Unverified Commit 4180b4a7 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

add example to COUPLE folder demonstrating loading LAMMPS as a plugin.

parent 7434267f

examples/COUPLE/plugin/README

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This directory has a simple C code that shows how

LAMMPS can be linked to a driver application as a library. The purpose

is to illustrate how another code could perform computations while

using LAMMPS to perform MD on all or a subset of the processors, or

how an umbrella code or script could call both LAMMPS and some other

code to perform a coupled calculation.



simple.c           is the C driver

liblammpsplugin.c  is the LAMMPS library plugin loader



The 3 codes do the same thing, so you can compare them to see how to

drive LAMMPS from each language.  See lammps/python/example/simple.py

to do something similar from Python.  The Fortran driver requires an

additional wrapper library that interfaces the C interface of the

LAMMPS library to Fortran and also translates the MPI communicator

from Fortran to C.



First build LAMMPS as a library (see examples/COUPLE/README), e.g. 



cd $HOME/lammps/src

make mode=shlib mpi



or 



cd $HOME/lammps

mkdir build-shared

cd build-shared

cmake -D BUILD_LIB=on -D BUILD_SHARED_LIBS=on ../cmake

make



You can then build any of the driver codes with compile lines like

these, which include paths to the LAMMPS library interface, and

linking with FFTW (only needed if you built LAMMPS as a library with

its PPPM solver).



mpicc -c simple.c

mpicc simple.o -llammps -lfftw -o simpleC





You then run simpleC on a parallel machine

on some number of processors Q with 3 arguments:



% mpirun -np Q simpleC P in.lj $HOME/lammps/src/liblammps.so



or



% mpirun -np Q simpleC P in.lj $HOME/lammps/build-shared/liblammps.so



P is the number of procs you want LAMMPS to run on (must be <= Q) and

in.lj is a LAMMPS input script and the last argument is the path to

the LAMMPS shared library. This either has to be an absolute path, or

liblammps.so has to be in a folder that is included in the environment

variable LD_LIBRARY_PATH so it will be found by the dynamic object loader.



The driver will launch LAMMPS on P procs, read the input script a line

at a time, and pass each command line to LAMMPS.  The final line of

the script is a "run" command, so LAMMPS will run the problem.



The driver then requests all the atom coordinates from LAMMPS, moves

one of the atoms a small amount "epsilon", passes the coordinates back

to LAMMPS, and runs LAMMPS again.  If you look at the output, you

should see a small energy change between runs, due to the moved atom.



The C driver is calling C-style routines in the src/library.cpp file

of LAMMPS through the function pointers in the liblammpsplugin_t struct.

This has the benefit that your binary is not linked to liblammps.so directly

and thus you can change the name of the shared library (e.g. to have 

different variants compiled, or to load a different LAMMPS versions without

having to update your executable).

examples/COUPLE/plugin/in.lj

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# 3d Lennard-Jones melt



units		lj

atom_style	atomic

atom_modify	map array



lattice		fcc 0.8442

region		box block 0 4 0 4 0 4

create_box	1 box

create_atoms	1 box

mass		1 1.0



velocity	all create 1.44 87287 loop geom



pair_style	lj/cut 2.5

pair_coeff	1 1 1.0 1.0 2.5



neighbor	0.3 bin

neigh_modify	delay 0 every 20 check no



fix		1 all nve



variable        fx atom fx



run		10

examples/COUPLE/plugin/liblammpsplugin.c

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/* -*- 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.

------------------------------------------------------------------------- */



/*

   Variant of the C style library interface to LAMMPS

   that uses a shared library and dynamically opens it,

   so this can be used as a prototype code to integrate

   a LAMMPS plugin to some other software.

*/



#include "library.h"

#include "liblammpsplugin.h"

#include <stdlib.h>

#include <dlfcn.h>



liblammpsplugin_t *liblammpsplugin_load(const char *lib)

{

  liblammpsplugin_t *lmp;

  void *handle;



  if (lib == NULL) return NULL;

  handle = dlopen(lib,RTLD_NOW|RTLD_GLOBAL);

  if (handle == NULL) return NULL;

  

  lmp = (liblammpsplugin_t *) malloc(sizeof(liblammpsplugin_t));

  lmp->handle = handle;



#define ADDSYM(symbol) lmp->symbol = dlsym(handle,"lammps_" #symbol)

  ADDSYM(open);

  ADDSYM(open_no_mpi);

  ADDSYM(close);

  ADDSYM(version);

  ADDSYM(file);

  ADDSYM(command);

  ADDSYM(commands_list);

  ADDSYM(commands_string);

  ADDSYM(free);

  ADDSYM(extract_setting);

  ADDSYM(extract_global);

  ADDSYM(extract_box);

  ADDSYM(extract_atom);

  ADDSYM(extract_compute);

  ADDSYM(extract_fix);

  ADDSYM(extract_variable);



  ADDSYM(get_thermo);

  ADDSYM(get_natoms);



  ADDSYM(set_variable);

  ADDSYM(reset_box);



  ADDSYM(gather_atoms);

  ADDSYM(gather_atoms_concat);

  ADDSYM(gather_atoms_subset);

  ADDSYM(scatter_atoms);

  ADDSYM(scatter_atoms_subset);



  ADDSYM(set_fix_external_callback);



  ADDSYM(config_has_package);

  ADDSYM(config_package_count);

  ADDSYM(config_package_name);

  ADDSYM(config_has_gzip_support);

  ADDSYM(config_has_png_support);

  ADDSYM(config_has_jpeg_support);

  ADDSYM(config_has_ffmpeg_support);

  ADDSYM(config_has_exceptions);

  ADDSYM(create_atoms);

#ifdef LAMMPS_EXCEPTIONS

  lmp->has_exceptions = 1;

  ADDSYM(has_error);

  ADDSYM(get_last_error_message);

#else

  lmp->has_exceptions = 0;

  lmp->has_error = NULL;

  lmp->get_last_error_message = NULL;

#endif

  return lmp;

}



int liblammpsplugin_release(liblammpsplugin_t *lmp)

{

  if (lmp == NULL) return 1;

  if (lmp->handle == NULL) return 2;



  dlclose(lmp->handle);

  free((void *)lmp);

  return 0;

}

examples/COUPLE/plugin/liblammpsplugin.h

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/* -*- 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.

------------------------------------------------------------------------- */



#ifndef LIBLAMMPSPLUGIN_H

#define LIBLAMMPSPLUGIN_H

/*

   Variant of the C style library interface to LAMMPS

   that uses a shared library and dynamically opens it,

   so this can be used as a prototype code to integrate

   a LAMMPS plugin to some other software.

*/



/*

 * Follow the behavior of regular LAMMPS compilation and assume

 * -DLAMMPS_SMALLBIG when no define is set.

 */

#if !defined(LAMMPS_BIGBIG) && !defined(LAMMPS_SMALLBIG) && !defined(LAMMPS_SMALLSMALL)

#define LAMMPS_SMALLBIG

#endif



#include <mpi.h>

#if defined(LAMMPS_BIGBIG) || defined(LAMMPS_SMALLBIG)

#include <inttypes.h>  /* for int64_t */

#endif



#ifdef __cplusplus

extern "C" {

#endif



#if defined(LAMMPS_BIGBIG)

typedef void (*FixExternalFnPtr)(void *, int64_t, int, int64_t *, double **, double **);

#elif defined(LAMMPS_SMALLBIG)

typedef void (*FixExternalFnPtr)(void *, int64_t, int, int *, double **, double **);

#else

typedef void (*FixExternalFnPtr)(void *, int, int, int *, double **, double **);

#endif



  

struct _liblammpsplugin {

  int abiversion;

  int has_exceptions;

  void *handle;

  void (*open)(int, char **, MPI_Comm, void **);

  void (*open_no_mpi)(int, char **, void **);

  void (*close)(void *);

  int  (*version)(void *);

  void (*file)(void *, char *);

  char *(*command)(void *, char *);

  void (*commands_list)(void *, int, char **);

  void (*commands_string)(void *, char *);

  void (*free)(void *);

  int (*extract_setting)(void *, char *);

  void *(*extract_global)(void *, char *);

  void (*extract_box)(void *, double *, double *,

		      double *, double *, double *, int *, int *);

  void *(*extract_atom)(void *, char *);

  void *(*extract_compute)(void *, char *, int, int);

  void *(*extract_fix)(void *, char *, int, int, int, int);

  void *(*extract_variable)(void *, char *, char *);



  double (*get_thermo)(void *, char *);

  int (*get_natoms)(void *);



  int (*set_variable)(void *, char *, char *);

  void (*reset_box)(void *, double *, double *, double, double, double);



  void (*gather_atoms)(void *, char *, int, int, void *);

  void (*gather_atoms_concat)(void *, char *, int, int, void *);

  void (*gather_atoms_subset)(void *, char *, int, int, int, int *, void *);

  void (*scatter_atoms)(void *, char *, int, int, void *);

  void (*scatter_atoms_subset)(void *, char *, int, int, int, int *, void *);



  void (*set_fix_external_callback)(void *, char *, FixExternalFnPtr, void*);



  int (*config_has_package)(char * package_name);

  int (*config_package_count)();

  int (*config_package_name)(int index, char * buffer, int max_size);

  int (*config_has_gzip_support)();

  int (*config_has_png_support)();

  int (*config_has_jpeg_support)();

  int (*config_has_ffmpeg_support)();

  int (*config_has_exceptions)();



  int (*find_pair_neighlist)(void* ptr, char * style, int exact, int nsub, int request);

  int (*find_fix_neighlist)(void* ptr, char * id, int request);

  int (*find_compute_neighlist)(void* ptr, char * id, int request);

  int (*neighlist_num_elements)(void* ptr, int idx);

  void (*neighlist_element_neighbors)(void * ptr, int idx, int element, int * iatom, int * numneigh, int ** neighbors);



// lammps_create_atoms() takes tagint and imageint as args

// ifdef insures they are compatible with rest of LAMMPS

// caller must match to how LAMMPS library is built



#ifdef LAMMPS_BIGBIG

  void (*create_atoms)(void *, int, int64_t *, int *,

                         double *, double *, int64_t *, int);

#else

  void (*create_atoms)(void *, int, int *, int *,

                         double *, double *, int *, int);

#endif



  int (*has_error)(void *);

  int (*get_last_error_message)(void *, char *, int);

};



typedef struct _liblammpsplugin liblammpsplugin_t;



liblammpsplugin_t *liblammpsplugin_load(const char *);

int liblammpsplugin_release(liblammpsplugin_t *);

  

#undef LAMMPS

#ifdef __cplusplus

}

#endif



#endif

examples/COUPLE/plugin/log.simple.plugin.1

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LAMMPS (18 Feb 2020)

Lattice spacing in x,y,z = 1.6796 1.6796 1.6796

Created orthogonal box = (0 0 0) to (6.71838 6.71838 6.71838)

  1 by 1 by 1 MPI processor grid

Created 256 atoms

  create_atoms CPU = 0.000297844 secs

Neighbor list info ...

  update every 20 steps, delay 0 steps, check no

  max neighbors/atom: 2000, page size: 100000

  master list distance cutoff = 2.8

  ghost atom cutoff = 2.8

  binsize = 1.4, bins = 5 5 5

  1 neighbor lists, perpetual/occasional/extra = 1 0 0

  (1) pair lj/cut, perpetual

      attributes: half, newton on

      pair build: half/bin/atomonly/newton

      stencil: half/bin/3d/newton

      bin: standard

Setting up Verlet run ...

  Unit style    : lj

  Current step  : 0

  Time step     : 0.005

Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes

Step Temp E_pair E_mol TotEng Press 

       0         1.44   -6.7733681            0   -4.6218056   -5.0244179 

      10    1.1298532   -6.3095502            0   -4.6213906   -2.6058175 

Loop time of 0.00164276 on 1 procs for 10 steps with 256 atoms



Performance: 2629719.113 tau/day, 6087.313 timesteps/s

93.7% CPU use with 1 MPI tasks x no OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.0014956  | 0.0014956  | 0.0014956  |   0.0 | 91.04

Neigh   | 0          | 0          | 0          |   0.0 |  0.00

Comm    | 8.045e-05  | 8.045e-05  | 8.045e-05  |   0.0 |  4.90

Output  | 1.1399e-05 | 1.1399e-05 | 1.1399e-05 |   0.0 |  0.69

Modify  | 3.7431e-05 | 3.7431e-05 | 3.7431e-05 |   0.0 |  2.28

Other   |            | 1.789e-05  |            |       |  1.09



Nlocal:    256 ave 256 max 256 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost:    1431 ave 1431 max 1431 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs:    9984 ave 9984 max 9984 min

Histogram: 1 0 0 0 0 0 0 0 0 0



Total # of neighbors = 9984

Ave neighs/atom = 39

Neighbor list builds = 0

Dangerous builds not checked

Setting up Verlet run ...

  Unit style    : lj

  Current step  : 10

  Time step     : 0.005

Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes

Step Temp E_pair E_mol TotEng Press 

      10    1.1298532   -6.3095502            0   -4.6213906   -2.6058175 

      20    0.6239063    -5.557644            0   -4.6254403   0.97451173 

Loop time of 0.00199768 on 1 procs for 10 steps with 256 atoms



Performance: 2162504.180 tau/day, 5005.797 timesteps/s

99.8% CPU use with 1 MPI tasks x no OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.0018518  | 0.0018518  | 0.0018518  |   0.0 | 92.70

Neigh   | 0          | 0          | 0          |   0.0 |  0.00

Comm    | 7.9768e-05 | 7.9768e-05 | 7.9768e-05 |   0.0 |  3.99

Output  | 1.1433e-05 | 1.1433e-05 | 1.1433e-05 |   0.0 |  0.57

Modify  | 3.6904e-05 | 3.6904e-05 | 3.6904e-05 |   0.0 |  1.85

Other   |            | 1.773e-05  |            |       |  0.89



Nlocal:    256 ave 256 max 256 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost:    1431 ave 1431 max 1431 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs:    9952 ave 9952 max 9952 min

Histogram: 1 0 0 0 0 0 0 0 0 0



Total # of neighbors = 9952

Ave neighs/atom = 38.875

Neighbor list builds = 0

Dangerous builds not checked

Setting up Verlet run ...

  Unit style    : lj

  Current step  : 20

  Time step     : 0.005

Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes

Step Temp E_pair E_mol TotEng Press 

      20    0.6239063   -5.5404291            0   -4.6082254    1.0394285 

      21   0.63845863   -5.5628733            0   -4.6089263   0.99398278 

Loop time of 0.000304321 on 1 procs for 1 steps with 256 atoms



Performance: 1419553.695 tau/day, 3286.004 timesteps/s

98.9% CPU use with 1 MPI tasks x no OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.00027815 | 0.00027815 | 0.00027815 |   0.0 | 91.40

Neigh   | 0          | 0          | 0          |   0.0 |  0.00

Comm    | 8.321e-06  | 8.321e-06  | 8.321e-06  |   0.0 |  2.73

Output  | 1.0513e-05 | 1.0513e-05 | 1.0513e-05 |   0.0 |  3.45

Modify  | 3.968e-06  | 3.968e-06  | 3.968e-06  |   0.0 |  1.30

Other   |            | 3.365e-06  |            |       |  1.11



Nlocal:    256 ave 256 max 256 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost:    1431 ave 1431 max 1431 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs:    9705 ave 9705 max 9705 min

Histogram: 1 0 0 0 0 0 0 0 0 0



Total # of neighbors = 9705

Ave neighs/atom = 37.9102

Neighbor list builds = 0

Dangerous builds not checked

Force on 1 atom via extract_atom: 26.9581

Force on 1 atom via extract_variable: 26.9581

Setting up Verlet run ...

  Unit style    : lj

  Current step  : 21

  Time step     : 0.005

Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes

Step Temp E_pair E_mol TotEng Press 

      21   0.63845863   -5.5628733            0   -4.6089263   0.99398278 

      31    0.7494946   -5.7306417            0   -4.6107913   0.41043597 

Loop time of 0.00196027 on 1 procs for 10 steps with 256 atoms



Performance: 2203779.175 tau/day, 5101.341 timesteps/s

99.7% CPU use with 1 MPI tasks x no OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.0018146  | 0.0018146  | 0.0018146  |   0.0 | 92.57

Neigh   | 0          | 0          | 0          |   0.0 |  0.00

Comm    | 8.0268e-05 | 8.0268e-05 | 8.0268e-05 |   0.0 |  4.09

Output  | 1.0973e-05 | 1.0973e-05 | 1.0973e-05 |   0.0 |  0.56

Modify  | 3.6913e-05 | 3.6913e-05 | 3.6913e-05 |   0.0 |  1.88

Other   |            | 1.756e-05  |            |       |  0.90



Nlocal:    256 ave 256 max 256 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost:    1431 ave 1431 max 1431 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs:    9688 ave 9688 max 9688 min

Histogram: 1 0 0 0 0 0 0 0 0 0



Total # of neighbors = 9688

Ave neighs/atom = 37.8438

Neighbor list builds = 0

Dangerous builds not checked

Setting up Verlet run ...

  Unit style    : lj

  Current step  : 31

  Time step     : 0.005

Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes

Step Temp E_pair E_mol TotEng Press 

      31    0.7494946   -5.7306417            0   -4.6107913   0.41043597 

      51   0.71349216   -5.6772387            0   -4.6111811   0.52117681 

Loop time of 0.00433063 on 1 procs for 20 steps with 256 atoms



Performance: 1995088.941 tau/day, 4618.261 timesteps/s

99.3% CPU use with 1 MPI tasks x no OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.0035121  | 0.0035121  | 0.0035121  |   0.0 | 81.10

Neigh   | 0.00050258 | 0.00050258 | 0.00050258 |   0.0 | 11.61

Comm    | 0.00019444 | 0.00019444 | 0.00019444 |   0.0 |  4.49

Output  | 1.2092e-05 | 1.2092e-05 | 1.2092e-05 |   0.0 |  0.28

Modify  | 7.2917e-05 | 7.2917e-05 | 7.2917e-05 |   0.0 |  1.68

Other   |            | 3.647e-05  |            |       |  0.84



Nlocal:    256 ave 256 max 256 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost:    1421 ave 1421 max 1421 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs:    9700 ave 9700 max 9700 min

Histogram: 1 0 0 0 0 0 0 0 0 0



Total # of neighbors = 9700

Ave neighs/atom = 37.8906

Neighbor list builds = 1

Dangerous builds not checked

Setting up Verlet run ...

  Unit style    : lj

  Current step  : 51

  Time step     : 0.005

Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes

Step Temp E_pair E_mol TotEng Press 

      51   0.71349216   -5.6772387            0   -4.6111811   0.52117681 

      61   0.78045421   -5.7781094            0   -4.6120011  0.093808941 

Loop time of 0.00196567 on 1 procs for 10 steps with 256 atoms



Performance: 2197727.285 tau/day, 5087.332 timesteps/s

99.7% CPU use with 1 MPI tasks x no OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.0018222  | 0.0018222  | 0.0018222  |   0.0 | 92.70

Neigh   | 0          | 0          | 0          |   0.0 |  0.00

Comm    | 7.8285e-05 | 7.8285e-05 | 7.8285e-05 |   0.0 |  3.98

Output  | 1.0862e-05 | 1.0862e-05 | 1.0862e-05 |   0.0 |  0.55

Modify  | 3.6719e-05 | 3.6719e-05 | 3.6719e-05 |   0.0 |  1.87

Other   |            | 1.764e-05  |            |       |  0.90



Nlocal:    256 ave 256 max 256 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost:    1421 ave 1421 max 1421 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs:    9700 ave 9700 max 9700 min

Histogram: 1 0 0 0 0 0 0 0 0 0



Total # of neighbors = 9700

Ave neighs/atom = 37.8906

Neighbor list builds = 0

Dangerous builds not checked

Setting up Verlet run ...

  Unit style    : lj

  Current step  : 61

  Time step     : 0.005

Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes

Step Temp E_pair E_mol TotEng Press 

      61   0.78045421   -5.7781094            0   -4.6120011  0.093808941 

      81   0.77743907   -5.7735004            0   -4.6118971  0.090822641 

Loop time of 0.00430528 on 1 procs for 20 steps with 256 atoms



Performance: 2006838.581 tau/day, 4645.460 timesteps/s

99.8% CPU use with 1 MPI tasks x no OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.0034931  | 0.0034931  | 0.0034931  |   0.0 | 81.13

Neigh   | 0.00050437 | 0.00050437 | 0.00050437 |   0.0 | 11.72

Comm    | 0.0001868  | 0.0001868  | 0.0001868  |   0.0 |  4.34

Output  | 1.1699e-05 | 1.1699e-05 | 1.1699e-05 |   0.0 |  0.27

Modify  | 7.3308e-05 | 7.3308e-05 | 7.3308e-05 |   0.0 |  1.70

Other   |            | 3.604e-05  |            |       |  0.84



Nlocal:    256 ave 256 max 256 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost:    1405 ave 1405 max 1405 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs:    9701 ave 9701 max 9701 min

Histogram: 1 0 0 0 0 0 0 0 0 0



Total # of neighbors = 9701

Ave neighs/atom = 37.8945

Neighbor list builds = 1

Dangerous builds not checked

Deleted 256 atoms, new total = 0

Setting up Verlet run ...

  Unit style    : lj

  Current step  : 81

  Time step     : 0.005

Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes

Step Temp E_pair E_mol TotEng Press 

      81    0.6239063   -5.5404291            0   -4.6082254    1.0394285 

      91   0.75393007   -5.7375259            0   -4.6110484   0.39357367 

Loop time of 0.00195843 on 1 procs for 10 steps with 256 atoms



Performance: 2205851.941 tau/day, 5106.139 timesteps/s

99.7% CPU use with 1 MPI tasks x no OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.0018143  | 0.0018143  | 0.0018143  |   0.0 | 92.64

Neigh   | 0          | 0          | 0          |   0.0 |  0.00

Comm    | 7.8608e-05 | 7.8608e-05 | 7.8608e-05 |   0.0 |  4.01

Output  | 1.0786e-05 | 1.0786e-05 | 1.0786e-05 |   0.0 |  0.55

Modify  | 3.7106e-05 | 3.7106e-05 | 3.7106e-05 |   0.0 |  1.89

Other   |            | 1.762e-05  |            |       |  0.90



Nlocal:    256 ave 256 max 256 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost:    1431 ave 1431 max 1431 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs:    9705 ave 9705 max 9705 min

Histogram: 1 0 0 0 0 0 0 0 0 0



Total # of neighbors = 9705

Ave neighs/atom = 37.9102

Neighbor list builds = 0

Dangerous builds not checked

Total wall time: 0:00:00

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