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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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mmeineke |
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#ifdef IS_MPI |
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#include <mpi.h> |
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#include <mpi++.h> |
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#endif //is_mpi |
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mmeineke |
270 |
#include "ForceFields.hpp" |
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#include "SRI.hpp" |
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#include "simError.h" |
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mmeineke |
294 |
#include <fortranWrappers.hpp> |
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mmeineke |
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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 |
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mmeineke |
270 |
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mmeineke |
348 |
namespace LJ_NS{ |
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mmeineke |
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mmeineke |
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// Declare the structures that will be passed by the parser and 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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int ident; |
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int last; // 0 -> default |
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// 1 -> in MPI: tells nodes to stop listening |
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} atomStruct; |
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mmeineke |
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mmeineke |
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int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ); |
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mmeineke |
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#ifdef IS_MPI |
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mmeineke |
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MPI_Datatype mpiAtomStructType; |
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mmeineke |
270 |
#endif |
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mmeineke |
291 |
} |
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mmeineke |
270 |
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mmeineke |
348 |
using namespace LJ_NS; |
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mmeineke |
270 |
|
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//**************************************************************** |
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// begins the actual forcefield stuff. |
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//**************************************************************** |
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LJ_FF::LJ_FF(){ |
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char fileName[200]; |
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char* ffPath_env = "FORCE_PARAM_PATH"; |
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char* ffPath; |
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char temp[200]; |
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char errMsg[1000]; |
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// do the funtion wrapping |
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mmeineke |
294 |
wrapMeFF( this ); |
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mmeineke |
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|
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#ifdef IS_MPI |
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int i; |
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// ********************************************************************** |
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// Init the atomStruct mpi type |
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atomStruct atomProto; // mpiPrototype |
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int atomBC[3] = {15,3,2}; // block counts |
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MPI_Aint atomDspls[3]; // displacements |
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MPI_Datatype atomMbrTypes[3]; // member mpi types |
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MPI_Address(&atomProto.name, &atomDspls[0]); |
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MPI_Address(&atomProto.mass, &atomDspls[1]); |
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MPI_Address(&atomProto.ident, &atomDspls[2]); |
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atomMbrTypes[0] = MPI_CHAR; |
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atomMbrTypes[1] = MPI_DOUBLE; |
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atomMbrTypes[2] = MPI_INT; |
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for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0]; |
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MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType); |
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MPI_Type_commit(&mpiAtomStructType); |
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// *********************************************************************** |
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if( worldRank == 0 ){ |
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#endif |
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// generate the force file name |
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strcpy( fileName, "LJ_FF.frc" ); |
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// fprintf( stderr,"Trying to open %s\n", fileName ); |
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// attempt to open the file in the current directory first. |
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frcFile = fopen( fileName, "r" ); |
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if( frcFile == NULL ){ |
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// next see if the force path enviorment variable is set |
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ffPath = getenv( ffPath_env ); |
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if( ffPath == NULL ) { |
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mmeineke |
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STR_DEFINE(ffPath, FRC_PATH ); |
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mmeineke |
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} |
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strcpy( temp, ffPath ); |
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strcat( temp, "/" ); |
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strcat( temp, fileName ); |
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strcpy( fileName, temp ); |
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frcFile = fopen( fileName, "r" ); |
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if( frcFile == NULL ){ |
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sprintf( painCave.errMsg, |
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"Error opening the force field parameter file: %s\n" |
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"Have you tried setting the FORCE_PARAM_PATH environment " |
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"vairable?\n", |
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fileName ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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#ifdef IS_MPI |
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} |
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sprintf( checkPointMsg, "LJ_FF file opened sucessfully." ); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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} |
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LJ_FF::~LJ_FF(){ |
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#ifdef IS_MPI |
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if( worldRank == 0 ){ |
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#endif // is_mpi |
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fclose( frcFile ); |
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#ifdef IS_MPI |
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} |
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#endif // is_mpi |
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} |
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mmeineke |
362 |
void LJ_FF::initForceField( int ljMixRule ){ |
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initFortran( ljMixRule, 0 ); |
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} |
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mmeineke |
270 |
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void LJ_FF::initializeAtoms( void ){ |
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class LinkedType { |
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public: |
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LinkedType(){ |
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next = NULL; |
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name[0] = '\0'; |
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} |
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~LinkedType(){ if( next != NULL ) delete next; } |
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LinkedType* 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 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 LJ atom type \"%s\" found in " |
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"the LJ_FF 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 LinkedType(); |
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strcpy(next->name, info.name); |
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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->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.mass = mass; |
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info.epslon = epslon; |
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info.sigma = sigma; |
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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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double mass; |
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double epslon; |
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double sigma; |
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int ident; |
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LinkedType* next; |
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}; |
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LinkedType* headAtomType; |
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LinkedType* currentAtomType; |
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atomStruct info; |
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info.last = 1; // initialize last to have the last set. |
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// if things go well, last will be set to 0 |
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int i; |
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int identNum; |
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Atom** the_atoms; |
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int nAtoms; |
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the_atoms = entry_plug->atoms; |
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nAtoms = entry_plug->n_atoms; |
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#ifdef IS_MPI |
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if( worldRank == 0 ){ |
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#endif |
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// read in the atom types. |
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headAtomType = new LinkedType; |
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fastForward( "AtomTypes", "initializeAtoms" ); |
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// we are now at the AtomTypes section. |
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eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
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lineNum++; |
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// read a line, and start parseing out the atom types |
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if( eof_test == NULL ){ |
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sprintf( painCave.errMsg, |
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"Error in reading Atoms from force file at line %d.\n", |
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lineNum ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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identNum = 1; |
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// stop reading at end of file, or at next section |
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while( readLine[0] != '#' && eof_test != NULL ){ |
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// toss comment lines |
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if( readLine[0] != '!' ){ |
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// the parser returns 0 if the line was blank |
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mmeineke |
348 |
if( parseAtom( readLine, lineNum, info ) ){ |
276 |
mmeineke |
270 |
info.ident = identNum; |
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headAtomType->add( info );; |
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identNum++; |
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} |
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} |
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eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
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lineNum++; |
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} |
284 |
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285 |
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#ifdef IS_MPI |
286 |
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287 |
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// send out the linked list to all the other processes |
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sprintf( checkPointMsg, |
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"LJ_FF atom structures read successfully." ); |
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MPIcheckPoint(); |
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currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
294 |
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while( currentAtomType != NULL ){ |
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currentAtomType->duplicate( info ); |
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298 |
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299 |
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sendFrcStruct( &info, mpiAtomStructType ); |
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sprintf( checkPointMsg, |
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"successfully sent lJ force type: \"%s\"\n", |
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info.name ); |
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MPIcheckPoint(); |
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currentAtomType = currentAtomType->next; |
307 |
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} |
308 |
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info.last = 1; |
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sendFrcStruct( &info, mpiAtomStructType ); |
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311 |
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} |
312 |
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else{ |
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// listen for node 0 to send out the force params |
316 |
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317 |
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MPIcheckPoint(); |
318 |
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319 |
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headAtomType = new LinkedType; |
320 |
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recieveFrcStruct( &info, mpiAtomStructType ); |
321 |
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322 |
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while( !info.last ){ |
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325 |
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326 |
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headAtomType->add( info ); |
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328 |
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MPIcheckPoint(); |
329 |
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330 |
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recieveFrcStruct( &info, mpiAtomStructType ); |
331 |
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} |
332 |
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} |
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#endif // is_mpi |
334 |
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335 |
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// call new A_types in fortran |
336 |
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337 |
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int isError; |
338 |
mmeineke |
296 |
|
339 |
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// dummy variables |
340 |
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int isLJ = 1; |
341 |
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int isDipole = 0; |
342 |
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int isSSD = 0; |
343 |
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int isGB = 0; |
344 |
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double w0 = 0.0; |
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double v0 = 0.0; |
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double dipole = 0.0; |
347 |
mmeineke |
365 |
double GB_dummy = 0.0; |
348 |
mmeineke |
296 |
|
349 |
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350 |
mmeineke |
270 |
currentAtomType = headAtomType; |
351 |
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while( currentAtomType != NULL ){ |
352 |
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353 |
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if( currentAtomType->name[0] != '\0' ){ |
354 |
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isError = 0; |
355 |
mmeineke |
348 |
makeAtype( &(currentAtomType->ident), |
356 |
mmeineke |
362 |
&isLJ, |
357 |
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&isSSD, |
358 |
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&isDipole, |
359 |
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&isGB, |
360 |
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&(currentAtomType->epslon), |
361 |
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&(currentAtomType->sigma), |
362 |
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&dipole, |
363 |
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&w0, |
364 |
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&v0, |
365 |
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&GB_dummy, |
366 |
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&GB_dummy, |
367 |
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&GB_dummy, |
368 |
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&GB_dummy, |
369 |
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&GB_dummy, |
370 |
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&GB_dummy, |
371 |
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&isError ); |
372 |
mmeineke |
270 |
if( isError ){ |
373 |
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sprintf( painCave.errMsg, |
374 |
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"Error initializing the \"%s\" atom type in fortran\n", |
375 |
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currentAtomType->name ); |
376 |
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painCave.isFatal = 1; |
377 |
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simError(); |
378 |
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} |
379 |
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} |
380 |
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currentAtomType = currentAtomType->next; |
381 |
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} |
382 |
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383 |
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#ifdef IS_MPI |
384 |
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sprintf( checkPointMsg, |
385 |
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"LJ_FF atom structures successfully sent to fortran\n" ); |
386 |
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MPIcheckPoint(); |
387 |
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#endif // is_mpi |
388 |
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389 |
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390 |
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391 |
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// initialize the atoms |
392 |
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393 |
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double bigSigma = 0.0; |
394 |
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Atom* thisAtom; |
395 |
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396 |
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for( i=0; i<nAtoms; i++ ){ |
397 |
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398 |
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currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
399 |
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if( currentAtomType == NULL ){ |
400 |
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sprintf( painCave.errMsg, |
401 |
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"AtomType error, %s not found in force file.\n", |
402 |
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the_atoms[i]->getType() ); |
403 |
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painCave.isFatal = 1; |
404 |
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simError(); |
405 |
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} |
406 |
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407 |
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the_atoms[i]->setMass( currentAtomType->mass ); |
408 |
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the_atoms[i]->setEpslon( currentAtomType->epslon ); |
409 |
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the_atoms[i]->setSigma( currentAtomType->sigma ); |
410 |
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the_atoms[i]->setIdent( currentAtomType->ident ); |
411 |
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the_atoms[i]->setLJ(); |
412 |
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413 |
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if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma; |
414 |
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} |
415 |
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416 |
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417 |
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#ifdef IS_MPI |
418 |
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double tempBig = bigSigma; |
419 |
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MPI::COMM_WORLD.Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX ); |
420 |
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#endif //is_mpi |
421 |
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422 |
|
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//calc rCut and rList |
423 |
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|
424 |
|
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entry_plug->rCut = 2.5 * bigSigma; |
425 |
mmeineke |
362 |
if(entry_plug->rCut > (entry_plug->box_x / 2.0)) |
426 |
|
|
entry_plug->rCut = entry_plug->box_x / 2.0; |
427 |
|
|
if(entry_plug->rCut > (entry_plug->box_y / 2.0)) |
428 |
|
|
entry_plug->rCut = entry_plug->box_y / 2.0; |
429 |
|
|
if(entry_plug->rCut > (entry_plug->box_z / 2.0)) |
430 |
|
|
entry_plug->rCut = entry_plug->box_z / 2.0; |
431 |
mmeineke |
270 |
|
432 |
|
|
entry_plug->rList = entry_plug->rCut + 1.0; |
433 |
|
|
|
434 |
mmeineke |
362 |
entry_plug->useLJ = 1; |
435 |
|
|
|
436 |
mmeineke |
270 |
// clean up the memory |
437 |
|
|
|
438 |
|
|
delete headAtomType; |
439 |
|
|
|
440 |
|
|
#ifdef IS_MPI |
441 |
|
|
sprintf( checkPointMsg, "LJ_FF atoms initialized succesfully" ); |
442 |
|
|
MPIcheckPoint(); |
443 |
|
|
#endif // is_mpi |
444 |
|
|
|
445 |
|
|
} |
446 |
|
|
|
447 |
|
|
void LJ_FF::initializeBonds( bond_pair* the_bonds ){ |
448 |
|
|
|
449 |
|
|
if( entry_plug->n_bonds ){ |
450 |
|
|
sprintf( painCave.errMsg, |
451 |
|
|
"LJ_FF does not support bonds.\n" ); |
452 |
|
|
painCave.isFatal = 1; |
453 |
|
|
simError(); |
454 |
|
|
} |
455 |
|
|
#ifdef IS_MPI |
456 |
|
|
MPIcheckPoint(); |
457 |
|
|
#endif // is_mpi |
458 |
|
|
|
459 |
|
|
} |
460 |
|
|
|
461 |
|
|
void LJ_FF::initializeBends( bend_set* the_bends ){ |
462 |
|
|
|
463 |
|
|
if( entry_plug->n_bends ){ |
464 |
|
|
sprintf( painCave.errMsg, |
465 |
|
|
"LJ_FF does not support bends.\n" ); |
466 |
|
|
painCave.isFatal = 1; |
467 |
|
|
simError(); |
468 |
|
|
} |
469 |
|
|
#ifdef IS_MPI |
470 |
|
|
MPIcheckPoint(); |
471 |
|
|
#endif // is_mpi |
472 |
|
|
|
473 |
|
|
} |
474 |
|
|
|
475 |
|
|
void LJ_FF::initializeTorsions( torsion_set* the_torsions ){ |
476 |
|
|
|
477 |
|
|
if( entry_plug->n_torsions ){ |
478 |
|
|
sprintf( painCave.errMsg, |
479 |
|
|
"LJ_FF does not support torsions.\n" ); |
480 |
|
|
painCave.isFatal = 1; |
481 |
|
|
simError(); |
482 |
|
|
} |
483 |
|
|
#ifdef IS_MPI |
484 |
|
|
MPIcheckPoint(); |
485 |
|
|
#endif // is_mpi |
486 |
|
|
|
487 |
|
|
} |
488 |
|
|
|
489 |
|
|
void LJ_FF::fastForward( char* stopText, char* searchOwner ){ |
490 |
|
|
|
491 |
|
|
int foundText = 0; |
492 |
|
|
char* the_token; |
493 |
|
|
|
494 |
|
|
rewind( frcFile ); |
495 |
|
|
lineNum = 0; |
496 |
|
|
|
497 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
498 |
|
|
lineNum++; |
499 |
|
|
if( eof_test == NULL ){ |
500 |
|
|
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
501 |
|
|
" file is empty.\n", |
502 |
|
|
searchOwner ); |
503 |
|
|
painCave.isFatal = 1; |
504 |
|
|
simError(); |
505 |
|
|
} |
506 |
|
|
|
507 |
|
|
|
508 |
|
|
while( !foundText ){ |
509 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
510 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
511 |
|
|
lineNum++; |
512 |
|
|
} |
513 |
|
|
if( eof_test == NULL ){ |
514 |
|
|
sprintf( painCave.errMsg, |
515 |
|
|
"Error fast forwarding force file for %s at " |
516 |
|
|
"line %d: file ended unexpectedly.\n", |
517 |
|
|
searchOwner, |
518 |
|
|
lineNum ); |
519 |
|
|
painCave.isFatal = 1; |
520 |
|
|
simError(); |
521 |
|
|
} |
522 |
|
|
|
523 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
524 |
|
|
foundText = !strcmp( stopText, the_token ); |
525 |
|
|
|
526 |
|
|
if( !foundText ){ |
527 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
528 |
|
|
lineNum++; |
529 |
|
|
|
530 |
|
|
if( eof_test == NULL ){ |
531 |
|
|
sprintf( painCave.errMsg, |
532 |
|
|
"Error fast forwarding force file for %s at " |
533 |
|
|
"line %d: file ended unexpectedly.\n", |
534 |
|
|
searchOwner, |
535 |
|
|
lineNum ); |
536 |
|
|
painCave.isFatal = 1; |
537 |
|
|
simError(); |
538 |
|
|
} |
539 |
|
|
} |
540 |
|
|
} |
541 |
|
|
} |
542 |
|
|
|
543 |
|
|
|
544 |
|
|
|
545 |
mmeineke |
367 |
int LJ_NS::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){ |
546 |
mmeineke |
270 |
|
547 |
|
|
char* the_token; |
548 |
|
|
|
549 |
|
|
the_token = strtok( lineBuffer, " \n\t,;" ); |
550 |
|
|
if( the_token != NULL ){ |
551 |
|
|
|
552 |
|
|
strcpy( info.name, the_token ); |
553 |
|
|
|
554 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
555 |
|
|
sprintf( painCave.errMsg, |
556 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
557 |
|
|
painCave.isFatal = 1; |
558 |
|
|
simError(); |
559 |
|
|
} |
560 |
|
|
|
561 |
|
|
info.mass = atof( the_token ); |
562 |
|
|
|
563 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
564 |
|
|
sprintf( painCave.errMsg, |
565 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
566 |
|
|
painCave.isFatal = 1; |
567 |
|
|
simError(); |
568 |
|
|
} |
569 |
|
|
|
570 |
|
|
info.epslon = atof( the_token ); |
571 |
|
|
|
572 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
573 |
|
|
sprintf( painCave.errMsg, |
574 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
575 |
|
|
painCave.isFatal = 1; |
576 |
|
|
simError(); |
577 |
|
|
} |
578 |
|
|
|
579 |
|
|
info.sigma = atof( the_token ); |
580 |
|
|
|
581 |
|
|
return 1; |
582 |
|
|
} |
583 |
|
|
else return 0; |
584 |
|
|
} |