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Fix example CIF files #19

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f311d07
Add mandatory CIF 2.0 header comment
vaitkus Jun 5, 2026
e264ca3
Remove commas from CIF 2.0 lists
vaitkus Jun 5, 2026
fee027f
Prefix '...' with a comment symbol to produce a parseable CIF
vaitkus Jun 5, 2026
cd1f9c8
CIF 2.0 does not permit square brackets to appear in unquoted values
vaitkus Jun 5, 2026
863ccf8
Fix data names
vaitkus Jun 5, 2026
71f65ac
Fix placement of '.' in data names
vaitkus Jun 5, 2026
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12 changes: 6 additions & 6 deletions Examples/01_Org_MCPT_Minimal/csp_input.cif
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Expand Up @@ -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
Expand All @@ -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
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1 change: 1 addition & 0 deletions Examples/01_Org_MCPT_Minimal/csp_workflows.cif
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@@ -1,3 +1,4 @@
#\#CIF_2.0
data_workflow
# Data blocks details
_csp_data_block.class Workflow
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1 change: 1 addition & 0 deletions Examples/01_Org_MCPT_Minimal/structure_1.cif
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@@ -1,3 +1,4 @@
#\#CIF_2.0
data_structure_1_step0
# Datablock Details
_csp_data_block.class "Theoretical Structure"
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3 changes: 2 additions & 1 deletion Examples/01_Org_MCPT_Minimal/structure_generation_methods.cif
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@@ -1,3 +1,4 @@
#\#CIF_2.0
# Monte Carlo Parallel Tempering
data_mcpt
# Datablock Details
Expand All @@ -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
6 changes: 3 additions & 3 deletions Examples/01_Org_MCPT_Minimal/structure_ranking_methods.cif
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Expand Up @@ -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"
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17 changes: 9 additions & 8 deletions Examples/02_Org_Multi_Stoich/csp_input.cif
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@@ -1,3 +1,4 @@
#\#CIF_2.0
data_cbn_tmp
# Datablock Details
_csp_data_block.class "Input"
Expand All @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
_csp_input.composition_coefficients [[2 1] [1 1] [1 2]] # 2:1, 1:1, 1:2 stoichiometries considered
1 change: 1 addition & 0 deletions Examples/02_Org_Multi_Stoich/csp_workflows.cif
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#\#CIF_2.0
data_workflow
# Data blocks details
_csp_data_block.class Workflow
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33 changes: 17 additions & 16 deletions Examples/02_Org_Multi_Stoich/structure_A1B1_1.cif
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#\#CIF_2.0
data_structure_A1B1_1_step0
# Datablock Details
_csp_data_block.class "Theoretical Structure"
Expand Down Expand Up @@ -156,7 +157,7 @@ data_structure_A1B1_1_step1
_theoretical_structure.rank 3

# Crystal
...
# ...

data_structure_A1B1_1_step2
# Datablock Details
Expand Down Expand Up @@ -189,7 +190,7 @@ data_structure_A1B1_1_step2
_theoretical_structure.rank 4

# Crystal
...
# ...

data_structure_A1B1_1_step3
# Datablock Details
Expand Down Expand Up @@ -222,7 +223,7 @@ data_structure_A1B1_1_step3
_theoretical_structure.rank 2

# Crystal
...
# ...

data_structure_A1B1_1_step4
# Datablock Details
Expand Down Expand Up @@ -255,7 +256,7 @@ data_structure_A1B1_1_step4
_theoretical_structure.rank 6

# Crystal
...
# ...

data_structure_A1B1_1_step5
# Datablock Details
Expand Down Expand Up @@ -288,7 +289,7 @@ data_structure_A1B1_1_step5
_theoretical_structure.rank 4

# Crystal
...
# ...

data_structure_A1B1_1_step6
# Datablock Details
Expand Down Expand Up @@ -321,7 +322,7 @@ data_structure_A1B1_1_step6
_theoretical_structure.rank 6

# Crystal
...
# ...

data_structure_A1B1_1_step7
# Datablock Details
Expand Down Expand Up @@ -354,7 +355,7 @@ data_structure_A1B1_1_step7
_theoretical_structure.rank 6

# Crystal
...
# ...

data_structure_A1B1_1_step8_t100
# Datablock Details
Expand All @@ -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
Expand All @@ -389,7 +390,7 @@ data_structure_A1B1_1_step8_t100
_theoretical_structure.rank 6

# Crystal
...
# ...

data_structure_A1B1_1_step8_t200
# Datablock Details
Expand All @@ -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
Expand All @@ -424,7 +425,7 @@ data_structure_A1B1_1_step8_t200
_theoretical_structure.rank 7

# Crystal
...
# ...

data_structure_A1B1_1_step8_t300
# Datablock Details
Expand All @@ -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
Expand All @@ -459,4 +460,4 @@ data_structure_A1B1_1_step8_t300
_theoretical_structure.rank 7

# Crystal
...
# ...
17 changes: 9 additions & 8 deletions Examples/02_Org_Multi_Stoich/structure_generation_methods.cif
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#\#CIF_2.0
# Random Search
data_rs
# Datablock Details
Expand Down Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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
9 changes: 5 additions & 4 deletions Examples/02_Org_Multi_Stoich/structure_ranking_methods.cif
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#\#CIF_2.0
# Forcefield
data_gaff
# Datablock Details
Expand All @@ -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

Expand All @@ -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"
Expand Down
1 change: 1 addition & 0 deletions Examples/03_Org_ROY/csp_workflows.cif
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#\#CIF_2.0
data_workflow
# Data blocks details
_csp_data_block.class Workflow
Expand Down
5 changes: 3 additions & 2 deletions Examples/03_Org_ROY/structure_generation_methods.cif
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#\#CIF_2.0
# Random Search
data_rs
# Datablock Details
Expand All @@ -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"
Expand Down
16 changes: 8 additions & 8 deletions Examples/03_Org_ROY/structure_ranking_methods.cif
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Expand Up @@ -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"
Expand All @@ -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"
Expand Down Expand Up @@ -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"
Expand All @@ -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"
Expand Down
2 changes: 1 addition & 1 deletion Examples/03_Org_ROY/structures.cif
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#\#CIF_2.0
#######################################################################
#
# Cambridge Crystallographic Data Centre
Expand Down