diff --git a/Examples/01_Org_MCPT_Minimal/csp_input.cif b/Examples/01_Org_MCPT_Minimal/csp_input.cif index aaacb81..6e06e4a 100644 --- a/Examples/01_Org_MCPT_Minimal/csp_input.cif +++ b/Examples/01_Org_MCPT_Minimal/csp_input.cif @@ -19,10 +19,10 @@ loop_ loop_ _csp_input_atom.molecular_entity_number _csp_input_atom.molecular_entity_identifier - _chemical.conn_atom_number + _chemical_conn_atom.number _csp_input_atom.label - _chemical.conn_atom_type_symbol - _chemical.conn_atom_charge + _chemical_conn_atom.type_symbol + _chemical_conn_atom.charge 1 B29 1 C1 C 0.0799 1 B29 2 O1 O -0.4751 1 B29 3 C2 C 0.2712 @@ -48,9 +48,9 @@ loop_ # Bonds loop_ - _chemical.conn_bond_atom_1 - _chemical.conn_bond_atom_2 - _chemical.conn_bond_type + _chemical_conn_bond.atom_1 + _chemical_conn_bond.atom_2 + _chemical_conn_bond.type 1 2 sing 2 3 sing 3 4 doub diff --git a/Examples/01_Org_MCPT_Minimal/csp_workflows.cif b/Examples/01_Org_MCPT_Minimal/csp_workflows.cif index a860a3e..f55c109 100644 --- a/Examples/01_Org_MCPT_Minimal/csp_workflows.cif +++ b/Examples/01_Org_MCPT_Minimal/csp_workflows.cif @@ -1,3 +1,4 @@ +#\#CIF_2.0 data_workflow # Data blocks details _csp_data_block.class Workflow diff --git a/Examples/01_Org_MCPT_Minimal/structure_1.cif b/Examples/01_Org_MCPT_Minimal/structure_1.cif index fb6adcf..fe26068 100644 --- a/Examples/01_Org_MCPT_Minimal/structure_1.cif +++ b/Examples/01_Org_MCPT_Minimal/structure_1.cif @@ -1,3 +1,4 @@ +#\#CIF_2.0 data_structure_1_step0 # Datablock Details _csp_data_block.class "Theoretical Structure" diff --git a/Examples/01_Org_MCPT_Minimal/structure_generation_methods.cif b/Examples/01_Org_MCPT_Minimal/structure_generation_methods.cif index 31ebc5e..82c5bd5 100644 --- a/Examples/01_Org_MCPT_Minimal/structure_generation_methods.cif +++ b/Examples/01_Org_MCPT_Minimal/structure_generation_methods.cif @@ -1,3 +1,4 @@ +#\#CIF_2.0 # Monte Carlo Parallel Tempering data_mcpt # Datablock Details @@ -16,7 +17,7 @@ data_mcpt _csp.structure_generation_density_upper_limit 1750 _csp.structure_generation_space_group_number_list [14 2 15 61 19 4 33 29 5 1] - _csp_structure_generation_stopping_criteria.description ["Max Structures", "Low-Energy Structures Unchanged"] + _csp_structure_generation_stopping_criteria.description ["Max Structures" "Low-Energy Structures Unchanged"] _csp_structure_generation_stopping_criteria.max_structures_evaluated 100000 _csp_structure_generation_stopping_criteria.iterations_without_improvement 20 _csp_structure_generation_stopping_criteria.energy_range 10.0 diff --git a/Examples/01_Org_MCPT_Minimal/structure_ranking_methods.cif b/Examples/01_Org_MCPT_Minimal/structure_ranking_methods.cif index 1f0163b..0fdbd46 100644 --- a/Examples/01_Org_MCPT_Minimal/structure_ranking_methods.cif +++ b/Examples/01_Org_MCPT_Minimal/structure_ranking_methods.cif @@ -18,9 +18,9 @@ data_psi_mol _forcefield.vdw_term "Buckingham" loop_ - _forcefield_parameterization.term - _forcefield_parameterization.description - _forcefield_parameterization.method + _forcefield_parameterisation.term + _forcefield_parameterisation.description + _forcefield_parameterisation.method intra "Transferable parameters based on atom types" "PBE0/6-31G(d,p)" electrostatic "Fitting to gas-phase QM data" "PBE0/6-31G(d,p)" vdw "Transferable parameters based on atom types" "FIT" diff --git a/Examples/02_Org_Multi_Stoich/csp_input.cif b/Examples/02_Org_Multi_Stoich/csp_input.cif index 725b205..862b2fe 100644 --- a/Examples/02_Org_Multi_Stoich/csp_input.cif +++ b/Examples/02_Org_Multi_Stoich/csp_input.cif @@ -1,3 +1,4 @@ +#\#CIF_2.0 data_cbn_tmp # Datablock Details _csp_data_block.class "Input" @@ -13,17 +14,17 @@ loop_ _csp_input_molecular_entity.identifier _csp_input_molecular_entity.smiles _chemical.name_common - 1 CBN CCCCCc1cc(O)c2c(OC(C)(C)c3ccc([CH6])cc23)c1 cannabinol + 1 CBN 'CCCCCc1cc(O)c2c(OC(C)(C)c3ccc([CH6])cc23)c1' cannabinol 2 TMP Cc1nc(C)c(C)nc1C tetramethylpyrazine # Atoms in molecules loop_ _csp_input_atom.molecular_entity_number _csp_input_atom.molecular_entity_identifier - _chemical.conn_atom_number + _chemical_conn_atom.number _csp_input_atom.label - _chemical.conn_atom_type_symbol - _chemical.conn_atom_charge + _chemical_conn_atom.type_symbol + _chemical_conn_atom.charge 1 CBN 1 O8 O -0.4823 1 CBN 2 O1 O -0.5071 1 CBN 3 H1 H 0.2931 @@ -100,9 +101,9 @@ loop_ # Bonds loop_ - _chemical.conn_bond_atom_1 - _chemical.conn_bond_atom_2 - _chemical.conn_bond_type + _chemical_conn_bond.atom_1 + _chemical_conn_bond.atom_2 + _chemical_conn_bond.type 1 10 sing 1 14 sing 2 3 sing @@ -179,4 +180,4 @@ loop_ # Type of Composition Search _csp_input.composition_calculation "fixed" -_csp_input.composition_coefficients [[2 1] [1 1] [1 2]] # 2:1, 1:1, 1:2 stoichiometries considered \ No newline at end of file +_csp_input.composition_coefficients [[2 1] [1 1] [1 2]] # 2:1, 1:1, 1:2 stoichiometries considered diff --git a/Examples/02_Org_Multi_Stoich/csp_workflows.cif b/Examples/02_Org_Multi_Stoich/csp_workflows.cif index c96c07f..173c941 100644 --- a/Examples/02_Org_Multi_Stoich/csp_workflows.cif +++ b/Examples/02_Org_Multi_Stoich/csp_workflows.cif @@ -1,3 +1,4 @@ +#\#CIF_2.0 data_workflow # Data blocks details _csp_data_block.class Workflow diff --git a/Examples/02_Org_Multi_Stoich/structure_A1B1_1.cif b/Examples/02_Org_Multi_Stoich/structure_A1B1_1.cif index 4036ca4..fd15b88 100644 --- a/Examples/02_Org_Multi_Stoich/structure_A1B1_1.cif +++ b/Examples/02_Org_Multi_Stoich/structure_A1B1_1.cif @@ -1,3 +1,4 @@ +#\#CIF_2.0 data_structure_A1B1_1_step0 # Datablock Details _csp_data_block.class "Theoretical Structure" @@ -156,7 +157,7 @@ data_structure_A1B1_1_step1 _theoretical_structure.rank 3 # Crystal - ... + # ... data_structure_A1B1_1_step2 # Datablock Details @@ -189,7 +190,7 @@ data_structure_A1B1_1_step2 _theoretical_structure.rank 4 # Crystal - ... + # ... data_structure_A1B1_1_step3 # Datablock Details @@ -222,7 +223,7 @@ data_structure_A1B1_1_step3 _theoretical_structure.rank 2 # Crystal - ... + # ... data_structure_A1B1_1_step4 # Datablock Details @@ -255,7 +256,7 @@ data_structure_A1B1_1_step4 _theoretical_structure.rank 6 # Crystal - ... + # ... data_structure_A1B1_1_step5 # Datablock Details @@ -288,7 +289,7 @@ data_structure_A1B1_1_step5 _theoretical_structure.rank 4 # Crystal - ... + # ... data_structure_A1B1_1_step6 # Datablock Details @@ -321,7 +322,7 @@ data_structure_A1B1_1_step6 _theoretical_structure.rank 6 # Crystal - ... + # ... data_structure_A1B1_1_step7 # Datablock Details @@ -354,7 +355,7 @@ data_structure_A1B1_1_step7 _theoretical_structure.rank 6 # Crystal - ... + # ... data_structure_A1B1_1_step8_t100 # Datablock Details @@ -377,8 +378,8 @@ data_structure_A1B1_1_step8_t100 _theoretical_structure.csp_ranking_stage_description pbe0_mbd_qha _theoretical_structure.csp_ranking_stage_id 2b9deed1-116f-454a-922e-be61c8d946c5 - _theoretical_structure.csp_reference_temperature 100.0 - _theoretical_structure.csp_reference_pressure 100000.0 + _theoretical_structure.reference_temperature 100.0 + _theoretical_structure.reference_pressure 100000.0 _theoretical_structure.csp_previous_stage_structure_description structure_A1B1_1_step7 _theoretical_structure.csp_previous_stage_structure_id 094f5430-0785-4d8f-8aa4-3e31fb579ec4 @@ -389,7 +390,7 @@ data_structure_A1B1_1_step8_t100 _theoretical_structure.rank 6 # Crystal - ... + # ... data_structure_A1B1_1_step8_t200 # Datablock Details @@ -412,8 +413,8 @@ data_structure_A1B1_1_step8_t200 _theoretical_structure.csp_ranking_stage_description pbe0_mbd_qha _theoretical_structure.csp_ranking_stage_id 2b9deed1-116f-454a-922e-be61c8d946c5 - _theoretical_structure.csp_reference_temperature 200.0 - _theoretical_structure.csp_reference_pressure 100000.0 + _theoretical_structure.reference_temperature 200.0 + _theoretical_structure.reference_pressure 100000.0 _theoretical_structure.csp_previous_stage_structure_description structure_A1B1_1_step7 _theoretical_structure.csp_previous_stage_structure_id 094f5430-0785-4d8f-8aa4-3e31fb579ec4 @@ -424,7 +425,7 @@ data_structure_A1B1_1_step8_t200 _theoretical_structure.rank 7 # Crystal - ... + # ... data_structure_A1B1_1_step8_t300 # Datablock Details @@ -447,8 +448,8 @@ data_structure_A1B1_1_step8_t300 _theoretical_structure.csp_ranking_stage_description pbe0_mbd_qha _theoretical_structure.csp_ranking_stage_id 2b9deed1-116f-454a-922e-be61c8d946c5 - _theoretical_structure.csp_reference_temperature 300.0 - _theoretical_structure.csp_reference_pressure 100000.0 + _theoretical_structure.reference_temperature 300.0 + _theoretical_structure.reference_pressure 100000.0 _theoretical_structure.csp_previous_stage_structure_description structure_A1B1_1_step7 _theoretical_structure.csp_previous_stage_structure_id 094f5430-0785-4d8f-8aa4-3e31fb579ec4 @@ -459,4 +460,4 @@ data_structure_A1B1_1_step8_t300 _theoretical_structure.rank 7 # Crystal - ... + # ... diff --git a/Examples/02_Org_Multi_Stoich/structure_generation_methods.cif b/Examples/02_Org_Multi_Stoich/structure_generation_methods.cif index d492c58..5f71343 100644 --- a/Examples/02_Org_Multi_Stoich/structure_generation_methods.cif +++ b/Examples/02_Org_Multi_Stoich/structure_generation_methods.cif @@ -1,3 +1,4 @@ +#\#CIF_2.0 # Random Search data_rs # Datablock Details @@ -49,7 +50,7 @@ data_mcpt _csp.structure_generation_density_upper_limit 1500 _csp.structure_generation_space_group_number_list [14 2 15 61 19 4 33 29 5 1] - _csp_structure_generation_stopping_criteria.description ["Max Structures", "Low-Energy Structures Unchanged"] + _csp_structure_generation_stopping_criteria.description ["Max Structures" "Low-Energy Structures Unchanged"] _csp_structure_generation_stopping_criteria.max_structures_evaluated 100000 _csp_structure_generation_stopping_criteria.iterations_without_improvement 20 _csp_structure_generation_stopping_criteria.energy_range 10.0 @@ -63,18 +64,18 @@ data_ea # Method Details _csp.structure_generation_method "Evolutionary Algorithm" - _csp_evolutionary_algorithm.initial_population_size 50 - _csp_evolutionary_algorithm.population_size 50 - _csp_evolutionary_algorithm.parents_structure_fraction 0.6 - _csp_evolutionary_algorithm.mutation_fraction 0.5 - _csp_evolutionary_algorithm.heredity_fraction 0.5 # Crossover or recombination + _csp_evolutionary_algorithms.initial_population_size 50 + _csp_evolutionary_algorithms.population_size 50 + _csp_evolutionary_algorithms.parents_structure_fraction 0.6 + _csp_evolutionary_algorithms.mutation_fraction 0.5 + _csp_evolutionary_algorithms.heredity_fraction 0.5 # Crossover or recombination # Search Space & Stopping Criteria _csp.structure_generation_density_lower_limit 1000 _csp.structure_generation_density_upper_limit 1500 _csp.structure_generation_space_group_number_list [14 2 15 61 19 4 33 29 5 1] - _csp_structure_generation_stopping_criteria.description ["Max Structures", "Low-Energy Structures Unchanged"] + _csp_structure_generation_stopping_criteria.description ["Max Structures" "Low-Energy Structures Unchanged"] _csp_structure_generation_stopping_criteria.max_structures_evaluated 100000 _csp_structure_generation_stopping_criteria.iterations_without_improvement 20 _csp_structure_generation_stopping_criteria.energy_range 10.0 @@ -101,7 +102,7 @@ data_pso _csp.structure_generation_density_upper_limit 1500 _csp.structure_generation_space_group_number_list [14 2 15 61 19 4 33 29 5 1] - _csp_structure_generation_stopping_criteria.description ["Max Structures", "Low-Energy Structures Unchanged"] + _csp_structure_generation_stopping_criteria.description ["Max Structures" "Low-Energy Structures Unchanged"] _csp_structure_generation_stopping_criteria.max_structures_evaluated 100000 _csp_structure_generation_stopping_criteria.iterations_without_improvement 20 _csp_structure_generation_stopping_criteria.energy_range 10.0 diff --git a/Examples/02_Org_Multi_Stoich/structure_ranking_methods.cif b/Examples/02_Org_Multi_Stoich/structure_ranking_methods.cif index 530da4a..f16d390 100644 --- a/Examples/02_Org_Multi_Stoich/structure_ranking_methods.cif +++ b/Examples/02_Org_Multi_Stoich/structure_ranking_methods.cif @@ -1,3 +1,4 @@ +#\#CIF_2.0 # Forcefield data_gaff # Datablock Details @@ -15,7 +16,7 @@ data_gaff _forcefield.angle_type "Harmonic" _forcefield.improper_type "Harmonic" _forcefield.dihedral_type "Periodic" - _forcefield.1-4_pairs True + _forcefield.1_4_pairs True _forcefield.fudgeQQ 0.8333 _forcefield.fudgeLJ 0.5 @@ -28,9 +29,9 @@ data_gaff _forcefield.combination_rule "Lorentz-Berthelot" loop_ - _forcefield_parameterization.term - _forcefield_parameterization.description - _forcefield_parameterization.method + _forcefield_parameterisation.term + _forcefield_parameterisation.description + _forcefield_parameterisation.method intra "Transferable parameters based on atom types" "GAFF2" electrostatic "Fitting to gas-phase QM data" "MP2/6-31G(d,p)" vdw "Transferable parameters based on atom types" "AMBER" diff --git a/Examples/03_Org_ROY/csp_workflows.cif b/Examples/03_Org_ROY/csp_workflows.cif index 8430108..9b388bf 100644 --- a/Examples/03_Org_ROY/csp_workflows.cif +++ b/Examples/03_Org_ROY/csp_workflows.cif @@ -1,3 +1,4 @@ +#\#CIF_2.0 data_workflow # Data blocks details _csp_data_block.class Workflow diff --git a/Examples/03_Org_ROY/structure_generation_methods.cif b/Examples/03_Org_ROY/structure_generation_methods.cif index 1b39614..2f6fab5 100644 --- a/Examples/03_Org_ROY/structure_generation_methods.cif +++ b/Examples/03_Org_ROY/structure_generation_methods.cif @@ -1,3 +1,4 @@ +#\#CIF_2.0 # Random Search data_rs # Datablock Details @@ -7,8 +8,8 @@ data_rs # Method Details _csp.structure_generation_method "Random Search" - _csp_random_searc.algorithm_type "Quasi-random" - _csp_random_searc.algorithm "Sobol" + _csp_random_search.algorithm_type "Quasi-random" + _csp_random_search.algorithm "Sobol" _csp.structure_generation_space_group_list [P1, P-1, P21, P21/c, P21212, P212121, Pna21, Pca21, Pbca, Pbcn, C2/c, Cc, C2, Pc, Cm, P21/m, C2/m, P2/c, C2221, Pmn21, Cmc21, Aba2, Fdd2, Iba2, Pnna, Pccn, Pbcm, Pnnm, Pmmn, Pnma, Fddd, Ibam, P41, P43, I-4, P4/n, P42/n, I4/m, I41/a, P41212, P43212, P-421c, I-42d, P31, P32, R3, P-3, R-3, P3121, P3221, R3c, R-3c, P61, P63, P63/m, P213, Pa-3, Cmcm, Cmca] _csp_structure_generation_stopping_criteria.description "Max Structures" diff --git a/Examples/03_Org_ROY/structure_ranking_methods.cif b/Examples/03_Org_ROY/structure_ranking_methods.cif index 6fc114a..6411eab 100644 --- a/Examples/03_Org_ROY/structure_ranking_methods.cif +++ b/Examples/03_Org_ROY/structure_ranking_methods.cif @@ -15,7 +15,7 @@ data_PCLAMS _forcefield.angle_type "Quadratic" _forcefield.improper_type "Quadratic" _forcefield.dihedral_type "Periodic" - _forcefield.1-4_pairs False + _forcefield.1_4_pairs False _forcefield.electrostatic_term "Point-Charges" _forcefield.long_range_electrostatic "PME" @@ -26,9 +26,9 @@ data_PCLAMS _forcefield.combination_rule "Lorentz-Berthelot" loop_ - _forcefield_parameterization.term - _forcefield_parameterization.description - _forcefield_parameterization.method + _forcefield_parameterisation.term + _forcefield_parameterisation.description + _forcefield_parameterisation.method intra "Local Approximate Models fit to QM data" "CrystPredLAMs" electrostatic "Fitting to gas-phase QM data" "B3LYP/6-31G(d,p)" vdw "Transferable parameters based on atom types" "FIT" @@ -56,7 +56,7 @@ data_MPLAMS _forcefield.angle_type "Quadratic" _forcefield.improper_type "Quadratic" _forcefield.dihedral_type "Periodic" - _forcefield.1-4_pairs False + _forcefield.1_4_pairs False _forcefield.electrostatic_term "Multipoles" _forcefield.long_range_electrostatic "PME" @@ -67,9 +67,9 @@ data_MPLAMS _forcefield.combination_rule "Lorentz-Berthelot" loop_ - _forcefield_parameterization.term - _forcefield_parameterization.description - _forcefield_parameterization.method + _forcefield_parameterisation.term + _forcefield_parameterisation.description + _forcefield_parameterisation.method intra "Local Approximate Models fit to QM data" "CrystOptLAMs" electrostatic "Fitting to gas-phase QM data" "B3LYP/6-31G(d,p)" vdw "Transferable parameters based on atom types" "FIT" diff --git a/Examples/03_Org_ROY/structures.cif b/Examples/03_Org_ROY/structures.cif index 9e95040..81e81eb 100644 --- a/Examples/03_Org_ROY/structures.cif +++ b/Examples/03_Org_ROY/structures.cif @@ -1,4 +1,4 @@ - +#\#CIF_2.0 ####################################################################### # # Cambridge Crystallographic Data Centre