Added FixMSST in package shock

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4275 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/SHOCK/Install.sh

@@ -0,0 +1,19 @@
+# Install/unInstall package files in LAMMPS
+
+if (test $1 = 1) then
+
+  cp fix_msst.cpp ..
+  cp compute_vsum.cpp ..
+
+  cp fix_msst.h ..
+  cp compute_vsum.h ..
+
+elif (test $1 = 0) then
+
+  rm ../fix_msst.cpp
+  rm ../compute_vsum.cpp
+
+  rm ../fix_msst.h
+  rm ../compute_vsum.h
+
+fi

src/SHOCK/compute_vsum.cpp

@@ -0,0 +1,77 @@
+/* ----------------------------------------------------------------------
+   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 "mpi.h"
+#include "compute_vsum.h"
+#include "atom.h"
+#include "force.h"
+#include "modify.h"
+#include "fix.h"
+#include "group.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+ComputeVsum::ComputeVsum(LAMMPS *lmp, int narg, char **arg) : 
+  Compute(lmp, narg, arg)
+{
+  if (narg != 3) error->all("Illegal compute temp command");
+
+  scalar_flag = vector_flag = 1;
+  size_vector = 6;
+  extscalar = 0;
+  tempflag = 1;
+
+  vector = new double[6];
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeVsum::~ComputeVsum()
+{
+  delete [] vector;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeVsum::init()
+{
+  ;
+}
+
+/* ---------------------------------------------------------------------- */
+
+/* ---------------------------------------------------------------------- */
+
+double ComputeVsum::compute_scalar()
+{
+  double **v = atom->v;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+
+  double t = 0.0;
+
+  for (int i = 0; i < nlocal; i++) {
+    if (mask[i] & groupbit) {
+      t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) ;
+    }
+  }
+
+  MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
+  return scalar;
+}
+
+/* ---------------------------------------------------------------------- */
+

src/SHOCK/compute_vsum.h

@@ -0,0 +1,42 @@
+/* ----------------------------------------------------------------------
+   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.
+------------------------------------------------------------------------- */
+
+// Compute the sum of the squared velocities, without usual mass terms
+// for the kinetic energy.  This is used for the MSST (Larry Fried).
+
+#ifdef COMPUTE_CLASS
+
+ComputeStyle(vsum,ComputeVsum)
+
+#else
+
+#ifndef COMPUTE_VSUM_H
+#define COMPUTE_VSUM_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+class ComputeVsum : public Compute {
+ public:
+  ComputeVsum(class LAMMPS *, int, char **);
+  ~ComputeVsum();
+  void init();
+  double compute_scalar();
+
+};
+
+}
+
+#endif
+#endif

src/SHOCK/fix_msst.h

@@ -0,0 +1,108 @@
+/* ----------------------------------------------------------------------
+   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.
+------------------------------------------------------------------------- */
+/* Implementation of the Multi-Scale Shock Method.
+   See Reed, Fried, Joannopoulos, Phys. Rev. Lett., 90, 235503(2003).
+   Implementation by Laurence Fried, LLNL, 4/2007.
+*/
+
+#ifdef FIX_CLASS
+
+FixStyle(msst,FixMSST)
+
+#else
+
+#ifndef FIX_MSST_H
+#define FIX_MSST_H
+
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+class FixMSST : public Fix {
+ public:
+  FixMSST(class LAMMPS *, int, char **);
+  ~FixMSST();
+  int setmask();
+  void init();
+  void setup(int);
+  void initial_integrate(int);
+  void final_integrate();
+  void initial_integrate_respa(int,int,int);
+  void final_integrate_respa(int);
+  double compute_scalar();
+  double compute_vector(int);
+  void write_restart(FILE *);
+  void restart(char *);
+  int modify_param(int, char **);
+
+ private:
+  double dtv,dtf,dthalf;           // Full and half step sizes.
+  double boltz,nktv2p, mvv2e;      // Boltzmann factor and unit conversions.
+  double total_mass;               // Mass of the computational cell.
+
+  double omega[3];                 // Time derivative of the volume.
+  double p_current[3],dilation[3];
+  double qmass;                    // Effective cell mass.
+  double mu;                       // Effective cell viscosity.
+  double tscale;                   // Converts thermal energy to compressive 
+                                   // strain ke at simulation start
+  
+  double velocity_sum;             // Sum of the velocities squared.
+
+  double **old_velocity;           // Saved velocities.
+
+  int kspace_flag;                 // 1 if KSpace invoked, 0 if not
+  int nrigid;                      // number of rigid fixes
+  int *rfix;                       // indices of rigid fixes
+
+  char *id_temp,*id_press;         // Strings with identifiers of
+  char *id_vsum, *id_pe;           // created computes.
+
+  class Compute *temperature;      // Computes created to evaluate 
+  class Compute *pressure;         // thermodynamic quantities.
+  class Compute *vsum; 
+  class Compute *pe;
+  int tflag,pflag,vsflag,peflag;   // Flags to keep track of computes that
+                                   // were created.
+
+  // shock initial conditions.
+
+  double e0;                       // Initial energy
+  double v0;                       // Initial volume
+  double p0;                       // Initial pressure
+  double velocity;                 // Velocity of the shock.
+  double lagrangian_position;      // Lagrangian location of computational cell  
+  int direction;                   // Direction of shock
+  int p0_set;                      // Is pressure set.
+  int v0_set;                      // Is volume set.
+  int e0_set;                      // Is energy set.
+    
+  int atoms_allocated;             // The number of allocated atoms in old_velocity.
+
+  // functions 
+
+  void couple();
+  void remap(int);
+  void check_alloc(int n);
+  double compute_etotal();
+  double compute_vol();
+  double compute_hugoniot();
+  double compute_rayleigh();
+  double compute_lagrangian_speed();
+  double compute_lagrangian_position();
+};
+
+}
+
+#endif
+#endif