/************************************************************************************************************* The MIT License Copyright (C) 2006-2019 David Dubbeldam, Sofia Calero, Thijs Vlugt, Donald E. Ellis, and Randall Q. Snurr. D.Dubbeldam@uva.nl http://www.uva.nl/profiel/d/u/d.dubbeldam/d.dubbeldam.html scaldia@upo.es http://www.upo.es/raspa/ t.j.h.vlugt@tudelft.nl http://homepage.tudelft.nl/v9k6y don-ellis@northwestern.edu http://dvworld.northwestern.edu/ snurr@northwestern.edu http://zeolites.cqe.northwestern.edu/ Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. **************************************************************************************************************/ #ifndef FRAMEWORK_H #define FRAMEWORK_H #ifdef HAVE_CONFIG_H #include #endif #include #include "vector.h" enum {FLEXIBLE_FILE_TYPE_RASPA,FLEXIBLE_FILE_TYPE_DLPOLY}; enum {IMPROPER_TORSION_SCAN_GENERAL,IMPROPER_TORSION_SCAN_UNIQUE}; extern int CorrectNetChargeOnPseudoAtom; extern REAL CorrectNetChargeOnPseudoAtomValue; typedef struct citation_information { char CitationId[80]; char CitationAuthorName[256]; char CitationCoordinateLinkage[80]; char CitationTitle[1024]; char CitationCountry[80]; char CitationPageFirst[80]; char CitationPageLast[80]; char CitationYear[80]; char CitationJournalAbbrev[80]; char CitationJournalVolume[80]; char CitationJournalIssue[80]; char CitationJournalID_ASTM[80]; char CitationJournalID_ISSN[80]; char CitationBookTitle[80]; char CitationBookPublisher[80]; char CitationBookID_ISBN[80]; char CitationSpecialDetails[80]; } CITATION_INFORMATION; typedef struct crystallographic_statistics { VECTOR *Position; VECTOR *PositionSquared; VECTOR *Distance; REAL *Occupation; REAL *AverageDistance; REAL Unclassified; REAL *RelativeOccupation; int *NumberOfCationSites; REAL *Count; REAL_MATRIX3x3 *TemperatureFactor; REAL count; REAL count2; } CRYSTALLOGRAPHIC_STATISTICS; extern CRYSTALLOGRAPHIC_STATISTICS *crystallographic_stats; typedef struct framework_asymmetric_atom { char AtomNumberCode[32]; int Type; // the pseudo-atom Type of the atom REAL Charge; int Replacable; int AssymetricType; int Identifier; POINT Position; } FRAMEWORK_ASYMMETRIC_ATOM; extern REAL CutOffIons; extern int AsymmetricIons; extern int SpaceGroupIons; extern int NumberOfSingleSubstitutionRules; extern char (*SubstitutionSingleFrameworkAtom)[3][256]; extern int (*SubstitutionSingleFrameworkAtomTypes)[3]; extern int NumberOfRandomSubstitutions; extern int NumberOfSubstitutionRules; extern char (*SubstitutionFrameworkAtoms)[3][256]; extern int (*SubstitutionFrameworkAtomTypes)[3]; extern int NumberOfSubstitutions; extern int (*ListOfAtomSubstitutions)[3]; enum {MODIFY_FRAMEWORKATOM_CONNECTED_TO,MODIFY_FRAMEWORKATOM_DIMER,MODIFY_FRAMEWORKATOM_TRIPLE,MODIFY_FRAMEWORKATOM_PLANAR}; extern int NumberOfModificationRules; extern int *ModificationRuleType; extern char (*ModifyFrameworkAtoms)[10][256]; extern int (*ModifyFrameworkAtomTypes)[10]; extern int NumberOfForbiddenConnectivityRules; extern char (*ForbiddenConnectivityAtoms)[3][256]; extern int (*ForbiddenConnectivityTypes)[3]; void CheckFrameworkCharges(void); void AddAsymmetricAtom(FRAMEWORK_ASYMMETRIC_ATOM atom); void SetBoundaryCondition(int system, REAL eps_angle, REAL eps_length, REAL alpha, REAL beta, REAL gamma, REAL A, REAL B, REAL C); void SetBoundaryConditionFromSystem(int system, REAL eps_angle, REAL eps_length); void ReadFrameworkDefinitionCSSR(void); void ReadFrameworkDefinitionDLPOLY(void); void CreateAsymetricFrameworkAtoms(void); void WriteSymmetricFrameworkCssr(void); void WriteFrameworkCssr(void); void MakeConnectivityList(void); void AllocateConnectivityList(void); void FreeAllocateConnectivityList(void); void SubstituteAtoms(void); void ModifyAtomsConnectedToDefinedNeighbours(void); extern VECTOR *UnitCellSize; extern INT_VECTOR3 *NumberOfUnitCells; extern REAL_MATRIX3x3 *UnitCellBox; extern REAL_MATRIX3x3 *InverseUnitCellBox; extern int *Lowenstein; int BlockedPocket(VECTOR pos); int BlockedPocketGridTest(VECTOR pos); void ReadCageCenters(void); void ReadBlockingPockets(void); extern int RemoveBondNeighboursFromLongRangeInteraction; extern int RemoveBendNeighboursFromLongRangeInteraction; extern int RemoveTorsionNeighboursFromLongRangeInteraction; extern int Remove12NeighboursFromVDWInteraction; extern int Remove13NeighboursFromVDWInteraction; extern int Remove14NeighboursFromVDWInteraction; extern int Remove12NeighboursFromChargeChargeInteraction; extern int Remove13NeighboursFromChargeChargeInteraction; extern int Remove14NeighboursFromChargeChargeInteraction; extern int Remove11NeighboursFromChargeBondDipoleInteraction; extern int Remove12NeighboursFromChargeBondDipoleInteraction; extern int Remove13NeighboursFromChargeBondDipoleInteraction; extern int Remove14NeighboursFromChargeBondDipoleInteraction; extern int Remove12NeighboursFromBondDipoleBondDipoleInteraction; extern int Remove13NeighboursFromBondDipoleBondDipoleInteraction; extern int Remove14NeighboursFromBondDipoleBondDipoleInteraction; extern int ImproperTorsionScanType; extern int InternalFrameworkLennardJonesInteractions; typedef struct FrameworkComponent { char (*Name)[256]; // the name of the frameworks int TotalNumberOfAtoms; // the total number of atoms of the frameworks int TotalNumberOfCharges; // the total number of charges of the frameworks int TotalNumberOfUnitCellAtoms; // the total number of atoms of the unit cell REAL FrameworkDensity; // the total density of the frameworks REAL FrameworkMass; // the total mass of the frameworks int NumberOfFrameworks; // the number of frameworks REAL *FrameworkDensityPerComponent; // the density per framework REAL *FrameworkMassPerComponent; // the mass per framework int *NumberOfAtoms; // the number of atoms per framework int *NumberOfCharges; // the number of atoms per framework int *NumberOfFixedAtoms; // the number of fixed atoms per framework int *NumberOfFreeAtoms; // the number of free atoms per framework int *NumberOfUnitCellAtoms; // the number of unit cell atoms per framework int *MaxNumberOfAtoms; ATOM **Atoms; // list of framework-atoms per framework int **CellListHead; // the starting atom per cell int **CellList; // linked list of framework atoms // Added by Ambroise de Izarra //------------------------------------------------------------------- REAL ***scaling_pair14VDW; // Store 14 atoms in the box for VDW. REAL ***scaling_pair14ChargeCharge; // Store 14 atoms in the box for chargecharge. PAIR **list14pair; // Store 14 atom pairs for Ewald summation. int *pair14VDW_size; int *pair14ChargeCharge_size; int *list14pair_size; //------------------------------------------------------------------- REAL *FrameworkProbability; int FrameworkExclusion; int RemoveHydrogenDisorder; int *NumberOfCitations; CITATION_INFORMATION **CitationInformation; int FrameworkModel; int *FrameworkModels; VECTOR *ShiftUnitCell; int *Asymmetric; int *SpaceGroupIdentifier; int *CalculateSpaceGroup; int *RemoveAtomNumberCodeFromLabel; int *AddAtomNumberCodeToLabel; int *InputFileType; int ForceSpaceGroupDetection; char FrameworkDefinitions[256]; int FlexibleModelInputType; int AnisotropicType; VECTOR IntialCenterOfMassPosition; REAL SurfaceArea; // in units of Angstrom^2 REAL *SurfaceAreas; REAL SurfaceAreaCations; char SurfaceAreaProbeAtom[256]; int SurfaceAreaSamplingPointsPerShere; REAL SurfaceAreaProbeDistance; REAL PoreSizeDistributionProbeDistance; int TranslationDirection; int *NumberOfAsymmetricAtoms; FRAMEWORK_ASYMMETRIC_ATOM **AtomsAsymmetric; char NameIons[256]; // the Name of the component ("methane","C12","propane" etc). int NumberOfIons; int MaxNumberOfIons; ATOM *Ions; int NumberOfAsymmetricIons; FRAMEWORK_ASYMMETRIC_ATOM *IonsAsymmetric; int RestrictFrameworkAtomsToBox; int ReadCIFAsCartesian; // Added by Ambroise de Izarra //------------------------------------------------------------------- int * PrintInteractionIndex; //------------------------------------------------------------------- char ***ExclusionMatrix; int **Connectivity; int ***Neighbours; int *NumberOfCoreShells; int **CoreShellConnectivity; int NumberOfCoreShellDefinitions; PAIR *CoreShellDefinitions; int *NumberOfCoreShellsPerType; REAL Intra14VDWScalingValue; REAL Intra14ChargeChargeScalingValue; int NumberOfIntra12Interactions; int NumberOfIntra13Interactions; int NumberOfIntra14Interactions; int NumberOfIntra123Interactions; int NumberOfIntra1234Interactions; int NumberOfBondsDefinitions; // the number of bond definitions int *BondDefinitionType; // the type of the bonds (i.e. HARMONIC_BOND) PAIR *BondDefinitions; // the pair of pseudo-atoms in the bond definition REAL (*BondArgumentDefinitions)[MAX_BOND_POTENTIAL_ARGUMENTS]; // the parameters corresponding to this bond int *NumberOfBondsPerType; // the number of bonds for this type int *NumberOfBonds; // the number of Bonds (per framework) int *MaxNumberOfBonds; // the currently allocated memory for bonds (per framework) PAIR **Bonds; // the list of bond-pairs (per framework) int **BondType; // the type of the bond for each Bond-pair (per framework) REAL (**BondArguments)[MAX_BOND_POTENTIAL_ARGUMENTS]; // the bond arguments for this bond-pair (per framework) // the bondarguments are sometimes modified, e.g. taking the bond equilibrium distance from the crystal-structure // the distances could be different for each bond-pair int NumberOfBondDipoleDefinitions; // the number of bond-dipole definitions PAIR *BondDipoleDefinitions; // the pair of pseudo-atoms in the bond-dipole definition REAL *BondDipoleArgumentDefinition; // the magntitude corresponding to this bond-dipole int *NumberOfBondDipolesPerType; // the number of bond-dipoles for this type int *NumberOfBondDipoles; // the number of bond-dipoles (per framework) int *MaxNumberOfBondDipoles; // the currently allocated memory for bond-dipoles (per framework) PAIR **BondDipoles; // the list of bond-dipole-pairs (per framework) REAL **BondDipoleMagnitude; // the magntiude of the bond-dipole for this bond-pair (per framework) int NumberOfUreyBradleyDefinitions; // the number of Urey-Bradley definitions int *UreyBradleyDefinitionType; // the type of the Urey-Bradleys TRIPLE *UreyBradleyDefinitions; // the triple of pseudo-atoms in the Urey-Bradley definition REAL (*UreyBradleyArgumentDefinitions)[MAX_UREYBRADLEY_POTENTIAL_ARGUMENTS]; // the parameters corresponding to this Urey-Bradley int *NumberOfUreyBradleysPerType; // the number of Urey-Bradleys for this type int *NumberOfUreyBradleys; // the number of Urey-Bradleys (per framework) int *MaxNumberOfUreyBradleys; // the currently allocated memory for Urey-Bradleys (per framework) TRIPLE **UreyBradleys; // the list of Urey-Bradley-triples (per framework) int **UreyBradleyType; // the type of the Urey-Bradley for each Urey-Bradley-triple (per framework) REAL (**UreyBradleyArguments)[MAX_UREYBRADLEY_POTENTIAL_ARGUMENTS]; // the Urey-Bradley arguments for this triple (per framework) int NumberOfBendDefinitions; // the number of bend definitions int *BendDefinitionType; // the type of the bend QUAD *BendDefinitions; // the triple of pseudo-atoms in the bend definition REAL (*BendArgumentDefinitions)[MAX_BEND_POTENTIAL_ARGUMENTS]; // the parameters corresponding to this bend int *NumberOfBendsPerType; // the number of bends for this type int *NumberOfBends; // the number of bends (per framework) int *MaxNumberOfBends; // the currently allocated memory for bends (per framework) QUAD **Bends; // the list of bend-triples (per framework) int **BendType; // the type of the bend for each bend-triple (per framework) REAL (**BendArguments)[MAX_BEND_POTENTIAL_ARGUMENTS]; // the bend arguments for this triple (per framework) int NumberOfInversionBendDefinitions; // the number of inversion bend definitions int *InversionBendDefinitionType; // the type of the inversion bend QUAD *InversionBendDefinitions; // the quad of pseudo-atoms in the inversion bend definition REAL (*InversionBendArgumentDefinitions)[MAX_INVERSION_BEND_POTENTIAL_ARGUMENTS]; // the parameters corresponding to this inversion bend int *NumberOfInversionBendsPerType; // the number of inversion bends for this type int *NumberOfInversionBends; // the number of inversion bends (per framework) int *MaxNumberOfInversionBends; // the currently allocated memory for inversion bends (per framework) QUAD **InversionBends; // the list of inversion bend-triples (per framework) int **InversionBendType; // the type of the inv bend for each inversion bend-triple (per framework) REAL (**InversionBendArguments)[MAX_INVERSION_BEND_POTENTIAL_ARGUMENTS]; // the inversion bend arguments for this triple (per framework) int NumberOfTorsionDefinitions; // the number of torsion definitions int *TorsionDefinitionType; // the type of the torsion QUAD *TorsionDefinitions; // the quad of pseudo-atoms in the torsion definition REAL (*TorsionArgumentDefinitions)[MAX_TORSION_POTENTIAL_ARGUMENTS]; // the parameters corresponding to this torsion int *NumberOfTorsionsPerType; // the number of torsions for this type int *NumberOfTorsions; // the number of torsions (per framework) int *MaxNumberOfTorsions; // the currently allocated memory for torsions (per framework) QUAD **Torsions; // the list of torsion-quads (per framework) int **TorsionType; // the type of the torsions for each torsion-quad (per framework) REAL (**TorsionArguments)[MAX_TORSION_POTENTIAL_ARGUMENTS]; // the torsion arguments for this quad (per framework) int NumberOfImproperTorsionDefinitions; // the number of improper torsion definitions int *ImproperTorsionDefinitionType; // the type of the improper torsion QUAD *ImproperTorsionDefinitions; // the quad of pseudo-atoms in the improper torsion definition REAL (*ImproperTorsionArgumentDefinitions)[MAX_IMPROPER_TORSION_POTENTIAL_ARGUMENTS]; // the parameters corresponding to this improper torsion int *NumberOfImproperTorsionsPerType; // the number of improper torsions for this type int *NumberOfImproperTorsions; // the number of improper torsions (per framework) int *MaxNumberOfImproperTorsions; // the currently allocated memory for improper torsions (per framework) QUAD **ImproperTorsions; // the list of improper torsion-quads (per framework) int **ImproperTorsionType; // the type of the torsions for each improper torsion-quad (per framework) REAL (**ImproperTorsionArguments)[MAX_IMPROPER_TORSION_POTENTIAL_ARGUMENTS]; // the improper torsion arguments for this quad (per framework) int NumberOfOutOfPlaneDefinitions; // the number of out-of-plane definitions int *OutOfPlaneDefinitionType; // the type of the out-of-plane QUAD *OutOfPlaneDefinitions; // the quad of pseudo-atoms in the out-of-plane definition REAL (*OutOfPlaneArgumentDefinitions)[MAX_OUT_OF_PLANE_POTENTIAL_ARGUMENTS]; // the parameters corresponding to this out-of-plane int *NumberOfOutOfPlanesPerType; // the number of out-of-planes for this type int *NumberOfOutOfPlanes; // the number of out-of-planes (per framework) int *MaxNumberOfOutOfPlanes; // the currently allocated memory for out-of-plane (per framework) QUAD **OutOfPlanes; // the list of out-of-plane-quads (per framework) int **OutOfPlaneType; // the type of the out-of-plane for each out-of-plane-quad (per framework) REAL (**OutOfPlaneArguments)[MAX_OUT_OF_PLANE_POTENTIAL_ARGUMENTS]; // the out-of-plane arguments for this quad (per framework) int NumberOfBondBondDefinitions; // the number of Bonds of the component int *BondBondDefinitionType; TRIPLE *BondBondDefinitions; REAL (*BondBondArgumentDefinitions)[MAX_BOND_BOND_POTENTIAL_ARGUMENTS]; int *NumberOfBondBondsPerType; int *NumberOfBondBonds; int *MaxNumberOfBondBonds; TRIPLE **BondBonds; int **BondBondType; REAL (**BondBondArguments)[MAX_BOND_BOND_POTENTIAL_ARGUMENTS]; int NumberOfBondBendDefinitions; // the number of Bonds of the component int *BondBendDefinitionType; TRIPLE *BondBendDefinitions; REAL (*BondBendArgumentDefinitions)[MAX_BOND_BEND_POTENTIAL_ARGUMENTS]; int *NumberOfBondBendsPerType; int *NumberOfBondBends; int *MaxNumberOfBondBends; TRIPLE **BondBends; int **BondBendType; REAL (**BondBendArguments)[MAX_BOND_BEND_POTENTIAL_ARGUMENTS]; int NumberOfBendBendDefinitions; // the number of Bonds of the component int *BendBendDefinitionType; QUAD *BendBendDefinitions; REAL (*BendBendArgumentDefinitions)[MAX_BEND_BEND_POTENTIAL_ARGUMENTS]; int *NumberOfBendBendsPerType; int *NumberOfBendBends; int *MaxNumberOfBendBends; QUAD **BendBends; int **BendBendType; REAL (**BendBendArguments)[MAX_BEND_BEND_POTENTIAL_ARGUMENTS]; int NumberOfBondTorsionDefinitions; int *BondTorsionDefinitionType; QUAD *BondTorsionDefinitions; REAL (*BondTorsionArgumentDefinitions)[MAX_BOND_TORSION_POTENTIAL_ARGUMENTS]; int *NumberOfBondTorsionsPerType; int *NumberOfBondTorsions; int *MaxNumberOfBondTorsions; QUAD **BondTorsions; int **BondTorsionType; REAL (**BondTorsionArguments)[MAX_BOND_TORSION_POTENTIAL_ARGUMENTS]; int NumberOfBendTorsionDefinitions; int *BendTorsionDefinitionType; QUAD *BendTorsionDefinitions; REAL (*BendTorsionArgumentDefinitions)[MAX_BEND_TORSION_POTENTIAL_ARGUMENTS]; int *NumberOfBendTorsionsPerType; int *NumberOfBendTorsions; int *MaxNumberOfBendTorsions; QUAD **BendTorsions; int **BendTorsionType; REAL (**BendTorsionArguments)[MAX_BEND_TORSION_POTENTIAL_ARGUMENTS]; int *NumberOfIntraVDW; int *NumberOfExcludedIntraVDW; int *NumberOfIntraCharges; int *NumberOfIntraChargeBondDipoles; int *NumberOfIntraBondDipoles; // lists for the Ewald erf-subtraction int *NumberOfExcludedIntraChargeCharge; int *MaxNumberOfExcludedIntraChargeCharge; PAIR **ExcludedIntraChargeCharge; int *NumberOfExcludedIntraChargeBondDipole; int *MaxNumberOfExcludedIntraChargeBondDipole; PAIR **ExcludedIntraChargeBondDipole; int *NumberOfExcludedIntraBondDipoleBondDipole; int *MaxNumberOfExcludedIntraBondDipoleBondDipole; PAIR **ExcludedIntraBondDipoleBondDipole; } FRAMEWORK_COMPONENT; extern FRAMEWORK_COMPONENT *Framework; extern int CurrentFramework; void AllocateFrameworkCellList(void); void MakeFrameworkCellList(void); void AllocateAnisotropicNeighbors(void); void ReadFrameworkDefinitionMOL(void); void ReadFrameworkSpecificDefinition(void); int ReadFrameworkDefinition(void); void WriteFrameworkDefinitionDLPOLY(void); void CellProperties(REAL_MATRIX3x3 *in,REAL_MATRIX3x3 *out,REAL *Volume); void ReadIonSitingDefinition(void); void PrintFrameworkStatus(void); int ReadFrameworkComponentDefinition(void); void PrintFlexibleFrameworkModel(void); VECTOR GetFrameworkCenterOfMass(void); VECTOR GetIndividualFrameworkCenterOfMass(int f1); VECTOR GetFrameworkCenterOfMassPosition(void); VECTOR GetFrameworkCenterOfMassVelocity(void); void InitializeFrameworkVelocities(void); VECTOR MeasureFrameworkVelocityDrift(void); void RemoveFrameworkVelocityDrift(void); REAL GetFrameworkKineticEnergy(void); void SetFrameworkVelocitesToZero(void); void ScaleFrameworkVelocitesToTemperature(void); void UpdateCrystallographics(void); void GetFAUStructure(void); void GetFAU2Structure(void); void GetLTAStructure(void); void PrintConnectivityList(void); void PrintReplicaConnectivityList(void); int BondNeighbours(int A,int B); int BendNeighbours(int A,int C); int TorsionNeighbours(int A,int D); void QuenchCoreSHellVelocities(void); int ClosestCrystallographicPosition(VECTOR pos); void ClosestCrystallographicPosition2(VECTOR pos,int *closest,REAL *minimum_distance); void AllocateList14atomsVDWandEwald(int system); void MakeExclusionMatrix(int system); void MakeExcludedInteractionLists(int system); int CheckSurfaceAreaOverlap(int typeA,VECTOR posA,int skipf,int skipfa,int skipcm,int skipca); void ExpandAsymmetricFrameworkToFullFramework(void); void ExpandAsymmetricIonsToFullCell(void); void IndexFrameworkAtomsToAtomIndices(void); void ConstructBondDipolesFromBondsFramework(void); int IsDefinedBondType(int,int,int,int); int IsDefinedBendType(int,int,int,int,int); int isDefinedBend(int system, int f1, int Aref, int Cref); int IsDefinedTorsionType(int,int,int,int,int,int); void WriteRestartFramework(FILE *FilePtr); void ReadRestartFramework(FILE *FilePtr); void DetermineSpaceGroup(void); void GenerateFramework(void); int ReturnNumberOfAsymmetricAtoms(int sp); void WriteAsymmetricUnitCell(int sp); void ReadFrameworkDefinitionCIF(void); void WriteFrameworkDefinitionCIF(char * string); void WriteFrameworkDefinitionShell(char * string); void WriteFrameworkDefinitionCSSR(char *string); void WriteFrameworkDefinitionGulp(char *string); void WriteFrameworkDefinitionVASP(char *string); void WriteFrameworkDefinitionPDB(char *string); void WriteFrameworkDefinitionTinker(char *string); void WriteFrameworkDefinitionMOL(char *string); void PutNoiseOnFrameworkAtomicPositions(void); // Added by Ambroise de Izarra //------------------------------------------------------------------- void printInteractionIndexAtoms(int system); //------------------------------------------------------------------- #endif