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#include <iostream> |
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#include <cmath> |
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|
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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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|
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#include "ReadWrite.hpp" |
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|
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|
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InitializeFromFile :: InitializeFromFile( char *in_name ){ |
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|
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c_in_file = fopen(in_name, "r"); |
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if(c_in_file == NULL){ |
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printf("Cannot open file: %s\n", in_name); |
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exit(8); |
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} |
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|
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strcpy( c_in_name, in_name); |
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return; |
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} |
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|
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InitializeFromFile :: ~InitializeFromFile( ){ |
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|
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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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fprintf( stderr, "Error closing %s\n", c_in_name ); |
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} |
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return; |
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} |
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|
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|
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void InitializeFromFile :: read_xyz( SimInfo* entry_plug ){ |
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|
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int i; // loop counter |
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|
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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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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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|
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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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|
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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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|
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(void)sscanf(read_buffer, "%d", &n_atoms); |
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|
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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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fprintf( stderr, |
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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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exit(8); |
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} |
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|
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//read and toss the comment line |
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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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printf("error in reading commment in %s\n", c_in_name); |
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exit(8); |
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} |
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|
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for( i=0; i < n_atoms; i++){ |
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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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printf("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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exit(8); |
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} |
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|
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foo = strtok(read_buffer, " ,;\t"); |
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|
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// check the atom name to the current atom |
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|
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if( strcmp( foo, atoms[i]->getType() ) ){ |
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fprintf( stderr, |
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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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exit(8); |
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} |
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|
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// get the positions |
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|
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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printf("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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exit(8); |
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} |
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(void)sscanf( foo, "%lf", &rx ); |
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|
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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printf("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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exit(8); |
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} |
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(void)sscanf( foo, "%lf", &ry ); |
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|
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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printf("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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exit(8); |
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} |
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(void)sscanf( foo, "%lf", &rz ); |
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|
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// get the velocities |
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|
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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printf("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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exit(8); |
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} |
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(void)sscanf( foo, "%lf", &vx ); |
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|
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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printf("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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exit(8); |
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} |
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(void)sscanf( foo, "%lf", &vy ); |
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|
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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printf("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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exit(8); |
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} |
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(void)sscanf( foo, "%lf", &vz ); |
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|
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|
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// get the quaternions |
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|
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if( atoms[i]->isDirectional() ){ |
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|
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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printf("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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exit(8); |
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} |
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(void)sscanf( foo, "%lf", &q[0] ); |
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|
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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printf("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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exit(8); |
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} |
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(void)sscanf( foo, "%lf", &q[1] ); |
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|
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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printf("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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exit(8); |
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} |
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(void)sscanf( foo, "%lf", &q[2] ); |
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|
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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printf("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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exit(8); |
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} |
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(void)sscanf( foo, "%lf", &q[3] ); |
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|
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// get the angular velocities |
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|
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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printf("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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exit(8); |
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} |
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(void)sscanf( foo, "%lf", &jx ); |
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|
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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printf("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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exit(8); |
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} |
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(void)sscanf( foo, "%lf", &jy ); |
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|
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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printf("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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exit(8); |
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} |
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(void)sscanf( foo, "%lf", &jz ); |
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|
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dAtom = ( DirectionalAtom* )atoms[i]; |
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|
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// check that the quaternion vector is normalized |
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|
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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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|
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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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|
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dAtom->setQ( q ); |
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|
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// add the angular velocities |
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|
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dAtom->setJx( jx ); |
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dAtom->setJy( jy ); |
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dAtom->setJz( jz ); |
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} |
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|
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// add the positions and velocities to the atom |
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|
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atoms[i]->setX( rx ); |
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atoms[i]->setY( ry ); |
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atoms[i]->setZ( rz ); |
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|
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atoms[i]->set_vx( vx ); |
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atoms[i]->set_vy( vy ); |
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atoms[i]->set_vz( vz ); |
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|
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} |
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} |
