1 |
gezelter |
830 |
#define _FILE_OFFSET_BITS 64 |
2 |
mmeineke |
377 |
#include <iostream> |
3 |
gezelter |
829 |
#include <math.h> |
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mmeineke |
377 |
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5 |
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#include <stdio.h> |
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#include <stdlib.h> |
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#include <string.h> |
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#include <unistd.h> |
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#include <sys/types.h> |
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#include <sys/stat.h> |
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#include "ReadWrite.hpp" |
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#include "simError.h" |
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#ifdef IS_MPI |
16 |
gezelter |
417 |
#include <mpi.h> |
17 |
mmeineke |
377 |
#include "mpiSimulation.hpp" |
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chuckv |
436 |
#define TAKE_THIS_TAG_CHAR 0 |
19 |
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#define TAKE_THIS_TAG_INT 1 |
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21 |
mmeineke |
440 |
namespace initFile{ |
22 |
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void nodeZeroError( void ); |
23 |
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void anonymousNodeDie( void ); |
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} |
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chuckv |
436 |
|
26 |
mmeineke |
440 |
using namespace initFile; |
27 |
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28 |
mmeineke |
377 |
#endif // is_mpi |
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30 |
tim |
689 |
InitializeFromFile::InitializeFromFile( char *in_name ){ |
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mmeineke |
377 |
#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif |
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c_in_file = fopen(in_name, "r"); |
37 |
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if(c_in_file == NULL){ |
38 |
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sprintf(painCave.errMsg, |
39 |
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"Cannot open file: %s\n", in_name); |
40 |
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painCave.isFatal = 1; |
41 |
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simError(); |
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} |
43 |
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44 |
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strcpy( c_in_name, in_name); |
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#ifdef IS_MPI |
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} |
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strcpy( checkPointMsg, "Infile opened for reading successfully." ); |
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MPIcheckPoint(); |
49 |
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#endif |
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return; |
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} |
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53 |
tim |
689 |
InitializeFromFile::~InitializeFromFile( ){ |
54 |
mmeineke |
377 |
#ifdef IS_MPI |
55 |
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if (worldRank == 0) { |
56 |
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#endif |
57 |
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int error; |
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error = fclose( c_in_file ); |
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if( error ){ |
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sprintf( painCave.errMsg, |
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"Error closing %s\n", c_in_name ); |
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simError(); |
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} |
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#ifdef IS_MPI |
65 |
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} |
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strcpy( checkPointMsg, "Infile closed successfully." ); |
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MPIcheckPoint(); |
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#endif |
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return; |
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} |
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mmeineke |
641 |
void InitializeFromFile :: readInit( SimInfo* the_simnfo ){ |
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mmeineke |
377 |
|
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mmeineke |
787 |
int i, j; |
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#ifdef IS_MPI |
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int done, which_node, which_atom; // loop counter |
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#endif //is_mpi |
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mmeineke |
377 |
|
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const int BUFFERSIZE = 2000; // size of the read buffer |
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int n_atoms; // the number of atoms |
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char read_buffer[BUFFERSIZE]; //the line buffer for reading |
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char *eof_test; // ptr to see when we reach the end of the file |
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char *parseErr; |
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mmeineke |
787 |
|
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mmeineke |
644 |
double currTime; |
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mmeineke |
586 |
double boxMat[9]; |
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mmeineke |
590 |
double theBoxMat3[3][3]; |
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mmeineke |
377 |
|
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mmeineke |
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simnfo = the_simnfo; |
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mmeineke |
377 |
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#ifndef IS_MPI |
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
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if( eof_test == NULL ){ |
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sprintf( painCave.errMsg, |
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"InitializeFromFile error: error reading 1st line of \"%s\"\n", |
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c_in_name ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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n_atoms = atoi( read_buffer ); |
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mmeineke |
586 |
if( n_atoms != simnfo->n_atoms ){ |
109 |
mmeineke |
377 |
sprintf( painCave.errMsg, |
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"Initialize from File error. %s n_atoms, %d, " |
111 |
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"does not match the BASS file's n_atoms, %d.\n", |
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mmeineke |
586 |
c_in_name, n_atoms, simnfo->n_atoms ); |
113 |
mmeineke |
377 |
painCave.isFatal = 1; |
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simError(); |
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} |
116 |
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117 |
mmeineke |
586 |
//read the box mat from the comment line |
118 |
mmeineke |
377 |
|
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
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if(eof_test == NULL){ |
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sprintf( painCave.errMsg, |
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"error in reading commment in %s\n", c_in_name); |
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painCave.isFatal = 1; |
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simError(); |
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} |
126 |
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127 |
mmeineke |
644 |
parseErr = parseBoxLine( read_buffer, boxMat, currTime ); |
128 |
mmeineke |
586 |
if( parseErr != NULL ){ |
129 |
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strcpy( painCave.errMsg, parseErr ); |
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painCave.isFatal = 1; |
131 |
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simError(); |
132 |
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} |
133 |
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134 |
mmeineke |
590 |
for(i=0;i<3;i++) |
135 |
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for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
136 |
mmeineke |
586 |
|
137 |
mmeineke |
590 |
simnfo->setBoxM( theBoxMat3 ); |
138 |
mmeineke |
644 |
simnfo->setTime( currTime ); |
139 |
mmeineke |
586 |
|
140 |
mmeineke |
590 |
|
141 |
mmeineke |
377 |
for( i=0; i < n_atoms; i++){ |
142 |
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143 |
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
144 |
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if(eof_test == NULL){ |
145 |
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sprintf(painCave.errMsg, |
146 |
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"error in reading file %s\n" |
147 |
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"natoms = %d; index = %d\n" |
148 |
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"error reading the line from the file.\n", |
149 |
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c_in_name, n_atoms, i ); |
150 |
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painCave.isFatal = 1; |
151 |
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simError(); |
152 |
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} |
153 |
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154 |
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155 |
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parseErr = parseDumpLine( read_buffer, i ); |
156 |
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if( parseErr != NULL ){ |
157 |
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strcpy( painCave.errMsg, parseErr ); |
158 |
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painCave.isFatal = 1; |
159 |
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simError(); |
160 |
mmeineke |
586 |
} |
161 |
mmeineke |
377 |
} |
162 |
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163 |
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164 |
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// MPI Section of code.......... |
165 |
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#else //IS_MPI |
166 |
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167 |
chuckv |
436 |
// first thing first, suspend fatalities. |
168 |
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painCave.isEventLoop = 1; |
169 |
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170 |
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int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
171 |
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int haveError; |
172 |
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173 |
mmeineke |
447 |
MPI_Status istatus; |
174 |
gezelter |
417 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
175 |
mmeineke |
377 |
|
176 |
chuckv |
436 |
|
177 |
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haveError = 0; |
178 |
mmeineke |
377 |
if (worldRank == 0) { |
179 |
chuckv |
436 |
|
180 |
mmeineke |
377 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
181 |
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if( eof_test == NULL ){ |
182 |
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sprintf( painCave.errMsg, |
183 |
mmeineke |
787 |
"Error reading 1st line of %s \n ",c_in_name); |
184 |
chuckv |
436 |
haveError = 1; |
185 |
mmeineke |
377 |
simError(); |
186 |
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} |
187 |
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188 |
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n_atoms = atoi( read_buffer ); |
189 |
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190 |
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// Check to see that the number of atoms in the intial configuration file is the |
191 |
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// same as declared in simBass. |
192 |
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193 |
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if( n_atoms != mpiSim->getTotAtoms() ){ |
194 |
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sprintf( painCave.errMsg, |
195 |
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"Initialize from File error. %s n_atoms, %d, " |
196 |
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"does not match the BASS file's n_atoms, %d.\n", |
197 |
mmeineke |
586 |
c_in_name, n_atoms, simnfo->n_atoms ); |
198 |
chuckv |
436 |
haveError= 1; |
199 |
mmeineke |
377 |
simError(); |
200 |
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} |
201 |
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202 |
mmeineke |
586 |
//read the boxMat from the comment line |
203 |
mmeineke |
377 |
|
204 |
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
205 |
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if(eof_test == NULL){ |
206 |
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sprintf( painCave.errMsg, |
207 |
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"error in reading commment in %s\n", c_in_name); |
208 |
mmeineke |
586 |
haveError = 1; |
209 |
mmeineke |
377 |
simError(); |
210 |
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} |
211 |
mmeineke |
586 |
|
212 |
mmeineke |
644 |
parseErr = parseBoxLine( read_buffer, boxMat, currTime ); |
213 |
mmeineke |
586 |
if( parseErr != NULL ){ |
214 |
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strcpy( painCave.errMsg, parseErr ); |
215 |
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haveError = 1; |
216 |
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simError(); |
217 |
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} |
218 |
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219 |
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MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
220 |
mmeineke |
644 |
MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
221 |
mmeineke |
377 |
|
222 |
chuckv |
436 |
if(haveError) nodeZeroError(); |
223 |
gezelter |
417 |
|
224 |
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for (i=0 ; i < mpiSim->getTotAtoms(); i++) { |
225 |
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226 |
mmeineke |
377 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
227 |
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if(eof_test == NULL){ |
228 |
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sprintf(painCave.errMsg, |
229 |
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"error in reading file %s\n" |
230 |
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"natoms = %d; index = %d\n" |
231 |
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"error reading the line from the file.\n", |
232 |
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c_in_name, n_atoms, i ); |
233 |
chuckv |
436 |
haveError= 1; |
234 |
mmeineke |
377 |
simError(); |
235 |
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} |
236 |
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237 |
chuckv |
436 |
if(haveError) nodeZeroError(); |
238 |
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239 |
gezelter |
417 |
// Get the Node number which wants this atom: |
240 |
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which_node = AtomToProcMap[i]; |
241 |
chuckv |
436 |
if (which_node == 0) { |
242 |
gezelter |
417 |
parseErr = parseDumpLine( read_buffer, i ); |
243 |
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if( parseErr != NULL ){ |
244 |
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strcpy( painCave.errMsg, parseErr ); |
245 |
chuckv |
436 |
haveError = 1; |
246 |
gezelter |
417 |
simError(); |
247 |
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} |
248 |
chuckv |
436 |
if(haveError) nodeZeroError(); |
249 |
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} |
250 |
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251 |
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else { |
252 |
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253 |
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myStatus = 1; |
254 |
mmeineke |
447 |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
255 |
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TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
256 |
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MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
257 |
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TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
258 |
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MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
259 |
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MPI_COMM_WORLD); |
260 |
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MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
261 |
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MPI_COMM_WORLD, &istatus); |
262 |
chuckv |
436 |
|
263 |
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if(!myStatus) nodeZeroError(); |
264 |
mmeineke |
377 |
} |
265 |
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} |
266 |
chuckv |
436 |
myStatus = -1; |
267 |
gezelter |
417 |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
268 |
mmeineke |
447 |
MPI_Send( &myStatus, 1, MPI_INT, j, |
269 |
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TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
270 |
gezelter |
417 |
} |
271 |
gezelter |
419 |
|
272 |
gezelter |
417 |
} else { |
273 |
gezelter |
419 |
|
274 |
mmeineke |
586 |
MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
275 |
mmeineke |
644 |
MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
276 |
mmeineke |
586 |
|
277 |
gezelter |
417 |
done = 0; |
278 |
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while (!done) { |
279 |
chuckv |
436 |
|
280 |
mmeineke |
447 |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
281 |
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TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
282 |
chuckv |
436 |
|
283 |
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if(!myStatus) anonymousNodeDie(); |
284 |
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285 |
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if(myStatus < 0) break; |
286 |
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287 |
mmeineke |
447 |
MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
288 |
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TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
289 |
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MPI_Recv(&which_atom, 1, MPI_INT, 0, |
290 |
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TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
291 |
chuckv |
436 |
|
292 |
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myStatus = 1; |
293 |
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parseErr = parseDumpLine( read_buffer, which_atom ); |
294 |
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if( parseErr != NULL ){ |
295 |
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strcpy( painCave.errMsg, parseErr ); |
296 |
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myStatus = 0;; |
297 |
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simError(); |
298 |
mmeineke |
377 |
} |
299 |
chuckv |
436 |
|
300 |
mmeineke |
447 |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
301 |
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TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
302 |
chuckv |
436 |
|
303 |
mmeineke |
377 |
} |
304 |
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} |
305 |
chuckv |
436 |
|
306 |
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// last thing last, enable fatalities. |
307 |
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painCave.isEventLoop = 0; |
308 |
mmeineke |
586 |
|
309 |
mmeineke |
590 |
for(i=0;i<3;i++) |
310 |
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for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
311 |
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312 |
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simnfo->setBoxM( theBoxMat3 ); |
313 |
mmeineke |
644 |
simnfo->setTime( currTime ); |
314 |
mmeineke |
590 |
|
315 |
chuckv |
436 |
|
316 |
mmeineke |
377 |
#endif |
317 |
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} |
318 |
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|
319 |
gezelter |
419 |
char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){ |
320 |
mmeineke |
377 |
|
321 |
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char *foo; // the pointer to the current string token |
322 |
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|
323 |
mmeineke |
670 |
double pos[3]; // position place holders |
324 |
|
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double vel[3]; // velocity placeholders |
325 |
mmeineke |
377 |
double q[4]; // the quaternions |
326 |
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double jx, jy, jz; // angular velocity placeholders; |
327 |
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double qSqr, qLength; // needed to normalize the quaternion vector. |
328 |
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|
329 |
mmeineke |
586 |
Atom **atoms = simnfo->atoms; |
330 |
mmeineke |
377 |
DirectionalAtom* dAtom; |
331 |
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|
332 |
mmeineke |
787 |
int n_atoms, atomIndex; |
333 |
mmeineke |
377 |
|
334 |
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#ifdef IS_MPI |
335 |
mmeineke |
787 |
int j; |
336 |
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|
337 |
mmeineke |
377 |
n_atoms = mpiSim->getTotAtoms(); |
338 |
gezelter |
419 |
atomIndex=-1; |
339 |
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for (j=0; j < mpiSim->getMyNlocal(); j++) { |
340 |
|
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if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j; |
341 |
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} |
342 |
|
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if (atomIndex == -1) { |
343 |
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sprintf( painCave.errMsg, |
344 |
|
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"Initialize from file error. Atom at index %d " |
345 |
|
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"in file %s does not exist on processor %d .\n", |
346 |
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globalIndex, c_in_name, mpiSim->getMyNode() ); |
347 |
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return strdup( painCave.errMsg ); |
348 |
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} |
349 |
mmeineke |
377 |
#else |
350 |
mmeineke |
586 |
n_atoms = simnfo->n_atoms; |
351 |
gezelter |
419 |
atomIndex = globalIndex; |
352 |
mmeineke |
377 |
#endif // is_mpi |
353 |
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|
354 |
|
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// set the string tokenizer |
355 |
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|
356 |
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foo = strtok(readLine, " ,;\t"); |
357 |
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|
358 |
|
|
// check the atom name to the current atom |
359 |
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|
360 |
|
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if( strcmp( foo, atoms[atomIndex]->getType() ) ){ |
361 |
|
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sprintf( painCave.errMsg, |
362 |
|
|
"Initialize from file error. Atom %s at index %d " |
363 |
|
|
"in file %s does not" |
364 |
|
|
" match the BASS atom %s.\n", |
365 |
|
|
foo, atomIndex, c_in_name, atoms[atomIndex]->getType() ); |
366 |
|
|
return strdup( painCave.errMsg ); |
367 |
|
|
} |
368 |
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|
369 |
|
|
// get the positions |
370 |
|
|
|
371 |
|
|
foo = strtok(NULL, " ,;\t"); |
372 |
|
|
if(foo == NULL){ |
373 |
|
|
sprintf( painCave.errMsg, |
374 |
|
|
"error in reading postition x from %s\n" |
375 |
|
|
"natoms = %d, index = %d\n", |
376 |
|
|
c_in_name, n_atoms, atomIndex ); |
377 |
|
|
return strdup( painCave.errMsg ); |
378 |
|
|
} |
379 |
mmeineke |
670 |
pos[0] = atof( foo ); |
380 |
mmeineke |
377 |
|
381 |
|
|
foo = strtok(NULL, " ,;\t"); |
382 |
|
|
if(foo == NULL){ |
383 |
|
|
sprintf( painCave.errMsg, |
384 |
|
|
"error in reading postition y from %s\n" |
385 |
|
|
"natoms = %d, index = %d\n", |
386 |
|
|
c_in_name, n_atoms, atomIndex ); |
387 |
|
|
return strdup( painCave.errMsg ); |
388 |
|
|
} |
389 |
mmeineke |
670 |
pos[1] = atof( foo ); |
390 |
mmeineke |
377 |
|
391 |
|
|
foo = strtok(NULL, " ,;\t"); |
392 |
|
|
if(foo == NULL){ |
393 |
|
|
sprintf( painCave.errMsg, |
394 |
|
|
"error in reading postition z from %s\n" |
395 |
|
|
"natoms = %d, index = %d\n", |
396 |
|
|
c_in_name, n_atoms, atomIndex ); |
397 |
|
|
return strdup( painCave.errMsg ); |
398 |
|
|
} |
399 |
mmeineke |
670 |
pos[2] = atof( foo ); |
400 |
mmeineke |
377 |
|
401 |
|
|
|
402 |
|
|
// get the velocities |
403 |
|
|
|
404 |
|
|
foo = strtok(NULL, " ,;\t"); |
405 |
|
|
if(foo == NULL){ |
406 |
|
|
sprintf( painCave.errMsg, |
407 |
|
|
"error in reading velocity x from %s\n" |
408 |
|
|
"natoms = %d, index = %d\n", |
409 |
|
|
c_in_name, n_atoms, atomIndex ); |
410 |
|
|
return strdup( painCave.errMsg ); |
411 |
|
|
} |
412 |
mmeineke |
670 |
vel[0] = atof( foo ); |
413 |
mmeineke |
377 |
|
414 |
|
|
foo = strtok(NULL, " ,;\t"); |
415 |
|
|
if(foo == NULL){ |
416 |
|
|
sprintf( painCave.errMsg, |
417 |
|
|
"error in reading velocity y from %s\n" |
418 |
|
|
"natoms = %d, index = %d\n", |
419 |
|
|
c_in_name, n_atoms, atomIndex ); |
420 |
|
|
return strdup( painCave.errMsg ); |
421 |
|
|
} |
422 |
mmeineke |
670 |
vel[1] = atof( foo ); |
423 |
mmeineke |
377 |
|
424 |
|
|
foo = strtok(NULL, " ,;\t"); |
425 |
|
|
if(foo == NULL){ |
426 |
|
|
sprintf( painCave.errMsg, |
427 |
|
|
"error in reading velocity z from %s\n" |
428 |
|
|
"natoms = %d, index = %d\n", |
429 |
|
|
c_in_name, n_atoms, atomIndex ); |
430 |
|
|
return strdup( painCave.errMsg ); |
431 |
|
|
} |
432 |
mmeineke |
670 |
vel[2] = atof( foo ); |
433 |
mmeineke |
377 |
|
434 |
|
|
|
435 |
|
|
// get the quaternions |
436 |
|
|
|
437 |
|
|
if( atoms[atomIndex]->isDirectional() ){ |
438 |
|
|
|
439 |
|
|
foo = strtok(NULL, " ,;\t"); |
440 |
|
|
if(foo == NULL){ |
441 |
|
|
sprintf(painCave.errMsg, |
442 |
|
|
"error in reading quaternion 0 from %s\n" |
443 |
|
|
"natoms = %d, index = %d\n", |
444 |
|
|
c_in_name, n_atoms, atomIndex ); |
445 |
|
|
return strdup( painCave.errMsg ); |
446 |
|
|
} |
447 |
|
|
q[0] = atof( foo ); |
448 |
|
|
|
449 |
|
|
foo = strtok(NULL, " ,;\t"); |
450 |
|
|
if(foo == NULL){ |
451 |
|
|
sprintf( painCave.errMsg, |
452 |
|
|
"error in reading quaternion 1 from %s\n" |
453 |
|
|
"natoms = %d, index = %d\n", |
454 |
|
|
c_in_name, n_atoms, atomIndex ); |
455 |
|
|
return strdup( painCave.errMsg ); |
456 |
|
|
} |
457 |
|
|
q[1] = atof( foo ); |
458 |
|
|
|
459 |
|
|
foo = strtok(NULL, " ,;\t"); |
460 |
|
|
if(foo == NULL){ |
461 |
|
|
sprintf( painCave.errMsg, |
462 |
|
|
"error in reading quaternion 2 from %s\n" |
463 |
|
|
"natoms = %d, index = %d\n", |
464 |
|
|
c_in_name, n_atoms, atomIndex ); |
465 |
|
|
return strdup( painCave.errMsg ); |
466 |
|
|
} |
467 |
|
|
q[2] = atof( foo ); |
468 |
|
|
|
469 |
|
|
foo = strtok(NULL, " ,;\t"); |
470 |
|
|
if(foo == NULL){ |
471 |
|
|
sprintf( painCave.errMsg, |
472 |
|
|
"error in reading quaternion 3 from %s\n" |
473 |
|
|
"natoms = %d, index = %d\n", |
474 |
|
|
c_in_name, n_atoms, atomIndex ); |
475 |
|
|
return strdup( painCave.errMsg ); |
476 |
|
|
} |
477 |
|
|
q[3] = atof( foo ); |
478 |
|
|
|
479 |
|
|
// get the angular velocities |
480 |
|
|
|
481 |
|
|
foo = strtok(NULL, " ,;\t"); |
482 |
|
|
if(foo == NULL){ |
483 |
|
|
sprintf( painCave.errMsg, |
484 |
|
|
"error in reading angular momentum jx from %s\n" |
485 |
|
|
"natoms = %d, index = %d\n", |
486 |
|
|
c_in_name, n_atoms, atomIndex ); |
487 |
|
|
return strdup( painCave.errMsg ); |
488 |
|
|
} |
489 |
|
|
jx = atof( foo ); |
490 |
|
|
|
491 |
|
|
foo = strtok(NULL, " ,;\t"); |
492 |
|
|
if(foo == NULL){ |
493 |
|
|
sprintf( painCave.errMsg, |
494 |
|
|
"error in reading angular momentum jy from %s\n" |
495 |
|
|
"natoms = %d, index = %d\n", |
496 |
|
|
c_in_name, n_atoms, atomIndex ); |
497 |
|
|
return strdup( painCave.errMsg ); |
498 |
|
|
} |
499 |
|
|
jy = atof(foo ); |
500 |
|
|
|
501 |
|
|
foo = strtok(NULL, " ,;\t"); |
502 |
|
|
if(foo == NULL){ |
503 |
|
|
sprintf( painCave.errMsg, |
504 |
|
|
"error in reading angular momentum jz from %s\n" |
505 |
|
|
"natoms = %d, index = %d\n", |
506 |
|
|
c_in_name, n_atoms, atomIndex ); |
507 |
|
|
return strdup( painCave.errMsg ); |
508 |
|
|
} |
509 |
|
|
jz = atof( foo ); |
510 |
|
|
|
511 |
|
|
dAtom = ( DirectionalAtom* )atoms[atomIndex]; |
512 |
|
|
|
513 |
|
|
// check that the quaternion vector is normalized |
514 |
|
|
|
515 |
|
|
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
516 |
|
|
|
517 |
|
|
qLength = sqrt( qSqr ); |
518 |
|
|
q[0] = q[0] / qLength; |
519 |
|
|
q[1] = q[1] / qLength; |
520 |
|
|
q[2] = q[2] / qLength; |
521 |
|
|
q[3] = q[3] / qLength; |
522 |
|
|
|
523 |
|
|
dAtom->setQ( q ); |
524 |
|
|
|
525 |
|
|
// add the angular velocities |
526 |
|
|
|
527 |
|
|
dAtom->setJx( jx ); |
528 |
|
|
dAtom->setJy( jy ); |
529 |
|
|
dAtom->setJz( jz ); |
530 |
|
|
} |
531 |
|
|
|
532 |
|
|
// add the positions and velocities to the atom |
533 |
|
|
|
534 |
mmeineke |
670 |
atoms[atomIndex]->setPos( pos ); |
535 |
|
|
atoms[atomIndex]->setVel( vel ); |
536 |
mmeineke |
377 |
|
537 |
|
|
return NULL; |
538 |
|
|
} |
539 |
chuckv |
436 |
|
540 |
|
|
|
541 |
mmeineke |
644 |
char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9], |
542 |
|
|
double &time ){ |
543 |
mmeineke |
586 |
|
544 |
|
|
char *foo; // the pointer to the current string token |
545 |
|
|
|
546 |
|
|
// set the string tokenizer |
547 |
|
|
|
548 |
|
|
foo = strtok(readLine, " ,;\t"); |
549 |
mmeineke |
641 |
// set the timeToken. |
550 |
mmeineke |
586 |
|
551 |
mmeineke |
641 |
if(foo == NULL){ |
552 |
|
|
sprintf( painCave.errMsg, |
553 |
|
|
"error in reading Time from %s\n", |
554 |
|
|
c_in_name ); |
555 |
|
|
return strdup( painCave.errMsg ); |
556 |
|
|
} |
557 |
mmeineke |
644 |
time = atof( foo ); |
558 |
mmeineke |
586 |
|
559 |
|
|
// get the Hx vector |
560 |
|
|
|
561 |
|
|
foo = strtok(NULL, " ,;\t"); |
562 |
|
|
if(foo == NULL){ |
563 |
|
|
sprintf( painCave.errMsg, |
564 |
|
|
"error in reading Hx[0] from %s\n", |
565 |
|
|
c_in_name ); |
566 |
|
|
return strdup( painCave.errMsg ); |
567 |
|
|
} |
568 |
|
|
boxMat[0] = atof( foo ); |
569 |
|
|
|
570 |
|
|
foo = strtok(NULL, " ,;\t"); |
571 |
|
|
if(foo == NULL){ |
572 |
|
|
sprintf( painCave.errMsg, |
573 |
|
|
"error in reading Hx[1] from %s\n", |
574 |
|
|
c_in_name ); |
575 |
|
|
return strdup( painCave.errMsg ); |
576 |
|
|
} |
577 |
|
|
boxMat[1] = atof( foo ); |
578 |
|
|
|
579 |
|
|
foo = strtok(NULL, " ,;\t"); |
580 |
|
|
if(foo == NULL){ |
581 |
|
|
sprintf( painCave.errMsg, |
582 |
|
|
"error in reading Hx[2] from %s\n", |
583 |
|
|
c_in_name ); |
584 |
|
|
return strdup( painCave.errMsg ); |
585 |
|
|
} |
586 |
|
|
boxMat[2] = atof( foo ); |
587 |
|
|
|
588 |
|
|
// get the Hy vector |
589 |
|
|
|
590 |
|
|
foo = strtok(NULL, " ,;\t"); |
591 |
|
|
if(foo == NULL){ |
592 |
|
|
sprintf( painCave.errMsg, |
593 |
|
|
"error in reading Hy[0] from %s\n", |
594 |
|
|
c_in_name ); |
595 |
|
|
return strdup( painCave.errMsg ); |
596 |
|
|
} |
597 |
|
|
boxMat[3] = atof( foo ); |
598 |
|
|
|
599 |
|
|
foo = strtok(NULL, " ,;\t"); |
600 |
|
|
if(foo == NULL){ |
601 |
|
|
sprintf( painCave.errMsg, |
602 |
|
|
"error in reading Hy[1] from %s\n", |
603 |
|
|
c_in_name ); |
604 |
|
|
return strdup( painCave.errMsg ); |
605 |
|
|
} |
606 |
|
|
boxMat[4] = atof( foo ); |
607 |
|
|
|
608 |
|
|
foo = strtok(NULL, " ,;\t"); |
609 |
|
|
if(foo == NULL){ |
610 |
|
|
sprintf( painCave.errMsg, |
611 |
|
|
"error in reading Hy[2] from %s\n", |
612 |
|
|
c_in_name ); |
613 |
|
|
return strdup( painCave.errMsg ); |
614 |
|
|
} |
615 |
|
|
boxMat[5] = atof( foo ); |
616 |
|
|
|
617 |
|
|
// get the Hz vector |
618 |
|
|
|
619 |
|
|
foo = strtok(NULL, " ,;\t"); |
620 |
|
|
if(foo == NULL){ |
621 |
|
|
sprintf( painCave.errMsg, |
622 |
|
|
"error in reading Hz[0] from %s\n", |
623 |
|
|
c_in_name ); |
624 |
|
|
return strdup( painCave.errMsg ); |
625 |
|
|
} |
626 |
|
|
boxMat[6] = atof( foo ); |
627 |
|
|
|
628 |
|
|
foo = strtok(NULL, " ,;\t"); |
629 |
|
|
if(foo == NULL){ |
630 |
|
|
sprintf( painCave.errMsg, |
631 |
|
|
"error in reading Hz[1] from %s\n", |
632 |
|
|
c_in_name ); |
633 |
|
|
return strdup( painCave.errMsg ); |
634 |
|
|
} |
635 |
|
|
boxMat[7] = atof( foo ); |
636 |
|
|
|
637 |
|
|
foo = strtok(NULL, " ,;\t"); |
638 |
|
|
if(foo == NULL){ |
639 |
|
|
sprintf( painCave.errMsg, |
640 |
|
|
"error in reading Hz[2] from %s\n", |
641 |
|
|
c_in_name ); |
642 |
|
|
return strdup( painCave.errMsg ); |
643 |
|
|
} |
644 |
|
|
boxMat[8] = atof( foo ); |
645 |
|
|
|
646 |
|
|
return NULL; |
647 |
|
|
} |
648 |
|
|
|
649 |
|
|
|
650 |
chuckv |
436 |
#ifdef IS_MPI |
651 |
|
|
|
652 |
|
|
// a couple of functions to let us escape the read loop |
653 |
|
|
|
654 |
mmeineke |
440 |
void initFile::nodeZeroError( void ){ |
655 |
chuckv |
436 |
int j, myStatus; |
656 |
|
|
|
657 |
|
|
myStatus = 0; |
658 |
|
|
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
659 |
mmeineke |
447 |
MPI_Send( &myStatus, 1, MPI_INT, j, |
660 |
|
|
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
661 |
chuckv |
436 |
} |
662 |
|
|
|
663 |
|
|
|
664 |
|
|
MPI_Finalize(); |
665 |
|
|
exit (0); |
666 |
|
|
|
667 |
|
|
} |
668 |
|
|
|
669 |
mmeineke |
440 |
void initFile::anonymousNodeDie( void ){ |
670 |
chuckv |
436 |
|
671 |
|
|
MPI_Finalize(); |
672 |
|
|
exit (0); |
673 |
|
|
} |
674 |
|
|
|
675 |
|
|
#endif //is_mpi |