mdtools/md_code/InitializeFromFile.cpp

#include <iostream>
#include <cmath>

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include <sys/types.h>
#include <sys/stat.h>

#include "ReadWrite.hpp"
#include "simError.h"


InitializeFromFile :: InitializeFromFile( char *in_name ){

  c_in_file = fopen(in_name, "r");
  if(c_in_file == NULL){
    sprintf(painCave.errMsg,
            "Cannot open file: %s\n", in_name);
    painCave.isFatal = 1;
    simError();
  }
  
  strcpy( c_in_name, in_name);
  return;  
}

InitializeFromFile :: ~InitializeFromFile( ){
  
  int error;
  error = fclose( c_in_file );
  if( error ){
    sprintf( painCave.errMsg,
             "Error closing %s\n", c_in_name );
    simError();
  }
  return;
}


void InitializeFromFile :: read_xyz( SimInfo* entry_plug ){

  int i; // loop counter

  int n_atoms; // the number of atoms
  char read_buffer[2000]; //the line buffer for reading 
  char *eof_test; // ptr to see when we reach the end of the file 
  char *foo; // the pointer to the current string token 

  double rx, ry, rz; // position place holders
  double vx, vy, vz; // velocity placeholders
  double q[4]; // the quaternions
  double jx, jy, jz; // angular velocity placeholders;
  double qSqr, qLength; // needed to normalize the quaternion vector.

  eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
  if( eof_test == NULL ){
    std::cerr << "error reading 1st line of" << c_in_name << "\n";
  }

  (void)sscanf(read_buffer, "%d", &n_atoms);

  Atom **atoms = entry_plug->atoms;
  DirectionalAtom* dAtom;

  if( n_atoms != entry_plug->n_atoms ){
    sprintf( painCave.errMsg,
             "Initialize from File error. %s n_atoms, %d, "
             "does not match the BASS file's n_atoms, %d.\n",
             c_in_name, n_atoms, entry_plug->n_atoms );
    painCave.isFatal = 1;
    simError();
  }
  
  //read and toss the comment line 
  
  eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
  if(eof_test == NULL){
    sprintf( painCave.errMsg,
             "error in reading commment in %s\n", c_in_name);
    painCave.isFatal = 1;
    simError();
  }

  for( i=0; i < n_atoms; i++){
    
    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
    if(eof_test == NULL){
      sprintf(painCave.errMsg,
              "error in reading file %s\n"
              "natoms  = %d; index = %d\n"
              "error reading the line from the file.\n",
              c_in_name, n_atoms, i );
      painCave.isFatal = 1;
      simError();
    }

    foo = strtok(read_buffer, " ,;\t");
    
    // check the atom name to the current atom

    if( strcmp( foo, atoms[i]->getType() ) ){
      sprintf( painCave.errMsg,
               "Initialize from file error. Atom %s at index %d "
               "in file %s does not"
               " match the BASS atom %s.\n",
               foo, i, c_in_name, atoms[i]->getType() );
      painCave.isFatal = 1;
      simError();
    }
    
    // get the positions

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
               "error in reading postition x from %s\n"
               "natoms  = %d, index = %d\n",
               c_in_name, n_atoms, i );
      painCave.isFatal = 1;
      simError();
    }
    (void)sscanf( foo, "%lf", &rx );
   
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
               "error in reading postition y from %s\n"
               "natoms  = %d, index = %d\n",
               c_in_name, n_atoms, i );
      painCave.isFatal = 1;
      simError();
    }
    (void)sscanf( foo, "%lf", &ry );
     
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
               "error in reading postition z from %s\n"
               "natoms  = %d, index = %d\n",
               c_in_name, n_atoms, i );
      painCave.isFatal = 1;
      simError();
    }
    (void)sscanf( foo, "%lf", &rz );
    
    // get the velocities

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
               "error in reading velocity x from %s\n"
               "natoms  = %d, index = %d\n",
               c_in_name, n_atoms, i );
      painCave.isFatal = 1;
      simError();
    }
    (void)sscanf( foo, "%lf", &vx );
    
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
               "error in reading velocity y from %s\n"
               "natoms  = %d, index = %d\n",
               c_in_name, n_atoms, i );
      painCave.isFatal = 1;
      simError();
    }
    (void)sscanf( foo, "%lf", &vy );
    
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
               "error in reading velocity z from %s\n"
               "natoms  = %d, index = %d\n",
               c_in_name, n_atoms, i );
      painCave.isFatal = 1;
      simError();
    }
    (void)sscanf( foo, "%lf", &vz );
    
    
    // get the quaternions
    
    if( atoms[i]->isDirectional() ){
      
      foo = strtok(NULL, " ,;\t");
      if(foo == NULL){
        sprintf(painCave.errMsg,
                "error in reading quaternion 0 from %s\n"
                "natoms  = %d, index = %d\n",
                c_in_name, n_atoms, i );
        painCave.isFatal = 1;
        simError();
      }
      (void)sscanf( foo, "%lf", &q[0] );
      
      foo = strtok(NULL, " ,;\t");
      if(foo == NULL){
        sprintf( painCave.errMsg,
                 "error in reading quaternion 1 from %s\n"
                 "natoms  = %d, index = %d\n",
                 c_in_name, n_atoms, i );
        painCave.isFatal = 1;
        simError();
      }
      (void)sscanf( foo, "%lf", &q[1] );
      
      foo = strtok(NULL, " ,;\t");
      if(foo == NULL){
        sprintf( painCave.errMsg,
                 "error in reading quaternion 2 from %s\n"
                 "natoms  = %d, index = %d\n",
                 c_in_name, n_atoms, i );
        painCave.isFatal = 1;
        simError();
      }
      (void)sscanf( foo, "%lf", &q[2] );
      
      foo = strtok(NULL, " ,;\t");
      if(foo == NULL){
        sprintf( painCave.errMsg,
                 "error in reading quaternion 3 from %s\n"
                 "natoms  = %d, index = %d\n",
                 c_in_name, n_atoms, i );
        painCave.isFatal = 1;
        simError();
      }
      (void)sscanf( foo, "%lf", &q[3] );
      
      // get the angular velocities
      
      foo = strtok(NULL, " ,;\t");
      if(foo == NULL){
        sprintf( painCave.errMsg,
                 "error in reading angular momentum jx from %s\n"
                 "natoms  = %d, index = %d\n",
                 c_in_name, n_atoms, i );
        painCave.isFatal = 1;
        simError();
      }
      (void)sscanf( foo, "%lf", &jx );
      
      foo = strtok(NULL, " ,;\t");
      if(foo == NULL){
        sprintf( painCave.errMsg,
                 "error in reading angular momentum jy from %s\n"
                 "natoms  = %d, index = %d\n",
                 c_in_name, n_atoms, i );
        painCave.isFatal = 1;
        simError();
      }
      (void)sscanf( foo, "%lf", &jy );
      
      foo = strtok(NULL, " ,;\t");
      if(foo == NULL){
        sprintf( painCave.errMsg,
                 "error in reading angular momentum jz from %s\n"
                 "natoms  = %d, index = %d\n",
                 c_in_name, n_atoms, i );
        painCave.isFatal = 1;
        simError();
      }
      (void)sscanf( foo, "%lf", &jz );
      
      dAtom = ( DirectionalAtom* )atoms[i];

      // check that the quaternion vector is normalized

      qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
      
      qLength = sqrt( qSqr );
      q[0] = q[0] / qLength;
      q[1] = q[1] / qLength;
      q[2] = q[2] / qLength;
      q[3] = q[3] / qLength;
      
      dAtom->setQ( q );
      
      // add the angular velocities

      dAtom->setJx( jx );
      dAtom->setJy( jy );
      dAtom->setJz( jz );
    }
    
    // add the positions and velocities to the atom
    
    atoms[i]->setX( rx );
    atoms[i]->setY( ry );
    atoms[i]->setZ( rz );
    
    atoms[i]->set_vx( vx );
    atoms[i]->set_vy( vy );
    atoms[i]->set_vz( vz );
    
  }
}
Revision:	162
Committed:	Thu Oct 31 21:20:49 2002 UTC (22 years, 11 months ago) by mmeineke
File size:	7546 byte(s)
Log Message:	* empty log message *
#	Content
1	#include <iostream>
2	#include <cmath>
3
4	#include <stdio.h>
5	#include <stdlib.h>
6	#include <string.h>
7	#include <unistd.h>
8	#include <sys/types.h>
9	#include <sys/stat.h>
10
11	#include "ReadWrite.hpp"
12	#include "simError.h"
13
14
15	InitializeFromFile :: InitializeFromFile( char *in_name ){
16
17	c_in_file = fopen(in_name, "r");
18	if(c_in_file == NULL){
19	sprintf(painCave.errMsg,
20	"Cannot open file: %s\n", in_name);
21	painCave.isFatal = 1;
22	simError();
23	}
24
25	strcpy( c_in_name, in_name);
26	return;
27	}
28
29	InitializeFromFile :: ~InitializeFromFile( ){
30
31	int error;
32	error = fclose( c_in_file );
33	if( error ){
34	sprintf( painCave.errMsg,
35	"Error closing %s\n", c_in_name );
36	simError();
37	}
38	return;
39	}
40
41
42	void InitializeFromFile :: read_xyz( SimInfo* entry_plug ){
43
44	int i; // loop counter
45
46	int n_atoms; // the number of atoms
47	char read_buffer[2000]; //the line buffer for reading
48	char *eof_test; // ptr to see when we reach the end of the file
49	char *foo; // the pointer to the current string token
50
51	double rx, ry, rz; // position place holders
52	double vx, vy, vz; // velocity placeholders
53	double q[4]; // the quaternions
54	double jx, jy, jz; // angular velocity placeholders;
55	double qSqr, qLength; // needed to normalize the quaternion vector.
56
57	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
58	if( eof_test == NULL ){
59	std::cerr << "error reading 1st line of" << c_in_name << "\n";
60	}
61
62	(void)sscanf(read_buffer, "%d", &n_atoms);
63
64	Atom **atoms = entry_plug->atoms;
65	DirectionalAtom* dAtom;
66
67	if( n_atoms != entry_plug->n_atoms ){
68	sprintf( painCave.errMsg,
69	"Initialize from File error. %s n_atoms, %d, "
70	"does not match the BASS file's n_atoms, %d.\n",
71	c_in_name, n_atoms, entry_plug->n_atoms );
72	painCave.isFatal = 1;
73	simError();
74	}
75
76	//read and toss the comment line
77
78	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
79	if(eof_test == NULL){
80	sprintf( painCave.errMsg,
81	"error in reading commment in %s\n", c_in_name);
82	painCave.isFatal = 1;
83	simError();
84	}
85
86	for( i=0; i < n_atoms; i++){
87
88	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
89	if(eof_test == NULL){
90	sprintf(painCave.errMsg,
91	"error in reading file %s\n"
92	"natoms = %d; index = %d\n"
93	"error reading the line from the file.\n",
94	c_in_name, n_atoms, i );
95	painCave.isFatal = 1;
96	simError();
97	}
98
99	foo = strtok(read_buffer, " ,;\t");
100
101	// check the atom name to the current atom
102
103	if( strcmp( foo, atoms[i]->getType() ) ){
104	sprintf( painCave.errMsg,
105	"Initialize from file error. Atom %s at index %d "
106	"in file %s does not"
107	" match the BASS atom %s.\n",
108	foo, i, c_in_name, atoms[i]->getType() );
109	painCave.isFatal = 1;
110	simError();
111	}
112
113	// get the positions
114
115	foo = strtok(NULL, " ,;\t");
116	if(foo == NULL){
117	sprintf( painCave.errMsg,
118	"error in reading postition x from %s\n"
119	"natoms = %d, index = %d\n",
120	c_in_name, n_atoms, i );
121	painCave.isFatal = 1;
122	simError();
123	}
124	(void)sscanf( foo, "%lf", &rx );
125
126	foo = strtok(NULL, " ,;\t");
127	if(foo == NULL){
128	sprintf( painCave.errMsg,
129	"error in reading postition y from %s\n"
130	"natoms = %d, index = %d\n",
131	c_in_name, n_atoms, i );
132	painCave.isFatal = 1;
133	simError();
134	}
135	(void)sscanf( foo, "%lf", &ry );
136
137	foo = strtok(NULL, " ,;\t");
138	if(foo == NULL){
139	sprintf( painCave.errMsg,
140	"error in reading postition z from %s\n"
141	"natoms = %d, index = %d\n",
142	c_in_name, n_atoms, i );
143	painCave.isFatal = 1;
144	simError();
145	}
146	(void)sscanf( foo, "%lf", &rz );
147
148	// get the velocities
149
150	foo = strtok(NULL, " ,;\t");
151	if(foo == NULL){
152	sprintf( painCave.errMsg,
153	"error in reading velocity x from %s\n"
154	"natoms = %d, index = %d\n",
155	c_in_name, n_atoms, i );
156	painCave.isFatal = 1;
157	simError();
158	}
159	(void)sscanf( foo, "%lf", &vx );
160
161	foo = strtok(NULL, " ,;\t");
162	if(foo == NULL){
163	sprintf( painCave.errMsg,
164	"error in reading velocity y from %s\n"
165	"natoms = %d, index = %d\n",
166	c_in_name, n_atoms, i );
167	painCave.isFatal = 1;
168	simError();
169	}
170	(void)sscanf( foo, "%lf", &vy );
171
172	foo = strtok(NULL, " ,;\t");
173	if(foo == NULL){
174	sprintf( painCave.errMsg,
175	"error in reading velocity z from %s\n"
176	"natoms = %d, index = %d\n",
177	c_in_name, n_atoms, i );
178	painCave.isFatal = 1;
179	simError();
180	}
181	(void)sscanf( foo, "%lf", &vz );
182
183
184	// get the quaternions
185
186	if( atoms[i]->isDirectional() ){
187
188	foo = strtok(NULL, " ,;\t");
189	if(foo == NULL){
190	sprintf(painCave.errMsg,
191	"error in reading quaternion 0 from %s\n"
192	"natoms = %d, index = %d\n",
193	c_in_name, n_atoms, i );
194	painCave.isFatal = 1;
195	simError();
196	}
197	(void)sscanf( foo, "%lf", &q[0] );
198
199	foo = strtok(NULL, " ,;\t");
200	if(foo == NULL){
201	sprintf( painCave.errMsg,
202	"error in reading quaternion 1 from %s\n"
203	"natoms = %d, index = %d\n",
204	c_in_name, n_atoms, i );
205	painCave.isFatal = 1;
206	simError();
207	}
208	(void)sscanf( foo, "%lf", &q[1] );
209
210	foo = strtok(NULL, " ,;\t");
211	if(foo == NULL){
212	sprintf( painCave.errMsg,
213	"error in reading quaternion 2 from %s\n"
214	"natoms = %d, index = %d\n",
215	c_in_name, n_atoms, i );
216	painCave.isFatal = 1;
217	simError();
218	}
219	(void)sscanf( foo, "%lf", &q[2] );
220
221	foo = strtok(NULL, " ,;\t");
222	if(foo == NULL){
223	sprintf( painCave.errMsg,
224	"error in reading quaternion 3 from %s\n"
225	"natoms = %d, index = %d\n",
226	c_in_name, n_atoms, i );
227	painCave.isFatal = 1;
228	simError();
229	}
230	(void)sscanf( foo, "%lf", &q[3] );
231
232	// get the angular velocities
233
234	foo = strtok(NULL, " ,;\t");
235	if(foo == NULL){
236	sprintf( painCave.errMsg,
237	"error in reading angular momentum jx from %s\n"
238	"natoms = %d, index = %d\n",
239	c_in_name, n_atoms, i );
240	painCave.isFatal = 1;
241	simError();
242	}
243	(void)sscanf( foo, "%lf", &jx );
244
245	foo = strtok(NULL, " ,;\t");
246	if(foo == NULL){
247	sprintf( painCave.errMsg,
248	"error in reading angular momentum jy from %s\n"
249	"natoms = %d, index = %d\n",
250	c_in_name, n_atoms, i );
251	painCave.isFatal = 1;
252	simError();
253	}
254	(void)sscanf( foo, "%lf", &jy );
255
256	foo = strtok(NULL, " ,;\t");
257	if(foo == NULL){
258	sprintf( painCave.errMsg,
259	"error in reading angular momentum jz from %s\n"
260	"natoms = %d, index = %d\n",
261	c_in_name, n_atoms, i );
262	painCave.isFatal = 1;
263	simError();
264	}
265	(void)sscanf( foo, "%lf", &jz );
266
267	dAtom = ( DirectionalAtom* )atoms[i];
268
269	// check that the quaternion vector is normalized
270
271	qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
272
273	qLength = sqrt( qSqr );
274	q[0] = q[0] / qLength;
275	q[1] = q[1] / qLength;
276	q[2] = q[2] / qLength;
277	q[3] = q[3] / qLength;
278
279	dAtom->setQ( q );
280
281	// add the angular velocities
282
283	dAtom->setJx( jx );
284	dAtom->setJy( jy );
285	dAtom->setJz( jz );
286	}
287
288	// add the positions and velocities to the atom
289
290	atoms[i]->setX( rx );
291	atoms[i]->setY( ry );
292	atoms[i]->setZ( rz );
293
294	atoms[i]->set_vx( vx );
295	atoms[i]->set_vy( vy );
296	atoms[i]->set_vz( vz );
297
298	}
299	}