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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8070 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2012-05-17 17:49:21 +00:00
parent 0f3c9e1e3d
commit 56933a0bd1
2 changed files with 60 additions and 21 deletions
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73
src/USER-MISC/dihedral_table.cpp
View File

@ -25,6 +25,7 @@
#include <iostream>
#define NDEBUG //(disable assert())
#include <cassert>
#include <sstream>
using namespace std;
#include "atom.h"
@ -38,6 +39,7 @@ using namespace std;
#include "dihedral_table.h"
// Additional header files available for numerical debugging:
//#undef NDEBUG
//#define DIH_DEBUG_NUM
//#ifdef DIH_DEBUG_NUM
//#include "dihedral_table_dbg.h" //in "supporting_files/debug_numerical/"
@ -127,8 +129,8 @@ void DihedralTable::compute(int eflag, int vflag)
// n123 & n234: These two unit vectors are normal to the planes
// defined by atoms 1,2,3 and 2,3,4.
double n123[g_dim]; //n123=vb12 x vb23 / |vb12 x vb23| ("x" is cross product)
double n234[g_dim]; //n234=vb34 x vb23 / |vb34 x vb23| ("x" is cross product)
double n123[g_dim]; //n123=vb23 x vb12 / |vb23 x vb12| ("x" is cross product)
double n234[g_dim]; //n234=vb23 x vb34 / |vb23 x vb34| ("x" is cross product)
double proj12on23[g_dim];
// proj12on23[d] = (vb23[d]/|vb23|) * DotProduct(vb12,vb23)/|vb12|*|vb23|
@ -215,8 +217,8 @@ void DihedralTable::compute(int eflag, int vflag)
if (perp34on23_len != 0.0) inv_perp34on23 = 1.0 / perp34on23_len;
for (int d=0; d < g_dim; ++d) {
dphi_dx1[d] = n123[d] * inv_perp12on23;
dphi_dx4[d] = n234[d] * inv_perp34on23;
dphi_dx1[d] = n123[d] * inv_perp12on23;
dphi_dx4[d] = n234[d] * inv_perp34on23;
}
// --- Compute the gradient vectors dphi/dx2 and dphi/dx3: ---
@ -433,7 +435,7 @@ void DihedralTable::coeff(int narg, char **arg)
int ilo,ihi;
force->bounds(arg[0],atom->ndihedraltypes,ilo,ihi);
int me;
MPI_Comm_rank(world,&me);
tables = (Table *)
@ -457,9 +459,13 @@ void DihedralTable::coeff(int narg, char **arg)
// check for monotonicity
for (int i=0; i < tb->ninput-1; i++) {
if (tb->phifile[i] >= tb->phifile[i+1]) {
stringstream i_str;
i_str << i+1;
string err_msg =
string("Dihedral table values are not increasing (") +
string(arg[2]) + string(").");
string("Dihedral table values are not increasing (") +
string(arg[2]) + string(", ")+i_str.str()+string("th entry)");
if (i==0)
err_msg += string("\n(This is probably a mistake with your table format.)\n");
error->all(FLERR,err_msg.c_str());
}
}
@ -597,7 +603,6 @@ void DihedralTable::coeff(int narg, char **arg)
} // if (checkF_fname && (strlen(checkF_fname) != 0))
} // if (me == 0)
// store ptr to table in tabindex
int count = 0;
for (int i = ilo; i <= ihi; i++)
@ -611,6 +616,7 @@ void DihedralTable::coeff(int narg, char **arg)
if (count == 0)
error->all(FLERR,"Illegal dihedral_coeff command");
} //DihedralTable::coeff()
@ -634,7 +640,9 @@ void DihedralTable::read_restart(FILE *fp)
fread(&tabstyle,sizeof(int),1,fp);
fread(&tablength,sizeof(int),1,fp);
}
MPI_Bcast(&tabstyle,1,MPI_DOUBLE,0,world);
//MPI_Bcast(&tabstyle,1,MPI_DOUBLE,0,world); <-looks like a bug. Andrew 2012
MPI_Bcast(&tabstyle,1,MPI_INT,0,world);
MPI_Bcast(&tablength,1,MPI_INT,0,world);
allocate();
@ -689,8 +697,11 @@ void DihedralTable::read_table(Table *tb, char *file, char *keyword)
// loop until section found with matching keyword
while (1) {
if (fgets(line,MAXLINE,fp) == NULL)
error->one(FLERR,"Did not find keyword in dihedral table file");
if (fgets(line,MAXLINE,fp) == NULL) {
string err_msg=string("Did not find keyword \"")
+string(keyword)+string("\" in dihedral table file.");
error->one(FLERR, err_msg.c_str());
}
if (strspn(line," \t\n\r") == strlen(line)) continue; // blank line
if (line[0] == '#') continue; // comment
if (strstr(line,keyword) == line) break; // matching keyword
@ -715,12 +726,40 @@ void DihedralTable::read_table(Table *tb, char *file, char *keyword)
int itmp;
for (int i = 0; i < tb->ninput; i++) {
fgets(line,MAXLINE,fp);
if (tb->f_unspecified)
sscanf(line,"%d %lg %lg",
&itmp,&tb->phifile[i],&tb->efile[i]);
else
sscanf(line,"%d %lg %lg %lg",
&itmp,&tb->phifile[i],&tb->efile[i],&tb->ffile[i]);
// Skip blank lines and delete text following a '#' character
char *pe = strchr(line, '#');
if (pe != NULL) *pe = '\0'; //terminate string at '#' character
char *pc = line;
while ((*pc != '\0') && isspace(*pc))
pc++;
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]);
line_ss >> itmp;
line_ss >> tb->phifile[i];
line_ss >> tb->efile[i];
line_ss >> tb->ffile[i];
}
if (! line_ss) {
stringstream err_msg;
err_msg << "Read error in table "<< keyword<<", near line "<<i+1<<"\n"
<< " (Check to make sure the number of colums is correct.)";
if ((! tb->f_unspecified) && (i==0))
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.
i--;
}
fclose(fp);

8
src/USER-MISC/dihedral_table.h
View File

@ -51,8 +51,8 @@ class DihedralTable : public Dihedral {
struct Table {
int ninput;
//double phi0; <-equilibrium angles not supported
bool f_unspecified;
bool use_degrees;
int f_unspecified; // boolean (but MPI does not like type "bool")
int use_degrees; // boolean (but MPI does not like type "bool")
double *phifile,*efile,*ffile;
double *e2file,*f2file;
double delta,invdelta,deltasq6;
@ -299,8 +299,8 @@ inline double Phi(double const *x1, //array holding x,y,z coords atom 1
//--- Compute the normal to the planes formed by atoms 1,2,3 and 2,3,4 ---
CrossProduct(vb12, vb23, n123); // <- n123=vb12 x vb23
CrossProduct(vb34, vb23, n234); // <- n234=vb34 x vb23
CrossProduct(vb23, vb12, n123); // <- n123=vb23 x vb12
CrossProduct(vb23, vb34, n234); // <- n234=vb23 x vb34
Normalize(n123);
Normalize(n234);