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#define _FILE_OFFSET_BITS 64 |
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#include <iostream> |
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#include <cmath> |
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#include <math.h> |
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#include <stdio.h> |
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#include <stdlib.h> |
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#endif // is_mpi |
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InitializeFromFile :: InitializeFromFile( char *in_name ){ |
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InitializeFromFile::InitializeFromFile( char *in_name ){ |
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|
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif |
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return; |
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} |
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InitializeFromFile :: ~InitializeFromFile( ){ |
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InitializeFromFile::~InitializeFromFile( ){ |
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif |
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} |
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void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){ |
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void InitializeFromFile :: readInit( SimInfo* the_simnfo ){ |
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int i, j, done, which_node, which_atom; // loop counter |
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int i, j; |
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|
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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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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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#ifdef IS_MPI |
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char send_buffer[BUFFERSIZE]; |
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#endif |
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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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int procIndex; |
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entry_plug = the_entry_plug; |
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double currTime; |
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double boxMat[9]; |
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double theBoxMat3[3][3]; |
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simnfo = the_simnfo; |
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|
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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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n_atoms = atoi( read_buffer ); |
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Atom **atoms = entry_plug->atoms; |
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DirectionalAtom* dAtom; |
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|
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if( n_atoms != entry_plug->n_atoms ){ |
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if( n_atoms != simnfo->n_atoms ){ |
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sprintf( painCave.errMsg, |
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"Initialize from File error. %s n_atoms, %d, " |
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"does not match the BASS file's n_atoms, %d.\n", |
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c_in_name, n_atoms, entry_plug->n_atoms ); |
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c_in_name, n_atoms, simnfo->n_atoms ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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//read and toss the comment line |
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//read the box mat from the comment line |
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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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simError(); |
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} |
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parseErr = parseBoxLine( read_buffer, boxMat, currTime ); |
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if( parseErr != NULL ){ |
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strcpy( painCave.errMsg, parseErr ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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for(i=0;i<3;i++) |
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for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
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|
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simnfo->setBoxM( theBoxMat3 ); |
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simnfo->setTime( currTime ); |
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|
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|
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for( i=0; i < n_atoms; i++){ |
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
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strcpy( painCave.errMsg, parseErr ); |
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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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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 reading 1st line of %d \n ",c_in_name); |
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"Error reading 1st line of %s \n ",c_in_name); |
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haveError = 1; |
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simError(); |
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} |
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n_atoms = atoi( read_buffer ); |
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Atom **atoms = entry_plug->atoms; |
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DirectionalAtom* dAtom; |
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|
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// Check to see that the number of atoms in the intial configuration file is the |
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// same as declared in simBass. |
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sprintf( painCave.errMsg, |
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"Initialize from File error. %s n_atoms, %d, " |
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"does not match the BASS file's n_atoms, %d.\n", |
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c_in_name, n_atoms, entry_plug->n_atoms ); |
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c_in_name, n_atoms, simnfo->n_atoms ); |
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haveError= 1; |
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simError(); |
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} |
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//read and toss the comment line |
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//read the boxMat from the comment line |
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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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haveError= 1; |
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haveError = 1; |
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simError(); |
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} |
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|
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parseErr = parseBoxLine( read_buffer, boxMat, currTime ); |
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if( parseErr != NULL ){ |
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strcpy( painCave.errMsg, parseErr ); |
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haveError = 1; |
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simError(); |
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} |
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|
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MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
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MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
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if(haveError) nodeZeroError(); |
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} else { |
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MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
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MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
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|
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done = 0; |
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while (!done) { |
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// last thing last, enable fatalities. |
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painCave.isEventLoop = 0; |
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|
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for(i=0;i<3;i++) |
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for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
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|
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simnfo->setBoxM( theBoxMat3 ); |
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simnfo->setTime( currTime ); |
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|
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#endif |
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} |
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char *foo; // the pointer to the current string token |
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double rx, ry, rz; // position place holders |
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double vx, vy, vz; // velocity placeholders |
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double pos[3]; // position place holders |
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double vel[3]; // velocity placeholders |
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double q[4]; // the quaternions |
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double jx, jy, jz; // angular velocity placeholders; |
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double qSqr, qLength; // needed to normalize the quaternion vector. |
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Atom **atoms = entry_plug->atoms; |
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Atom **atoms = simnfo->atoms; |
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DirectionalAtom* dAtom; |
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int j, n_atoms, atomIndex; |
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> |
int n_atoms, atomIndex; |
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|
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#ifdef IS_MPI |
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int j; |
336 |
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|
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n_atoms = mpiSim->getTotAtoms(); |
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atomIndex=-1; |
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for (j=0; j < mpiSim->getMyNlocal(); j++) { |
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return strdup( painCave.errMsg ); |
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} |
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#else |
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n_atoms = entry_plug->n_atoms; |
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> |
n_atoms = simnfo->n_atoms; |
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atomIndex = globalIndex; |
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#endif // is_mpi |
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c_in_name, n_atoms, atomIndex ); |
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return strdup( painCave.errMsg ); |
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} |
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rx = atof( foo ); |
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> |
pos[0] = atof( foo ); |
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|
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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c_in_name, n_atoms, atomIndex ); |
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return strdup( painCave.errMsg ); |
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} |
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ry = atof( foo ); |
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> |
pos[1] = atof( foo ); |
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|
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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c_in_name, n_atoms, atomIndex ); |
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return strdup( painCave.errMsg ); |
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} |
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rz = atof( foo ); |
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> |
pos[2] = atof( foo ); |
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// get the velocities |
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c_in_name, n_atoms, atomIndex ); |
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return strdup( painCave.errMsg ); |
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} |
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< |
vx = atof( foo ); |
412 |
> |
vel[0] = atof( foo ); |
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|
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foo = strtok(NULL, " ,;\t"); |
415 |
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if(foo == NULL){ |
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c_in_name, n_atoms, atomIndex ); |
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return strdup( painCave.errMsg ); |
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} |
422 |
< |
vy = atof( foo ); |
422 |
> |
vel[1] = atof( foo ); |
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|
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foo = strtok(NULL, " ,;\t"); |
425 |
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if(foo == NULL){ |
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c_in_name, n_atoms, atomIndex ); |
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return strdup( painCave.errMsg ); |
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} |
432 |
< |
vz = atof( foo ); |
432 |
> |
vel[2] = atof( foo ); |
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|
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|
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// get the quaternions |
531 |
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|
532 |
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// add the positions and velocities to the atom |
533 |
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|
534 |
< |
atoms[atomIndex]->setX( rx ); |
535 |
< |
atoms[atomIndex]->setY( ry ); |
500 |
< |
atoms[atomIndex]->setZ( rz ); |
501 |
< |
|
502 |
< |
atoms[atomIndex]->set_vx( vx ); |
503 |
< |
atoms[atomIndex]->set_vy( vy ); |
504 |
< |
atoms[atomIndex]->set_vz( vz ); |
534 |
> |
atoms[atomIndex]->setPos( pos ); |
535 |
> |
atoms[atomIndex]->setVel( vel ); |
536 |
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|
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return NULL; |
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} |
539 |
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|
540 |
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|
541 |
+ |
char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9], |
542 |
+ |
double &time ){ |
543 |
+ |
|
544 |
+ |
char *foo; // the pointer to the current string token |
545 |
+ |
|
546 |
+ |
// set the string tokenizer |
547 |
+ |
|
548 |
+ |
foo = strtok(readLine, " ,;\t"); |
549 |
+ |
// set the timeToken. |
550 |
+ |
|
551 |
+ |
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 |
+ |
time = atof( foo ); |
558 |
+ |
|
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 |
|
#ifdef IS_MPI |
651 |
|
|
652 |
|
// a couple of functions to let us escape the read loop |