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gezelter |
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#include <stdlib.h> |
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#include <stdio.h> |
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#include <string.h> |
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#include <iostream> |
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using namespace std; |
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tim |
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#include "UseTheForce/ForceFields.hpp" |
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#include "primitives/SRI.hpp" |
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#include "utils/simError.h" |
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gezelter |
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tim |
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#include "UseTheForce/fortranWrappers.hpp" |
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gezelter |
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#ifdef IS_MPI |
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tim |
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#include "UseTheForce/mpiForceField.h" |
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gezelter |
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#endif // is_mpi |
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// define some bond Types |
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#define FIXED_BOND 0 |
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#define HARMONIC_BOND 1 |
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namespace DUFF_NS { // restrict the access of the folowing to this file only. |
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// Declare the structures that will be passed by MPI |
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typedef struct{ |
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char name[15]; |
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double mass; |
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double epslon; |
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double sigma; |
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double charge; |
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double dipole; |
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double w0; |
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double v0; |
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double v0p; |
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double rl; |
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double ru; |
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double rlp; |
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double rup; |
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int isSSD; |
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int isCharge; |
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int isDipole; |
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int ident; |
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int last; // 0 -> default |
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// 1 -> tells nodes to stop listening |
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} atomStruct; |
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typedef struct{ |
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char nameA[15]; |
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char nameB[15]; |
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double d0; |
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double k0; |
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int last; // 0 -> default |
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// 1 -> tells nodes to stop listening |
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int type; |
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} bondStruct; |
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typedef struct{ |
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char nameA[15]; |
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char nameB[15]; |
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char nameC[15]; |
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char type[30]; |
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double k1, k2, k3, t0; |
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int last; // 0 -> default |
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// 1 -> tells nodes to stop listening |
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} bendStruct; |
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typedef struct{ |
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char nameA[15]; |
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char nameB[15]; |
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char nameC[15]; |
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char nameD[15]; |
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char type[30]; |
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double k1, k2, k3, k4; |
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int last; // 0 -> default |
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// 1 -> tells nodes to stop listening |
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} torsionStruct; |
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int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ); |
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int parseBond( char *lineBuffer, int lineNum, bondStruct &info ); |
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int parseBend( char *lineBuffer, int lineNum, bendStruct &info ); |
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int parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ); |
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#ifdef IS_MPI |
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MPI_Datatype mpiAtomStructType; |
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MPI_Datatype mpiBondStructType; |
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MPI_Datatype mpiBendStructType; |
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MPI_Datatype mpiTorsionStructType; |
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#endif |
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class LinkedAtomType { |
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public: |
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LinkedAtomType(){ |
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next = NULL; |
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name[0] = '\0'; |
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} |
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~LinkedAtomType(){ if( next != NULL ) delete next; } |
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LinkedAtomType* find(char* key){ |
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if( !strcmp(name, key) ) return this; |
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if( next != NULL ) return next->find(key); |
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return NULL; |
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} |
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void printMe( void ){ |
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std::cerr << "LinkedAtype " << name << ": ident = " << ident << "\n"; |
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// if( next != NULL ) next->printMe(); |
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} |
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void add( atomStruct &info ){ |
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// check for duplicates |
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if( !strcmp( info.name, name ) ){ |
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sprintf( painCave.errMsg, |
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"Duplicate DUFF atom type \"%s\" found in " |
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"the DUFF param file./n", |
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name ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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if( next != NULL ) next->add(info); |
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else{ |
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next = new LinkedAtomType(); |
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strcpy(next->name, info.name); |
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next->isDipole = info.isDipole; |
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next->isSSD = info.isSSD; |
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next->mass = info.mass; |
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next->epslon = info.epslon; |
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next->sigma = info.sigma; |
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next->dipole = info.dipole; |
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next->w0 = info.w0; |
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next->v0 = info.v0; |
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next->v0p = info.v0p; |
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next->rl = info.rl; |
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next->ru = info.ru; |
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next->rlp = info.rlp; |
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next->rup = info.rup; |
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next->ident = info.ident; |
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} |
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} |
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#ifdef IS_MPI |
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void duplicate( atomStruct &info ){ |
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strcpy(info.name, name); |
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info.isDipole = isDipole; |
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info.isSSD = isSSD; |
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info.mass = mass; |
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info.epslon = epslon; |
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info.sigma = sigma; |
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info.dipole = dipole; |
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info.w0 = w0; |
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info.v0 = v0; |
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info.v0p = v0p; |
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info.rl = rl; |
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info.ru = ru; |
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info.rlp = rlp; |
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info.rup = rup; |
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info.ident = ident; |
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info.last = 0; |
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} |
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#endif |
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char name[15]; |
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int isDipole; |
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int isSSD; |
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double mass; |
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double epslon; |
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double sigma; |
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double dipole; |
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double w0; |
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double v0; |
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double v0p; |
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double rl; |
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double ru; |
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double rlp; |
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double rup; |
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int ident; |
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LinkedAtomType* next; |
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}; |
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class LinkedBondType { |
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public: |
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LinkedBondType(){ |
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next = NULL; |
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nameA[0] = '\0'; |
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nameB[0] = '\0'; |
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} |
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~LinkedBondType(){ if( next != NULL ) delete next; } |
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LinkedBondType* find(char* key1, char* key2){ |
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if( !strcmp(nameA, key1 ) && !strcmp( nameB, key2 ) ) return this; |
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if( !strcmp(nameA, key2 ) && !strcmp( nameB, key1 ) ) return this; |
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if( next != NULL ) return next->find(key1, key2); |
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return NULL; |
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} |
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void add( bondStruct &info ){ |
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// check for duplicates |
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int dup = 0; |
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if( !strcmp(nameA, info.nameA ) && !strcmp( nameB, info.nameB ) ) dup = 1; |
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if( !strcmp(nameA, info.nameB ) && !strcmp( nameB, info.nameA ) ) dup = 1; |
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if(dup){ |
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sprintf( painCave.errMsg, |
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"Duplicate DUFF bond type \"%s - %s\" found in " |
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"the DUFF param file./n", |
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nameA, nameB ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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if( next != NULL ) next->add(info); |
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else{ |
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next = new LinkedBondType(); |
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strcpy(next->nameA, info.nameA); |
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strcpy(next->nameB, info.nameB); |
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next->type = info.type; |
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next->d0 = info.d0; |
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next->k0 = info.k0; |
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} |
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} |
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#ifdef IS_MPI |
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void duplicate( bondStruct &info ){ |
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strcpy(info.nameA, nameA); |
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strcpy(info.nameB, nameB); |
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info.type = type; |
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info.d0 = d0; |
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info.k0 = k0; |
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info.last = 0; |
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} |
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#endif |
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char nameA[15]; |
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char nameB[15]; |
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int type; |
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double d0; |
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double k0; |
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LinkedBondType* next; |
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}; |
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class LinkedBendType { |
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public: |
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LinkedBendType(){ |
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next = NULL; |
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nameA[0] = '\0'; |
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nameB[0] = '\0'; |
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nameC[0] = '\0'; |
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type[0] = '\0'; |
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} |
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~LinkedBendType(){ if( next != NULL ) delete next; } |
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LinkedBendType* find( char* key1, char* key2, char* key3 ){ |
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if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) |
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&& !strcmp( nameC, key3 ) ) return this; |
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if( !strcmp( nameA, key3 ) && !strcmp( nameB, key2 ) |
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&& !strcmp( nameC, key1 ) ) return this; |
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if( next != NULL ) return next->find(key1, key2, key3); |
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return NULL; |
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} |
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void add( bendStruct &info ){ |
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// check for duplicates |
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int dup = 0; |
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if( !strcmp( nameA, info.nameA ) && !strcmp( nameB, info.nameB ) |
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&& !strcmp( nameC, info.nameC ) ) dup = 1; |
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if( !strcmp( nameA, info.nameC ) && !strcmp( nameB, info.nameB ) |
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&& !strcmp( nameC, info.nameA ) ) dup = 1; |
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if(dup){ |
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sprintf( painCave.errMsg, |
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"Duplicate DUFF bend type \"%s - %s - %s\" found in " |
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"the DUFF param file./n", |
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nameA, nameB, nameC ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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if( next != NULL ) next->add(info); |
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else{ |
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next = new LinkedBendType(); |
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strcpy(next->nameA, info.nameA); |
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strcpy(next->nameB, info.nameB); |
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strcpy(next->nameC, info.nameC); |
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strcpy(next->type, info.type); |
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next->k1 = info.k1; |
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next->k2 = info.k2; |
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next->k3 = info.k3; |
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next->t0 = info.t0; |
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} |
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} |
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#ifdef IS_MPI |
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void duplicate( bendStruct &info ){ |
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strcpy(info.nameA, nameA); |
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strcpy(info.nameB, nameB); |
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strcpy(info.nameC, nameC); |
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strcpy(info.type, type); |
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info.k1 = k1; |
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info.k2 = k2; |
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info.k3 = k3; |
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info.t0 = t0; |
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info.last = 0; |
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} |
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#endif // is_mpi |
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char nameA[15]; |
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char nameB[15]; |
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char nameC[15]; |
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char type[30]; |
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double k1, k2, k3, t0; |
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LinkedBendType* next; |
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}; |
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class LinkedTorsionType { |
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public: |
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LinkedTorsionType(){ |
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next = NULL; |
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nameA[0] = '\0'; |
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nameB[0] = '\0'; |
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nameC[0] = '\0'; |
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type[0] = '\0'; |
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} |
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~LinkedTorsionType(){ if( next != NULL ) delete next; } |
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LinkedTorsionType* find( char* key1, char* key2, char* key3, char* key4 ){ |
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if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) && |
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!strcmp( nameC, key3 ) && !strcmp( nameD, key4 ) ) return this; |
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if( !strcmp( nameA, key4 ) && !strcmp( nameB, key3 ) && |
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!strcmp( nameC, key2 ) && !strcmp( nameD, key1 ) ) return this; |
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if( next != NULL ) return next->find(key1, key2, key3, key4); |
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return NULL; |
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} |
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void add( torsionStruct &info ){ |
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373 |
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// check for duplicates |
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int dup = 0; |
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if( !strcmp( nameA, info.nameA ) && !strcmp( nameB, info.nameB ) && |
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!strcmp( nameC, info.nameC ) && !strcmp( nameD, info.nameD ) ) dup = 1; |
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if( !strcmp( nameA, info.nameD ) && !strcmp( nameB, info.nameC ) && |
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!strcmp( nameC, info.nameB ) && !strcmp( nameD, info.nameA ) ) dup = 1; |
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if(dup){ |
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sprintf( painCave.errMsg, |
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"Duplicate DUFF torsion type \"%s - %s - %s - %s\" found in " |
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"the DUFF param file./n", nameA, nameB, nameC, nameD ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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390 |
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if( next != NULL ) next->add(info); |
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else{ |
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next = new LinkedTorsionType(); |
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strcpy(next->nameA, info.nameA); |
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strcpy(next->nameB, info.nameB); |
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strcpy(next->nameC, info.nameC); |
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strcpy(next->nameD, info.nameD); |
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strcpy(next->type, info.type); |
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next->k1 = info.k1; |
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next->k2 = info.k2; |
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next->k3 = info.k3; |
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next->k4 = info.k4; |
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} |
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} |
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406 |
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#ifdef IS_MPI |
407 |
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408 |
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void duplicate( torsionStruct &info ){ |
409 |
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strcpy(info.nameA, nameA); |
410 |
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strcpy(info.nameB, nameB); |
411 |
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strcpy(info.nameC, nameC); |
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|
|
strcpy(info.nameD, nameD); |
413 |
|
|
strcpy(info.type, type); |
414 |
|
|
info.k1 = k1; |
415 |
|
|
info.k2 = k2; |
416 |
|
|
info.k3 = k3; |
417 |
|
|
info.k4 = k4; |
418 |
|
|
info.last = 0; |
419 |
|
|
} |
420 |
|
|
|
421 |
|
|
#endif |
422 |
|
|
|
423 |
|
|
char nameA[15]; |
424 |
|
|
char nameB[15]; |
425 |
|
|
char nameC[15]; |
426 |
|
|
char nameD[15]; |
427 |
|
|
char type[30]; |
428 |
|
|
double k1, k2, k3, k4; |
429 |
|
|
|
430 |
|
|
LinkedTorsionType* next; |
431 |
|
|
}; |
432 |
|
|
|
433 |
|
|
|
434 |
|
|
LinkedAtomType* headAtomType; |
435 |
|
|
LinkedAtomType* currentAtomType; |
436 |
|
|
LinkedBondType* headBondType; |
437 |
|
|
LinkedBondType* currentBondType; |
438 |
|
|
LinkedBendType* headBendType; |
439 |
|
|
LinkedBendType* currentBendType; |
440 |
|
|
LinkedTorsionType* headTorsionType; |
441 |
|
|
LinkedTorsionType* currentTorsionType; |
442 |
|
|
|
443 |
|
|
} // namespace |
444 |
|
|
|
445 |
|
|
using namespace DUFF_NS; |
446 |
|
|
|
447 |
|
|
|
448 |
|
|
//**************************************************************** |
449 |
|
|
// begins the actual forcefield stuff. |
450 |
|
|
//**************************************************************** |
451 |
|
|
|
452 |
|
|
|
453 |
|
|
DUFF::DUFF(){ |
454 |
|
|
|
455 |
|
|
char fileName[200]; |
456 |
|
|
char* ffPath_env = "FORCE_PARAM_PATH"; |
457 |
|
|
char* ffPath; |
458 |
|
|
char temp[200]; |
459 |
|
|
|
460 |
|
|
headAtomType = NULL; |
461 |
|
|
currentAtomType = NULL; |
462 |
|
|
headBondType = NULL; |
463 |
|
|
currentBondType = NULL; |
464 |
|
|
headBendType = NULL; |
465 |
|
|
currentBendType = NULL; |
466 |
|
|
headTorsionType = NULL; |
467 |
|
|
currentTorsionType = NULL; |
468 |
|
|
|
469 |
|
|
// do the funtion wrapping |
470 |
|
|
wrapMeFF( this ); |
471 |
|
|
|
472 |
|
|
|
473 |
|
|
#ifdef IS_MPI |
474 |
|
|
int i; |
475 |
|
|
|
476 |
|
|
// ********************************************************************** |
477 |
|
|
// Init the atomStruct mpi type |
478 |
|
|
|
479 |
|
|
atomStruct atomProto; // mpiPrototype |
480 |
|
|
int atomBC[3] = {15,12,5}; // block counts |
481 |
|
|
MPI_Aint atomDspls[3]; // displacements |
482 |
|
|
MPI_Datatype atomMbrTypes[3]; // member mpi types |
483 |
|
|
|
484 |
|
|
MPI_Address(&atomProto.name, &atomDspls[0]); |
485 |
|
|
MPI_Address(&atomProto.mass, &atomDspls[1]); |
486 |
|
|
MPI_Address(&atomProto.isSSD, &atomDspls[2]); |
487 |
|
|
|
488 |
|
|
atomMbrTypes[0] = MPI_CHAR; |
489 |
|
|
atomMbrTypes[1] = MPI_DOUBLE; |
490 |
|
|
atomMbrTypes[2] = MPI_INT; |
491 |
|
|
|
492 |
|
|
for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0]; |
493 |
|
|
|
494 |
|
|
MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType); |
495 |
|
|
MPI_Type_commit(&mpiAtomStructType); |
496 |
|
|
|
497 |
|
|
|
498 |
|
|
// ********************************************************************** |
499 |
|
|
// Init the bondStruct mpi type |
500 |
|
|
|
501 |
|
|
bondStruct bondProto; // mpiPrototype |
502 |
|
|
int bondBC[3] = {30,2,2}; // block counts |
503 |
|
|
MPI_Aint bondDspls[3]; // displacements |
504 |
|
|
MPI_Datatype bondMbrTypes[3]; // member mpi types |
505 |
|
|
|
506 |
|
|
MPI_Address(&bondProto.nameA, &bondDspls[0]); |
507 |
|
|
MPI_Address(&bondProto.d0, &bondDspls[1]); |
508 |
|
|
MPI_Address(&bondProto.last, &bondDspls[2]); |
509 |
|
|
|
510 |
|
|
bondMbrTypes[0] = MPI_CHAR; |
511 |
|
|
bondMbrTypes[1] = MPI_DOUBLE; |
512 |
|
|
bondMbrTypes[2] = MPI_INT; |
513 |
|
|
|
514 |
|
|
for (i=2; i >= 0; i--) bondDspls[i] -= bondDspls[0]; |
515 |
|
|
|
516 |
|
|
MPI_Type_struct(3, bondBC, bondDspls, bondMbrTypes, &mpiBondStructType); |
517 |
|
|
MPI_Type_commit(&mpiBondStructType); |
518 |
|
|
|
519 |
|
|
|
520 |
|
|
// ********************************************************************** |
521 |
|
|
// Init the bendStruct mpi type |
522 |
|
|
|
523 |
|
|
bendStruct bendProto; // mpiPrototype |
524 |
|
|
int bendBC[3] = {75,4,1}; // block counts |
525 |
|
|
MPI_Aint bendDspls[3]; // displacements |
526 |
|
|
MPI_Datatype bendMbrTypes[3]; // member mpi types |
527 |
|
|
|
528 |
|
|
MPI_Address(&bendProto.nameA, &bendDspls[0]); |
529 |
|
|
MPI_Address(&bendProto.k1, &bendDspls[1]); |
530 |
|
|
MPI_Address(&bendProto.last, &bendDspls[2]); |
531 |
|
|
|
532 |
|
|
bendMbrTypes[0] = MPI_CHAR; |
533 |
|
|
bendMbrTypes[1] = MPI_DOUBLE; |
534 |
|
|
bendMbrTypes[2] = MPI_INT; |
535 |
|
|
|
536 |
|
|
for (i=2; i >= 0; i--) bendDspls[i] -= bendDspls[0]; |
537 |
|
|
|
538 |
|
|
MPI_Type_struct(3, bendBC, bendDspls, bendMbrTypes, &mpiBendStructType); |
539 |
|
|
MPI_Type_commit(&mpiBendStructType); |
540 |
|
|
|
541 |
|
|
|
542 |
|
|
// ********************************************************************** |
543 |
|
|
// Init the torsionStruct mpi type |
544 |
|
|
|
545 |
|
|
torsionStruct torsionProto; // mpiPrototype |
546 |
|
|
int torsionBC[3] = {90,4,1}; // block counts |
547 |
|
|
MPI_Aint torsionDspls[3]; // displacements |
548 |
|
|
MPI_Datatype torsionMbrTypes[3]; // member mpi types |
549 |
|
|
|
550 |
|
|
MPI_Address(&torsionProto.nameA, &torsionDspls[0]); |
551 |
|
|
MPI_Address(&torsionProto.k1, &torsionDspls[1]); |
552 |
|
|
MPI_Address(&torsionProto.last, &torsionDspls[2]); |
553 |
|
|
|
554 |
|
|
torsionMbrTypes[0] = MPI_CHAR; |
555 |
|
|
torsionMbrTypes[1] = MPI_DOUBLE; |
556 |
|
|
torsionMbrTypes[2] = MPI_INT; |
557 |
|
|
|
558 |
|
|
for (i=2; i >= 0; i--) torsionDspls[i] -= torsionDspls[0]; |
559 |
|
|
|
560 |
|
|
MPI_Type_struct(3, torsionBC, torsionDspls, torsionMbrTypes, |
561 |
|
|
&mpiTorsionStructType); |
562 |
|
|
MPI_Type_commit(&mpiTorsionStructType); |
563 |
|
|
|
564 |
|
|
// *********************************************************************** |
565 |
|
|
|
566 |
|
|
if( worldRank == 0 ){ |
567 |
|
|
#endif |
568 |
|
|
|
569 |
|
|
// generate the force file name |
570 |
|
|
|
571 |
|
|
strcpy( fileName, "DUFF.frc" ); |
572 |
|
|
// fprintf( stderr,"Trying to open %s\n", fileName ); |
573 |
|
|
|
574 |
|
|
// attempt to open the file in the current directory first. |
575 |
|
|
|
576 |
|
|
frcFile = fopen( fileName, "r" ); |
577 |
|
|
|
578 |
|
|
if( frcFile == NULL ){ |
579 |
|
|
|
580 |
|
|
// next see if the force path enviorment variable is set |
581 |
|
|
|
582 |
|
|
ffPath = getenv( ffPath_env ); |
583 |
|
|
if( ffPath == NULL ) { |
584 |
|
|
STR_DEFINE(ffPath, FRC_PATH ); |
585 |
|
|
} |
586 |
|
|
|
587 |
|
|
|
588 |
|
|
strcpy( temp, ffPath ); |
589 |
|
|
strcat( temp, "/" ); |
590 |
|
|
strcat( temp, fileName ); |
591 |
|
|
strcpy( fileName, temp ); |
592 |
|
|
|
593 |
|
|
frcFile = fopen( fileName, "r" ); |
594 |
|
|
|
595 |
|
|
if( frcFile == NULL ){ |
596 |
|
|
|
597 |
|
|
sprintf( painCave.errMsg, |
598 |
|
|
"Error opening the force field parameter file:\n" |
599 |
|
|
"\t%s\n" |
600 |
|
|
"\tHave you tried setting the FORCE_PARAM_PATH environment " |
601 |
|
|
"variable?\n", |
602 |
|
|
fileName ); |
603 |
|
|
painCave.severity = OOPSE_ERROR; |
604 |
|
|
painCave.isFatal = 1; |
605 |
|
|
simError(); |
606 |
|
|
} |
607 |
|
|
} |
608 |
|
|
|
609 |
|
|
#ifdef IS_MPI |
610 |
|
|
} |
611 |
|
|
|
612 |
|
|
sprintf( checkPointMsg, "DUFF file opened sucessfully." ); |
613 |
|
|
MPIcheckPoint(); |
614 |
|
|
|
615 |
|
|
#endif // is_mpi |
616 |
|
|
} |
617 |
|
|
|
618 |
|
|
|
619 |
|
|
DUFF::~DUFF(){ |
620 |
|
|
|
621 |
|
|
if( headAtomType != NULL ) delete headAtomType; |
622 |
|
|
if( headBondType != NULL ) delete headBondType; |
623 |
|
|
if( headBendType != NULL ) delete headBendType; |
624 |
|
|
if( headTorsionType != NULL ) delete headTorsionType; |
625 |
|
|
|
626 |
|
|
#ifdef IS_MPI |
627 |
|
|
if( worldRank == 0 ){ |
628 |
|
|
#endif // is_mpi |
629 |
|
|
|
630 |
|
|
fclose( frcFile ); |
631 |
|
|
|
632 |
|
|
#ifdef IS_MPI |
633 |
|
|
} |
634 |
|
|
#endif // is_mpi |
635 |
|
|
} |
636 |
|
|
|
637 |
|
|
void DUFF::cleanMe( void ){ |
638 |
|
|
|
639 |
|
|
#ifdef IS_MPI |
640 |
|
|
|
641 |
|
|
// keep the linked lists in the mpi version |
642 |
|
|
|
643 |
|
|
#else // is_mpi |
644 |
|
|
|
645 |
|
|
// delete the linked lists in the single processor version |
646 |
|
|
|
647 |
|
|
if( headAtomType != NULL ) delete headAtomType; |
648 |
|
|
if( headBondType != NULL ) delete headBondType; |
649 |
|
|
if( headBendType != NULL ) delete headBendType; |
650 |
|
|
if( headTorsionType != NULL ) delete headTorsionType; |
651 |
|
|
|
652 |
|
|
#endif // is_mpi |
653 |
|
|
} |
654 |
|
|
|
655 |
|
|
|
656 |
|
|
void DUFF::initForceField( int ljMixRule ){ |
657 |
|
|
|
658 |
|
|
initFortran( ljMixRule, entry_plug->useReactionField ); |
659 |
|
|
} |
660 |
|
|
|
661 |
|
|
double DUFF::getAtomTypeMass (char* atomType) { |
662 |
|
|
|
663 |
|
|
currentAtomType = headAtomType->find( atomType ); |
664 |
|
|
if( currentAtomType == NULL ){ |
665 |
|
|
sprintf( painCave.errMsg, |
666 |
|
|
"AtomType error, %s not found in force file.\n", |
667 |
|
|
atomType ); |
668 |
|
|
painCave.isFatal = 1; |
669 |
|
|
simError(); |
670 |
|
|
} |
671 |
|
|
|
672 |
|
|
return currentAtomType->mass; |
673 |
|
|
} |
674 |
|
|
|
675 |
|
|
void DUFF::readParams( void ){ |
676 |
|
|
|
677 |
|
|
int identNum; |
678 |
|
|
|
679 |
|
|
atomStruct atomInfo; |
680 |
|
|
bondStruct bondInfo; |
681 |
|
|
bendStruct bendInfo; |
682 |
|
|
torsionStruct torsionInfo; |
683 |
|
|
|
684 |
|
|
bigSigma = 0.0; |
685 |
|
|
|
686 |
|
|
atomInfo.last = 1; |
687 |
|
|
bondInfo.last = 1; |
688 |
|
|
bendInfo.last = 1; |
689 |
|
|
torsionInfo.last = 1; |
690 |
|
|
|
691 |
|
|
// read in the atom info |
692 |
|
|
|
693 |
|
|
#ifdef IS_MPI |
694 |
|
|
if( worldRank == 0 ){ |
695 |
|
|
#endif |
696 |
|
|
|
697 |
|
|
// read in the atom types. |
698 |
|
|
|
699 |
|
|
headAtomType = new LinkedAtomType; |
700 |
|
|
|
701 |
|
|
fastForward( "AtomTypes", "initializeAtoms" ); |
702 |
|
|
|
703 |
|
|
// we are now at the AtomTypes section. |
704 |
|
|
|
705 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
706 |
|
|
lineNum++; |
707 |
|
|
|
708 |
|
|
|
709 |
|
|
// read a line, and start parseing out the atom types |
710 |
|
|
|
711 |
|
|
if( eof_test == NULL ){ |
712 |
|
|
sprintf( painCave.errMsg, |
713 |
|
|
"Error in reading Atoms from force file at line %d.\n", |
714 |
|
|
lineNum ); |
715 |
|
|
painCave.isFatal = 1; |
716 |
|
|
simError(); |
717 |
|
|
} |
718 |
|
|
|
719 |
|
|
identNum = 1; |
720 |
|
|
// stop reading at end of file, or at next section |
721 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
722 |
|
|
|
723 |
|
|
// toss comment lines |
724 |
|
|
if( readLine[0] != '!' ){ |
725 |
|
|
|
726 |
|
|
// the parser returns 0 if the line was blank |
727 |
|
|
if( parseAtom( readLine, lineNum, atomInfo ) ){ |
728 |
|
|
atomInfo.ident = identNum; |
729 |
|
|
headAtomType->add( atomInfo );; |
730 |
|
|
identNum++; |
731 |
|
|
} |
732 |
|
|
} |
733 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
734 |
|
|
lineNum++; |
735 |
|
|
} |
736 |
|
|
|
737 |
|
|
#ifdef IS_MPI |
738 |
|
|
|
739 |
|
|
// send out the linked list to all the other processes |
740 |
|
|
|
741 |
|
|
sprintf( checkPointMsg, |
742 |
|
|
"DUFF atom structures read successfully." ); |
743 |
|
|
MPIcheckPoint(); |
744 |
|
|
|
745 |
|
|
currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
746 |
|
|
while( currentAtomType != NULL ){ |
747 |
|
|
currentAtomType->duplicate( atomInfo ); |
748 |
|
|
|
749 |
|
|
sendFrcStruct( &atomInfo, mpiAtomStructType ); |
750 |
|
|
|
751 |
|
|
sprintf( checkPointMsg, |
752 |
|
|
"successfully sent DUFF force type: \"%s\"\n", |
753 |
|
|
atomInfo.name ); |
754 |
|
|
MPIcheckPoint(); |
755 |
|
|
|
756 |
|
|
currentAtomType = currentAtomType->next; |
757 |
|
|
} |
758 |
|
|
atomInfo.last = 1; |
759 |
|
|
sendFrcStruct( &atomInfo, mpiAtomStructType ); |
760 |
|
|
|
761 |
|
|
} |
762 |
|
|
|
763 |
|
|
else{ |
764 |
|
|
|
765 |
|
|
// listen for node 0 to send out the force params |
766 |
|
|
|
767 |
|
|
MPIcheckPoint(); |
768 |
|
|
|
769 |
|
|
headAtomType = new LinkedAtomType; |
770 |
|
|
receiveFrcStruct( &atomInfo, mpiAtomStructType ); |
771 |
|
|
|
772 |
|
|
while( !atomInfo.last ){ |
773 |
|
|
|
774 |
|
|
headAtomType->add( atomInfo ); |
775 |
|
|
|
776 |
|
|
MPIcheckPoint(); |
777 |
|
|
|
778 |
|
|
receiveFrcStruct( &atomInfo, mpiAtomStructType ); |
779 |
|
|
} |
780 |
|
|
} |
781 |
|
|
|
782 |
|
|
#endif // is_mpi |
783 |
|
|
|
784 |
|
|
|
785 |
|
|
|
786 |
|
|
// call new A_types in fortran |
787 |
|
|
|
788 |
|
|
int isError; |
789 |
|
|
|
790 |
|
|
// dummy variables |
791 |
|
|
|
792 |
|
|
int isGB = 0; |
793 |
|
|
int isLJ = 1; |
794 |
|
|
int isEAM =0; |
795 |
|
|
int isCharge = 0; |
796 |
|
|
double charge=0.0; |
797 |
|
|
|
798 |
|
|
currentAtomType = headAtomType->next;; |
799 |
|
|
while( currentAtomType != NULL ){ |
800 |
|
|
|
801 |
|
|
if(currentAtomType->isDipole) entry_plug->useDipoles = 1; |
802 |
|
|
if(currentAtomType->isSSD) { |
803 |
|
|
entry_plug->useSticky = 1; |
804 |
|
|
set_sticky_params( &(currentAtomType->w0), &(currentAtomType->v0), |
805 |
|
|
&(currentAtomType->v0p), |
806 |
|
|
&(currentAtomType->rl), &(currentAtomType->ru), |
807 |
|
|
&(currentAtomType->rlp), &(currentAtomType->rup)); |
808 |
|
|
} |
809 |
|
|
|
810 |
|
|
if( currentAtomType->name[0] != '\0' ){ |
811 |
|
|
isError = 0; |
812 |
|
|
makeAtype( &(currentAtomType->ident), |
813 |
|
|
&isLJ, |
814 |
|
|
&(currentAtomType->isSSD), |
815 |
|
|
&(currentAtomType->isDipole), |
816 |
|
|
&isGB, |
817 |
|
|
&isEAM, |
818 |
|
|
&isCharge, |
819 |
|
|
&(currentAtomType->epslon), |
820 |
|
|
&(currentAtomType->sigma), |
821 |
|
|
&charge, |
822 |
|
|
&(currentAtomType->dipole), |
823 |
|
|
&isError ); |
824 |
|
|
if( isError ){ |
825 |
|
|
sprintf( painCave.errMsg, |
826 |
|
|
"Error initializing the \"%s\" atom type in fortran\n", |
827 |
|
|
currentAtomType->name ); |
828 |
|
|
painCave.isFatal = 1; |
829 |
|
|
simError(); |
830 |
|
|
} |
831 |
|
|
} |
832 |
|
|
currentAtomType = currentAtomType->next; |
833 |
|
|
} |
834 |
|
|
|
835 |
|
|
#ifdef IS_MPI |
836 |
|
|
sprintf( checkPointMsg, |
837 |
|
|
"DUFF atom structures successfully sent to fortran\n" ); |
838 |
|
|
MPIcheckPoint(); |
839 |
|
|
#endif // is_mpi |
840 |
|
|
|
841 |
|
|
|
842 |
|
|
|
843 |
|
|
// read in the bonds |
844 |
|
|
|
845 |
|
|
#ifdef IS_MPI |
846 |
|
|
if( worldRank == 0 ){ |
847 |
|
|
#endif |
848 |
|
|
|
849 |
|
|
// read in the bond types. |
850 |
|
|
|
851 |
|
|
headBondType = new LinkedBondType; |
852 |
|
|
|
853 |
|
|
fastForward( "BondTypes", "initializeBonds" ); |
854 |
|
|
|
855 |
|
|
// we are now at the bondTypes section |
856 |
|
|
|
857 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
858 |
|
|
lineNum++; |
859 |
|
|
|
860 |
|
|
|
861 |
|
|
// read a line, and start parseing out the atom types |
862 |
|
|
|
863 |
|
|
if( eof_test == NULL ){ |
864 |
|
|
sprintf( painCave.errMsg, |
865 |
|
|
"Error in reading bonds from force file at line %d.\n", |
866 |
|
|
lineNum ); |
867 |
|
|
painCave.isFatal = 1; |
868 |
|
|
simError(); |
869 |
|
|
} |
870 |
|
|
|
871 |
|
|
// stop reading at end of file, or at next section |
872 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
873 |
|
|
|
874 |
|
|
// toss comment lines |
875 |
|
|
if( readLine[0] != '!' ){ |
876 |
|
|
|
877 |
|
|
// the parser returns 0 if the line was blank |
878 |
|
|
if( parseBond( readLine, lineNum, bondInfo ) ){ |
879 |
|
|
headBondType->add( bondInfo ); |
880 |
|
|
} |
881 |
|
|
} |
882 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
883 |
|
|
lineNum++; |
884 |
|
|
} |
885 |
|
|
|
886 |
|
|
#ifdef IS_MPI |
887 |
|
|
|
888 |
|
|
// send out the linked list to all the other processes |
889 |
|
|
|
890 |
|
|
sprintf( checkPointMsg, |
891 |
|
|
"DUFF bond structures read successfully." ); |
892 |
|
|
MPIcheckPoint(); |
893 |
|
|
|
894 |
|
|
currentBondType = headBondType->next; |
895 |
|
|
while( currentBondType != NULL ){ |
896 |
|
|
currentBondType->duplicate( bondInfo ); |
897 |
|
|
sendFrcStruct( &bondInfo, mpiBondStructType ); |
898 |
|
|
currentBondType = currentBondType->next; |
899 |
|
|
} |
900 |
|
|
bondInfo.last = 1; |
901 |
|
|
sendFrcStruct( &bondInfo, mpiBondStructType ); |
902 |
|
|
|
903 |
|
|
} |
904 |
|
|
|
905 |
|
|
else{ |
906 |
|
|
|
907 |
|
|
// listen for node 0 to send out the force params |
908 |
|
|
|
909 |
|
|
MPIcheckPoint(); |
910 |
|
|
|
911 |
|
|
headBondType = new LinkedBondType; |
912 |
|
|
receiveFrcStruct( &bondInfo, mpiBondStructType ); |
913 |
|
|
while( !bondInfo.last ){ |
914 |
|
|
|
915 |
|
|
headBondType->add( bondInfo ); |
916 |
|
|
receiveFrcStruct( &bondInfo, mpiBondStructType ); |
917 |
|
|
} |
918 |
|
|
} |
919 |
|
|
|
920 |
|
|
sprintf( checkPointMsg, |
921 |
|
|
"DUFF bond structures broadcast successfully." ); |
922 |
|
|
MPIcheckPoint(); |
923 |
|
|
|
924 |
|
|
#endif // is_mpi |
925 |
|
|
|
926 |
|
|
|
927 |
|
|
// read in the bends |
928 |
|
|
|
929 |
|
|
#ifdef IS_MPI |
930 |
|
|
if( worldRank == 0 ){ |
931 |
|
|
#endif |
932 |
|
|
|
933 |
|
|
// read in the bend types. |
934 |
|
|
|
935 |
|
|
headBendType = new LinkedBendType; |
936 |
|
|
|
937 |
|
|
fastForward( "BendTypes", "initializeBends" ); |
938 |
|
|
|
939 |
|
|
// we are now at the bendTypes section |
940 |
|
|
|
941 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
942 |
|
|
lineNum++; |
943 |
|
|
|
944 |
|
|
// read a line, and start parseing out the bend types |
945 |
|
|
|
946 |
|
|
if( eof_test == NULL ){ |
947 |
|
|
sprintf( painCave.errMsg, |
948 |
|
|
"Error in reading bends from force file at line %d.\n", |
949 |
|
|
lineNum ); |
950 |
|
|
painCave.isFatal = 1; |
951 |
|
|
simError(); |
952 |
|
|
} |
953 |
|
|
|
954 |
|
|
// stop reading at end of file, or at next section |
955 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
956 |
|
|
|
957 |
|
|
// toss comment lines |
958 |
|
|
if( readLine[0] != '!' ){ |
959 |
|
|
|
960 |
|
|
// the parser returns 0 if the line was blank |
961 |
|
|
if( parseBend( readLine, lineNum, bendInfo ) ){ |
962 |
|
|
headBendType->add( bendInfo ); |
963 |
|
|
} |
964 |
|
|
} |
965 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
966 |
|
|
lineNum++; |
967 |
|
|
} |
968 |
|
|
|
969 |
|
|
#ifdef IS_MPI |
970 |
|
|
|
971 |
|
|
// send out the linked list to all the other processes |
972 |
|
|
|
973 |
|
|
sprintf( checkPointMsg, |
974 |
|
|
"DUFF bend structures read successfully." ); |
975 |
|
|
MPIcheckPoint(); |
976 |
|
|
|
977 |
|
|
currentBendType = headBendType->next; |
978 |
|
|
while( currentBendType != NULL ){ |
979 |
|
|
currentBendType->duplicate( bendInfo ); |
980 |
|
|
sendFrcStruct( &bendInfo, mpiBendStructType ); |
981 |
|
|
currentBendType = currentBendType->next; |
982 |
|
|
} |
983 |
|
|
bendInfo.last = 1; |
984 |
|
|
sendFrcStruct( &bendInfo, mpiBendStructType ); |
985 |
|
|
|
986 |
|
|
} |
987 |
|
|
|
988 |
|
|
else{ |
989 |
|
|
|
990 |
|
|
// listen for node 0 to send out the force params |
991 |
|
|
|
992 |
|
|
MPIcheckPoint(); |
993 |
|
|
|
994 |
|
|
headBendType = new LinkedBendType; |
995 |
|
|
receiveFrcStruct( &bendInfo, mpiBendStructType ); |
996 |
|
|
while( !bendInfo.last ){ |
997 |
|
|
|
998 |
|
|
headBendType->add( bendInfo ); |
999 |
|
|
receiveFrcStruct( &bendInfo, mpiBendStructType ); |
1000 |
|
|
} |
1001 |
|
|
} |
1002 |
|
|
|
1003 |
|
|
sprintf( checkPointMsg, |
1004 |
|
|
"DUFF bend structures broadcast successfully." ); |
1005 |
|
|
MPIcheckPoint(); |
1006 |
|
|
|
1007 |
|
|
#endif // is_mpi |
1008 |
|
|
|
1009 |
|
|
|
1010 |
|
|
// read in the torsions |
1011 |
|
|
|
1012 |
|
|
#ifdef IS_MPI |
1013 |
|
|
if( worldRank == 0 ){ |
1014 |
|
|
#endif |
1015 |
|
|
|
1016 |
|
|
// read in the torsion types. |
1017 |
|
|
|
1018 |
|
|
headTorsionType = new LinkedTorsionType; |
1019 |
|
|
|
1020 |
|
|
fastForward( "TorsionTypes", "initializeTorsions" ); |
1021 |
|
|
|
1022 |
|
|
// we are now at the torsionTypes section |
1023 |
|
|
|
1024 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1025 |
|
|
lineNum++; |
1026 |
|
|
|
1027 |
|
|
|
1028 |
|
|
// read a line, and start parseing out the atom types |
1029 |
|
|
|
1030 |
|
|
if( eof_test == NULL ){ |
1031 |
|
|
sprintf( painCave.errMsg, |
1032 |
|
|
"Error in reading torsions from force file at line %d.\n", |
1033 |
|
|
lineNum ); |
1034 |
|
|
painCave.isFatal = 1; |
1035 |
|
|
simError(); |
1036 |
|
|
} |
1037 |
|
|
|
1038 |
|
|
// stop reading at end of file, or at next section |
1039 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
1040 |
|
|
|
1041 |
|
|
// toss comment lines |
1042 |
|
|
if( readLine[0] != '!' ){ |
1043 |
|
|
|
1044 |
|
|
// the parser returns 0 if the line was blank |
1045 |
|
|
if( parseTorsion( readLine, lineNum, torsionInfo ) ){ |
1046 |
|
|
headTorsionType->add( torsionInfo ); |
1047 |
|
|
|
1048 |
|
|
} |
1049 |
|
|
} |
1050 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1051 |
|
|
lineNum++; |
1052 |
|
|
} |
1053 |
|
|
|
1054 |
|
|
#ifdef IS_MPI |
1055 |
|
|
|
1056 |
|
|
// send out the linked list to all the other processes |
1057 |
|
|
|
1058 |
|
|
sprintf( checkPointMsg, |
1059 |
|
|
"DUFF torsion structures read successfully." ); |
1060 |
|
|
MPIcheckPoint(); |
1061 |
|
|
|
1062 |
|
|
currentTorsionType = headTorsionType->next; |
1063 |
|
|
while( currentTorsionType != NULL ){ |
1064 |
|
|
currentTorsionType->duplicate( torsionInfo ); |
1065 |
|
|
sendFrcStruct( &torsionInfo, mpiTorsionStructType ); |
1066 |
|
|
currentTorsionType = currentTorsionType->next; |
1067 |
|
|
} |
1068 |
|
|
torsionInfo.last = 1; |
1069 |
|
|
sendFrcStruct( &torsionInfo, mpiTorsionStructType ); |
1070 |
|
|
|
1071 |
|
|
} |
1072 |
|
|
|
1073 |
|
|
else{ |
1074 |
|
|
|
1075 |
|
|
// listen for node 0 to send out the force params |
1076 |
|
|
|
1077 |
|
|
MPIcheckPoint(); |
1078 |
|
|
|
1079 |
|
|
headTorsionType = new LinkedTorsionType; |
1080 |
|
|
receiveFrcStruct( &torsionInfo, mpiTorsionStructType ); |
1081 |
|
|
while( !torsionInfo.last ){ |
1082 |
|
|
|
1083 |
|
|
headTorsionType->add( torsionInfo ); |
1084 |
|
|
receiveFrcStruct( &torsionInfo, mpiTorsionStructType ); |
1085 |
|
|
} |
1086 |
|
|
} |
1087 |
|
|
|
1088 |
|
|
sprintf( checkPointMsg, |
1089 |
|
|
"DUFF torsion structures broadcast successfully." ); |
1090 |
|
|
MPIcheckPoint(); |
1091 |
|
|
|
1092 |
|
|
#endif // is_mpi |
1093 |
|
|
|
1094 |
|
|
entry_plug->useLJ = 1; |
1095 |
|
|
} |
1096 |
|
|
|
1097 |
|
|
|
1098 |
|
|
|
1099 |
|
|
void DUFF::initializeAtoms( int nAtoms, Atom** the_atoms ){ |
1100 |
|
|
|
1101 |
|
|
|
1102 |
|
|
////////////////////////////////////////////////// |
1103 |
|
|
// a quick water fix |
1104 |
|
|
|
1105 |
|
|
double waterI[3][3]; |
1106 |
|
|
waterI[0][0] = 1.76958347772500; |
1107 |
|
|
waterI[0][1] = 0.0; |
1108 |
|
|
waterI[0][2] = 0.0; |
1109 |
|
|
|
1110 |
|
|
waterI[1][0] = 0.0; |
1111 |
|
|
waterI[1][1] = 0.614537057924513; |
1112 |
|
|
waterI[1][2] = 0.0; |
1113 |
|
|
|
1114 |
|
|
waterI[2][0] = 0.0; |
1115 |
|
|
waterI[2][1] = 0.0; |
1116 |
|
|
waterI[2][2] = 1.15504641980049; |
1117 |
|
|
|
1118 |
|
|
|
1119 |
|
|
double headI[3][3]; |
1120 |
|
|
headI[0][0] = 1125; |
1121 |
|
|
headI[0][1] = 0.0; |
1122 |
|
|
headI[0][2] = 0.0; |
1123 |
|
|
|
1124 |
|
|
headI[1][0] = 0.0; |
1125 |
|
|
headI[1][1] = 1125; |
1126 |
|
|
headI[1][2] = 0.0; |
1127 |
|
|
|
1128 |
|
|
headI[2][0] = 0.0; |
1129 |
|
|
headI[2][1] = 0.0; |
1130 |
|
|
headI[2][2] = 250; |
1131 |
|
|
|
1132 |
|
|
////////////////////////////////////////////////// |
1133 |
|
|
|
1134 |
|
|
|
1135 |
|
|
// initialize the atoms |
1136 |
|
|
|
1137 |
|
|
DirectionalAtom* dAtom; |
1138 |
|
|
double ji[3]; |
1139 |
|
|
|
1140 |
|
|
for(int i=0; i<nAtoms; i++ ){ |
1141 |
|
|
|
1142 |
|
|
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
1143 |
|
|
if( currentAtomType == NULL ){ |
1144 |
|
|
sprintf( painCave.errMsg, |
1145 |
|
|
"AtomType error, %s not found in force file.\n", |
1146 |
|
|
the_atoms[i]->getType() ); |
1147 |
|
|
painCave.isFatal = 1; |
1148 |
|
|
simError(); |
1149 |
|
|
} |
1150 |
|
|
|
1151 |
|
|
the_atoms[i]->setMass( currentAtomType->mass ); |
1152 |
|
|
the_atoms[i]->setIdent( currentAtomType->ident ); |
1153 |
|
|
|
1154 |
|
|
if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma; |
1155 |
|
|
|
1156 |
|
|
if( currentAtomType->isDipole ){ |
1157 |
|
|
if( the_atoms[i]->isDirectional() ){ |
1158 |
|
|
|
1159 |
|
|
dAtom = (DirectionalAtom *) the_atoms[i]; |
1160 |
|
|
dAtom->setHasDipole( 1 ); |
1161 |
|
|
|
1162 |
|
|
ji[0] = 0.0; |
1163 |
|
|
ji[1] = 0.0; |
1164 |
|
|
ji[2] = 0.0; |
1165 |
|
|
|
1166 |
|
|
dAtom->setJ( ji ); |
1167 |
|
|
|
1168 |
|
|
if(!strcmp("SSD",the_atoms[i]->getType())){ |
1169 |
|
|
dAtom->setI( waterI ); |
1170 |
|
|
} |
1171 |
|
|
else if(!strcmp("HEAD",the_atoms[i]->getType())){ |
1172 |
|
|
dAtom->setI( headI ); |
1173 |
|
|
} |
1174 |
|
|
else{ |
1175 |
|
|
sprintf(painCave.errMsg, |
1176 |
|
|
"AtmType error, %s does not have a moment of inertia set.\n", |
1177 |
|
|
the_atoms[i]->getType() ); |
1178 |
|
|
painCave.isFatal = 1; |
1179 |
|
|
simError(); |
1180 |
|
|
} |
1181 |
|
|
entry_plug->n_dipoles++; |
1182 |
|
|
} |
1183 |
|
|
else{ |
1184 |
|
|
|
1185 |
|
|
sprintf( painCave.errMsg, |
1186 |
|
|
"DUFF error: Atom \"%s\" is a dipole, yet no standard" |
1187 |
|
|
" orientation was specifed in the meta-data file.\n", |
1188 |
|
|
currentAtomType->name ); |
1189 |
|
|
painCave.isFatal = 1; |
1190 |
|
|
simError(); |
1191 |
|
|
} |
1192 |
|
|
} |
1193 |
|
|
else{ |
1194 |
|
|
if( the_atoms[i]->isDirectional() ){ |
1195 |
|
|
sprintf( painCave.errMsg, |
1196 |
|
|
"DUFF error: Atom \"%s\" was given a standard " |
1197 |
|
|
"orientation in the meta-data file, yet it is not a dipole.\n", |
1198 |
|
|
currentAtomType->name); |
1199 |
|
|
painCave.isFatal = 1; |
1200 |
|
|
simError(); |
1201 |
|
|
} |
1202 |
|
|
} |
1203 |
|
|
} |
1204 |
|
|
} |
1205 |
|
|
|
1206 |
|
|
void DUFF::initializeBonds( int nBonds, Bond** bondArray, |
1207 |
|
|
bond_pair* the_bonds ){ |
1208 |
|
|
int i,a,b; |
1209 |
|
|
char* atomA; |
1210 |
|
|
char* atomB; |
1211 |
|
|
|
1212 |
|
|
Atom** the_atoms; |
1213 |
|
|
the_atoms = entry_plug->atoms; |
1214 |
|
|
|
1215 |
|
|
|
1216 |
|
|
// initialize the Bonds |
1217 |
|
|
|
1218 |
|
|
for( i=0; i<nBonds; i++ ){ |
1219 |
|
|
|
1220 |
|
|
a = the_bonds[i].a; |
1221 |
|
|
b = the_bonds[i].b; |
1222 |
|
|
|
1223 |
|
|
atomA = the_atoms[a]->getType(); |
1224 |
|
|
atomB = the_atoms[b]->getType(); |
1225 |
|
|
currentBondType = headBondType->find( atomA, atomB ); |
1226 |
|
|
if( currentBondType == NULL ){ |
1227 |
|
|
sprintf( painCave.errMsg, |
1228 |
|
|
"BondType error, %s - %s not found in force file.\n", |
1229 |
|
|
atomA, atomB ); |
1230 |
|
|
painCave.isFatal = 1; |
1231 |
|
|
simError(); |
1232 |
|
|
} |
1233 |
|
|
|
1234 |
|
|
switch( currentBondType->type ){ |
1235 |
|
|
|
1236 |
|
|
case FIXED_BOND: |
1237 |
|
|
|
1238 |
|
|
bondArray[i] = new ConstrainedBond( *the_atoms[a], |
1239 |
|
|
*the_atoms[b], |
1240 |
|
|
currentBondType->d0 ); |
1241 |
|
|
entry_plug->n_constraints++; |
1242 |
|
|
break; |
1243 |
|
|
|
1244 |
|
|
case HARMONIC_BOND: |
1245 |
|
|
|
1246 |
|
|
bondArray[i] = new HarmonicBond( *the_atoms[a], |
1247 |
|
|
*the_atoms[b], |
1248 |
|
|
currentBondType->d0, |
1249 |
|
|
currentBondType->k0 ); |
1250 |
|
|
break; |
1251 |
|
|
|
1252 |
|
|
default: |
1253 |
|
|
|
1254 |
|
|
break; |
1255 |
|
|
// do nothing |
1256 |
|
|
} |
1257 |
|
|
} |
1258 |
|
|
} |
1259 |
|
|
|
1260 |
|
|
void DUFF::initializeBends( int nBends, Bend** bendArray, |
1261 |
|
|
bend_set* the_bends ){ |
1262 |
|
|
|
1263 |
|
|
QuadraticBend* qBend; |
1264 |
|
|
GhostBend* gBend; |
1265 |
|
|
Atom** the_atoms; |
1266 |
|
|
the_atoms = entry_plug->atoms; |
1267 |
|
|
|
1268 |
|
|
int i, a, b, c; |
1269 |
|
|
char* atomA; |
1270 |
|
|
char* atomB; |
1271 |
|
|
char* atomC; |
1272 |
|
|
|
1273 |
|
|
// initialize the Bends |
1274 |
|
|
|
1275 |
|
|
for( i=0; i<nBends; i++ ){ |
1276 |
|
|
|
1277 |
|
|
a = the_bends[i].a; |
1278 |
|
|
b = the_bends[i].b; |
1279 |
|
|
c = the_bends[i].c; |
1280 |
|
|
|
1281 |
|
|
atomA = the_atoms[a]->getType(); |
1282 |
|
|
atomB = the_atoms[b]->getType(); |
1283 |
|
|
|
1284 |
|
|
if( the_bends[i].isGhost ) atomC = "GHOST"; |
1285 |
|
|
else atomC = the_atoms[c]->getType(); |
1286 |
|
|
|
1287 |
|
|
currentBendType = headBendType->find( atomA, atomB, atomC ); |
1288 |
|
|
if( currentBendType == NULL ){ |
1289 |
|
|
sprintf( painCave.errMsg, "BendType error, %s - %s - %s not found" |
1290 |
|
|
" in force file.\n", |
1291 |
|
|
atomA, atomB, atomC ); |
1292 |
|
|
painCave.isFatal = 1; |
1293 |
|
|
simError(); |
1294 |
|
|
} |
1295 |
|
|
|
1296 |
|
|
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
1297 |
|
|
|
1298 |
|
|
if( the_bends[i].isGhost){ |
1299 |
|
|
|
1300 |
|
|
if( the_bends[i].ghost == b ){ |
1301 |
|
|
// do nothing |
1302 |
|
|
} |
1303 |
|
|
else if( the_bends[i].ghost == a ){ |
1304 |
|
|
c = a; |
1305 |
|
|
a = b; |
1306 |
|
|
b = c; |
1307 |
|
|
} |
1308 |
|
|
else{ |
1309 |
|
|
sprintf( painCave.errMsg, |
1310 |
|
|
"BendType error, %s - %s - %s,\n" |
1311 |
|
|
" --> central atom is not " |
1312 |
|
|
"correctly identified with the " |
1313 |
|
|
"\"ghostVectorSource = \" tag.\n", |
1314 |
|
|
atomA, atomB, atomC ); |
1315 |
|
|
painCave.isFatal = 1; |
1316 |
|
|
simError(); |
1317 |
|
|
} |
1318 |
|
|
|
1319 |
|
|
gBend = new GhostBend( *the_atoms[a], |
1320 |
|
|
*the_atoms[b]); |
1321 |
|
|
|
1322 |
|
|
gBend->setConstants( currentBendType->k1, |
1323 |
|
|
currentBendType->k2, |
1324 |
|
|
currentBendType->k3, |
1325 |
|
|
currentBendType->t0 ); |
1326 |
|
|
bendArray[i] = gBend; |
1327 |
|
|
} |
1328 |
|
|
else{ |
1329 |
|
|
qBend = new QuadraticBend( *the_atoms[a], |
1330 |
|
|
*the_atoms[b], |
1331 |
|
|
*the_atoms[c] ); |
1332 |
|
|
qBend->setConstants( currentBendType->k1, |
1333 |
|
|
currentBendType->k2, |
1334 |
|
|
currentBendType->k3, |
1335 |
|
|
currentBendType->t0 ); |
1336 |
|
|
bendArray[i] = qBend; |
1337 |
|
|
} |
1338 |
|
|
} |
1339 |
|
|
} |
1340 |
|
|
} |
1341 |
|
|
|
1342 |
|
|
void DUFF::initializeTorsions( int nTorsions, Torsion** torsionArray, |
1343 |
|
|
torsion_set* the_torsions ){ |
1344 |
|
|
|
1345 |
|
|
int i, a, b, c, d; |
1346 |
|
|
char* atomA; |
1347 |
|
|
char* atomB; |
1348 |
|
|
char* atomC; |
1349 |
|
|
char* atomD; |
1350 |
|
|
|
1351 |
|
|
CubicTorsion* cTors; |
1352 |
|
|
Atom** the_atoms; |
1353 |
|
|
the_atoms = entry_plug->atoms; |
1354 |
|
|
|
1355 |
|
|
// initialize the Torsions |
1356 |
|
|
|
1357 |
|
|
for( i=0; i<nTorsions; i++ ){ |
1358 |
|
|
|
1359 |
|
|
a = the_torsions[i].a; |
1360 |
|
|
b = the_torsions[i].b; |
1361 |
|
|
c = the_torsions[i].c; |
1362 |
|
|
d = the_torsions[i].d; |
1363 |
|
|
|
1364 |
|
|
atomA = the_atoms[a]->getType(); |
1365 |
|
|
atomB = the_atoms[b]->getType(); |
1366 |
|
|
atomC = the_atoms[c]->getType(); |
1367 |
|
|
atomD = the_atoms[d]->getType(); |
1368 |
|
|
currentTorsionType = headTorsionType->find( atomA, atomB, atomC, atomD ); |
1369 |
|
|
if( currentTorsionType == NULL ){ |
1370 |
|
|
sprintf( painCave.errMsg, |
1371 |
|
|
"TorsionType error, %s - %s - %s - %s not found" |
1372 |
|
|
" in force file.\n", |
1373 |
|
|
atomA, atomB, atomC, atomD ); |
1374 |
|
|
painCave.isFatal = 1; |
1375 |
|
|
simError(); |
1376 |
|
|
} |
1377 |
|
|
|
1378 |
|
|
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
1379 |
|
|
|
1380 |
|
|
cTors = new CubicTorsion( *the_atoms[a], *the_atoms[b], |
1381 |
|
|
*the_atoms[c], *the_atoms[d] ); |
1382 |
|
|
cTors->setConstants( currentTorsionType->k1, currentTorsionType->k2, |
1383 |
|
|
currentTorsionType->k3, currentTorsionType->k4 ); |
1384 |
|
|
torsionArray[i] = cTors; |
1385 |
|
|
} |
1386 |
|
|
} |
1387 |
|
|
} |
1388 |
|
|
|
1389 |
|
|
void DUFF::fastForward( char* stopText, char* searchOwner ){ |
1390 |
|
|
|
1391 |
|
|
int foundText = 0; |
1392 |
|
|
char* the_token; |
1393 |
|
|
|
1394 |
|
|
rewind( frcFile ); |
1395 |
|
|
lineNum = 0; |
1396 |
|
|
|
1397 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1398 |
|
|
lineNum++; |
1399 |
|
|
if( eof_test == NULL ){ |
1400 |
|
|
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
1401 |
|
|
" file is empty.\n", |
1402 |
|
|
searchOwner ); |
1403 |
|
|
painCave.isFatal = 1; |
1404 |
|
|
simError(); |
1405 |
|
|
} |
1406 |
|
|
|
1407 |
|
|
|
1408 |
|
|
while( !foundText ){ |
1409 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
1410 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1411 |
|
|
lineNum++; |
1412 |
|
|
} |
1413 |
|
|
if( eof_test == NULL ){ |
1414 |
|
|
sprintf( painCave.errMsg, |
1415 |
|
|
"Error fast forwarding force file for %s at " |
1416 |
|
|
"line %d: file ended unexpectedly.\n", |
1417 |
|
|
searchOwner, |
1418 |
|
|
lineNum ); |
1419 |
|
|
painCave.isFatal = 1; |
1420 |
|
|
simError(); |
1421 |
|
|
} |
1422 |
|
|
|
1423 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
1424 |
|
|
foundText = !strcmp( stopText, the_token ); |
1425 |
|
|
|
1426 |
|
|
if( !foundText ){ |
1427 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1428 |
|
|
lineNum++; |
1429 |
|
|
|
1430 |
|
|
if( eof_test == NULL ){ |
1431 |
|
|
sprintf( painCave.errMsg, |
1432 |
|
|
"Error fast forwarding force file for %s at " |
1433 |
|
|
"line %d: file ended unexpectedly.\n", |
1434 |
|
|
searchOwner, |
1435 |
|
|
lineNum ); |
1436 |
|
|
painCave.isFatal = 1; |
1437 |
|
|
simError(); |
1438 |
|
|
} |
1439 |
|
|
} |
1440 |
|
|
} |
1441 |
|
|
} |
1442 |
|
|
|
1443 |
|
|
|
1444 |
|
|
int DUFF_NS::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){ |
1445 |
|
|
|
1446 |
|
|
char* the_token; |
1447 |
|
|
|
1448 |
|
|
the_token = strtok( lineBuffer, " \n\t,;" ); |
1449 |
|
|
if( the_token != NULL ){ |
1450 |
|
|
|
1451 |
|
|
strcpy( info.name, the_token ); |
1452 |
|
|
|
1453 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1454 |
|
|
sprintf( painCave.errMsg, |
1455 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1456 |
|
|
painCave.isFatal = 1; |
1457 |
|
|
simError(); |
1458 |
|
|
} |
1459 |
|
|
|
1460 |
|
|
info.isDipole = atoi( the_token ); |
1461 |
|
|
|
1462 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1463 |
|
|
sprintf( painCave.errMsg, |
1464 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1465 |
|
|
painCave.isFatal = 1; |
1466 |
|
|
simError(); |
1467 |
|
|
} |
1468 |
|
|
|
1469 |
|
|
info.isSSD = atoi( the_token ); |
1470 |
|
|
|
1471 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1472 |
|
|
sprintf( painCave.errMsg, |
1473 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1474 |
|
|
painCave.isFatal = 1; |
1475 |
|
|
simError(); |
1476 |
|
|
} |
1477 |
|
|
|
1478 |
|
|
info.mass = atof( the_token ); |
1479 |
|
|
|
1480 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1481 |
|
|
sprintf( painCave.errMsg, |
1482 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1483 |
|
|
painCave.isFatal = 1; |
1484 |
|
|
simError(); |
1485 |
|
|
} |
1486 |
|
|
|
1487 |
|
|
info.epslon = atof( the_token ); |
1488 |
|
|
|
1489 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1490 |
|
|
sprintf( painCave.errMsg, |
1491 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1492 |
|
|
painCave.isFatal = 1; |
1493 |
|
|
simError(); |
1494 |
|
|
} |
1495 |
|
|
|
1496 |
|
|
info.sigma = atof( the_token ); |
1497 |
|
|
|
1498 |
|
|
if( info.isDipole ){ |
1499 |
|
|
|
1500 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1501 |
|
|
sprintf( painCave.errMsg, |
1502 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1503 |
|
|
painCave.isFatal = 1; |
1504 |
|
|
simError(); |
1505 |
|
|
} |
1506 |
|
|
|
1507 |
|
|
info.dipole = atof( the_token ); |
1508 |
|
|
} |
1509 |
|
|
else info.dipole = 0.0; |
1510 |
|
|
|
1511 |
|
|
if( info.isSSD ){ |
1512 |
|
|
|
1513 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1514 |
|
|
sprintf( painCave.errMsg, |
1515 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1516 |
|
|
painCave.isFatal = 1; |
1517 |
|
|
simError(); |
1518 |
|
|
} |
1519 |
|
|
|
1520 |
|
|
info.w0 = atof( the_token ); |
1521 |
|
|
|
1522 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1523 |
|
|
sprintf( painCave.errMsg, |
1524 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1525 |
|
|
painCave.isFatal = 1; |
1526 |
|
|
simError(); |
1527 |
|
|
} |
1528 |
|
|
|
1529 |
|
|
info.v0 = atof( the_token ); |
1530 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1531 |
|
|
sprintf( painCave.errMsg, |
1532 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1533 |
|
|
painCave.isFatal = 1; |
1534 |
|
|
simError(); |
1535 |
|
|
} |
1536 |
|
|
|
1537 |
|
|
info.v0p = atof( the_token ); |
1538 |
|
|
|
1539 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1540 |
|
|
sprintf( painCave.errMsg, |
1541 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1542 |
|
|
painCave.isFatal = 1; |
1543 |
|
|
simError(); |
1544 |
|
|
} |
1545 |
|
|
|
1546 |
|
|
info.rl = atof( the_token ); |
1547 |
|
|
|
1548 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1549 |
|
|
sprintf( painCave.errMsg, |
1550 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1551 |
|
|
painCave.isFatal = 1; |
1552 |
|
|
simError(); |
1553 |
|
|
} |
1554 |
|
|
|
1555 |
|
|
info.ru = atof( the_token ); |
1556 |
|
|
|
1557 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1558 |
|
|
sprintf( painCave.errMsg, |
1559 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1560 |
|
|
painCave.isFatal = 1; |
1561 |
|
|
simError(); |
1562 |
|
|
} |
1563 |
|
|
|
1564 |
|
|
info.rlp = atof( the_token ); |
1565 |
|
|
|
1566 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1567 |
|
|
sprintf( painCave.errMsg, |
1568 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1569 |
|
|
painCave.isFatal = 1; |
1570 |
|
|
simError(); |
1571 |
|
|
} |
1572 |
|
|
|
1573 |
|
|
info.rup = atof( the_token ); |
1574 |
|
|
} |
1575 |
|
|
else info.v0 = info.w0 = info.v0p = info.rl = info.ru = info.rlp = info.rup = 0.0; |
1576 |
|
|
|
1577 |
|
|
return 1; |
1578 |
|
|
} |
1579 |
|
|
else return 0; |
1580 |
|
|
} |
1581 |
|
|
|
1582 |
|
|
int DUFF_NS::parseBond( char *lineBuffer, int lineNum, bondStruct &info ){ |
1583 |
|
|
|
1584 |
|
|
char* the_token; |
1585 |
|
|
char bondType[30]; |
1586 |
|
|
|
1587 |
|
|
the_token = strtok( lineBuffer, " \n\t,;" ); |
1588 |
|
|
if( the_token != NULL ){ |
1589 |
|
|
|
1590 |
|
|
strcpy( info.nameA, the_token ); |
1591 |
|
|
|
1592 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1593 |
|
|
sprintf( painCave.errMsg, |
1594 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1595 |
|
|
painCave.isFatal = 1; |
1596 |
|
|
simError(); |
1597 |
|
|
} |
1598 |
|
|
|
1599 |
|
|
strcpy( info.nameB, the_token ); |
1600 |
|
|
|
1601 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1602 |
|
|
sprintf( painCave.errMsg, |
1603 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1604 |
|
|
painCave.isFatal = 1; |
1605 |
|
|
simError(); |
1606 |
|
|
} |
1607 |
|
|
|
1608 |
|
|
strcpy( bondType, the_token ); |
1609 |
|
|
|
1610 |
|
|
if( !strcmp( bondType, "fixed" ) ){ |
1611 |
|
|
info.type = FIXED_BOND; |
1612 |
|
|
|
1613 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1614 |
|
|
sprintf( painCave.errMsg, |
1615 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1616 |
|
|
painCave.isFatal = 1; |
1617 |
|
|
simError(); |
1618 |
|
|
} |
1619 |
|
|
|
1620 |
|
|
info.d0 = atof( the_token ); |
1621 |
|
|
|
1622 |
|
|
info.k0=0.0; |
1623 |
|
|
} |
1624 |
|
|
else if( !strcmp( bondType, "harmonic" ) ){ |
1625 |
|
|
info.type = HARMONIC_BOND; |
1626 |
|
|
|
1627 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1628 |
|
|
sprintf( painCave.errMsg, |
1629 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1630 |
|
|
painCave.isFatal = 1; |
1631 |
|
|
simError(); |
1632 |
|
|
} |
1633 |
|
|
|
1634 |
|
|
info.d0 = atof( the_token ); |
1635 |
|
|
|
1636 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1637 |
|
|
sprintf( painCave.errMsg, |
1638 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1639 |
|
|
painCave.isFatal = 1; |
1640 |
|
|
simError(); |
1641 |
|
|
} |
1642 |
|
|
|
1643 |
|
|
info.k0 = atof( the_token ); |
1644 |
|
|
} |
1645 |
|
|
|
1646 |
|
|
else{ |
1647 |
|
|
sprintf( painCave.errMsg, |
1648 |
|
|
"Unknown DUFF bond type \"%s\" at line %d\n", |
1649 |
|
|
bondType, |
1650 |
|
|
lineNum ); |
1651 |
|
|
painCave.isFatal = 1; |
1652 |
|
|
simError(); |
1653 |
|
|
} |
1654 |
|
|
|
1655 |
|
|
return 1; |
1656 |
|
|
} |
1657 |
|
|
else return 0; |
1658 |
|
|
} |
1659 |
|
|
|
1660 |
|
|
|
1661 |
|
|
int DUFF_NS::parseBend( char *lineBuffer, int lineNum, bendStruct &info ){ |
1662 |
|
|
|
1663 |
|
|
char* the_token; |
1664 |
|
|
|
1665 |
|
|
the_token = strtok( lineBuffer, " \n\t,;" ); |
1666 |
|
|
if( the_token != NULL ){ |
1667 |
|
|
|
1668 |
|
|
strcpy( info.nameA, the_token ); |
1669 |
|
|
|
1670 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1671 |
|
|
sprintf( painCave.errMsg, |
1672 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1673 |
|
|
painCave.isFatal = 1; |
1674 |
|
|
simError(); |
1675 |
|
|
} |
1676 |
|
|
|
1677 |
|
|
strcpy( info.nameB, the_token ); |
1678 |
|
|
|
1679 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1680 |
|
|
sprintf( painCave.errMsg, |
1681 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1682 |
|
|
painCave.isFatal = 1; |
1683 |
|
|
simError(); |
1684 |
|
|
} |
1685 |
|
|
|
1686 |
|
|
strcpy( info.nameC, the_token ); |
1687 |
|
|
|
1688 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1689 |
|
|
sprintf( painCave.errMsg, |
1690 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1691 |
|
|
painCave.isFatal = 1; |
1692 |
|
|
simError(); |
1693 |
|
|
} |
1694 |
|
|
|
1695 |
|
|
strcpy( info.type, the_token ); |
1696 |
|
|
|
1697 |
|
|
if( !strcmp( info.type, "quadratic" ) ){ |
1698 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1699 |
|
|
sprintf( painCave.errMsg, |
1700 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1701 |
|
|
painCave.isFatal = 1; |
1702 |
|
|
simError(); |
1703 |
|
|
} |
1704 |
|
|
|
1705 |
|
|
info.k1 = atof( the_token ); |
1706 |
|
|
|
1707 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1708 |
|
|
sprintf( painCave.errMsg, |
1709 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1710 |
|
|
painCave.isFatal = 1; |
1711 |
|
|
simError(); |
1712 |
|
|
} |
1713 |
|
|
|
1714 |
|
|
info.k2 = atof( the_token ); |
1715 |
|
|
|
1716 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1717 |
|
|
sprintf( painCave.errMsg, |
1718 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1719 |
|
|
painCave.isFatal = 1; |
1720 |
|
|
simError(); |
1721 |
|
|
} |
1722 |
|
|
|
1723 |
|
|
info.k3 = atof( the_token ); |
1724 |
|
|
|
1725 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1726 |
|
|
sprintf( painCave.errMsg, |
1727 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1728 |
|
|
painCave.isFatal = 1; |
1729 |
|
|
simError(); |
1730 |
|
|
} |
1731 |
|
|
|
1732 |
|
|
info.t0 = atof( the_token ); |
1733 |
|
|
} |
1734 |
|
|
|
1735 |
|
|
else{ |
1736 |
|
|
sprintf( painCave.errMsg, |
1737 |
|
|
"Unknown DUFF bend type \"%s\" at line %d\n", |
1738 |
|
|
info.type, |
1739 |
|
|
lineNum ); |
1740 |
|
|
painCave.isFatal = 1; |
1741 |
|
|
simError(); |
1742 |
|
|
} |
1743 |
|
|
|
1744 |
|
|
return 1; |
1745 |
|
|
} |
1746 |
|
|
else return 0; |
1747 |
|
|
} |
1748 |
|
|
|
1749 |
|
|
int DUFF_NS::parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ){ |
1750 |
|
|
|
1751 |
|
|
char* the_token; |
1752 |
|
|
|
1753 |
|
|
the_token = strtok( lineBuffer, " \n\t,;" ); |
1754 |
|
|
if( the_token != NULL ){ |
1755 |
|
|
|
1756 |
|
|
strcpy( info.nameA, the_token ); |
1757 |
|
|
|
1758 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1759 |
|
|
sprintf( painCave.errMsg, |
1760 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1761 |
|
|
painCave.isFatal = 1; |
1762 |
|
|
simError(); |
1763 |
|
|
} |
1764 |
|
|
|
1765 |
|
|
strcpy( info.nameB, the_token ); |
1766 |
|
|
|
1767 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1768 |
|
|
sprintf( painCave.errMsg, |
1769 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1770 |
|
|
painCave.isFatal = 1; |
1771 |
|
|
simError(); |
1772 |
|
|
} |
1773 |
|
|
|
1774 |
|
|
strcpy( info.nameC, the_token ); |
1775 |
|
|
|
1776 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1777 |
|
|
sprintf( painCave.errMsg, |
1778 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1779 |
|
|
painCave.isFatal = 1; |
1780 |
|
|
simError(); |
1781 |
|
|
} |
1782 |
|
|
|
1783 |
|
|
strcpy( info.nameD, the_token ); |
1784 |
|
|
|
1785 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1786 |
|
|
sprintf( painCave.errMsg, |
1787 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1788 |
|
|
painCave.isFatal = 1; |
1789 |
|
|
simError(); |
1790 |
|
|
} |
1791 |
|
|
|
1792 |
|
|
strcpy( info.type, the_token ); |
1793 |
|
|
|
1794 |
|
|
if( !strcmp( info.type, "cubic" ) ){ |
1795 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1796 |
|
|
sprintf( painCave.errMsg, |
1797 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1798 |
|
|
painCave.isFatal = 1; |
1799 |
|
|
simError(); |
1800 |
|
|
} |
1801 |
|
|
|
1802 |
|
|
info.k1 = atof( the_token ); |
1803 |
|
|
|
1804 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1805 |
|
|
sprintf( painCave.errMsg, |
1806 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1807 |
|
|
painCave.isFatal = 1; |
1808 |
|
|
simError(); |
1809 |
|
|
} |
1810 |
|
|
|
1811 |
|
|
info.k2 = atof( the_token ); |
1812 |
|
|
|
1813 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1814 |
|
|
sprintf( painCave.errMsg, |
1815 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1816 |
|
|
painCave.isFatal = 1; |
1817 |
|
|
simError(); |
1818 |
|
|
} |
1819 |
|
|
|
1820 |
|
|
info.k3 = atof( the_token ); |
1821 |
|
|
|
1822 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1823 |
|
|
sprintf( painCave.errMsg, |
1824 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1825 |
|
|
painCave.isFatal = 1; |
1826 |
|
|
simError(); |
1827 |
|
|
} |
1828 |
|
|
|
1829 |
|
|
info.k4 = atof( the_token ); |
1830 |
|
|
|
1831 |
|
|
} |
1832 |
|
|
|
1833 |
|
|
else{ |
1834 |
|
|
sprintf( painCave.errMsg, |
1835 |
|
|
"Unknown DUFF torsion type \"%s\" at line %d\n", |
1836 |
|
|
info.type, |
1837 |
|
|
lineNum ); |
1838 |
|
|
painCave.isFatal = 1; |
1839 |
|
|
simError(); |
1840 |
|
|
} |
1841 |
|
|
|
1842 |
|
|
return 1; |
1843 |
|
|
} |
1844 |
|
|
|
1845 |
|
|
else return 0; |
1846 |
|
|
} |