convert several more table styles to use utils::sfgets() (c42b2698) · Commits · 郑智淋 / lammps

src/MOLECULE/angle_table.cpp

+21 −10

Original line number	Diff line number	Diff line
		@@ -27,6 +27,7 @@
		#include "math_const.h"
		#include "memory.h"
		#include "error.h"
		#include "utils.h"

		using namespace LAMMPS_NS;
		using namespace MathConst;
		@@ -382,16 +383,17 @@ void AngleTable::read_table(Table tb, char file, char *keyword)
		if (line[0] == '#') continue; // comment
		char *word = strtok(line," \t\n\r");
		if (strcmp(word,keyword) == 0) break; // matching keyword
		fgets(line,MAXLINE,fp); // no match, skip section
		utils::sfgets(FLERR,line,MAXLINE,fp,file,error); // no match, skip section
		param_extract(tb,line);
		fgets(line,MAXLINE,fp);
		for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp);
		utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
		for (int i = 0; i < tb->ninput; i++)
		utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
		}

		// read args on 2nd line of section
		// allocate table arrays for file values

		fgets(line,MAXLINE,fp);
		utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
		param_extract(tb,line);
		memory->create(tb->afile,tb->ninput,"angle:afile");
		memory->create(tb->efile,tb->ninput,"angle:efile");
		@@ -399,15 +401,24 @@ void AngleTable::read_table(Table tb, char file, char *keyword)

		// read a,e,f table values from file

		int itmp;
		fgets(line,MAXLINE,fp);
		int cerror = 0;
		utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
		for (int i = 0; i < tb->ninput; i++) {
		fgets(line,MAXLINE,fp);
		sscanf(line,"%d %lg %lg %lg",
		&itmp,&tb->afile[i],&tb->efile[i],&tb->ffile[i]);
		utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
		if (3 != sscanf(line,"%*d %lg %lg %lg",
		&tb->afile[i],&tb->efile[i],&tb->ffile[i])) ++cerror;
		}

		fclose(fp);

		// warn if data was read incompletely, e.g. columns were missing

		if (cerror) {
		char str[128];
		sprintf(str,"%d of %d lines in table were incomplete or could not be"
		" parsed completely",cerror,tb->ninput);
		error->warning(FLERR,str);
		}
		}

		/* ----------------------------------------------------------------------

src/MOLECULE/bond_table.cpp

+10 −11

Original line number	Diff line number	Diff line
		@@ -26,6 +26,7 @@
		#include "force.h"
		#include "memory.h"
		#include "error.h"
		#include "utils.h"

		using namespace LAMMPS_NS;

		@@ -311,16 +312,17 @@ void BondTable::read_table(Table tb, char file, char *keyword)
		if (line[0] == '#') continue; // comment
		char *word = strtok(line," \t\n\r");
		if (strcmp(word,keyword) == 0) break; // matching keyword
		fgets(line,MAXLINE,fp); // no match, skip section
		utils::sfgets(FLERR,line,MAXLINE,fp,file,error); // no match, skip section
		param_extract(tb,line);
		fgets(line,MAXLINE,fp);
		for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp);
		utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
		for (int i = 0; i < tb->ninput; i++)
		utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
		}

		// read args on 2nd line of section
		// allocate table arrays for file values

		fgets(line,MAXLINE,fp);
		utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
		param_extract(tb,line);
		memory->create(tb->rfile,tb->ninput,"bond:rfile");
		memory->create(tb->efile,tb->ninput,"bond:efile");
		@@ -328,16 +330,15 @@ void BondTable::read_table(Table tb, char file, char *keyword)

		// read r,e,f table values from file

		int itmp;
		int cerror = 0;
		int r0idx = -1;

		fgets(line,MAXLINE,fp);
		utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
		for (int i = 0; i < tb->ninput; i++) {
		if (NULL == fgets(line,MAXLINE,fp))
		error->one(FLERR,"Premature end of file in bond table");
		if (4 != sscanf(line,"%d %lg %lg %lg",
		&itmp,&tb->rfile[i],&tb->efile[i],&tb->ffile[i])) ++cerror;
		if (3 != sscanf(line,"%*d %lg %lg %lg",
		&tb->rfile[i],&tb->efile[i],&tb->ffile[i])) ++cerror;
		if (tb->efile[i] < emin) {
		emin = tb->efile[i];
		r0idx = i;
		@@ -369,8 +370,6 @@ void BondTable::read_table(Table tb, char file, char *keyword)
		fright = - (enext-e) / (rnext-r);
		if (f < fleft && f < fright) ferror++;
		if (f > fleft && f > fright) ferror++;
		//printf("Values %d: %g %g %g\n",i,r,e,f);
		//printf(" secant %d %d %g: %g %g %g\n",i,ferror,r,fleft,fright,f);
		}

		if (ferror) {

src/USER-MISC/dihedral_table.cpp

+11 −17

Original line number	Diff line number	Diff line
		@@ -35,6 +35,7 @@
		#include "memory.h"
		#include "error.h"
		#include "dihedral_table.h"
		#include "utils.h"

		#include "math_const.h"
		#include "math_extra.h"
		@@ -51,7 +52,7 @@ using namespace MathExtra;
		// ------------------------------------------------------------------------

		// -------------------------------------------------------------------
		// --------- The function was stolen verbatim from the ---------
		// --------- The function was taken verbatim from the ---------
		// --------- GNU Scientific Library (GSL, version 1.15) ---------
		// -------------------------------------------------------------------

		@@ -1091,17 +1092,17 @@ void DihedralTable::read_table(Table tb, char file, char *keyword)
		if (line[0] == '#') continue; // comment
		char *word = strtok(line," \t\n\r");
		if (strcmp(word,keyword) == 0) break; // matching keyword
		fgets(line,MAXLINE,fp); // no match, skip section
		utils::sfgets(FLERR,line,MAXLINE,fp,file,error); // no match, skip section
		param_extract(tb,line);
		fgets(line,MAXLINE,fp);
		utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
		for (int i = 0; i < tb->ninput; i++)
		fgets(line,MAXLINE,fp);
		utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
		}

		// read args on 2nd line of section
		// allocate table arrays for file values

		fgets(line,MAXLINE,fp);
		utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
		param_extract(tb,line);
		memory->create(tb->phifile,tb->ninput,"dihedral:phifile");
		memory->create(tb->efile,tb->ninput,"dihedral:efile");
		@@ -1111,9 +1112,8 @@ void DihedralTable::read_table(Table tb, char file, char *keyword)

		int itmp;
		for (int i = 0; i < tb->ninput; i++) {
		// Read the next line. Make sure the file is long enough.
		if (! fgets(line,MAXLINE,fp))
		error->one(FLERR, "Dihedral table does not contain enough entries.");
		utils::sfgets(FLERR,line,MAXLINE,fp,file,error);

		// Skip blank lines and delete text following a '#' character
		char *pe = strchr(line, '#');
		if (pe != NULL) *pe = '\0'; //terminate string at '#' character
		@@ -1123,15 +1123,10 @@ void DihedralTable::read_table(Table tb, char file, char *keyword)
		if (*pc != '\0') { //If line is not a blank line
		stringstream line_ss(line);
		if (tb->f_unspecified) {
		//sscanf(line,"%d %lg %lg",
		// &itmp,&tb->phifile[i],&tb->efile[i]);
		line_ss >> itmp;
		line_ss >> tb->phifile[i];
		line_ss >> tb->efile[i];
		}
		else {
		//sscanf(line,"%d %lg %lg %lg",
		// &itmp,&tb->phifile[i],&tb->efile[i],&tb->ffile[i]);
		} else {
		line_ss >> itmp;
		line_ss >> tb->phifile[i];
		line_ss >> tb->efile[i];
		@@ -1145,8 +1140,7 @@ void DihedralTable::read_table(Table tb, char file, char *keyword)
		err_msg << "\n (This sometimes occurs if users forget to specify the \"NOF\" option.)\n";
		error->one(FLERR, err_msg.str().c_str());
		}
		}
		else //if it is a blank line, then skip it.
		} else //if it is a blank line, then skip it.
		i--;
		} //for (int i = 0; (i < tb->ninput) && fp; i++) {

src/USER-MISC/dihedral_table_cut.cpp

+11 −16

Original line number	Diff line number	Diff line
		@@ -37,6 +37,7 @@
		#include "math_extra.h"
		#include "memory.h"
		#include "error.h"
		#include "utils.h"

		using namespace LAMMPS_NS;
		using namespace MathConst;
		@@ -45,7 +46,7 @@ using namespace MathExtra;


		static const char cite_dihedral_tablecut[] =
		"dihedral_style tablecut command:\n\n"
		"dihedral_style table/cut command:\n\n"
		"@Article{Salerno17,\n"
		" author = {K. M. Salerno and N. Bernstein},\n"
		" title = {Persistence Length, End-to-End Distance, and Structure of Coarse-Grained Polymers},\n"
		@@ -66,7 +67,7 @@ static const char cite_dihedral_tablecut[] =
		// ------------------------------------------------------------------------

		// -------------------------------------------------------------------
		// --------- The function was stolen verbatim from the ---------
		// --------- The function was taken verbatim from the ---------
		// --------- GNU Scientific Library (GSL, version 1.15) ---------
		// -------------------------------------------------------------------

		@@ -1151,17 +1152,17 @@ void DihedralTableCut::read_table(Table tb, char file, char *keyword)
		if (line[0] == '#') continue; // comment
		char *word = strtok(line," \t\n\r");
		if (strcmp(word,keyword) == 0) break; // matching keyword
		fgets(line,MAXLINE,fp); // no match, skip section
		utils::sfgets(FLERR,line,MAXLINE,fp,file,error); // no match, skip section
		param_extract(tb,line);
		fgets(line,MAXLINE,fp);
		utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
		for (int i = 0; i < tb->ninput; i++)
		fgets(line,MAXLINE,fp);
		utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
		}

		// read args on 2nd line of section
		// allocate table arrays for file values

		fgets(line,MAXLINE,fp);
		utils::sfgets(FLERR,line,MAXLINE,fp,file,error);
		param_extract(tb,line);
		memory->create(tb->phifile,tb->ninput,"dihedral:phifile");
		memory->create(tb->efile,tb->ninput,"dihedral:efile");
		@@ -1172,8 +1173,8 @@ void DihedralTableCut::read_table(Table tb, char file, char *keyword)
		int itmp;
		for (int i = 0; i < tb->ninput; i++) {
		// Read the next line. Make sure the file is long enough.
		if (! fgets(line,MAXLINE,fp))
		error->one(FLERR, "Dihedral table does not contain enough entries.");
		utils::sfgets(FLERR,line,MAXLINE,fp,file,error);

		// Skip blank lines and delete text following a '#' character
		char *pe = strchr(line, '#');
		if (pe != NULL) *pe = '\0'; //terminate string at '#' character
		@@ -1183,15 +1184,10 @@ void DihedralTableCut::read_table(Table tb, char file, char *keyword)
		if (*pc != '\0') { //If line is not a blank line
		stringstream line_ss(line);
		if (tb->f_unspecified) {
		//sscanf(line,"%d %lg %lg",
		// &itmp,&tb->phifile[i],&tb->efile[i]);
		line_ss >> itmp;
		line_ss >> tb->phifile[i];
		line_ss >> tb->efile[i];
		}
		else {
		//sscanf(line,"%d %lg %lg %lg",
		// &itmp,&tb->phifile[i],&tb->efile[i],&tb->ffile[i]);
		} else {
		line_ss >> itmp;
		line_ss >> tb->phifile[i];
		line_ss >> tb->efile[i];
		@@ -1205,8 +1201,7 @@ void DihedralTableCut::read_table(Table tb, char file, char *keyword)
		err_msg << "\n (This sometimes occurs if users forget to specify the \"NOF\" option.)\n";
		error->one(FLERR, err_msg.str().c_str());
		}
		}
		else //if it is a blank line, then skip it.
		} else //if it is a blank line, then skip it.
		i--;
		} //for (int i = 0; (i < tb->ninput) && fp; i++) {

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