improved whitespace handling in msi2lmp for force fields and topologies (22ce6718) · Commits · 郑智淋 / lammps

tools/msi2lmp/README

+6 −1

Original line number	Diff line number	Diff line
		Axel Kohlmeyer is the current maintainer of the msi2lmp tool.
		Please send any inquiries about msi2lmp to the lammps-users mailing list.

		06 Oct 2016 Axel Kohlmeyer <akohlmey@gmail.com>

		Improved whitespace handling in parsing topology and force field
		files to avoid bogus warnings about type name truncation.

		24 Oct 2015 Axel Kohlmeyer <akohlmey@gmail.com>

		Added check to make certain that force field files
		are consistent with the notation of non-bonded parameters
		that the msi2lmp code expects. For Class 1 and OPLS-AA
		the A-B notation with geometric mixing is expected and for
		Class 2 the r-eps notation with sixthpower mixing.(
		Class 2 the r-eps notation with sixthpower mixing.

		11 Sep 2014 Axel Kohlmeyer <akohlmey@gmail.com>

tools/msi2lmp/src/ReadMdfFile.c

+8 −8

Original line number	Diff line number	Diff line
		@@ -74,9 +74,9 @@ void ReadMdfFile(void)
		at_end = 1;
		} else if (strncmp(line,"@column",7) == 0) {

		temp_string = strtok(line," ");
		col_no = strtok(NULL," ");
		col_name = strtok(NULL," ");
		temp_string = strtok(line,WHITESPACE);
		col_no = strtok(NULL,WHITESPACE);
		col_name = strtok(NULL,WHITESPACE);
		if (strncmp(col_name,"charge",6) == 0) {
		if (strlen(col_name) < 8) {
		q_col_no = atoi(col_no);
		@@ -285,7 +285,7 @@ int get_molecule(char *line, int connect_col_no, int q_col_no,
		/* Get atom name */
		cur_field = strtok(line,":");
		sscanf(cur_field, "%s", atoms[*counter].residue_string);
		cur_field = strtok(NULL," ");
		cur_field = strtok(NULL,WHITESPACE);
		/* Compare atom name with that in .car file */
		if (strcmp(atoms[*counter].name, cur_field)) {
		printf("Names %s from .car file and %s from .mdf file do not match\n",
		@@ -297,18 +297,18 @@ int get_molecule(char *line, int connect_col_no, int q_col_no,

		/* Skip unwanted fields until charge column, then update charge */

		for (i=1; i < q_col_no; i++) strtok(NULL," ");
		cur_field = strtok(NULL, " ");
		for (i=1; i < q_col_no; i++) strtok(NULL,WHITESPACE);
		cur_field = strtok(NULL, WHITESPACE);
		atoms[*counter].q = atof(cur_field);

		/* Continue skipping unwanted fields until connectivity records begin */

		for ( i = (q_col_no + 1); i < connect_col_no; i++) strtok(NULL," ");
		for ( i = (q_col_no + 1); i < connect_col_no; i++) strtok(NULL,WHITESPACE);

		/* Process connections */

		connect_no = 0; /* reset connections counter */
		while ((cur_field = strtok(NULL," ")) && (connect_no < MAX_CONNECTIONS)) {
		while ((cur_field = strtok(NULL,WHITESPACE)) && (connect_no < MAX_CONNECTIONS)) {
		sscanf(cur_field, "%s", atoms[*counter].connections[connect_no++]);
		}
		atoms[*counter].no_connect = connect_no;

tools/msi2lmp/src/SearchAndFill.c

+7 −7

Original line number	Diff line number	Diff line
		@@ -45,9 +45,9 @@ const char SearchAndCheck(const char keyword)
		exit(1);
		}
		if (line[0] == '@') {
		if (string_match(strtok(line+1," '\t\n'("),keyword)) {
		if (string_match(strtok(line+1," '\t\n\r\f("),keyword)) {
		got_it = 1;
		status = strtok(NULL," '\t\n(");
		status = strtok(NULL," '\t\n\r\f(");
		if (status != NULL)
		return strdup(status);
		}
		@@ -79,7 +79,7 @@ void SearchAndFill(struct FrcFieldItem *item)
		exit(1);
		}
		if (line[0] == '#') {
		if (string_match(strtok(line," '\t'("),item->keyword)) got_it = 1;
		if (string_match(strtok(line," '\t\r\n("),item->keyword)) got_it = 1;
		}
		/* if (strncmp(line, item->keyword,strlen(item->keyword))==0) got_it = 1; */
		}
		@@ -132,13 +132,13 @@ void SearchAndFill(struct FrcFieldItem *item)

		/* version number and reference number */

		version = atof(strtok(line, " "));
		reference = atoi(strtok(NULL, " "));
		version = atof(strtok(line, WHITESPACE));
		reference = atoi(strtok(NULL, WHITESPACE));

		/* equivalences */

		for(i = 0; i < item->number_of_members; i++ ) {
		charptr = strtok(NULL, " ");
		charptr = strtok(NULL, WHITESPACE);
		if (strlen(charptr) > 4) {
		fprintf(stderr,"Warning: type name overflow for '%s'. "
		"Truncating to 4 characters.\n",charptr);
		@@ -150,7 +150,7 @@ void SearchAndFill(struct FrcFieldItem *item)
		endbontor have to be treated carefully */

		for( i = 0; i < item->number_of_parameters; i++ ) {
		charptr = strtok(NULL, " ");
		charptr = strtok(NULL, WHITESPACE);
		if(charptr == NULL) {
		for ( j = i; j < item->number_of_parameters; j++ )
		parameters[j] = parameters[j-i];

tools/msi2lmp/src/msi2lmp.c

+3 −0

Original line number	Diff line number	Diff line
		@@ -2,6 +2,9 @@
		*
		* msi2lmp.exe
		*
		* v3.9.8 AK- Improved whitespace handling in parsing topology and force
		* field files to avoid bogus warnings about type name truncation
		*
		* v3.9.7 AK- Add check to enforce that Class1/OPLS-AA use A-B parameter
		* conventions in force field file and Class2 us r-eps conventions
		*

tools/msi2lmp/src/msi2lmp.h

+3 −1

Original line number	Diff line number	Diff line
		@@ -36,7 +36,7 @@

		# include <stdio.h>

		#define MSI2LMP_VERSION "v3.9.7 / 24 Oct 2015"
		#define MSI2LMP_VERSION "v3.9.8 / 06 Oct 2016"

		#define PI_180 0.01745329251994329576

		@@ -45,6 +45,8 @@
		#define MAX_STRING 64
		#define MAX_NAME 16

		#define WHITESPACE " \t\r\n\f"

		#define MAX_ATOM_TYPES 100
		#define MAX_BOND_TYPES 200
		#define MAX_ANGLE_TYPES 300

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