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some small formating change but does not work anymore

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This commit is contained in:
Emile Maras
2017-05-18 16:48:20 +02:00
parent 640edbc1d4
commit 8daba01151
4 changed files with 647 additions and 735 deletions
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112
src/REPLICA/neb.cpp
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@ -9,7 +9,7 @@
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
------------------------------------------------------------------------- */
// lmptype.h must be first b/c this file uses MAXBIGINT and includes mpi.h
// due to OpenMPI bug which sets INT64_MAX via its mpi.h
@ -37,8 +37,10 @@
#include "memory.h"
#include "error.h"
#include "force.h"
#include "math_const.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define MAXLINE 256
#define CHUNK 1024
@ -50,7 +52,7 @@ NEB::NEB(LAMMPS *lmp) : Pointers(lmp) {}
/* ----------------------------------------------------------------------
internal NEB constructor, called from TAD
------------------------------------------------------------------------- */
------------------------------------------------------------------------- */
NEB::NEB(LAMMPS *lmp, double etol_in, double ftol_in, int n1steps_in,
int n2steps_in, int nevery_in, double *buf_init, double *buf_final)
@ -103,7 +105,7 @@ NEB::~NEB()
/* ----------------------------------------------------------------------
perform NEB on multiple replicas
------------------------------------------------------------------------- */
------------------------------------------------------------------------- */
void NEB::command(int narg, char **arg)
{
@ -153,7 +155,7 @@ void NEB::command(int narg, char **arg)
} else if (strcmp(arg[5],"none") == 0) {
if (narg != 6 and narg !=7) error->universe_all(FLERR,"Illegal NEB command");
} else error->universe_all(FLERR,"Illegal NEB command");
Verbose=false;
if (strcmp(arg[narg-1],"verbose") == 0) Verbose=true;
// run the NEB calculation
@ -163,7 +165,7 @@ void NEB::command(int narg, char **arg)
/* ----------------------------------------------------------------------
run NEB on multiple replicas
------------------------------------------------------------------------- */
------------------------------------------------------------------------- */
void NEB::run()
{
@ -215,27 +217,27 @@ void NEB::run()
if (universe->uscreen)
if (Verbose)
fprintf(universe->uscreen,"Step MaxReplicaForce MaxAtomForce "
"GradV0 GradV1 GradVc "
"EBF EBR RDT "
"RD1 PE1 RD2 PE2 ... RDN PEN pathangle1 angletangrad1 anglegrad1 gradV1 ReplicaForce1 MaxAtomForce1 pathangle2 angletangrad2 ... ReplicaForceN MaxAtomForceN\n");
"GradV0 GradV1 GradVc "
"EBF EBR RDT "
"RD1 PE1 RD2 PE2 ... RDN PEN pathangle1 angletangrad1 anglegrad1 gradV1 ReplicaForce1 MaxAtomForce1 pathangle2 angletangrad2 ... ReplicaForceN MaxAtomForceN\n");
else
fprintf(universe->uscreen,"Step MaxReplicaForce MaxAtomForce "
"GradV0 GradV1 GradVc "
"EBF EBR RDT "
"RD1 PE1 RD2 PE2 ... RDN PEN\n");
fprintf(universe->uscreen,"Step MaxReplicaForce MaxAtomForce "
"GradV0 GradV1 GradVc "
"EBF EBR RDT "
"RD1 PE1 RD2 PE2 ... RDN PEN\n");
if (universe->ulogfile)
if (Verbose)
fprintf(universe->ulogfile,"Step MaxReplicaForce MaxAtomForce "
"GradV0 GradV1 GradVc "
"EBF EBR RDT "
"RD1 PE1 RD2 PE2 ... RDN PEN pathangle1 angletangrad1 anglegrad1 gradV1 ReplicaForce1 MaxAtomForce1 pathangle2 angletangrad2 ... ReplicaForceN MaxAtomForceN\n");
"GradV0 GradV1 GradVc "
"EBF EBR RDT "
"RD1 PE1 RD2 PE2 ... RDN PEN pathangle1 angletangrad1 anglegrad1 gradV1 ReplicaForce1 MaxAtomForce1 pathangle2 angletangrad2 ... ReplicaForceN MaxAtomForceN\n");
else
fprintf(universe->ulogfile,"Step MaxReplicaForce MaxAtomForce "
"GradV0 GradV1 GradVc "
"EBF EBR RDT "
"RD1 PE1 RD2 PE2 ... RDN PEN\n");
fprintf(universe->ulogfile,"Step MaxReplicaForce MaxAtomForce "
"GradV0 GradV1 GradVc "
"EBF EBR RDT "
"RD1 PE1 RD2 PE2 ... RDN PEN\n");
}
print_status();
@ -299,26 +301,26 @@ void NEB::run()
if (universe->uscreen)
if (Verbose)
fprintf(universe->uscreen,"Step MaxReplicaForce MaxAtomForce "
"GradV0 GradV1 GradVc "
"EBF EBR RDT "
"RD1 PE1 RD2 PE2 ... RDN PEN pathangle1 angletangrad1 anglegrad1 gradV1 ReplicaForce1 MaxAtomForce1 pathangle2 angletangrad2 ... ReplicaForceN MaxAtomForceN\n");
"GradV0 GradV1 GradVc "
"EBF EBR RDT "
"RD1 PE1 RD2 PE2 ... RDN PEN pathangle1 angletangrad1 anglegrad1 gradV1 ReplicaForce1 MaxAtomForce1 pathangle2 angletangrad2 ... ReplicaForceN MaxAtomForceN\n");
else
fprintf(universe->uscreen,"Step MaxReplicaForce MaxAtomForce "
"GradV0 GradV1 GradVc "
"EBF EBR RDT "
"RD1 PE1 RD2 PE2 ... RDN PEN\n");
"GradV0 GradV1 GradVc "
"EBF EBR RDT "
"RD1 PE1 RD2 PE2 ... RDN PEN\n");
if (universe->ulogfile)
if (Verbose)
fprintf(universe->ulogfile,"Step MaxReplicaForce MaxAtomForce "
"GradV0 GradV1 GradVc "
"EBF EBR RDT "
"RD1 PE1 RD2 PE2 ... RDN PEN pathangle1 angletangrad1 anglegrad1 gradV1 ReplicaForce1 MaxAtomForce1 pathangle2 angletangrad2 ... ReplicaForceN MaxAtomForceN\n");
"GradV0 GradV1 GradVc "
"EBF EBR RDT "
"RD1 PE1 RD2 PE2 ... RDN PEN pathangle1 angletangrad1 anglegrad1 gradV1 ReplicaForce1 MaxAtomForce1 pathangle2 angletangrad2 ... ReplicaForceN MaxAtomForceN\n");
else
fprintf(universe->ulogfile,"Step MaxReplicaForce MaxAtomForce "
"GradV0 GradV1 GradVc "
"EBF EBR RDT "
"RD1 PE1 RD2 PE2 ... RDN PEN\n");
fprintf(universe->ulogfile,"Step MaxReplicaForce MaxAtomForce "
"GradV0 GradV1 GradVc "
"EBF EBR RDT "
"RD1 PE1 RD2 PE2 ... RDN PEN\n");
}
print_status();
@ -351,17 +353,17 @@ void NEB::run()
/* ----------------------------------------------------------------------
read initial config atom coords from file
flag = 0
only first replica opens file and reads it
first replica bcasts lines to all replicas
final replica stores coords
intermediate replicas interpolate from coords
new coord = replica fraction between current and final state
initial replica does nothing
only first replica opens file and reads it
first replica bcasts lines to all replicas
final replica stores coords
intermediate replicas interpolate from coords
new coord = replica fraction between current and final state
initial replica does nothing
flag = 1
each replica (except first) opens file and reads it
each replica stores coords
initial replica does nothing
------------------------------------------------------------------------- */
each replica (except first) opens file and reads it
each replica stores coords
initial replica does nothing
------------------------------------------------------------------------- */
void NEB::readfile(char *file, int flag)
{
@ -524,7 +526,7 @@ void NEB::readfile(char *file, int flag)
/* ----------------------------------------------------------------------
universe proc 0 opens NEB data file
test if gzipped
------------------------------------------------------------------------- */
------------------------------------------------------------------------- */
void NEB::open(char *file)
{
@ -558,7 +560,7 @@ void NEB::open(char *file)
/* ----------------------------------------------------------------------
query fix NEB for info on each replica
universe proc 0 prints current NEB status
------------------------------------------------------------------------- */
------------------------------------------------------------------------- */
void NEB::print_status()
{
@ -568,7 +570,7 @@ void NEB::print_status()
double fnorminf = update->minimize->fnorm_inf();
double fmaxatom;
MPI_Allreduce(&fnorminf,&fmaxatom,1,MPI_DOUBLE,MPI_MAX,roots);
if (Verbose)
{
freplica = new double[nreplica];
@ -585,9 +587,9 @@ void NEB::print_status()
if (Verbose)
{
one[4] = fneb->dotpath;
one[5] = fneb->dottangrad;
one[6] = fneb->dotgrad;
one[4] = fneb->dotpath;
one[5] = fneb->dottangrad;
one[6] = fneb->dotgrad;
}
@ -632,7 +634,7 @@ void NEB::print_status()
ebf = all[irep][0]-all[0][0];
ebr = all[irep][0]-all[nreplica-1][0];
}
double pi=3.14159265;
if (me_universe == 0) {
if (universe->uscreen) {
fprintf(universe->uscreen,BIGINT_FORMAT " %12.8g %12.8g ",
@ -643,10 +645,10 @@ void NEB::print_status()
for (int i = 0; i < nreplica; i++)
fprintf(universe->uscreen,"%12.8g %12.8g ",rdist[i],all[i][0]);
if (Verbose)
{fprintf(universe->uscreen,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",NAN,180-acos(all[0][5])*180/pi,180-acos(all[0][6])*180/pi,all[0][3],freplica[0],fmaxatomInRepl[0]);
{fprintf(universe->uscreen,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",NAN,180-acos(all[0][5])*180/MY_PI,180-acos(all[0][6])*180/MY_PI,all[0][3],freplica[0],fmaxatomInRepl[0]);
for (int i = 1; i < nreplica-1; i++)
fprintf(universe->uscreen,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",180-acos(all[i][4])*180/pi,180-acos(all[i][5])*180/pi,180-acos(all[i][6])*180/pi,all[i][3],freplica[i],fmaxatomInRepl[i]);
fprintf(universe->uscreen,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",NAN,180-acos(all[nreplica-1][5])*180/pi,NAN,all[nreplica-1][3],freplica[nreplica-1],fmaxatomInRepl[nreplica-1]);
fprintf(universe->uscreen,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",180-acos(all[i][4])*180/MY_PI,180-acos(all[i][5])*180/MY_PI,180-acos(all[i][6])*180/MY_PI,all[i][3],freplica[i],fmaxatomInRepl[i]);
fprintf(universe->uscreen,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",NAN,180-acos(all[nreplica-1][5])*180/MY_PI,NAN,all[nreplica-1][3],freplica[nreplica-1],fmaxatomInRepl[nreplica-1]);
}
fprintf(universe->uscreen,"\n");
}
@ -660,10 +662,10 @@ void NEB::print_status()
for (int i = 0; i < nreplica; i++)
fprintf(universe->ulogfile,"%12.8g %12.8g ",rdist[i],all[i][0]);
if (Verbose)
{fprintf(universe->ulogfile,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",NAN,180-acos(all[0][5])*180/pi,180-acos(all[0][6])*180/pi,all[0][3],freplica[0],fmaxatomInRepl[0]);
{fprintf(universe->ulogfile,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",NAN,180-acos(all[0][5])*180/MY_PI,180-acos(all[0][6])*180/MY_PI,all[0][3],freplica[0],fmaxatomInRepl[0]);
for (int i = 1; i < nreplica-1; i++)
fprintf(universe->ulogfile,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",180-acos(all[i][4])*180/pi,180-acos(all[i][5])*180/pi,180-acos(all[i][6])*180/pi,all[i][3],freplica[i],fmaxatomInRepl[i]);
fprintf(universe->ulogfile,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",NAN,180-acos(all[nreplica-1][5])*180/pi,NAN,all[nreplica-1][3],freplica[nreplica-1],fmaxatomInRepl[nreplica-1]);
fprintf(universe->ulogfile,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",180-acos(all[i][4])*180/MY_PI,180-acos(all[i][5])*180/MY_PI,180-acos(all[i][6])*180/MY_PI,all[i][3],freplica[i],fmaxatomInRepl[i]);
fprintf(universe->ulogfile,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",NAN,180-acos(all[nreplica-1][5])*180/MY_PI,NAN,all[nreplica-1][3],freplica[nreplica-1],fmaxatomInRepl[nreplica-1]);
}
fprintf(universe->ulogfile,"\n");
fflush(universe->ulogfile);