Merge pull request #310 from EfremBraun/master

Fix nvk implemented

doc/src/Section_commands.txt

@@ -702,6 +702,7 @@ package"_Section_start.html#start_3.
 "manifoldforce"_fix_manifoldforce.html,
 "meso/stationary"_fix_meso_stationary.html,
 "nve/manifold/rattle"_fix_nve_manifold_rattle.html,
+"nvk"_fix_nvk.html,
 "nvt/manifold/rattle"_fix_nvt_manifold_rattle.html,
 "nph/eff"_fix_nh_eff.html,
 "npt/eff"_fix_nh_eff.html,

doc/src/fix_nvk.txt

@@ -0,0 +1,71 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix nvk command :h3
+
+[Syntax:]
+
+fix ID group-ID nvk :pre
+
+ID, group-ID are documented in "fix"_fix.html command
+nvk = style name of this fix command :ul
+
+[Examples:]
+
+fix 1 all nvk :pre
+
+[Description:]
+
+Perform constant kinetic energy integration using the Gaussian
+thermostat to update position and velocity for atoms in the group each
+timestep.  V is volume; K is kinetic energy. This creates a system
+trajectory consistent with the isokinetic ensemble.
+
+The equations of motion used are those of Minary et al in
+"(Minary)"_#nvk-Minary, a variant of those initially given by Zhang in 
+"(Zhang)"_#nvk-Zhang.
+
+The kinetic energy will be held constant at its value given when fix
+nvk is initiated. If a different kinetic energy is desired, the
+"velocity"_velocity.html command should be used to change the kinetic
+energy prior to this fix.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various "output
+commands"_Section_howto.html#howto_15.  No parameter of this fix can
+be used with the {start/stop} keywords of the "run"_run.html command.
+This fix is not invoked during "energy minimization"_minimize.html.
+
+[Restrictions:]
+
+The Gaussian thermostat only works when it is applied to all atoms in
+the simulation box. Therefore, the group must be set to all.
+
+This fix has not yet been implemented to work with the RESPA integrator.
+
+This fix is part of the USER-MISC package.  It is only enabled if LAMMPS
+was built with that package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:] none
+
+[Default:] none
+
+:line
+
+:link(nvk-Minary)
+[(Minary)] Minary, Martyna, and Tuckerman, J Chem Phys, 18, 2510 (2003).
+
+:link(nvk-Zhang)
+[(Zhang)] Zhang, J Chem Phys, 106, 6102 (1997).

doc/src/fixes.txt

@@ -90,6 +90,7 @@ Fixes :h1
    fix_nve_noforce
    fix_nve_sphere
    fix_nve_tri
+   fix_nvk
    fix_nvt_asphere
    fix_nvt_body
    fix_nvt_manifold_rattle

src/USER-MISC/README

@@ -43,6 +43,7 @@ fix gle, Michele Ceriotti (EPFL Lausanne), michele.ceriotti at gmail.com, 24 Nov
 fix grem, David Stelter, dstelter@bu.edu, 22 Nov 16
 fix imd, Axel Kohlmeyer, akohlmey at gmail.com, 9 Nov 2009
 fix ipi, Michele Ceriotti (EPFL Lausanne), michele.ceriotti at gmail.com, 24 Nov 2014
+fix nvk, Efrem Braun (UC Berkeley), efrem.braun at gmail.com, https://github.com/lammps/lammps/pull/310
 fix pimd, Yuxing Peng (U Chicago), yuxing at uchicago.edu, 24 Nov 2014
 fix smd, Axel Kohlmeyer, akohlmey at gmail.com, 19 May 2008
 fix ti/spring, Rodrigo Freitas (Unicamp/Brazil), rodrigohb at gmail.com, 7 Nov 2013

src/USER-MISC/fix_nvk.cpp

@@ -0,0 +1,219 @@
+/* ----------------------------------------------------------------------
+   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.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+     Contributing author: Efrem Braun (UC Berkeley)
+------------------------------------------------------------------------- */
+
+#include <math.h>
+#include <stdio.h>
+#include <string.h>
+#include "fix_nvk.h"
+#include "atom.h"
+#include "force.h"
+#include "update.h"
+#include "respa.h"
+#include "error.h"
+#include "compute.h"
+#include "math_extra.h"
+#include "domain.h"
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+FixNVK::FixNVK(LAMMPS *lmp, int narg, char **arg) :
+  Fix(lmp, narg, arg)
+{
+  if (narg < 3)
+    error->all(FLERR,"Illegal fix nvk command");
+  if (igroup) error->all(FLERR,"Fix nvk only supports group all");
+
+  dynamic_group_allow = 1;
+  time_integrate = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixNVK::setmask()
+{
+  int mask = 0;
+  mask |= INITIAL_INTEGRATE;
+  mask |= FINAL_INTEGRATE;
+  mask |= INITIAL_INTEGRATE_RESPA;
+  mask |= FINAL_INTEGRATE_RESPA;
+  return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNVK::init()
+{
+  dtv = update->dt;
+  dtf = 0.5 * update->dt;
+
+  if (strstr(update->integrate_style,"respa")) {
+    error->all(FLERR,"Fix nvk not yet enabled for RESPA");
+    step_respa = ((Respa *) update->integrate)->step;
+  }
+
+  // compute initial kinetic energy
+  // make better by calling compute_ke instead of copy/pasting code from compute_ke.cpp
+  double pfactor = 0.5 * force->mvv2e;
+  double **v = atom->v;
+  double *rmass = atom->rmass;
+  double *mass = atom->mass;
+  int *mask = atom->mask;
+  int *type = atom->type;
+  int nlocal = atom->nlocal;
+  double ke = 0.0;
+  if (rmass) {
+    for (int i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit)
+        ke += rmass[i] * (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
+  } else {
+    for (int i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit)
+        ke += mass[type[i]] *
+          (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
+  }
+  MPI_Allreduce(&ke,&K_target,1,MPI_DOUBLE,MPI_SUM,world);
+  K_target *= pfactor;
+}
+
+/* ----------------------------------------------------------------------
+   allow for both per-type and per-atom mass
+------------------------------------------------------------------------- */
+
+void FixNVK::initial_integrate(int vflag)
+{
+  double sm;
+  double a,b,sqtb,s,sdot;
+
+  double **x = atom->x;
+  double **v = atom->v;
+  double **f = atom->f;
+  double *rmass = atom->rmass;
+  double *mass = atom->mass;
+  int *type = atom->type;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+  if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+  // calculate s and sdot from Minary 2003, equations 4.12 and 4.13
+  double a_local = 0.0;
+  double b_local = 0.0;
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      a_local += MathExtra::dot3(f[i], v[i]);
+      if (rmass) b_local += MathExtra::dot3(f[i], f[i]) / rmass[i];
+      else b_local += MathExtra::dot3(f[i], f[i]) / mass[type[i]];
+    }
+  MPI_Allreduce(&a_local,&a,1,MPI_DOUBLE,MPI_SUM,world);
+  MPI_Allreduce(&b_local,&b,1,MPI_DOUBLE,MPI_SUM,world);
+  a /= (2.0*K_target); // units of inverse time
+  b /= (2.0*K_target * force->mvv2e); // units of inverse time squared
+  sqtb = sqrt(b);
+  s = a/b * (cosh(dtf*sqtb) - 1.0) + sinh(dtf*sqtb) / sqtb;
+  sdot = a/b * sqtb * sinh(dtf*sqtb) + cosh(dtf*sqtb);
+
+  // update v and x of atoms in group per Minary 2003, equations 4.15-4.17
+  // note that equation 4.15, 4.17 should read p = (p+F*s/m)/sdot
+  // note that equation 4.16 should read r = r + delt*p/m
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      if (rmass) sm = s / rmass[i];
+      else sm = s / mass[type[i]];
+      v[i][0] = (v[i][0] + f[i][0] * sm * force->ftm2v) / sdot;
+      v[i][1] = (v[i][1] + f[i][1] * sm * force->ftm2v) / sdot;
+      v[i][2] = (v[i][2] + f[i][2] * sm * force->ftm2v) / sdot;
+      x[i][0] += dtv * v[i][0];
+      x[i][1] += dtv * v[i][1];
+      x[i][2] += dtv * v[i][2];
+    }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNVK::final_integrate()
+{
+  double sm;
+  double a,b,sqtb,s,sdot;
+
+  double **v = atom->v;
+  double **f = atom->f;
+  double *rmass = atom->rmass;
+  double *mass = atom->mass;
+  int *type = atom->type;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+  if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+  // calculate s and sdot from Minary 2003, equations 4.12 and 4.13
+  double a_local = 0.0;
+  double b_local = 0.0;
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      a_local += MathExtra::dot3(f[i], v[i]);
+      if (rmass) b_local += MathExtra::dot3(f[i], f[i]) / rmass[i];
+      else b_local += MathExtra::dot3(f[i], f[i]) / mass[type[i]];
+    }
+  MPI_Allreduce(&a_local,&a,1,MPI_DOUBLE,MPI_SUM,world);
+  MPI_Allreduce(&b_local,&b,1,MPI_DOUBLE,MPI_SUM,world);
+  a /= (2.0*K_target); // units of inverse time
+  b /= (2.0*K_target * force->mvv2e); // units of inverse time squared
+  sqtb = sqrt(b);
+  s = a/b * (cosh(dtf*sqtb) - 1.0) + sinh(dtf*sqtb) / sqtb;
+  sdot = a/b * sqtb * sinh(dtf*sqtb) + cosh(dtf*sqtb);
+
+  // update v and x of atoms in group per Minary 2003, equations 4.15-4.17
+  // note that equation 4.15, 4.17 should read p = (p+F*s/m)/sdot
+  // note that equation 4.16 should read r = r + delt*p/m
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      if (rmass) sm = s / rmass[i];
+      else sm = s / mass[type[i]];
+      v[i][0] = (v[i][0] + f[i][0] * sm * force->ftm2v) / sdot;
+      v[i][1] = (v[i][1] + f[i][1] * sm * force->ftm2v) / sdot;
+      v[i][2] = (v[i][2] + f[i][2] * sm * force->ftm2v) / sdot;
+    }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNVK::initial_integrate_respa(int vflag, int ilevel, int iloop)
+{
+  dtv = step_respa[ilevel];
+  dtf = 0.5 * step_respa[ilevel];
+
+  // innermost level - NVK update of v and x
+  // all other levels - NVK update of v
+
+  if (ilevel == 0) initial_integrate(vflag);
+  else final_integrate();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNVK::final_integrate_respa(int ilevel, int iloop)
+{
+  dtf = 0.5 * step_respa[ilevel];
+  final_integrate();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixNVK::reset_dt()
+{
+  dtv = update->dt;
+  dtf = 0.5 * update->dt;
+}

src/USER-MISC/fix_nvk.h

@@ -0,0 +1,67 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   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(nvk,FixNVK)
+
+#else
+
+#ifndef LMP_FIX_NVK_H
+#define LMP_FIX_NVK_H
+
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+class FixNVK : public Fix {
+ public:
+  FixNVK(class LAMMPS *, int, char **);
+  virtual ~FixNVK() {}
+  int setmask();
+  virtual void init();
+  virtual void initial_integrate(int);
+  virtual void final_integrate();
+  virtual void initial_integrate_respa(int, int, int);
+  virtual void final_integrate_respa(int, int);
+  virtual void reset_dt();
+
+ protected:
+  double dtv,dtf;
+  double *step_respa;
+  int mass_require;
+  double K_target;
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Fix nvk only supports group all
+
+Self-explanatory.
+
+E: Fix nvk not yet enabled for RESPA
+
+Self-explanatory.
+
+*/