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binary_file.c
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binary_file.c
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// This file is part of the ESPResSo distribution (http://www.espresso.mpg.de).
// It is therefore subject to the ESPResSo license agreement which you accepted upon receiving the distribution
// and by which you are legally bound while utilizing this file in any form or way.
// There is NO WARRANTY, not even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
// You should have received a copy of that license along with this program;
// if not, refer to http://www.espresso.mpg.de/license.html where its current version can be found, or
// write to Max-Planck-Institute for Polymer Research, Theory Group, PO Box 3148, 55021 Mainz, Germany.
// Copyright (c) 2002-2006; all rights reserved unless otherwise stated.
/** \file binary_file.c
Implementation of \ref binary_file.h "binary_file.h".
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "utils.h"
#include "binary_file.h"
#include "global.h"
#include "communication.h"
#include "grid.h"
#include "interaction_data.h"
/* cwz-build-comman: ssh chakotay "builtin cd /nhomes/janeway/axel/progs/Espresso; make"
cwz-build-command: make
*/
int writemd(ClientData data, Tcl_Interp *interp,
int argc, char **argv)
{
static int end_num = -1;
char *row;
int p, i;
struct MDHeader header;
int tcl_file_mode;
Tcl_Channel channel;
if (argc < 3) {
Tcl_AppendResult(interp, "wrong # args: should be \"",
argv[0], " <file> ?posx|posy|posz|q|vx|vy|vz|fx|fy|fz|type?* ...\"",
(char *) NULL);
return (TCL_ERROR);
}
if ((channel = Tcl_GetChannel(interp, argv[1], &tcl_file_mode)) == NULL)
return (TCL_ERROR);
if (!(tcl_file_mode & TCL_WRITABLE)) {
Tcl_AppendResult(interp, "\"", argv[1], "\" not writeable", (char *) NULL);
return (TCL_ERROR);
}
/* tune channel to binary translation, e.g. none */
Tcl_SetChannelOption(interp, channel, "-translation", "binary");
/* assemble rows */
argc -= 2;
argv += 2;
row = malloc(sizeof(char)*argc);
for (i = 0; i < argc; i++) {
if (!strncmp(*argv, "posx", strlen(*argv))) {
row[i] = POSX;
}
else if (!strncmp(*argv, "posy", strlen(*argv))) {
row[i] = POSY;
}
else if (!strncmp(*argv, "posz", strlen(*argv))) {
row[i] = POSZ;
}
#ifdef MASS
else if (!strncmp(*argv, "mass", strlen(*argv))) {
row[i] = MASSES;
}
#endif
else if (!strncmp(*argv, "q", strlen(*argv))) {
row[i] = Q;
}
else if (!strncmp(*argv, "vx", strlen(*argv))) {
row[i] = VX;
}
else if (!strncmp(*argv, "vy", strlen(*argv))) {
row[i] = VY;
}
else if (!strncmp(*argv, "vz", strlen(*argv))) {
row[i] = VZ;
}
else if (!strncmp(*argv, "fx", strlen(*argv))) {
row[i] = FX;
}
else if (!strncmp(*argv, "fy", strlen(*argv))) {
row[i] = FY;
}
else if (!strncmp(*argv, "fz", strlen(*argv))) {
row[i] = FZ;
}
else if (!strncmp(*argv, "type", strlen(*argv))) {
row[i] = TYPE;
}
else {
Tcl_AppendResult(interp, "no particle data field \"", *argv, "\"?",
(char *) NULL);
free(row);
return (TCL_ERROR);
}
argv++;
}
if (!particle_node)
build_particle_node();
/* write header and row data */
memcpy(header.magic, MDMAGIC, 4*sizeof(char));
header.n_rows = argc;
Tcl_Write(channel, (char *)&header, sizeof(header));
Tcl_Write(channel, row, header.n_rows*sizeof(char));
for (p = 0; p <= max_seen_particle; p++) {
Particle data;
if (get_particle_data(p, &data)) {
unfold_position(data.r.p, data.l.i);
/* write particle index */
Tcl_Write(channel, (char *)&p, sizeof(int));
for (i = 0; i < header.n_rows; i++) {
switch (row[i]) {
case POSX: Tcl_Write(channel, (char *)&data.r.p[0], sizeof(double)); break;
case POSY: Tcl_Write(channel, (char *)&data.r.p[1], sizeof(double)); break;
case POSZ: Tcl_Write(channel, (char *)&data.r.p[2], sizeof(double)); break;
case VX: Tcl_Write(channel, (char *)&data.m.v[0], sizeof(double)); break;
case VY: Tcl_Write(channel, (char *)&data.m.v[1], sizeof(double)); break;
case VZ: Tcl_Write(channel, (char *)&data.m.v[2], sizeof(double)); break;
case FX: Tcl_Write(channel, (char *)&data.f.f[0], sizeof(double)); break;
case FY: Tcl_Write(channel, (char *)&data.f.f[1], sizeof(double)); break;
case FZ: Tcl_Write(channel, (char *)&data.f.f[2], sizeof(double)); break;
#ifdef MASS
case MASSES: Tcl_Write(channel, (char *)&data.p.mass, sizeof(double)); break;
#endif
#ifdef ELECTROSTATICS
case Q: Tcl_Write(channel, (char *)&data.p.q, sizeof(double)); break;
#endif
case TYPE: Tcl_Write(channel, (char *)&data.p.type, sizeof(int)); break;
}
}
free_particle(&data);
}
}
/* end marker */
Tcl_Write(channel, (char *)&end_num, sizeof(int));
free(row);
return TCL_OK;
}
int readmd(ClientData dummy, Tcl_Interp *interp,
int argc, char **argv)
{
char *row;
int pos_row[3] = { -1 }, v_row[3] = { -1 }, f_row[3] = { -1 };
int av_pos = 0, av_v = 0, av_mass=0, av_f = 0, av_q = 0, av_type = 0;
int node, i;
struct MDHeader header;
Particle data;
int tcl_file_mode;
Tcl_Channel channel;
if (argc != 2) {
Tcl_AppendResult(interp, "wrong # args: should be \"",
argv[0], " <file>\"",
(char *) NULL);
return (TCL_ERROR);
}
if ((channel = Tcl_GetChannel(interp, argv[1], &tcl_file_mode)) == NULL)
return (TCL_ERROR);
/* tune channel to binary translation, e.g. none */
Tcl_SetChannelOption(interp, channel, "-translation", "binary");
Tcl_Read(channel, (char *)&header, sizeof(header));
/* check token */
if (strncmp(header.magic, MDMAGIC, 4) || header.n_rows < 0) {
Tcl_AppendResult(interp, "data file \"", argv[1],
"\" does not contain tcl MD data",
(char *) NULL);
return (TCL_ERROR);
}
if (!particle_node)
build_particle_node();
/* parse rows */
row = malloc(header.n_rows*sizeof(char));
for (i = 0; i < header.n_rows; i++) {
Tcl_Read(channel, (char *)&row[i], sizeof(char));
switch (row[i]) {
case POSX: pos_row[0] = i; break;
case POSY: pos_row[1] = i; break;
case POSZ: pos_row[2] = i; break;
case VX: v_row[0] = i; break;
case VY: v_row[1] = i; break;
case VZ: v_row[2] = i; break;
case FX: f_row[0] = i; break;
case FY: f_row[1] = i; break;
case FZ: f_row[2] = i; break;
case MASSES: av_mass = 1; break;
case Q: av_q = 1; break;
case TYPE: av_type = 1; break;
}
}
/* *_row[0] tells if * data is completely available -
* otherwise we ignore it */
if (pos_row[0] != -1 && pos_row[1] != -1 && pos_row[2] != -1) {
av_pos = 1;
}
if (v_row[0] != -1 && v_row[1] != -1 && v_row[2] != -1) {
av_v = 1;
}
if (f_row[0] != -1 && f_row[1] != -1 && f_row[2] != -1) {
av_f = 1;
}
while (!Tcl_Eof(channel)) {
Tcl_Read(channel, (char *)&data.p.identity, sizeof(int));
if (data.p.identity == -1)
break;
/* printf("id=%d\n", data.identity); */
if (data.p.identity < 0) {
Tcl_AppendResult(interp, "illegal data format in data file \"", argv[1],
"\", perhaps wrong file?",
(char *) NULL);
free(row);
return (TCL_ERROR);
}
for (i = 0; i < header.n_rows; i++) {
switch (row[i]) {
case POSX: Tcl_Read(channel, (char *)&data.r.p[0], sizeof(double)); break;
case POSY: Tcl_Read(channel, (char *)&data.r.p[1], sizeof(double)); break;
case POSZ: Tcl_Read(channel, (char *)&data.r.p[2], sizeof(double)); break;
case VX: Tcl_Read(channel, (char *)&data.m.v[0], sizeof(double)); break;
case VY: Tcl_Read(channel, (char *)&data.m.v[1], sizeof(double)); break;
case VZ: Tcl_Read(channel, (char *)&data.m.v[2], sizeof(double)); break;
case FX: Tcl_Read(channel, (char *)&data.f.f[0], sizeof(double)); break;
case FY: Tcl_Read(channel, (char *)&data.f.f[1], sizeof(double)); break;
case FZ: Tcl_Read(channel, (char *)&data.f.f[2], sizeof(double)); break;
case MASSES:
#ifdef MASS
Tcl_Read(channel, (char *)&data.p.mass, sizeof(double)); break;
#else
{
double dummy_mass;
Tcl_Read(channel, (char *)&dummy_mass, sizeof(double)); break;
}
#endif
#ifdef ELECTROSTATICS
case Q: Tcl_Read(channel, (char *)&data.p.q, sizeof(double)); break;
#endif
case TYPE: Tcl_Read(channel, (char *)&data.p.type, sizeof(int)); break;
}
}
node = (data.p.identity <= max_seen_particle) ? particle_node[data.p.identity] : -1;
if (node == -1) {
if (!av_pos) {
Tcl_AppendResult(interp, "new particle without position data",
(char *) NULL);
free(row);
return (TCL_ERROR);
}
}
if (av_pos)
place_particle(data.p.identity, data.r.p);
#ifdef MASS
if (av_mass)
set_particle_mass(data.p.identity, data.p.mass);
#endif
#ifdef ELECTROSTATICS
if (av_q)
set_particle_q(data.p.identity, data.p.q);
#endif
if (av_v)
set_particle_v(data.p.identity, data.m.v);
if (av_f)
set_particle_f(data.p.identity, data.f.f);
if (av_type)
set_particle_type(data.p.identity, data.p.type);
}
free(row);
return TCL_OK;
}