From c3414bf5f612dbe3e280b529dfc363cffc52cb04 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Fri, 18 Jun 2010 16:00:10 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4296
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/fix_adapt.cpp | 196 ++++++++++++++++++++++++++++++++++++++++++++++
src/fix_adapt.h | 50 ++++++++++++
2 files changed, 246 insertions(+)
create mode 100644 src/fix_adapt.cpp
create mode 100644 src/fix_adapt.h
diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp
new file mode 100644
index 0000000000..65397b1894
--- /dev/null
+++ b/src/fix_adapt.cpp
@@ -0,0 +1,196 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "string.h"
+#include "stdlib.h"
+#include "fix_adapt.h"
+#include "atom.h"
+#include "force.h"
+#include "pair.h"
+#include "input.h"
+#include "variable.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+enum{PAIR,ATOM};
+enum{DIAMETER};
+
+/* ---------------------------------------------------------------------- */
+
+FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
+{
+ if (narg < 4) error->all("Illegal fix adapt command");
+ nevery = atoi(arg[3]);
+ if (nevery <= 0) error->all("Illegal fix adapt command");
+
+ // count # of adaptations
+
+ nadapt = 0;
+
+ int iarg = 4;
+ while (iarg < narg) {
+ if (strcmp(arg[iarg],"pair") == 0) {
+ if (iarg+6 > narg) error->all("Illegal fix adapt command");
+ nadapt++;
+ iarg += 6;
+ } else if (strcmp(arg[iarg],"atom") == 0) {
+ if (iarg+3 > narg) error->all("Illegal fix adapt command");
+ nadapt++;
+ iarg += 3;
+ } else error->all("Illegal fix adapt command");
+ }
+
+ // allocate per-adapt vectors
+
+ which = new int[nadapt];
+ pair = new char*[nadapt];
+ param = new char*[nadapt];
+ ilo = new int[nadapt];
+ ihi = new int[nadapt];
+ jlo = new int[nadapt];
+ jhi = new int[nadapt];
+ var = new char*[nadapt];
+ ivar = new int[nadapt];
+ pairptr = new Pair*[nadapt];
+ pairindex = new int[nadapt];
+ awhich = new int[nadapt];
+
+ // parse keywords
+
+ nadapt = 0;
+
+ iarg = 4;
+ while (iarg < narg) {
+ if (strcmp(arg[iarg],"pair") == 0) {
+ if (iarg+6 > narg) error->all("Illegal fix adapt command");
+ which[nadapt] = PAIR;
+ int n = strlen(arg[iarg+1]) + 1;
+ pair[nadapt] = new char[n];
+ strcpy(pair[nadapt],arg[iarg+1]);
+ n = strlen(arg[iarg+2]) + 1;
+ param[nadapt] = new char[n];
+ strcpy(param[nadapt],arg[iarg+2]);
+ force->bounds(arg[iarg+3],atom->ntypes,ilo[nadapt],ihi[nadapt]);
+ force->bounds(arg[iarg+4],atom->ntypes,jlo[nadapt],jhi[nadapt]);
+ n = strlen(arg[iarg+5]) + 1;
+ var[nadapt] = new char[n];
+ strcpy(var[nadapt],arg[iarg+5]);
+ nadapt++;
+ iarg += 6;
+ } else if (strcmp(arg[iarg],"atom") == 0) {
+ if (iarg+3 > narg) error->all("Illegal fix adapt command");
+ which[nadapt] = ATOM;
+ int n = strlen(arg[iarg+1]) + 1;
+ param[nadapt] = new char[n];
+ strcpy(param[nadapt],arg[iarg+1]);
+ n = strlen(arg[iarg+2]) + 1;
+ var[nadapt] = new char[n];
+ strcpy(var[nadapt],arg[iarg+2]);
+ nadapt++;
+ iarg += 3;
+ } else error->all("Illegal fix adapt command");
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+FixAdapt::~FixAdapt()
+{
+ for (int i = 0; i < nadapt; i++) {
+ if (which[i] == PAIR) delete [] pair[i];
+ delete [] param[i];
+ delete [] var[i];
+ }
+ delete [] which;
+ delete [] pair;
+ delete [] param;
+ delete [] ilo;
+ delete [] ihi;
+ delete [] jlo;
+ delete [] jhi;
+ delete [] var;
+ delete [] ivar;
+ delete [] pairptr;
+ delete [] pairindex;
+ delete [] awhich;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixAdapt::setmask()
+{
+ int mask = 0;
+ mask |= PRE_FORCE;
+ return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixAdapt::init()
+{
+ // error checks
+
+ for (int m = 0; m < nadapt; m++) {
+ if (which[m] == PAIR) {
+ pairptr[m] = force->pair_match(pair[m],1);
+ if (pairptr[m] == NULL)
+ error->all("Fix adapt pair style does not exist");
+ pairindex[m] =
+ pairptr[m]->pre_adapt(param[m],ilo[m],ihi[m],jlo[m],jhi[m]);
+ if (pairindex[m] < 0)
+ error->all("Fix adapt pair style is not compatible");
+ } else if (which[m] == ATOM) {
+ if (strcmp(param[m],"diameter") == 0) {
+ awhich[m] = DIAMETER;
+ if (!atom->radius_flag)
+ error->all("Fix adapt requires atom attribute radius");
+ } else error->all("Invalid fix adapt atom attribute");
+ }
+
+ ivar[m] = input->variable->find(var[m]);
+ if (ivar[m] < 0) error->all("Variable name for fix adapt does not exist");
+ if (!input->variable->equalstyle(ivar[m]))
+ error->all("Variable for fix adapt is not equal style");
+ }
+
+ // set params to values for initial force calculation
+ // needs to happen here in init() instead of setup()
+ // because modify->setup() is called after pre-Verlet forces are computed
+
+ pre_force(0);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixAdapt::pre_force(int vflag)
+{
+ for (int m = 0; m < nadapt; m++) {
+ double value = input->variable->compute_equal(ivar[m]);
+
+ if (which[m] == PAIR)
+ pairptr[m]->adapt(pairindex[m],ilo[m],ihi[m],jlo[m],jhi[m],value);
+
+ else if (which[m] == ATOM) {
+ double *radius = atom->radius;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+
+ if (awhich[m] == DIAMETER) {
+ for (int i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit)
+ radius[i] = 0.5*value;
+ }
+ }
+ }
+}
diff --git a/src/fix_adapt.h b/src/fix_adapt.h
new file mode 100644
index 0000000000..1411708e71
--- /dev/null
+++ b/src/fix_adapt.h
@@ -0,0 +1,50 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+
+FixStyle(adapt,FixAdapt)
+
+#else
+
+#ifndef LMP_FIX_ADAPT_H
+#define LMP_FIX_ADAPT_H
+
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+class FixAdapt : public Fix {
+ public:
+ FixAdapt(class LAMMPS *, int, char **);
+ ~FixAdapt();
+ int setmask();
+ void init();
+ void pre_force(int);
+
+ private:
+ int nadapt;
+ int *which;
+ char **pair,**param,**var;
+ int *ilo,*ihi,*jlo,*jhi;
+
+ int *ivar;
+ class Pair **pairptr;
+ int *pairindex;
+ int *awhich;
+};
+
+}
+
+#endif
+#endif
--
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