From d392e4d0ce6cf1abddb3a02503f68d7dac8ce7e1 Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Fri, 7 Dec 2018 10:40:19 +0100
Subject: [PATCH] Removed lammps patch
See #414
---
patches/lammps-6Apr13.config | 40 ----
patches/lammps-6Apr13.diff | 0
patches/lammps-6Apr13/Install.sh | 33 ---
patches/lammps-6Apr13/fix_plumed.cpp | 291 ---------------------------
patches/lammps-6Apr13/fix_plumed.h | 53 -----
5 files changed, 417 deletions(-)
delete mode 100644 patches/lammps-6Apr13.config
delete mode 100644 patches/lammps-6Apr13.diff
delete mode 100755 patches/lammps-6Apr13/Install.sh
delete mode 100644 patches/lammps-6Apr13/fix_plumed.cpp
delete mode 100644 patches/lammps-6Apr13/fix_plumed.h
diff --git a/patches/lammps-6Apr13.config b/patches/lammps-6Apr13.config
deleted file mode 100644
index 87e957536..000000000
--- a/patches/lammps-6Apr13.config
+++ /dev/null
@@ -1,40 +0,0 @@
-
-
-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
-}
diff --git a/patches/lammps-6Apr13.diff b/patches/lammps-6Apr13.diff
deleted file mode 100644
index e69de29bb..000000000
diff --git a/patches/lammps-6Apr13/Install.sh b/patches/lammps-6Apr13/Install.sh
deleted file mode 100755
index 848893f2f..000000000
--- a/patches/lammps-6Apr13/Install.sh
+++ /dev/null
@@ -1,33 +0,0 @@
-# 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
diff --git a/patches/lammps-6Apr13/fix_plumed.cpp b/patches/lammps-6Apr13/fix_plumed.cpp
deleted file mode 100644
index 91afd367b..000000000
--- a/patches/lammps-6Apr13/fix_plumed.cpp
+++ /dev/null
@@ -1,291 +0,0 @@
-#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;
-}
-
-
diff --git a/patches/lammps-6Apr13/fix_plumed.h b/patches/lammps-6Apr13/fix_plumed.h
deleted file mode 100644
index 055dc6f1d..000000000
--- a/patches/lammps-6Apr13/fix_plumed.h
+++ /dev/null
@@ -1,53 +0,0 @@
-
-#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
--
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