forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8070 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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@ -25,6 +25,7 @@
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#include <iostream>
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#define NDEBUG //(disable assert())
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#include <cassert>
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#include <sstream>
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using namespace std;
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#include "atom.h"
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@ -38,6 +39,7 @@ using namespace std;
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#include "dihedral_table.h"
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// Additional header files available for numerical debugging:
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//#undef NDEBUG
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//#define DIH_DEBUG_NUM
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//#ifdef DIH_DEBUG_NUM
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//#include "dihedral_table_dbg.h" //in "supporting_files/debug_numerical/"
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@ -127,8 +129,8 @@ void DihedralTable::compute(int eflag, int vflag)
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// n123 & n234: These two unit vectors are normal to the planes
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// defined by atoms 1,2,3 and 2,3,4.
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double n123[g_dim]; //n123=vb12 x vb23 / |vb12 x vb23| ("x" is cross product)
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double n234[g_dim]; //n234=vb34 x vb23 / |vb34 x vb23| ("x" is cross product)
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double n123[g_dim]; //n123=vb23 x vb12 / |vb23 x vb12| ("x" is cross product)
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double n234[g_dim]; //n234=vb23 x vb34 / |vb23 x vb34| ("x" is cross product)
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double proj12on23[g_dim];
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// proj12on23[d] = (vb23[d]/|vb23|) * DotProduct(vb12,vb23)/|vb12|*|vb23|
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@ -457,9 +459,13 @@ void DihedralTable::coeff(int narg, char **arg)
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// check for monotonicity
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for (int i=0; i < tb->ninput-1; i++) {
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if (tb->phifile[i] >= tb->phifile[i+1]) {
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stringstream i_str;
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i_str << i+1;
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string err_msg =
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string("Dihedral table values are not increasing (") +
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string(arg[2]) + string(").");
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string(arg[2]) + string(", ")+i_str.str()+string("th entry)");
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if (i==0)
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err_msg += string("\n(This is probably a mistake with your table format.)\n");
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error->all(FLERR,err_msg.c_str());
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}
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}
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@ -597,7 +603,6 @@ void DihedralTable::coeff(int narg, char **arg)
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} // if (checkF_fname && (strlen(checkF_fname) != 0))
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} // if (me == 0)
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// store ptr to table in tabindex
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int count = 0;
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for (int i = ilo; i <= ihi; i++)
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@ -611,6 +616,7 @@ void DihedralTable::coeff(int narg, char **arg)
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if (count == 0)
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error->all(FLERR,"Illegal dihedral_coeff command");
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} //DihedralTable::coeff()
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@ -634,7 +640,9 @@ void DihedralTable::read_restart(FILE *fp)
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fread(&tabstyle,sizeof(int),1,fp);
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fread(&tablength,sizeof(int),1,fp);
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}
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MPI_Bcast(&tabstyle,1,MPI_DOUBLE,0,world);
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//MPI_Bcast(&tabstyle,1,MPI_DOUBLE,0,world); <-looks like a bug. Andrew 2012
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MPI_Bcast(&tabstyle,1,MPI_INT,0,world);
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MPI_Bcast(&tablength,1,MPI_INT,0,world);
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allocate();
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@ -689,8 +697,11 @@ void DihedralTable::read_table(Table *tb, char *file, char *keyword)
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// loop until section found with matching keyword
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while (1) {
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if (fgets(line,MAXLINE,fp) == NULL)
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error->one(FLERR,"Did not find keyword in dihedral table file");
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if (fgets(line,MAXLINE,fp) == NULL) {
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string err_msg=string("Did not find keyword \"")
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+string(keyword)+string("\" in dihedral table file.");
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error->one(FLERR, err_msg.c_str());
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}
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if (strspn(line," \t\n\r") == strlen(line)) continue; // blank line
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if (line[0] == '#') continue; // comment
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if (strstr(line,keyword) == line) break; // matching keyword
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@ -715,12 +726,40 @@ void DihedralTable::read_table(Table *tb, char *file, char *keyword)
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int itmp;
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for (int i = 0; i < tb->ninput; i++) {
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fgets(line,MAXLINE,fp);
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if (tb->f_unspecified)
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sscanf(line,"%d %lg %lg",
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&itmp,&tb->phifile[i],&tb->efile[i]);
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else
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sscanf(line,"%d %lg %lg %lg",
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&itmp,&tb->phifile[i],&tb->efile[i],&tb->ffile[i]);
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// Skip blank lines and delete text following a '#' character
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char *pe = strchr(line, '#');
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if (pe != NULL) *pe = '\0'; //terminate string at '#' character
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char *pc = line;
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while ((*pc != '\0') && isspace(*pc))
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pc++;
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if (*pc != '\0') { //If line is not a blank line
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stringstream line_ss(line);
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if (tb->f_unspecified) {
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//sscanf(line,"%d %lg %lg",
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// &itmp,&tb->phifile[i],&tb->efile[i]);
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line_ss >> itmp;
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line_ss >> tb->phifile[i];
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line_ss >> tb->efile[i];
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}
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else {
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//sscanf(line,"%d %lg %lg %lg",
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// &itmp,&tb->phifile[i],&tb->efile[i],&tb->ffile[i]);
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line_ss >> itmp;
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line_ss >> tb->phifile[i];
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line_ss >> tb->efile[i];
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line_ss >> tb->ffile[i];
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}
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if (! line_ss) {
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stringstream err_msg;
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err_msg << "Read error in table "<< keyword<<", near line "<<i+1<<"\n"
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<< " (Check to make sure the number of colums is correct.)";
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if ((! tb->f_unspecified) && (i==0))
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err_msg << "\n (This sometimes occurs if users forget to specify the \"NOF\" option.)\n";
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error->one(FLERR, err_msg.str().c_str());
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}
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}
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else //if it is a blank line, then skip it.
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i--;
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}
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fclose(fp);
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@ -51,8 +51,8 @@ class DihedralTable : public Dihedral {
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struct Table {
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int ninput;
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//double phi0; <-equilibrium angles not supported
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bool f_unspecified;
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bool use_degrees;
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int f_unspecified; // boolean (but MPI does not like type "bool")
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int use_degrees; // boolean (but MPI does not like type "bool")
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double *phifile,*efile,*ffile;
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double *e2file,*f2file;
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double delta,invdelta,deltasq6;
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@ -299,8 +299,8 @@ inline double Phi(double const *x1, //array holding x,y,z coords atom 1
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//--- Compute the normal to the planes formed by atoms 1,2,3 and 2,3,4 ---
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CrossProduct(vb12, vb23, n123); // <- n123=vb12 x vb23
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CrossProduct(vb34, vb23, n234); // <- n234=vb34 x vb23
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CrossProduct(vb23, vb12, n123); // <- n123=vb23 x vb12
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CrossProduct(vb23, vb34, n234); // <- n234=vb23 x vb34
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Normalize(n123);
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Normalize(n234);
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