| 1 |
#include <cstdlib> |
| 2 |
#include <cstdio> |
| 3 |
#include <cstring> |
| 4 |
|
| 5 |
#include <iostream> |
| 6 |
using namespace std; |
| 7 |
|
| 8 |
#include "ForceFields.hpp" |
| 9 |
#include "SRI.hpp" |
| 10 |
#include "simError.h" |
| 11 |
|
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|
| 13 |
// Declare the structures that will be passed by the parser and MPI |
| 14 |
|
| 15 |
typedef struct{ |
| 16 |
char name[15]; |
| 17 |
double mass; |
| 18 |
double epslon; |
| 19 |
double sigma; |
| 20 |
int ident; |
| 21 |
int last; // 0 -> default |
| 22 |
// 1 -> in MPI: tells nodes to stop listening |
| 23 |
} atomStruct; |
| 24 |
|
| 25 |
int parseAtomLJ( char *lineBuffer, int lineNum, atomStruct &info ); |
| 26 |
|
| 27 |
#ifdef IS_MPI |
| 28 |
|
| 29 |
#include "mpiForceField.h" |
| 30 |
|
| 31 |
MPI_Datatype mpiAtomStructType; |
| 32 |
|
| 33 |
#endif |
| 34 |
|
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|
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// declaration of functions needed to wrap the fortran module |
| 37 |
|
| 38 |
extern "C" { |
| 39 |
void forcefactory_( char* forceName, |
| 40 |
int* status, |
| 41 |
void (*wrapFunction)( void (* |
| 42 |
|
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|
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|
| 45 |
LJ_FF::LJ_FF(){ |
| 46 |
|
| 47 |
char fileName[200]; |
| 48 |
char* ffPath_env = "FORCE_PARAM_PATH"; |
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char* ffPath; |
| 50 |
char temp[200]; |
| 51 |
char errMsg[1000]; |
| 52 |
|
| 53 |
#ifdef IS_MPI |
| 54 |
int i; |
| 55 |
|
| 56 |
// ********************************************************************** |
| 57 |
// Init the atomStruct mpi type |
| 58 |
|
| 59 |
atomStruct atomProto; // mpiPrototype |
| 60 |
int atomBC[3] = {15,3,2}; // block counts |
| 61 |
MPI_Aint atomDspls[3]; // displacements |
| 62 |
MPI_Datatype atomMbrTypes[3]; // member mpi types |
| 63 |
|
| 64 |
MPI_Address(&atomProto.name, &atomDspls[0]); |
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MPI_Address(&atomProto.mass, &atomDspls[1]); |
| 66 |
MPI_Address(&atomProto.ident, &atomDspls[2]); |
| 67 |
|
| 68 |
atomMbrTypes[0] = MPI_CHAR; |
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atomMbrTypes[1] = MPI_DOUBLE; |
| 70 |
atomMbrTypes[2] = MPI_INT; |
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|
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for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0]; |
| 73 |
|
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MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType); |
| 75 |
MPI_Type_commit(&mpiAtomStructType); |
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|
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// *********************************************************************** |
| 78 |
|
| 79 |
if( worldRank == 0 ){ |
| 80 |
#endif |
| 81 |
|
| 82 |
// generate the force file name |
| 83 |
|
| 84 |
strcpy( fileName, "LJ_FF.frc" ); |
| 85 |
// fprintf( stderr,"Trying to open %s\n", fileName ); |
| 86 |
|
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// attempt to open the file in the current directory first. |
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|
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frcFile = fopen( fileName, "r" ); |
| 90 |
|
| 91 |
if( frcFile == NULL ){ |
| 92 |
|
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// next see if the force path enviorment variable is set |
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|
| 95 |
ffPath = getenv( ffPath_env ); |
| 96 |
if( ffPath == NULL ) { |
| 97 |
sprintf( painCave.errMsg, |
| 98 |
"Error opening the force field parameter file: %s\n" |
| 99 |
"Have you tried setting the FORCE_PARAM_PATH environment " |
| 100 |
"vairable?\n", |
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fileName ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
| 105 |
|
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|
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strcpy( temp, ffPath ); |
| 108 |
strcat( temp, "/" ); |
| 109 |
strcat( temp, fileName ); |
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strcpy( fileName, temp ); |
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|
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frcFile = fopen( fileName, "r" ); |
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|
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if( frcFile == NULL ){ |
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|
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sprintf( painCave.errMsg, |
| 117 |
"Error opening the force field parameter file: %s\n" |
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"Have you tried setting the FORCE_PARAM_PATH environment " |
| 119 |
"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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|
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#ifdef IS_MPI |
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} |
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|
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sprintf( checkPointMsg, "LJ_FF file opened sucessfully." ); |
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MPIcheckPoint(); |
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|
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#endif // is_mpi |
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} |
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|
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|
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LJ_FF::~LJ_FF(){ |
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|
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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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|
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fclose( frcFile ); |
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|
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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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|
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void LJ_FF::initializeAtoms( void ){ |
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|
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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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|
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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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|
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|
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void add( atomStruct &info ){ |
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|
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// check for duplicates |
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|
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if( !strcmp( info.name, name ) ){ |
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sprintf( simError.painCave, |
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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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|
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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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|
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|
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#ifdef IS_MPI |
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|
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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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|
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|
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#endif |
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|
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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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|
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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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|
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int i; |
| 220 |
int identNum; |
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|
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Atom** the_atoms; |
| 223 |
int nAtoms; |
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the_atoms = entry_plug->atoms; |
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nAtoms = entry_plug->n_atoms; |
| 226 |
|
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|
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#ifdef IS_MPI |
| 229 |
if( worldRank == 0 ){ |
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#endif |
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|
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// read in the atom types. |
| 233 |
|
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headAtomType = new LinkedType; |
| 235 |
|
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fastFoward( "AtomTypes", "initializeAtoms" ); |
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|
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// we are now at the AtomTypes section. |
| 239 |
|
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eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 241 |
lineNum++; |
| 242 |
|
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|
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// read a line, and start parseing out the atom types |
| 245 |
|
| 246 |
if( eof_test == NULL ){ |
| 247 |
sprintf( painCave.errMsg, |
| 248 |
"Error in reading Atoms from force file at line %d.\n", |
| 249 |
lineNum ); |
| 250 |
painCave.isFatal = 1; |
| 251 |
simError(); |
| 252 |
} |
| 253 |
|
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identNum = 1; |
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// stop reading at end of file, or at next section |
| 256 |
while( readLine[0] != '#' && eof_test != NULL ){ |
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|
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// toss comment lines |
| 259 |
if( readLine[0] != '!' ){ |
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|
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// the parser returns 0 if the line was blank |
| 262 |
if( parseAtomLJ( readLine, lineNum, info ) ){ |
| 263 |
info.ident = identNum; |
| 264 |
headAtomType->add( info );; |
| 265 |
identNum++; |
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} |
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} |
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eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 269 |
lineNum++; |
| 270 |
} |
| 271 |
|
| 272 |
#ifdef IS_MPI |
| 273 |
|
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// send out the linked list to all the other processes |
| 275 |
|
| 276 |
sprintf( checkPointMsg, |
| 277 |
"LJ_FF atom structures read successfully." ); |
| 278 |
MPIcheckPoint(); |
| 279 |
|
| 280 |
currentAtomType = headAtomType; |
| 281 |
while( currentAtomType != NULL ){ |
| 282 |
currentAtomType->duplicate( info ); |
| 283 |
sendFrcStruct( &info, mpiAtomStructType ); |
| 284 |
currentAtomType = currentAtomType->next; |
| 285 |
} |
| 286 |
info.last = 1; |
| 287 |
sendFrcStruct( &info, mpiAtomStructType ); |
| 288 |
|
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} |
| 290 |
|
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else{ |
| 292 |
|
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// listen for node 0 to send out the force params |
| 294 |
|
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MPIcheckPoint(); |
| 296 |
|
| 297 |
headAtomType = new LinkedType; |
| 298 |
recieveFrcStruct( &info, mpiAtomStructType ); |
| 299 |
while( !info.last ){ |
| 300 |
|
| 301 |
headAtomType->add( info ); |
| 302 |
recieveFrcStruct( &info, mpiAtomStructType ); |
| 303 |
} |
| 304 |
} |
| 305 |
#endif // is_mpi |
| 306 |
|
| 307 |
// call new A_types in fortran |
| 308 |
|
| 309 |
|
| 310 |
// initialize the atoms |
| 311 |
|
| 312 |
Atom* thisAtom; |
| 313 |
|
| 314 |
for( i=0; i<nAtoms; i++ ){ |
| 315 |
|
| 316 |
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
| 317 |
if( currentAtomType == NULL ){ |
| 318 |
sprintf( painCave.errMsg, |
| 319 |
"AtomType error, %s not found in force file.\n", |
| 320 |
the_atoms[i]->getType() ); |
| 321 |
painCave.isFatal = 1; |
| 322 |
simError(); |
| 323 |
} |
| 324 |
|
| 325 |
the_atoms[i]->setMass( currentAtomType->mass ); |
| 326 |
the_atoms[i]->setEpslon( currentAtomType->epslon ); |
| 327 |
the_atoms[i]->setSigma( currentAtomType->sigma ); |
| 328 |
the_atoms[i]->setIdent( currentAtomType->ident ); |
| 329 |
the_atoms[i]->setLJ(); |
| 330 |
} |
| 331 |
|
| 332 |
|
| 333 |
// clean up the memory |
| 334 |
|
| 335 |
delete headAtomType; |
| 336 |
|
| 337 |
#ifdef IS_MPI |
| 338 |
sprintf( checkPointMsg, "LJ_FF atoms initialized succesfully" ); |
| 339 |
MPIcheckPoint(); |
| 340 |
#endif // is_mpi |
| 341 |
|
| 342 |
} |
| 343 |
|
| 344 |
void LJ_FF::initializeBonds( bond_pair* the_bonds ){ |
| 345 |
|
| 346 |
if( entry_plug->n_bonds ){ |
| 347 |
sprintf( painCave.errMsg, |
| 348 |
"LJ_FF does not support bonds.\n" ); |
| 349 |
painCave.isFatal = 1; |
| 350 |
simError(); |
| 351 |
} |
| 352 |
#ifdef IS_MPI |
| 353 |
MPIcheckPoint(); |
| 354 |
#endif // is_mpi |
| 355 |
|
| 356 |
} |
| 357 |
|
| 358 |
void LJ_FF::initializeBends( bend_set* the_bends ){ |
| 359 |
|
| 360 |
if( entry_plug->n_bends ){ |
| 361 |
sprintf( painCave.errMsg, |
| 362 |
"LJ_FF does not support bends.\n" ); |
| 363 |
painCave.isFatal = 1; |
| 364 |
simError(); |
| 365 |
} |
| 366 |
#ifdef IS_MPI |
| 367 |
MPIcheckPoint(); |
| 368 |
#endif // is_mpi |
| 369 |
|
| 370 |
} |
| 371 |
|
| 372 |
void LJ_FF::initializeTorsions( torsion_set* the_torsions ){ |
| 373 |
|
| 374 |
if( entry_plug->n_torsions ){ |
| 375 |
sprintf( painCave.errMsg, |
| 376 |
"LJ_FF does not support torsions.\n" ); |
| 377 |
painCave.isFatal = 1; |
| 378 |
simError(); |
| 379 |
} |
| 380 |
#ifdef IS_MPI |
| 381 |
MPIcheckPoint(); |
| 382 |
#endif // is_mpi |
| 383 |
|
| 384 |
} |
| 385 |
|
| 386 |
|
| 387 |
void LJ_FF::fastForward( char* stopText, char* searchOwner ){ |
| 388 |
|
| 389 |
int foundText = 0; |
| 390 |
char* the_token; |
| 391 |
|
| 392 |
rewind( frcFile ); |
| 393 |
lineNum = 0; |
| 394 |
|
| 395 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 396 |
lineNum++; |
| 397 |
if( eof_test == NULL ){ |
| 398 |
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
| 399 |
" file is empty.\n", |
| 400 |
searchOwner ); |
| 401 |
painCave.isFatal = 1; |
| 402 |
simError(); |
| 403 |
} |
| 404 |
|
| 405 |
|
| 406 |
while( !foundText ){ |
| 407 |
while( eof_test != NULL && readLine[0] != '#' ){ |
| 408 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 409 |
lineNum++; |
| 410 |
} |
| 411 |
if( eof_test == NULL ){ |
| 412 |
sprintf( painCave.errMsg, |
| 413 |
"Error fast forwarding force file for %s at " |
| 414 |
"line %d: file ended unexpectedly.\n", |
| 415 |
searchOwner, |
| 416 |
lineNum ); |
| 417 |
painCave.isFatal = 1; |
| 418 |
simError(); |
| 419 |
} |
| 420 |
|
| 421 |
the_token = strtok( readLine, " ,;\t#\n" ); |
| 422 |
foundText = !strcmp( stopText, the_token ); |
| 423 |
|
| 424 |
if( !foundText ){ |
| 425 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 426 |
lineNum++; |
| 427 |
|
| 428 |
if( eof_test == NULL ){ |
| 429 |
sprintf( painCave.errMsg, |
| 430 |
"Error fast forwarding force file for %s at " |
| 431 |
"line %d: file ended unexpectedly.\n", |
| 432 |
searchOwner, |
| 433 |
lineNum ); |
| 434 |
painCave.isFatal = 1; |
| 435 |
simError(); |
| 436 |
} |
| 437 |
} |
| 438 |
} |
| 439 |
} |
| 440 |
|
| 441 |
|
| 442 |
|
| 443 |
int parseAtomLJ( char *lineBuffer, int lineNum, atomStruct &info ){ |
| 444 |
|
| 445 |
char* the_token; |
| 446 |
|
| 447 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
| 448 |
if( the_token != NULL ){ |
| 449 |
|
| 450 |
strcpy( info.name, the_token ); |
| 451 |
|
| 452 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 453 |
sprintf( painCave.errMsg, |
| 454 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 455 |
painCave.isFatal = 1; |
| 456 |
simError(); |
| 457 |
} |
| 458 |
|
| 459 |
info.mass = atof( the_token ); |
| 460 |
|
| 461 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 462 |
sprintf( painCave.errMsg, |
| 463 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 464 |
painCave.isFatal = 1; |
| 465 |
simError(); |
| 466 |
} |
| 467 |
|
| 468 |
info.epslon = atof( the_token ); |
| 469 |
|
| 470 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 471 |
sprintf( painCave.errMsg, |
| 472 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 473 |
painCave.isFatal = 1; |
| 474 |
simError(); |
| 475 |
} |
| 476 |
|
| 477 |
info.sigma = atof( the_token ); |
| 478 |
|
| 479 |
return 1; |
| 480 |
} |
| 481 |
else return 0; |
| 482 |
} |
