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mmeineke |
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#include <iostream> |
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#include <cmath> |
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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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mmeineke |
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#include "simError.h" |
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mmeineke |
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InitializeFromFile :: InitializeFromFile( char *in_name ){ |
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chuckv |
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif |
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mmeineke |
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c_in_file = fopen(in_name, "r"); |
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if(c_in_file == NULL){ |
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mmeineke |
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sprintf(painCave.errMsg, |
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"Cannot open file: %s\n", in_name); |
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painCave.isFatal = 1; |
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simError(); |
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mmeineke |
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} |
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strcpy( c_in_name, in_name); |
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chuckv |
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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(); |
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#endif |
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mmeineke |
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return; |
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} |
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InitializeFromFile :: ~InitializeFromFile( ){ |
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chuckv |
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif |
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mmeineke |
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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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mmeineke |
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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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mmeineke |
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} |
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chuckv |
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#ifdef IS_MPI |
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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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mmeineke |
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return; |
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} |
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chuckv |
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void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){ |
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mmeineke |
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int i; // loop counter |
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int n_atoms; // the number of atoms |
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char read_buffer[2000]; //the line buffer for reading |
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chuckv |
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#ifdef IS_MPI |
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char send_buffer[2000]; |
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#endif |
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mmeineke |
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char *eof_test; // ptr to see when we reach the end of the file |
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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 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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chuckv |
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entry_plug = the_entry_plug |
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#ifndef IS_MPI |
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mmeineke |
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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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std::cerr << "error reading 1st line of" << c_in_name << "\n"; |
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} |
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(void)sscanf(read_buffer, "%d", &n_atoms); |
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Atom **atoms = entry_plug->atoms; |
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DirectionalAtom* dAtom; |
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if( n_atoms != entry_plug->n_atoms ){ |
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mmeineke |
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sprintf( painCave.errMsg, |
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mmeineke |
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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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mmeineke |
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painCave.isFatal = 1; |
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simError(); |
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mmeineke |
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} |
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//read and toss 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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mmeineke |
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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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mmeineke |
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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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if(eof_test == NULL){ |
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mmeineke |
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sprintf(painCave.errMsg, |
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"error in reading file %s\n" |
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"natoms = %d; index = %d\n" |
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"error reading the line from the file.\n", |
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c_in_name, n_atoms, i ); |
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painCave.isFatal = 1; |
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simError(); |
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mmeineke |
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} |
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foo = strtok(read_buffer, " ,;\t"); |
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// check the atom name to the current atom |
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if( strcmp( foo, atoms[i]->getType() ) ){ |
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mmeineke |
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sprintf( painCave.errMsg, |
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mmeineke |
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"Initialize from file error. Atom %s at index %d " |
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"in file %s does not" |
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" match the BASS atom %s.\n", |
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foo, i, c_in_name, atoms[i]->getType() ); |
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mmeineke |
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painCave.isFatal = 1; |
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simError(); |
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mmeineke |
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} |
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// get the positions |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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mmeineke |
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sprintf( painCave.errMsg, |
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"error in reading postition x from %s\n" |
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"natoms = %d, index = %d\n", |
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c_in_name, n_atoms, i ); |
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painCave.isFatal = 1; |
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simError(); |
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mmeineke |
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} |
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(void)sscanf( foo, "%lf", &rx ); |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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mmeineke |
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sprintf( painCave.errMsg, |
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"error in reading postition y from %s\n" |
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"natoms = %d, index = %d\n", |
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c_in_name, n_atoms, i ); |
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painCave.isFatal = 1; |
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simError(); |
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mmeineke |
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} |
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(void)sscanf( foo, "%lf", &ry ); |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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mmeineke |
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sprintf( painCave.errMsg, |
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"error in reading postition z from %s\n" |
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"natoms = %d, index = %d\n", |
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c_in_name, n_atoms, i ); |
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painCave.isFatal = 1; |
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simError(); |
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mmeineke |
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} |
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(void)sscanf( foo, "%lf", &rz ); |
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// get the velocities |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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mmeineke |
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sprintf( painCave.errMsg, |
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"error in reading velocity x from %s\n" |
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"natoms = %d, index = %d\n", |
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c_in_name, n_atoms, i ); |
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painCave.isFatal = 1; |
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simError(); |
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mmeineke |
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} |
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(void)sscanf( foo, "%lf", &vx ); |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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mmeineke |
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sprintf( painCave.errMsg, |
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"error in reading velocity y from %s\n" |
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"natoms = %d, index = %d\n", |
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c_in_name, n_atoms, i ); |
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painCave.isFatal = 1; |
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simError(); |
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mmeineke |
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} |
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(void)sscanf( foo, "%lf", &vy ); |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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mmeineke |
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sprintf( painCave.errMsg, |
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"error in reading velocity z from %s\n" |
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"natoms = %d, index = %d\n", |
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c_in_name, n_atoms, i ); |
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painCave.isFatal = 1; |
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simError(); |
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mmeineke |
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} |
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(void)sscanf( foo, "%lf", &vz ); |
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// get the quaternions |
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if( atoms[i]->isDirectional() ){ |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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mmeineke |
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sprintf(painCave.errMsg, |
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"error in reading quaternion 0 from %s\n" |
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"natoms = %d, index = %d\n", |
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c_in_name, n_atoms, i ); |
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painCave.isFatal = 1; |
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simError(); |
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mmeineke |
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} |
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(void)sscanf( foo, "%lf", &q[0] ); |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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mmeineke |
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sprintf( painCave.errMsg, |
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"error in reading quaternion 1 from %s\n" |
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"natoms = %d, index = %d\n", |
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c_in_name, n_atoms, i ); |
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painCave.isFatal = 1; |
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simError(); |
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mmeineke |
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} |
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(void)sscanf( foo, "%lf", &q[1] ); |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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mmeineke |
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sprintf( painCave.errMsg, |
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"error in reading quaternion 2 from %s\n" |
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"natoms = %d, index = %d\n", |
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c_in_name, n_atoms, i ); |
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painCave.isFatal = 1; |
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simError(); |
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mmeineke |
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} |
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(void)sscanf( foo, "%lf", &q[2] ); |
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mmeineke |
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mmeineke |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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mmeineke |
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sprintf( painCave.errMsg, |
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"error in reading quaternion 3 from %s\n" |
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"natoms = %d, index = %d\n", |
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c_in_name, n_atoms, i ); |
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painCave.isFatal = 1; |
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simError(); |
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mmeineke |
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} |
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(void)sscanf( foo, "%lf", &q[3] ); |
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// get the angular velocities |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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mmeineke |
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sprintf( painCave.errMsg, |
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"error in reading angular momentum jx from %s\n" |
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"natoms = %d, index = %d\n", |
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c_in_name, n_atoms, i ); |
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painCave.isFatal = 1; |
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simError(); |
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mmeineke |
10 |
} |
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(void)sscanf( foo, "%lf", &jx ); |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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mmeineke |
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sprintf( painCave.errMsg, |
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"error in reading angular momentum jy from %s\n" |
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"natoms = %d, index = %d\n", |
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c_in_name, n_atoms, i ); |
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painCave.isFatal = 1; |
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simError(); |
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mmeineke |
10 |
} |
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(void)sscanf( foo, "%lf", &jy ); |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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mmeineke |
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sprintf( painCave.errMsg, |
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"error in reading angular momentum jz from %s\n" |
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"natoms = %d, index = %d\n", |
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c_in_name, n_atoms, i ); |
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painCave.isFatal = 1; |
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simError(); |
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mmeineke |
10 |
} |
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(void)sscanf( foo, "%lf", &jz ); |
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dAtom = ( DirectionalAtom* )atoms[i]; |
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// check that the quaternion vector is normalized |
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qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
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qLength = sqrt( qSqr ); |
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q[0] = q[0] / qLength; |
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q[1] = q[1] / qLength; |
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q[2] = q[2] / qLength; |
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q[3] = q[3] / qLength; |
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dAtom->setQ( q ); |
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// add the angular velocities |
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dAtom->setJx( jx ); |
308 |
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dAtom->setJy( jy ); |
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dAtom->setJz( jz ); |
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} |
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// add the positions and velocities to the atom |
313 |
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atoms[i]->setX( rx ); |
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atoms[i]->setY( ry ); |
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atoms[i]->setZ( rz ); |
317 |
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atoms[i]->set_vx( vx ); |
319 |
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atoms[i]->set_vy( vy ); |
320 |
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atoms[i]->set_vz( vz ); |
321 |
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} |
323 |
chuckv |
206 |
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// MPI Section of code.......... |
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#else //IS_MPI |
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329 |
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330 |
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if (worldRank == 0) { |
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
333 |
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if( eof_test == NULL ){ |
334 |
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sprintf( painCave.errMsg, |
335 |
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"Error reading 1st line of %d \n ",c_in_name); |
336 |
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painCave.isFatal = 1; |
337 |
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simError(); |
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} |
339 |
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340 |
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(void)sscanf(read_buffer, "%d", &n_atoms); |
341 |
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342 |
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Atom **atoms = entry_plug->atoms; |
343 |
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DirectionalAtom* dAtom; |
344 |
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345 |
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if( n_atoms != entry_plug->n_atoms ){ |
346 |
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sprintf( painCave.errMsg, |
347 |
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"Initialize from File error. %s n_atoms, %d, " |
348 |
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"does not match the BASS file's n_atoms, %d.\n", |
349 |
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c_in_name, n_atoms, entry_plug->n_atoms ); |
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painCave.isFatal = 1; |
351 |
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simError(); |
352 |
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} |
353 |
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354 |
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//read and toss the comment line |
355 |
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356 |
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
357 |
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if(eof_test == NULL){ |
358 |
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sprintf( painCave.errMsg, |
359 |
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"error in reading commment in %s\n", c_in_name); |
360 |
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painCave.isFatal = 1; |
361 |
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simError(); |
362 |
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} |
363 |
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} |
364 |
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for( i=0; i < n_atoms; i++){ |
365 |
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366 |
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
367 |
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if(eof_test == NULL){ |
368 |
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sprintf(painCave.errMsg, |
369 |
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"error in reading file %s\n" |
370 |
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"natoms = %d; index = %d\n" |
371 |
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"error reading the line from the file.\n", |
372 |
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c_in_name, n_atoms, i ); |
373 |
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painCave.isFatal = 1; |
374 |
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simError(); |
375 |
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} |
376 |
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377 |
|
|
foo = strtok(read_buffer, " ,;\t"); |
378 |
|
|
|
379 |
|
|
// check the atom name to the current atom |
380 |
|
|
|
381 |
|
|
if( strcmp( foo, atoms[i]->getType() ) ){ |
382 |
|
|
sprintf( painCave.errMsg, |
383 |
|
|
"Initialize from file error. Atom %s at index %d " |
384 |
|
|
"in file %s does not" |
385 |
|
|
" match the BASS atom %s.\n", |
386 |
|
|
foo, i, c_in_name, atoms[i]->getType() ); |
387 |
|
|
painCave.isFatal = 1; |
388 |
|
|
simError(); |
389 |
|
|
} |
390 |
|
|
|
391 |
|
|
// get the positions |
392 |
|
|
|
393 |
|
|
foo = strtok(NULL, " ,;\t"); |
394 |
|
|
if(foo == NULL){ |
395 |
|
|
sprintf( painCave.errMsg, |
396 |
|
|
"error in reading postition x from %s\n" |
397 |
|
|
"natoms = %d, index = %d\n", |
398 |
|
|
c_in_name, n_atoms, i ); |
399 |
|
|
painCave.isFatal = 1; |
400 |
|
|
simError(); |
401 |
|
|
} |
402 |
|
|
(void)sscanf( foo, "%lf", &rx ); |
403 |
|
|
|
404 |
|
|
foo = strtok(NULL, " ,;\t"); |
405 |
|
|
if(foo == NULL){ |
406 |
|
|
sprintf( painCave.errMsg, |
407 |
|
|
"error in reading postition y from %s\n" |
408 |
|
|
"natoms = %d, index = %d\n", |
409 |
|
|
c_in_name, n_atoms, i ); |
410 |
|
|
painCave.isFatal = 1; |
411 |
|
|
simError(); |
412 |
|
|
} |
413 |
|
|
(void)sscanf( foo, "%lf", &ry ); |
414 |
|
|
|
415 |
|
|
foo = strtok(NULL, " ,;\t"); |
416 |
|
|
if(foo == NULL){ |
417 |
|
|
sprintf( painCave.errMsg, |
418 |
|
|
"error in reading postition z from %s\n" |
419 |
|
|
"natoms = %d, index = %d\n", |
420 |
|
|
c_in_name, n_atoms, i ); |
421 |
|
|
painCave.isFatal = 1; |
422 |
|
|
simError(); |
423 |
|
|
} |
424 |
|
|
(void)sscanf( foo, "%lf", &rz ); |
425 |
|
|
|
426 |
|
|
// get the velocities |
427 |
|
|
|
428 |
|
|
foo = strtok(NULL, " ,;\t"); |
429 |
|
|
if(foo == NULL){ |
430 |
|
|
sprintf( painCave.errMsg, |
431 |
|
|
"error in reading velocity x from %s\n" |
432 |
|
|
"natoms = %d, index = %d\n", |
433 |
|
|
c_in_name, n_atoms, i ); |
434 |
|
|
painCave.isFatal = 1; |
435 |
|
|
simError(); |
436 |
|
|
} |
437 |
|
|
(void)sscanf( foo, "%lf", &vx ); |
438 |
|
|
|
439 |
|
|
foo = strtok(NULL, " ,;\t"); |
440 |
|
|
if(foo == NULL){ |
441 |
|
|
sprintf( painCave.errMsg, |
442 |
|
|
"error in reading velocity y from %s\n" |
443 |
|
|
"natoms = %d, index = %d\n", |
444 |
|
|
c_in_name, n_atoms, i ); |
445 |
|
|
painCave.isFatal = 1; |
446 |
|
|
simError(); |
447 |
|
|
} |
448 |
|
|
(void)sscanf( foo, "%lf", &vy ); |
449 |
|
|
|
450 |
|
|
foo = strtok(NULL, " ,;\t"); |
451 |
|
|
if(foo == NULL){ |
452 |
|
|
sprintf( painCave.errMsg, |
453 |
|
|
"error in reading velocity z from %s\n" |
454 |
|
|
"natoms = %d, index = %d\n", |
455 |
|
|
c_in_name, n_atoms, i ); |
456 |
|
|
painCave.isFatal = 1; |
457 |
|
|
simError(); |
458 |
|
|
} |
459 |
|
|
(void)sscanf( foo, "%lf", &vz ); |
460 |
|
|
|
461 |
|
|
|
462 |
|
|
// get the quaternions |
463 |
|
|
|
464 |
|
|
if( atoms[i]->isDirectional() ){ |
465 |
|
|
|
466 |
|
|
foo = strtok(NULL, " ,;\t"); |
467 |
|
|
if(foo == NULL){ |
468 |
|
|
sprintf(painCave.errMsg, |
469 |
|
|
"error in reading quaternion 0 from %s\n" |
470 |
|
|
"natoms = %d, index = %d\n", |
471 |
|
|
c_in_name, n_atoms, i ); |
472 |
|
|
painCave.isFatal = 1; |
473 |
|
|
simError(); |
474 |
|
|
} |
475 |
|
|
(void)sscanf( foo, "%lf", &q[0] ); |
476 |
|
|
|
477 |
|
|
foo = strtok(NULL, " ,;\t"); |
478 |
|
|
if(foo == NULL){ |
479 |
|
|
sprintf( painCave.errMsg, |
480 |
|
|
"error in reading quaternion 1 from %s\n" |
481 |
|
|
"natoms = %d, index = %d\n", |
482 |
|
|
c_in_name, n_atoms, i ); |
483 |
|
|
painCave.isFatal = 1; |
484 |
|
|
simError(); |
485 |
|
|
} |
486 |
|
|
(void)sscanf( foo, "%lf", &q[1] ); |
487 |
|
|
|
488 |
|
|
foo = strtok(NULL, " ,;\t"); |
489 |
|
|
if(foo == NULL){ |
490 |
|
|
sprintf( painCave.errMsg, |
491 |
|
|
"error in reading quaternion 2 from %s\n" |
492 |
|
|
"natoms = %d, index = %d\n", |
493 |
|
|
c_in_name, n_atoms, i ); |
494 |
|
|
painCave.isFatal = 1; |
495 |
|
|
simError(); |
496 |
|
|
} |
497 |
|
|
(void)sscanf( foo, "%lf", &q[2] ); |
498 |
|
|
|
499 |
|
|
foo = strtok(NULL, " ,;\t"); |
500 |
|
|
if(foo == NULL){ |
501 |
|
|
sprintf( painCave.errMsg, |
502 |
|
|
"error in reading quaternion 3 from %s\n" |
503 |
|
|
"natoms = %d, index = %d\n", |
504 |
|
|
c_in_name, n_atoms, i ); |
505 |
|
|
painCave.isFatal = 1; |
506 |
|
|
simError(); |
507 |
|
|
} |
508 |
|
|
(void)sscanf( foo, "%lf", &q[3] ); |
509 |
|
|
|
510 |
|
|
// get the angular velocities |
511 |
|
|
|
512 |
|
|
foo = strtok(NULL, " ,;\t"); |
513 |
|
|
if(foo == NULL){ |
514 |
|
|
sprintf( painCave.errMsg, |
515 |
|
|
"error in reading angular momentum jx from %s\n" |
516 |
|
|
"natoms = %d, index = %d\n", |
517 |
|
|
c_in_name, n_atoms, i ); |
518 |
|
|
painCave.isFatal = 1; |
519 |
|
|
simError(); |
520 |
|
|
} |
521 |
|
|
(void)sscanf( foo, "%lf", &jx ); |
522 |
|
|
|
523 |
|
|
foo = strtok(NULL, " ,;\t"); |
524 |
|
|
if(foo == NULL){ |
525 |
|
|
sprintf( painCave.errMsg, |
526 |
|
|
"error in reading angular momentum jy from %s\n" |
527 |
|
|
"natoms = %d, index = %d\n", |
528 |
|
|
c_in_name, n_atoms, i ); |
529 |
|
|
painCave.isFatal = 1; |
530 |
|
|
simError(); |
531 |
|
|
} |
532 |
|
|
(void)sscanf( foo, "%lf", &jy ); |
533 |
|
|
|
534 |
|
|
foo = strtok(NULL, " ,;\t"); |
535 |
|
|
if(foo == NULL){ |
536 |
|
|
sprintf( painCave.errMsg, |
537 |
|
|
"error in reading angular momentum jz from %s\n" |
538 |
|
|
"natoms = %d, index = %d\n", |
539 |
|
|
c_in_name, n_atoms, i ); |
540 |
|
|
painCave.isFatal = 1; |
541 |
|
|
simError(); |
542 |
|
|
} |
543 |
|
|
(void)sscanf( foo, "%lf", &jz ); |
544 |
|
|
|
545 |
|
|
dAtom = ( DirectionalAtom* )atoms[i]; |
546 |
|
|
|
547 |
|
|
// check that the quaternion vector is normalized |
548 |
|
|
|
549 |
|
|
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
550 |
|
|
|
551 |
|
|
qLength = sqrt( qSqr ); |
552 |
|
|
q[0] = q[0] / qLength; |
553 |
|
|
q[1] = q[1] / qLength; |
554 |
|
|
q[2] = q[2] / qLength; |
555 |
|
|
q[3] = q[3] / qLength; |
556 |
|
|
|
557 |
|
|
dAtom->setQ( q ); |
558 |
|
|
|
559 |
|
|
// add the angular velocities |
560 |
|
|
|
561 |
|
|
dAtom->setJx( jx ); |
562 |
|
|
dAtom->setJy( jy ); |
563 |
|
|
dAtom->setJz( jz ); |
564 |
|
|
} |
565 |
|
|
|
566 |
|
|
// add the positions and velocities to the atom |
567 |
|
|
|
568 |
|
|
atoms[i]->setX( rx ); |
569 |
|
|
atoms[i]->setY( ry ); |
570 |
|
|
atoms[i]->setZ( rz ); |
571 |
|
|
|
572 |
|
|
atoms[i]->set_vx( vx ); |
573 |
|
|
atoms[i]->set_vy( vy ); |
574 |
|
|
atoms[i]->set_vz( vz ); |
575 |
|
|
|
576 |
|
|
} |
577 |
|
|
#endif |
578 |
mmeineke |
10 |
} |
579 |
chuckv |
206 |
|
580 |
|
|
char* IntitializeFromFile::parseDumpLine(char* readLine); |