From df3390e224074b18ffe95f9623aef1f1c5be3261 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 2 Nov 2018 21:33:30 -0400
Subject: [PATCH] update formatting to closer match LAMMPS' programming style
---
src/USER-PLUMED/fix_plumed.cpp | 187 ++++++++++++++++++---------------
1 file changed, 102 insertions(+), 85 deletions(-)
diff --git a/src/USER-PLUMED/fix_plumed.cpp b/src/USER-PLUMED/fix_plumed.cpp
index b326940d94..feb12716b8 100644
--- a/src/USER-PLUMED/fix_plumed.cpp
+++ b/src/USER-PLUMED/fix_plumed.cpp
@@ -55,6 +55,8 @@
#include "plumed/wrapper/Plumed.h"
+/* -------------------------------------------------------------------- */
+
using namespace LAMMPS_NS;
using namespace FixConst;
@@ -62,76 +64,88 @@ using namespace FixConst;
FixPlumed::FixPlumed(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
- p(NULL),
- nlocal(0),
- gatindex(NULL),
- masses(NULL),
- charges(NULL),
- id_pe(NULL),
- id_press(NULL)
+ p(NULL), nlocal(0), gatindex(NULL), masses(NULL), charges(NULL),
+ id_pe(NULL), id_press(NULL)
{
-// Not sure this is really necessary:
- if (!atom->tag_enable) error->all(FLERR,"fix plumed requires atom tags");
-// Initialize plumed:
+
+ if (!atom->tag_enable)
+ error->all(FLERR,"Fix plumed requires atom tags");
+
+ if (igroup != 0 && comm->me == 0)
+ error->warning(FLERR,"Fix group for fix plumed is not 'all'. "
+ "Group will be ignored.");
+
+
p=new PLMD::Plumed;
-// Check API version
- int api_version; p->cmd("getApiVersion",&api_version);
- if( api_version>6 ) error->all(FLERR,"invalid api version for PLUMED");
-// If the -partition option is activated then enable inter-partition communication
+ // Check API version
+
+ int api_version;
+ p->cmd("getApiVersion",&api_version);
+ if (api_version > 6)
+ error->all(FLERR,"Incompatible API version for PLUMED in fix 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);
+ 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.
+ // 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
+ // Set up units
+ // LAMMPS units wrt kj/mol - nm - ps
+ // Set up units
- if (force->boltz == 1.0){
-// LAMMPS units lj
+ 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
+ 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
+ } 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
+ } 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
+ } 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
+ } else if (force->boltz == 3.16681534e-6) {
+ // LAMMPS units electron :: Hartree, bohr, fs
energyUnits=2625.5257;
lengthUnits=0.052917725;
timeUnits=0.001;
@@ -141,12 +155,13 @@ FixPlumed::FixPlumed(LAMMPS *lmp, int narg, char **arg) :
p->cmd("setMDTimeUnits",&timeUnits);
}
-// Read fix parameters:
+ // 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){
+ 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];
@@ -160,16 +175,16 @@ FixPlumed::FixPlumed(LAMMPS *lmp, int narg, char **arg) :
p->cmd("setLogFile",arg[i]);
next=0;
}
- }
- else if(!strcmp(arg[i],"plumedfile"))next=2;
- else if(next==2){
+ } 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' ");
+ } else error->all(FLERR,"Syntax error - use 'fix <fix-ID> 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");
+ 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");
@@ -183,10 +198,12 @@ FixPlumed::FixPlumed(LAMMPS *lmp, int narg, char **arg) :
thermo_virial=1;
scalar_flag = 1;
-// This is the real initialization:
+ // This is the real initialization:
+
p->cmd("init");
-// Define compute to calculate potential energy
+ // Define compute to calculate potential energy
+
id_pe = new char[7];
id_pe = (char *) "plmd_pe";
char **newarg = new char*[3];
@@ -220,7 +237,7 @@ FixPlumed::FixPlumed(LAMMPS *lmp, int narg, char **arg) :
strncmp(modify->fix[i]->style,"npt",3) ||
strncmp(modify->fix[i]->style,"npt_sphere",10) )
error->all(FLERR,"Fix plumed must be called before fix_nh derived fixes, "
- "for instance nph and npt fixes");
+ "for instance nph and npt fixes");
}
}
@@ -248,7 +265,7 @@ void FixPlumed::init()
nlevels_respa = ((Respa *) update->integrate)->nlevels;
// This avoids nan pressure if compute_pressure is called
// in a setup method
- for(int i=0;i<6;i++) virial[i] = 0.;
+ for (int i=0;i<6;i++) virial[i] = 0.;
}
void FixPlumed::setup(int vflag)
@@ -281,22 +298,22 @@ void FixPlumed::min_setup(int vflag)
void FixPlumed::post_force(int /* vflag */)
{
// Check tag is enabled
- if( !atom->tag_enable ) error->all(FLERR,"to run PLUMED you must have tag_enable==1");
+ if ( !atom->tag_enable ) error->all(FLERR,"to run PLUMED you must have tag_enable==1");
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;
+ 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){
+ for (int i=0;i<nlocal;i++) {
+ if (gatindex[i]!=atom->tag[i]-1) {
update_gatindex=1;
break;
}
@@ -306,19 +323,19 @@ void FixPlumed::post_force(int /* vflag */)
// 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;
+ if (update_gatindex) {
+ for (int i=0;i<nlocal;i++) gatindex[i]=atom->tag[i]-1;
// Get masses
- if(atom->rmass_flag) {
- for(int i=0;i<nlocal;i++) masses[i]=atom->rmass[i];
+ if (atom->rmass_flag) {
+ for (int i=0;i<nlocal;i++) masses[i]=atom->rmass[i];
} else {
- for(int i=0;i<nlocal;i++) masses[i]=atom->mass[atom->type[i]];
+ for (int i=0;i<nlocal;i++) masses[i]=atom->mass[atom->type[i]];
}
// Get charges
- if(atom->q_flag) {
- for(int i=0;i<nlocal;i++) charges[i]=atom->q[i];
+ if (atom->q_flag) {
+ for (int i=0;i<nlocal;i++) charges[i]=atom->q[i];
} else {
- for(int i=0;i<nlocal;i++) charges[i]=0.0;
+ for (int i=0;i<nlocal;i++) charges[i]=0.0;
}
p->cmd("setAtomsNlocal",&nlocal);
p->cmd("setAtomsGatindex",gatindex);
@@ -327,9 +344,9 @@ void FixPlumed::post_force(int /* vflag */)
// set up local virial/box. plumed uses full 3x3 matrices
double plmd_virial[3][3];
- for(int i=0;i<3;i++) for(int j=0;j<3;j++) plmd_virial[i][j]=0.0;
+ for (int i=0;i<3;i++) for (int j=0;j<3;j++) plmd_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;
+ 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];
@@ -338,7 +355,7 @@ void FixPlumed::post_force(int /* vflag */)
box[1][0]=domain->h[5];
// Make initial of virial of this fix zero
// The following line is very important, otherwise the compute pressure will include
- for(int i=0;i<6;++i) virial[i] = 0.;
+ for (int i=0;i<6;++i) virial[i] = 0.;
// local variable with timestep:
int step=update->ntimestep;
@@ -349,7 +366,7 @@ void FixPlumed::post_force(int /* vflag */)
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]);
+ if (atom->q) p->cmd("setCharges",&charges[0]);
p->cmd("getBias",&bias);
// Pass virial to plumed
// If energy is needed virial_plmd is equal to Lammps' virial
@@ -368,9 +385,9 @@ void FixPlumed::post_force(int /* vflag */)
// Error if tail corrections are included
if (force->pair && force->pair->tail_flag)
error->all(FLERR,"Tail corrections to the pair potential included."
- " The energy cannot be biased in this case."
- " Remove the tail corrections by removing the"
- " command: pair_modify tail yes");
+ " The energy cannot be biased in this case."
+ " Remove the tail corrections by removing the"
+ " command: pair_modify tail yes");
// compute the potential energy
double pot_energy = 0.;
c_pe->compute_scalar();
@@ -386,7 +403,7 @@ void FixPlumed::post_force(int /* vflag */)
virial_lmp = c_press->vector;
// Check if pressure is finite
if (!std::isfinite(virial_lmp[0]) || !std::isfinite(virial_lmp[1]) || !std::isfinite(virial_lmp[2])
- || !std::isfinite(virial_lmp[3]) || !std::isfinite(virial_lmp[4]) || !std::isfinite(virial_lmp[5]))
+ || !std::isfinite(virial_lmp[3]) || !std::isfinite(virial_lmp[4]) || !std::isfinite(virial_lmp[5]))
error->all(FLERR,"Non-numeric virial - Plumed cannot work with that");
// Convert pressure to virial per number of MPI processes
// From now on all virials are divided by the number of MPI processes
@@ -397,7 +414,7 @@ void FixPlumed::post_force(int /* vflag */)
} else {
inv_volume = 1.0 / (domain->xprd * domain->yprd);
}
- for(int i=0;i<6;i++) virial_lmp[i] /= (inv_volume * nktv2p * nprocs);
+ for (int i=0;i<6;i++) virial_lmp[i] /= (inv_volume * nktv2p * nprocs);
// Convert virial from lammps to plumed representation
plmd_virial[0][0]=-virial_lmp[0];
plmd_virial[1][1]=-virial_lmp[1];
@@ -407,7 +424,7 @@ void FixPlumed::post_force(int /* vflag */)
plmd_virial[1][2]=-virial_lmp[5];
} else {
virial_lmp = new double[6];
- for(int i=0;i<6;i++) virial_lmp[i] = 0.;
+ for (int i=0;i<6;i++) virial_lmp[i] = 0.;
}
// do the real calculation:
p->cmd("performCalc");
--
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