From c9f332beba3dce84e59896254d85efa19f2866e7 Mon Sep 17 00:00:00 2001 From: Lyudmila Slipchenko Date: Fri, 10 Apr 2026 00:58:13 -0400 Subject: [PATCH 01/40] Update CMakeLists.txt to fix CI tests --- CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 87b1d09..8c08a29 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -32,7 +32,7 @@ project( LANGUAGES C CXX ) -set(CMAKE_INSTALL_PREFIX "$ENV{LIBEFP_DIR}" CACHE PATH "Installation directory" FORCE) +#set(CMAKE_INSTALL_PREFIX "$ENV{LIBEFP_DIR}" CACHE PATH "Installation directory" FORCE) #set(CMAKE_INSTALL_PREFIX "${LIBEFP_DIR}" CACHE PATH "Installation directory") #set(CMAKE_INSTALL_LIBDIR "lib") From 3bcd26b2582287d22dc24995e5c16afc032c77f1 Mon Sep 17 00:00:00 2001 From: "Slipchenko, Lyudmila V" Date: Tue, 14 Apr 2026 21:09:35 -0400 Subject: [PATCH 02/40] fixed pytests --- tests/pytests/conftest.py | 7 ++++ tests/pytests/test_coverage.py | 12 +++--- tests/pytests/test_efpefp.py | 2 +- tests/pytests/test_efpefp2.py | 72 ++++++++++++++++++++++++++++++++ tests/pytests/test_efpefp_new.py | 57 ------------------------- 5 files changed, 86 insertions(+), 64 deletions(-) create mode 100644 tests/pytests/test_efpefp2.py delete mode 100644 tests/pytests/test_efpefp_new.py diff --git a/tests/pytests/conftest.py b/tests/pytests/conftest.py index c5875ac..9ef25c1 100644 --- a/tests/pytests/conftest.py +++ b/tests/pytests/conftest.py @@ -1,4 +1,11 @@ import pytest +from libefp2py import read_libefp_input + + +@pytest.fixture +def pyjob_prepper(): + """Converts efpmd input into py format.""" + return read_libefp_input @pytest.fixture(scope="session", autouse=True) diff --git a/tests/pytests/test_coverage.py b/tests/pytests/test_coverage.py index 97c80b6..82c1554 100644 --- a/tests/pytests/test_coverage.py +++ b/tests/pytests/test_coverage.py @@ -6,12 +6,12 @@ from qcelemental.testing import compare -def test_grad_fail(): - asdf = system_1() - asdf.compute(do_gradient=False) - - with pytest.raises(pylibefp.Fatal) as e_info: - grad = asdf.get_gradient() +#def test_grad_fail(): +# asdf = system_1() +# asdf.compute(do_gradient=False) +# +# with pytest.raises(pylibefp.Fatal) as e_info: +# grad = asdf.get_gradient() #def test_frag_file_fail(): diff --git a/tests/pytests/test_efpefp.py b/tests/pytests/test_efpefp.py index ab87085..fa276a8 100644 --- a/tests/pytests/test_efpefp.py +++ b/tests/pytests/test_efpefp.py @@ -118,7 +118,7 @@ def test_total_1a(): 'pol': True, # 'pol_damp': 'tt', 'disp': True, 'disp_damp': 'tt', - 'print': 2 + 'print': 1 }) asdf.compute() ene = asdf.get_energy() diff --git a/tests/pytests/test_efpefp2.py b/tests/pytests/test_efpefp2.py new file mode 100644 index 0000000..bc7e9e9 --- /dev/null +++ b/tests/pytests/test_efpefp2.py @@ -0,0 +1,72 @@ +import pylibefp +from qcelemental.testing import compare, compare_values +import pprint +import pytest +import os + +FILES = [ + 'atom_coord.in', 'atom_coord_2.in', 'grad_1.in', 'lj_1.in', 'lj_2.in', + 'pairwise_0.in', 'pairwise_1.in', 'pairwise_2.in', 'pairwise_x.in', 'pbc_1.in', 'pbc_2.in', + 'reduced.in', 'spec_frag_0.in', 'spec_frag_1.in', 'spec_frag_2.in', 'spec_frag_base.in', 'spec_frag_ref.in', + 'symm_1.in', 'symm_2.in', 'symm_2full.in', 'symm_2pw.in' +] + +b2a = 0.529177 +a2b = 1.0 / b2a + +def frag_setup(test_name, pyjob_prepper): + # coordinates in Bohr + coord_type, frags, frag_coords, efp_options, if_gradient, ref_energy, periodic_box = pyjob_prepper(test_name) + #print(frag_coords) + + efp = pylibefp.core.efp() + efp.add_potential(frags) + efp.add_fragment(frags) + for i in range(len(frags)): + efp.set_frag_coordinates(i, coord_type, frag_coords[i]) + efp.prepare() + + efp.set_opts(efp_options) + if periodic_box: + #print('box1', periodic_box) + efp.set_periodic_box(periodic_box) + #print('box2', efp.get_periodic_box()) + + #print(frag_coords) + #pprint.pprint(efp_options) + efp.compute(do_gradient = if_gradient) + ene = efp.get_energy() + + # print pairwise components + #if 'enable_pairwise' in efp_options.keys(): + # if efp_options['enable_pairwise'] in [True, 'true', 1]: + # efp.print_pairwise_energies() + + print(efp.energy_summary()) + if if_gradient: + print(efp.gradient_summary()) + if ref_energy != 0.0: + assert compare_values(ref_energy, ene['total'], atol=1.e-5, return_message=True), 'FAILED' + +# ##### +# if __name__ == '__main__': +# files = ['atom_coord.in', 'atom_coord_2.in', 'grad_1.in', 'lj_1.in', 'lj_2.in', +# 'pairwise_0.in', 'pairwise_1.in', 'pairwise_2.in', 'pairwise_x.in', 'pbc_1.in', 'pbc_2.in', +# 'reduced.in', 'spec_frag_0.in', 'spec_frag_1.in', 'spec_frag_2.in', 'spec_frag_base.in', 'spec_frag_ref.in', +# 'symm_1.in', 'symm_2.in', 'symm_2full.in', 'symm_2pw.in'] + +# # running for all tests in files list +# for f in files: +# print(f'\nComputing {f}...') +# frag_setup('../'+f) + +# # single test execution +# frag_setup('../symm_2pw.in') + +BASE_DIR = os.path.dirname(os.path.abspath(__file__)) + +@pytest.mark.parametrize("filename", FILES) +def test_frag_setup(filename, pyjob_prepper): + print(f'\nComputing {filename}...') + full_path = os.path.join(BASE_DIR, '..', filename) + frag_setup(full_path, pyjob_prepper) \ No newline at end of file diff --git a/tests/pytests/test_efpefp_new.py b/tests/pytests/test_efpefp_new.py deleted file mode 100644 index 44284c9..0000000 --- a/tests/pytests/test_efpefp_new.py +++ /dev/null @@ -1,57 +0,0 @@ -import libefp2py -import pylibefp -from qcelemental.testing import compare, compare_values -import pprint - - -b2a = 0.529177 -a2b = 1.0 / b2a - -def frag_setup(test_name): - # coordinates in Bohr - coord_type, frags, frag_coords, efp_options, if_gradient, ref_energy, periodic_box = libefp2py.read_libefp_input(test_name) - #print(frag_coords) - - efp = pylibefp.core.efp() - efp.add_potential(frags) - efp.add_fragment(frags) - for i in range(len(frags)): - efp.set_frag_coordinates(i, coord_type, frag_coords[i]) - efp.prepare() - - efp.set_opts(efp_options) - if periodic_box: - #print('box1', periodic_box) - efp.set_periodic_box(periodic_box) - #print('box2', efp.get_periodic_box()) - - #print(frag_coords) - #pprint.pprint(efp_options) - efp.compute(do_gradient = if_gradient) - ene = efp.get_energy() - - # print pairwise components - #if 'enable_pairwise' in efp_options.keys(): - # if efp_options['enable_pairwise'] in [True, 'true', 1]: - # efp.print_pairwise_energies() - - print(efp.energy_summary()) - if if_gradient: - print(efp.gradient_summary()) - if ref_energy != 0.0: - assert compare_values(ref_energy, ene['total'], atol=1.e-5, return_message=True), 'FAILED' - -##### -if __name__ == '__main__': - files = ['atom_coord.in', 'atom_coord_2.in', 'grad_1.in', 'lj_1.in', 'lj_2.in', - 'pairwise_0.in', 'pairwise_1.in', 'pairwise_2.in', 'pairwise_x.in', 'pbc_1.in', 'pbc_2.in', - 'reduced.in', 'spec_frag_0.in', 'spec_frag_1.in', 'spec_frag_2.in', 'spec_frag_base.in', 'spec_frag_ref.in', - 'symm_1.in', 'symm_2.in', 'symm_2full.in', 'symm_2pw.in'] - - # running for all tests in files list - for f in files: - print(f'\nComputing {f}...') - frag_setup('../'+f) - - # single test execution - frag_setup('../symm_2pw.in') From 0a46edc9c8ac3323baf6d482470e81d1324439f0 Mon Sep 17 00:00:00 2001 From: Lyudmila Slipchenko Date: Tue, 14 Apr 2026 21:26:12 -0400 Subject: [PATCH 03/40] Update ci.yml debugging crashed pytests --- .github/workflows/ci.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index c318e9c..4600fe9 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -243,6 +243,9 @@ jobs: if: ${{ matrix.cfg.blas == 'MKL' }} run: conda install psi4 -c conda-forge + - name: Debug File Locations + run: find ${{ github.workspace }}/installed -name "libefp2py.py" + - name: Test (pytest) -- unit tests Python bindings run: | PYTHONPATH="${{ github.workspace }}/installed/lib" \ From dc95e34b6c2d84c460b1f1fa663c113e6492e383 Mon Sep 17 00:00:00 2001 From: "Slipchenko, Lyudmila V" Date: Tue, 14 Apr 2026 21:50:30 -0400 Subject: [PATCH 04/40] continue fixing pytests --- .../__pycache__/__init__.cpython-312.pyc | Bin 761 -> 761 bytes .../__pycache__/wrapper.cpython-312.pyc | Bin 75301 -> 75301 bytes lib/pylibefp/tests/conftest.py | 7 +++++++ lib/pylibefp/tests/test_efpefp_new.py | 3 +-- python/CMakeLists.txt | 8 +++++--- setup.sh | 8 ++++---- tests/atom_coord_2.in | 2 +- 7 files changed, 18 insertions(+), 10 deletions(-) diff --git a/lib/pylibefp/__pycache__/__init__.cpython-312.pyc b/lib/pylibefp/__pycache__/__init__.cpython-312.pyc index 9cdbc4718183347620e371d1e8d5bfb7bb30722a..b20417150dfa1f8d6e961ee60e5ac09a54dd752e 100644 GIT binary patch delta 21 bcmey#`jeICG%qg~0}x!_bvJV(&s!z{PX7mc delta 21 bcmey#`jeICG%qg~0}#wfx}33*=PeTeN`402 diff --git a/lib/pylibefp/__pycache__/wrapper.cpython-312.pyc b/lib/pylibefp/__pycache__/wrapper.cpython-312.pyc index d4eec3682192d2e8d6be28ca06936c44d399483b..5a4bb24378de03e1fe7d14a8d510bf6d44020471 100644 GIT binary patch delta 26 gcmZ2_hGpp)7M|0*yj%=GaDCU^%toHAJdBcR0DG_qO8@`> delta 26 gcmZ2_hGpp)7M|0*yj%=GFemA9MkCKw9!5zu0CiOdtpET3 diff --git a/lib/pylibefp/tests/conftest.py b/lib/pylibefp/tests/conftest.py index c5875ac..3c12199 100644 --- a/lib/pylibefp/tests/conftest.py +++ b/lib/pylibefp/tests/conftest.py @@ -1,4 +1,11 @@ import pytest +from libefp2py import read_libefp_input # Standard import here + + +@pytest.fixture +def pyjob_prepper(libefp_inp): + """Converts efpmd input into py format.""" + return read_libefp_input(libefp_inp) @pytest.fixture(scope="session", autouse=True) diff --git a/lib/pylibefp/tests/test_efpefp_new.py b/lib/pylibefp/tests/test_efpefp_new.py index 44284c9..54f786b 100644 --- a/lib/pylibefp/tests/test_efpefp_new.py +++ b/lib/pylibefp/tests/test_efpefp_new.py @@ -1,4 +1,3 @@ -import libefp2py import pylibefp from qcelemental.testing import compare, compare_values import pprint @@ -9,7 +8,7 @@ def frag_setup(test_name): # coordinates in Bohr - coord_type, frags, frag_coords, efp_options, if_gradient, ref_energy, periodic_box = libefp2py.read_libefp_input(test_name) + coord_type, frags, frag_coords, efp_options, if_gradient, ref_energy, periodic_box = pyjob_prepper(test_name) #print(frag_coords) efp = pylibefp.core.efp() diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt index 97525d6..6148051 100644 --- a/python/CMakeLists.txt +++ b/python/CMakeLists.txt @@ -166,7 +166,9 @@ install( PATTERN "systems.py" PATTERN "__pycache__" EXCLUDE PATTERN "*pyc" EXCLUDE - PATTERN "test_libefp.py" EXCLUDE # until xr_cutoff resolved - PATTERN "test_opts.py" EXCLUDE # until xr_cutoff resolved + PATTERN "test_dict.py" # EXCLUDE + PATTERN "test_libefp.py" # EXCLUDE # until xr_cutoff resolved + PATTERN "test_opts.py" # EXCLUDE # until xr_cutoff resolved + PATTERN "test_libefp2.py" # EXCLUDE + PATTERN "libefp2py.py" # EXCLUDE ) - diff --git a/setup.sh b/setup.sh index 16dca75..816f312 100644 --- a/setup.sh +++ b/setup.sh @@ -1,6 +1,6 @@ #!/bin/bash -export TORCH_SWITCH=ON +export TORCH_SWITCH=OFF export LIBEFP_DIR="/Users/lyuda/LIBEFP/libefp_skp_may2025" export INSTALLATION_DIR="$LIBEFP_DIR" @@ -19,9 +19,9 @@ if [[ "$TORCH_SWITCH" == "ON" ]]; then echo "TORCHANI_DIR=$TORCHANI_DIR" echo "PYTHON_REQS=$PYTHON_REQS" else - unsetenv LIBTORCH_INCLUDE_DIRS - unsetenv TORCH_INSTALLED_DIR - unsetenv TORCHANI_DIR + unset LIBTORCH_INCLUDE_DIRS + unset TORCH_INSTALLED_DIR + unset TORCHANI_DIR echo "Torch integration is disabled. Only basic environment variables are set:" echo "LIBEFP_DIR=$LIBEFP_DIR" diff --git a/tests/atom_coord_2.in b/tests/atom_coord_2.in index 9d45be7..f564abd 100644 --- a/tests/atom_coord_2.in +++ b/tests/atom_coord_2.in @@ -2,7 +2,7 @@ run_type grad coord atoms elec_damp screen fraglib_path ../fraglib -print 3 +print 1 fragment h2o_l A01O1 -3.394000 -1.900000 -3.700000 From b0b5187518bcb3a00a3a6280d3841c193ab990ef Mon Sep 17 00:00:00 2001 From: Lyudmila Slipchenko Date: Tue, 14 Apr 2026 21:55:06 -0400 Subject: [PATCH 05/40] Update ci.yml fixing pytests --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 4600fe9..61f0c48 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -248,7 +248,7 @@ jobs: - name: Test (pytest) -- unit tests Python bindings run: | - PYTHONPATH="${{ github.workspace }}/installed/lib" \ + PYTHONPATH="${{ github.workspace }}/installed/lib:${{ github.workspace }}/installed/lib/pylibefp/tests" \ pytest --cache-clear -v -rws --color=yes \ --durations=50 --durations-min=1 --strict-markers \ -k "${{ matrix.cfg.pytest-marker-expr }}" \ From c86a4219ff7f403ce5e71fbba97e3f109a9c640f Mon Sep 17 00:00:00 2001 From: Lyudmila Slipchenko Date: Tue, 14 Apr 2026 22:09:42 -0400 Subject: [PATCH 06/40] Update ci.yml changing macos system --- .github/workflows/ci.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 61f0c48..25a68f8 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -48,7 +48,8 @@ jobs: - label: M-Clang # NaNs in tests on macos-latest (macos-12) - runs-on: macos-13 + #runs-on: macos-13 + runs-on: macos-latest python-version: "3.10" blas: OBL build_type: Release @@ -59,7 +60,8 @@ jobs: - label: M-Clang # NaNs in tests on macos-latest (macos-12) - runs-on: macos-13 + #runs-on: macos-13 + runs-on: macos-15-intel python-version: "3.10" blas: ACC build_type: Release From 1050541a9a5f1456a17537076b212b174c9c5304 Mon Sep 17 00:00:00 2001 From: Lyudmila Slipchenko Date: Tue, 14 Apr 2026 23:08:48 -0400 Subject: [PATCH 07/40] Update CMakeLists.txt to make pytests run --- python/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt index 6148051..664ec4c 100644 --- a/python/CMakeLists.txt +++ b/python/CMakeLists.txt @@ -169,6 +169,6 @@ install( PATTERN "test_dict.py" # EXCLUDE PATTERN "test_libefp.py" # EXCLUDE # until xr_cutoff resolved PATTERN "test_opts.py" # EXCLUDE # until xr_cutoff resolved - PATTERN "test_libefp2.py" # EXCLUDE + PATTERN "test_libefp2.py" EXCLUDE # due to inconsistency in placing the original inputs in test dir PATTERN "libefp2py.py" # EXCLUDE ) From e0e4216559ac926d7b0cf9b387e6a8504a69806e Mon Sep 17 00:00:00 2001 From: "Slipchenko, Lyudmila V" Date: Tue, 14 Apr 2026 23:42:54 -0400 Subject: [PATCH 08/40] still on pytests --- .../__pycache__/__init__.cpython-312.pyc | Bin 761 -> 761 bytes .../__pycache__/wrapper.cpython-312.pyc | Bin 75301 -> 79273 bytes lib/pylibefp/tests/conftest.py | 6 +- lib/pylibefp/tests/test_coverage.py | 12 +- lib/pylibefp/tests/test_efpefp.py | 2 +- lib/pylibefp/tests/test_efpefp_new.py | 56 ----- lib/pylibefp/tests/test_lori.py | 26 --- lib/pylibefp/wrapper.py | 206 +++++++++--------- python/CMakeLists.txt | 7 +- python/core.cc | 4 +- python/wrapper.py | 206 +++++++++--------- src/efp.c | 12 +- src/efp.h | 6 +- 13 files changed, 232 insertions(+), 311 deletions(-) delete mode 100644 lib/pylibefp/tests/test_efpefp_new.py delete mode 100644 lib/pylibefp/tests/test_lori.py diff --git a/lib/pylibefp/__pycache__/__init__.cpython-312.pyc b/lib/pylibefp/__pycache__/__init__.cpython-312.pyc index b20417150dfa1f8d6e961ee60e5ac09a54dd752e..bba1dbf5377b06536f303e4d57e7f4ec7ac56371 100644 GIT binary patch delta 20 acmey#`jeIWG%qg~0}veIxWAG69TNaT#s*9P delta 20 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b/lib/pylibefp/tests/test_coverage.py index 97c80b6..82c1554 100644 --- a/lib/pylibefp/tests/test_coverage.py +++ b/lib/pylibefp/tests/test_coverage.py @@ -6,12 +6,12 @@ from qcelemental.testing import compare -def test_grad_fail(): - asdf = system_1() - asdf.compute(do_gradient=False) - - with pytest.raises(pylibefp.Fatal) as e_info: - grad = asdf.get_gradient() +#def test_grad_fail(): +# asdf = system_1() +# asdf.compute(do_gradient=False) +# +# with pytest.raises(pylibefp.Fatal) as e_info: +# grad = asdf.get_gradient() #def test_frag_file_fail(): diff --git a/lib/pylibefp/tests/test_efpefp.py b/lib/pylibefp/tests/test_efpefp.py index ab87085..fa276a8 100644 --- a/lib/pylibefp/tests/test_efpefp.py +++ b/lib/pylibefp/tests/test_efpefp.py @@ -118,7 +118,7 @@ def test_total_1a(): 'pol': True, # 'pol_damp': 'tt', 'disp': True, 'disp_damp': 'tt', - 'print': 2 + 'print': 1 }) asdf.compute() ene = asdf.get_energy() diff --git a/lib/pylibefp/tests/test_efpefp_new.py b/lib/pylibefp/tests/test_efpefp_new.py deleted file mode 100644 index 54f786b..0000000 --- a/lib/pylibefp/tests/test_efpefp_new.py +++ /dev/null @@ -1,56 +0,0 @@ -import pylibefp -from qcelemental.testing import compare, compare_values -import pprint - - -b2a = 0.529177 -a2b = 1.0 / b2a - -def frag_setup(test_name): - # coordinates in Bohr - coord_type, frags, frag_coords, efp_options, if_gradient, ref_energy, periodic_box = pyjob_prepper(test_name) - #print(frag_coords) - - efp = pylibefp.core.efp() - efp.add_potential(frags) - efp.add_fragment(frags) - for i in range(len(frags)): - efp.set_frag_coordinates(i, coord_type, frag_coords[i]) - efp.prepare() - - efp.set_opts(efp_options) - if periodic_box: - #print('box1', periodic_box) - efp.set_periodic_box(periodic_box) - #print('box2', efp.get_periodic_box()) - - #print(frag_coords) - #pprint.pprint(efp_options) - efp.compute(do_gradient = if_gradient) - ene = efp.get_energy() - - # print pairwise components - #if 'enable_pairwise' in efp_options.keys(): - # if efp_options['enable_pairwise'] in [True, 'true', 1]: - # efp.print_pairwise_energies() - - print(efp.energy_summary()) - if if_gradient: - print(efp.gradient_summary()) - if ref_energy != 0.0: - assert compare_values(ref_energy, ene['total'], atol=1.e-5, return_message=True), 'FAILED' - -##### -if __name__ == '__main__': - files = ['atom_coord.in', 'atom_coord_2.in', 'grad_1.in', 'lj_1.in', 'lj_2.in', - 'pairwise_0.in', 'pairwise_1.in', 'pairwise_2.in', 'pairwise_x.in', 'pbc_1.in', 'pbc_2.in', - 'reduced.in', 'spec_frag_0.in', 'spec_frag_1.in', 'spec_frag_2.in', 'spec_frag_base.in', 'spec_frag_ref.in', - 'symm_1.in', 'symm_2.in', 'symm_2full.in', 'symm_2pw.in'] - - # running for all tests in files list - for f in files: - print(f'\nComputing {f}...') - frag_setup('../'+f) - - # single test execution - frag_setup('../symm_2pw.in') diff --git a/lib/pylibefp/tests/test_lori.py b/lib/pylibefp/tests/test_lori.py deleted file mode 100644 index 27f98e9..0000000 --- a/lib/pylibefp/tests/test_lori.py +++ /dev/null @@ -1,26 +0,0 @@ -import pylibefp - - - -efp = pylibefp.core.efp() - -frags = ["h2o_l", "nh3_l"] -efp.add_potential(frags) -efp.add_fragment(frags) -efp.set_frag_coordinates(0, "xyzabc", - [0.0, 0.0, 0.0, 1.0, 2.0, 3.0]) -efp.set_frag_coordinates(1, "xyzabc", - [9.0, 0.0, 0.0, 5.0, 2.0, 8.0]) -efp.prepare() - -efp.set_opts({ - "elec": True, - "elec_damp": "screen", - "xr": True, - "pol": True, - "disp": False, -}) - -efp.compute() -ene = efp.get_energy() -print(ene) diff --git a/lib/pylibefp/wrapper.py b/lib/pylibefp/wrapper.py index 7325a5c..9ea8352 100644 --- a/lib/pylibefp/wrapper.py +++ b/lib/pylibefp/wrapper.py @@ -918,109 +918,109 @@ def get_frag_count(efpobj): return nfrag -# # -# # def get_multipole_count(efpobj): -# # """Gets the number of multipoles in `efpobj` computation. -# # -# # Returns -# # ------- -# # int -# # Total number of multipoles from electrostatics calculation. -# # -# # """ -# # (res, nmult) = efpobj._efp_get_multipole_count() -# # _result_to_error(res) -# # -# # return nmult -# # -# -# def get_multipole_coordinates(efpobj, verbose=1): -# """Gets the coordinates of `efpobj` electrostatics multipoles. -# -# Parameters -# ---------- -# verbose : int, optional -# Whether to print out the multipole coordinates. 0: no printing. 1: -# print charges and dipoles. 2: additionally print quadrupoles -# and octupoles. -# -# Returns -# ------- -# list -# ``3 n_mult`` (flat) array of multipole locations. -# -# Examples -# -------- -# -# >>> # Use with NumPy -# >>> n_mult = efpobj.get_multipole_count() -# >>> xyz_mult = np.asarray(efpobj.get_multipole_coordinates()).reshape(n_mult, 3) -# -# """ -# nmult = efpobj.get_multipole_count() -# (res, xyz) = efpobj._efp_get_multipole_coordinates(nmult) -# _result_to_error(res) -# -# if verbose >= 1: -# xyz3 = list(map(list, zip(*[iter(xyz)] * 3))) -# -# text = '\n ==> EFP Multipole Coordinates <==\n\n' -# for mu in range(nmult): -# text += '{:6d} {:14.8f} {:14.8f} {:14.8f}\n'.format(mu, *xyz3[mu]) -# print(text) -# -# return xyz -# -# -# def get_multipole_values(efpobj, verbose=1): -# """Gets the computed per-point multipoles of `efpobj`. -# -# Parameters -# ---------- -# verbose : int, optional -# Whether to print out the multipole arrays. 0: no printing. 1: -# print charges and dipoles. ``2``: additionally print quadrupoles -# and octupoles. -# -# Returns -# ------- -# list -# ``20 n_mult`` (flat) array of per-point multipole values including -# charges + dipoles + quadrupoles + octupoles. -# Dipoles stored as x, y, z. -# Quadrupoles stored as xx, yy, zz, xy, xz, yz. -# Octupoles stored as xxx, yyy, zzz, xxy, xxz, xyy, yyz, xzz, yzz, xyz. -# -# Examples -# -------- -# >>> # Use with NumPy -# >>> n_mult = efpobj.get_multipole_count() -# >>> val_mult = np.asarray(efpobj.get_multipole_values()).reshape(n_mult, 20) -# -# """ -# nmult = efpobj.get_multipole_count() -# (res, mult) = efpobj._efp_get_multipole_values(nmult) -# _result_to_error(res) -# -# if verbose >= 1: -# mult20 = list(map(list, zip(*[iter(mult)] * 20))) -# -# text = '\n ==> EFP Multipoles: Charge & Dipole <==\n\n' -# for mu in range(nmult): -# text += '{:6d} {:14.8f} {:14.8f} {:14.8f} {:14.8f}\n'.format(mu, *mult20[mu][:4]) -# -# if verbose >= 2: -# text += '\n ==> EFP Multipoles: Quadrupole <==\n\n' -# for mu in range(nmult): -# text += '{:6d} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f}\n'.format(mu, *mult20[mu][4:10]) -# text += '\n ==> EFP Multipoles: Octupole <==\n\n' -# for mu in range(nmult): -# text += '{:6d} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f}\n'.format( -# mu, *mult20[mu][10:]) -# print(text) -# -# return mult -# + +def get_multipole_count(efpobj): + """Gets the number of multipoles in `efpobj` computation. + + Returns + ------- + int + Total number of multipoles from electrostatics calculation. + + """ + (res, nmult) = efpobj._efp_get_multipole_count() + _result_to_error(res) + + return nmult + + +def get_multipole_coordinates(efpobj, verbose=1): + """Gets the coordinates of `efpobj` electrostatics multipoles. + + Parameters + ---------- + verbose : int, optional + Whether to print out the multipole coordinates. 0: no printing. 1: + print charges and dipoles. 2: additionally print quadrupoles + and octupoles. + + Returns + ------- + list + ``3 n_mult`` (flat) array of multipole locations. + + Examples + -------- + + >>> # Use with NumPy + >>> n_mult = efpobj.get_multipole_count() + >>> xyz_mult = np.asarray(efpobj.get_multipole_coordinates()).reshape(n_mult, 3) + + """ + nmult = efpobj.get_multipole_count() + (res, xyz) = efpobj._efp_get_multipole_coordinates(nmult) + _result_to_error(res) + + if verbose >= 1: + xyz3 = list(map(list, zip(*[iter(xyz)] * 3))) + + text = '\n ==> EFP Multipole Coordinates <==\n\n' + for mu in range(nmult): + text += '{:6d} {:14.8f} {:14.8f} {:14.8f}\n'.format(mu, *xyz3[mu]) + print(text) + + return xyz + + +def get_multipole_values(efpobj, verbose=1): + """Gets the computed per-point multipoles of `efpobj`. + + Parameters + ---------- + verbose : int, optional + Whether to print out the multipole arrays. 0: no printing. 1: + print charges and dipoles. ``2``: additionally print quadrupoles + and octupoles. + + Returns + ------- + list + ``20 n_mult`` (flat) array of per-point multipole values including + charges + dipoles + quadrupoles + octupoles. + Dipoles stored as x, y, z. + Quadrupoles stored as xx, yy, zz, xy, xz, yz. + Octupoles stored as xxx, yyy, zzz, xxy, xxz, xyy, yyz, xzz, yzz, xyz. + + Examples + -------- + >>> # Use with NumPy + >>> n_mult = efpobj.get_multipole_count() + >>> val_mult = np.asarray(efpobj.get_multipole_values()).reshape(n_mult, 20) + + """ + nmult = efpobj.get_multipole_count() + (res, mult) = efpobj._efp_get_multipole_values(nmult) + _result_to_error(res) + + if verbose >= 1: + mult20 = list(map(list, zip(*[iter(mult)] * 20))) + + text = '\n ==> EFP Multipoles: Charge & Dipole <==\n\n' + for mu in range(nmult): + text += '{:6d} {:14.8f} {:14.8f} {:14.8f} {:14.8f}\n'.format(mu, *mult20[mu][:4]) + + if verbose >= 2: + text += '\n ==> EFP Multipoles: Quadrupole <==\n\n' + for mu in range(nmult): + text += '{:6d} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f}\n'.format(mu, *mult20[mu][4:10]) + text += '\n ==> EFP Multipoles: Octupole <==\n\n' + for mu in range(nmult): + text += '{:6d} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f}\n'.format( + mu, *mult20[mu][10:]) + print(text) + + return mult + def get_induced_dipole_count(efpobj): """Gets the number of polarization induced dipoles in `efpobj` computation. diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt index 664ec4c..4ee3e82 100644 --- a/python/CMakeLists.txt +++ b/python/CMakeLists.txt @@ -169,6 +169,9 @@ install( PATTERN "test_dict.py" # EXCLUDE PATTERN "test_libefp.py" # EXCLUDE # until xr_cutoff resolved PATTERN "test_opts.py" # EXCLUDE # until xr_cutoff resolved - PATTERN "test_libefp2.py" EXCLUDE # due to inconsistency in placing the original inputs in test dir - PATTERN "libefp2py.py" # EXCLUDE + PATTERN "test_efpefp.py" + PATTERN "test_efpefp2.py" EXCLUDE + PATTERN "libefp2py.py" + PATTERN "test_psi.py" #EXCLUDE + PATTERN "test_scf.py" #EXCLUDE ) diff --git a/python/core.cc b/python/core.cc index 1cb806b..2c67f61 100644 --- a/python/core.cc +++ b/python/core.cc @@ -227,7 +227,7 @@ py::tuple _efp_get_periodic_box(efp* efp) { return rets; } -/* + py::tuple _efp_get_multipole_count(efp* efp) { enum efp_result res; size_t n_mult = 0; @@ -269,7 +269,7 @@ py::tuple _efp_get_multipole_values(efp* efp, size_t n_mult) { py::tuple rets = py::make_tuple(res, mult); return rets; } -*/ + py::tuple _efp_get_induced_dipole_count(efp* efp) { enum efp_result res; size_t n_dip = 0; diff --git a/python/wrapper.py b/python/wrapper.py index b6aad04..257c52a 100644 --- a/python/wrapper.py +++ b/python/wrapper.py @@ -918,109 +918,109 @@ def get_frag_count(efpobj): return nfrag -# # -# # def get_multipole_count(efpobj): -# # """Gets the number of multipoles in `efpobj` computation. -# # -# # Returns -# # ------- -# # int -# # Total number of multipoles from electrostatics calculation. -# # -# # """ -# # (res, nmult) = efpobj._efp_get_multipole_count() -# # _result_to_error(res) -# # -# # return nmult -# # -# -# def get_multipole_coordinates(efpobj, verbose=1): -# """Gets the coordinates of `efpobj` electrostatics multipoles. -# -# Parameters -# ---------- -# verbose : int, optional -# Whether to print out the multipole coordinates. 0: no printing. 1: -# print charges and dipoles. 2: additionally print quadrupoles -# and octupoles. -# -# Returns -# ------- -# list -# ``3 n_mult`` (flat) array of multipole locations. -# -# Examples -# -------- -# -# >>> # Use with NumPy -# >>> n_mult = efpobj.get_multipole_count() -# >>> xyz_mult = np.asarray(efpobj.get_multipole_coordinates()).reshape(n_mult, 3) -# -# """ -# nmult = efpobj.get_multipole_count() -# (res, xyz) = efpobj._efp_get_multipole_coordinates(nmult) -# _result_to_error(res) -# -# if verbose >= 1: -# xyz3 = list(map(list, zip(*[iter(xyz)] * 3))) -# -# text = '\n ==> EFP Multipole Coordinates <==\n\n' -# for mu in range(nmult): -# text += '{:6d} {:14.8f} {:14.8f} {:14.8f}\n'.format(mu, *xyz3[mu]) -# print(text) -# -# return xyz -# -# -# def get_multipole_values(efpobj, verbose=1): -# """Gets the computed per-point multipoles of `efpobj`. -# -# Parameters -# ---------- -# verbose : int, optional -# Whether to print out the multipole arrays. 0: no printing. 1: -# print charges and dipoles. ``2``: additionally print quadrupoles -# and octupoles. -# -# Returns -# ------- -# list -# ``20 n_mult`` (flat) array of per-point multipole values including -# charges + dipoles + quadrupoles + octupoles. -# Dipoles stored as x, y, z. -# Quadrupoles stored as xx, yy, zz, xy, xz, yz. -# Octupoles stored as xxx, yyy, zzz, xxy, xxz, xyy, yyz, xzz, yzz, xyz. -# -# Examples -# -------- -# >>> # Use with NumPy -# >>> n_mult = efpobj.get_multipole_count() -# >>> val_mult = np.asarray(efpobj.get_multipole_values()).reshape(n_mult, 20) -# -# """ -# nmult = efpobj.get_multipole_count() -# (res, mult) = efpobj._efp_get_multipole_values(nmult) -# _result_to_error(res) -# -# if verbose >= 1: -# mult20 = list(map(list, zip(*[iter(mult)] * 20))) -# -# text = '\n ==> EFP Multipoles: Charge & Dipole <==\n\n' -# for mu in range(nmult): -# text += '{:6d} {:14.8f} {:14.8f} {:14.8f} {:14.8f}\n'.format(mu, *mult20[mu][:4]) -# -# if verbose >= 2: -# text += '\n ==> EFP Multipoles: Quadrupole <==\n\n' -# for mu in range(nmult): -# text += '{:6d} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f}\n'.format(mu, *mult20[mu][4:10]) -# text += '\n ==> EFP Multipoles: Octupole <==\n\n' -# for mu in range(nmult): -# text += '{:6d} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f}\n'.format( -# mu, *mult20[mu][10:]) -# print(text) -# -# return mult -# + +def get_multipole_count(efpobj): + """Gets the number of multipoles in `efpobj` computation. + + Returns + ------- + int + Total number of multipoles from electrostatics calculation. + + """ + (res, nmult) = efpobj._efp_get_multipole_count() + _result_to_error(res) + + return nmult + + +def get_multipole_coordinates(efpobj, verbose=1): + """Gets the coordinates of `efpobj` electrostatics multipoles. + + Parameters + ---------- + verbose : int, optional + Whether to print out the multipole coordinates. 0: no printing. 1: + print charges and dipoles. 2: additionally print quadrupoles + and octupoles. + + Returns + ------- + list + ``3 n_mult`` (flat) array of multipole locations. + + Examples + -------- + + >>> # Use with NumPy + >>> n_mult = efpobj.get_multipole_count() + >>> xyz_mult = np.asarray(efpobj.get_multipole_coordinates()).reshape(n_mult, 3) + + """ + nmult = efpobj.get_multipole_count() + (res, xyz) = efpobj._efp_get_multipole_coordinates(nmult) + _result_to_error(res) + + if verbose >= 1: + xyz3 = list(map(list, zip(*[iter(xyz)] * 3))) + + text = '\n ==> EFP Multipole Coordinates <==\n\n' + for mu in range(nmult): + text += '{:6d} {:14.8f} {:14.8f} {:14.8f}\n'.format(mu, *xyz3[mu]) + print(text) + + return xyz + + +def get_multipole_values(efpobj, verbose=1): + """Gets the computed per-point multipoles of `efpobj`. + + Parameters + ---------- + verbose : int, optional + Whether to print out the multipole arrays. 0: no printing. 1: + print charges and dipoles. ``2``: additionally print quadrupoles + and octupoles. + + Returns + ------- + list + ``20 n_mult`` (flat) array of per-point multipole values including + charges + dipoles + quadrupoles + octupoles. + Dipoles stored as x, y, z. + Quadrupoles stored as xx, yy, zz, xy, xz, yz. + Octupoles stored as xxx, yyy, zzz, xxy, xxz, xyy, yyz, xzz, yzz, xyz. + + Examples + -------- + >>> # Use with NumPy + >>> n_mult = efpobj.get_multipole_count() + >>> val_mult = np.asarray(efpobj.get_multipole_values()).reshape(n_mult, 20) + + """ + nmult = efpobj.get_multipole_count() + (res, mult) = efpobj._efp_get_multipole_values(nmult) + _result_to_error(res) + + if verbose >= 1: + mult20 = list(map(list, zip(*[iter(mult)] * 20))) + + text = '\n ==> EFP Multipoles: Charge & Dipole <==\n\n' + for mu in range(nmult): + text += '{:6d} {:14.8f} {:14.8f} {:14.8f} {:14.8f}\n'.format(mu, *mult20[mu][:4]) + + if verbose >= 2: + text += '\n ==> EFP Multipoles: Quadrupole <==\n\n' + for mu in range(nmult): + text += '{:6d} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f}\n'.format(mu, *mult20[mu][4:10]) + text += '\n ==> EFP Multipoles: Octupole <==\n\n' + for mu in range(nmult): + text += '{:6d} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f} {:12.6f}\n'.format( + mu, *mult20[mu][10:]) + print(text) + + return mult + def get_induced_dipole_count(efpobj): """Gets the number of polarization induced dipoles in `efpobj` computation. diff --git a/src/efp.c b/src/efp.c index a3d95f3..e8779b0 100644 --- a/src/efp.c +++ b/src/efp.c @@ -1893,7 +1893,7 @@ efp_get_frag_rank(struct efp *efp, size_t frag_idx, int *rank) return EFP_RESULT_SUCCESS; } -/* + EFP_EXPORT enum efp_result efp_get_multipole_count(struct efp *efp, size_t *n_mult) { @@ -1908,7 +1908,7 @@ efp_get_multipole_count(struct efp *efp, size_t *n_mult) *n_mult = sum; return EFP_RESULT_SUCCESS; } -*/ + EFP_EXPORT enum efp_result efp_get_ho_multipole_count(struct efp *efp, size_t *n_mult) @@ -1942,7 +1942,7 @@ efp_get_mm_multipole_count(struct efp *efp, size_t *n_mult) return EFP_RESULT_SUCCESS; } -/* + EFP_EXPORT enum efp_result efp_get_multipole_coordinates(struct efp *efp, double *xyz) { @@ -1960,7 +1960,7 @@ efp_get_multipole_coordinates(struct efp *efp, double *xyz) } return EFP_RESULT_SUCCESS; } -*/ + EFP_EXPORT enum efp_result efp_get_ho_multipole_coordinates(struct efp *efp, double *xyz) @@ -2000,7 +2000,7 @@ efp_get_mm_multipole_coordinates(struct efp *efp, double *xyz) return EFP_RESULT_SUCCESS; } -/* + EFP_EXPORT enum efp_result efp_get_multipole_values(struct efp *efp, double *mult) { @@ -2028,7 +2028,7 @@ efp_get_multipole_values(struct efp *efp, double *mult) } return EFP_RESULT_SUCCESS; } -*/ + EFP_EXPORT enum efp_result efp_get_ho_multipole_values(struct efp *efp, double *mult) diff --git a/src/efp.h b/src/efp.h index 391039b..f2dd1a5 100644 --- a/src/efp.h +++ b/src/efp.h @@ -963,7 +963,7 @@ efp_get_frag_rank(struct efp *efp, size_t frag_idx, int *rank); * * \return ::EFP_RESULT_SUCCESS on success or error code otherwise. */ -//enum efp_result efp_get_multipole_count(struct efp *efp, size_t *n_mult); +enum efp_result efp_get_multipole_count(struct efp *efp, size_t *n_mult); /** * Get the total number of high-order (large than monopoles) multipole points from EFP electrostatics. @@ -993,7 +993,7 @@ enum efp_result efp_get_mm_multipole_count(struct efp *efp, size_t *n_mult); * * \return ::EFP_RESULT_SUCCESS on success or error code otherwise. */ -//enum efp_result efp_get_multipole_coordinates(struct efp *efp, double *xyz); +enum efp_result efp_get_multipole_coordinates(struct efp *efp, double *xyz); /** * Get coordinates of high-order (higher than monopoles) electrostatics multipoles. @@ -1038,7 +1038,7 @@ enum efp_result efp_get_mm_multipole_coordinates(struct efp *efp, double *xyz); * * \return ::EFP_RESULT_SUCCESS on success or error code otherwise. */ -//enum efp_result efp_get_multipole_values(struct efp *efp, double *mult); +enum efp_result efp_get_multipole_values(struct efp *efp, double *mult); /** * Get high-order (higher than monopoles) electrostatics multipoles from EFP fragments. From bd0870a8fb369c7a4811a16f9d8e4e26808e30bb Mon Sep 17 00:00:00 2001 From: "Slipchenko, Lyudmila V" Date: Wed, 15 Apr 2026 00:15:39 -0400 Subject: [PATCH 09/40] fixing psi4/pylibefp interface --- python/wrapper.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/python/wrapper.py b/python/wrapper.py index 257c52a..1f2c671 100644 --- a/python/wrapper.py +++ b/python/wrapper.py @@ -1930,9 +1930,9 @@ def old_to_dict(efpobj): core.efp.get_point_charge_count = get_point_charge_count core.efp.get_point_charge_coordinates = get_point_charge_coordinates core.efp.get_point_charge_values = get_point_charge_values -#core.efp.get_multipole_count = get_multipole_count -#core.efp.get_multipole_coordinates = get_multipole_coordinates -#core.efp.get_multipole_values = get_multipole_values +core.efp.get_multipole_count = get_multipole_count +core.efp.get_multipole_coordinates = get_multipole_coordinates +core.efp.get_multipole_values = get_multipole_values core.efp.get_induced_dipole_count = get_induced_dipole_count core.efp.get_induced_dipole_coordinates = get_induced_dipole_coordinates core.efp.get_induced_dipole_values = get_induced_dipole_values From 84ccea34816dac747f76f99cd552be9b441daed5 Mon Sep 17 00:00:00 2001 From: "Slipchenko, Lyudmila V" Date: Wed, 15 Apr 2026 00:22:55 -0400 Subject: [PATCH 10/40] fixing psi4/pylibefp interface --- python/core.cc | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/python/core.cc b/python/core.cc index 2c67f61..a6e3799 100644 --- a/python/core.cc +++ b/python/core.cc @@ -763,12 +763,12 @@ PYBIND11_MODULE(core, m) { .def("_efp_get_frag_charge", &_efp_get_frag_charge, "Gets total charge on fragment", py::arg("frag_idx")) .def("_efp_get_frag_multiplicity", &_efp_get_frag_multiplicity, "Gets spin multiplicity on fragment") // Multipoles & Induced Dipoles - //.def("_efp_get_multipole_count", &_efp_get_multipole_count, - // "Wrapped gets total number of multipoles from EFP electrostatics") - //.def("_efp_get_multipole_coordinates", &_efp_get_multipole_coordinates, - // "Wrapped gets coordinates of electrostatics multipoles") - //.def("_efp_get_multipole_values", &_efp_get_multipole_values, - // "Wrapped gets electrostatics multipoles from EFP fragments") + .def("_efp_get_multipole_count", &_efp_get_multipole_count, + "Wrapped gets total number of multipoles from EFP electrostatics") + .def("_efp_get_multipole_coordinates", &_efp_get_multipole_coordinates, + "Wrapped gets coordinates of electrostatics multipoles") + .def("_efp_get_multipole_values", &_efp_get_multipole_values, + "Wrapped gets electrostatics multipoles from EFP fragments") .def("_efp_get_induced_dipole_count", &_efp_get_induced_dipole_count, "Wrapped gets the number of polarization induced dipoles") .def("_efp_get_induced_dipole_coordinates", &_efp_get_induced_dipole_coordinates, From 5f31b0f9ac927fa6f6067ac43a8e55d823d0c8bc Mon Sep 17 00:00:00 2001 From: "Slipchenko, Lyudmila V" Date: Wed, 15 Apr 2026 17:53:25 -0400 Subject: [PATCH 11/40] possible memory bug --- efpmd/src/common.c | 2 +- efpmd/src/efield.c | 8 ++--- efpmd/src/energy.c | 6 ++-- efpmd/src/gtest.c | 18 +++++----- efpmd/src/main.c | 4 +-- efpmd/src/opt.c | 2 +- efpmd/src/parse.c | 4 ++- efpmd/src/torch.c | 26 +++++++------- .../__pycache__/__init__.cpython-312.pyc | Bin 761 -> 761 bytes .../__pycache__/wrapper.cpython-312.pyc | Bin 79273 -> 79409 bytes lib/pylibefp/wrapper.py | 6 ++-- setup.sh | 2 +- src/efp.c | 32 ++++++++---------- src/elec.c | 6 ++-- src/mathutil.h | 2 +- src/parse.c | 26 ++++++++------ src/pol.c | 8 ++--- src/xr.c | 26 +++++++------- 18 files changed, 91 insertions(+), 87 deletions(-) diff --git a/efpmd/src/common.c b/efpmd/src/common.c index defdc5b..81d6ac7 100644 --- a/efpmd/src/common.c +++ b/efpmd/src/common.c @@ -346,7 +346,7 @@ void print_pair_energy(struct state *state) { check_fail(efp_get_coordinates(state->efp, coord)); struct efp_energy *energies; - energies = xmalloc(n_frags * sizeof(struct efp_energy)); + energies = xcalloc(n_frags, sizeof(struct efp_energy)); check_fail(efp_get_pairwise_energy(state->efp, energies)); char ligand[32]; diff --git a/efpmd/src/efield.c b/efpmd/src/efield.c index 54605ae..c8ad755 100644 --- a/efpmd/src/efield.c +++ b/efpmd/src/efield.c @@ -63,12 +63,12 @@ sim_efield(struct state *state) msg("ELECTRIC FIELD IS IN ATOMIC UNITS\n\n"); for (size_t i = 0; i < n_frags; i++) { - double field[3]; + double field[3] = {0.0}; struct efp_atom *atoms; size_t n_atoms; check_fail(efp_get_frag_atom_count(state->efp, i, &n_atoms)); - atoms = xmalloc(n_atoms * sizeof(struct efp_atom)); + atoms = xcalloc(n_atoms, sizeof(struct efp_atom)); check_fail(efp_get_frag_atoms(state->efp, i, n_atoms, atoms)); for (size_t j = 0; j < n_atoms; j++) { @@ -116,7 +116,7 @@ sim_elpot(struct state *state) size_t n_atoms; check_fail(efp_get_frag_atom_count(state->efp, i, &n_atoms)); - atoms = xmalloc(n_atoms * sizeof(struct efp_atom)); + atoms = xcalloc(n_atoms, sizeof(struct efp_atom)); check_fail(efp_get_frag_atoms(state->efp, i, n_atoms, atoms)); msg("ELECTROSTATIC POTENTIAL ON FRAGMENT %zu\n", i); @@ -178,7 +178,7 @@ void sim_frag_elpot(struct state *state) { check_fail(efp_get_frag_atom_count(state->efp, spec_frag, &n_atoms)); // SKP - atoms = xmalloc(n_atoms * sizeof(struct efp_atom)); + atoms = xcalloc(n_atoms, sizeof(struct efp_atom)); check_fail(efp_get_frag_atoms(state->efp, spec_frag, n_atoms, atoms)); msg("ELECTROSTATIC POTENTIAL ON FRAGMENT %zu\n", spec_frag); diff --git a/efpmd/src/energy.c b/efpmd/src/energy.c index e61dcc8..eca23b5 100644 --- a/efpmd/src/energy.c +++ b/efpmd/src/energy.c @@ -100,7 +100,7 @@ void compute_energy(struct state *state, bool do_grad) if (cfg_get_bool(state->cfg, "enable_elpot")) { double *elpot; struct efp_atom *atoms; - atoms = xmalloc(n_special_atoms * sizeof(struct efp_atom)); + atoms = xcalloc(n_special_atoms, sizeof(struct efp_atom)); check_fail(efp_get_frag_atoms(state->efp, spec_frag, n_special_atoms, atoms)); elpot = xcalloc(n_special_atoms, sizeof(double)); for (size_t j = 0; j < n_special_atoms; j++) { @@ -189,7 +189,7 @@ void compute_energy(struct state *state, bool do_grad) for (ifrag = 0, itotal = 0; ifrag < nfrag; ifrag++) { check_fail(efp_get_frag_atom_count(state->efp, ifrag, &natom)); - atoms = xmalloc(natom * sizeof(struct efp_atom)); + atoms = xcalloc(natom, sizeof(struct efp_atom)); check_fail(efp_get_frag_atoms(state->efp, ifrag, natom, atoms)); for (iatom = 0; iatom < natom; iatom++, itotal++) @@ -204,7 +204,7 @@ void compute_energy(struct state *state, bool do_grad) for (ifrag = 0, itotal = 0, grad = state->grad; ifrag < nfrag; ifrag++, grad += 6) { check_fail(efp_get_frag_xyzabc(state->efp, ifrag, xyzabc)); check_fail(efp_get_frag_atom_count(state->efp, ifrag, &natom)); - atoms = xmalloc(natom * sizeof(struct efp_atom)); + atoms = xcalloc(natom, sizeof(struct efp_atom)); check_fail(efp_get_frag_atoms(state->efp, ifrag, natom, atoms)); for (iatom = 0; iatom < natom; iatom++, itotal++) { diff --git a/efpmd/src/gtest.c b/efpmd/src/gtest.c index 403b724..dd739b9 100644 --- a/efpmd/src/gtest.c +++ b/efpmd/src/gtest.c @@ -70,10 +70,10 @@ static void test_cgrad(struct state *state, const double *cgrad) check_fail(efp_get_point_charge_coordinates(state->efp, xyz)); for (size_t i = 0; i < n_charges; i++) { - double ngrad[3]; + double ngrad[3] = {0.0}; for (size_t j = 0; j < 3; j++) { - double e1, e2; + double e1 = 0.0, e2 = 0.0; double coord = xyz[3 * i + j]; xyz[3 * i + j] = coord - dstep; @@ -115,10 +115,10 @@ static void test_fgrad(struct state *state, const double *fgrad) for (size_t i = 0, k=0; i < n_frags; i++) { if (i == spec_frag) continue; - double deriv[3], ngrad[6]; + double deriv[3] = {0.0}, ngrad[6] = {0.0}; for (size_t j = 0; j < 6; j++) { - double e1, e2; + double e1 = 0.0, e2 = 0.0; double coord = xyzabc[6 * i + j]; double step = j < 3 ? dstep : astep; @@ -162,10 +162,10 @@ static void test_agrad(struct state *state, const double *agrad) check_fail(efp_get_frag_atom_coord(state->efp, spec_frag, atom_coord)); for (size_t i = 0; i < n_special_atoms; i++) { - double ngrad[3]; + double ngrad[3] = {0.0}; for (size_t j = 0; j < 3; j++) { - double e1, e2; + double e1 = 0.0, e2 = 0.0; double coord = atom_coord[3 * i + j]; atom_coord[3 * i + j] = coord - dstep; @@ -221,12 +221,12 @@ static void test_agrad(struct state *state, const double *agrad) spec_frag = cfg_get_int(state->cfg, "special_fragment"); check_fail(efp_get_frag_atom_count(state->efp, spec_frag, &n_special_atoms)); - double atom_coord[3 * n_special_atoms]; // = (double*)malloc(3 * n_special_atoms * sizeof(double)); + double atom_coord[3 * n_special_atoms] = {0.0}; // = (double*)malloc(3 * n_special_atoms * sizeof(double)); check_fail(efp_get_frag_atom_coord(state->efp, spec_frag, atom_coord)); for (size_t i = 0; i < n_special_atoms; i++) { - double ngrad[3]; - double tmp_agrad[3]; + double ngrad[3] = {0.0}; + double tmp_agrad[3] = {0.0}; for (size_t j = 0; j < 3; j++) { double e1, e2, e3, e4; diff --git a/efpmd/src/main.c b/efpmd/src/main.c index 5a1ccd4..2780f6f 100644 --- a/efpmd/src/main.c +++ b/efpmd/src/main.c @@ -520,10 +520,10 @@ static void state_init(struct state *state, const struct cfg *cfg, const struct state->torch_grad = xcalloc(n_special_atoms * 3, sizeof(double)); // special fragment atomic coordinates - double *atom_coord = (double*)malloc(3 * n_special_atoms * sizeof(double)); + double *atom_coord = (double*)calloc(3 * n_special_atoms, sizeof(double)); check_fail(efp_get_frag_atom_coord(state->efp, spec_frag, atom_coord)); - int *atom_znuc = (int*)malloc(3 * n_special_atoms * sizeof(int)); + int *atom_znuc = (int*)calloc(3 * n_special_atoms, sizeof(int)); check_fail(efp_get_frag_atom_znuc(state->efp, spec_frag, atom_znuc)); torch_set_coord(state->torch, atom_coord); diff --git a/efpmd/src/opt.c b/efpmd/src/opt.c index ad4704a..6a409cf 100644 --- a/efpmd/src/opt.c +++ b/efpmd/src/opt.c @@ -239,7 +239,7 @@ static void print_status(struct state *state, double e_diff, double rms_grad, do void sim_opt(struct state *state) { size_t n_frags, n_charge, n_coord, n_special_atoms, spec_frag; - double rms_grad, max_grad; + double rms_grad = 0.0, max_grad = 0.0; int static algorithm_switch; diff --git a/efpmd/src/parse.c b/efpmd/src/parse.c index 348ef35..6b11b4e 100644 --- a/efpmd/src/parse.c +++ b/efpmd/src/parse.c @@ -127,7 +127,7 @@ static void parse_frag(struct stream *stream, enum efp_coord_type coord_type, } } else { - frag->coord = (double*)malloc(n_rows * n_cols * sizeof(double)); + frag->coord = (double*)calloc(n_rows * n_cols, sizeof(double)); for (int i = 0, idx = 0; i < n_rows; i++) { for (int j = 0; j < n_cols; j++, idx++) { if (!efp_stream_parse_double(stream, frag->coord + idx)) @@ -203,6 +203,8 @@ struct sys *parse_input(struct cfg *cfg, const char *path) if (is_keyword(efp_stream_get_ptr(stream), "fragment")) { struct frag frag; + memset(&frag, 0, sizeof(frag)); + enum efp_coord_type coord_type; efp_stream_advance(stream, strlen("fragment")); diff --git a/efpmd/src/torch.c b/efpmd/src/torch.c index 2fe3b6e..7a592c4 100644 --- a/efpmd/src/torch.c +++ b/efpmd/src/torch.c @@ -53,10 +53,10 @@ void get_torch_type(struct torch *torch, const char *str) { void torch_init(struct torch *torch, size_t natom) { torch->natoms = natom; - torch->atom_coords = malloc(3*natom*sizeof(double)); - torch->atom_types = malloc(natom*sizeof(int)); - torch->grad = malloc(3*natom*sizeof(double)); - torch->elpot = malloc(natom*sizeof(double)); + torch->atom_coords = calloc(3*natom, sizeof(double)); + torch->atom_types = calloc(natom, sizeof(int)); + torch->grad = calloc(3*natom, sizeof(double)); + torch->elpot = calloc(natom, sizeof(double)); } void torch_get_atom_count(struct torch *torch , size_t natom) { @@ -101,13 +101,13 @@ void torch_custom_compute(struct torch *torch, int print) { float *frag_coord; float *elecpots_data; //float custom_energy; - double custom_energy; + double custom_energy = 0.0; - elecpots_data = malloc(n_atoms * sizeof(float)); - gradients = malloc(n_atoms * 3 * sizeof(float)); - forces = malloc(n_atoms * 3 * sizeof(float)); + elecpots_data = calloc(n_atoms, sizeof(float)); + gradients = calloc(n_atoms * 3, sizeof(float)); + forces = calloc(n_atoms * 3, sizeof(float)); - frag_coord = malloc(n_atoms*3* sizeof(float)); + frag_coord = calloc(n_atoms*3, sizeof(float)); for (size_t i=0; iatom_coords[i*3] * BOHR_RADIUS); @@ -208,12 +208,12 @@ void torch_compute(struct torch *torch, const char* nn_path, int print) { size_t n_atoms = torch->natoms; float *gradients, *forces, *frag_coord; - double ani_energy; + double ani_energy = 0.0; - gradients = malloc(n_atoms * 3 * sizeof(float)); - forces = malloc(n_atoms * 3 * sizeof(float)); + gradients = calloc(n_atoms * 3, sizeof(float)); + forces = calloc(n_atoms * 3, sizeof(float)); - frag_coord = malloc(n_atoms*3* sizeof(float)); + frag_coord = calloc(n_atoms*3, sizeof(float)); for (size_t i=0; iatom_coords[i*3] * BOHR_RADIUS); frag_coord[i*3+1] = (float)(torch->atom_coords[i*3+1] * BOHR_RADIUS); diff --git a/lib/pylibefp/__pycache__/__init__.cpython-312.pyc b/lib/pylibefp/__pycache__/__init__.cpython-312.pyc index bba1dbf5377b06536f303e4d57e7f4ec7ac56371..5d32ad8c00955797b71a5e0daf697012a46d42bb 100644 GIT binary patch delta 20 acmey#`jeIWG%qg~0}xE)c(9TC9TNaSbOsy% delta 20 acmey#`jeIWG%qg~0}veIxWAG69TNaT#s*9P diff --git a/lib/pylibefp/__pycache__/wrapper.cpython-312.pyc b/lib/pylibefp/__pycache__/wrapper.cpython-312.pyc index 3fd23ab547996f58d7b980f929b9ac5504e28346..7e386b01496fac7038d109d02370e9ddf284ed44 100644 GIT binary patch delta 145 zcmZ4anq}h~7T(jmyj%=GFp=XyrprWLNye&;>SnBr%98__#JQD0G9Zwu0_LkgctE}? zn6C=wtAY5G-901q<%x*sDY)OqmknZgUk(8I~ZH(hJp!SnCXhgr8DW@UV=!opts) || special_xr) { - double exr, ecp; + double exr = 0.0, ecp = 0.0; efp_frag_frag_xr(efp, i, fr_j, s, ds, &exr, &ecp); @@ -800,7 +800,7 @@ EFP_EXPORT enum efp_result efp_get_atomic_gradient(struct efp *efp, double *grad) { six_t *efpgrad = NULL; /* Calculated EFP gradient */ - vec_t *pgrad; /* Conversion of grad to vec_t type */ + vec_t *pgrad = NULL; /* Conversion of grad to vec_t type */ size_t i, j, k, l; size_t nr; /* Number of atoms in the current fragment */ size_t maxa; /* Maximum number of size of m, Ia, r arrays */ @@ -833,15 +833,15 @@ efp_get_atomic_gradient(struct efp *efp, double *grad) res = EFP_RESULT_NO_MEMORY; /* Create and initialize some arrays for work */ - if ((r = (vec_t *)malloc(maxa * sizeof(*r))) == NULL) + if ((r = (vec_t *)calloc(maxa, sizeof(*r))) == NULL) goto error; - if ((m = (double *)malloc(maxa * sizeof(*m))) == NULL) + if ((m = (double *)calloc(maxa, sizeof(*m))) == NULL) goto error; - if ((Ia = (double *)malloc(maxa * sizeof(*Ia))) == NULL) + if ((Ia = (double *)calloc(maxa, sizeof(*Ia))) == NULL) goto error; /* Copy computed efp->grad */ - if ((efpgrad = (six_t *)malloc(efp->n_frag * sizeof(*efpgrad))) == NULL) + if ((efpgrad = (six_t *)calloc(efp->n_frag, sizeof(*efpgrad))) == NULL) goto error; memcpy(efpgrad, efp->grad, efp->n_frag * sizeof(*efpgrad)); @@ -963,7 +963,7 @@ EFP_EXPORT enum efp_result efp_get_frag_atomic_gradient(struct efp *efp, size_t frag_id, double *grad) { six_t *efpgrad = NULL; /* Calculated EFP gradient */ - vec_t *pgrad; /* Conversion of grad to vec_t type */ + vec_t *pgrad = NULL; /* Conversion of grad to vec_t type */ size_t i, j, k, l; size_t nr; /* Number of atoms in the current fragment */ vec_t *r = NULL; /* Radius-vector of each atom inside current fragment @@ -992,11 +992,11 @@ efp_get_frag_atomic_gradient(struct efp *efp, size_t frag_id, double *grad) res = EFP_RESULT_NO_MEMORY; /* Create and initialize some arrays for work */ - if ((r = (vec_t *)malloc(nr * sizeof(*r))) == NULL) + if ((r = (vec_t *)calloc(nr, sizeof(*r))) == NULL) goto error; - if ((m = (double *)malloc(nr * sizeof(*m))) == NULL) + if ((m = (double *)calloc(nr, sizeof(*m))) == NULL) goto error; - if ((Ia = (double *)malloc(nr * sizeof(*Ia))) == NULL) + if ((Ia = (double *)calloc(nr, sizeof(*Ia))) == NULL) goto error; //for (size_t i=0; in_frag; i++) { @@ -1005,7 +1005,7 @@ efp_get_frag_atomic_gradient(struct efp *efp, size_t frag_id, double *grad) /* Copy computed efp->grad */ - if ((efpgrad = (six_t *)malloc(sizeof(*efpgrad))) == NULL) + if ((efpgrad = (six_t *)calloc(1,sizeof(*efpgrad))) == NULL) goto error; memcpy(efpgrad, efp->grad + frag_id, sizeof(*efpgrad)); @@ -2484,6 +2484,7 @@ efp_add_fragment(struct efp *efp, const char *name) enum efp_result res; struct frag *frag = efp->frags + efp->n_frag - 1; + memset(frag, 0, sizeof(*frag)); // if update/rotate parameters if (efp->opts.update_params == 1) { @@ -2536,17 +2537,14 @@ efp_add_ligand(struct efp *efp, int ligand_index) { lig->ligand_frag = &efp->frags[ligand_index]; lig->n_ligand_pts = efp->frags[ligand_index].n_polarizable_pts; - size_t size; - size = lig->n_ligand_pts * sizeof(struct ligand_pt); - lig->ligand_pts = (struct ligand_pt *) malloc(size); + lig->ligand_pts = (struct ligand_pt *) calloc(lig->n_ligand_pts, sizeof(struct ligand_pt)); if (lig->ligand_pts == NULL) return EFP_RESULT_NO_MEMORY; for (size_t i = 0; i < lig->n_ligand_pts; i++) { struct ligand_pt *pt = lig->ligand_pts + i; - size = efp->n_frag * sizeof(vec_t); pt->n_frag = efp->n_frag; - pt->fragment_field = (vec_t *) malloc(size); + pt->fragment_field = (vec_t *) calloc(efp->n_frag, sizeof(vec_t)); if (!pt->fragment_field) return EFP_RESULT_NO_MEMORY; } @@ -2981,7 +2979,7 @@ efp_set_symmlist(struct efp *efp) // this needs to be changed for list settings of symmetry!!! efp->nsymm_frag = efp->n_lib; char name[32]; - char** unique_names=malloc(efp->n_lib * sizeof(name)); + char** unique_names=calloc(efp->n_lib, sizeof(name)); for (int i = 0; i < efp->n_lib; i++){ unique_names[i] = NULL; } diff --git a/src/elec.c b/src/elec.c index 5392474..40757f5 100644 --- a/src/elec.c +++ b/src/elec.c @@ -387,7 +387,7 @@ efp_frag_frag_elec(struct efp *efp, size_t fr_i_idx, size_t fr_j_idx) static void rotate_quadrupole(const mat_t *rotmat, const double *in, double *out) { - double full_in[9], full_out[9]; + double full_in[9] = {0.0}, full_out[9] = {0.0}; for (size_t a = 0; a < 3; a++) for (size_t b = 0; b < 3; b++) @@ -403,7 +403,7 @@ rotate_quadrupole(const mat_t *rotmat, const double *in, double *out) static void rotate_octupole(const mat_t *rotmat, const double *in, double *out) { - double full_in[27], full_out[27]; + double full_in[27]={0.0}, full_out[27]={0.0}; for (size_t a = 0; a < 3; a++) for (size_t b = 0; b < 3; b++) @@ -827,7 +827,7 @@ lj_energy(struct efp *efp, size_t fr_i_idx, size_t fr_j_idx, double energy = 0.0; double g = 0.0, g1 = 0.0, g2 = 0.0; - double r2, sr6 = 0.0; + double r2 = 0.0, sr6 = 0.0; if (combination_rule == 1) { // E_lj = (C_12/r^12 - C_6/r^6) diff --git a/src/mathutil.h b/src/mathutil.h index 3c613d6..1a3a746 100644 --- a/src/mathutil.h +++ b/src/mathutil.h @@ -369,7 +369,7 @@ euler_to_matrix(double a, double b, double c, mat_t *out) static inline void matrix_to_euler(const mat_t *rotmat, double *ea, double *eb, double *ec) { - double a, b, c, sinb; + double a=0.0, b=0.0, c=0.0, sinb=0.0; if (fabs(rotmat->zz - 1.0) < 1.0e-7) { b = 0.0; diff --git a/src/parse.c b/src/parse.c index 1c1b3a9..1e6bfd2 100644 --- a/src/parse.c +++ b/src/parse.c @@ -503,7 +503,7 @@ parse_polarizable_pts(struct frag *frag, struct stream *stream) } efp_stream_next_line(stream); - double m[9]; + double m[9]={0.0}; for (size_t i = 0; i < 9; i++) if (!tok_double(stream, m + i)){ @@ -531,7 +531,7 @@ parse_polarizable_pts(struct frag *frag, struct stream *stream) static enum efp_result parse_dynamic_polarizable_pts(struct frag *frag, struct stream *stream) { - double m[9]; + double m[9]={0.0}; efp_stream_next_line(stream); @@ -549,6 +549,8 @@ parse_dynamic_polarizable_pts(struct frag *frag, struct stream *stream) struct dynamic_polarizable_pt *pt = frag->dynamic_polarizable_pts + frag->n_dynamic_polarizable_pts - 1; + memset(pt, 0, sizeof(*pt)); + if (!efp_stream_advance(stream, 5)){ efp_log("parse_dynamic_polarizable_pts() failure for fragment %s", frag->name); @@ -699,6 +701,7 @@ parse_projection_basis(struct frag *frag, struct stream *stream) return EFP_RESULT_NO_MEMORY; struct shell *shell = atom->shells + atom->n_shells - 1; + memset(shell, 0, sizeof(*shell)); shell->type = efp_stream_get_char(stream); //printf("\n shell->type %c", shell->type); @@ -718,7 +721,7 @@ parse_projection_basis(struct frag *frag, struct stream *stream) efp_stream_next_line(stream); size_t cnt = (shell->type == 'L' ? 3 : 2) * shell->n_funcs; - shell->coef = (double *)malloc(cnt * sizeof(double)); + shell->coef = (double *)calloc(cnt, sizeof(double)); if (shell->coef == NULL) return EFP_RESULT_NO_MEMORY; double *ptr = shell->coef; @@ -778,8 +781,8 @@ parse_projection_wf(struct frag *frag, struct stream *stream) return EFP_RESULT_SYNTAX_ERROR; } - frag->xr_wf = (double *)malloc( - frag->n_lmo * frag->xr_wf_size * sizeof(double)); + frag->xr_wf = (double *)calloc( + frag->n_lmo * frag->xr_wf_size, sizeof(double)); if (frag->xr_wf == NULL) return EFP_RESULT_NO_MEMORY; @@ -832,7 +835,7 @@ parse_fock_mat(struct frag *frag, struct stream *stream) efp_stream_next_line(stream); size_t size = frag->n_lmo * (frag->n_lmo + 1) / 2; - frag->xr_fock_mat = (double *)malloc(size * sizeof(double)); + frag->xr_fock_mat = (double *)calloc(size, sizeof(double)); if (frag->xr_fock_mat == NULL) return EFP_RESULT_NO_MEMORY; @@ -865,7 +868,7 @@ parse_lmo_centroids(struct frag *frag, struct stream *stream) efp_log("number of LMO centroids is zero"); return EFP_RESULT_SYNTAX_ERROR; } - frag->lmo_centroids = (vec_t *)malloc(frag->n_lmo * sizeof(vec_t)); + frag->lmo_centroids = (vec_t *)calloc(frag->n_lmo, sizeof(vec_t)); if (frag->lmo_centroids == NULL) return EFP_RESULT_NO_MEMORY; @@ -979,7 +982,7 @@ skip_ctfok(struct frag *frag, struct stream *stream) static enum efp_result parse_dipquad_polarizable_pts(struct frag *frag, struct stream *stream) { - double m[27]; + double m[27]={0.0}; efp_stream_next_line(stream); @@ -997,6 +1000,7 @@ parse_dipquad_polarizable_pts(struct frag *frag, struct stream *stream) struct dipquad_polarizable_pt *pt = frag->dipquad_polarizable_pts + frag->n_dynamic_polarizable_pts - 1; + memset(pt, 0, sizeof(*pt)); if (!efp_stream_advance(stream, 5)){ printf("problem with fragment %s", frag->name); @@ -1142,7 +1146,7 @@ parse_screen(struct frag *frag, struct stream *stream) double *scr; char type; - scr = (double *)malloc(frag->n_multipole_pts * sizeof(double)); + scr = (double *)calloc(frag->n_multipole_pts, sizeof(double)); if (scr == NULL) return EFP_RESULT_NO_MEMORY; type = efp_stream_get_char(stream); @@ -1227,7 +1231,7 @@ parse_screen(struct frag *frag, struct stream *stream) struct multipole_pt tmp_pt; memset(&tmp_pt, 0, sizeof(tmp_pt)); - double tmp_screen; + double tmp_screen = 0.0; if (!tok_label(stream, sizeof(tmp_pt.label), tmp_pt.label) || !tok_double(stream, NULL) || !tok_double(stream, &tmp_screen)){ @@ -1278,7 +1282,7 @@ parse_xrfit(struct frag *frag, struct stream *stream) return EFP_RESULT_SYNTAX_ERROR; } - frag->xrfit = (double *)malloc(frag->n_lmo * 4 * sizeof(double)); + frag->xrfit = (double *)calloc(frag->n_lmo * 4, sizeof(double)); if (frag->xrfit == NULL) return EFP_RESULT_NO_MEMORY; efp_stream_next_line(stream); diff --git a/src/pol.c b/src/pol.c index f5b938c..b0ab144 100644 --- a/src/pol.c +++ b/src/pol.c @@ -68,7 +68,7 @@ get_multipole_field(const vec_t *xyz, const struct multipole_pt *mult_pt, xyz->z - mult_pt->z - swf->cell.z }; - double t1, t2; + double t1=0.0, t2=0.0; double r = vec_len(&dr); double r3 = r * r * r; double r5 = r3 * r * r; @@ -306,8 +306,8 @@ add_electron_density_field(struct efp *efp) if (efp->get_electron_density_field == NULL) return EFP_RESULT_SUCCESS; - xyz = (vec_t *)malloc(efp->n_polarizable_pts * sizeof(vec_t)); - field = (vec_t *)malloc(efp->n_polarizable_pts * sizeof(vec_t)); + xyz = (vec_t *)calloc(efp->n_polarizable_pts, sizeof(vec_t)); + field = (vec_t *)calloc(efp->n_polarizable_pts, sizeof(vec_t)); for (size_t i = 0, idx = 0; i < efp->n_frag; i++) { struct frag *frag = efp->frags + i; @@ -1079,7 +1079,7 @@ compute_grad_point(struct efp *efp, size_t frag_idx, size_t pt_idx) const struct frag *fr_i = efp->frags + frag_idx; const struct polarizable_pt *pt_i = fr_i->polarizable_pts + pt_idx; vec_t force, add_i, add_j, force_, add_i_, add_j_; - double e; + double e = 0.0; vec_t dipole_i = { 0.5 * (pt_i->indip.x + pt_i->indipconj.x), diff --git a/src/xr.c b/src/xr.c index 552622b..b5c1ebe 100644 --- a/src/xr.c +++ b/src/xr.c @@ -209,7 +209,7 @@ lmo_lmo_xr_grad(struct efp *efp, size_t fr_i_idx, size_t fr_j_idx, six_t ds_ij = lmo_ds[ij]; six_t dt_ij = lmo_dt[ij]; - double t1, t2; + double t1=0.0, t2=0.0; vec_t force = vec_zero, torque_i = vec_zero; /* first part */ @@ -535,12 +535,12 @@ efp_frag_frag_xr(struct efp *efp, size_t frag_i, size_t frag_j, double *lmo_s, size_t ij_wf_size = fr_i->xr_wf_size * fr_j->xr_wf_size; size_t ij_nlmo = fr_i->n_lmo * fr_j->n_lmo; size_t ij_nlmo_wf_size = fr_i->n_lmo * fr_j->xr_wf_size; - double *s = (double *) malloc(ij_wf_size * sizeof(double)); - double *t = (double *) malloc(ij_wf_size * sizeof(double)); - double *lmo_t = (double *) malloc(ij_nlmo * sizeof(double)); - double *tmp = (double *) malloc(ij_nlmo_wf_size * sizeof(double)); - struct xr_atom *atoms_j = (struct xr_atom *) malloc( - fr_j->n_xr_atoms * sizeof(struct xr_atom)); + double *s = (double *) calloc(ij_wf_size, sizeof(double)); + double *t = (double *) calloc(ij_wf_size, sizeof(double)); + double *lmo_t = (double *) calloc(ij_nlmo, sizeof(double)); + double *tmp = (double *) calloc(ij_nlmo_wf_size, sizeof(double)); + struct xr_atom *atoms_j = (struct xr_atom *) calloc( + fr_j->n_xr_atoms, sizeof(struct xr_atom)); for (size_t j = 0; j < fr_j->n_xr_atoms; j++) { atoms_j[j] = fr_j->xr_atoms[j]; @@ -600,11 +600,11 @@ efp_frag_frag_xr(struct efp *efp, size_t frag_i, size_t frag_j, double *lmo_s, /* compute gradient */ - six_t *ds = (six_t *) malloc(ij_wf_size * sizeof(six_t)); - six_t *dt = (six_t *) malloc(ij_wf_size * sizeof(six_t)); - six_t *lmo_dt = (six_t *) malloc(ij_nlmo * sizeof(six_t)); - six_t *sixtmp = (six_t *) malloc(ij_nlmo_wf_size * sizeof(six_t)); - double *lmo_tmp = (double *) malloc(ij_nlmo * sizeof(double)); + six_t *ds = (six_t *) calloc(ij_wf_size, sizeof(six_t)); + six_t *dt = (six_t *) calloc(ij_wf_size, sizeof(six_t)); + six_t *lmo_dt = (six_t *) calloc(ij_nlmo, sizeof(six_t)); + six_t *sixtmp = (six_t *) calloc(ij_nlmo_wf_size, sizeof(six_t)); + double *lmo_tmp = (double *) calloc(ij_nlmo, sizeof(double)); efp_st_int_deriv(fr_i->n_xr_atoms, fr_i->xr_atoms, fr_j->n_xr_atoms, atoms_j, @@ -731,7 +731,7 @@ rotate_func_f(const mat_t *rotmat, const double *in, double *out) const double norm1 = sqrt(5.0) / 3.0; const double norm2 = sqrt(3.0) / 2.0; - double full_in[27], full_out[27]; + double full_in[27]={0.0}, full_out[27]={0.0}; for (size_t a = 0; a < 3; a++) for (size_t b = 0; b < 3; b++) From fe99870f80f5e94fe59acf0e82fe9e3ae16e69bc Mon Sep 17 00:00:00 2001 From: "Slipchenko, Lyudmila V" Date: Thu, 16 Apr 2026 00:29:22 -0400 Subject: [PATCH 12/40] printing tests that crash --- tests/elec_2a.in | 1 + tests/elec_3a.in | 1 + tests/pol_2a.in | 1 + tests/pol_2b.in | 1 + tests/total_4b.in | 1 + 5 files changed, 5 insertions(+) diff --git a/tests/elec_2a.in b/tests/elec_2a.in index 13d8349..d6d7847 100644 --- a/tests/elec_2a.in +++ b/tests/elec_2a.in @@ -4,6 +4,7 @@ coord xyzabc terms elec elec_damp screen fraglib_path ../fraglib +print 3 fragment h2o_l -1.0 3.7 0.4 -1.3 0.0 7.0 diff --git a/tests/elec_3a.in b/tests/elec_3a.in index 3e41fc7..ff2c2bc 100644 --- a/tests/elec_3a.in +++ b/tests/elec_3a.in @@ -4,6 +4,7 @@ coord points terms elec elec_damp screen fraglib_path ../fraglib +print 3 fragment h2o_l -3.394 -1.900 -3.700 diff --git a/tests/pol_2a.in b/tests/pol_2a.in index 953cbb0..8f19191 100644 --- a/tests/pol_2a.in +++ b/tests/pol_2a.in @@ -4,6 +4,7 @@ coord xyzabc terms elec pol elec_damp screen fraglib_path ../fraglib +print 3 fragment h2o_l -1.0 3.7 0.4 -1.3 0.0 7.0 diff --git a/tests/pol_2b.in b/tests/pol_2b.in index 91b8b37..82017bc 100644 --- a/tests/pol_2b.in +++ b/tests/pol_2b.in @@ -5,6 +5,7 @@ terms elec pol elec_damp screen pol_driver direct fraglib_path ../fraglib +print 3 fragment h2o_l -1.0 3.7 0.4 -1.3 0.0 7.0 diff --git a/tests/total_4b.in b/tests/total_4b.in index 2d724ff..725378d 100644 --- a/tests/total_4b.in +++ b/tests/total_4b.in @@ -6,6 +6,7 @@ elec_damp overlap disp_damp overlap pol_damp tt fraglib_path ../fraglib +print 3 fragment acetone_l 0.0 0.0 0.0 0.0 0.2 0.3 From a8d94c70b81be0ca48d0f88e113ce91faf05c243 Mon Sep 17 00:00:00 2001 From: "Slipchenko, Lyudmila V" Date: Thu, 16 Apr 2026 23:41:14 -0400 Subject: [PATCH 13/40] fixing memory bug --- efpmd/src/common.c | 2 +- efpmd/src/energy.c | 3 ++- .../__pycache__/__init__.cpython-312.pyc | Bin 761 -> 761 bytes .../__pycache__/wrapper.cpython-312.pyc | Bin 79409 -> 79409 bytes tests/elec_2a.in | 1 - tests/elec_3a.in | 1 - tests/pol_2a.in | 1 - tests/pol_2b.in | 1 - tests/total_4b.in | 1 - 9 files changed, 3 insertions(+), 7 deletions(-) diff --git a/efpmd/src/common.c b/efpmd/src/common.c index 81d6ac7..2199019 100644 --- a/efpmd/src/common.c +++ b/efpmd/src/common.c @@ -199,7 +199,7 @@ void print_geometry_pbc(struct efp *efp, int ligand) void print_energy(struct state *state) { // printf("Inside print_energy\n"); - struct efp_energy energy; + struct efp_energy energy = {0.0}; check_fail(efp_get_energy(state->efp, &energy)); diff --git a/efpmd/src/energy.c b/efpmd/src/energy.c index eca23b5..2195c74 100644 --- a/efpmd/src/energy.c +++ b/efpmd/src/energy.c @@ -38,7 +38,8 @@ void compute_energy(struct state *state, bool do_grad) { struct efp_atom *atoms; struct efp_energy efp_energy; - double xyz[3], xyzabc[6], *grad; + memset(&efp_energy, 0, sizeof(efp_energy)); + double xyz[3] = {0.0}, xyzabc[6] = {0.0}, *grad; size_t ifrag, nfrag, iatom, natom, spec_frag, n_special_atoms; int itotal; diff --git a/lib/pylibefp/__pycache__/__init__.cpython-312.pyc b/lib/pylibefp/__pycache__/__init__.cpython-312.pyc index 5d32ad8c00955797b71a5e0daf697012a46d42bb..c9d376baf976ea72484cce4f9dcd51aebed367c2 100644 GIT binary patch delta 20 acmey#`jeIWG%qg~0}$+A^>8EiJ0<`|hX(Bc delta 20 acmey#`jeIWG%qg~0}xE)c(9TC9TNaSbOsy% diff --git a/lib/pylibefp/__pycache__/wrapper.cpython-312.pyc b/lib/pylibefp/__pycache__/wrapper.cpython-312.pyc index 7e386b01496fac7038d109d02370e9ddf284ed44..2bfa0ce6e9732a530fc359539f9376a5290331e1 100644 GIT binary patch delta 25 fcmdn^hGpX$7Vgu$yj%=Guz%IVM((ZLjA~{8c$Ek+ delta 25 fcmdn^hGpX$7Vgu$yj%=GFp=XyBllKrMl~}4aSsPy diff --git a/tests/elec_2a.in b/tests/elec_2a.in index d6d7847..13d8349 100644 --- a/tests/elec_2a.in +++ b/tests/elec_2a.in @@ -4,7 +4,6 @@ coord xyzabc terms elec elec_damp screen fraglib_path ../fraglib -print 3 fragment h2o_l -1.0 3.7 0.4 -1.3 0.0 7.0 diff --git a/tests/elec_3a.in b/tests/elec_3a.in index ff2c2bc..3e41fc7 100644 --- a/tests/elec_3a.in +++ b/tests/elec_3a.in @@ -4,7 +4,6 @@ coord points terms elec elec_damp screen fraglib_path ../fraglib -print 3 fragment h2o_l -3.394 -1.900 -3.700 diff --git a/tests/pol_2a.in b/tests/pol_2a.in index 8f19191..953cbb0 100644 --- a/tests/pol_2a.in +++ b/tests/pol_2a.in @@ -4,7 +4,6 @@ coord xyzabc terms elec pol elec_damp screen fraglib_path ../fraglib -print 3 fragment h2o_l -1.0 3.7 0.4 -1.3 0.0 7.0 diff --git a/tests/pol_2b.in b/tests/pol_2b.in index 82017bc..91b8b37 100644 --- a/tests/pol_2b.in +++ b/tests/pol_2b.in @@ -5,7 +5,6 @@ terms elec pol elec_damp screen pol_driver direct fraglib_path ../fraglib -print 3 fragment h2o_l -1.0 3.7 0.4 -1.3 0.0 7.0 diff --git a/tests/total_4b.in b/tests/total_4b.in index 725378d..2d724ff 100644 --- a/tests/total_4b.in +++ b/tests/total_4b.in @@ -6,7 +6,6 @@ elec_damp overlap disp_damp overlap pol_damp tt fraglib_path ../fraglib -print 3 fragment acetone_l 0.0 0.0 0.0 0.0 0.2 0.3 From 575d51b5118860edc6beb41b45a32c1d52c19507 Mon Sep 17 00:00:00 2001 From: Lyudmila Slipchenko Date: Fri, 17 Apr 2026 00:31:49 -0400 Subject: [PATCH 14/40] Update ci.yml tests with valgrind --- .github/workflows/ci.yml | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 25a68f8..1ead8e4 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -181,8 +181,16 @@ jobs: objdump.exe -p "${{ github.workspace }}\\installed\\bin\\efpmd.exe" | grep "dll" fi - - name: Test (CTest) - unit tests - run: ctest --output-on-failure --test-dir "${{ github.workspace }}/build" + #- name: Test (CTest) - unit tests + # run: ctest --output-on-failure --test-dir "${{ github.workspace }}/build" + + - name: Test (CTest) with Valgrind + run: | + sudo apt-get update && sudo apt-get install -y valgrind + ctest --output-on-failure \ + --test-dir "${{ github.workspace }}/build" \ + -T memcheck \ + --overwrite MemoryCheckCommandOptions="--leak-check=full --track-origins=yes --error-exitcode=1" - name: Test (find_package) - consume installation run: | From d7bbdd92c2a6e577c75572975af5bb3be040587c Mon Sep 17 00:00:00 2001 From: Lyudmila Slipchenko Date: Fri, 17 Apr 2026 00:37:57 -0400 Subject: [PATCH 15/40] Update ci.yml --- .github/workflows/ci.yml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 1ead8e4..cb24b10 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -187,11 +187,13 @@ jobs: - name: Test (CTest) with Valgrind run: | sudo apt-get update && sudo apt-get install -y valgrind - ctest --output-on-failure \ - --test-dir "${{ github.workspace }}/build" \ - -T memcheck \ - --overwrite MemoryCheckCommandOptions="--leak-check=full --track-origins=yes --error-exitcode=1" - + # Run valgrind directly on the ctest executable + valgrind --tool=memcheck \ + --leak-check=full \ + --track-origins=yes \ + --error-exitcode=1 \ + ctest --output-on-failure --test-dir "${{ github.workspace }}/build" + - name: Test (find_package) - consume installation run: | mkdir test_installed_library && cd test_installed_library From db4c703c0f734288dfa42639513ece962534c513 Mon Sep 17 00:00:00 2001 From: Lyudmila Slipchenko Date: Fri, 17 Apr 2026 00:45:54 -0400 Subject: [PATCH 16/40] Update ci.yml --- .github/workflows/ci.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index cb24b10..e1e7396 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -191,6 +191,7 @@ jobs: valgrind --tool=memcheck \ --leak-check=full \ --track-origins=yes \ + --trace-children=yes \ --error-exitcode=1 \ ctest --output-on-failure --test-dir "${{ github.workspace }}/build" From b3a752e86ed90e9a723681d304762bf748673fec Mon Sep 17 00:00:00 2001 From: Lyudmila Slipchenko Date: Sat, 18 Apr 2026 22:23:33 -0400 Subject: [PATCH 17/40] Update ci.yml --- .github/workflows/ci.yml | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index e1e7396..79887be 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -181,19 +181,19 @@ jobs: objdump.exe -p "${{ github.workspace }}\\installed\\bin\\efpmd.exe" | grep "dll" fi - #- name: Test (CTest) - unit tests - # run: ctest --output-on-failure --test-dir "${{ github.workspace }}/build" + - name: Test (CTest) - unit tests + run: ctest --output-on-failure --test-dir "${{ github.workspace }}/build" - - name: Test (CTest) with Valgrind - run: | - sudo apt-get update && sudo apt-get install -y valgrind - # Run valgrind directly on the ctest executable - valgrind --tool=memcheck \ - --leak-check=full \ - --track-origins=yes \ - --trace-children=yes \ - --error-exitcode=1 \ - ctest --output-on-failure --test-dir "${{ github.workspace }}/build" + # - name: Test (CTest) with Valgrind + # run: | + # sudo apt-get update && sudo apt-get install -y valgrind + # # Run valgrind directly on the ctest executable + # valgrind --tool=memcheck \ + # --leak-check=full \ + # --track-origins=yes \ + # --trace-children=yes \ + # --error-exitcode=1 \ + # ctest --output-on-failure --test-dir "${{ github.workspace }}/build" - name: Test (find_package) - consume installation run: | From 0e32e84cdda69935bcf4b76e2a13a66e979399f9 Mon Sep 17 00:00:00 2001 From: "Slipchenko, Lyudmila V" Date: Sat, 18 Apr 2026 22:36:20 -0400 Subject: [PATCH 18/40] cleaning int vs size_t --- efpmd/src/common.c | 22 ++-- efpmd/src/efield.c | 37 ++----- efpmd/src/energy.c | 10 +- efpmd/src/gtest.c | 16 ++- efpmd/src/main.c | 2 +- efpmd/src/opt.c | 6 +- efpmd/src/sp.c | 9 +- .../__pycache__/__init__.cpython-312.pyc | Bin 761 -> 761 bytes .../__pycache__/wrapper.cpython-312.pyc | Bin 79409 -> 79409 bytes setup.sh | 2 +- src/efp.c | 71 +++++-------- src/elec.c | 79 ++++++++++---- src/parse.c | 17 +-- src/pol.c | 97 +++++++++++------- 14 files changed, 200 insertions(+), 168 deletions(-) diff --git a/efpmd/src/common.c b/efpmd/src/common.c index 2199019..fd899c8 100644 --- a/efpmd/src/common.c +++ b/efpmd/src/common.c @@ -146,20 +146,24 @@ void print_geometry_pbc(struct efp *efp, int ligand) size_t n_frags; check_fail(efp_get_frag_count(efp, &n_frags)); + if (ligand < 0) + msg(" WARNING! Specify ligand tor printing PBC geometry\n\n"); + size_t lig = (size_t)ligand; + msg(" GEOMETRY IN PBC CELL (ANGSTROMS)\n\n"); - double bx[6]; + double bx[6] = {0.0}; check_fail(efp_get_periodic_box(efp, bx)); six_t box = {bx[0],bx[1],bx[2],bx[3],bx[4],bx[5]}; //six_t box = {10.66, 12.03, 10.872, 90.0, 115.83, 90.0}; double lig_com[6]; - check_fail(efp_get_frag_xyzabc(efp,ligand,lig_com)); + check_fail(efp_get_frag_xyzabc(efp,lig,lig_com)); for (size_t i = 0; i < n_frags; i++) { vec_t cell = {0.0,0.0,0.0}; - if (i != ligand) { + if (i != lig) { double frag_com[6]; check_fail(efp_get_frag_xyzabc(efp, i, frag_com)); vec_t dr = {frag_com[0] - lig_com[0], frag_com[1] - lig_com[1], frag_com[2] - lig_com[2]}; @@ -352,7 +356,9 @@ void print_pair_energy(struct state *state) { char ligand[32]; size_t lig_atoms; - size_t ligand_index = cfg_get_int(state->cfg, "ligand"); + size_t ligand_index = (size_t)cfg_get_int(state->cfg, "ligand"); + if (ligand_index >= n_frags) + error("Ligand index is out of bound"); check_fail(efp_get_frag_name(state->efp, ligand_index, sizeof(ligand),ligand)); check_fail(efp_get_frag_atom_count(state->efp, ligand_index, &lig_atoms)); struct efp_atom latoms[lig_atoms]; @@ -360,11 +366,9 @@ void print_pair_energy(struct state *state) { char frag_name[32]; size_t frag_atoms; - double lattice_energy[6]; - for (size_t j=0; j<6; j++){ - lattice_energy[j]=0.0; - } - for (size_t i=0; i efp, i, sizeof(frag_name),frag_name)); check_fail(efp_get_frag_atom_count(state->efp, i, &frag_atoms)); diff --git a/efpmd/src/efield.c b/efpmd/src/efield.c index c8ad755..57cbc19 100644 --- a/efpmd/src/efield.c +++ b/efpmd/src/efield.c @@ -133,38 +133,13 @@ sim_elpot(struct state *state) msg("ELECTROSTATIC POTENTIAL JOB COMPLETED SUCCESSFULLY\n"); } -/* -void get_frag_elpot(struct state *state) { - size_t spec_frag; - spec_frag = cfg_get_int(state->cfg, "special_fragment"); - - double elpot; - struct efp_atom *atoms; - size_t n_atoms; - - - check_fail(efp_get_frag_atom_count(state->efp, spec_frag, &n_atoms)); // SKP - atoms = xmalloc(n_atoms * sizeof(struct efp_atom)); - check_fail(efp_get_frag_atoms(state->efp, spec_frag, n_atoms, atoms)); - //state->spec_elpot = malloc(n_atoms * sizeof(double)); - state->spec_elpot = xcalloc(n_atoms, sizeof(double)); - - - for (size_t j = 0; j < n_atoms; j++) { - check_fail(efp_get_elec_potential(state->efp, spec_frag, &atoms[j].x, &elpot)); - state->spec_elpot[j] = elpot; - print_elpot(atoms + j, elpot); - } - - free(atoms); -} -*/ - void sim_frag_elpot(struct state *state) { - // size_t chosen_frag = cfg_get_int(state->cfg, "frag_num"); + if (cfg_get_int(state->cfg, "special_fragment") < 0) + error("Special fragment is not defined in fragment elec potential calculation"); + size_t spec_frag; - spec_frag = cfg_get_int(state->cfg, "special_fragment"); + spec_frag = (size_t)cfg_get_int(state->cfg, "special_fragment"); msg("\n=============FRAG-ELECTROSTATIC POTENTIAL JOB======================\n\n"); @@ -172,12 +147,12 @@ void sim_frag_elpot(struct state *state) { msg("\nCOORDINATES IN ANGSTROMS, ELECTROSTATIC POTENTIAL IN ATOMIC UNITS\n"); msg(" ATOM X Y Z ELPOT \n\n"); - double elpot; + double elpot = 0.0; struct efp_atom *atoms; size_t n_atoms; - check_fail(efp_get_frag_atom_count(state->efp, spec_frag, &n_atoms)); // SKP + check_fail(efp_get_frag_atom_count(state->efp, spec_frag, &n_atoms)); atoms = xcalloc(n_atoms, sizeof(struct efp_atom)); check_fail(efp_get_frag_atoms(state->efp, spec_frag, n_atoms, atoms)); diff --git a/efpmd/src/energy.c b/efpmd/src/energy.c index 2195c74..9c6de4e 100644 --- a/efpmd/src/energy.c +++ b/efpmd/src/energy.c @@ -37,8 +37,7 @@ void compute_energy(struct state *state, bool do_grad) { struct efp_atom *atoms; - struct efp_energy efp_energy; - memset(&efp_energy, 0, sizeof(efp_energy)); + struct efp_energy efp_energy = {0.0}; double xyz[3] = {0.0}, xyzabc[6] = {0.0}, *grad; size_t ifrag, nfrag, iatom, natom, spec_frag, n_special_atoms; int itotal; @@ -95,8 +94,11 @@ void compute_energy(struct state *state, bool do_grad) if (cfg_get_bool(state->cfg, "enable_torch") && cfg_get_int(state->cfg, "opt_special_frag") > -1) { - spec_frag = cfg_get_int(state->cfg, "special_fragment"); - check_fail(efp_get_frag_atom_count(state->efp, spec_frag, &n_special_atoms)); // SKP + spec_frag = (size_t)cfg_get_int(state->cfg, "special_fragment"); + check_fail(efp_get_frag_atom_count(state->efp, spec_frag, &n_special_atoms)); + + if (n_special_atoms < 1) + error("ML special fragment does not have any atoms!"); if (cfg_get_bool(state->cfg, "enable_elpot")) { double *elpot; diff --git a/efpmd/src/gtest.c b/efpmd/src/gtest.c index dd739b9..fb102b4 100644 --- a/efpmd/src/gtest.c +++ b/efpmd/src/gtest.c @@ -105,10 +105,13 @@ static void test_fgrad(struct state *state, const double *fgrad) size_t n_frags, spec_frag; check_fail(efp_get_frag_count(state->efp, &n_frags)); - spec_frag = n_frags + 1; // make in inactive if torch model is off + spec_frag = n_frags + 1; // make it inactive if torch model is off if (cfg_get_bool(state->cfg, "enable_torch") ) - spec_frag = cfg_get_int(state->cfg, "special_fragment"); + if (cfg_get_int(state->cfg, "special_fragment") < 0) + error("Special fragment is not defined in ML model"); + spec_frag = (size_t)cfg_get_int(state->cfg, "special_fragment"); + double xyzabc[6 * n_frags]; check_fail(efp_get_coordinates(state->efp, xyzabc)); @@ -155,7 +158,9 @@ static void test_agrad(struct state *state, const double *agrad) size_t spec_frag, n_special_atoms; - spec_frag = cfg_get_int(state->cfg, "special_fragment"); + if (cfg_get_int(state->cfg, "special_fragment") < 0) + error("Special fragment is not defined in ML model!"); + spec_frag = (size_t)cfg_get_int(state->cfg, "special_fragment"); check_fail(efp_get_frag_atom_count(state->efp, spec_frag, &n_special_atoms)); double atom_coord[3 * n_special_atoms]; // = (double*)malloc(3 * n_special_atoms * sizeof(double)); @@ -300,7 +305,10 @@ static void test_grad(struct state *state) #ifdef TORCH_SWITCH // models with libtorch optimized fragment if (cfg_get_bool(state->cfg, "enable_torch")) { - spec_frag = cfg_get_int(state->cfg, "special_fragment"); + if (cfg_get_int(state->cfg, "special_fragment") < 0) + error("Special fragment is not defined in ML model"); + + spec_frag = (size_t)cfg_get_int(state->cfg, "special_fragment"); check_fail(efp_get_frag_atom_count(state->efp, spec_frag, &n_special_atoms)); // check efp and charges gradient on non-special fragment diff --git a/efpmd/src/main.c b/efpmd/src/main.c index 2780f6f..f7e3f0c 100644 --- a/efpmd/src/main.c +++ b/efpmd/src/main.c @@ -513,7 +513,7 @@ static void state_init(struct state *state, const struct cfg *cfg, const struct if (state->torch->nn_type != 3) load_ani_model(state->torch->ani_model, state->torch->nn_type, cfg_get_string(state->cfg, "ml_path")); if (state->torch->nn_type == 3) load_custom_ani_model(state->torch->ani_model, state->torch->aev, state->torch->custom_model, ml_location); - spec_frag = cfg_get_int(cfg, "special_fragment"); + spec_frag = (size_t)cfg_get_int(cfg, "special_fragment"); check_fail(efp_get_frag_atom_count(state->efp, spec_frag, &n_special_atoms)); torch_init(state->torch, n_special_atoms); diff --git a/efpmd/src/opt.c b/efpmd/src/opt.c index 6a409cf..08b6ced 100644 --- a/efpmd/src/opt.c +++ b/efpmd/src/opt.c @@ -48,7 +48,7 @@ static double compute_efp(size_t n, const double *x, double *gx, void *data) if (cfg_get_bool(state->cfg, "enable_torch") && cfg_get_int(state->cfg, "opt_special_frag") > -1) { // prepare for optimization of atom coordinates of a special fragment // through forces provided externally - spec_frag = cfg_get_int(state->cfg, "special_fragment"); + spec_frag = (size_t)cfg_get_int(state->cfg, "special_fragment"); check_fail(efp_get_frag_atom_count(state->efp, spec_frag, &n_special_atoms)); switch(cfg_get_int(state->cfg, "opt_special_frag")) { @@ -238,7 +238,7 @@ static void print_status(struct state *state, double e_diff, double rms_grad, do void sim_opt(struct state *state) { - size_t n_frags, n_charge, n_coord, n_special_atoms, spec_frag; + size_t n_frags=0, n_charge=0, n_coord=0, n_special_atoms=0, spec_frag; double rms_grad = 0.0, max_grad = 0.0; int static algorithm_switch; @@ -275,7 +275,7 @@ void sim_opt(struct state *state) #ifdef TORCH_SWITCH if (cfg_get_bool(state->cfg, "enable_torch") && cfg_get_int(state->cfg, "opt_special_frag") > -1) { - spec_frag = cfg_get_int(state->cfg, "special_fragment"); + spec_frag = (size_t)cfg_get_int(state->cfg, "special_fragment"); check_fail(efp_get_frag_atom_count(state->efp, spec_frag, &n_special_atoms)); if (cfg_get_int(state->cfg, "opt_special_frag") == 0) diff --git a/efpmd/src/sp.c b/efpmd/src/sp.c index db540c3..d1ba038 100644 --- a/efpmd/src/sp.c +++ b/efpmd/src/sp.c @@ -33,11 +33,14 @@ void sim_sp(struct state *state) msg("SINGLE POINT ENERGY JOB\n\n\n"); print_geometry(state->efp); - if (cfg_get_bool(state->cfg, "print_pbc") && cfg_get_bool(state->cfg, "enable_pbc")) - print_geometry_pbc(state->efp,cfg_get_int(state->cfg, "ligand")); + if (cfg_get_bool(state->cfg, "print_pbc") && cfg_get_bool(state->cfg, "enable_pbc") ) + if (cfg_get_int(state->cfg, "ligand") > -1) + print_geometry_pbc(state->efp,cfg_get_int(state->cfg, "ligand")); + else + error("Ligand is not specified for printing PBC geometry"); compute_energy(state, false); - if (cfg_get_bool(state->cfg, "enable_pairwise") && cfg_get_int(state->cfg, "ligand") != -1){ + if (cfg_get_bool(state->cfg, "enable_pairwise") && cfg_get_int(state->cfg, "ligand") > -1){ print_pair_energy(state); } print_energy(state); diff --git a/lib/pylibefp/__pycache__/__init__.cpython-312.pyc b/lib/pylibefp/__pycache__/__init__.cpython-312.pyc index c9d376baf976ea72484cce4f9dcd51aebed367c2..40bd5ae8d72ea3ae2b795e1f7a4b75007c6ca80e 100644 GIT binary patch delta 20 acmey#`jeIWG%qg~0}yPpd9soF9TNaU!v=W( delta 20 acmey#`jeIWG%qg~0}$+A^>8EiJ0<`|hX(Bc diff --git a/lib/pylibefp/__pycache__/wrapper.cpython-312.pyc b/lib/pylibefp/__pycache__/wrapper.cpython-312.pyc index 2bfa0ce6e9732a530fc359539f9376a5290331e1..474e18efc034c1dca144348292b29b6eaf195642 100644 GIT binary patch delta 25 fcmdn^hGpX$7Vgu$yj%=Gu+8R4BllKrMl~}4bae;3 delta 25 fcmdn^hGpX$7Vgu$yj%=Guz%IVM((ZLjA~{8c$Ek+ diff --git a/setup.sh b/setup.sh index c32afcf..816f312 100644 --- a/setup.sh +++ b/setup.sh @@ -1,6 +1,6 @@ #!/bin/bash -export TORCH_SWITCH=ON +export TORCH_SWITCH=OFF export LIBEFP_DIR="/Users/lyuda/LIBEFP/libefp_skp_may2025" export INSTALLATION_DIR="$LIBEFP_DIR" diff --git a/src/efp.c b/src/efp.c index 231bb39..14a93a4 100644 --- a/src/efp.c +++ b/src/efp.c @@ -341,36 +341,6 @@ copy_frag(struct frag *dest, const struct frag *src) return EFP_RESULT_SUCCESS; } -/* -static enum efp_result -copy_ligand(struct ligand *dest, const struct ligand *src) { - size_t size; - - memcpy(dest, src, sizeof(*dest)); - - if (src->ligand_frag) - copy_frag(dest->ligand_frag, src->ligand_frag); - - if (src->ligand_pts) { - size = src->n_ligand_pts * sizeof(struct ligand_pt); - dest->ligand_pts = (struct ligand_pt *) malloc(size); - if (!dest->ligand_pts) - return EFP_RESULT_NO_MEMORY; - memcpy(dest->ligand_pts, src->ligand_pts, size); - - for (size_t i=0; in_ligand_pts; i++) { - const struct ligand_pt *src_pt = src->ligand_pts + i; - struct ligand_pt *dest_pt = dest->ligand_pts + i; - size = src_pt->n_frag * sizeof(vec_t); - dest_pt->fragment_field = (vec_t *)malloc(size); - if (!dest_pt->fragment_field) - return EFP_RESULT_NO_MEMORY; - memcpy(dest_pt->fragment_field, src_pt->fragment_field, size); - } - } -} -*/ - // updates (shifts) parameters of fragment based on coordinates of fragment atoms static enum efp_result update_params(struct efp_atom *atoms, const struct frag *lib_orig, const struct frag *lib_current) { @@ -566,12 +536,15 @@ compute_two_body_range(struct efp *efp, size_t frag_from, size_t frag_to, size_t fr_j = j % efp->n_frag; // special fragment - additional check on special terms - bool if_special_fragment = efp->opts.special_fragment == i || efp->opts.special_fragment == fr_j; - bool special_xr = if_special_fragment && (efp->opts.special_terms & EFP_SPEC_TERM_XR); - bool special_elec = if_special_fragment && (efp->opts.special_terms & EFP_SPEC_TERM_ELEC); - bool special_disp = if_special_fragment && (efp->opts.special_terms & EFP_SPEC_TERM_DISP); - bool special_qq = (!if_special_fragment) || (if_special_fragment && (efp->opts.special_terms & EFP_SPEC_TERM_QQ)); - bool special_lj = if_special_fragment && (efp->opts.special_terms & EFP_SPEC_TERM_LJ); + bool if_special_fragment=false, special_xr=false, special_elec=false, special_disp=false, special_qq=false, special_lj=false; + if (efp->opts.special_fragment >=0) { + if_special_fragment = (size_t)efp->opts.special_fragment == i || (size_t)efp->opts.special_fragment == fr_j; + } + special_xr = if_special_fragment && (efp->opts.special_terms & EFP_SPEC_TERM_XR); + special_elec = if_special_fragment && (efp->opts.special_terms & EFP_SPEC_TERM_ELEC); + special_disp = if_special_fragment && (efp->opts.special_terms & EFP_SPEC_TERM_DISP); + special_qq = (!if_special_fragment) || (if_special_fragment && (efp->opts.special_terms & EFP_SPEC_TERM_QQ)); + special_lj = if_special_fragment && (efp->opts.special_terms & EFP_SPEC_TERM_LJ); if (!efp_skip_frag_pair(efp, i, fr_j)) { double *s; @@ -613,8 +586,9 @@ compute_two_body_range(struct efp *efp, size_t frag_from, size_t frag_to, printf(" WARNING: elec energy between fragments %zu and %zu is %lf \n", i, fr_j, e_elec_tmp); // zeroing the energy contribution on the special fragment in torch custom models - if (efp->opts.enable_elpot && if_special_fragment) e_elec_tmp = 0.0; - //e_elec_tmp = efp_frag_frag_elec(efp, i, fr_j); + if (efp->opts.enable_elpot && if_special_fragment) + e_elec_tmp = 0.0; + e_elec += e_elec_tmp; /* */ if (if_pairwise) { @@ -626,8 +600,7 @@ compute_two_body_range(struct efp *efp, size_t frag_from, size_t frag_to, } if ((do_disp(&efp->opts) || special_disp) && efp->frags[i].n_dynamic_polarizable_pts > 0 && efp->frags[fr_j].n_dynamic_polarizable_pts > 0) { - e_disp_tmp = efp_frag_frag_disp(efp, - i, fr_j, s, ds); + e_disp_tmp = efp_frag_frag_disp(efp, i, fr_j, s, ds); e_disp += e_disp_tmp; /* */ if (if_pairwise) { @@ -1208,7 +1181,11 @@ update_special_fragment(struct efp *efp, const double *coord) assert(efp); assert(coord); //printf("Inside update_special_fragment\n"); - size_t fr_i = efp->opts.special_fragment; + if (efp->opts.special_fragment < 0) { + efp_log("special fragment not set"); + return EFP_RESULT_FATAL; + } + size_t fr_i = (size_t)efp->opts.special_fragment; struct frag *spec_frag = efp->frags + fr_i; if (set_coord_atoms(spec_frag, coord)) { @@ -1224,11 +1201,11 @@ update_gradient_special_fragment(struct efp *efp) { assert(efp); if (efp->opts.special_fragment < 0) { - efp_log("special fragment not set, continue"); - return EFP_RESULT_SUCCESS; + efp_log("special fragment not set"); + return EFP_RESULT_FATAL; } - size_t fr_i = efp->opts.special_fragment; + size_t fr_i = (size_t)efp->opts.special_fragment; struct frag *spec_frag = efp->frags + fr_i; for (size_t i=0; in_atoms; i++) { @@ -2743,10 +2720,14 @@ EFP_EXPORT enum efp_result efp_get_atom_mm_info(struct efp *efp, double *charges assert(coords); assert(charges); + if (efp->opts.special_fragment < 0) { + efp_log("special fragment is not defined"); + return EFP_RESULT_FATAL; + } int natom = 0; for (size_t fr_i = 0; fr_i < efp->n_frag; fr_i++) { // assume that this function is always used in QM/MM like models with QM fragment - if (efp->opts.special_fragment == fr_i) continue; + if ((size_t)efp->opts.special_fragment == fr_i) continue; struct frag *frag = efp->frags + fr_i; for (size_t j = 0; j < frag->n_atoms; j++) { struct efp_atom *atom = frag->atoms + j; diff --git a/src/elec.c b/src/elec.c index 40757f5..fcf1ab8 100644 --- a/src/elec.c +++ b/src/elec.c @@ -327,15 +327,31 @@ mult_mult_grad(struct efp *efp, size_t fr_i_idx, size_t fr_j_idx, // gradient is not added to the special fragment in this case // this assumes that we use ml/efp fragment that induces field to other fragments due to its efp nature (multipoles and ind dipoles) // this might need to be changed if ml fragment uses ml-predicted charges instead - - if (!efp->opts.enable_elpot || (efp->opts.special_fragment != fr_i_idx && efp->opts.special_fragment != fr_j_idx)) { + if (!efp->opts.enable_elpot) { efp_add_force(efp->grad + fr_i_idx, CVEC(fr_i->x), CVEC(pt_i->x), &force, &torque_i); efp_sub_force(efp->grad + fr_j_idx, CVEC(fr_j->x), CVEC(pt_j->x), &force, &torque_j); - } - else if (efp->opts.enable_elpot && efp->opts.special_fragment == fr_i_idx) - efp_sub_force(efp->grad + fr_j_idx, CVEC(fr_j->x), CVEC(pt_j->x), &force, &torque_j); - else if (efp->opts.enable_elpot && efp->opts.special_fragment == fr_j_idx) - efp_add_force(efp->grad + fr_i_idx, CVEC(fr_i->x), CVEC(pt_i->x), &force, &torque_i); + } + else if ( efp->opts.special_fragment >= 0) { + if ((size_t)efp->opts.special_fragment != fr_i_idx && (size_t)efp->opts.special_fragment != fr_j_idx) { + efp_add_force(efp->grad + fr_i_idx, CVEC(fr_i->x), CVEC(pt_i->x), &force, &torque_i); + efp_sub_force(efp->grad + fr_j_idx, CVEC(fr_j->x), CVEC(pt_j->x), &force, &torque_j); + } + else if ((size_t)efp->opts.special_fragment == fr_i_idx) + efp_sub_force(efp->grad + fr_j_idx, CVEC(fr_j->x), CVEC(pt_j->x), &force, &torque_j); + else if ((size_t)efp->opts.special_fragment == fr_j_idx) + efp_add_force(efp->grad + fr_i_idx, CVEC(fr_i->x), CVEC(pt_i->x), &force, &torque_i); + } + else + printf("\nERROR: special fragment is not defined in elpot model!\n"); + + // if (!efp->opts.enable_elpot || (efp->opts.special_fragment != fr_i_idx && efp->opts.special_fragment != fr_j_idx)) { + // efp_add_force(efp->grad + fr_i_idx, CVEC(fr_i->x), CVEC(pt_i->x), &force, &torque_i); + // efp_sub_force(efp->grad + fr_j_idx, CVEC(fr_j->x), CVEC(pt_j->x), &force, &torque_j); + // } + // else if (efp->opts.enable_elpot && efp->opts.special_fragment == fr_i_idx) + // efp_sub_force(efp->grad + fr_j_idx, CVEC(fr_j->x), CVEC(pt_j->x), &force, &torque_j); + // else if (efp->opts.enable_elpot && efp->opts.special_fragment == fr_j_idx) + // efp_add_force(efp->grad + fr_i_idx, CVEC(fr_i->x), CVEC(pt_i->x), &force, &torque_i); } double @@ -373,13 +389,23 @@ efp_frag_frag_elec(struct efp *efp, size_t fr_i_idx, size_t fr_j_idx) // a check for torch special model with elpot on special fragment // gradient is not added to the special fragment in this case - if (!efp->opts.enable_elpot || (efp->opts.special_fragment != fr_i_idx && efp->opts.special_fragment != fr_j_idx)) { + if (!efp->opts.enable_elpot) { six_atomic_add_xyz(efp->grad + fr_i_idx, &force); six_atomic_sub_xyz(efp->grad + fr_j_idx, &force); } - else if (efp->opts.enable_elpot && efp->opts.special_fragment == fr_i_idx) six_atomic_sub_xyz(efp->grad + fr_j_idx, &force); - else if (efp->opts.enable_elpot && efp->opts.special_fragment == fr_j_idx) six_atomic_add_xyz(efp->grad + fr_i_idx, &force); - + else if ( efp->opts.special_fragment >= 0) { + if ((size_t)efp->opts.special_fragment != fr_i_idx && (size_t)efp->opts.special_fragment != fr_j_idx) { + six_atomic_add_xyz(efp->grad + fr_i_idx, &force); + six_atomic_sub_xyz(efp->grad + fr_j_idx, &force); + } + else if ((size_t)efp->opts.special_fragment == fr_i_idx) + six_atomic_sub_xyz(efp->grad + fr_j_idx, &force); + else if ((size_t)efp->opts.special_fragment == fr_j_idx) + six_atomic_add_xyz(efp->grad + fr_i_idx, &force); + } + else { + printf("\nERROR: special fragment is not defined in elpot model!\n"); + } return energy * swf.swf; } } @@ -601,8 +627,8 @@ compute_ai_elec_frag(struct efp *efp, size_t frag_idx) } */ for (size_t i = 0; i < fr_i->n_multipole_pts; i++) { + struct multipole_pt *pt_i = fr_i->multipole_pts + i; for (size_t j = 0; j < efp->n_ptc; j++) { - struct multipole_pt *pt_i = fr_i->multipole_pts + i; vec_t dr = vec_sub(CVEC(pt_i->x), efp->ptc_xyz + j); /* charge - monopole */ @@ -712,9 +738,11 @@ compute_ai_elec_range(struct efp *efp, size_t from, size_t to, void *data) #pragma omp parallel for schedule(dynamic) reduction(+:energy) #endif for (size_t i = from; i < to; i++) { + energy_tmp = 0.0; // skip special fragment - if (i == efp->opts.special_fragment) - continue; + if (efp->opts.special_fragment >= -1) + if (i == (size_t)efp->opts.special_fragment) + continue; energy_tmp = compute_ai_elec_frag(efp, i); energy += energy_tmp; @@ -960,12 +988,23 @@ efp_frag_frag_qq(struct efp *efp, size_t fr_i_idx, size_t fr_j_idx) // a check for torch special model with elpot on special fragment // gradient is not added to the special fragment in this case - if (!efp->opts.enable_elpot || (efp->opts.special_fragment != fr_i_idx && efp->opts.special_fragment != fr_j_idx)) { + if (!efp->opts.enable_elpot) { six_atomic_add_xyz(efp->grad + fr_i_idx, &force); six_atomic_sub_xyz(efp->grad + fr_j_idx, &force); } - else if (efp->opts.enable_elpot && efp->opts.special_fragment == fr_i_idx) six_atomic_sub_xyz(efp->grad + fr_j_idx, &force); - else if (efp->opts.enable_elpot && efp->opts.special_fragment == fr_j_idx) six_atomic_add_xyz(efp->grad + fr_i_idx, &force); + else if ( efp->opts.special_fragment >= 0) { + if ((size_t)efp->opts.special_fragment != fr_i_idx && (size_t)efp->opts.special_fragment != fr_j_idx) { + six_atomic_add_xyz(efp->grad + fr_i_idx, &force); + six_atomic_sub_xyz(efp->grad + fr_j_idx, &force); + } + else if ((size_t)efp->opts.special_fragment == fr_i_idx) + six_atomic_sub_xyz(efp->grad + fr_j_idx, &force); + else if ((size_t)efp->opts.special_fragment == fr_j_idx) + six_atomic_add_xyz(efp->grad + fr_i_idx, &force); + } + else { + printf("\nERROR: special fragment is not defined in elpot model!\n"); + } } return energy * swf.swf; @@ -1063,9 +1102,11 @@ compute_ai_qq_range(struct efp *efp, size_t from, size_t to, void *data) #pragma omp parallel for schedule(dynamic) reduction(+:energy) #endif for (size_t i = from; i < to; i++) { + energy_tmp = 0.0; // skip special fragment - if (i == efp->opts.special_fragment) - continue; + if (efp->opts.special_fragment >= -1) + if (i == (size_t)efp->opts.special_fragment) + continue; // where are switching functions??? diff --git a/src/parse.c b/src/parse.c index 1e6bfd2..b53f03b 100644 --- a/src/parse.c +++ b/src/parse.c @@ -34,7 +34,7 @@ #include "private.h" static void init_multipole_pt(struct multipole_pt *pt) { - memset(pt, 0, sizeof(*pt)); + memset(pt, 0, sizeof(struct multipole_pt)); pt->screen2 = 10.0; pt->screen0 = 10.0; pt->if_znuc = false; @@ -46,10 +46,6 @@ static void init_multipole_pt(struct multipole_pt *pt) { pt->if_scr0 = false; } -static void init_pol_pt(struct polarizable_pt *pt) { - memset(pt, 0, sizeof(*pt)); -} - static int tok(struct stream *stream, const char *id) { @@ -158,9 +154,7 @@ parse_coordinates(struct frag *frag, struct stream *stream) return EFP_RESULT_SUCCESS; } - struct efp_atom atom; - - memset(&atom, 0, sizeof(atom)); + struct efp_atom atom = {0.0}; if (!tok_label(stream, sizeof(atom.label), atom.label) || !tok_double(stream, &atom.x) || !tok_double(stream, &atom.y) || @@ -488,8 +482,8 @@ parse_polarizable_pts(struct frag *frag, struct stream *stream) struct polarizable_pt *pt = frag->polarizable_pts + frag->n_polarizable_pts - 1; // zero out all entries - init_pol_pt(pt); - + memset(pt, 0, sizeof(struct polarizable_pt)); + if (!efp_stream_advance(stream, 4)){ efp_log("parse_polarizable_pts() failure for fragment %s", frag->name); return EFP_RESULT_SYNTAX_ERROR; @@ -1449,8 +1443,7 @@ parse_mm_atomtype(struct frag *frag, struct stream *stream) counter, frag->n_atoms, frag->name); return EFP_RESULT_SUCCESS; } - struct efp_atom atom; - memset(&atom, 0, sizeof(atom)); + struct efp_atom atom = {0.0}; if (!tok_label(stream, sizeof(atom.label), atom.label) || !tok_label(stream, sizeof(atom.ff_label), atom.ff_label)){ printf("problem with fragment %s", frag->name); diff --git a/src/pol.c b/src/pol.c index b0ab144..1c0c6d1 100644 --- a/src/pol.c +++ b/src/pol.c @@ -75,7 +75,7 @@ get_multipole_field(const vec_t *xyz, const struct multipole_pt *mult_pt, double r7 = r5 * r * r; /* charge */ - if (mult_pt->if_mon || mult_pt->if_dip) { + if (mult_pt->if_mon || mult_pt->if_znuc) { field.x += swf->swf * (mult_pt->monopole + mult_pt->znuc) * dr.x / r3; field.y += swf->swf * (mult_pt->monopole + mult_pt->znuc) * dr.y / r3; field.z += swf->swf * (mult_pt->monopole + mult_pt->znuc) * dr.z / r3; @@ -178,6 +178,8 @@ get_elec_field(const struct efp *efp, size_t frag_idx, size_t pt_idx) const struct polarizable_pt *pt = fr_j->polarizable_pts + pt_idx; vec_t elec_field = vec_zero; + // ATTENTION! field due to MM atoms is not added here. Is it needed in any circumstances? + for (size_t i = 0; i < efp->n_frag; i++) { if (i == frag_idx ) continue; @@ -186,8 +188,9 @@ get_elec_field(const struct efp *efp, size_t frag_idx, size_t pt_idx) continue; // this might need to be changed to a more careful separation of // elec and pol contributions to the field - if (i == efp->opts.special_fragment && !(efp->opts.special_terms & EFP_SPEC_TERM_POL)) - continue; + if (efp->opts.special_fragment >=0) + if (i == (size_t)efp->opts.special_fragment && !(efp->opts.special_terms & EFP_SPEC_TERM_POL)) + continue; const struct frag *fr_i = efp->frags + i; struct swf swf = efp_make_swf(efp, fr_i, fr_j, 0); if (swf.swf == 0.0) @@ -247,8 +250,8 @@ get_ligand_field(const struct efp *efp, size_t frag_idx, size_t pt_idx, int liga /* ligand is not QM */ if (ligand_idx != -1) { - const struct frag *fr_i = efp->frags + ligand_idx; - if (efp_skip_frag_pair(efp, ligand_idx, frag_idx)) + const struct frag *fr_i = efp->frags + (size_t)ligand_idx; + if (efp_skip_frag_pair(efp, (size_t)ligand_idx, frag_idx)) return elec_field; struct swf swf = efp_make_swf(efp, fr_i, fr_j, 0); @@ -349,9 +352,10 @@ compute_elec_field_range(struct efp *efp, size_t from, size_t to, void *data) #pragma omp parallel for schedule(dynamic) #endif for (size_t i = from; i < to; i++) { - if (i == efp->opts.special_fragment && - !(efp->opts.special_terms & EFP_SPEC_TERM_POL)) - continue; + if (efp->opts.special_fragment >=0) + if (i == (size_t)efp->opts.special_fragment && + !(efp->opts.special_terms & EFP_SPEC_TERM_POL)) + continue; // const struct frag *frag = efp->frags + i; struct frag *frag = efp->frags + i; @@ -488,9 +492,10 @@ get_induced_dipole_field(struct efp *efp, size_t frag_idx, if (efp->opts.symmetry == 0 && efp_skip_frag_pair(efp, frag_idx, j)) continue; - if (j == efp->opts.special_fragment && - !(efp->opts.special_terms & EFP_SPEC_TERM_POL)) - continue; + if (efp->opts.special_fragment >=0) + if (j == (size_t)efp->opts.special_fragment && + !(efp->opts.special_terms & EFP_SPEC_TERM_POL)) + continue; struct frag *fr_j = efp->frags + j; struct swf swf = efp_make_swf(efp, fr_i, fr_j, 0); @@ -616,9 +621,10 @@ compute_id_range(struct efp *efp, size_t from, size_t to, void *data) #endif for (size_t i = from; i < to; i++) { - if (i == efp->opts.special_fragment && - !(efp->opts.special_terms & EFP_SPEC_TERM_POL)) - continue; + if (efp->opts.special_fragment >=0) + if (i == (size_t)efp->opts.special_fragment && + !(efp->opts.special_terms & EFP_SPEC_TERM_POL)) + continue; struct frag *frag = efp->frags + i; @@ -776,16 +782,18 @@ compute_energy_range(struct efp *efp, size_t from, size_t to, void *data) #endif for (size_t i = from; i < to; i++) { + // zeroing out polarization pair energies is a must + efp->pair_energies[i].polarization = 0.0; + // skip energy contribution for a special fragment in case of torch model with elpot // this assumes that we use ml/efp fragment that induces field to other fragments due to its efp nature (multipoles and ind dipoles) // this needs to be changed if ml fragment uses ml-predicted charges instead - if (efp->opts.enable_elpot && efp->opts.special_fragment == i) continue; + if (efp->opts.enable_elpot && efp->opts.special_fragment >=0) + if ((size_t)efp->opts.special_fragment == i) + continue; struct frag *frag = efp->frags + i; - // zeroing out polarization pair energies is a must - efp->pair_energies[i].polarization = 0.0; - for (size_t j = 0; j < frag->n_polarizable_pts; j++) { struct polarizable_pt *pt = frag->polarizable_pts + j; @@ -1079,7 +1087,7 @@ compute_grad_point(struct efp *efp, size_t frag_idx, size_t pt_idx) const struct frag *fr_i = efp->frags + frag_idx; const struct polarizable_pt *pt_i = fr_i->polarizable_pts + pt_idx; vec_t force, add_i, add_j, force_, add_i_, add_j_; - double e = 0.0; + double ene = 0.0, energy = 0.0; vec_t dipole_i = { 0.5 * (pt_i->indip.x + pt_i->indipconj.x), @@ -1088,6 +1096,10 @@ compute_grad_point(struct efp *efp, size_t frag_idx, size_t pt_idx) }; for (size_t j = 0; j < efp->n_frag; j++) { + + /* energy without switching applied */ + energy = 0.0; + if (j == frag_idx || efp_skip_frag_pair(efp, frag_idx, j)) continue; @@ -1096,24 +1108,32 @@ compute_grad_point(struct efp *efp, size_t frag_idx, size_t pt_idx) // this needs to be changed if ml fragment uses ml-predicted charges instead // this is true for normal cases not related to torch model with elpot - bool not_torch_elpot = !efp->opts.enable_elpot || (efp->opts.special_fragment != frag_idx && efp->opts.special_fragment != j); + bool not_torch_elpot = true; // true when torch with elpot is invoked and fr_idx is the ml fragment - bool torch_elpot_i = efp->opts.enable_elpot && (efp->opts.special_fragment == frag_idx); + bool torch_elpot_i = false; // true when torch with elpot is invoked and j is the ml fragment - bool torch_elpot_j = efp->opts.enable_elpot && (efp->opts.special_fragment == j); + bool torch_elpot_j = false; + + if (efp->opts.special_fragment >= 0) { + not_torch_elpot = !efp->opts.enable_elpot || + ((size_t)efp->opts.special_fragment != frag_idx && + (size_t)efp->opts.special_fragment != j); + torch_elpot_i = efp->opts.enable_elpot && ((size_t)efp->opts.special_fragment == frag_idx); + torch_elpot_j = efp->opts.enable_elpot && ((size_t)efp->opts.special_fragment == j); + } struct frag *fr_j = efp->frags + j; struct swf swf = efp_make_swf(efp, fr_i, fr_j, 0); if (swf.swf == 0.0) continue; - /* energy without switching applied */ - double energy = 0.0; /* induced dipole - multipoles */ for (size_t k = 0; k < fr_j->n_multipole_pts; k++) { struct multipole_pt *pt_j = fr_j->multipole_pts + k; + ene = 0.0; + vec_t dr = { pt_j->x - pt_i->x - swf.cell.x, pt_j->y - pt_i->y - swf.cell.y, @@ -1138,7 +1158,7 @@ compute_grad_point(struct efp *efp, size_t frag_idx, size_t pt_idx) /* induced dipole - charge+monopole */ if (pt_j->if_mon || pt_j->if_znuc) { double qj = pt_j->monopole + pt_j->znuc; - e = -efp_charge_dipole_energy(qj, &dipole_i, &dr); + ene = -efp_charge_dipole_energy(qj, &dipole_i, &dr); efp_charge_dipole_grad(qj, &dipole_i, &dr, &force_, &add_j_, &add_i_); vec_negate(&force_); @@ -1148,7 +1168,7 @@ compute_grad_point(struct efp *efp, size_t frag_idx, size_t pt_idx) /* induced dipole - dipole */ if (pt_j->if_dip) { - e += efp_dipole_dipole_energy(&dipole_i, + ene += efp_dipole_dipole_energy(&dipole_i, &pt_j->dipole, &dr); efp_dipole_dipole_grad(&dipole_i, &pt_j->dipole, &dr, &force_, &add_i_, &add_j_); @@ -1159,7 +1179,7 @@ compute_grad_point(struct efp *efp, size_t frag_idx, size_t pt_idx) /* induced dipole - quadrupole */ if (pt_j->if_quad) { - e += efp_dipole_quadrupole_energy(&dipole_i, + ene += efp_dipole_quadrupole_energy(&dipole_i, pt_j->quadrupole, &dr); efp_dipole_quadrupole_grad(&dipole_i, pt_j->quadrupole, &dr, &force_, &add_i_, &add_j_); @@ -1173,9 +1193,9 @@ compute_grad_point(struct efp *efp, size_t frag_idx, size_t pt_idx) vec_scale(&add_i, p1); vec_scale(&add_j, p1); - force.x += p2 * e * dr.x; - force.y += p2 * e * dr.y; - force.z += p2 * e * dr.z; + force.x += p2 * ene * dr.x; + force.y += p2 * ene * dr.y; + force.z += p2 * ene * dr.z; vec_scale(&force, swf.swf); vec_scale(&add_i, swf.swf); @@ -1187,7 +1207,7 @@ compute_grad_point(struct efp *efp, size_t frag_idx, size_t pt_idx) if (not_torch_elpot) { efp_add_force(efp->grad + frag_idx, CVEC(fr_i->x), CVEC(pt_i->x), &force, &add_i); efp_sub_force(efp->grad + j, CVEC(fr_j->x), CVEC(pt_j->x), &force, &add_j); - energy += p1 * e; + energy += p1 * ene; } // adding gradients to non-ML fragment only in torch elpot model @@ -1200,6 +1220,8 @@ compute_grad_point(struct efp *efp, size_t frag_idx, size_t pt_idx) struct polarizable_pt *pt_j = fr_j->polarizable_pts+jj; // size_t idx_j = fr_j->polarizable_offset+jj; + ene = 0.0; + vec_t dr = { pt_j->x - pt_i->x - swf.cell.x, pt_j->y - pt_i->y - swf.cell.y, @@ -1223,7 +1245,7 @@ compute_grad_point(struct efp *efp, size_t frag_idx, size_t pt_idx) fr_j->pol_damp); } - e = efp_dipole_dipole_energy(&half_dipole_i, &pt_j->indipconj, &dr); + ene = efp_dipole_dipole_energy(&half_dipole_i, &pt_j->indipconj, &dr); efp_dipole_dipole_grad(&half_dipole_i, &pt_j->indipconj, &dr, &force, &add_i, &add_j); vec_negate(&add_j); @@ -1231,9 +1253,9 @@ compute_grad_point(struct efp *efp, size_t frag_idx, size_t pt_idx) vec_scale(&add_i, p1); vec_scale(&add_j, p1); - force.x += p2 * e * dr.x; - force.y += p2 * e * dr.y; - force.z += p2 * e * dr.z; + force.x += p2 * ene * dr.x; + force.y += p2 * ene * dr.y; + force.z += p2 * ene * dr.z; vec_scale(&force, swf.swf); vec_scale(&add_i, swf.swf); @@ -1245,7 +1267,7 @@ compute_grad_point(struct efp *efp, size_t frag_idx, size_t pt_idx) if (not_torch_elpot) { efp_add_force(efp->grad + frag_idx, CVEC(fr_i->x), CVEC(pt_i->x), &force, &add_i); efp_sub_force(efp->grad + j, CVEC(fr_j->x), CVEC(pt_j->x), &force, &add_j); - energy += p1 * e; + energy += p1 * ene; } // adding gradients to non-ML fragment only in torch elpot model @@ -1340,6 +1362,9 @@ efp_get_electric_field(struct efp *efp, size_t frag_idx, const double *xyz, assert(xyz); assert(field); + // ATTENTION! This function does not include the electric field due to MM atoms + // might need to reconsider it! + const struct frag *frag = efp->frags + frag_idx; vec_t elec_field = vec_zero; From 4fa26637a20bc4b4be630e365feaa8b6c04e5b15 Mon Sep 17 00:00:00 2001 From: "Slipchenko, Lyudmila V" Date: Sat, 18 Apr 2026 23:35:10 -0400 Subject: [PATCH 19/40] mmm --- src/efp.c | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/efp.c b/src/efp.c index 14a93a4..f871202 100644 --- a/src/efp.c +++ b/src/efp.c @@ -536,7 +536,8 @@ compute_two_body_range(struct efp *efp, size_t frag_from, size_t frag_to, size_t fr_j = j % efp->n_frag; // special fragment - additional check on special terms - bool if_special_fragment=false, special_xr=false, special_elec=false, special_disp=false, special_qq=false, special_lj=false; + bool if_special_fragment=false, special_xr=false, special_elec=false, + special_disp=false, special_qq=false, special_lj=false; if (efp->opts.special_fragment >=0) { if_special_fragment = (size_t)efp->opts.special_fragment == i || (size_t)efp->opts.special_fragment == fr_j; } @@ -637,10 +638,10 @@ compute_two_body_range(struct efp *efp, size_t frag_from, size_t frag_to, efp->energy.qq += e_qq; efp->energy.lj += e_lj; - if (efp->opts.print > 1) { +// if (efp->opts.print > 1) { printf(" In compute_two_body_range() \n"); print_ene(&efp->energy); - } +// } if (efp->opts.print > 2 && efp->opts.enable_pairwise) print_energies(efp); } From ad30b1c66c3ad0419999962d741488af66e51229 Mon Sep 17 00:00:00 2001 From: Lyudmila Slipchenko Date: Sun, 19 Apr 2026 00:27:42 -0400 Subject: [PATCH 20/40] Update ci.yml --- .github/workflows/ci.yml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 79887be..96d20e6 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -20,6 +20,8 @@ jobs: cmargs: > -D BUILD_SHARED_LIBS=ON -D LIBEFP_ENABLE_OPENMP=ON + -D CMAKE_C_FLAGS="-fsanitize=thread -g" + -D CMAKE_EXE_LINKER_FLAGS="-fsanitize=thread" pytest-marker-expr: "test" # i.e., all - label: L-Gnu @@ -30,6 +32,8 @@ jobs: cmargs: > -D BUILD_SHARED_LIBS=ON -D LIBEFP_ENABLE_OPENMP=ON + -D CMAKE_C_FLAGS="-fsanitize=thread -g" + -D CMAKE_EXE_LINKER_FLAGS="-fsanitize=thread" pytest-marker-expr: "test" - label: L-Intel @@ -56,6 +60,8 @@ jobs: cmargs: > -D BUILD_SHARED_LIBS=ON -D LIBEFP_ENABLE_OPENMP=ON + -D CMAKE_C_FLAGS="-fsanitize=thread -g" + -D CMAKE_EXE_LINKER_FLAGS="-fsanitize=thread" pytest-marker-expr: "test" - label: M-Clang @@ -68,6 +74,8 @@ jobs: cmargs: > -D BUILD_SHARED_LIBS=ON -D LIBEFP_ENABLE_OPENMP=ON + -D CMAKE_C_FLAGS="-fsanitize=thread -g" + -D CMAKE_EXE_LINKER_FLAGS="-fsanitize=thread" pytest-marker-expr: "test" - label: W-MinGW From 6eeb1a486cea5a525ce18b65e39db451b27f1a80 Mon Sep 17 00:00:00 2001 From: "Slipchenko, Lyudmila V" Date: Sun, 19 Apr 2026 00:43:34 -0400 Subject: [PATCH 21/40] bug --- efpmd/src/sp.c | 3 +- src/elec.c | 28 ++++++------- tests/CMakeLists.txt | 96 ++++++++++++++++++++++---------------------- 3 files changed, 64 insertions(+), 63 deletions(-) diff --git a/efpmd/src/sp.c b/efpmd/src/sp.c index d1ba038..0882c6d 100644 --- a/efpmd/src/sp.c +++ b/efpmd/src/sp.c @@ -33,11 +33,12 @@ void sim_sp(struct state *state) msg("SINGLE POINT ENERGY JOB\n\n\n"); print_geometry(state->efp); - if (cfg_get_bool(state->cfg, "print_pbc") && cfg_get_bool(state->cfg, "enable_pbc") ) + if (cfg_get_bool(state->cfg, "print_pbc") && cfg_get_bool(state->cfg, "enable_pbc") ) { if (cfg_get_int(state->cfg, "ligand") > -1) print_geometry_pbc(state->efp,cfg_get_int(state->cfg, "ligand")); else error("Ligand is not specified for printing PBC geometry"); + } compute_energy(state, false); if (cfg_get_bool(state->cfg, "enable_pairwise") && cfg_get_int(state->cfg, "ligand") > -1){ diff --git a/src/elec.c b/src/elec.c index fcf1ab8..677f505 100644 --- a/src/elec.c +++ b/src/elec.c @@ -96,60 +96,60 @@ mult_mult_energy(struct efp *efp, size_t fr_i_idx, size_t fr_j_idx, } // charge - monopole - if (pt_i->if_znuc && pt_j->if_mon) + //if (pt_i->if_znuc && pt_j->if_mon) energy += ccdamp_j * efp_charge_charge_energy(pt_i->znuc, pt_j->monopole, &dr); // monopole - charge - if (pt_j->if_znuc && pt_i->if_mon) + //if (pt_j->if_znuc && pt_i->if_mon) energy += ccdamp_i * efp_charge_charge_energy(pt_j->znuc, pt_i->monopole, &dr); // charge-charge - if (pt_i->if_znuc && pt_j->if_znuc) + //if (pt_i->if_znuc && pt_j->if_znuc) energy += efp_charge_charge_energy(pt_i->znuc, pt_j->znuc, &dr); // monopole - monopole - if (pt_i->if_mon && pt_j->if_mon) + //if (pt_i->if_mon && pt_j->if_mon) energy += ccdamp * efp_charge_charge_energy(pt_i->monopole, pt_j->monopole, &dr); // monopole - dipole - if ((pt_i->if_znuc || pt_i->if_mon) && pt_j->if_dip) + //if ((pt_i->if_znuc || pt_i->if_mon) && pt_j->if_dip) energy += efp_charge_dipole_energy(qi, &pt_j->dipole, &dr); // dipole - monopole - if ((pt_j->if_znuc || pt_j->if_mon) && pt_i->if_dip) + //if ((pt_j->if_znuc || pt_j->if_mon) && pt_i->if_dip) energy -= efp_charge_dipole_energy(qj, &pt_i->dipole, &dr); // monopole - quadrupole - if ((pt_i->if_znuc || pt_i->if_mon) && pt_j->if_quad) + //if ((pt_i->if_znuc || pt_i->if_mon) && pt_j->if_quad) energy += efp_charge_quadrupole_energy(qi, pt_j->quadrupole, &dr); // quadrupole - monopole - if ((pt_j->if_znuc || pt_j->if_mon) && pt_i->if_quad) + //if ((pt_j->if_znuc || pt_j->if_mon) && pt_i->if_quad) energy += efp_charge_quadrupole_energy(qj, pt_i->quadrupole, &dr); // monopole - octupole - if ((pt_i->if_znuc || pt_i->if_mon) && pt_j->if_oct) + //if ((pt_i->if_znuc || pt_i->if_mon) && pt_j->if_oct) energy += efp_charge_octupole_energy(qi, pt_j->octupole, &dr); // octupole - monopole - if ((pt_j->if_znuc || pt_j->if_mon) && pt_i->if_oct) + //if ((pt_j->if_znuc || pt_j->if_mon) && pt_i->if_oct) energy -= efp_charge_octupole_energy(qj, pt_i->octupole, &dr); /* dipole - dipole */ - if (pt_i->if_dip && pt_j->if_dip) + //if (pt_i->if_dip && pt_j->if_dip) energy += efp_dipole_dipole_energy(&pt_i->dipole, &pt_j->dipole, &dr); /* dipole - quadrupole */ - if (pt_i->if_dip && pt_j->if_quad) + //if (pt_i->if_dip && pt_j->if_quad) energy += efp_dipole_quadrupole_energy(&pt_i->dipole, pt_j->quadrupole, &dr); /* quadrupole - dipole */ - if (pt_j->if_dip && pt_i->if_dip) + //if (pt_j->if_dip && pt_i->if_dip) energy -= efp_dipole_quadrupole_energy(&pt_j->dipole, pt_i->quadrupole, &dr); /* quadrupole - quadrupole */ - if (pt_i->if_quad && pt_j->if_quad) + //if (pt_i->if_quad && pt_j->if_quad) energy += efp_quadrupole_quadrupole_energy(pt_i->quadrupole, pt_j->quadrupole, &dr); diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt index 3ea0dd5..bab9b28 100644 --- a/tests/CMakeLists.txt +++ b/tests/CMakeLists.txt @@ -45,18 +45,18 @@ macro(add_mpi_test _name _prc) endmacro() foreach(test_name - atom_coord - constraint_1 - constraint_2 - constraint_3 - disp_1a - disp_1b - disp_1c - disp_2a - disp_2b - disp_3a - disp_3b - efield + #atom_coord + #constraint_1 + #constraint_2 + #constraint_3 + #disp_1a + #disp_1b + #disp_1c + #disp_2a + #disp_2b + #disp_3a + #disp_3b + #efield elec_1a elec_1b elec_1c @@ -64,37 +64,37 @@ foreach(test_name elec_2b elec_3a elec_3b - elpot - grad_1 - hess_1 - md_1 - md_2 - md_3 - opt_1 - pairwise_0 - pairwise_1 - pairwise_2 - pairwise_x - pbc_1 - pbc_2 + #elpot + #grad_1 + #hess_1 + #md_1 + #md_2 + #md_3 + #opt_1 + #pairwise_0 + #pairwise_1 + #pairwise_2 + #pairwise_x + #pbc_1 + #pbc_2 pol_1a pol_1b pol_2a pol_2b pol_3a pol_3b - print - qm_1a - qm_1b - qm_2a - qm_2b - reduced - sp_1 - symm_1 - symm_2full - symm_2 - symm_2pw - symm_2pw_printout + #print + #qm_1a + #qm_1b + #qm_2a + #qm_2b + #reduced + #sp_1 + #symm_1 + #symm_2full + #symm_2 + #symm_2pw + #symm_2pw_printout total_1a total_2a total_3a @@ -102,17 +102,17 @@ foreach(test_name total_4b total_4c total_4d - total_5a - total_5b - total_5c - total_5d - total_6a - total_6b - total_6c - total_6d - xr_1 - xr_2 - xr_3 + #total_5a + #total_5b + #total_5c + #total_5d + #total_6a + #total_6b + #total_6c + #total_6d + #xr_1 + #xr_2 + #xr_3 # crambin/opt.in not handled (cannot load ff geometry) ) From 618fcccc738fd7c2fc08242b40e5009ac71ddd46 Mon Sep 17 00:00:00 2001 From: "Slipchenko, Lyudmila V" Date: Sun, 19 Apr 2026 01:47:40 -0400 Subject: [PATCH 22/40] bug --- src/efp.c | 6 ++++-- src/util.c | 41 +++++++++++++++++++++++++++++++++++++++-- 2 files changed, 43 insertions(+), 4 deletions(-) diff --git a/src/efp.c b/src/efp.c index f871202..3c54ebd 100644 --- a/src/efp.c +++ b/src/efp.c @@ -516,8 +516,8 @@ static void compute_two_body_range(struct efp *efp, size_t frag_from, size_t frag_to, void *data) { - double e_elec = 0.0, e_disp = 0.0, e_xr = 0.0, e_cp = 0.0, e_elec_tmp = 0.0, e_disp_tmp = 0.0; - double e_lj = 0.0, e_qq = 0.0, e_qq_tmp = 0.0; + double e_elec = 0.0, e_disp = 0.0, e_xr = 0.0, e_cp = 0.0; + double e_lj = 0.0, e_qq = 0.0; (void)data; @@ -535,6 +535,8 @@ compute_two_body_range(struct efp *efp, size_t frag_from, size_t frag_to, for (size_t j = i + 1; j < i + 1 + cnt; j++) { size_t fr_j = j % efp->n_frag; + double e_elec_tmp = 0.0, e_disp_tmp = 0.0, e_qq_tmp = 0.0; + // special fragment - additional check on special terms bool if_special_fragment=false, special_xr=false, special_elec=false, special_disp=false, special_qq=false, special_lj=false; diff --git a/src/util.c b/src/util.c index c38e0ab..d7eec95 100644 --- a/src/util.c +++ b/src/util.c @@ -182,12 +182,48 @@ efp_find_lib(struct efp *efp, const char *name) return NULL; } +// void +// efp_add_stress(const vec_t *dr, const vec_t *force, mat_t *stress) +// { +// #ifdef _OPENMP +// #pragma omp critical +// #endif +// { +// stress->xx += dr->x * force->x; +// stress->xy += dr->x * force->y; +// stress->xz += dr->x * force->z; +// stress->yx += dr->y * force->x; +// stress->yy += dr->y * force->y; +// stress->yz += dr->y * force->z; +// stress->zx += dr->z * force->x; +// stress->zy += dr->z * force->y; +// stress->zz += dr->z * force->z; +// } +// } + void efp_add_stress(const vec_t *dr, const vec_t *force, mat_t *stress) { #ifdef _OPENMP -#pragma omp critical -#endif +#pragma omp atomic + stress->xx += dr->x * force->x; +#pragma omp atomic + stress->xy += dr->x * force->y; +#pragma omp atomic + stress->xz += dr->x * force->z; +#pragma omp atomic + stress->yx += dr->y * force->x; +#pragma omp atomic + stress->yy += dr->y * force->y; +#pragma omp atomic + stress->yz += dr->y * force->z; +#pragma omp atomic + stress->zx += dr->z * force->x; +#pragma omp atomic + stress->zy += dr->z * force->y; +#pragma omp atomic + stress->zz += dr->z * force->z; +#else { stress->xx += dr->x * force->x; stress->xy += dr->x * force->y; @@ -199,6 +235,7 @@ efp_add_stress(const vec_t *dr, const vec_t *force, mat_t *stress) stress->zy += dr->z * force->y; stress->zz += dr->z * force->z; } +#endif } void From 90628a826b82bff563324f25421d6116a2505dd0 Mon Sep 17 00:00:00 2001 From: "Slipchenko, Lyudmila V" Date: Sun, 19 Apr 2026 20:16:00 -0400 Subject: [PATCH 23/40] memory bug fixed --- CMakeLists.txt | 2 +- src/elec.c | 6 ++---- src/pol.c | 13 ++++++------- 3 files changed, 9 insertions(+), 12 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 8c08a29..94a7196 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -81,7 +81,7 @@ if((${BUILD_SHARED_LIBS}) AND NOT ${BUILD_FPIC}) endif() ### This option turns OPENMP ON and OFF! -option_with_print(LIBEFP_ENABLE_OPENMP "Enable OpenMP parallelization. Psi4 wants OFF" OFF) +option_with_print(LIBEFP_ENABLE_OPENMP "Enable OpenMP parallelization. Psi4 wants OFF" ON) option_with_print(ENABLE_GENERIC "Enable mostly static linking in shared library" OFF) include(xhost) # defines: option(ENABLE_XHOST "Enable processor-specific optimization" ON) diff --git a/src/elec.c b/src/elec.c index 677f505..0da7417 100644 --- a/src/elec.c +++ b/src/elec.c @@ -730,7 +730,6 @@ static void compute_ai_elec_range(struct efp *efp, size_t from, size_t to, void *data) { double energy = 0.0; - double energy_tmp = 0.0; (void)data; @@ -738,7 +737,7 @@ compute_ai_elec_range(struct efp *efp, size_t from, size_t to, void *data) #pragma omp parallel for schedule(dynamic) reduction(+:energy) #endif for (size_t i = from; i < to; i++) { - energy_tmp = 0.0; + double energy_tmp = 0.0; // skip special fragment if (efp->opts.special_fragment >= -1) if (i == (size_t)efp->opts.special_fragment) @@ -1094,7 +1093,6 @@ static void compute_ai_qq_range(struct efp *efp, size_t from, size_t to, void *data) { double energy = 0.0; - double energy_tmp = 0.0; (void)data; @@ -1102,7 +1100,7 @@ compute_ai_qq_range(struct efp *efp, size_t from, size_t to, void *data) #pragma omp parallel for schedule(dynamic) reduction(+:energy) #endif for (size_t i = from; i < to; i++) { - energy_tmp = 0.0; + double energy_tmp = 0.0; // skip special fragment if (efp->opts.special_fragment >= -1) if (i == (size_t)efp->opts.special_fragment) diff --git a/src/pol.c b/src/pol.c index 1c0c6d1..3309d2b 100644 --- a/src/pol.c +++ b/src/pol.c @@ -390,13 +390,12 @@ compute_fragment_field_range(struct efp *efp, size_t from, size_t to, void *data { (void)data; - struct ligand *ligand = efp->ligand; - #ifdef _OPENMP #pragma omp parallel for schedule(dynamic) #endif for (size_t i = from; i < to; i++) { - struct frag *frag = efp->frags + i; + // struct frag *frag = efp->frags + i; + struct ligand *ligand = efp->ligand; for (size_t j = 0; j < ligand->n_ligand_pts; j++) { struct ligand_pt *pt = ligand->ligand_pts + j; @@ -773,10 +772,6 @@ compute_energy_range(struct efp *efp, size_t from, size_t to, void *data) // if_pairwise tells whether pairwise calculations with EFP (not QM) ligand bool if_pairwise = efp->opts.enable_pairwise && efp->opts.ligand > -1; - struct ligand *ligand; - if (if_pairwise) - ligand = efp->ligand; - #ifdef _OPENMP #pragma omp parallel for schedule(dynamic) reduction(+:energy) #endif @@ -785,6 +780,10 @@ compute_energy_range(struct efp *efp, size_t from, size_t to, void *data) // zeroing out polarization pair energies is a must efp->pair_energies[i].polarization = 0.0; + struct ligand *ligand; + if (if_pairwise) + ligand = efp->ligand; + // skip energy contribution for a special fragment in case of torch model with elpot // this assumes that we use ml/efp fragment that induces field to other fragments due to its efp nature (multipoles and ind dipoles) // this needs to be changed if ml fragment uses ml-predicted charges instead From 5193c36a0720e8da99609c5ad9732c56594aa32b Mon Sep 17 00:00:00 2001 From: Lyudmila Slipchenko Date: Sun, 19 Apr 2026 20:27:05 -0400 Subject: [PATCH 24/40] Update ci.yml --- .github/workflows/ci.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 96d20e6..d990c6c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -62,6 +62,7 @@ jobs: -D LIBEFP_ENABLE_OPENMP=ON -D CMAKE_C_FLAGS="-fsanitize=thread -g" -D CMAKE_EXE_LINKER_FLAGS="-fsanitize=thread" + -D CMAKE_SHARED_LINKER_FLAGS="-fsanitize=thread" pytest-marker-expr: "test" - label: M-Clang @@ -76,6 +77,7 @@ jobs: -D LIBEFP_ENABLE_OPENMP=ON -D CMAKE_C_FLAGS="-fsanitize=thread -g" -D CMAKE_EXE_LINKER_FLAGS="-fsanitize=thread" + -D CMAKE_SHARED_LINKER_FLAGS="-fsanitize=thread" pytest-marker-expr: "test" - label: W-MinGW From 3aa34f68ca09d2b5c2676d27109b2ccbbd633252 Mon Sep 17 00:00:00 2001 From: Lyudmila Slipchenko Date: Sun, 19 Apr 2026 20:35:29 -0400 Subject: [PATCH 25/40] Update ci.yml --- .github/workflows/ci.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d990c6c..b75caa5 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -60,8 +60,8 @@ jobs: cmargs: > -D BUILD_SHARED_LIBS=ON -D LIBEFP_ENABLE_OPENMP=ON - -D CMAKE_C_FLAGS="-fsanitize=thread -g" - -D CMAKE_EXE_LINKER_FLAGS="-fsanitize=thread" + -D CMAKE_C_FLAGS="-fsanitize=thread -g -fPIE" + -D CMAKE_EXE_LINKER_FLAGS="-fsanitize=thread -pie" -D CMAKE_SHARED_LINKER_FLAGS="-fsanitize=thread" pytest-marker-expr: "test" @@ -75,8 +75,8 @@ jobs: cmargs: > -D BUILD_SHARED_LIBS=ON -D LIBEFP_ENABLE_OPENMP=ON - -D CMAKE_C_FLAGS="-fsanitize=thread -g" - -D CMAKE_EXE_LINKER_FLAGS="-fsanitize=thread" + -D CMAKE_C_FLAGS="-fsanitize=thread -g -fPIE" + -D CMAKE_EXE_LINKER_FLAGS="-fsanitize=thread -pie" -D CMAKE_SHARED_LINKER_FLAGS="-fsanitize=thread" pytest-marker-expr: "test" From e6e92189dd265e5971bf878f1904d13360de2814 Mon Sep 17 00:00:00 2001 From: Lyudmila Slipchenko Date: Sun, 19 Apr 2026 20:41:19 -0400 Subject: [PATCH 26/40] Update ci.yml --- .github/workflows/ci.yml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b75caa5..6a5ee8d 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -60,10 +60,10 @@ jobs: cmargs: > -D BUILD_SHARED_LIBS=ON -D LIBEFP_ENABLE_OPENMP=ON - -D CMAKE_C_FLAGS="-fsanitize=thread -g -fPIE" - -D CMAKE_EXE_LINKER_FLAGS="-fsanitize=thread -pie" - -D CMAKE_SHARED_LINKER_FLAGS="-fsanitize=thread" - pytest-marker-expr: "test" + -D CMAKE_C_FLAGS="-fsanitize=thread -g" + -D CMAKE_SHARED_LINKER_FLAGS="-fsanitize=thread -L$(dirname $(clang -print-file-name=libclang_rt.tsan_osx_dynamic.dylib))" + -D CMAKE_EXE_LINKER_FLAGS="-fsanitize=thread -L$(dirname $(clang -print-file-name=libclang_rt.tsan_osx_dynamic.dylib))" + pytest-marker-expr: "test" - label: M-Clang # NaNs in tests on macos-latest (macos-12) @@ -75,9 +75,9 @@ jobs: cmargs: > -D BUILD_SHARED_LIBS=ON -D LIBEFP_ENABLE_OPENMP=ON - -D CMAKE_C_FLAGS="-fsanitize=thread -g -fPIE" - -D CMAKE_EXE_LINKER_FLAGS="-fsanitize=thread -pie" - -D CMAKE_SHARED_LINKER_FLAGS="-fsanitize=thread" + -D CMAKE_C_FLAGS="-fsanitize=thread -g" + -D CMAKE_SHARED_LINKER_FLAGS="-fsanitize=thread -L$(dirname $(clang -print-file-name=libclang_rt.tsan_osx_dynamic.dylib))" + -D CMAKE_EXE_LINKER_FLAGS="-fsanitize=thread -L$(dirname $(clang -print-file-name=libclang_rt.tsan_osx_dynamic.dylib))" pytest-marker-expr: "test" - label: W-MinGW From 4c4c15ab1547f0f139ab51b9496a443a2a75608d Mon Sep 17 00:00:00 2001 From: Lyudmila Slipchenko Date: Sun, 19 Apr 2026 20:48:32 -0400 Subject: [PATCH 27/40] Update ci.yml --- .github/workflows/ci.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 6a5ee8d..4d4c597 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -61,8 +61,8 @@ jobs: -D BUILD_SHARED_LIBS=ON -D LIBEFP_ENABLE_OPENMP=ON -D CMAKE_C_FLAGS="-fsanitize=thread -g" - -D CMAKE_SHARED_LINKER_FLAGS="-fsanitize=thread -L$(dirname $(clang -print-file-name=libclang_rt.tsan_osx_dynamic.dylib))" - -D CMAKE_EXE_LINKER_FLAGS="-fsanitize=thread -L$(dirname $(clang -print-file-name=libclang_rt.tsan_osx_dynamic.dylib))" + -D CMAKE_SHARED_LINKER_FLAGS="-fsanitize=thread -L${CONDA_PREFIX}/lib/clang/19/lib/darwin/" + -D CMAKE_EXE_LINKER_FLAGS="-fsanitize=thread -L${CONDA_PREFIX}/lib/clang/19/lib/darwin/" pytest-marker-expr: "test" - label: M-Clang @@ -76,8 +76,8 @@ jobs: -D BUILD_SHARED_LIBS=ON -D LIBEFP_ENABLE_OPENMP=ON -D CMAKE_C_FLAGS="-fsanitize=thread -g" - -D CMAKE_SHARED_LINKER_FLAGS="-fsanitize=thread -L$(dirname $(clang -print-file-name=libclang_rt.tsan_osx_dynamic.dylib))" - -D CMAKE_EXE_LINKER_FLAGS="-fsanitize=thread -L$(dirname $(clang -print-file-name=libclang_rt.tsan_osx_dynamic.dylib))" + -D CMAKE_SHARED_LINKER_FLAGS="-fsanitize=thread -shared-libsan" + -D CMAKE_EXE_LINKER_FLAGS="-fsanitize=thread -shared-libsan" pytest-marker-expr: "test" - label: W-MinGW From b2fa6d0c7ff6540cc7431d3baae525d2ae74b7a6 Mon Sep 17 00:00:00 2001 From: Lyudmila Slipchenko Date: Sun, 19 Apr 2026 22:17:56 -0400 Subject: [PATCH 28/40] Update ci.yml --- .github/workflows/ci.yml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 4d4c597..24897a3 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -60,9 +60,6 @@ jobs: cmargs: > -D BUILD_SHARED_LIBS=ON -D LIBEFP_ENABLE_OPENMP=ON - -D CMAKE_C_FLAGS="-fsanitize=thread -g" - -D CMAKE_SHARED_LINKER_FLAGS="-fsanitize=thread -L${CONDA_PREFIX}/lib/clang/19/lib/darwin/" - -D CMAKE_EXE_LINKER_FLAGS="-fsanitize=thread -L${CONDA_PREFIX}/lib/clang/19/lib/darwin/" pytest-marker-expr: "test" - label: M-Clang @@ -75,9 +72,6 @@ jobs: cmargs: > -D BUILD_SHARED_LIBS=ON -D LIBEFP_ENABLE_OPENMP=ON - -D CMAKE_C_FLAGS="-fsanitize=thread -g" - -D CMAKE_SHARED_LINKER_FLAGS="-fsanitize=thread -shared-libsan" - -D CMAKE_EXE_LINKER_FLAGS="-fsanitize=thread -shared-libsan" pytest-marker-expr: "test" - label: W-MinGW From bc84b1cbcdb0aa1c6745e7628fb05962e10d3815 Mon Sep 17 00:00:00 2001 From: Lyudmila Slipchenko Date: Sun, 19 Apr 2026 23:10:57 -0400 Subject: [PATCH 29/40] Update ci.yml --- .github/workflows/ci.yml | 21 +++++++++++++++------ 1 file changed, 15 insertions(+), 6 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 24897a3..a4da99a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -130,11 +130,21 @@ jobs: : sed -E -i.bak "s;#${{ matrix.cfg.blas }};;g" export.yaml fi + # does not work with thread-sanitizing + # if [[ "${{ runner.os }}" == "Windows" ]]; then + # : + # sed -i "s;fortran-compiler;m2w64-gcc-fortran;g" export.yaml + # sed -i "s;#${{ matrix.cfg.blas }};;g" export.yaml + # sed -i "s;openmp;pthreads;g" export.yaml # W openblas is pthreads + # sed -i "s;#- libpython;- libpython;g" export.yaml + # fi if [[ "${{ runner.os }}" == "Windows" ]]; then - : - sed -i "s;fortran-compiler;m2w64-gcc-fortran;g" export.yaml + # Use the modern conda-forge compilers instead of the ancient m2w64 ones + sed -i "s;c-compiler;gcc;g" export.yaml + sed -i "s;cxx-compiler;gxx;g" export.yaml + sed -i "s;fortran-compiler;gfortran;g" export.yaml sed -i "s;#${{ matrix.cfg.blas }};;g" export.yaml - sed -i "s;openmp;pthreads;g" export.yaml # W openblas is pthreads + sed -i "s;openmp;pthreads;g" export.yaml sed -i "s;#- libpython;- libpython;g" export.yaml fi # model sed for L/W @@ -259,12 +269,11 @@ jobs: - name: Install Psi4 for QM/EFP testing if: ${{ matrix.cfg.blas == 'MKL' }} run: conda install psi4 -c conda-forge - - - name: Debug File Locations - run: find ${{ github.workspace }}/installed -name "libefp2py.py" - name: Test (pytest) -- unit tests Python bindings run: | + # needed only when thread-sanitizing + export LD_PRELOAD=/usr/share/miniconda/envs/libefp-dev/lib/libtsan.so.2 PYTHONPATH="${{ github.workspace }}/installed/lib:${{ github.workspace }}/installed/lib/pylibefp/tests" \ pytest --cache-clear -v -rws --color=yes \ --durations=50 --durations-min=1 --strict-markers \ From 3446cddb83e30504e501920bfdcb855477a29321 Mon Sep 17 00:00:00 2001 From: "Slipchenko, Lyudmila V" Date: Mon, 20 Apr 2026 00:03:14 -0400 Subject: [PATCH 30/40] psi4 test fixed --- .../__pycache__/__init__.cpython-312.pyc | Bin 761 -> 761 bytes .../__pycache__/wrapper.cpython-312.pyc | Bin 79409 -> 79409 bytes src/efp.c | 4 +- tests/pytests/output.dat | 8 ++ tests/pytests/test_scf.py | 19 ++-- tests/pytests/timer.dat | 96 ++++++++++++++++++ 6 files changed, 118 insertions(+), 9 deletions(-) create mode 100644 tests/pytests/output.dat create mode 100644 tests/pytests/timer.dat diff --git a/lib/pylibefp/__pycache__/__init__.cpython-312.pyc b/lib/pylibefp/__pycache__/__init__.cpython-312.pyc index 40bd5ae8d72ea3ae2b795e1f7a4b75007c6ca80e..c91e565ed5b53734f7530f036dfcbd318f55dcbc 100644 GIT binary patch delta 20 acmey#`jeIWG%qg~0}xnEe7ceQ9TNaTVg^$H delta 20 acmey#`jeIWG%qg~0}yPpd9soF9TNaU!v=W( diff --git a/lib/pylibefp/__pycache__/wrapper.cpython-312.pyc b/lib/pylibefp/__pycache__/wrapper.cpython-312.pyc index 474e18efc034c1dca144348292b29b6eaf195642..9b10d52246a2f2a4b71c823e80e8421cd15543e8 100644 GIT binary patch delta 25 fcmdn^hGpX$7Vgu$yj%=GU^Ve+BllKrMl~}4a-s*8 delta 25 fcmdn^hGpX$7Vgu$yj%=Gu+8R4BllKrMl~}4bae;3 diff --git a/src/efp.c b/src/efp.c index 3c54ebd..fe834bc 100644 --- a/src/efp.c +++ b/src/efp.c @@ -640,10 +640,10 @@ compute_two_body_range(struct efp *efp, size_t frag_from, size_t frag_to, efp->energy.qq += e_qq; efp->energy.lj += e_lj; -// if (efp->opts.print > 1) { + if (efp->opts.print > 1) { printf(" In compute_two_body_range() \n"); print_ene(&efp->energy); -// } + } if (efp->opts.print > 2 && efp->opts.enable_pairwise) print_energies(efp); } diff --git a/tests/pytests/output.dat b/tests/pytests/output.dat new file mode 100644 index 0000000..6d40fd6 --- /dev/null +++ b/tests/pytests/output.dat @@ -0,0 +1,8 @@ + => Loading Basis Set <= + + Name: 6-31G* + Role: ORBITAL + Keyword: BASIS + atoms 1 entry O line 145 file /Users/lyuda/anaconda3/envs/psi4_2026/share/psi4/basis/6-31gs.gbs + atoms 2-3 entry H line 44 file /Users/lyuda/anaconda3/envs/psi4_2026/share/psi4/basis/6-31gs.gbs + diff --git a/tests/pytests/test_scf.py b/tests/pytests/test_scf.py index 4d1ca33..9cf9c4d 100644 --- a/tests/pytests/test_scf.py +++ b/tests/pytests/test_scf.py @@ -102,13 +102,14 @@ def modify_Fock_permanent(mol, nbf, efpobj): for pole in range(20): efp_ints[pole] = np.asarray(p4_efp_ints[pole]) - # add frag atom Z into multipole charge (when pos'n of atom matches mp) - for ifr in range(n_fr): - atoms = efpobj.get_frag_atoms(ifr) - for iat in range(natoms[ifr]): - xyz_atom = [atoms[iat]['x'], atoms[iat]['y'], atoms[iat]['z']] - if np.allclose(xyz_atom, origin, atol=1e-10): - val_mp[imp, 0] += atoms[iat]['Z'] + # LVS: atom Z charges are already included in multipoles as of 2025 + # # add frag atom Z into multipole charge (when pos'n of atom matches mp) + # for ifr in range(n_fr): + # atoms = efpobj.get_frag_atoms(ifr) + # for iat in range(natoms[ifr]): + # xyz_atom = [atoms[iat]['x'], atoms[iat]['y'], atoms[iat]['z']] + # if np.allclose(xyz_atom, origin, atol=1e-10): + # val_mp[imp, 0] += atoms[iat]['Z'] # scale multipole integrals by multipole magnitudes. result goes into V for pole in range(20): @@ -380,6 +381,10 @@ def field_fn(xyz): # <-- efp: add in permanent moment contribution and cache Vefp = modify_Fock_permanent(mol, nbf, efpmol) + + print("Vefp") + print(Vefp) + assert compare(1, np.allclose(Vefp, ref_V2), 'EFP permanent Fock contrib') H = H + Vefp Horig = H.copy() diff --git a/tests/pytests/timer.dat b/tests/pytests/timer.dat new file mode 100644 index 0000000..1efbf3b --- /dev/null +++ b/tests/pytests/timer.dat @@ -0,0 +1,96 @@ + +Host: MacBook-Pro-5.local + +Timers On : Sun Apr 19 22:37:26 2026 +Timers Off: Sun Apr 19 22:37:35 2026 + +Wall Time: 9.11 seconds + + Time (seconds) +Module User System Wall Calls +Libint2ERI::Libint2ERI : 0.000u 0.000s 0.001w 1 calls + +-------------------------------------------------------------------------------------- +Libint2ERI::Libint2ERI : 0.000u 0.000s 0.001w 1 calls + +************************************************************************************** + +Host: MacBook-Pro-5.local + +Timers On : Sun Apr 19 22:45:19 2026 +Timers Off: Sun Apr 19 22:45:20 2026 + +Wall Time: 0.46 seconds + + Time (seconds) +Module User System Wall Calls +Libint2ERI::Libint2ERI : 0.000u 0.000s 0.007w 1 calls + +-------------------------------------------------------------------------------------- +Libint2ERI::Libint2ERI : 0.000u 0.000s 0.007w 1 calls + +************************************************************************************** + +Host: MacBook-Pro-5.local + +Timers On : Sun Apr 19 22:47:15 2026 +Timers Off: Sun Apr 19 22:47:16 2026 + +Wall Time: 0.44 seconds + + Time (seconds) +Module User System Wall Calls +Libint2ERI::Libint2ERI : 0.000u 0.000s 0.005w 1 calls + +-------------------------------------------------------------------------------------- +Libint2ERI::Libint2ERI : 0.000u 0.000s 0.005w 1 calls + +************************************************************************************** + +Host: MacBook-Pro-5.local + +Timers On : Sun Apr 19 23:26:35 2026 +Timers Off: Sun Apr 19 23:26:36 2026 + +Wall Time: 0.45 seconds + + Time (seconds) +Module User System Wall Calls +Libint2ERI::Libint2ERI : 0.000u 0.000s 0.006w 1 calls + +-------------------------------------------------------------------------------------- +Libint2ERI::Libint2ERI : 0.000u 0.000s 0.006w 1 calls + +************************************************************************************** + +Host: MacBook-Pro-5.local + +Timers On : Sun Apr 19 23:27:15 2026 +Timers Off: Sun Apr 19 23:27:15 2026 + +Wall Time: 0.36 seconds + + Time (seconds) +Module User System Wall Calls +Libint2ERI::Libint2ERI : 0.000u 0.000s 0.006w 1 calls + +-------------------------------------------------------------------------------------- +Libint2ERI::Libint2ERI : 0.000u 0.000s 0.006w 1 calls + +************************************************************************************** + +Host: MacBook-Pro-5.local + +Timers On : Mon Apr 20 00:02:21 2026 +Timers Off: Mon Apr 20 00:02:30 2026 + +Wall Time: 9.12 seconds + + Time (seconds) +Module User System Wall Calls +Libint2ERI::Libint2ERI : 0.000u 0.017s 0.006w 1 calls + +-------------------------------------------------------------------------------------- +Libint2ERI::Libint2ERI : 0.000u 0.017s 0.006w 1 calls + +************************************************************************************** From 387d5bdcc29c973fac837d77fd31f1d227096100 Mon Sep 17 00:00:00 2001 From: Lyudmila Slipchenko Date: Mon, 20 Apr 2026 00:06:26 -0400 Subject: [PATCH 31/40] Update ci.yml --- .github/workflows/ci.yml | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index a4da99a..39b82fe 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -272,8 +272,13 @@ jobs: - name: Test (pytest) -- unit tests Python bindings run: | - # needed only when thread-sanitizing - export LD_PRELOAD=/usr/share/miniconda/envs/libefp-dev/lib/libtsan.so.2 + # Only apply LD_PRELOAD on Linux if we are thread-sanitizing + if [[ "${{ runner.os }}" == "Linux" && "${{ matrix.cfg.cmargs }}" == *"-fsanitize=thread"* ]]; then + export LD_PRELOAD=$(find /usr/share/miniconda -name libtsan.so.2 | head -n 1) + echo "Using LD_PRELOAD=$LD_PRELOAD" + fi + #export LD_PRELOAD=/usr/share/miniconda/envs/libefp-dev/lib/libtsan.so.2 + PYTHONPATH="${{ github.workspace }}/installed/lib:${{ github.workspace }}/installed/lib/pylibefp/tests" \ pytest --cache-clear -v -rws --color=yes \ --durations=50 --durations-min=1 --strict-markers \ From 9026c3c6f31c68a07d9fa4b960aabef549723164 Mon Sep 17 00:00:00 2001 From: Lyudmila Slipchenko Date: Mon, 20 Apr 2026 00:18:43 -0400 Subject: [PATCH 32/40] Update ci.yml --- .github/workflows/ci.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 39b82fe..ee5e55a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -277,8 +277,6 @@ jobs: export LD_PRELOAD=$(find /usr/share/miniconda -name libtsan.so.2 | head -n 1) echo "Using LD_PRELOAD=$LD_PRELOAD" fi - #export LD_PRELOAD=/usr/share/miniconda/envs/libefp-dev/lib/libtsan.so.2 - PYTHONPATH="${{ github.workspace }}/installed/lib:${{ github.workspace }}/installed/lib/pylibefp/tests" \ pytest --cache-clear -v -rws --color=yes \ --durations=50 --durations-min=1 --strict-markers \ From c8af01559b1dae610a17369a671b711820a48fd3 Mon Sep 17 00:00:00 2001 From: Lyudmila Slipchenko Date: Mon, 20 Apr 2026 10:29:03 -0400 Subject: [PATCH 33/40] Update ci.yml --- .github/workflows/ci.yml | 30 ++++++++++++++++++++++-------- 1 file changed, 22 insertions(+), 8 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ee5e55a..91c2439 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -272,13 +272,27 @@ jobs: - name: Test (pytest) -- unit tests Python bindings run: | - # Only apply LD_PRELOAD on Linux if we are thread-sanitizing - if [[ "${{ runner.os }}" == "Linux" && "${{ matrix.cfg.cmargs }}" == *"-fsanitize=thread"* ]]; then - export LD_PRELOAD=$(find /usr/share/miniconda -name libtsan.so.2 | head -n 1) + # 1. Fix the Linux LD_PRELOAD logic with safer quoting + # We check the environment variable directly rather than the expanded string + if [[ "${{ runner.os }}" == "Linux" ]] && [[ "${{ matrix.cfg.cmargs }}" == *"-fsanitize=thread"* ]]; then + TSAN_LIB=$(find /usr/share/miniconda -name libtsan.so.2 | head -n 1) + if [ -f "$TSAN_LIB" ]; then + export LD_PRELOAD="$TSAN_LIB" echo "Using LD_PRELOAD=$LD_PRELOAD" fi - PYTHONPATH="${{ github.workspace }}/installed/lib:${{ github.workspace }}/installed/lib/pylibefp/tests" \ - pytest --cache-clear -v -rws --color=yes \ - --durations=50 --durations-min=1 --strict-markers \ - -k "${{ matrix.cfg.pytest-marker-expr }}" \ - "${{ github.workspace }}/installed/" + fi + + # 2. Fix the Windows/Linux PYTHONPATH separator issue + # We use a small python snippet to get the correct OS separator (: or ;) + SEP=$(python -c "import os; print(os.pathsep)") + LIB_PATH="${{ github.workspace }}/installed/lib" + TEST_PATH="${{ github.workspace }}/installed/lib/pylibefp/tests" + + export PYTHONPATH="${LIB_PATH}${SEP}${TEST_PATH}" + echo "PYTHONPATH is set to: $PYTHONPATH" + + # PYTHONPATH="${{ github.workspace }}/installed/lib:${{ github.workspace }}/installed/lib/pylibefp/tests" \ + pytest --cache-clear -v -rws --color=yes \ + --durations=50 --durations-min=1 --strict-markers \ + -k "${{ matrix.cfg.pytest-marker-expr }}" \ + "${{ github.workspace }}/installed/" From 2dc36a7594a54142e600601347c08e00d5f55e64 Mon Sep 17 00:00:00 2001 From: Lyudmila Slipchenko Date: Mon, 20 Apr 2026 13:08:36 -0400 Subject: [PATCH 34/40] Update ci.yml --- .github/workflows/ci.yml | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 91c2439..36beb80 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -272,26 +272,27 @@ jobs: - name: Test (pytest) -- unit tests Python bindings run: | - # 1. Fix the Linux LD_PRELOAD logic with safer quoting - # We check the environment variable directly rather than the expanded string - if [[ "${{ runner.os }}" == "Linux" ]] && [[ "${{ matrix.cfg.cmargs }}" == *"-fsanitize=thread"* ]]; then + # 1. Capture the cmargs into a variable first to avoid quote nesting issues + CM_ARGS='${{ matrix.cfg.cmargs }}' + + # 2. Logic for TSan on Linux + if [[ "${{ runner.os }}" == "Linux" && "$CM_ARGS" == *"-fsanitize=thread"* ]]; then TSAN_LIB=$(find /usr/share/miniconda -name libtsan.so.2 | head -n 1) - if [ -f "$TSAN_LIB" ]; then + if [ -n "$TSAN_LIB" ] && [ -f "$TSAN_LIB" ]; then export LD_PRELOAD="$TSAN_LIB" echo "Using LD_PRELOAD=$LD_PRELOAD" fi fi - - # 2. Fix the Windows/Linux PYTHONPATH separator issue - # We use a small python snippet to get the correct OS separator (: or ;) + + # 3. Setup PYTHONPATH SEP=$(python -c "import os; print(os.pathsep)") LIB_PATH="${{ github.workspace }}/installed/lib" TEST_PATH="${{ github.workspace }}/installed/lib/pylibefp/tests" - export PYTHONPATH="${LIB_PATH}${SEP}${TEST_PATH}" echo "PYTHONPATH is set to: $PYTHONPATH" - # PYTHONPATH="${{ github.workspace }}/installed/lib:${{ github.workspace }}/installed/lib/pylibefp/tests" \ + + # 4. Run Pytest pytest --cache-clear -v -rws --color=yes \ --durations=50 --durations-min=1 --strict-markers \ -k "${{ matrix.cfg.pytest-marker-expr }}" \ From f7280b5e07b679787282496b20aa30b33452495c Mon Sep 17 00:00:00 2001 From: Lyudmila Slipchenko Date: Mon, 20 Apr 2026 14:04:27 -0400 Subject: [PATCH 35/40] Update ci.yml --- .github/workflows/ci.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 36beb80..cdbffef 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -280,7 +280,8 @@ jobs: TSAN_LIB=$(find /usr/share/miniconda -name libtsan.so.2 | head -n 1) if [ -n "$TSAN_LIB" ] && [ -f "$TSAN_LIB" ]; then export LD_PRELOAD="$TSAN_LIB" - echo "Using LD_PRELOAD=$LD_PRELOAD" + # FORCE TSAN TO EXIT IMMEDIATELY ON FIRST ERROR TO SAVE LOG SPACE + export TSAN_OPTIONS="halt_on_error=1:second_deadlock_stack=1" fi fi @@ -293,7 +294,7 @@ jobs: # PYTHONPATH="${{ github.workspace }}/installed/lib:${{ github.workspace }}/installed/lib/pylibefp/tests" \ # 4. Run Pytest - pytest --cache-clear -v -rws --color=yes \ + pytest -s --cache-clear -v -rws --color=yes \ --durations=50 --durations-min=1 --strict-markers \ -k "${{ matrix.cfg.pytest-marker-expr }}" \ "${{ github.workspace }}/installed/" From 8fe5eb21b11786381177c1d569bc9dcb92fe50a1 Mon Sep 17 00:00:00 2001 From: Lyudmila Slipchenko Date: Mon, 20 Apr 2026 16:13:27 -0400 Subject: [PATCH 36/40] Update ci.yml --- .github/workflows/ci.yml | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index cdbffef..5f57625 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -20,8 +20,10 @@ jobs: cmargs: > -D BUILD_SHARED_LIBS=ON -D LIBEFP_ENABLE_OPENMP=ON - -D CMAKE_C_FLAGS="-fsanitize=thread -g" - -D CMAKE_EXE_LINKER_FLAGS="-fsanitize=thread" + # uncomment the following two options to look for possible memory-related bugs in openmp + # however, the tests will take ~10 times longer + #-D CMAKE_C_FLAGS="-fsanitize=thread -g" + #-D CMAKE_EXE_LINKER_FLAGS="-fsanitize=thread" pytest-marker-expr: "test" # i.e., all - label: L-Gnu @@ -32,8 +34,11 @@ jobs: cmargs: > -D BUILD_SHARED_LIBS=ON -D LIBEFP_ENABLE_OPENMP=ON - -D CMAKE_C_FLAGS="-fsanitize=thread -g" - -D CMAKE_EXE_LINKER_FLAGS="-fsanitize=thread" + # uncomment the following two options to look for possible memory-related bugs in openmp + # however, the tests will take ~10 times longer + # this workflow was crashing with these options in pytests due to conflict of TSan and libgomp + #-D CMAKE_C_FLAGS="-fsanitize=thread -g" + #-D CMAKE_EXE_LINKER_FLAGS="-fsanitize=thread" pytest-marker-expr: "test" - label: L-Intel @@ -130,7 +135,6 @@ jobs: : sed -E -i.bak "s;#${{ matrix.cfg.blas }};;g" export.yaml fi - # does not work with thread-sanitizing # if [[ "${{ runner.os }}" == "Windows" ]]; then # : # sed -i "s;fortran-compiler;m2w64-gcc-fortran;g" export.yaml @@ -139,7 +143,7 @@ jobs: # sed -i "s;#- libpython;- libpython;g" export.yaml # fi if [[ "${{ runner.os }}" == "Windows" ]]; then - # Use the modern conda-forge compilers instead of the ancient m2w64 ones + # Use the modern conda-forge compilers instead of the old m2w64 ones sed -i "s;c-compiler;gcc;g" export.yaml sed -i "s;cxx-compiler;gxx;g" export.yaml sed -i "s;fortran-compiler;gfortran;g" export.yaml @@ -201,7 +205,7 @@ jobs: # - name: Test (CTest) with Valgrind # run: | # sudo apt-get update && sudo apt-get install -y valgrind - # # Run valgrind directly on the ctest executable + # # Run valgrind directly on the ctest executable. The tests will take forever # valgrind --tool=memcheck \ # --leak-check=full \ # --track-origins=yes \ From 018e559381b61984e4467bf97b4b454748ba49be Mon Sep 17 00:00:00 2001 From: Lyudmila Slipchenko Date: Mon, 20 Apr 2026 16:21:35 -0400 Subject: [PATCH 37/40] Update ci.yml --- .github/workflows/ci.yml | 26 ++++++++++++-------------- 1 file changed, 12 insertions(+), 14 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 5f57625..0d37927 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -276,20 +276,18 @@ jobs: - name: Test (pytest) -- unit tests Python bindings run: | - # 1. Capture the cmargs into a variable first to avoid quote nesting issues - CM_ARGS='${{ matrix.cfg.cmargs }}' - - # 2. Logic for TSan on Linux - if [[ "${{ runner.os }}" == "Linux" && "$CM_ARGS" == *"-fsanitize=thread"* ]]; then - TSAN_LIB=$(find /usr/share/miniconda -name libtsan.so.2 | head -n 1) - if [ -n "$TSAN_LIB" ] && [ -f "$TSAN_LIB" ]; then - export LD_PRELOAD="$TSAN_LIB" - # FORCE TSAN TO EXIT IMMEDIATELY ON FIRST ERROR TO SAVE LOG SPACE - export TSAN_OPTIONS="halt_on_error=1:second_deadlock_stack=1" - fi - fi + # needed with thread sanitizer + # CM_ARGS='${{ matrix.cfg.cmargs }}' + # if [[ "${{ runner.os }}" == "Linux" && "$CM_ARGS" == *"-fsanitize=thread"* ]]; then + # TSAN_LIB=$(find /usr/share/miniconda -name libtsan.so.2 | head -n 1) + # if [ -n "$TSAN_LIB" ] && [ -f "$TSAN_LIB" ]; then + # export LD_PRELOAD="$TSAN_LIB" + # # FORCE TSAN TO EXIT IMMEDIATELY ON FIRST ERROR TO SAVE LOG SPACE + # export TSAN_OPTIONS="halt_on_error=1:second_deadlock_stack=1" + # fi + # fi - # 3. Setup PYTHONPATH + # Setup PYTHONPATH SEP=$(python -c "import os; print(os.pathsep)") LIB_PATH="${{ github.workspace }}/installed/lib" TEST_PATH="${{ github.workspace }}/installed/lib/pylibefp/tests" @@ -297,7 +295,7 @@ jobs: echo "PYTHONPATH is set to: $PYTHONPATH" # PYTHONPATH="${{ github.workspace }}/installed/lib:${{ github.workspace }}/installed/lib/pylibefp/tests" \ - # 4. Run Pytest + # Run Pytest pytest -s --cache-clear -v -rws --color=yes \ --durations=50 --durations-min=1 --strict-markers \ -k "${{ matrix.cfg.pytest-marker-expr }}" \ From 6824c787abad24cea6765865e54c861b3474ec47 Mon Sep 17 00:00:00 2001 From: Lyudmila Slipchenko Date: Mon, 20 Apr 2026 17:48:29 -0400 Subject: [PATCH 38/40] Update ci.yml --- .github/workflows/ci.yml | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 0d37927..20f8b0f 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -276,17 +276,6 @@ jobs: - name: Test (pytest) -- unit tests Python bindings run: | - # needed with thread sanitizer - # CM_ARGS='${{ matrix.cfg.cmargs }}' - # if [[ "${{ runner.os }}" == "Linux" && "$CM_ARGS" == *"-fsanitize=thread"* ]]; then - # TSAN_LIB=$(find /usr/share/miniconda -name libtsan.so.2 | head -n 1) - # if [ -n "$TSAN_LIB" ] && [ -f "$TSAN_LIB" ]; then - # export LD_PRELOAD="$TSAN_LIB" - # # FORCE TSAN TO EXIT IMMEDIATELY ON FIRST ERROR TO SAVE LOG SPACE - # export TSAN_OPTIONS="halt_on_error=1:second_deadlock_stack=1" - # fi - # fi - # Setup PYTHONPATH SEP=$(python -c "import os; print(os.pathsep)") LIB_PATH="${{ github.workspace }}/installed/lib" From c19aab72485008c2c1e183aac7996ce680de43eb Mon Sep 17 00:00:00 2001 From: "Slipchenko, Lyudmila V" Date: Mon, 20 Apr 2026 20:14:38 -0400 Subject: [PATCH 39/40] fixing special_term --- setup.sh | 2 +- src/efp.c | 14 +++--- tests/CMakeLists.txt | 105 ++++++++++++++++++++++------------------ tests/spec_frag_0.in | 12 ----- tests/spec_frag_1.in | 3 +- tests/spec_frag_2.in | 3 +- tests/spec_frag_base.in | 3 +- 7 files changed, 71 insertions(+), 71 deletions(-) delete mode 100644 tests/spec_frag_0.in diff --git a/setup.sh b/setup.sh index 816f312..c32afcf 100644 --- a/setup.sh +++ b/setup.sh @@ -1,6 +1,6 @@ #!/bin/bash -export TORCH_SWITCH=OFF +export TORCH_SWITCH=ON export LIBEFP_DIR="/Users/lyuda/LIBEFP/libefp_skp_may2025" export INSTALLATION_DIR="$LIBEFP_DIR" diff --git a/src/efp.c b/src/efp.c index fe834bc..144ff0a 100644 --- a/src/efp.c +++ b/src/efp.c @@ -560,7 +560,7 @@ compute_two_body_range(struct efp *efp, size_t frag_from, size_t frag_to, s = (double *) calloc(n_lmo_ij, sizeof(double)); ds = (six_t *) calloc(n_lmo_ij, sizeof(six_t)); - if (do_xr(&efp->opts) || special_xr) { + if ((do_xr(&efp->opts) && !if_special_fragment) || special_xr) { double exr = 0.0, ecp = 0.0; efp_frag_frag_xr(efp, i, fr_j, @@ -581,8 +581,8 @@ compute_two_body_range(struct efp *efp, size_t frag_from, size_t frag_to, } } } - if ((do_elec(&efp->opts) || special_elec) && efp->frags[i].n_multipole_pts > 0 && - efp->frags[fr_j].n_multipole_pts > 0) { + if (((do_elec(&efp->opts) && !if_special_fragment) || special_elec) + && efp->frags[i].n_multipole_pts > 0 && efp->frags[fr_j].n_multipole_pts > 0) { e_elec_tmp = efp_frag_frag_elec(efp, i, fr_j); if (efp->opts.print > 0 && fabs(e_elec_tmp) > 1.0) @@ -601,8 +601,8 @@ compute_two_body_range(struct efp *efp, size_t frag_from, size_t frag_to, efp->pair_energies[i].electrostatic = e_elec_tmp; } } - if ((do_disp(&efp->opts) || special_disp) && efp->frags[i].n_dynamic_polarizable_pts > 0 && - efp->frags[fr_j].n_dynamic_polarizable_pts > 0) { + if (((do_disp(&efp->opts) && !if_special_fragment) || special_disp) + && efp->frags[i].n_dynamic_polarizable_pts > 0 && efp->frags[fr_j].n_dynamic_polarizable_pts > 0) { e_disp_tmp = efp_frag_frag_disp(efp, i, fr_j, s, ds); e_disp += e_disp_tmp; /* */ @@ -614,11 +614,11 @@ compute_two_body_range(struct efp *efp, size_t frag_from, size_t frag_to, } } // LJ terms - if (do_lj(&efp->opts) || special_lj) { + if ((do_lj(&efp->opts) && !if_special_fragment) || special_lj) { e_lj += efp_frag_frag_lj(efp, i, fr_j); } // MM-like charge-charge interactions - if (do_qq(&efp->opts) && special_qq) { + if ((do_qq(&efp->opts) && !if_special_fragment) || special_qq) { e_qq_tmp = efp_frag_frag_qq(efp, i, fr_j); // zeroing the energy contribution on the special fragment in torch custom models diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt index bab9b28..8eded85 100644 --- a/tests/CMakeLists.txt +++ b/tests/CMakeLists.txt @@ -45,18 +45,18 @@ macro(add_mpi_test _name _prc) endmacro() foreach(test_name - #atom_coord - #constraint_1 - #constraint_2 - #constraint_3 - #disp_1a - #disp_1b - #disp_1c - #disp_2a - #disp_2b - #disp_3a - #disp_3b - #efield + atom_coord + constraint_1 + constraint_2 + constraint_3 + disp_1a + disp_1b + disp_1c + disp_2a + disp_2b + disp_3a + disp_3b + efield elec_1a elec_1b elec_1c @@ -64,37 +64,46 @@ foreach(test_name elec_2b elec_3a elec_3b - #elpot - #grad_1 - #hess_1 - #md_1 - #md_2 - #md_3 - #opt_1 - #pairwise_0 - #pairwise_1 - #pairwise_2 - #pairwise_x - #pbc_1 - #pbc_2 + elpot + elpot_frag + grad_1 + hess_1 + lj_1 + lj_2 + md_1 + md_2 + md_3 + opt_1 + pairwise_0 + pairwise_1 + pairwise_2 + pairwise_x + pbc_1 + pbc_2 pol_1a pol_1b pol_2a pol_2b pol_3a pol_3b - #print - #qm_1a - #qm_1b - #qm_2a - #qm_2b - #reduced - #sp_1 - #symm_1 - #symm_2full - #symm_2 - #symm_2pw - #symm_2pw_printout + polab_0 + polab_1 + print + qm_1a + qm_1b + qm_2a + qm_2b + reduced + sp_1 + sp_2 + spec_frag_1 + spec_frag_2 + spec_frag_base + symm_1 + symm_2full + symm_2 + symm_2pw + symm_2pw_printout total_1a total_2a total_3a @@ -102,17 +111,17 @@ foreach(test_name total_4b total_4c total_4d - #total_5a - #total_5b - #total_5c - #total_5d - #total_6a - #total_6b - #total_6c - #total_6d - #xr_1 - #xr_2 - #xr_3 + total_5a + total_5b + total_5c + total_5d + total_6a + total_6b + total_6c + total_6d + xr_1 + xr_2 + xr_3 # crambin/opt.in not handled (cannot load ff geometry) ) diff --git a/tests/spec_frag_0.in b/tests/spec_frag_0.in deleted file mode 100644 index 9ad9244..0000000 --- a/tests/spec_frag_0.in +++ /dev/null @@ -1,12 +0,0 @@ -run_type sp -coord xyzabc -terms elec pol disp xr -disp_damp off -fraglib_path ../fraglib - -fragment h2o_l - 0.000 0.000 0.000 0.000 0.000 0.000 -fragment h2o_l - 5.000 0.000 0.000 2.000 0.000 2.000 -fragment nh3_l - 0.000 5.000 0.000 5.000 0.000 -3.000 diff --git a/tests/spec_frag_1.in b/tests/spec_frag_1.in index c8917f9..0ad2d34 100644 --- a/tests/spec_frag_1.in +++ b/tests/spec_frag_1.in @@ -1,4 +1,5 @@ -run_type sp +run_type etest +ref_energy 0.0000841901 coord xyzabc terms elec pol disp xr disp_damp off diff --git a/tests/spec_frag_2.in b/tests/spec_frag_2.in index 2e0dd0f..1985c0d 100644 --- a/tests/spec_frag_2.in +++ b/tests/spec_frag_2.in @@ -1,4 +1,5 @@ -run_type sp +run_type etest +ref_energy -0.0000982356 coord xyzabc terms elec pol disp xr disp_damp off diff --git a/tests/spec_frag_base.in b/tests/spec_frag_base.in index 03db67f..53973cb 100644 --- a/tests/spec_frag_base.in +++ b/tests/spec_frag_base.in @@ -1,4 +1,5 @@ -run_type sp +run_type etest +ref_energy -0.0000850092 coord xyzabc terms elec pol disp xr disp_damp off From 996362324de3e9ca243358befa2ffdfb1c925192 Mon Sep 17 00:00:00 2001 From: "Slipchenko, Lyudmila V" Date: Mon, 20 Apr 2026 20:33:52 -0400 Subject: [PATCH 40/40] small fixes --- .../__pycache__/__init__.cpython-312.pyc | Bin 761 -> 761 bytes .../__pycache__/wrapper.cpython-312.pyc | Bin 79409 -> 79409 bytes src/elec.c | 28 +++++++-------- tests/pytests/test_efpefp2.py | 2 +- tests/pytests/timer.dat | 32 ++++++++++++++++++ 5 files changed, 47 insertions(+), 15 deletions(-) diff --git a/lib/pylibefp/__pycache__/__init__.cpython-312.pyc b/lib/pylibefp/__pycache__/__init__.cpython-312.pyc index c91e565ed5b53734f7530f036dfcbd318f55dcbc..b376489a52e712c808851e4af0659b12098b4caa 100644 GIT binary patch delta 20 acmey#`jeIWG%qg~0}v=3eYTPN9TNaT_XcnP delta 20 acmey#`jeIWG%qg~0}xnEe7ceQ9TNaTVg^$H diff --git a/lib/pylibefp/__pycache__/wrapper.cpython-312.pyc b/lib/pylibefp/__pycache__/wrapper.cpython-312.pyc index 9b10d52246a2f2a4b71c823e80e8421cd15543e8..871c3d7fef022fe2a891487eb003e442087c7293 100644 GIT binary patch delta 25 fcmdn^hGpX$7Vgu$yj%=Gpmg+EBllKrMl~}4bB+hI delta 25 fcmdn^hGpX$7Vgu$yj%=GU^Ve+BllKrMl~}4a-s*8 diff --git a/src/elec.c b/src/elec.c index 0da7417..3382029 100644 --- a/src/elec.c +++ b/src/elec.c @@ -96,60 +96,60 @@ mult_mult_energy(struct efp *efp, size_t fr_i_idx, size_t fr_j_idx, } // charge - monopole - //if (pt_i->if_znuc && pt_j->if_mon) + if (pt_i->if_znuc && pt_j->if_mon) energy += ccdamp_j * efp_charge_charge_energy(pt_i->znuc, pt_j->monopole, &dr); // monopole - charge - //if (pt_j->if_znuc && pt_i->if_mon) + if (pt_j->if_znuc && pt_i->if_mon) energy += ccdamp_i * efp_charge_charge_energy(pt_j->znuc, pt_i->monopole, &dr); // charge-charge - //if (pt_i->if_znuc && pt_j->if_znuc) + if (pt_i->if_znuc && pt_j->if_znuc) energy += efp_charge_charge_energy(pt_i->znuc, pt_j->znuc, &dr); // monopole - monopole - //if (pt_i->if_mon && pt_j->if_mon) + if (pt_i->if_mon && pt_j->if_mon) energy += ccdamp * efp_charge_charge_energy(pt_i->monopole, pt_j->monopole, &dr); // monopole - dipole - //if ((pt_i->if_znuc || pt_i->if_mon) && pt_j->if_dip) + if ((pt_i->if_znuc || pt_i->if_mon) && pt_j->if_dip) energy += efp_charge_dipole_energy(qi, &pt_j->dipole, &dr); // dipole - monopole - //if ((pt_j->if_znuc || pt_j->if_mon) && pt_i->if_dip) + if ((pt_j->if_znuc || pt_j->if_mon) && pt_i->if_dip) energy -= efp_charge_dipole_energy(qj, &pt_i->dipole, &dr); // monopole - quadrupole - //if ((pt_i->if_znuc || pt_i->if_mon) && pt_j->if_quad) + if ((pt_i->if_znuc || pt_i->if_mon) && pt_j->if_quad) energy += efp_charge_quadrupole_energy(qi, pt_j->quadrupole, &dr); // quadrupole - monopole - //if ((pt_j->if_znuc || pt_j->if_mon) && pt_i->if_quad) + if ((pt_j->if_znuc || pt_j->if_mon) && pt_i->if_quad) energy += efp_charge_quadrupole_energy(qj, pt_i->quadrupole, &dr); // monopole - octupole - //if ((pt_i->if_znuc || pt_i->if_mon) && pt_j->if_oct) + if ((pt_i->if_znuc || pt_i->if_mon) && pt_j->if_oct) energy += efp_charge_octupole_energy(qi, pt_j->octupole, &dr); // octupole - monopole - //if ((pt_j->if_znuc || pt_j->if_mon) && pt_i->if_oct) + if ((pt_j->if_znuc || pt_j->if_mon) && pt_i->if_oct) energy -= efp_charge_octupole_energy(qj, pt_i->octupole, &dr); /* dipole - dipole */ - //if (pt_i->if_dip && pt_j->if_dip) + if (pt_i->if_dip && pt_j->if_dip) energy += efp_dipole_dipole_energy(&pt_i->dipole, &pt_j->dipole, &dr); /* dipole - quadrupole */ - //if (pt_i->if_dip && pt_j->if_quad) + if (pt_i->if_dip && pt_j->if_quad) energy += efp_dipole_quadrupole_energy(&pt_i->dipole, pt_j->quadrupole, &dr); /* quadrupole - dipole */ - //if (pt_j->if_dip && pt_i->if_dip) + if (pt_j->if_dip && pt_i->if_dip) energy -= efp_dipole_quadrupole_energy(&pt_j->dipole, pt_i->quadrupole, &dr); /* quadrupole - quadrupole */ - //if (pt_i->if_quad && pt_j->if_quad) + if (pt_i->if_quad && pt_j->if_quad) energy += efp_quadrupole_quadrupole_energy(pt_i->quadrupole, pt_j->quadrupole, &dr); diff --git a/tests/pytests/test_efpefp2.py b/tests/pytests/test_efpefp2.py index bc7e9e9..6b125f2 100644 --- a/tests/pytests/test_efpefp2.py +++ b/tests/pytests/test_efpefp2.py @@ -7,7 +7,7 @@ FILES = [ 'atom_coord.in', 'atom_coord_2.in', 'grad_1.in', 'lj_1.in', 'lj_2.in', 'pairwise_0.in', 'pairwise_1.in', 'pairwise_2.in', 'pairwise_x.in', 'pbc_1.in', 'pbc_2.in', - 'reduced.in', 'spec_frag_0.in', 'spec_frag_1.in', 'spec_frag_2.in', 'spec_frag_base.in', 'spec_frag_ref.in', + 'reduced.in', 'spec_frag_1.in', 'spec_frag_2.in', 'spec_frag_base.in', 'symm_1.in', 'symm_2.in', 'symm_2full.in', 'symm_2pw.in' ] diff --git a/tests/pytests/timer.dat b/tests/pytests/timer.dat index 1efbf3b..b6fc97b 100644 --- a/tests/pytests/timer.dat +++ b/tests/pytests/timer.dat @@ -94,3 +94,35 @@ Libint2ERI::Libint2ERI : 0.000u 0.017s 0.006w 1 Libint2ERI::Libint2ERI : 0.000u 0.017s 0.006w 1 calls ************************************************************************************** + +Host: MacBook-Pro-5.local + +Timers On : Mon Apr 20 20:30:41 2026 +Timers Off: Mon Apr 20 20:30:50 2026 + +Wall Time: 9.24 seconds + + Time (seconds) +Module User System Wall Calls +Libint2ERI::Libint2ERI : 0.000u 0.000s 0.006w 1 calls + +-------------------------------------------------------------------------------------- +Libint2ERI::Libint2ERI : 0.000u 0.000s 0.006w 1 calls + +************************************************************************************** + +Host: MacBook-Pro-5.local + +Timers On : Mon Apr 20 20:32:58 2026 +Timers Off: Mon Apr 20 20:33:07 2026 + +Wall Time: 8.90 seconds + + Time (seconds) +Module User System Wall Calls +Libint2ERI::Libint2ERI : 0.000u 0.000s 0.005w 1 calls + +-------------------------------------------------------------------------------------- +Libint2ERI::Libint2ERI : 0.000u 0.000s 0.005w 1 calls + +**************************************************************************************