Removed lammps patch

See #414

patches/lammps-6Apr13.config

-
-
-function plumed_preliminary_test(){
-# check if the README contains the word LAMMPS
-  grep -q LAMMPS README 1>/dev/null 2>/dev/null
-}
-
-function plumed_before_patch(){
-  mkdir src/USER-PLUMED
-  test -d $otherfiles/ && cp $otherfiles/* src/USER-PLUMED/
-}
-
-function plumed_after_revert(){
-  rm -fr src/USER-PLUMED/
-}
-
-function plumed_patch_info(){
-cat << EOF
-
-PLUMED can be incorporated into LAMMPS using a simple patching procedure.
-Patching must be done _before_ LAMMPS is configured.
-After patching, one should enable PLUMED using the command
-make yes-user-plumed
-In the same way, before reverting one should disable PLUMED using the command
-make no-user-plumed
-
-Also notice that command "fix plumed" should be used in lammps input
-file *after* the relevant input parameters have been set (e.g. after "timestep" command)
-
-\bug The provided patch does not pass the virial correctly to PLUMED (see https://github.com/plumed/plumed2/issues/377).
-     If you need to perform constant pressure simulations you should download a LAMMPS version newer than November 2018, where the mentioned bug
-     has been fixed, that natively supports PLUMED 2.4.
-
-See also http://lammps.sandia.gov/doc/Section_commands.html for
-further info on processing LAMMPS input, as well as
-this discussion on github: http://github.com/plumed/plumed2/issues/67.
-
-For more information on LAMMPS you should visit http://lammps.sandia.gov/
-EOF
-}

patches/lammps-6Apr13/Install.sh

-# Install/unInstall package files in LAMMPS
-# edit 2 Makefile.package files to include/exclude ATC info
-
-if (test $1 = 1) then
-
-  if (test -e ../Makefile.package) then
-    sed -i -e 's|^PKG_LIB =[ \t]*|& $(PLUMED_LOAD) |' ../Makefile.package
-  fi
-
-  if (test -e ../Makefile.package.settings) then
-    # multiline form needed for BSD sed on Macs
-    sed -i -e '4 i \
-include ..\/..\/Plumed.inc
-' ../Makefile.package.settings
-  fi
-
-  cp fix_plumed.cpp ..
-  cp fix_plumed.h ..
-
-elif (test $1 = 0) then
-
-  if (test -e ../Makefile.package) then
-    sed -i -e 's/[^ \t]* \$(PLUMED_LOAD)[^ \t]* //' ../Makefile.package
-  fi
-
-  if (test -e ../Makefile.package.settings) then
-    sed -i -e '/^include.*Plumed\.inc.*$/d' ../Makefile.package.settings
-  fi
-
-  rm -f ../fix_plumed.cpp
-  rm -f ../fix_plumed.h
-
-fi

patches/lammps-6Apr13/fix_plumed.cpp

-#include "math.h"
-#include "stdlib.h"
-#include "string.h"
-#include "atom.h"
-#include "update.h"
-#include "force.h"
-#include "respa.h"
-#include "domain.h"
-#include "error.h"
-#include "group.h"
-#include "fix_plumed.h"
-#include "universe.h"
-#include "compute.h"
-#include "modify.h"
-#include "pair.h"
-
-using namespace LAMMPS_NS;
-using namespace PLMD;
-using namespace FixConst;
-
-#define INVOKED_SCALAR 1
-
-FixPlumed::FixPlumed(LAMMPS *lmp, int narg, char **arg) :
-  Fix(lmp, narg, arg),
-  p(NULL),
-  nlocal(0),
-  gatindex(NULL),
-  masses(NULL),
-  charges(NULL)
-{
-// Not sure this is really necessary:
-  if (!atom->tag_enable) error->all(FLERR,"fix plumed requires atom tags");
-// Initialize plumed:
-  p=new PLMD::Plumed;
-
-// If the -partition option is activated then enable inter-partition communication
-  if (universe->existflag == 1) {
-     int me;
-     MPI_Comm inter_comm;
-     MPI_Comm_rank(world,&me);
-     // Change MPI_COMM_WORLD to universe->uworld which seems more appropriate
-     MPI_Comm_split(universe->uworld,me,0,&inter_comm);
-     p->cmd("GREX setMPIIntracomm",&world);
-     if (me == 0) {
-        // The inter-partition communicator is only defined for the root in
-        //    each partition (a.k.a. world). This is due to the way in which
-        //    it is defined inside plumed.
-        p->cmd("GREX setMPIIntercomm",&inter_comm);
-     }
-     p->cmd("GREX init",NULL);
-  }
-  // The general communicator is independent of the existence of partitions,
-  //   if there are partitions, world is defined within each partition,
-  //   whereas if partitions are not defined then world is equal to MPI_COMM_WORLD.
-  p->cmd("setMPIComm",&world);
-
-// Set up units
-// LAMMPS units wrt kj/mol - nm - ps
-// Set up units
-
-  if (force->boltz == 1.0){
-// LAMMPS units lj
-    p->cmd("setNaturalUnits");
-  } else {
-    double energyUnits=1.0;
-    double lengthUnits=1.0;
-    double timeUnits=1.0;
-    if (force->boltz == 0.0019872067){
-// LAMMPS units real :: kcal/mol; angstrom; fs
-      energyUnits=4.184;
-      lengthUnits=0.1;
-      timeUnits=0.001;
-    } else if (force->boltz == 8.617343e-5){
-// LAMMPS units metal :: eV; angstrom; ps
-      energyUnits=96.48530749925792;
-      lengthUnits=0.1;
-      timeUnits=1.0;
-    } else if (force->boltz == 1.3806504e-23){
-// LAMMPS units si :: Joule, m; s
-      energyUnits=0.001;
-      lengthUnits=1.e-9;
-      timeUnits=1.e-12;
-    } else if (force->boltz == 1.3806504e-16){
-// LAMMPS units cgs :: erg; cms;, s
-      energyUnits=6.0221418e13;
-      lengthUnits=1.e-7;
-      timeUnits=1.e-12;
-    } else if (force->boltz == 3.16681534e-6){
-// LAMMPS units electron :: Hartree, bohr, fs
-      energyUnits=2625.5257;
-      lengthUnits=0.052917725;
-      timeUnits=0.001;
-    } else error->all(FLERR,"Odd LAMMPS units, plumed cannot work with that");
-    p->cmd("setMDEnergyUnits",&energyUnits);
-    p->cmd("setMDLengthUnits",&lengthUnits);
-    p->cmd("setMDTimeUnits",&timeUnits);
-  }
-
-// Read fix parameters:
-  int next=0;
-  for(int i=3;i<narg;++i){
-    if(!strcmp(arg[i],"outfile")) next=1;
-    else if(next==1){
-      if(universe->existflag == 1){
-        // Each replica writes an independent log file
-        //  with suffix equal to the replica id
-        char str_num[32], logFile[1024];
-        sprintf(str_num,".%d",universe->iworld);
-        strncpy(logFile,arg[i],1024-32);
-        strcat(logFile,str_num);
-        p->cmd("setLogFile",logFile);
-        next=0;
-      } else {
-        // partition option not used
-        p->cmd("setLogFile",arg[i]);
-        next=0;
-      }
-    }
-    else if(!strcmp(arg[i],"plumedfile"))next=2;
-    else if(next==2){
-      p->cmd("setPlumedDat",arg[i]);
-      next=0;
-    }
-    else error->all(FLERR,"syntax error in fix plumed - use 'fix name plumed plumedfile plumed.dat outfile plumed.out' ");
-  }
-  if(next==1) error->all(FLERR,"missing argument for outfile option");
-  if(next==2) error->all(FLERR,"missing argument for plumedfile option");
-
-  p->cmd("setMDEngine","LAMMPS");
-
-  int natoms=int(atom->natoms);
-  p->cmd("setNatoms",&natoms);
-
-  double dt=update->dt;
-  p->cmd("setTimestep",&dt);
-
-  virial_flag=1;
-  scalar_flag = 1;
-
-// This is the real initialization:
-  p->cmd("init");
-
-// Define compute to calculate potential energy
-  char *id_pe = (char *) "thermo_pe";
-  int ipe = modify->find_compute(id_pe);
-  c_pe = modify->compute[ipe];
-  // Trigger computation of potential energy every step
-  c_pe->addstep(update->ntimestep+1);
-}
-
-FixPlumed::~FixPlumed()
-{
-  delete p;
-}
-
-int FixPlumed::setmask()
-{
-  // set with a bitmask how and when apply the force from plumed
-  int mask = 0;
-  mask |= POST_FORCE;
-  mask |= THERMO_ENERGY;
-  mask |= POST_FORCE_RESPA;
-  mask |= MIN_POST_FORCE;
-  return mask;
-}
-
-void FixPlumed::init()
-{
-  if (strcmp(update->integrate_style,"respa") == 0)
-    nlevels_respa = ((Respa *) update->integrate)->nlevels;
-}
-
-void FixPlumed::setup(int vflag)
-{
-  if (strcmp(update->integrate_style,"verlet") == 0)
-    post_force(vflag);
-  else {
-    ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
-    post_force_respa(vflag,nlevels_respa-1,0);
-    ((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
-  }
-}
-
-void FixPlumed::min_setup(int vflag)
-{
-  post_force(vflag);
-}
-
-void FixPlumed::post_force(int vflag)
-{
-  int update_gatindex=0;
-// Try to find out if the domain decomposition has been updated:
-  if(nlocal!=atom->nlocal){
-    if(charges) delete [] charges;
-    if(masses) delete [] masses;
-    if(gatindex) delete [] gatindex;
-    nlocal=atom->nlocal;
-    gatindex=new int [nlocal];
-    masses=new double [nlocal];
-    charges=new double [nlocal];
-    update_gatindex=1;
-  } else {
-    for(int i=0;i<nlocal;i++){
-      if(gatindex[i]!=atom->tag[i]-1){
-        update_gatindex=1;
-        break;
-      }
-    }
-  }
-  MPI_Allreduce(MPI_IN_PLACE,&update_gatindex,1,MPI_INT,MPI_SUM,world);
-
-// In case it has been updated, rebuild the local mass/charges array
-// and tell plumed about the change:
-  if(update_gatindex){
-    for(int i=0;i<nlocal;i++){
-      gatindex[i]=atom->tag[i]-1;
-      masses[i]=atom->mass[atom->type[i]];
-      if(atom->q) charges[i]=atom->q[atom->type[i]];
-    }
-    p->cmd("setAtomsNlocal",&nlocal);
-    p->cmd("setAtomsGatindex",gatindex);
-  }
-
-
-// set up local virial/box. plumed uses full 3x3 matrices
-  double virial[3][3];
-  for(int i=0;i<3;i++) for(int j=0;j<3;j++) virial[i][j]=0.0;
-  double box[3][3];
-  for(int i=0;i<3;i++) for(int j=0;j<3;j++) box[i][j]=0.0;
-  box[0][0]=domain->h[0];
-  box[1][1]=domain->h[1];
-  box[2][2]=domain->h[2];
-  box[2][1]=domain->h[3];
-  box[2][0]=domain->h[4];
-  box[1][0]=domain->h[5];
-
-// local variable with timestep:
-  int step=update->ntimestep;
-
-// pass all pointers to plumed:
-  p->cmd("setStep",&step);
-  p->cmd("setPositions",&atom->x[0][0]);
-  p->cmd("setBox",&box[0][0]);
-  p->cmd("setForces",&atom->f[0][0]);
-  p->cmd("setMasses",&masses[0]);
-  if(atom->q) p->cmd("setCharges",&charges[0]);
-  p->cmd("setVirial",&virial[0][0]);
-  p->cmd("getBias",&bias);
-
-// pass the energy
-  double pot_energy = 0.;
-  c_pe->compute_scalar();
-  c_pe->invoked_flag |= INVOKED_SCALAR;
-  pot_energy = c_pe->scalar;
-  int nprocs;
-  // Divide energy by number of processors 
-  // Plumed wants it this way
-  MPI_Comm_size(world,&nprocs);
-  pot_energy /= nprocs;
-  p->cmd("setEnergy",&pot_energy);
-  // Trigger computation of potential energy every step
-  c_pe->addstep(update->ntimestep+1);
-
-// do the real calculation:
-  p->cmd("calc");
-
-// retransform virial to lammps representation:
-  Fix::virial[0]=-virial[0][0];
-  Fix::virial[1]=-virial[1][1];
-  Fix::virial[2]=-virial[2][2];
-  Fix::virial[3]=-virial[0][1];
-  Fix::virial[4]=-virial[0][2];
-  Fix::virial[5]=-virial[1][2];
-}
-
-void FixPlumed::post_force_respa(int vflag, int ilevel, int iloop)
-{
-  if (ilevel == nlevels_respa-1) post_force(vflag);
-}
-
-void FixPlumed::min_post_force(int vflag)
-{
-  post_force(vflag);
-}
-
-double FixPlumed::compute_scalar()
-{
-  return bias;
-}
-
-

patches/lammps-6Apr13/fix_plumed.h

-
-#ifdef FIX_CLASS
-
-FixStyle(plumed,FixPlumed)
-
-#else
-
-#ifndef LMP_FIX_PLUMED_H
-#define LMP_FIX_PLUMED_H
-
-#include "fix.h"
-#include "compute.h"
-// the plumed header that defines the class//
-#include "../Plumed.h"
-
-namespace LAMMPS_NS {
-
-class FixPlumed : public Fix {
- public:
-  FixPlumed(class LAMMPS *, int, char **);
-  ~FixPlumed();
-  int setmask();
-  void init();
-  void setup(int);
-  void min_setup(int);
-  void post_force(int);
-  void post_force_respa(int, int, int);
-  void min_post_force(int);
-  double compute_scalar();
-
- private:
-// pointer to plumed object:
-  PLMD::Plumed*p;
-// number of atoms local to this process:
-  int nlocal;
-// array of atom indexes local to this process:
-  int*gatindex;
-// array of masses for local atoms:
-  double*masses;
-// array of charges for local atoms:
-  double*charges;
-// this is something to enable respa
-  int nlevels_respa;
-// output bias potential
-  double bias;
-// Compute for the energy
-  class Compute *c_pe; 
-};
-
-};
-
-#endif
-#endif