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mmeineke |
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#include <cstdlib> |
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#include <cstdio> |
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#include <cstring> |
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#include <iostream> |
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using namespace std; |
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#include "ForceFields.hpp" |
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#include "SRI.hpp" |
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#include "simError.h" |
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#include "fortranWrappers.hpp" |
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#ifdef IS_MPI |
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#include "mpiForceField.h" |
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#endif // is_mpi |
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mmeineke |
564 |
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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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mmeineke |
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namespace DUFF_NS { // restrict the access of the folowing to this file only. |
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mmeineke |
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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 dipole; |
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double w0; |
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double v0; |
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gezelter |
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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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mmeineke |
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int isSSD; |
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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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mmeineke |
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double k0; |
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mmeineke |
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int last; // 0 -> default |
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// 1 -> tells nodes to stop listening |
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mmeineke |
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int type; |
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mmeineke |
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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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mmeineke |
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"Duplicate DUFF atom type \"%s\" found in " |
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"the DUFF param file./n", |
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mmeineke |
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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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gezelter |
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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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mmeineke |
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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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gezelter |
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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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mmeineke |
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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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gezelter |
635 |
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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mmeineke |
559 |
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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mmeineke |
561 |
"Duplicate DUFF bond type \"%s - %s\" found in " |
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"the DUFF param file./n", |
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mmeineke |
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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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mmeineke |
564 |
next->type = info.type; |
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mmeineke |
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next->d0 = info.d0; |
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mmeineke |
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next->k0 = info.k0; |
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mmeineke |
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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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mmeineke |
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info.type = type; |
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mmeineke |
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info.d0 = d0; |
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mmeineke |
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info.k0 = k0; |
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mmeineke |
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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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mmeineke |
564 |
int type; |
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mmeineke |
559 |
double d0; |
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mmeineke |
564 |
double k0; |
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mmeineke |
559 |
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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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mmeineke |
561 |
"Duplicate DUFF bend type \"%s - %s - %s\" found in " |
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"the DUFF param file./n", |
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mmeineke |
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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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// 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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mmeineke |
561 |
"Duplicate DUFF torsion type \"%s - %s - %s - %s\" found in " |
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"the DUFF param file./n", nameA, nameB, nameC, nameD ); |
384 |
mmeineke |
559 |
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 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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#ifdef IS_MPI |
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|
406 |
|
|
void duplicate( torsionStruct &info ){ |
407 |
|
|
strcpy(info.nameA, nameA); |
408 |
|
|
strcpy(info.nameB, nameB); |
409 |
|
|
strcpy(info.nameC, nameC); |
410 |
|
|
strcpy(info.nameD, nameD); |
411 |
|
|
strcpy(info.type, type); |
412 |
|
|
info.k1 = k1; |
413 |
|
|
info.k2 = k2; |
414 |
|
|
info.k3 = k3; |
415 |
|
|
info.k4 = k4; |
416 |
|
|
info.last = 0; |
417 |
|
|
} |
418 |
|
|
|
419 |
|
|
#endif |
420 |
|
|
|
421 |
|
|
char nameA[15]; |
422 |
|
|
char nameB[15]; |
423 |
|
|
char nameC[15]; |
424 |
|
|
char nameD[15]; |
425 |
|
|
char type[30]; |
426 |
|
|
double k1, k2, k3, k4; |
427 |
|
|
|
428 |
|
|
LinkedTorsionType* next; |
429 |
|
|
}; |
430 |
|
|
|
431 |
|
|
|
432 |
|
|
LinkedAtomType* headAtomType; |
433 |
|
|
LinkedAtomType* currentAtomType; |
434 |
|
|
LinkedBondType* headBondType; |
435 |
|
|
LinkedBondType* currentBondType; |
436 |
|
|
LinkedBendType* headBendType; |
437 |
|
|
LinkedBendType* currentBendType; |
438 |
|
|
LinkedTorsionType* headTorsionType; |
439 |
|
|
LinkedTorsionType* currentTorsionType; |
440 |
|
|
|
441 |
|
|
} // namespace |
442 |
|
|
|
443 |
mmeineke |
594 |
using namespace DUFF_NS; |
444 |
mmeineke |
559 |
|
445 |
|
|
|
446 |
|
|
//**************************************************************** |
447 |
|
|
// begins the actual forcefield stuff. |
448 |
|
|
//**************************************************************** |
449 |
|
|
|
450 |
|
|
|
451 |
mmeineke |
561 |
DUFF::DUFF(){ |
452 |
mmeineke |
559 |
|
453 |
|
|
char fileName[200]; |
454 |
|
|
char* ffPath_env = "FORCE_PARAM_PATH"; |
455 |
|
|
char* ffPath; |
456 |
|
|
char temp[200]; |
457 |
|
|
char errMsg[1000]; |
458 |
|
|
|
459 |
|
|
headAtomType = NULL; |
460 |
|
|
currentAtomType = NULL; |
461 |
|
|
headBondType = NULL; |
462 |
|
|
currentBondType = NULL; |
463 |
|
|
headBendType = NULL; |
464 |
|
|
currentBendType = NULL; |
465 |
|
|
headTorsionType = NULL; |
466 |
|
|
currentTorsionType = NULL; |
467 |
|
|
|
468 |
|
|
// do the funtion wrapping |
469 |
|
|
wrapMeFF( this ); |
470 |
|
|
|
471 |
|
|
|
472 |
|
|
#ifdef IS_MPI |
473 |
|
|
int i; |
474 |
|
|
|
475 |
|
|
// ********************************************************************** |
476 |
|
|
// Init the atomStruct mpi type |
477 |
|
|
|
478 |
|
|
atomStruct atomProto; // mpiPrototype |
479 |
|
|
int atomBC[3] = {15,6,4}; // block counts |
480 |
|
|
MPI_Aint atomDspls[3]; // displacements |
481 |
|
|
MPI_Datatype atomMbrTypes[3]; // member mpi types |
482 |
|
|
|
483 |
|
|
MPI_Address(&atomProto.name, &atomDspls[0]); |
484 |
|
|
MPI_Address(&atomProto.mass, &atomDspls[1]); |
485 |
|
|
MPI_Address(&atomProto.isSSD, &atomDspls[2]); |
486 |
|
|
|
487 |
|
|
atomMbrTypes[0] = MPI_CHAR; |
488 |
|
|
atomMbrTypes[1] = MPI_DOUBLE; |
489 |
|
|
atomMbrTypes[2] = MPI_INT; |
490 |
|
|
|
491 |
|
|
for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0]; |
492 |
|
|
|
493 |
|
|
MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType); |
494 |
|
|
MPI_Type_commit(&mpiAtomStructType); |
495 |
|
|
|
496 |
|
|
|
497 |
|
|
// ********************************************************************** |
498 |
|
|
// Init the bondStruct mpi type |
499 |
|
|
|
500 |
|
|
bondStruct bondProto; // mpiPrototype |
501 |
mmeineke |
564 |
int bondBC[3] = {30,2,2}; // block counts |
502 |
mmeineke |
559 |
MPI_Aint bondDspls[3]; // displacements |
503 |
|
|
MPI_Datatype bondMbrTypes[3]; // member mpi types |
504 |
|
|
|
505 |
|
|
MPI_Address(&bondProto.nameA, &bondDspls[0]); |
506 |
|
|
MPI_Address(&bondProto.d0, &bondDspls[1]); |
507 |
|
|
MPI_Address(&bondProto.last, &bondDspls[2]); |
508 |
|
|
|
509 |
|
|
bondMbrTypes[0] = MPI_CHAR; |
510 |
|
|
bondMbrTypes[1] = MPI_DOUBLE; |
511 |
|
|
bondMbrTypes[2] = MPI_INT; |
512 |
|
|
|
513 |
|
|
for (i=2; i >= 0; i--) bondDspls[i] -= bondDspls[0]; |
514 |
|
|
|
515 |
|
|
MPI_Type_struct(3, bondBC, bondDspls, bondMbrTypes, &mpiBondStructType); |
516 |
|
|
MPI_Type_commit(&mpiBondStructType); |
517 |
|
|
|
518 |
|
|
|
519 |
|
|
// ********************************************************************** |
520 |
|
|
// Init the bendStruct mpi type |
521 |
|
|
|
522 |
|
|
bendStruct bendProto; // mpiPrototype |
523 |
|
|
int bendBC[3] = {75,4,1}; // block counts |
524 |
|
|
MPI_Aint bendDspls[3]; // displacements |
525 |
|
|
MPI_Datatype bendMbrTypes[3]; // member mpi types |
526 |
|
|
|
527 |
|
|
MPI_Address(&bendProto.nameA, &bendDspls[0]); |
528 |
|
|
MPI_Address(&bendProto.k1, &bendDspls[1]); |
529 |
|
|
MPI_Address(&bendProto.last, &bendDspls[2]); |
530 |
|
|
|
531 |
|
|
bendMbrTypes[0] = MPI_CHAR; |
532 |
|
|
bendMbrTypes[1] = MPI_DOUBLE; |
533 |
|
|
bendMbrTypes[2] = MPI_INT; |
534 |
|
|
|
535 |
|
|
for (i=2; i >= 0; i--) bendDspls[i] -= bendDspls[0]; |
536 |
|
|
|
537 |
|
|
MPI_Type_struct(3, bendBC, bendDspls, bendMbrTypes, &mpiBendStructType); |
538 |
|
|
MPI_Type_commit(&mpiBendStructType); |
539 |
|
|
|
540 |
|
|
|
541 |
|
|
// ********************************************************************** |
542 |
|
|
// Init the torsionStruct mpi type |
543 |
|
|
|
544 |
|
|
torsionStruct torsionProto; // mpiPrototype |
545 |
|
|
int torsionBC[3] = {90,4,1}; // block counts |
546 |
|
|
MPI_Aint torsionDspls[3]; // displacements |
547 |
|
|
MPI_Datatype torsionMbrTypes[3]; // member mpi types |
548 |
|
|
|
549 |
|
|
MPI_Address(&torsionProto.nameA, &torsionDspls[0]); |
550 |
|
|
MPI_Address(&torsionProto.k1, &torsionDspls[1]); |
551 |
|
|
MPI_Address(&torsionProto.last, &torsionDspls[2]); |
552 |
|
|
|
553 |
|
|
torsionMbrTypes[0] = MPI_CHAR; |
554 |
|
|
torsionMbrTypes[1] = MPI_DOUBLE; |
555 |
|
|
torsionMbrTypes[2] = MPI_INT; |
556 |
|
|
|
557 |
|
|
for (i=2; i >= 0; i--) torsionDspls[i] -= torsionDspls[0]; |
558 |
|
|
|
559 |
|
|
MPI_Type_struct(3, torsionBC, torsionDspls, torsionMbrTypes, |
560 |
|
|
&mpiTorsionStructType); |
561 |
|
|
MPI_Type_commit(&mpiTorsionStructType); |
562 |
|
|
|
563 |
|
|
// *********************************************************************** |
564 |
|
|
|
565 |
|
|
if( worldRank == 0 ){ |
566 |
|
|
#endif |
567 |
|
|
|
568 |
|
|
// generate the force file name |
569 |
|
|
|
570 |
mmeineke |
561 |
strcpy( fileName, "DUFF.frc" ); |
571 |
mmeineke |
559 |
// fprintf( stderr,"Trying to open %s\n", fileName ); |
572 |
|
|
|
573 |
|
|
// attempt to open the file in the current directory first. |
574 |
|
|
|
575 |
|
|
frcFile = fopen( fileName, "r" ); |
576 |
|
|
|
577 |
|
|
if( frcFile == NULL ){ |
578 |
|
|
|
579 |
|
|
// next see if the force path enviorment variable is set |
580 |
|
|
|
581 |
|
|
ffPath = getenv( ffPath_env ); |
582 |
|
|
if( ffPath == NULL ) { |
583 |
|
|
STR_DEFINE(ffPath, FRC_PATH ); |
584 |
|
|
} |
585 |
|
|
|
586 |
|
|
|
587 |
|
|
strcpy( temp, ffPath ); |
588 |
|
|
strcat( temp, "/" ); |
589 |
|
|
strcat( temp, fileName ); |
590 |
|
|
strcpy( fileName, temp ); |
591 |
|
|
|
592 |
|
|
frcFile = fopen( fileName, "r" ); |
593 |
|
|
|
594 |
|
|
if( frcFile == NULL ){ |
595 |
|
|
|
596 |
|
|
sprintf( painCave.errMsg, |
597 |
|
|
"Error opening the force field parameter file: %s\n" |
598 |
|
|
"Have you tried setting the FORCE_PARAM_PATH environment " |
599 |
|
|
"vairable?\n", |
600 |
|
|
fileName ); |
601 |
|
|
painCave.isFatal = 1; |
602 |
|
|
simError(); |
603 |
|
|
} |
604 |
|
|
} |
605 |
|
|
|
606 |
|
|
#ifdef IS_MPI |
607 |
|
|
} |
608 |
|
|
|
609 |
mmeineke |
561 |
sprintf( checkPointMsg, "DUFF file opened sucessfully." ); |
610 |
mmeineke |
559 |
MPIcheckPoint(); |
611 |
|
|
|
612 |
|
|
#endif // is_mpi |
613 |
|
|
} |
614 |
|
|
|
615 |
|
|
|
616 |
mmeineke |
561 |
DUFF::~DUFF(){ |
617 |
mmeineke |
559 |
|
618 |
|
|
if( headAtomType != NULL ) delete headAtomType; |
619 |
|
|
if( headBondType != NULL ) delete headBondType; |
620 |
|
|
if( headBendType != NULL ) delete headBendType; |
621 |
|
|
if( headTorsionType != NULL ) delete headTorsionType; |
622 |
|
|
|
623 |
|
|
#ifdef IS_MPI |
624 |
|
|
if( worldRank == 0 ){ |
625 |
|
|
#endif // is_mpi |
626 |
|
|
|
627 |
|
|
fclose( frcFile ); |
628 |
|
|
|
629 |
|
|
#ifdef IS_MPI |
630 |
|
|
} |
631 |
|
|
#endif // is_mpi |
632 |
|
|
} |
633 |
|
|
|
634 |
mmeineke |
561 |
void DUFF::cleanMe( void ){ |
635 |
mmeineke |
559 |
|
636 |
|
|
#ifdef IS_MPI |
637 |
|
|
|
638 |
|
|
// keep the linked lists in the mpi version |
639 |
|
|
|
640 |
|
|
#else // is_mpi |
641 |
|
|
|
642 |
|
|
// delete the linked lists in the single processor version |
643 |
|
|
|
644 |
|
|
if( headAtomType != NULL ) delete headAtomType; |
645 |
|
|
if( headBondType != NULL ) delete headBondType; |
646 |
|
|
if( headBendType != NULL ) delete headBendType; |
647 |
|
|
if( headTorsionType != NULL ) delete headTorsionType; |
648 |
|
|
|
649 |
|
|
#endif // is_mpi |
650 |
|
|
} |
651 |
|
|
|
652 |
|
|
|
653 |
mmeineke |
561 |
void DUFF::initForceField( int ljMixRule ){ |
654 |
mmeineke |
559 |
|
655 |
|
|
initFortran( ljMixRule, entry_plug->useReactionField ); |
656 |
|
|
} |
657 |
|
|
|
658 |
|
|
|
659 |
mmeineke |
561 |
void DUFF::readParams( void ){ |
660 |
mmeineke |
559 |
|
661 |
|
|
int i, a, b, c, d; |
662 |
|
|
int identNum; |
663 |
|
|
char* atomA; |
664 |
|
|
char* atomB; |
665 |
|
|
char* atomC; |
666 |
|
|
char* atomD; |
667 |
|
|
|
668 |
|
|
atomStruct atomInfo; |
669 |
|
|
bondStruct bondInfo; |
670 |
|
|
bendStruct bendInfo; |
671 |
|
|
torsionStruct torsionInfo; |
672 |
|
|
|
673 |
|
|
bigSigma = 0.0; |
674 |
|
|
|
675 |
|
|
atomInfo.last = 1; |
676 |
|
|
bondInfo.last = 1; |
677 |
|
|
bendInfo.last = 1; |
678 |
|
|
torsionInfo.last = 1; |
679 |
|
|
|
680 |
|
|
// read in the atom info |
681 |
|
|
|
682 |
|
|
#ifdef IS_MPI |
683 |
|
|
if( worldRank == 0 ){ |
684 |
|
|
#endif |
685 |
|
|
|
686 |
|
|
// read in the atom types. |
687 |
|
|
|
688 |
|
|
headAtomType = new LinkedAtomType; |
689 |
|
|
|
690 |
|
|
fastForward( "AtomTypes", "initializeAtoms" ); |
691 |
|
|
|
692 |
|
|
// we are now at the AtomTypes section. |
693 |
|
|
|
694 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
695 |
|
|
lineNum++; |
696 |
|
|
|
697 |
|
|
|
698 |
|
|
// read a line, and start parseing out the atom types |
699 |
|
|
|
700 |
|
|
if( eof_test == NULL ){ |
701 |
|
|
sprintf( painCave.errMsg, |
702 |
|
|
"Error in reading Atoms from force file at line %d.\n", |
703 |
|
|
lineNum ); |
704 |
|
|
painCave.isFatal = 1; |
705 |
|
|
simError(); |
706 |
|
|
} |
707 |
|
|
|
708 |
|
|
identNum = 1; |
709 |
|
|
// stop reading at end of file, or at next section |
710 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
711 |
|
|
|
712 |
|
|
// toss comment lines |
713 |
|
|
if( readLine[0] != '!' ){ |
714 |
|
|
|
715 |
|
|
// the parser returns 0 if the line was blank |
716 |
|
|
if( parseAtom( readLine, lineNum, atomInfo ) ){ |
717 |
|
|
atomInfo.ident = identNum; |
718 |
|
|
headAtomType->add( atomInfo );; |
719 |
|
|
identNum++; |
720 |
|
|
} |
721 |
|
|
} |
722 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
723 |
|
|
lineNum++; |
724 |
|
|
} |
725 |
|
|
|
726 |
|
|
#ifdef IS_MPI |
727 |
|
|
|
728 |
|
|
// send out the linked list to all the other processes |
729 |
|
|
|
730 |
|
|
sprintf( checkPointMsg, |
731 |
mmeineke |
561 |
"DUFF atom structures read successfully." ); |
732 |
mmeineke |
559 |
MPIcheckPoint(); |
733 |
|
|
|
734 |
|
|
currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
735 |
|
|
while( currentAtomType != NULL ){ |
736 |
|
|
currentAtomType->duplicate( atomInfo ); |
737 |
|
|
|
738 |
|
|
|
739 |
|
|
|
740 |
|
|
sendFrcStruct( &atomInfo, mpiAtomStructType ); |
741 |
|
|
|
742 |
|
|
sprintf( checkPointMsg, |
743 |
mmeineke |
561 |
"successfully sent DUFF force type: \"%s\"\n", |
744 |
mmeineke |
559 |
atomInfo.name ); |
745 |
|
|
MPIcheckPoint(); |
746 |
|
|
|
747 |
|
|
currentAtomType = currentAtomType->next; |
748 |
|
|
} |
749 |
|
|
atomInfo.last = 1; |
750 |
|
|
sendFrcStruct( &atomInfo, mpiAtomStructType ); |
751 |
|
|
|
752 |
|
|
} |
753 |
|
|
|
754 |
|
|
else{ |
755 |
|
|
|
756 |
|
|
// listen for node 0 to send out the force params |
757 |
|
|
|
758 |
|
|
MPIcheckPoint(); |
759 |
|
|
|
760 |
|
|
headAtomType = new LinkedAtomType; |
761 |
|
|
recieveFrcStruct( &atomInfo, mpiAtomStructType ); |
762 |
|
|
|
763 |
|
|
while( !atomInfo.last ){ |
764 |
|
|
|
765 |
|
|
|
766 |
|
|
|
767 |
|
|
headAtomType->add( atomInfo ); |
768 |
|
|
|
769 |
|
|
MPIcheckPoint(); |
770 |
|
|
|
771 |
|
|
recieveFrcStruct( &atomInfo, mpiAtomStructType ); |
772 |
|
|
} |
773 |
|
|
} |
774 |
|
|
|
775 |
|
|
#endif // is_mpi |
776 |
|
|
|
777 |
|
|
|
778 |
|
|
|
779 |
|
|
// call new A_types in fortran |
780 |
|
|
|
781 |
|
|
int isError; |
782 |
|
|
|
783 |
|
|
// dummy variables |
784 |
|
|
|
785 |
|
|
int isGB = 0; |
786 |
|
|
int isLJ = 1; |
787 |
chuckv |
631 |
int isEAM =0; |
788 |
mmeineke |
559 |
double GB_dummy = 0.0; |
789 |
|
|
|
790 |
|
|
|
791 |
|
|
currentAtomType = headAtomType->next;; |
792 |
|
|
while( currentAtomType != NULL ){ |
793 |
|
|
|
794 |
|
|
if(currentAtomType->isDipole) entry_plug->useDipole = 1; |
795 |
|
|
if(currentAtomType->isSSD) { |
796 |
|
|
entry_plug->useSticky = 1; |
797 |
gezelter |
635 |
set_sticky_params( &(currentAtomType->w0), &(currentAtomType->v0), |
798 |
|
|
&(currentAtomType->v0p), |
799 |
|
|
&(currentAtomType->rl), &(currentAtomType->ru), |
800 |
|
|
&(currentAtomType->rlp), &(currentAtomType->rup)); |
801 |
mmeineke |
559 |
} |
802 |
|
|
|
803 |
|
|
if( currentAtomType->name[0] != '\0' ){ |
804 |
|
|
isError = 0; |
805 |
|
|
makeAtype( &(currentAtomType->ident), |
806 |
|
|
&isLJ, |
807 |
|
|
&(currentAtomType->isSSD), |
808 |
|
|
&(currentAtomType->isDipole), |
809 |
|
|
&isGB, |
810 |
chuckv |
631 |
&isEAM, |
811 |
mmeineke |
559 |
&(currentAtomType->epslon), |
812 |
|
|
&(currentAtomType->sigma), |
813 |
|
|
&(currentAtomType->dipole), |
814 |
|
|
&isError ); |
815 |
|
|
if( isError ){ |
816 |
|
|
sprintf( painCave.errMsg, |
817 |
|
|
"Error initializing the \"%s\" atom type in fortran\n", |
818 |
|
|
currentAtomType->name ); |
819 |
|
|
painCave.isFatal = 1; |
820 |
|
|
simError(); |
821 |
|
|
} |
822 |
|
|
} |
823 |
|
|
currentAtomType = currentAtomType->next; |
824 |
|
|
} |
825 |
|
|
|
826 |
|
|
#ifdef IS_MPI |
827 |
|
|
sprintf( checkPointMsg, |
828 |
mmeineke |
561 |
"DUFF atom structures successfully sent to fortran\n" ); |
829 |
mmeineke |
559 |
MPIcheckPoint(); |
830 |
|
|
#endif // is_mpi |
831 |
|
|
|
832 |
|
|
|
833 |
|
|
|
834 |
|
|
// read in the bonds |
835 |
|
|
|
836 |
|
|
#ifdef IS_MPI |
837 |
|
|
if( worldRank == 0 ){ |
838 |
|
|
#endif |
839 |
|
|
|
840 |
|
|
// read in the bond types. |
841 |
|
|
|
842 |
|
|
headBondType = new LinkedBondType; |
843 |
|
|
|
844 |
|
|
fastForward( "BondTypes", "initializeBonds" ); |
845 |
|
|
|
846 |
|
|
// we are now at the bondTypes section |
847 |
|
|
|
848 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
849 |
|
|
lineNum++; |
850 |
|
|
|
851 |
|
|
|
852 |
|
|
// read a line, and start parseing out the atom types |
853 |
|
|
|
854 |
|
|
if( eof_test == NULL ){ |
855 |
|
|
sprintf( painCave.errMsg, |
856 |
|
|
"Error in reading bonds from force file at line %d.\n", |
857 |
|
|
lineNum ); |
858 |
|
|
painCave.isFatal = 1; |
859 |
|
|
simError(); |
860 |
|
|
} |
861 |
|
|
|
862 |
|
|
// stop reading at end of file, or at next section |
863 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
864 |
|
|
|
865 |
|
|
// toss comment lines |
866 |
|
|
if( readLine[0] != '!' ){ |
867 |
|
|
|
868 |
|
|
// the parser returns 0 if the line was blank |
869 |
|
|
if( parseBond( readLine, lineNum, bondInfo ) ){ |
870 |
|
|
headBondType->add( bondInfo ); |
871 |
|
|
} |
872 |
|
|
} |
873 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
874 |
|
|
lineNum++; |
875 |
|
|
} |
876 |
|
|
|
877 |
|
|
#ifdef IS_MPI |
878 |
|
|
|
879 |
|
|
// send out the linked list to all the other processes |
880 |
|
|
|
881 |
|
|
sprintf( checkPointMsg, |
882 |
mmeineke |
561 |
"DUFF bond structures read successfully." ); |
883 |
mmeineke |
559 |
MPIcheckPoint(); |
884 |
|
|
|
885 |
|
|
currentBondType = headBondType->next; |
886 |
|
|
while( currentBondType != NULL ){ |
887 |
|
|
currentBondType->duplicate( bondInfo ); |
888 |
|
|
sendFrcStruct( &bondInfo, mpiBondStructType ); |
889 |
|
|
currentBondType = currentBondType->next; |
890 |
|
|
} |
891 |
|
|
bondInfo.last = 1; |
892 |
|
|
sendFrcStruct( &bondInfo, mpiBondStructType ); |
893 |
|
|
|
894 |
|
|
} |
895 |
|
|
|
896 |
|
|
else{ |
897 |
|
|
|
898 |
|
|
// listen for node 0 to send out the force params |
899 |
|
|
|
900 |
|
|
MPIcheckPoint(); |
901 |
|
|
|
902 |
|
|
headBondType = new LinkedBondType; |
903 |
|
|
recieveFrcStruct( &bondInfo, mpiBondStructType ); |
904 |
|
|
while( !bondInfo.last ){ |
905 |
|
|
|
906 |
|
|
headBondType->add( bondInfo ); |
907 |
|
|
recieveFrcStruct( &bondInfo, mpiBondStructType ); |
908 |
|
|
} |
909 |
|
|
} |
910 |
|
|
|
911 |
|
|
sprintf( checkPointMsg, |
912 |
mmeineke |
561 |
"DUFF bond structures broadcast successfully." ); |
913 |
mmeineke |
559 |
MPIcheckPoint(); |
914 |
|
|
|
915 |
|
|
#endif // is_mpi |
916 |
|
|
|
917 |
|
|
|
918 |
|
|
// read in the bends |
919 |
|
|
|
920 |
|
|
#ifdef IS_MPI |
921 |
|
|
if( worldRank == 0 ){ |
922 |
|
|
#endif |
923 |
|
|
|
924 |
|
|
// read in the bend types. |
925 |
|
|
|
926 |
|
|
headBendType = new LinkedBendType; |
927 |
|
|
|
928 |
|
|
fastForward( "BendTypes", "initializeBends" ); |
929 |
|
|
|
930 |
|
|
// we are now at the bendTypes section |
931 |
|
|
|
932 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
933 |
|
|
lineNum++; |
934 |
|
|
|
935 |
|
|
// read a line, and start parseing out the bend types |
936 |
|
|
|
937 |
|
|
if( eof_test == NULL ){ |
938 |
|
|
sprintf( painCave.errMsg, |
939 |
|
|
"Error in reading bends from force file at line %d.\n", |
940 |
|
|
lineNum ); |
941 |
|
|
painCave.isFatal = 1; |
942 |
|
|
simError(); |
943 |
|
|
} |
944 |
|
|
|
945 |
|
|
// stop reading at end of file, or at next section |
946 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
947 |
|
|
|
948 |
|
|
// toss comment lines |
949 |
|
|
if( readLine[0] != '!' ){ |
950 |
|
|
|
951 |
|
|
// the parser returns 0 if the line was blank |
952 |
|
|
if( parseBend( readLine, lineNum, bendInfo ) ){ |
953 |
|
|
headBendType->add( bendInfo ); |
954 |
|
|
} |
955 |
|
|
} |
956 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
957 |
|
|
lineNum++; |
958 |
|
|
} |
959 |
|
|
|
960 |
|
|
#ifdef IS_MPI |
961 |
|
|
|
962 |
|
|
// send out the linked list to all the other processes |
963 |
|
|
|
964 |
|
|
sprintf( checkPointMsg, |
965 |
mmeineke |
561 |
"DUFF bend structures read successfully." ); |
966 |
mmeineke |
559 |
MPIcheckPoint(); |
967 |
|
|
|
968 |
|
|
currentBendType = headBendType->next; |
969 |
|
|
while( currentBendType != NULL ){ |
970 |
|
|
currentBendType->duplicate( bendInfo ); |
971 |
|
|
sendFrcStruct( &bendInfo, mpiBendStructType ); |
972 |
|
|
currentBendType = currentBendType->next; |
973 |
|
|
} |
974 |
|
|
bendInfo.last = 1; |
975 |
|
|
sendFrcStruct( &bendInfo, mpiBendStructType ); |
976 |
|
|
|
977 |
|
|
} |
978 |
|
|
|
979 |
|
|
else{ |
980 |
|
|
|
981 |
|
|
// listen for node 0 to send out the force params |
982 |
|
|
|
983 |
|
|
MPIcheckPoint(); |
984 |
|
|
|
985 |
|
|
headBendType = new LinkedBendType; |
986 |
|
|
recieveFrcStruct( &bendInfo, mpiBendStructType ); |
987 |
|
|
while( !bendInfo.last ){ |
988 |
|
|
|
989 |
|
|
headBendType->add( bendInfo ); |
990 |
|
|
recieveFrcStruct( &bendInfo, mpiBendStructType ); |
991 |
|
|
} |
992 |
|
|
} |
993 |
|
|
|
994 |
|
|
sprintf( checkPointMsg, |
995 |
mmeineke |
561 |
"DUFF bend structures broadcast successfully." ); |
996 |
mmeineke |
559 |
MPIcheckPoint(); |
997 |
|
|
|
998 |
|
|
#endif // is_mpi |
999 |
|
|
|
1000 |
|
|
|
1001 |
|
|
// read in the torsions |
1002 |
|
|
|
1003 |
|
|
#ifdef IS_MPI |
1004 |
|
|
if( worldRank == 0 ){ |
1005 |
|
|
#endif |
1006 |
|
|
|
1007 |
|
|
// read in the torsion types. |
1008 |
|
|
|
1009 |
|
|
headTorsionType = new LinkedTorsionType; |
1010 |
|
|
|
1011 |
|
|
fastForward( "TorsionTypes", "initializeTorsions" ); |
1012 |
|
|
|
1013 |
|
|
// we are now at the torsionTypes section |
1014 |
|
|
|
1015 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1016 |
|
|
lineNum++; |
1017 |
|
|
|
1018 |
|
|
|
1019 |
|
|
// read a line, and start parseing out the atom types |
1020 |
|
|
|
1021 |
|
|
if( eof_test == NULL ){ |
1022 |
|
|
sprintf( painCave.errMsg, |
1023 |
|
|
"Error in reading torsions from force file at line %d.\n", |
1024 |
|
|
lineNum ); |
1025 |
|
|
painCave.isFatal = 1; |
1026 |
|
|
simError(); |
1027 |
|
|
} |
1028 |
|
|
|
1029 |
|
|
// stop reading at end of file, or at next section |
1030 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
1031 |
|
|
|
1032 |
|
|
// toss comment lines |
1033 |
|
|
if( readLine[0] != '!' ){ |
1034 |
|
|
|
1035 |
|
|
// the parser returns 0 if the line was blank |
1036 |
|
|
if( parseTorsion( readLine, lineNum, torsionInfo ) ){ |
1037 |
|
|
headTorsionType->add( torsionInfo ); |
1038 |
|
|
|
1039 |
|
|
} |
1040 |
|
|
} |
1041 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1042 |
|
|
lineNum++; |
1043 |
|
|
} |
1044 |
|
|
|
1045 |
|
|
#ifdef IS_MPI |
1046 |
|
|
|
1047 |
|
|
// send out the linked list to all the other processes |
1048 |
|
|
|
1049 |
|
|
sprintf( checkPointMsg, |
1050 |
mmeineke |
561 |
"DUFF torsion structures read successfully." ); |
1051 |
mmeineke |
559 |
MPIcheckPoint(); |
1052 |
|
|
|
1053 |
|
|
currentTorsionType = headTorsionType->next; |
1054 |
|
|
while( currentTorsionType != NULL ){ |
1055 |
|
|
currentTorsionType->duplicate( torsionInfo ); |
1056 |
|
|
sendFrcStruct( &torsionInfo, mpiTorsionStructType ); |
1057 |
|
|
currentTorsionType = currentTorsionType->next; |
1058 |
|
|
} |
1059 |
|
|
torsionInfo.last = 1; |
1060 |
|
|
sendFrcStruct( &torsionInfo, mpiTorsionStructType ); |
1061 |
|
|
|
1062 |
|
|
} |
1063 |
|
|
|
1064 |
|
|
else{ |
1065 |
|
|
|
1066 |
|
|
// listen for node 0 to send out the force params |
1067 |
|
|
|
1068 |
|
|
MPIcheckPoint(); |
1069 |
|
|
|
1070 |
|
|
headTorsionType = new LinkedTorsionType; |
1071 |
|
|
recieveFrcStruct( &torsionInfo, mpiTorsionStructType ); |
1072 |
|
|
while( !torsionInfo.last ){ |
1073 |
|
|
|
1074 |
|
|
headTorsionType->add( torsionInfo ); |
1075 |
|
|
recieveFrcStruct( &torsionInfo, mpiTorsionStructType ); |
1076 |
|
|
} |
1077 |
|
|
} |
1078 |
|
|
|
1079 |
|
|
sprintf( checkPointMsg, |
1080 |
mmeineke |
561 |
"DUFF torsion structures broadcast successfully." ); |
1081 |
mmeineke |
559 |
MPIcheckPoint(); |
1082 |
|
|
|
1083 |
|
|
#endif // is_mpi |
1084 |
|
|
|
1085 |
|
|
entry_plug->useLJ = 1; |
1086 |
|
|
} |
1087 |
|
|
|
1088 |
|
|
|
1089 |
|
|
|
1090 |
mmeineke |
561 |
void DUFF::initializeAtoms( int nAtoms, Atom** the_atoms ){ |
1091 |
mmeineke |
559 |
|
1092 |
|
|
|
1093 |
|
|
////////////////////////////////////////////////// |
1094 |
|
|
// a quick water fix |
1095 |
|
|
|
1096 |
|
|
double waterI[3][3]; |
1097 |
|
|
waterI[0][0] = 1.76958347772500; |
1098 |
|
|
waterI[0][1] = 0.0; |
1099 |
|
|
waterI[0][2] = 0.0; |
1100 |
|
|
|
1101 |
|
|
waterI[1][0] = 0.0; |
1102 |
|
|
waterI[1][1] = 0.614537057924513; |
1103 |
|
|
waterI[1][2] = 0.0; |
1104 |
|
|
|
1105 |
|
|
waterI[2][0] = 0.0; |
1106 |
|
|
waterI[2][1] = 0.0; |
1107 |
|
|
waterI[2][2] = 1.15504641980049; |
1108 |
|
|
|
1109 |
|
|
|
1110 |
|
|
double headI[3][3]; |
1111 |
|
|
headI[0][0] = 1125; |
1112 |
|
|
headI[0][1] = 0.0; |
1113 |
|
|
headI[0][2] = 0.0; |
1114 |
|
|
|
1115 |
|
|
headI[1][0] = 0.0; |
1116 |
|
|
headI[1][1] = 1125; |
1117 |
|
|
headI[1][2] = 0.0; |
1118 |
|
|
|
1119 |
|
|
headI[2][0] = 0.0; |
1120 |
|
|
headI[2][1] = 0.0; |
1121 |
|
|
headI[2][2] = 250; |
1122 |
|
|
|
1123 |
|
|
////////////////////////////////////////////////// |
1124 |
|
|
|
1125 |
|
|
|
1126 |
|
|
// initialize the atoms |
1127 |
|
|
|
1128 |
|
|
DirectionalAtom* dAtom; |
1129 |
|
|
|
1130 |
|
|
for(int i=0; i<nAtoms; i++ ){ |
1131 |
|
|
|
1132 |
|
|
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
1133 |
|
|
if( currentAtomType == NULL ){ |
1134 |
|
|
sprintf( painCave.errMsg, |
1135 |
|
|
"AtomType error, %s not found in force file.\n", |
1136 |
|
|
the_atoms[i]->getType() ); |
1137 |
|
|
painCave.isFatal = 1; |
1138 |
|
|
simError(); |
1139 |
|
|
} |
1140 |
|
|
|
1141 |
|
|
the_atoms[i]->setMass( currentAtomType->mass ); |
1142 |
|
|
the_atoms[i]->setEpslon( currentAtomType->epslon ); |
1143 |
|
|
the_atoms[i]->setSigma( currentAtomType->sigma ); |
1144 |
|
|
the_atoms[i]->setIdent( currentAtomType->ident ); |
1145 |
|
|
the_atoms[i]->setLJ(); |
1146 |
|
|
|
1147 |
|
|
if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma; |
1148 |
|
|
|
1149 |
|
|
if( currentAtomType->isDipole ){ |
1150 |
|
|
if( the_atoms[i]->isDirectional() ){ |
1151 |
|
|
|
1152 |
|
|
dAtom = (DirectionalAtom *) the_atoms[i]; |
1153 |
|
|
dAtom->setMu( currentAtomType->dipole ); |
1154 |
|
|
dAtom->setHasDipole( 1 ); |
1155 |
|
|
dAtom->setJx( 0.0 ); |
1156 |
|
|
dAtom->setJy( 0.0 ); |
1157 |
|
|
dAtom->setJz( 0.0 ); |
1158 |
|
|
|
1159 |
|
|
if(!strcmp("SSD",the_atoms[i]->getType())){ |
1160 |
|
|
dAtom->setI( waterI ); |
1161 |
|
|
dAtom->setSSD( 1 ); |
1162 |
|
|
} |
1163 |
|
|
else if(!strcmp("HEAD",the_atoms[i]->getType())){ |
1164 |
|
|
dAtom->setI( headI ); |
1165 |
|
|
dAtom->setSSD( 0 ); |
1166 |
|
|
} |
1167 |
|
|
else{ |
1168 |
|
|
sprintf(painCave.errMsg, |
1169 |
|
|
"AtmType error, %s does not have a moment of inertia set.\n", |
1170 |
|
|
the_atoms[i]->getType() ); |
1171 |
|
|
painCave.isFatal = 1; |
1172 |
|
|
simError(); |
1173 |
|
|
} |
1174 |
|
|
entry_plug->n_dipoles++; |
1175 |
|
|
} |
1176 |
|
|
else{ |
1177 |
|
|
|
1178 |
|
|
sprintf( painCave.errMsg, |
1179 |
mmeineke |
561 |
"DUFF error: Atom \"%s\" is a dipole, yet no standard" |
1180 |
mmeineke |
559 |
" orientation was specifed in the BASS file.\n", |
1181 |
|
|
currentAtomType->name ); |
1182 |
|
|
painCave.isFatal = 1; |
1183 |
|
|
simError(); |
1184 |
|
|
} |
1185 |
|
|
} |
1186 |
|
|
else{ |
1187 |
|
|
if( the_atoms[i]->isDirectional() ){ |
1188 |
|
|
sprintf( painCave.errMsg, |
1189 |
mmeineke |
561 |
"DUFF error: Atom \"%s\" was given a standard" |
1190 |
mmeineke |
559 |
"orientation in the BASS file, yet it is not a dipole.\n", |
1191 |
|
|
currentAtomType->name); |
1192 |
|
|
painCave.isFatal = 1; |
1193 |
|
|
simError(); |
1194 |
|
|
} |
1195 |
|
|
} |
1196 |
|
|
} |
1197 |
|
|
} |
1198 |
|
|
|
1199 |
mmeineke |
561 |
void DUFF::initializeBonds( int nBonds, Bond** bondArray, |
1200 |
mmeineke |
559 |
bond_pair* the_bonds ){ |
1201 |
|
|
int i,a,b; |
1202 |
|
|
char* atomA; |
1203 |
|
|
char* atomB; |
1204 |
|
|
|
1205 |
|
|
Atom** the_atoms; |
1206 |
|
|
the_atoms = entry_plug->atoms; |
1207 |
|
|
|
1208 |
|
|
|
1209 |
|
|
// initialize the Bonds |
1210 |
|
|
|
1211 |
|
|
for( i=0; i<nBonds; i++ ){ |
1212 |
|
|
|
1213 |
|
|
a = the_bonds[i].a; |
1214 |
|
|
b = the_bonds[i].b; |
1215 |
|
|
|
1216 |
|
|
atomA = the_atoms[a]->getType(); |
1217 |
|
|
atomB = the_atoms[b]->getType(); |
1218 |
|
|
currentBondType = headBondType->find( atomA, atomB ); |
1219 |
|
|
if( currentBondType == NULL ){ |
1220 |
|
|
sprintf( painCave.errMsg, |
1221 |
|
|
"BondType error, %s - %s not found in force file.\n", |
1222 |
|
|
atomA, atomB ); |
1223 |
|
|
painCave.isFatal = 1; |
1224 |
|
|
simError(); |
1225 |
|
|
} |
1226 |
|
|
|
1227 |
mmeineke |
564 |
switch( currentBondType->type ){ |
1228 |
|
|
|
1229 |
|
|
case FIXED_BOND: |
1230 |
|
|
|
1231 |
mmeineke |
559 |
bondArray[i] = new ConstrainedBond( *the_atoms[a], |
1232 |
|
|
*the_atoms[b], |
1233 |
|
|
currentBondType->d0 ); |
1234 |
|
|
entry_plug->n_constraints++; |
1235 |
mmeineke |
564 |
break; |
1236 |
|
|
|
1237 |
|
|
case HARMONIC_BOND: |
1238 |
|
|
|
1239 |
|
|
bondArray[i] = new HarmonicBond( *the_atoms[a], |
1240 |
|
|
*the_atoms[b], |
1241 |
|
|
currentBondType->d0, |
1242 |
|
|
currentBondType->k0 ); |
1243 |
|
|
break; |
1244 |
|
|
|
1245 |
|
|
default: |
1246 |
|
|
|
1247 |
|
|
break; |
1248 |
|
|
// do nothing |
1249 |
mmeineke |
559 |
} |
1250 |
|
|
} |
1251 |
|
|
} |
1252 |
|
|
|
1253 |
mmeineke |
561 |
void DUFF::initializeBends( int nBends, Bend** bendArray, |
1254 |
mmeineke |
559 |
bend_set* the_bends ){ |
1255 |
|
|
|
1256 |
|
|
QuadraticBend* qBend; |
1257 |
|
|
GhostBend* gBend; |
1258 |
|
|
Atom** the_atoms; |
1259 |
|
|
the_atoms = entry_plug->atoms; |
1260 |
|
|
|
1261 |
|
|
int i, a, b, c; |
1262 |
|
|
char* atomA; |
1263 |
|
|
char* atomB; |
1264 |
|
|
char* atomC; |
1265 |
|
|
|
1266 |
|
|
// initialize the Bends |
1267 |
|
|
|
1268 |
|
|
for( i=0; i<nBends; i++ ){ |
1269 |
|
|
|
1270 |
|
|
a = the_bends[i].a; |
1271 |
|
|
b = the_bends[i].b; |
1272 |
|
|
c = the_bends[i].c; |
1273 |
|
|
|
1274 |
|
|
atomA = the_atoms[a]->getType(); |
1275 |
|
|
atomB = the_atoms[b]->getType(); |
1276 |
|
|
|
1277 |
|
|
if( the_bends[i].isGhost ) atomC = "GHOST"; |
1278 |
|
|
else atomC = the_atoms[c]->getType(); |
1279 |
|
|
|
1280 |
|
|
currentBendType = headBendType->find( atomA, atomB, atomC ); |
1281 |
|
|
if( currentBendType == NULL ){ |
1282 |
|
|
sprintf( painCave.errMsg, "BendType error, %s - %s - %s not found" |
1283 |
|
|
" in force file.\n", |
1284 |
|
|
atomA, atomB, atomC ); |
1285 |
|
|
painCave.isFatal = 1; |
1286 |
|
|
simError(); |
1287 |
|
|
} |
1288 |
|
|
|
1289 |
|
|
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
1290 |
|
|
|
1291 |
|
|
if( the_bends[i].isGhost){ |
1292 |
|
|
|
1293 |
|
|
if( the_bends[i].ghost == b ){ |
1294 |
|
|
// do nothing |
1295 |
|
|
} |
1296 |
|
|
else if( the_bends[i].ghost == a ){ |
1297 |
|
|
c = a; |
1298 |
|
|
a = b; |
1299 |
|
|
b = c; |
1300 |
|
|
} |
1301 |
|
|
else{ |
1302 |
|
|
sprintf( painCave.errMsg, |
1303 |
|
|
"BendType error, %s - %s - %s,\n" |
1304 |
|
|
" --> central atom is not " |
1305 |
|
|
"correctly identified with the " |
1306 |
|
|
"\"ghostVectorSource = \" tag.\n", |
1307 |
|
|
atomA, atomB, atomC ); |
1308 |
|
|
painCave.isFatal = 1; |
1309 |
|
|
simError(); |
1310 |
|
|
} |
1311 |
|
|
|
1312 |
|
|
gBend = new GhostBend( *the_atoms[a], |
1313 |
tim |
704 |
*the_atoms[b], |
1314 |
|
|
*the_atoms[c] ); |
1315 |
|
|
|
1316 |
mmeineke |
559 |
gBend->setConstants( currentBendType->k1, |
1317 |
|
|
currentBendType->k2, |
1318 |
|
|
currentBendType->k3, |
1319 |
|
|
currentBendType->t0 ); |
1320 |
|
|
bendArray[i] = gBend; |
1321 |
|
|
} |
1322 |
|
|
else{ |
1323 |
|
|
qBend = new QuadraticBend( *the_atoms[a], |
1324 |
|
|
*the_atoms[b], |
1325 |
|
|
*the_atoms[c] ); |
1326 |
|
|
qBend->setConstants( currentBendType->k1, |
1327 |
|
|
currentBendType->k2, |
1328 |
|
|
currentBendType->k3, |
1329 |
|
|
currentBendType->t0 ); |
1330 |
|
|
bendArray[i] = qBend; |
1331 |
tim |
704 |
} |
1332 |
mmeineke |
559 |
} |
1333 |
|
|
} |
1334 |
|
|
} |
1335 |
|
|
|
1336 |
mmeineke |
561 |
void DUFF::initializeTorsions( int nTorsions, Torsion** torsionArray, |
1337 |
mmeineke |
559 |
torsion_set* the_torsions ){ |
1338 |
|
|
|
1339 |
|
|
int i, a, b, c, d; |
1340 |
|
|
char* atomA; |
1341 |
|
|
char* atomB; |
1342 |
|
|
char* atomC; |
1343 |
|
|
char* atomD; |
1344 |
|
|
|
1345 |
|
|
CubicTorsion* cTors; |
1346 |
|
|
Atom** the_atoms; |
1347 |
|
|
the_atoms = entry_plug->atoms; |
1348 |
|
|
|
1349 |
|
|
// initialize the Torsions |
1350 |
|
|
|
1351 |
|
|
for( i=0; i<nTorsions; i++ ){ |
1352 |
|
|
|
1353 |
|
|
a = the_torsions[i].a; |
1354 |
|
|
b = the_torsions[i].b; |
1355 |
|
|
c = the_torsions[i].c; |
1356 |
|
|
d = the_torsions[i].d; |
1357 |
|
|
|
1358 |
|
|
atomA = the_atoms[a]->getType(); |
1359 |
|
|
atomB = the_atoms[b]->getType(); |
1360 |
|
|
atomC = the_atoms[c]->getType(); |
1361 |
|
|
atomD = the_atoms[d]->getType(); |
1362 |
|
|
currentTorsionType = headTorsionType->find( atomA, atomB, atomC, atomD ); |
1363 |
|
|
if( currentTorsionType == NULL ){ |
1364 |
|
|
sprintf( painCave.errMsg, |
1365 |
|
|
"TorsionType error, %s - %s - %s - %s not found" |
1366 |
|
|
" in force file.\n", |
1367 |
|
|
atomA, atomB, atomC, atomD ); |
1368 |
|
|
painCave.isFatal = 1; |
1369 |
|
|
simError(); |
1370 |
|
|
} |
1371 |
|
|
|
1372 |
|
|
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
1373 |
|
|
|
1374 |
|
|
cTors = new CubicTorsion( *the_atoms[a], *the_atoms[b], |
1375 |
|
|
*the_atoms[c], *the_atoms[d] ); |
1376 |
|
|
cTors->setConstants( currentTorsionType->k1, currentTorsionType->k2, |
1377 |
|
|
currentTorsionType->k3, currentTorsionType->k4 ); |
1378 |
|
|
torsionArray[i] = cTors; |
1379 |
|
|
} |
1380 |
|
|
} |
1381 |
|
|
} |
1382 |
|
|
|
1383 |
mmeineke |
561 |
void DUFF::fastForward( char* stopText, char* searchOwner ){ |
1384 |
mmeineke |
559 |
|
1385 |
|
|
int foundText = 0; |
1386 |
|
|
char* the_token; |
1387 |
|
|
|
1388 |
|
|
rewind( frcFile ); |
1389 |
|
|
lineNum = 0; |
1390 |
|
|
|
1391 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1392 |
|
|
lineNum++; |
1393 |
|
|
if( eof_test == NULL ){ |
1394 |
|
|
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
1395 |
|
|
" file is empty.\n", |
1396 |
|
|
searchOwner ); |
1397 |
|
|
painCave.isFatal = 1; |
1398 |
|
|
simError(); |
1399 |
|
|
} |
1400 |
|
|
|
1401 |
|
|
|
1402 |
|
|
while( !foundText ){ |
1403 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
1404 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1405 |
|
|
lineNum++; |
1406 |
|
|
} |
1407 |
|
|
if( eof_test == NULL ){ |
1408 |
|
|
sprintf( painCave.errMsg, |
1409 |
|
|
"Error fast forwarding force file for %s at " |
1410 |
|
|
"line %d: file ended unexpectedly.\n", |
1411 |
|
|
searchOwner, |
1412 |
|
|
lineNum ); |
1413 |
|
|
painCave.isFatal = 1; |
1414 |
|
|
simError(); |
1415 |
|
|
} |
1416 |
|
|
|
1417 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
1418 |
|
|
foundText = !strcmp( stopText, the_token ); |
1419 |
|
|
|
1420 |
|
|
if( !foundText ){ |
1421 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1422 |
|
|
lineNum++; |
1423 |
|
|
|
1424 |
|
|
if( eof_test == NULL ){ |
1425 |
|
|
sprintf( painCave.errMsg, |
1426 |
|
|
"Error fast forwarding force file for %s at " |
1427 |
|
|
"line %d: file ended unexpectedly.\n", |
1428 |
|
|
searchOwner, |
1429 |
|
|
lineNum ); |
1430 |
|
|
painCave.isFatal = 1; |
1431 |
|
|
simError(); |
1432 |
|
|
} |
1433 |
|
|
} |
1434 |
|
|
} |
1435 |
|
|
} |
1436 |
|
|
|
1437 |
|
|
|
1438 |
mmeineke |
594 |
int DUFF_NS::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){ |
1439 |
mmeineke |
559 |
|
1440 |
|
|
char* the_token; |
1441 |
|
|
|
1442 |
|
|
the_token = strtok( lineBuffer, " \n\t,;" ); |
1443 |
|
|
if( the_token != NULL ){ |
1444 |
|
|
|
1445 |
|
|
strcpy( info.name, the_token ); |
1446 |
|
|
|
1447 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1448 |
|
|
sprintf( painCave.errMsg, |
1449 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1450 |
|
|
painCave.isFatal = 1; |
1451 |
|
|
simError(); |
1452 |
|
|
} |
1453 |
|
|
|
1454 |
|
|
info.isDipole = atoi( the_token ); |
1455 |
|
|
|
1456 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1457 |
|
|
sprintf( painCave.errMsg, |
1458 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1459 |
|
|
painCave.isFatal = 1; |
1460 |
|
|
simError(); |
1461 |
|
|
} |
1462 |
|
|
|
1463 |
|
|
info.isSSD = atoi( the_token ); |
1464 |
|
|
|
1465 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1466 |
|
|
sprintf( painCave.errMsg, |
1467 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1468 |
|
|
painCave.isFatal = 1; |
1469 |
|
|
simError(); |
1470 |
|
|
} |
1471 |
|
|
|
1472 |
|
|
info.mass = atof( the_token ); |
1473 |
|
|
|
1474 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1475 |
|
|
sprintf( painCave.errMsg, |
1476 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1477 |
|
|
painCave.isFatal = 1; |
1478 |
|
|
simError(); |
1479 |
|
|
} |
1480 |
|
|
|
1481 |
|
|
info.epslon = atof( the_token ); |
1482 |
|
|
|
1483 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1484 |
|
|
sprintf( painCave.errMsg, |
1485 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1486 |
|
|
painCave.isFatal = 1; |
1487 |
|
|
simError(); |
1488 |
|
|
} |
1489 |
|
|
|
1490 |
|
|
info.sigma = atof( the_token ); |
1491 |
|
|
|
1492 |
|
|
if( info.isDipole ){ |
1493 |
|
|
|
1494 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1495 |
|
|
sprintf( painCave.errMsg, |
1496 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1497 |
|
|
painCave.isFatal = 1; |
1498 |
|
|
simError(); |
1499 |
|
|
} |
1500 |
|
|
|
1501 |
|
|
info.dipole = atof( the_token ); |
1502 |
|
|
} |
1503 |
|
|
else info.dipole = 0.0; |
1504 |
|
|
|
1505 |
|
|
if( info.isSSD ){ |
1506 |
|
|
|
1507 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1508 |
|
|
sprintf( painCave.errMsg, |
1509 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1510 |
|
|
painCave.isFatal = 1; |
1511 |
|
|
simError(); |
1512 |
|
|
} |
1513 |
|
|
|
1514 |
|
|
info.w0 = atof( the_token ); |
1515 |
|
|
|
1516 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1517 |
|
|
sprintf( painCave.errMsg, |
1518 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1519 |
|
|
painCave.isFatal = 1; |
1520 |
|
|
simError(); |
1521 |
|
|
} |
1522 |
|
|
|
1523 |
|
|
info.v0 = atof( the_token ); |
1524 |
gezelter |
635 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1525 |
|
|
sprintf( painCave.errMsg, |
1526 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1527 |
|
|
painCave.isFatal = 1; |
1528 |
|
|
simError(); |
1529 |
|
|
} |
1530 |
|
|
|
1531 |
|
|
info.v0p = atof( the_token ); |
1532 |
|
|
|
1533 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1534 |
|
|
sprintf( painCave.errMsg, |
1535 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1536 |
|
|
painCave.isFatal = 1; |
1537 |
|
|
simError(); |
1538 |
|
|
} |
1539 |
|
|
|
1540 |
|
|
info.rl = atof( the_token ); |
1541 |
|
|
|
1542 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1543 |
|
|
sprintf( painCave.errMsg, |
1544 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1545 |
|
|
painCave.isFatal = 1; |
1546 |
|
|
simError(); |
1547 |
|
|
} |
1548 |
|
|
|
1549 |
|
|
info.ru = atof( the_token ); |
1550 |
|
|
|
1551 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1552 |
|
|
sprintf( painCave.errMsg, |
1553 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1554 |
|
|
painCave.isFatal = 1; |
1555 |
|
|
simError(); |
1556 |
|
|
} |
1557 |
|
|
|
1558 |
|
|
info.rlp = atof( the_token ); |
1559 |
|
|
|
1560 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1561 |
|
|
sprintf( painCave.errMsg, |
1562 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1563 |
|
|
painCave.isFatal = 1; |
1564 |
|
|
simError(); |
1565 |
|
|
} |
1566 |
|
|
|
1567 |
|
|
info.rup = atof( the_token ); |
1568 |
mmeineke |
559 |
} |
1569 |
gezelter |
635 |
else info.v0 = info.w0 = info.v0p = info.rl = info.ru = info.rlp = info.rup = 0.0; |
1570 |
mmeineke |
559 |
|
1571 |
|
|
return 1; |
1572 |
|
|
} |
1573 |
|
|
else return 0; |
1574 |
|
|
} |
1575 |
|
|
|
1576 |
mmeineke |
594 |
int DUFF_NS::parseBond( char *lineBuffer, int lineNum, bondStruct &info ){ |
1577 |
mmeineke |
559 |
|
1578 |
|
|
char* the_token; |
1579 |
mmeineke |
564 |
char bondType[30]; |
1580 |
mmeineke |
559 |
|
1581 |
|
|
the_token = strtok( lineBuffer, " \n\t,;" ); |
1582 |
|
|
if( the_token != NULL ){ |
1583 |
|
|
|
1584 |
|
|
strcpy( info.nameA, the_token ); |
1585 |
|
|
|
1586 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1587 |
|
|
sprintf( painCave.errMsg, |
1588 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1589 |
|
|
painCave.isFatal = 1; |
1590 |
|
|
simError(); |
1591 |
|
|
} |
1592 |
|
|
|
1593 |
|
|
strcpy( info.nameB, the_token ); |
1594 |
|
|
|
1595 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1596 |
|
|
sprintf( painCave.errMsg, |
1597 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1598 |
|
|
painCave.isFatal = 1; |
1599 |
|
|
simError(); |
1600 |
|
|
} |
1601 |
|
|
|
1602 |
mmeineke |
564 |
strcpy( bondType, the_token ); |
1603 |
mmeineke |
559 |
|
1604 |
mmeineke |
564 |
if( !strcmp( bondType, "fixed" ) ){ |
1605 |
|
|
info.type = FIXED_BOND; |
1606 |
|
|
|
1607 |
mmeineke |
559 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1608 |
|
|
sprintf( painCave.errMsg, |
1609 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1610 |
|
|
painCave.isFatal = 1; |
1611 |
|
|
simError(); |
1612 |
|
|
} |
1613 |
|
|
|
1614 |
|
|
info.d0 = atof( the_token ); |
1615 |
mmeineke |
690 |
|
1616 |
|
|
info.k0=0.0; |
1617 |
mmeineke |
559 |
} |
1618 |
mmeineke |
564 |
else if( !strcmp( bondType, "harmonic" ) ){ |
1619 |
|
|
info.type = HARMONIC_BOND; |
1620 |
|
|
|
1621 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1622 |
|
|
sprintf( painCave.errMsg, |
1623 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1624 |
|
|
painCave.isFatal = 1; |
1625 |
|
|
simError(); |
1626 |
|
|
} |
1627 |
|
|
|
1628 |
|
|
info.d0 = atof( the_token ); |
1629 |
|
|
|
1630 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1631 |
|
|
sprintf( painCave.errMsg, |
1632 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1633 |
|
|
painCave.isFatal = 1; |
1634 |
|
|
simError(); |
1635 |
|
|
} |
1636 |
|
|
|
1637 |
|
|
info.k0 = atof( the_token ); |
1638 |
|
|
} |
1639 |
|
|
|
1640 |
mmeineke |
559 |
else{ |
1641 |
|
|
sprintf( painCave.errMsg, |
1642 |
mmeineke |
561 |
"Unknown DUFF bond type \"%s\" at line %d\n", |
1643 |
mmeineke |
559 |
info.type, |
1644 |
|
|
lineNum ); |
1645 |
|
|
painCave.isFatal = 1; |
1646 |
|
|
simError(); |
1647 |
|
|
} |
1648 |
|
|
|
1649 |
|
|
return 1; |
1650 |
|
|
} |
1651 |
|
|
else return 0; |
1652 |
|
|
} |
1653 |
|
|
|
1654 |
|
|
|
1655 |
mmeineke |
594 |
int DUFF_NS::parseBend( char *lineBuffer, int lineNum, bendStruct &info ){ |
1656 |
mmeineke |
559 |
|
1657 |
|
|
char* the_token; |
1658 |
|
|
|
1659 |
|
|
the_token = strtok( lineBuffer, " \n\t,;" ); |
1660 |
|
|
if( the_token != NULL ){ |
1661 |
|
|
|
1662 |
|
|
strcpy( info.nameA, the_token ); |
1663 |
|
|
|
1664 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1665 |
|
|
sprintf( painCave.errMsg, |
1666 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1667 |
|
|
painCave.isFatal = 1; |
1668 |
|
|
simError(); |
1669 |
|
|
} |
1670 |
|
|
|
1671 |
|
|
strcpy( info.nameB, the_token ); |
1672 |
|
|
|
1673 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1674 |
|
|
sprintf( painCave.errMsg, |
1675 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1676 |
|
|
painCave.isFatal = 1; |
1677 |
|
|
simError(); |
1678 |
|
|
} |
1679 |
|
|
|
1680 |
|
|
strcpy( info.nameC, the_token ); |
1681 |
|
|
|
1682 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1683 |
|
|
sprintf( painCave.errMsg, |
1684 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1685 |
|
|
painCave.isFatal = 1; |
1686 |
|
|
simError(); |
1687 |
|
|
} |
1688 |
|
|
|
1689 |
|
|
strcpy( info.type, the_token ); |
1690 |
|
|
|
1691 |
|
|
if( !strcmp( info.type, "quadratic" ) ){ |
1692 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1693 |
|
|
sprintf( painCave.errMsg, |
1694 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1695 |
|
|
painCave.isFatal = 1; |
1696 |
|
|
simError(); |
1697 |
|
|
} |
1698 |
|
|
|
1699 |
|
|
info.k1 = atof( the_token ); |
1700 |
|
|
|
1701 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1702 |
|
|
sprintf( painCave.errMsg, |
1703 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1704 |
|
|
painCave.isFatal = 1; |
1705 |
|
|
simError(); |
1706 |
|
|
} |
1707 |
|
|
|
1708 |
|
|
info.k2 = atof( the_token ); |
1709 |
|
|
|
1710 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1711 |
|
|
sprintf( painCave.errMsg, |
1712 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1713 |
|
|
painCave.isFatal = 1; |
1714 |
|
|
simError(); |
1715 |
|
|
} |
1716 |
|
|
|
1717 |
|
|
info.k3 = atof( the_token ); |
1718 |
|
|
|
1719 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1720 |
|
|
sprintf( painCave.errMsg, |
1721 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1722 |
|
|
painCave.isFatal = 1; |
1723 |
|
|
simError(); |
1724 |
|
|
} |
1725 |
|
|
|
1726 |
|
|
info.t0 = atof( the_token ); |
1727 |
|
|
} |
1728 |
|
|
|
1729 |
|
|
else{ |
1730 |
|
|
sprintf( painCave.errMsg, |
1731 |
mmeineke |
561 |
"Unknown DUFF bend type \"%s\" at line %d\n", |
1732 |
mmeineke |
559 |
info.type, |
1733 |
|
|
lineNum ); |
1734 |
|
|
painCave.isFatal = 1; |
1735 |
|
|
simError(); |
1736 |
|
|
} |
1737 |
|
|
|
1738 |
|
|
return 1; |
1739 |
|
|
} |
1740 |
|
|
else return 0; |
1741 |
|
|
} |
1742 |
|
|
|
1743 |
mmeineke |
594 |
int DUFF_NS::parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ){ |
1744 |
mmeineke |
559 |
|
1745 |
|
|
char* the_token; |
1746 |
|
|
|
1747 |
|
|
the_token = strtok( lineBuffer, " \n\t,;" ); |
1748 |
|
|
if( the_token != NULL ){ |
1749 |
|
|
|
1750 |
|
|
strcpy( info.nameA, the_token ); |
1751 |
|
|
|
1752 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1753 |
|
|
sprintf( painCave.errMsg, |
1754 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1755 |
|
|
painCave.isFatal = 1; |
1756 |
|
|
simError(); |
1757 |
|
|
} |
1758 |
|
|
|
1759 |
|
|
strcpy( info.nameB, the_token ); |
1760 |
|
|
|
1761 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1762 |
|
|
sprintf( painCave.errMsg, |
1763 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1764 |
|
|
painCave.isFatal = 1; |
1765 |
|
|
simError(); |
1766 |
|
|
} |
1767 |
|
|
|
1768 |
|
|
strcpy( info.nameC, the_token ); |
1769 |
|
|
|
1770 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1771 |
|
|
sprintf( painCave.errMsg, |
1772 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1773 |
|
|
painCave.isFatal = 1; |
1774 |
|
|
simError(); |
1775 |
|
|
} |
1776 |
|
|
|
1777 |
|
|
strcpy( info.nameD, the_token ); |
1778 |
|
|
|
1779 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1780 |
|
|
sprintf( painCave.errMsg, |
1781 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1782 |
|
|
painCave.isFatal = 1; |
1783 |
|
|
simError(); |
1784 |
|
|
} |
1785 |
|
|
|
1786 |
|
|
strcpy( info.type, the_token ); |
1787 |
|
|
|
1788 |
|
|
if( !strcmp( info.type, "cubic" ) ){ |
1789 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1790 |
|
|
sprintf( painCave.errMsg, |
1791 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1792 |
|
|
painCave.isFatal = 1; |
1793 |
|
|
simError(); |
1794 |
|
|
} |
1795 |
|
|
|
1796 |
|
|
info.k1 = atof( the_token ); |
1797 |
|
|
|
1798 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1799 |
|
|
sprintf( painCave.errMsg, |
1800 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1801 |
|
|
painCave.isFatal = 1; |
1802 |
|
|
simError(); |
1803 |
|
|
} |
1804 |
|
|
|
1805 |
|
|
info.k2 = atof( the_token ); |
1806 |
|
|
|
1807 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1808 |
|
|
sprintf( painCave.errMsg, |
1809 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1810 |
|
|
painCave.isFatal = 1; |
1811 |
|
|
simError(); |
1812 |
|
|
} |
1813 |
|
|
|
1814 |
|
|
info.k3 = atof( the_token ); |
1815 |
|
|
|
1816 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1817 |
|
|
sprintf( painCave.errMsg, |
1818 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1819 |
|
|
painCave.isFatal = 1; |
1820 |
|
|
simError(); |
1821 |
|
|
} |
1822 |
|
|
|
1823 |
|
|
info.k4 = atof( the_token ); |
1824 |
|
|
|
1825 |
|
|
} |
1826 |
|
|
|
1827 |
|
|
else{ |
1828 |
|
|
sprintf( painCave.errMsg, |
1829 |
mmeineke |
561 |
"Unknown DUFF torsion type \"%s\" at line %d\n", |
1830 |
mmeineke |
559 |
info.type, |
1831 |
|
|
lineNum ); |
1832 |
|
|
painCave.isFatal = 1; |
1833 |
|
|
simError(); |
1834 |
|
|
} |
1835 |
|
|
|
1836 |
|
|
return 1; |
1837 |
|
|
} |
1838 |
|
|
|
1839 |
|
|
else return 0; |
1840 |
|
|
} |