From 8492c4149e073c85583b3ba9d21863f905bfd6eb Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Tue, 23 Apr 2013 20:35:26 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9787
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/pair.h | 1 +
src/pair_coul_wolf.cpp | 5 ++++-
src/pair_lj_cut.cpp | 11 ++++++++++
src/pair_lj_cut.h | 1 +
src/read_data.cpp | 46 ++++++++++++++++++++++++++++++++++++++++--
src/read_data.h | 1 +
src/write_data.cpp | 28 ++++++++++++++++++++++---
src/write_data.h | 1 +
8 files changed, 88 insertions(+), 6 deletions(-)
diff --git a/src/pair.h b/src/pair.h
index 40f78934e4..8eb6854c09 100644
--- a/src/pair.h
+++ b/src/pair.h
@@ -153,6 +153,7 @@ class Pair : protected Pointers {
virtual void write_restart_settings(FILE *) {}
virtual void read_restart_settings(FILE *) {}
virtual void write_data(FILE *) {}
+ virtual void write_data_all(FILE *) {}
virtual int pack_comm(int, int *, double *, int, int *) {return 0;}
virtual void unpack_comm(int, int, double *) {}
diff --git a/src/pair_coul_wolf.cpp b/src/pair_coul_wolf.cpp
index af9751fa11..8cf821c2d7 100644
--- a/src/pair_coul_wolf.cpp
+++ b/src/pair_coul_wolf.cpp
@@ -34,7 +34,10 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
-PairCoulWolf::PairCoulWolf(LAMMPS *lmp) : Pair(lmp) {}
+PairCoulWolf::PairCoulWolf(LAMMPS *lmp) : Pair(lmp)
+{
+ writedata = 0;
+}
/* ---------------------------------------------------------------------- */
diff --git a/src/pair_lj_cut.cpp b/src/pair_lj_cut.cpp
index 15e7e7b855..becf294526 100644
--- a/src/pair_lj_cut.cpp
+++ b/src/pair_lj_cut.cpp
@@ -690,6 +690,17 @@ void PairLJCut::write_data(FILE *fp)
fprintf(fp,"%d %g %g\n",i,epsilon[i][i],sigma[i][i]);
}
+/* ----------------------------------------------------------------------
+ proc 0 writes all pairs to data file
+------------------------------------------------------------------------- */
+
+void PairLJCut::write_data_all(FILE *fp)
+{
+ for (int i = 1; i <= atom->ntypes; i++)
+ for (int j = i; j <= atom->ntypes; j++)
+ fprintf(fp,"%d %d %g %g %g\n",i,j,epsilon[i][i],sigma[i][i],cut[i][j]);
+}
+
/* ---------------------------------------------------------------------- */
double PairLJCut::single(int i, int j, int itype, int jtype, double rsq,
diff --git a/src/pair_lj_cut.h b/src/pair_lj_cut.h
index 46a7bf560d..cccd9d1c69 100644
--- a/src/pair_lj_cut.h
+++ b/src/pair_lj_cut.h
@@ -39,6 +39,7 @@ class PairLJCut : public Pair {
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
void write_data(FILE *);
+ void write_data_all(FILE *);
double single(int, int, int, int, double, double, double, double &);
void *extract(const char *, int &);
diff --git a/src/read_data.cpp b/src/read_data.cpp
index f03805cbca..56a7651e0a 100644
--- a/src/read_data.cpp
+++ b/src/read_data.cpp
@@ -47,7 +47,7 @@ using namespace LAMMPS_NS;
#define MAXBODY 20 // max # of lines in one body, also in Atom class
// customize for new sections
-#define NSECTIONS 24 // change when add to header::section_keywords
+#define NSECTIONS 25 // change when add to header::section_keywords
/* ---------------------------------------------------------------------- */
@@ -255,6 +255,10 @@ void ReadData::command(int narg, char **arg)
if (force->pair == NULL)
error->all(FLERR,"Must define pair_style before Pair Coeffs");
paircoeffs();
+ } else if (strcmp(keyword,"PairIJ Coeffs") == 0) {
+ if (force->pair == NULL)
+ error->all(FLERR,"Must define pair_style before PairIJ Coeffs");
+ pairIJcoeffs();
} else if (strcmp(keyword,"Bond Coeffs") == 0) {
if (atom->avec->bonds_allow == 0)
error->all(FLERR,"Invalid data file section: Bond Coeffs");
@@ -387,7 +391,7 @@ void ReadData::header(int flag)
const char *section_keywords[NSECTIONS] =
{"Atoms","Velocities","Ellipsoids","Lines","Triangles","Bodies",
"Bonds","Angles","Dihedrals","Impropers",
- "Masses","Pair Coeffs","Bond Coeffs","Angle Coeffs",
+ "Masses","Pair Coeffs","PairIJ Coeffs","Bond Coeffs","Angle Coeffs",
"Dihedral Coeffs","Improper Coeffs",
"BondBond Coeffs","BondAngle Coeffs","MiddleBondTorsion Coeffs",
"EndBondTorsion Coeffs","AngleTorsion Coeffs",
@@ -1062,6 +1066,40 @@ void ReadData::paircoeffs()
/* ---------------------------------------------------------------------- */
+void ReadData::pairIJcoeffs()
+{
+ int i,j,m;
+ char *buf = new char[atom->ntypes*(atom->ntypes+1)/2 * MAXLINE];
+ char *original = buf;
+
+ if (me == 0) {
+ char *eof;
+ m = 0;
+ for (i = 0; i < atom->ntypes; i++)
+ for (j = i; j < atom->ntypes; j++) {
+ eof = fgets(&buf[m],MAXLINE,fp);
+ if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
+ m += strlen(&buf[m]);
+ if (buf[m-1] != '\n') strcpy(&buf[m++],"\n");
+ buf[m-1] = '\0';
+ }
+ }
+
+ MPI_Bcast(&m,1,MPI_INT,0,world);
+ MPI_Bcast(buf,m,MPI_CHAR,0,world);
+
+ for (i = 0; i < atom->ntypes; i++)
+ for (j = i; j < atom->ntypes; j++) {
+ m = strlen(buf) + 1;
+ parse_coeffs(buf,NULL,0);
+ force->pair->coeff(narg,arg);
+ buf += m;
+ }
+ delete [] original;
+}
+
+/* ---------------------------------------------------------------------- */
+
void ReadData::bondcoeffs()
{
int i,m;
@@ -1305,6 +1343,10 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
if (force->pair == NULL)
error->one(FLERR,"Must define pair_style before Pair Coeffs");
skip_lines(atom->ntypes);
+ } else if (strcmp(keyword,"PairIJ Coeffs") == 0) {
+ if (force->pair == NULL)
+ error->one(FLERR,"Must define pair_style before Pair Coeffs");
+ skip_lines(atom->ntypes*(atom->ntypes+1)/2);
} else if (strcmp(keyword,"Bond Coeffs") == 0) {
if (atom->avec->bonds_allow == 0)
error->one(FLERR,"Invalid data file section: Bond Coeffs");
diff --git a/src/read_data.h b/src/read_data.h
index 4788cdacf7..b1d3bb48b1 100644
--- a/src/read_data.h
+++ b/src/read_data.h
@@ -72,6 +72,7 @@ class ReadData : protected Pointers {
void mass();
void paircoeffs();
+ void pairIJcoeffs();
void bondcoeffs();
void anglecoeffs(int);
void dihedralcoeffs(int);
diff --git a/src/write_data.cpp b/src/write_data.cpp
index cfb1f7855a..0f3de354ed 100644
--- a/src/write_data.cpp
+++ b/src/write_data.cpp
@@ -37,6 +37,7 @@
using namespace LAMMPS_NS;
enum{IGNORE,WARN,ERROR}; // same as thermo.cpp
+enum{II,IJ};
/* ---------------------------------------------------------------------- */
@@ -54,7 +55,8 @@ void WriteData::command(int narg, char **arg)
{
if (domain->box_exist == 0)
error->all(FLERR,"Write_data command before simulation box is defined");
- if (narg != 1) error->all(FLERR,"Illegal write_data command");
+
+ if (narg < 1) error->all(FLERR,"Illegal write_data command");
// if filename contains a "*", replace with current timestep
@@ -67,6 +69,21 @@ void WriteData::command(int narg, char **arg)
sprintf(file,"%s" BIGINT_FORMAT "%s",arg[0],update->ntimestep,ptr+1);
} else strcpy(file,arg[0]);
+ // read optional args
+
+ pairflag = II;
+
+ int iarg = 1;
+ while (iarg < narg) {
+ if (strcmp(arg[iarg],"pair") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal write_data command");
+ if (strcmp(arg[iarg+1],"ii") == 0) pairflag = II;
+ else if (strcmp(arg[iarg+1],"ij") == 0) pairflag = IJ;
+ else error->all(FLERR,"Illegal write_data command");
+ iarg += 2;
+ } else error->all(FLERR,"Illegal write_data command");
+ }
+
// init entire system since comm->exchange is done
// comm::init needs neighbor::init needs pair::init needs kspace::init, etc
@@ -224,8 +241,13 @@ void WriteData::type_arrays()
void WriteData::force_fields()
{
if (force->pair && force->pair->writedata) {
- fprintf(fp,"\nPair Coeffs\n\n");
- force->pair->write_data(fp);
+ if (pairflag == II) {
+ fprintf(fp,"\nPair Coeffs\n\n");
+ force->pair->write_data(fp);
+ } else if (pairflag == IJ) {
+ fprintf(fp,"\nPairIJ Coeffs\n\n");
+ force->pair->write_data_all(fp);
+ }
}
if (atom->avec->bonds_allow && force->bond && force->bond->writedata) {
fprintf(fp,"\nBond Coeffs\n\n");
diff --git a/src/write_data.h b/src/write_data.h
index 7b30441926..e879b00d76 100644
--- a/src/write_data.h
+++ b/src/write_data.h
@@ -33,6 +33,7 @@ class WriteData : protected Pointers {
private:
int me,nprocs;
+ int pairflag;
FILE *fp;
bigint nbonds_local,nbonds;
bigint nangles_local,nangles;
--
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