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lammps/lib/qmmm/libqmmm.c
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libqmmm.c
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/*
* This file is distributed under the terms of the
* GNU General Public License. See the file `License'
* in the root directory of the present distribution,
* or http://www.gnu.org/copyleft/gpl.txt .
*
* generic QM/MM support library
*/
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <ctype.h>
#include <time.h>
#include "libqmmm.h"
#define BUF_SIZE 1024
/* global variable for global QM/MM configuration */
qmmm_config_t qmmmcfg;
/* local helper function: advance char pointer beyond leading whitespace */
static char *skip_whitespace(char *ptr)
{
while ((*ptr == ' ') || (*ptr == '\t')
|| (*ptr == '\r') || (*ptr == '\n')) ++ptr;
return ptr;
}
/* local helper function: trim string to remove trailing whitespace */
static void trim_whitespace(char *ptr)
{
while ((*ptr != ' ') && (*ptr != '\t')
&& (*ptr != '\r') && (*ptr != '\n')) ++ptr;
*ptr = '\0';
}
/* read and parse global QM/MM configuration file and
store the result in a qmmm_config_t struct */
int read_qmmm_config(const char *file, qmmm_config_t *cfg)
{
FILE *fp;
char *ptr;
int i, lineno, len;
char buf[BUF_SIZE];
/* need to have config file and storage for config provided */
if ((file == NULL) || (cfg == NULL))
return QMMM_ERROR;
/* clear config */
memset(cfg, 0, sizeof(qmmm_config_t));
fp = fopen(file,"r");
if (fp == NULL) return QMMM_ERROR;
lineno = 0;
while (fgets(buf,BUF_SIZE,fp)) {
++lineno;
/* remove comments */
ptr = strchr(buf,'#');
if (ptr != NULL) *ptr = '\0';
/* skip over leading whitespace */
ptr = skip_whitespace(buf);
len = strlen(ptr);
if (len == 0) continue;
/* convert keyword to lower case */
for (i=0; i < len; ++i) {
if ((ptr[i]=='\0') || (ptr[i]==' ') || (ptr[i]=='\t'))
break;
ptr[i] = tolower(ptr[i]);
}
/* handle keywords */
if (strncmp(ptr,"mode",4) == 0) {
ptr = skip_whitespace(ptr+4);
if ((*ptr=='m') || (*ptr=='M'))
cfg->qmmm_mode = QMMM_MODE_MECH;
else if ((*ptr=='e') || (*ptr=='E'))
cfg->qmmm_mode = QMMM_MODE_ELEC;
else if ((*ptr=='o') || (*ptr=='O'))
cfg->qmmm_mode = QMMM_MODE_OFF;
else cfg->qmmm_mode = QMMM_ERROR;
} else if (strncmp(ptr,"comm",4) == 0) {
ptr = skip_whitespace(ptr+4);
if ((*ptr=='m') || (*ptr=='M'))
cfg->comm_mode = QMMM_COMM_MPI;
else if ((*ptr=='s') || (*ptr=='S'))
cfg->comm_mode = QMMM_COMM_SHM;
else cfg->comm_mode = QMMM_ERROR;
} else if (strncmp(ptr,"steps",5) == 0) {
ptr = skip_whitespace(ptr+5);
trim_whitespace(ptr);
cfg->steps = atoi(ptr);
} else if (strncmp(ptr,"verbose",7) == 0) {
ptr = skip_whitespace(ptr+7);
trim_whitespace(ptr);
cfg->verbose = atoi(ptr);
} else if (strncmp(ptr,"handle",6) == 0) {
ptr = skip_whitespace(ptr+6);
trim_whitespace(ptr);
if (cfg->handle) free(cfg->handle);
cfg->handle = strdup(ptr);
} else if (strncmp(ptr,"restart",7) == 0) {
ptr = skip_whitespace(ptr+7);
trim_whitespace(ptr);
if (cfg->restart) free(cfg->restart);
cfg->restart = strdup(ptr);
} else if (strncmp(ptr,"qmdir",5) == 0) {
ptr = skip_whitespace(ptr+5);
trim_whitespace(ptr);
if (cfg->qmdir) free(cfg->qmdir);
cfg->qmdir = strdup(ptr);
} else if (strncmp(ptr,"madir",5) == 0) {
ptr = skip_whitespace(ptr+5);
trim_whitespace(ptr);
if (cfg->madir) free(cfg->madir);
cfg->madir = strdup(ptr);
} else if (strncmp(ptr,"sldir",5) == 0) {
ptr = skip_whitespace(ptr+5);
trim_whitespace(ptr);
if (cfg->sldir) free(cfg->sldir);
cfg->sldir = strdup(ptr);
} else if (strncmp(ptr,"qminp",5) == 0) {
ptr = skip_whitespace(ptr+5);
trim_whitespace(ptr);
if (cfg->qminp) free(cfg->qminp);
cfg->qminp = strdup(ptr);
} else if (strncmp(ptr,"mainp",5) == 0) {
ptr = skip_whitespace(ptr+5);
trim_whitespace(ptr);
if (cfg->mainp) free(cfg->mainp);
cfg->mainp = strdup(ptr);
} else if (strncmp(ptr,"slinp",5) == 0) {
ptr = skip_whitespace(ptr+5);
trim_whitespace(ptr);
if (cfg->slinp) free(cfg->slinp);
cfg->slinp = strdup(ptr);
} else if (strncmp(ptr,"qmout",5) == 0) {
ptr = skip_whitespace(ptr+5);
trim_whitespace(ptr);
if (cfg->qmout) free(cfg->qmout);
cfg->qmout = strdup(ptr);
} else if (strncmp(ptr,"maout",5) == 0) {
ptr = skip_whitespace(ptr+5);
trim_whitespace(ptr);
if (cfg->maout) free(cfg->maout);
cfg->maout = strdup(ptr);
} else if (strncmp(ptr,"slout",5) == 0) {
ptr = skip_whitespace(ptr+5);
trim_whitespace(ptr);
if (cfg->slout) free(cfg->slout);
cfg->slout = strdup(ptr);
} else if (strncmp(ptr,"qmcmd",5) == 0) {
ptr = skip_whitespace(ptr+5);
if (cfg->qmcmd) free(cfg->qmcmd);
cfg->qmcmd = strdup(ptr);
} else if (strncmp(ptr,"macmd",5) == 0) {
ptr = skip_whitespace(ptr+5);
if (cfg->macmd) free(cfg->macmd);
cfg->macmd = strdup(ptr);
} else if (strncmp(ptr,"slcmd",5) == 0) {
ptr = skip_whitespace(ptr+5);
if (cfg->slcmd) free(cfg->slcmd);
cfg->slcmd = strdup(ptr);
} else if (strncmp(ptr,"qmarg",5) == 0) {
ptr = skip_whitespace(ptr+5);
if (cfg->qmarg) free(cfg->qmarg);
cfg->qmarg = strdup(ptr);
} else if (strncmp(ptr,"maarg",5) == 0) {
ptr = skip_whitespace(ptr+5);
if (cfg->maarg) free(cfg->maarg);
cfg->maarg = strdup(ptr);
} else if (strncmp(ptr,"slarg",5) == 0) {
ptr = skip_whitespace(ptr+5);
if (cfg->slarg) free(cfg->slarg);
cfg->slarg = strdup(ptr);
} else {
fprintf(stderr,"\nParse error in line %d of file %s\n>>%s<<\n\n",
lineno, file, buf);
return QMMM_ERROR;
}
if (feof(fp)) break;
}
fclose(fp);
return QMMM_OK;
}
/* perform consistency checks on a qmmm_config_t struct */
const char *check_qmmm_config(qmmm_config_t *cfg) {
const char *msg = NULL;
if (cfg->qmmm_mode == QMMM_MODE_NONE) {
msg = "QM/MM coupling mode not set";
} else if (cfg->steps < 1) {
msg = "Number of QM/MM steps must be > 0";
} else if (cfg->qmdir == NULL) {
msg = "QM directory not set";
} else if (cfg->madir == NULL) {
msg = "MM master directory not set";
} else if (cfg->sldir == NULL) {
msg = "MM slave directory not set";
} else if (cfg->qminp == NULL) {
msg = "QM input file not set";
} else if (cfg->mainp == NULL) {
msg = "MM master input file not set";
} else if (cfg->slinp == NULL) {
msg = "MM slave input file not set";
} else if (cfg->qmout == NULL) {
msg = "QM output file not set";
} else if (cfg->maout == NULL) {
msg = "MM master output file not set";
} else if (cfg->slout == NULL) {
msg = "MM slave output file not set";
}
return msg;
}
/* take the existing global QM/MM configuration and write it to a file */
int write_qmmm_config(const char *file, qmmm_config_t *cfg)
{
FILE *fp;
time_t now;
if (cfg == NULL)
return QMMM_ERROR;
if (file == NULL)
fp = stderr;
else {
fp = fopen(file,"w");
if (fp == NULL) return QMMM_ERROR;
}
now = time(NULL);
fprintf(fp,"# QM/MM global configuration. %s\n",ctime(&now));
fprintf(fp,"# comm_mode: %d\n", cfg->comm_mode);
if (cfg->qmmm_mode == QMMM_MODE_OFF) {
fputs("mode off\n",fp);
} else if (cfg->qmmm_mode == QMMM_MODE_NONE) {
fputs("mode none\n",fp);
} else if (cfg->qmmm_mode == QMMM_MODE_MECH) {
fputs("mode mechanical\n",fp);
} else if (cfg->qmmm_mode == QMMM_MODE_ELEC) {
fputs("mode electrostatic\n",fp);
} else fputs("mode unknown\n",fp);
if (cfg->restart) fprintf(fp,"restart %s\n",cfg->restart);
if (cfg->handle) fprintf(fp,"handle %s\n", cfg->handle);
fprintf(fp,"steps %d\n",cfg->steps);
fprintf(fp,"verbose %d\n",cfg->verbose);
fputs("\n# QM system configuration:\n",fp);
if (cfg->qmdir) fprintf(fp,"qmdir %s\n", cfg->qmdir);
else fputs("qmdir (required input not set)\n",fp);
if (cfg->qminp) fprintf(fp,"qminp %s\n", cfg->qminp);
else fputs("qminp (required input not set)\n",fp);
if (cfg->qmout) fprintf(fp,"qmout %s\n", cfg->qmout);
else fputs("qmout NULL\n",fp);
if (cfg->qmcmd) fprintf(fp,"qmcmd %s\n", cfg->qmcmd);
if (cfg->qmarg) fprintf(fp,"qmarg %s\n", cfg->qmarg);
fputs("\n# MM master system configuration:\n",fp);
if (cfg->madir) fprintf(fp,"madir %s\n", cfg->madir);
else fputs("madir (required input not set)\n",fp);
if (cfg->mainp) fprintf(fp,"mainp %s\n", cfg->mainp);
else fputs("mainp (required input not set)\n",fp);
if (cfg->maout) fprintf(fp,"maout %s\n", cfg->maout);
else fputs("maout NULL\n",fp);
if (cfg->macmd) fprintf(fp,"macmd %s\n", cfg->macmd);
if (cfg->maarg) fprintf(fp,"maarg %s\n", cfg->maarg);
fputs("\n# MM slave system configuration:\n",fp);
if (cfg->sldir) fprintf(fp,"sldir %s\n", cfg->sldir);
else fputs("sldir (required input not set)\n",fp);
if (cfg->slinp) fprintf(fp,"slinp %s\n", cfg->slinp);
else fputs("slinp (required input not set)\n",fp);
if (cfg->slout) fprintf(fp,"slout %s\n", cfg->slout);
else fputs("slout NULL\n",fp);
if (cfg->slcmd) fprintf(fp,"slcmd %s\n", cfg->slcmd);
if (cfg->slarg) fprintf(fp,"slarg %s\n", cfg->slarg);
if (file != NULL) fclose(fp);
return QMMM_OK;
}
/* free storage associated with qmmm_config_t struct */
void free_qmmm_config(qmmm_config_t *cfg) {
if (cfg->qmdir != NULL) free(cfg->qmdir);
if (cfg->madir != NULL) free(cfg->madir);
if (cfg->sldir != NULL) free(cfg->sldir);
if (cfg->qminp != NULL) free(cfg->qminp);
if (cfg->mainp != NULL) free(cfg->mainp);
if (cfg->slinp != NULL) free(cfg->slinp);
if (cfg->qmout != NULL) free(cfg->qmout);
if (cfg->maout != NULL) free(cfg->maout);
if (cfg->slout != NULL) free(cfg->slout);
if (cfg->qmcmd != NULL) free(cfg->qmcmd);
if (cfg->macmd != NULL) free(cfg->macmd);
if (cfg->slcmd != NULL) free(cfg->slcmd);
if (cfg->qmarg != NULL) free(cfg->qmarg);
if (cfg->maarg != NULL) free(cfg->maarg);
if (cfg->slarg != NULL) free(cfg->slarg);
}
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