forked from lijiext/lammps
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This commit is contained in:
sjplimp
parent
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This directory has examples of how to use LAMMPS as a library, either
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by itself or in tandem with another code or library.
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These examples is meant to illustrate what is possible when coupling
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codes or calling LAMMPS as a library. The examples are provided for
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demonstration purposes. The physics they calculate is too simple to
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model a realistic problem.
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See these sections of the LAMMPS manaul for details:
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2.4 Building LAMMPS as a library (doc/Section_start.html#2_4)
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4.10 Coupling LAMMPS to other codes (doc/Section_howto.html#4_10)
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In all of the examples included here, LAMMPS must first be built as a
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library. Basically, you type something like
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make makelib
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make -f Makefile.lib g++
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in the LAMMPS src directory to create liblmp_g++.a
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The library interface to LAMMPS is in src/library.cpp. Routines can
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be easily added to this file so an external program can perform the
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LAMMPS tasks desired.
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-------------------------------------------------------------------
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These are the sub-directories included in this directory:
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lammps_quest MD with quantum forces, coupling to Quest DFT code
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lammps_spparks grain-growth Monte Carlo with strain via MD,
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coupling to SPPARKS kinetic MC code
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library collection of useful inter-code communication routines
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simple simple example of driver code calling LAMMPS as library
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fortran a wrapper on the LAMMPS library API that
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can be called from Fortran
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Each sub-directory has its own README.
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libfwrapper.c is a C file that wraps the LAMMPS library API
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in src/library.h so that it can be called from Fortran.
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See the couple/simple/simple.f90 program for an example
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of a Fortran code that does this.
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See the README file in that dir for instructions
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on how to build a Fortran code that uses this
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wrapper and links to the LAMMPS library.
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@ -1,129 +0,0 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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www.cs.sandia.gov/~sjplimp/lammps.html
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Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* libwrapper = fortran wrappers for LAMMPS library functions.
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See README for compilation instructions */
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#include "mpi.h"
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#include "stdio.h"
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#include "stdlib.h"
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#include "string.h"
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#include "stdint.h"
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#include "library.h" /* this is a LAMMPS include file */
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/* wrapper for creating a lammps instance from fortran.
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since fortran has no simple way to emit a c-compatible
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argument array, we don't support it. for simplicity,
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the address of the pointer to the lammps object is
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stored in a 64-bit integer on all platforms. */
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void lammps_open_(MPI_Fint *comm, int64_t *ptr)
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{
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void *obj;
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MPI_Comm ccomm;
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/* convert MPI communicator from fortran to c */
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ccomm = MPI_Comm_f2c(*comm);
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lammps_open(0,NULL,ccomm,&obj);
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*ptr = (int64_t) obj;
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}
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/* no-MPI version of the wrapper from above. */
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void lammps_open_no_mpi_(int64_t *ptr)
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{
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void *obj;
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lammps_open_no_mpi(0,NULL,&obj);
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*ptr = (int64_t) obj;
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}
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/* wrapper for shutting down a lammps instance from fortran. */
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void lammps_close_(int64_t *ptr)
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{
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void *obj;
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obj = (void *) *ptr;
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lammps_close(obj);
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}
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/* wrapper for passing an input file to lammps from fortran.
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since fortran strings are not zero terminated, we have
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to pass the length explicitly and make a copy that is. */
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void lammps_file_(int64_t *ptr, char *fname, MPI_Fint *len)
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{
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void *obj;
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char *cpy;
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obj = (void *) *ptr;
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cpy = (char *)calloc(*len + 1,sizeof(char));
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memcpy(cpy,fname,*len);
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lammps_file(obj,cpy);
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free(cpy);
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}
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/* wrapper for passing a line input to lammps from fortran.
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since fortran strings are not zero terminated, we have
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to pass the length explicitly and make a copy that is. */
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void lammps_command_(int64_t *ptr, char *line, MPI_Fint *len)
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{
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void *obj;
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char *cpy;
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obj = (void *) *ptr;
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cpy = (char *)calloc(*len + 1,sizeof(char));
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memcpy(cpy,line,*len);
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lammps_command(obj,cpy);
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free(cpy);
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}
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/* fortran wrapper to get the number of atoms from lammps.
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return values require an interface in fortran, so we
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make the wrapper into a procedure. */
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void lammps_get_natoms_(int64_t *ptr, MPI_Fint *natoms)
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{
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void *obj;
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obj = (void *) *ptr;
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*natoms = lammps_get_natoms(obj);
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}
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/* wrapper to copy coordinates from lammps to fortran */
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void lammps_get_coords_(int64_t *ptr, double *coords)
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{
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void *obj;
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obj = (void *) *ptr;
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lammps_get_coords(obj,coords);
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}
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/* wrapper to copy coordinates from fortran to lammps */
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void lammps_put_coords_(int64_t *ptr, double *coords)
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{
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void *obj;
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obj = (void *) *ptr;
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lammps_put_coords(obj,coords);
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}
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# Makefile for MD with quantum forces via LAMMPS <-> Quest coupling
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SHELL = /bin/sh
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# System-specific settings
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LAMMPS = /home/sjplimp/lammps
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CC = g++
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CCFLAGS = -g -O -DMPICH_IGNORE_CXX_SEEK -I../library
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DEPFLAGS = -M
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LINK = g++
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LINKFLAGS = -g -O -L../library -L${LAMMPS}/src
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USRLIB = -lcouple -llmp_g++
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SYSLIB = -lfftw -lmpich -lpthread
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ARCHIVE = ar
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ARFLAGS = -rc
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SIZE = size
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# Files
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EXE = lmpqst
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SRC = $(wildcard *.cpp)
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INC = $(wildcard *.h)
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OBJ = $(SRC:.cpp=.o)
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# Targets
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$(EXE): $(OBJ)
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$(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
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$(SIZE) $(EXE)
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clean:
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rm $(EXE) *.o
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# Compilation rules
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%.o:%.cpp
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$(CC) $(CCFLAGS) -c $<
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%.d:%.cpp
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$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
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# Individual dependencies
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DEPENDS = $(OBJ:.o=.d)
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include $(DEPENDS)
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This directory has an application that runs classical MD via LAMMPS,
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but uses quantum forces calculated by the Quest DFT (density
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functional) code in place of the usual classical MD forces calculated
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by a pair style in LAMMPS.
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lmpqst.cpp main program
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it links LAMMPS as a library
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it invokes Quest as an executable
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in.lammps LAMMPS input script, without the run command
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si_111.in Quest input script for an 8-atom Si unit cell
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lmppath.h contains path to LAMMPS home directory
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qstexe.h contains full pathname to Quest executable
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After editing the Makefile, lmppath.h, and qstexe.h to make them
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suitable for your box, type:
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g++ -f Makefile.g++
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and you should get the lmpqst executable.
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NOTE: To run this coupled application, you must of course, have Quest
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built on your system. It's WWW site is http://dft.sandia.gov/Quest.
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It is not an open-source code, buy you can contact its authors to
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obtain a copy.
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You can run lmpqst in serial or parallel as:
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% lmpqst Niter in.lammps in.quest
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% mpirun -np 4 lmpqst Niter in.lammps in.quest
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where
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Niter = # of MD iterations
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in.lammps = LAMMPS input script
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in.quest = Quest input script
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The log files are for this run:
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% lmpqst 10 in.lammps si_111.in
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This application is an example of a coupling where the driver code
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(lmpqst) runs one code (LAMMPS) as an outer code and facilitates it
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calling the other code (Quest) as an inner code. Specifically, the
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driver (lmpqst) invokes one code (LAMMPS) to perform its timestep
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loop, and grabs information from the other code (Quest) during its
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timestep. This is done in LAMMPS using the fix external command,
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which makes a "callback" to the driver application (lmpqst), which in
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turn invokes Quest with new atom coordinates, lets Quest compute
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forces, and returns those forces to the LAMMPS fix external.
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The driver code launches LAMMPS in parallel. But Quest is only run on
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a single processor. It would be possible to change this by using a
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parallel build of Quest.
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Since Quest does not currently have a library interface, the driver
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code interfaces with Quest via input and output files.
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Note that essentially 100% of the run time for this coupled
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application is spent in Quest, as the quantum calculation of forces
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dominates the calculation.
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You can look at the log files in the directory to see sample LAMMPS
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output for this simulation. Dump files produced by LAMMPS are stored
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as dump.md.
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# LAMMPS input for coupling MD/Quantum
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units metal
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dimension 3
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atom_style atomic
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atom_modify sort 0 0.0
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lattice diamond 5.43
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region box block 0 1 0 1 0 1
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create_box 1 box
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create_atoms 1 box
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mass 1 28.08
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velocity all create 300.0 87293 loop geom
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fix 1 all nve
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fix 2 all external
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dump 1 all custom 1 dump.md id type x y z fx fy fz
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thermo 1
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@ -1 +0,0 @@
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#define LMPPATH /home/sjplimp/lammps
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// lmpqst = umbrella driver to couple LAMMPS + Quest
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// for MD using quantum forces
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// Syntax: lmpqst Niter in.lammps in.quest
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// Niter = # of MD iterations
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// in.lammps = LAMMPS input script
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// in.quest = Quest input script
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#include "mpi.h"
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#include "stdio.h"
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#include "stdlib.h"
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#include "string.h"
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#include "many2one.h"
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#include "one2many.h"
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#include "files.h"
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#include "memory.h"
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#include "error.h"
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#define QUOTE_(x) #x
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#define QUOTE(x) QUOTE_(x)
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#include "lmppath.h"
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#include QUOTE(LMPPATH/src/lammps.h)
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#include QUOTE(LMPPATH/src/library.h)
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#include QUOTE(LMPPATH/src/input.h)
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#include QUOTE(LMPPATH/src/modify.h)
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#include QUOTE(LMPPATH/src/fix.h)
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#include QUOTE(LMPPATH/src/fix_external.h)
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#include "qstexe.h"
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using namespace LAMMPS_NS;
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#define ANGSTROM_per_BOHR 0.529
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#define EV_per_RYDBERG 13.6056923
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void quest_callback(void *, int, int, int *, double **, double **);
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struct Info {
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int me;
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Memory *memory;
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LAMMPS *lmp;
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char *quest_input;
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};
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/* ---------------------------------------------------------------------- */
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int main(int narg, char **arg)
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{
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int n;
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char str[128];
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// setup MPI
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MPI_Init(&narg,&arg);
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MPI_Comm comm = MPI_COMM_WORLD;
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int me,nprocs;
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MPI_Comm_rank(comm,&me);
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MPI_Comm_size(comm,&nprocs);
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Memory *memory = new Memory(comm);
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Error *error = new Error(comm);
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// command-line args
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if (narg != 4) error->all("Syntax: lmpqst Niter in.lammps in.quest");
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int niter = atoi(arg[1]);
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n = strlen(arg[2]) + 1;
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char *lammps_input = new char[n];
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strcpy(lammps_input,arg[2]);
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n = strlen(arg[3]) + 1;
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char *quest_input = new char[n];
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strcpy(quest_input,arg[3]);
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// instantiate LAMMPS
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LAMMPS *lmp = new LAMMPS(0,NULL,MPI_COMM_WORLD);
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// create simulation in LAMMPS from in.lammps
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lmp->input->file(lammps_input);
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// make info avaiable to callback function
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Info info;
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info.me = me;
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info.memory = memory;
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info.lmp = lmp;
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info.quest_input = quest_input;
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// set callback to Quest inside fix external
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int ifix = lmp->modify->find_fix("2");
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FixExternal *fix = (FixExternal *) lmp->modify->fix[ifix];
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fix->set_callback(quest_callback,&info);
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// run LAMMPS for Niter
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// each time it needs forces, it will invoke quest_callback
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sprintf(str,"run %d",niter);
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lmp->input->one(str);
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// clean up
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delete lmp;
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delete memory;
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delete error;
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delete [] lammps_input;
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delete [] quest_input;
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MPI_Finalize();
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}
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/* ----------------------------------------------------------------------
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callback to Quest with atom IDs and coords from each proc
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invoke Quest to compute forces, load them into f for LAMMPS to use
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f can be NULL if proc owns no atoms
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------------------------------------------------------------------------- */
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void quest_callback(void *ptr, int ntimestep, int nlocal,
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int *id, double **x, double **f)
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{
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int i,j;
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char str[128];
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Info *info = (Info *) ptr;
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// boxlines = LAMMPS box size converted into Quest lattice vectors
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char **boxlines = NULL;
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if (info->me == 0) {
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boxlines = new char*[3];
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for (i = 0; i < 3; i++) boxlines[i] = new char[128];
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}
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double boxxlo = *((double *) lammps_extract_global(info->lmp,"boxxlo"));
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double boxxhi = *((double *) lammps_extract_global(info->lmp,"boxxhi"));
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double boxylo = *((double *) lammps_extract_global(info->lmp,"boxylo"));
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double boxyhi = *((double *) lammps_extract_global(info->lmp,"boxyhi"));
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double boxzlo = *((double *) lammps_extract_global(info->lmp,"boxzlo"));
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double boxzhi = *((double *) lammps_extract_global(info->lmp,"boxzhi"));
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double xprd = (boxxhi-boxxlo)/ANGSTROM_per_BOHR;
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double yprd = (boxyhi-boxylo)/ANGSTROM_per_BOHR;
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double zprd = (boxzhi-boxzlo)/ANGSTROM_per_BOHR;
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if (info->me == 0) {
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sprintf(boxlines[0],"%g %g %g\n",xprd,0.0,0.0);
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sprintf(boxlines[1],"%g %g %g\n",0.0,yprd,0.0);
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sprintf(boxlines[2],"%g %g %g\n",0.0,0.0,zprd);
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}
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// xlines = x for atoms on each proc converted to text lines
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// xlines is suitable for insertion into Quest input file
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// convert LAMMPS Angstroms to Quest bohr
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int natoms;
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MPI_Allreduce(&nlocal,&natoms,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD);
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Many2One *lmp2qst = new Many2One(MPI_COMM_WORLD);
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lmp2qst->setup(nlocal,id,natoms);
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char **xlines = NULL;
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double **xquest = NULL;
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if (info->me == 0) {
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xquest = info->memory->create_2d_double_array(natoms,3,"lmpqst:xquest");
|
||||
xlines = new char*[natoms];
|
||||
for (i = 0; i < natoms; i++) xlines[i] = new char[128];
|
||||
}
|
||||
|
||||
if (info->me == 0) lmp2qst->gather(&x[0][0],3,&xquest[0][0]);
|
||||
else lmp2qst->gather(&x[0][0],3,NULL);
|
||||
|
||||
if (info->me == 0) {
|
||||
for (i = 0; i < natoms; i++) {
|
||||
xquest[i][0] /= ANGSTROM_per_BOHR;
|
||||
xquest[i][1] /= ANGSTROM_per_BOHR;
|
||||
xquest[i][2] /= ANGSTROM_per_BOHR;
|
||||
}
|
||||
for (i = 0; i < natoms; i++) {
|
||||
sprintf(xlines[i],"%d %d %g %g %g\n",i+1,1,
|
||||
xquest[i][0],xquest[i][1],xquest[i][2]);
|
||||
}
|
||||
}
|
||||
|
||||
// one-processor tasks:
|
||||
// whack all lcao.* files
|
||||
// cp quest_input to lcao.in
|
||||
// replace atom coords section of lcao.in with new atom coords
|
||||
// run Quest on one proc, save screen output to file
|
||||
// flines = atom forces extracted from Quest screen file
|
||||
// fquest = atom forces
|
||||
// convert Quest Ryd/bohr to LAMMPS eV/Angstrom
|
||||
|
||||
char **flines = NULL;
|
||||
double **fquest = NULL;
|
||||
if (info->me == 0) {
|
||||
fquest = info->memory->create_2d_double_array(natoms,3,"lmpqst:fquest");
|
||||
flines = new char*[natoms];
|
||||
for (i = 0; i < natoms; i++) flines[i] = new char[128];
|
||||
}
|
||||
|
||||
if (info->me == 0) {
|
||||
system("rm lcao.*");
|
||||
sprintf(str,"cp %s lcao.in",info->quest_input);
|
||||
system(str);
|
||||
sprintf(str,"cp %s lcao.x",QUOTE(QUEST));
|
||||
system(str);
|
||||
replace("lcao.in","primitive lattice vectors",3,boxlines);
|
||||
replace("lcao.in","atom, type, position vector",natoms,xlines);
|
||||
system("lcao.x > lcao.screen");
|
||||
extract("lcao.screen","atom x force "
|
||||
"y force z force",natoms,flines);
|
||||
|
||||
int itmp;
|
||||
for (i = 0; i < natoms; i++)
|
||||
sscanf(flines[i],"%d %lg %lg %lg",&itmp,
|
||||
&fquest[i][0],&fquest[i][1],&fquest[i][2]);
|
||||
|
||||
for (i = 0; i < natoms; i++) {
|
||||
fquest[i][0] *= EV_per_RYDBERG / ANGSTROM_per_BOHR;
|
||||
fquest[i][1] *= EV_per_RYDBERG / ANGSTROM_per_BOHR;
|
||||
fquest[i][2] *= EV_per_RYDBERG / ANGSTROM_per_BOHR;
|
||||
}
|
||||
}
|
||||
|
||||
// convert fquest on one proc into f for atoms on each proc
|
||||
|
||||
One2Many *qst2lmp = new One2Many(MPI_COMM_WORLD);
|
||||
qst2lmp->setup(natoms,nlocal,id);
|
||||
double *fvec = NULL;
|
||||
if (f) fvec = &f[0][0];
|
||||
if (info->me == 0) qst2lmp->scatter(&fquest[0][0],3,fvec);
|
||||
else qst2lmp->scatter(NULL,3,fvec);
|
||||
|
||||
// clean up
|
||||
// some data only exists on proc 0
|
||||
|
||||
delete lmp2qst;
|
||||
delete qst2lmp;
|
||||
|
||||
info->memory->destroy_2d_double_array(xquest);
|
||||
info->memory->destroy_2d_double_array(fquest);
|
||||
|
||||
if (boxlines) {
|
||||
for (i = 0; i < 3; i++) delete [] boxlines[i];
|
||||
delete [] boxlines;
|
||||
}
|
||||
if (xlines) {
|
||||
for (i = 0; i < natoms; i++) delete [] xlines[i];
|
||||
delete [] xlines;
|
||||
}
|
||||
if (flines) {
|
||||
for (i = 0; i < natoms; i++) delete [] flines[i];
|
||||
delete [] flines;
|
||||
}
|
||||
}
|
||||
|
|
@ -1,58 +0,0 @@
|
|||
LAMMPS (20 Sep 2010)
|
||||
# LAMMPS input for coupling MD/Quantum
|
||||
|
||||
units metal
|
||||
dimension 3
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
lattice diamond 5.43
|
||||
Lattice spacing in x,y,z = 5.43 5.43 5.43
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (5.43 5.43 5.43)
|
||||
1 by 1 by 1 processor grid
|
||||
create_atoms 1 box
|
||||
Created 8 atoms
|
||||
mass 1 28.08
|
||||
|
||||
velocity all create 300.0 87293 loop geom
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all external
|
||||
|
||||
dump 1 all custom 1 dump.md id type x y z fx fy fz
|
||||
thermo 1
|
||||
run 10
|
||||
Memory usage per processor = 1.25982 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 0 0 0.2714463 1810.9378
|
||||
1 298.22165 0 0 0.26983722 1800.2029
|
||||
2 293.2839 0 0 0.26536943 1770.3964
|
||||
3 286.18537 0 0 0.25894654 1727.5464
|
||||
4 277.61576 0 0 0.25119258 1675.8163
|
||||
5 267.3325 0 0 0.24188807 1613.7418
|
||||
6 254.94702 0 0 0.23068142 1538.9774
|
||||
7 240.91176 0 0 0.21798202 1454.2541
|
||||
8 226.27996 0 0 0.20474287 1365.9298
|
||||
9 212.1059 0 0 0.19191788 1280.3687
|
||||
10 199.27609 0 0 0.18030919 1202.922
|
||||
Loop time of 80.663 on 1 procs for 10 steps with 8 atoms
|
||||
|
||||
Pair time (%) = 0 (0)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 4.91142e-05 (6.08882e-05)
|
||||
Outpt time (%) = 0.00111485 (0.0013821)
|
||||
Other time (%) = 80.6618 (99.9986)
|
||||
|
||||
Nlocal: 8 ave 8 max 8 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 10 ave 10 max 10 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
|
@ -1,58 +0,0 @@
|
|||
LAMMPS (20 Sep 2010)
|
||||
# LAMMPS input for coupling MD/Quantum
|
||||
|
||||
units metal
|
||||
dimension 3
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
lattice diamond 5.43
|
||||
Lattice spacing in x,y,z = 5.43 5.43 5.43
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (5.43 5.43 5.43)
|
||||
1 by 2 by 2 processor grid
|
||||
create_atoms 1 box
|
||||
Created 8 atoms
|
||||
mass 1 28.08
|
||||
|
||||
velocity all create 300.0 87293 loop geom
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all external
|
||||
|
||||
dump 1 all custom 1 dump.md id type x y z fx fy fz
|
||||
thermo 1
|
||||
run 10
|
||||
Memory usage per processor = 1.25928 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 0 0 0.2714463 1810.9378
|
||||
1 298.22166 0 0 0.26983722 1800.2029
|
||||
2 293.28391 0 0 0.26536944 1770.3964
|
||||
3 286.18538 0 0 0.25894655 1727.5464
|
||||
4 277.61578 0 0 0.25119259 1675.8164
|
||||
5 267.33252 0 0 0.24188809 1613.7419
|
||||
6 254.94703 0 0 0.23068143 1538.9774
|
||||
7 240.91175 0 0 0.21798202 1454.254
|
||||
8 226.27997 0 0 0.20474287 1365.9299
|
||||
9 212.10594 0 0 0.19191791 1280.3689
|
||||
10 199.27613 0 0 0.18030923 1202.9223
|
||||
Loop time of 79.8256 on 4 procs for 10 steps with 8 atoms
|
||||
|
||||
Pair time (%) = 0 (0)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000365376 (0.000457718)
|
||||
Outpt time (%) = 0.00169969 (0.00212925)
|
||||
Other time (%) = 79.8236 (99.9974)
|
||||
|
||||
Nlocal: 2 ave 2 max 2 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5 ave 5 max 5 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
|
@ -1 +0,0 @@
|
|||
#define QUEST /home/sjplimp/csrf/quest/src/lcao.x
|
||||
|
|
@ -1,161 +0,0 @@
|
|||
do setup
|
||||
do iters
|
||||
do force
|
||||
no relax
|
||||
setup data
|
||||
title
|
||||
Si 1x1x1 unit cell
|
||||
functional
|
||||
PBE
|
||||
dimensions of system (0=cluster ... 3=bulk)
|
||||
3
|
||||
primitive lattice vectors
|
||||
10.261212 0.000000 0.000000
|
||||
0.000000 10.261212 0.000000
|
||||
0.000000 0.000000 10.261212
|
||||
grid dimensions
|
||||
10 10 10
|
||||
atom types
|
||||
1
|
||||
type number, label:
|
||||
1 Si_pbe
|
||||
notes5
|
||||
Originally constructed by Peter A. Schultz, 12Apr01
|
||||
potential generated by new Hamann program PUNSLDX
|
||||
Cite use with: D.R. Hamann, unpublished.
|
||||
Potential: "standard" setting out to l=2
|
||||
Basis: amended Jun05 for better (2d/1d not 1d/1d) d-function
|
||||
effective nuclear charge (s2p2 to 10.0)
|
||||
4.00000000d+00
|
||||
pseudopotentials: Lmax, and effective gaussian range
|
||||
2 0.86000000d+00
|
||||
functional type used in generating potential:
|
||||
PBE
|
||||
radial mesh: number of points for local and non-local pot integrals
|
||||
80 67
|
||||
mesh points for nuclear potential; ham2dh
|
||||
0.02500000 0.02696978 0.02909477 0.03138719 0.03386023 0.03652812
|
||||
0.03940622 0.04251109 0.04586060 0.04947402 0.05337215 0.05757741
|
||||
0.06211402 0.06700807 0.07228773 0.07798338 0.08412779 0.09075634
|
||||
0.09790716 0.10562140 0.11394345 0.12292121 0.13260635 0.14305458
|
||||
0.15432605 0.16648562 0.17960325 0.19375443 0.20902061 0.22548964
|
||||
0.24325628 0.26242278 0.28309943 0.30540522 0.32946852 0.35542780
|
||||
0.38343245 0.41364362 0.44623518 0.48139466 0.51932441 0.56024270
|
||||
0.60438500 0.65200533 0.70337773 0.75879783 0.81858456 0.88308197
|
||||
0.95266121 1.02772271 1.10869840 1.19605428 1.29029305 1.39195702
|
||||
1.50163124 1.61994684 1.74758469 1.88527930 2.03382306 2.19407079
|
||||
2.36694466 2.55343950 2.75462852 2.97166951 3.20581145 3.45840177
|
||||
3.73089402 4.02485632 4.34198031 4.68409093 5.05315693 5.45130215
|
||||
5.88081777 6.34417553 6.84404189 7.38329340 7.96503329 8.59260927
|
||||
9.26963282 10.00000000
|
||||
radwts: weights for radial points
|
||||
0.00189603 0.00204542 0.00220659 0.00238045 0.00256800 0.00277034
|
||||
0.00298862 0.00322410 0.00347813 0.00375218 0.00404781 0.00436675
|
||||
0.00471081 0.00508198 0.00548240 0.00591436 0.00638036 0.00688308
|
||||
0.00742541 0.00801047 0.00864162 0.00932251 0.01005704 0.01084945
|
||||
0.01170429 0.01262649 0.01362135 0.01469459 0.01585240 0.01710143
|
||||
0.01844888 0.01990249 0.02147064 0.02316234 0.02498733 0.02695611
|
||||
0.02908002 0.03137128 0.03384307 0.03650961 0.03938625 0.04248955
|
||||
0.04583736 0.04944895 0.05334510 0.05754823 0.06208254 0.06697411
|
||||
0.07225109 0.07794385 0.08408515 0.09071034 0.09785753 0.10556786
|
||||
0.11388570 0.12285891 0.13253914 0.14298208 0.15424783 0.16640123
|
||||
0.17951222 0.19365623 0.20891467 0.22537535 0.24313298 0.26228977
|
||||
0.28295594 0.30525043 0.32930153 0.35524766 0.38323811 0.41343397
|
||||
0.44600900 0.48115067 0.51906119 0.55995874 0.60407867 0.65167486
|
||||
0.70302122 0.75841323
|
||||
non-local potential: l,potential*integration weight
|
||||
0 0.62022930 0.62128855 0.62243016 0.62366033 0.62498568 0.62641328
|
||||
0.62795061 0.62960563 0.63138673 0.63330275 0.63536294 0.63757692
|
||||
0.63995464 0.64250630 0.64524218 0.64817253 0.65130735 0.65465605
|
||||
0.65822713 0.66202767 0.66606269 0.67033437 0.67484108 0.67957602
|
||||
0.68452576 0.68966817 0.69497006 0.70038419 0.70584566 0.71126756
|
||||
0.71653578 0.72150290 0.72598113 0.72973436 0.73246932 0.73382636
|
||||
0.73337030 0.73058243 0.72485505 0.71549107 0.70171167 0.68267654
|
||||
0.65752236 0.62542611 0.58570073 0.53792896 0.48213811 0.41900888
|
||||
0.35009536 0.27800640 0.20646172 0.14009458 0.08384960 0.04186877
|
||||
0.01596164 0.00423035 0.00115036 0.00066636 0.00047879 0.00029939
|
||||
0.00016329 0.00007995 0.00003517 0.00001362 0.00000445 0.00000111
|
||||
0.00000016 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
|
||||
0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
|
||||
0.00000000 0.00000000
|
||||
non-local potential: l,potential*integration weight
|
||||
1 0.59551624 0.59463303 0.59368033 0.59265268 0.59154422 0.59034862
|
||||
0.58905906 0.58766819 0.58616811 0.58455033 0.58280567 0.58092430
|
||||
0.57889565 0.57670833 0.57435015 0.57180802 0.56906791 0.56611482
|
||||
0.56293268 0.55950435 0.55581158 0.55183493 0.54755377 0.54294628
|
||||
0.53798942 0.53265896 0.52692951 0.52077458 0.51416671 0.50707751
|
||||
0.49947790 0.49133817 0.48262822 0.47331766 0.46337588 0.45277197
|
||||
0.44147437 0.42945016 0.41666374 0.40307468 0.38863443 0.37328165
|
||||
0.35693601 0.33949042 0.32080256 0.30068740 0.27891443 0.25521609
|
||||
0.22931791 0.20100526 0.17024474 0.13737521 0.10336405 0.07007167
|
||||
0.04035673 0.01767907 0.00470635 0.00076638 0.00047880 0.00029939
|
||||
0.00016329 0.00007995 0.00003517 0.00001362 0.00000445 0.00000111
|
||||
0.00000016 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
|
||||
0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
|
||||
0.00000000 0.00000000
|
||||
non-local potential: l,potential*integration weight
|
||||
2 0.56305372 0.55961728 0.55591134 0.55191498 0.54760572 0.54295941
|
||||
0.53795013 0.53255008 0.52672947 0.52045641 0.51369682 0.50641433
|
||||
0.49857022 0.49012333 0.48103004 0.47124429 0.46071759 0.44939919
|
||||
0.43723624 0.42417413 0.41015690 0.39512792 0.37903070 0.36181001
|
||||
0.34341340 0.32379300 0.30290805 0.28072780 0.25723539 0.23243242
|
||||
0.20634465 0.17902876 0.15058041 0.12114359 0.09092117 0.06018665
|
||||
0.02929636 -0.00129833 -0.03104046 -0.05926034 -0.08517498 -0.10789810
|
||||
-0.12646610 -0.13988656 -0.14721657 -0.14767751 -0.14080976 -0.12666296
|
||||
-0.10600305 -0.08049270 -0.05276798 -0.02629475 -0.00486427 0.00837657
|
||||
0.01228139 0.00892332 0.00342796 0.00074936 0.00047880 0.00029939
|
||||
0.00016329 0.00007995 0.00003517 0.00001362 0.00000445 0.00000111
|
||||
0.00000016 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
|
||||
0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
|
||||
0.00000000 0.00000000
|
||||
number of radial functions **** Si PBE Ham-II basis 20Feb01-PAS ****
|
||||
5
|
||||
angular momentum, number of alphas
|
||||
0 4
|
||||
alphas - s - 4s/2/4s407 (bulk Si dzp Eopt+reopt c1)
|
||||
0.10460000d+00 0.27226300d+00 1.30050800d+00 2.60103000d+00
|
||||
wave function coefficients
|
||||
0.20995300d+00 0.55978200d+00 -0.99128200d+00 0.33487100d+00
|
||||
angular momentum, number of alphas
|
||||
1 3
|
||||
alphas - p - 3p/2/3p492 (bulk Si dzp Eopt + reopt c1)
|
||||
0.09424100d+00 0.31767900d+00 1.56114500d+00
|
||||
wave function coefficients
|
||||
0.06761600d+00 0.31821200d+00 -0.06638300d+00
|
||||
angular momentum, number of alphas
|
||||
0 1
|
||||
alphas - s - second zeta s polarization
|
||||
0.10460000d+00
|
||||
wave function coefficients
|
||||
1.00000000d+00
|
||||
angular momentum, number of alphas
|
||||
1 1
|
||||
alphas - p - second zeta p polarization
|
||||
0.09424100d+00
|
||||
wave function coefficients
|
||||
1.00000000d+00
|
||||
angular momentum, number of alphas
|
||||
2 2
|
||||
alphas - d - angular polarization (dzp Eopt)
|
||||
0.32000000d+00 1.40000000d+00
|
||||
wave function coefficients
|
||||
0.31557000d+00 1.00000000d+00
|
||||
shell occupancies for this silicon, Si: s(2.00)p(2.00)
|
||||
2.00000000 2.00000000 0.00000000 0.00000000 0.00000000 0.00000000
|
||||
end atom file
|
||||
number of atoms in unit cell
|
||||
8
|
||||
atom, type, position vector
|
||||
1 1 0.0000000000 0.0000000000 0.0000000000
|
||||
2 1 5.1306060590 5.1306060590 0.0000000000
|
||||
3 1 5.1306060590 0.0000000000 5.1306060590
|
||||
4 1 0.0000000000 5.1306060590 5.1306060590
|
||||
5 1 2.5653030295 2.5653030295 2.5653030295
|
||||
6 1 7.6959090885 7.6959090885 2.5653030295
|
||||
7 1 7.6959090885 2.5653030295 7.6959090885
|
||||
8 1 2.5653030295 7.6959090885 7.6959090885
|
||||
kgrid
|
||||
0 0 0
|
||||
end setup phase data
|
||||
run phase input data
|
||||
end of run phase data
|
||||
|
|
@ -1,48 +0,0 @@
|
|||
# Makefile for grain growth via LAMMPS <-> SPPARKS coupling
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
# System-specific settings
|
||||
|
||||
LAMMPS = /home/sjplimp/lammps
|
||||
SPPARKS = /home/sjplimp/spparks
|
||||
|
||||
CC = g++
|
||||
CCFLAGS = -g -O -DMPICH_IGNORE_CXX_SEEK -I../library
|
||||
DEPFLAGS = -M
|
||||
LINK = g++
|
||||
LINKFLAGS = -g -O -L../library -L${LAMMPS}/src -L${SPPARKS}/src
|
||||
USRLIB = -lcouple -llmp_g++ -lspk_g++
|
||||
SYSLIB = -lfftw -lmpich -lpthread
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
|
||||
# Files
|
||||
|
||||
EXE = lmpspk
|
||||
SRC = $(wildcard *.cpp)
|
||||
INC = $(wildcard *.h)
|
||||
OBJ = $(SRC:.cpp=.o)
|
||||
|
||||
# Targets
|
||||
|
||||
lmpspk: $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
clean:
|
||||
rm $(EXE) *.o
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
|
||||
|
||||
# Individual dependencies
|
||||
|
||||
DEPENDS = $(OBJ:.o=.d)
|
||||
include $(DEPENDS)
|
||||
|
|
@ -1,71 +0,0 @@
|
|||
This directory has an application that models grain growth in the
|
||||
presence of strain. The grain growth is simulated by a Potts model in
|
||||
a kinetic Monte Carlo code SPPARKS. Clusters of like spins on a
|
||||
lattice represent grains. The Hamiltonian for the energy due of a
|
||||
collection of spins includes a strain term and is described on this
|
||||
page in the SPPARKS documentation:
|
||||
|
||||
http://www.sandia.gov/~sjplimp/spparks/doc/app_potts_strain.html.
|
||||
|
||||
The strain is computed by LAMMPS as a particle displacement where
|
||||
pairs of atoms across a grain boundary are of different types and thus
|
||||
push off from each other due to a Lennard-Jones sigma between
|
||||
particles of different types that is larger than the sigma between
|
||||
particles of the same type (interior to grains).
|
||||
|
||||
lmpspk.cpp main program
|
||||
it links LAMMPS and SPPARKS as libraries
|
||||
in.spparks SPPARKS input script, without the run command
|
||||
lmppath.h contains path to LAMMPS home directory
|
||||
spkpath.h contains path to SPPARKS home directory
|
||||
|
||||
After editing the Makefile, lmppath.h, and spkpath.h to make them
|
||||
suitable for your box, type:
|
||||
|
||||
g++ -f Makefile.g++
|
||||
|
||||
and you should get the lmpspk executable.
|
||||
|
||||
NOTE: To build and run this coupled application, you must of course,
|
||||
have SPPARKS built on your system. It's WWW site is
|
||||
http://www.sandia.gov/~sjplimp/spparks.html. It is an open-source
|
||||
code, written by two of the LAMMPS authors.
|
||||
|
||||
You can run lmpspk in serial or parallel as:
|
||||
|
||||
% lmpspk Niter Ndelta Sfactor in.spparks
|
||||
% mpirun -np 4 lmpspk Niter Ndelta Sfactor in.spparks
|
||||
|
||||
where
|
||||
|
||||
Niter = # of outer iterations
|
||||
Ndelta = time to run MC in each iteration
|
||||
Sfactor = multiplier on strain effect
|
||||
in.spparks = SPPARKS input script
|
||||
|
||||
The log files are for this run:
|
||||
|
||||
% lmpspk 20 10.0 1 in.spparks
|
||||
|
||||
This application is an example of a coupling where the driver code
|
||||
(lmpspk) alternates back and forth between the 2 applications (LAMMPS
|
||||
and SPPARKS). Each outer timestep in the driver code, the following
|
||||
tasks are performed. One code (SPPARKS) is invoked for a few Monte
|
||||
Carlo steps. Some of its output (spin state) is passed to the other
|
||||
code (LAMMPS) as input (atom type). The the other code (LAMMPS) is
|
||||
invoked for a few timesteps. Some of its output (atom coords) is
|
||||
massaged to become an input (per-atom strain) for the original code
|
||||
(SPPARKS).
|
||||
|
||||
The driver code launches both SPPARKS and LAMMPS in parallel and they
|
||||
both decompose their spatial domains in the same manner. The datums
|
||||
in SPPARKS (lattice sites) are the same as the datums in LAMMPS
|
||||
(coarse-grained particles). If this were not the case, more
|
||||
sophisticated inter-code communication could be performed.
|
||||
|
||||
You can look at the log files in the directory to see sample LAMMPS
|
||||
and SPPARKS output for this simulation. Dump files produced by the
|
||||
run are stored as dump.mc and dump.md. The image*.png files show
|
||||
snapshots from both the LAMMPS and SPPARKS output. Note that the
|
||||
in.lammps and data.lammps files are not inputs; they are generated by
|
||||
the lmpspk driver.
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 280 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 321 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 329 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 260 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 229 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 261 KiB |
|
|
@ -1,23 +0,0 @@
|
|||
# SPPARKS input for coupling MD/MC
|
||||
|
||||
seed 56789
|
||||
|
||||
app_style potts/strain 100
|
||||
|
||||
dimension 2
|
||||
lattice sq/8n 1.0
|
||||
region box block 0 50 0 50 -0.5 0.5
|
||||
create_box box
|
||||
create_sites box
|
||||
set site range 1 100
|
||||
set d1 value 0.0
|
||||
|
||||
sector yes
|
||||
solve_style tree
|
||||
|
||||
diag_style energy
|
||||
|
||||
temperature 1.0
|
||||
|
||||
stats 10.0
|
||||
dump 1 10.0 dump.mc
|
||||
|
|
@ -1 +0,0 @@
|
|||
#define LMPPATH /home/sjplimp/lammps
|
||||
|
|
@ -1,223 +0,0 @@
|
|||
// lmpspk = umbrella driver to couple LAMMPS + SPPARKS
|
||||
// for a strain-induced grain growth model
|
||||
|
||||
// Syntax: lmpspk Niter Ndelta Sfactor in.spparks
|
||||
// Niter = # of outer iterations
|
||||
// Ndelta = time to run MC in each iteration
|
||||
// Sfactor = multiplier on strain effect
|
||||
// in.spparks = SPPARKS input script
|
||||
|
||||
#include "mpi.h"
|
||||
#include "stdio.h"
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
|
||||
#include "lammps_data_write.h"
|
||||
#include "many2many.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
#define QUOTE_(x) #x
|
||||
#define QUOTE(x) QUOTE_(x)
|
||||
|
||||
#include "spkpath.h"
|
||||
#include QUOTE(SPKPATH/src/spparks.h)
|
||||
#include QUOTE(SPKPATH/src/library.h)
|
||||
#include QUOTE(SPKPATH/src/input.h)
|
||||
|
||||
#include "lmppath.h"
|
||||
#include QUOTE(LMPPATH/src/lammps.h)
|
||||
#include QUOTE(LMPPATH/src/library.h)
|
||||
#include QUOTE(LMPPATH/src/input.h)
|
||||
#include QUOTE(LMPPATH/src/modify.h)
|
||||
#include QUOTE(LMPPATH/src/compute.h)
|
||||
|
||||
using namespace SPPARKS_NS;
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int main(int narg, char **arg)
|
||||
{
|
||||
int i,n;
|
||||
char str[128];
|
||||
|
||||
// setup MPI
|
||||
|
||||
MPI_Init(&narg,&arg);
|
||||
MPI_Comm comm = MPI_COMM_WORLD;
|
||||
|
||||
int me,nprocs;
|
||||
MPI_Comm_rank(comm,&me);
|
||||
MPI_Comm_size(comm,&nprocs);
|
||||
|
||||
Memory *memory = new Memory(comm);
|
||||
Error *error = new Error(comm);
|
||||
|
||||
// command-line args
|
||||
|
||||
if (narg != 5)
|
||||
error->all("Syntax: lmpspk Niter Ndelta Sfactor in.spparks");
|
||||
|
||||
int niter = atoi(arg[1]);
|
||||
double delta = atof(arg[2]);
|
||||
double sfactor = atof(arg[3]);
|
||||
n = strlen(arg[4]) + 1;
|
||||
char *spparks_input = new char[n];
|
||||
strcpy(spparks_input,arg[4]);
|
||||
|
||||
// instantiate LAMMPS and SPPARKS
|
||||
|
||||
SPPARKS *spk = new SPPARKS(0,NULL,MPI_COMM_WORLD);
|
||||
LAMMPS *lmp = new LAMMPS(0,NULL,MPI_COMM_WORLD);
|
||||
|
||||
// create simulation in SPPARKS from in.spparks
|
||||
|
||||
spk->input->file(spparks_input);
|
||||
|
||||
// extract permanent info from SPPARKS
|
||||
|
||||
int dimension,nglobal,nlocal_spparks,nspins;
|
||||
double boxxlo,boxxhi,boxylo,boxyhi,boxzlo,boxzhi;
|
||||
int *id_spparks,*spins;
|
||||
double **xyz;
|
||||
double *strain;
|
||||
|
||||
dimension = *((int *) spparks_extract(spk,"dimension"));
|
||||
nglobal = *((int *) spparks_extract(spk,"nglobal"));
|
||||
nlocal_spparks = *((int *) spparks_extract(spk,"nlocal"));
|
||||
|
||||
boxxlo = *((double *) spparks_extract(spk,"boxxlo"));
|
||||
boxxhi = *((double *) spparks_extract(spk,"boxxhi"));
|
||||
boxylo = *((double *) spparks_extract(spk,"boxylo"));
|
||||
boxyhi = *((double *) spparks_extract(spk,"boxyhi"));
|
||||
if (dimension == 3) {
|
||||
boxzlo = *((double *) spparks_extract(spk,"boxzlo"));
|
||||
boxzhi = *((double *) spparks_extract(spk,"boxzhi"));
|
||||
} else {
|
||||
boxzlo = -0.5;
|
||||
boxzhi = 0.5;
|
||||
}
|
||||
|
||||
id_spparks = (int *) spparks_extract(spk,"id");
|
||||
spins = (int *) spparks_extract(spk,"site");
|
||||
xyz = (double **) spparks_extract(spk,"xyz");
|
||||
|
||||
nspins = *((int *) spparks_extract(spk,"nspins"));
|
||||
strain = (double *) spparks_extract(spk,"strain");
|
||||
|
||||
// write a LAMMPS input script using SPPARKS params
|
||||
|
||||
if (me == 0) {
|
||||
FILE *fp = fopen("in.lammps","w");
|
||||
if (fp == NULL) error->one("Could not create LAMMPS input script");
|
||||
|
||||
fprintf(fp,"units lj\n");
|
||||
sprintf(str,"dimension %d\n",dimension);
|
||||
fprintf(fp,str);
|
||||
fprintf(fp,"atom_style atomic\n\n");
|
||||
|
||||
fprintf(fp,"read_data data.lammps\n");
|
||||
fprintf(fp,"mass * 1.0\n\n");
|
||||
|
||||
fprintf(fp,"pair_style lj/cut 2.5\n");
|
||||
fprintf(fp,"pair_coeff * * 1.0 1.2\n");
|
||||
for (i = 0; i < nspins; i++) {
|
||||
sprintf(str,"pair_coeff %d %d 1.0 1.0\n",i+1,i+1);
|
||||
fprintf(fp,str);
|
||||
}
|
||||
fprintf(fp,"\n");
|
||||
|
||||
fprintf(fp,"compute da all displace/atom\n\n");
|
||||
fprintf(fp,"dump 1 all atom 10 dump.md\n");
|
||||
fprintf(fp,"thermo 1\n");
|
||||
|
||||
fclose(fp);
|
||||
}
|
||||
|
||||
// write a LAMMPS data file using SPPARKS data
|
||||
|
||||
LAMMPSDataWrite *lwd = new LAMMPSDataWrite(MPI_COMM_WORLD);
|
||||
lwd->file("data.lammps");
|
||||
lwd->header("%d atoms",nglobal);
|
||||
lwd->header("%d atom types",nspins);
|
||||
lwd->header("%g %g xlo xhi",boxxlo,boxxhi);
|
||||
lwd->header("%g %g ylo yhi",boxylo,boxyhi);
|
||||
lwd->header("%g %g zlo zhi",boxzlo,boxzhi);
|
||||
lwd->atoms(nlocal_spparks);
|
||||
lwd->atoms(id_spparks);
|
||||
lwd->atoms(spins);
|
||||
lwd->atoms(3,xyz);
|
||||
lwd->execute();
|
||||
delete lwd;
|
||||
|
||||
// create simulation in LAMMPS from created input script
|
||||
|
||||
lmp->input->file("in.lammps");
|
||||
|
||||
// create transfer operators
|
||||
|
||||
Many2Many *spk2lmp = new Many2Many(MPI_COMM_WORLD);
|
||||
Many2Many *lmp2spk = new Many2Many(MPI_COMM_WORLD);
|
||||
|
||||
// timestep loop
|
||||
// run SPPARKS for delta time
|
||||
// use SPPARKS spins to reset LAMMPS atom types
|
||||
// perform LAMMPS minimization
|
||||
// use atom displacements to reset strain values in SPPARKS
|
||||
// realloc displace as necessary since nlocal_lammps may change
|
||||
// re-create both xfers every iteration since LAMMPS may migrate atoms
|
||||
|
||||
int nmax = 0;
|
||||
double *displace = NULL;
|
||||
|
||||
int nlocal_lammps;
|
||||
int *id_lammps,*type;
|
||||
double **displace_lammps;
|
||||
|
||||
for (int iter = 0; iter < niter; iter++) {
|
||||
sprintf(str,"run %g",delta);
|
||||
spk->input->one(str);
|
||||
|
||||
nlocal_lammps = *((int *) lammps_extract_global(lmp,"nlocal"));
|
||||
id_lammps = (int *) lammps_extract_atom(lmp,"id");
|
||||
type = (int *) lammps_extract_atom(lmp,"type");
|
||||
|
||||
spk2lmp->setup(nlocal_spparks,id_spparks,nlocal_lammps,id_lammps);
|
||||
spk2lmp->exchange(spins,type);
|
||||
|
||||
lmp->input->one("minimize 0.001 0.001 10 1000");
|
||||
|
||||
nlocal_lammps = *((int *) lammps_extract_global(lmp,"nlocal"));
|
||||
id_lammps = (int *) lammps_extract_atom(lmp,"id");
|
||||
displace_lammps = (double **) lammps_extract_compute(lmp,"da",1,2);
|
||||
|
||||
if (nlocal_lammps > nmax) {
|
||||
memory->sfree(displace);
|
||||
nmax = nlocal_lammps;
|
||||
displace = (double *)
|
||||
memory->smalloc(nmax*sizeof(double),"lmpspk:displace");
|
||||
}
|
||||
|
||||
for (i = 0; i < nlocal_lammps; i++)
|
||||
displace[i] = sfactor*displace_lammps[i][3];
|
||||
|
||||
lmp2spk->setup(nlocal_lammps,id_lammps,nlocal_spparks,id_spparks);
|
||||
lmp2spk->exchange(displace,strain);
|
||||
}
|
||||
|
||||
memory->sfree(displace);
|
||||
|
||||
// clean up
|
||||
|
||||
delete spk2lmp;
|
||||
delete lmp2spk;
|
||||
delete spk;
|
||||
delete lmp;
|
||||
|
||||
delete [] spparks_input;
|
||||
delete memory;
|
||||
delete error;
|
||||
|
||||
MPI_Finalize();
|
||||
}
|
||||
|
|
@ -1,978 +0,0 @@
|
|||
LAMMPS (20 Sep 2010)
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style atomic
|
||||
|
||||
read_data data.lammps
|
||||
orthogonal box = (0 0 -0.5) to (50 50 0.5)
|
||||
1 by 1 by 1 processor grid
|
||||
2500 atoms
|
||||
mass * 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.2
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 1.0 1.0
|
||||
pair_coeff 3 3 1.0 1.0
|
||||
pair_coeff 4 4 1.0 1.0
|
||||
pair_coeff 5 5 1.0 1.0
|
||||
pair_coeff 6 6 1.0 1.0
|
||||
pair_coeff 7 7 1.0 1.0
|
||||
pair_coeff 8 8 1.0 1.0
|
||||
pair_coeff 9 9 1.0 1.0
|
||||
pair_coeff 10 10 1.0 1.0
|
||||
pair_coeff 11 11 1.0 1.0
|
||||
pair_coeff 12 12 1.0 1.0
|
||||
pair_coeff 13 13 1.0 1.0
|
||||
pair_coeff 14 14 1.0 1.0
|
||||
pair_coeff 15 15 1.0 1.0
|
||||
pair_coeff 16 16 1.0 1.0
|
||||
pair_coeff 17 17 1.0 1.0
|
||||
pair_coeff 18 18 1.0 1.0
|
||||
pair_coeff 19 19 1.0 1.0
|
||||
pair_coeff 20 20 1.0 1.0
|
||||
pair_coeff 21 21 1.0 1.0
|
||||
pair_coeff 22 22 1.0 1.0
|
||||
pair_coeff 23 23 1.0 1.0
|
||||
pair_coeff 24 24 1.0 1.0
|
||||
pair_coeff 25 25 1.0 1.0
|
||||
pair_coeff 26 26 1.0 1.0
|
||||
pair_coeff 27 27 1.0 1.0
|
||||
pair_coeff 28 28 1.0 1.0
|
||||
pair_coeff 29 29 1.0 1.0
|
||||
pair_coeff 30 30 1.0 1.0
|
||||
pair_coeff 31 31 1.0 1.0
|
||||
pair_coeff 32 32 1.0 1.0
|
||||
pair_coeff 33 33 1.0 1.0
|
||||
pair_coeff 34 34 1.0 1.0
|
||||
pair_coeff 35 35 1.0 1.0
|
||||
pair_coeff 36 36 1.0 1.0
|
||||
pair_coeff 37 37 1.0 1.0
|
||||
pair_coeff 38 38 1.0 1.0
|
||||
pair_coeff 39 39 1.0 1.0
|
||||
pair_coeff 40 40 1.0 1.0
|
||||
pair_coeff 41 41 1.0 1.0
|
||||
pair_coeff 42 42 1.0 1.0
|
||||
pair_coeff 43 43 1.0 1.0
|
||||
pair_coeff 44 44 1.0 1.0
|
||||
pair_coeff 45 45 1.0 1.0
|
||||
pair_coeff 46 46 1.0 1.0
|
||||
pair_coeff 47 47 1.0 1.0
|
||||
pair_coeff 48 48 1.0 1.0
|
||||
pair_coeff 49 49 1.0 1.0
|
||||
pair_coeff 50 50 1.0 1.0
|
||||
pair_coeff 51 51 1.0 1.0
|
||||
pair_coeff 52 52 1.0 1.0
|
||||
pair_coeff 53 53 1.0 1.0
|
||||
pair_coeff 54 54 1.0 1.0
|
||||
pair_coeff 55 55 1.0 1.0
|
||||
pair_coeff 56 56 1.0 1.0
|
||||
pair_coeff 57 57 1.0 1.0
|
||||
pair_coeff 58 58 1.0 1.0
|
||||
pair_coeff 59 59 1.0 1.0
|
||||
pair_coeff 60 60 1.0 1.0
|
||||
pair_coeff 61 61 1.0 1.0
|
||||
pair_coeff 62 62 1.0 1.0
|
||||
pair_coeff 63 63 1.0 1.0
|
||||
pair_coeff 64 64 1.0 1.0
|
||||
pair_coeff 65 65 1.0 1.0
|
||||
pair_coeff 66 66 1.0 1.0
|
||||
pair_coeff 67 67 1.0 1.0
|
||||
pair_coeff 68 68 1.0 1.0
|
||||
pair_coeff 69 69 1.0 1.0
|
||||
pair_coeff 70 70 1.0 1.0
|
||||
pair_coeff 71 71 1.0 1.0
|
||||
pair_coeff 72 72 1.0 1.0
|
||||
pair_coeff 73 73 1.0 1.0
|
||||
pair_coeff 74 74 1.0 1.0
|
||||
pair_coeff 75 75 1.0 1.0
|
||||
pair_coeff 76 76 1.0 1.0
|
||||
pair_coeff 77 77 1.0 1.0
|
||||
pair_coeff 78 78 1.0 1.0
|
||||
pair_coeff 79 79 1.0 1.0
|
||||
pair_coeff 80 80 1.0 1.0
|
||||
pair_coeff 81 81 1.0 1.0
|
||||
pair_coeff 82 82 1.0 1.0
|
||||
pair_coeff 83 83 1.0 1.0
|
||||
pair_coeff 84 84 1.0 1.0
|
||||
pair_coeff 85 85 1.0 1.0
|
||||
pair_coeff 86 86 1.0 1.0
|
||||
pair_coeff 87 87 1.0 1.0
|
||||
pair_coeff 88 88 1.0 1.0
|
||||
pair_coeff 89 89 1.0 1.0
|
||||
pair_coeff 90 90 1.0 1.0
|
||||
pair_coeff 91 91 1.0 1.0
|
||||
pair_coeff 92 92 1.0 1.0
|
||||
pair_coeff 93 93 1.0 1.0
|
||||
pair_coeff 94 94 1.0 1.0
|
||||
pair_coeff 95 95 1.0 1.0
|
||||
pair_coeff 96 96 1.0 1.0
|
||||
pair_coeff 97 97 1.0 1.0
|
||||
pair_coeff 98 98 1.0 1.0
|
||||
pair_coeff 99 99 1.0 1.0
|
||||
pair_coeff 100 100 1.0 1.0
|
||||
|
||||
compute da all displace/atom
|
||||
|
||||
dump 1 all atom 10 dump.md
|
||||
thermo 1
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 2.85036 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 9.3150455 0 9.3150455 97.103602
|
||||
1 0 3.0727032 0 3.0727032 56.391395
|
||||
2 0 2.4831365 0 2.4831365 52.450383
|
||||
3 0 2.1851987 0 2.1851987 50.430755
|
||||
4 0 1.9671681 0 1.9671681 48.939108
|
||||
5 0 1.8292753 0 1.8292753 47.969182
|
||||
6 0 1.7386325 0 1.7386325 47.341991
|
||||
7 0 1.6672907 0 1.6672907 46.865385
|
||||
8 0 1.6046164 0 1.6046164 46.429986
|
||||
9 0 1.5099314 0 1.5099314 45.748095
|
||||
10 0 1.4106898 0 1.4106898 45.035856
|
||||
Loop time of 0.035866 on 1 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
9.31504545511 1.50993136661 1.41068980202
|
||||
Force two-norm initial, final = 14635.9 857.658
|
||||
Force max component initial, final = 332.921 80.6474
|
||||
Final line search alpha, max atom move = 0.0003705 0.0298798
|
||||
Iterations, force evaluations = 10 17
|
||||
|
||||
Pair time (%) = 0.0250154 (69.7467)
|
||||
Neigh time (%) = 0.00361013 (10.0656)
|
||||
Comm time (%) = 0.000285625 (0.796368)
|
||||
Outpt time (%) = 0.00396585 (11.0574)
|
||||
Other time (%) = 0.00298905 (8.33394)
|
||||
|
||||
Nlocal: 2500 ave 2500 max 2500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 526 ave 526 max 526 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 27247 ave 27247 max 27247 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 27247
|
||||
Ave neighs/atom = 10.8988
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 3.23183 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
10 0 12.002101 0 12.002101 114.02687
|
||||
11 0 5.3220163 0 5.3220163 70.950301
|
||||
12 0 4.1162407 0 4.1162407 62.953059
|
||||
13 0 3.2208482 0 3.2208482 56.887942
|
||||
14 0 2.8397825 0 2.8397825 54.301623
|
||||
15 0 2.019668 0 2.019668 48.619305
|
||||
16 0 1.8710381 0 1.8710381 47.601138
|
||||
17 0 1.5160328 0 1.5160328 45.108872
|
||||
18 0 1.3630386 0 1.3630386 44.05177
|
||||
19 0 1.1924745 0 1.1924745 42.849287
|
||||
20 0 1.0523828 0 1.0523828 41.861394
|
||||
Loop time of 0.0252161 on 1 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
12.0021008911 1.1924745171 1.0523827917
|
||||
Force two-norm initial, final = 21524.6 1259.91
|
||||
Force max component initial, final = 1527.37 241.935
|
||||
Final line search alpha, max atom move = 0.000346619 0.0838594
|
||||
Iterations, force evaluations = 10 10
|
||||
|
||||
Pair time (%) = 0.0147347 (58.4339)
|
||||
Neigh time (%) = 0.00360608 (14.3007)
|
||||
Comm time (%) = 0.000231743 (0.919027)
|
||||
Outpt time (%) = 0.00401402 (15.9185)
|
||||
Other time (%) = 0.00262952 (10.4279)
|
||||
|
||||
Nlocal: 2500 ave 2500 max 2500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 528 ave 528 max 528 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 27366 ave 27366 max 27366 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 27366
|
||||
Ave neighs/atom = 10.9464
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 3.23183 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
20 0 10.274114 0 10.274114 102.04597
|
||||
21 0 4.2587067 0 4.2587067 63.257085
|
||||
22 0 3.4579606 0 3.4579606 57.918783
|
||||
23 0 2.6091259 0 2.6091259 52.140871
|
||||
24 0 2.2414512 0 2.2414512 49.626887
|
||||
25 0 1.4257571 0 1.4257571 43.928929
|
||||
26 0 1.2604412 0 1.2604412 42.77986
|
||||
27 0 0.93381201 0 0.93381201 40.441383
|
||||
28 0 0.77305388 0 0.77305388 39.333891
|
||||
29 0 0.66272332 0 0.66272332 38.57176
|
||||
30 0 0.57357831 0 0.57357831 37.947153
|
||||
Loop time of 0.026665 on 1 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
10.2741143789 0.662723315031 0.57357831099
|
||||
Force two-norm initial, final = 20598.4 860.344
|
||||
Force max component initial, final = 1387.12 253.617
|
||||
Final line search alpha, max atom move = 0.00039155 0.0993038
|
||||
Iterations, force evaluations = 10 11
|
||||
|
||||
Pair time (%) = 0.0160739 (60.2811)
|
||||
Neigh time (%) = 0.00360513 (13.5201)
|
||||
Comm time (%) = 0.000238419 (0.894126)
|
||||
Outpt time (%) = 0.00400496 (15.0195)
|
||||
Other time (%) = 0.00274253 (10.2851)
|
||||
|
||||
Nlocal: 2500 ave 2500 max 2500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 533 ave 533 max 533 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 27534 ave 27534 max 27534 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 27534
|
||||
Ave neighs/atom = 11.0136
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 3.23183 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
30 0 8.9362793 0 8.9362793 92.757153
|
||||
31 0 3.9724633 0 3.9724633 60.7212
|
||||
32 0 2.6325511 0 2.6325511 51.784932
|
||||
33 0 1.9937863 0 1.9937863 47.422917
|
||||
34 0 1.6064073 0 1.6064073 44.757737
|
||||
35 0 1.1546808 0 1.1546808 41.600404
|
||||
36 0 0.93474074 0 0.93474074 40.067859
|
||||
37 0 0.67833269 0 0.67833269 38.264916
|
||||
38 0 0.51906207 0 0.51906207 37.145018
|
||||
39 0 0.31997654 0 0.31997654 35.736062
|
||||
40 0 0.18467885 0 0.18467885 34.785873
|
||||
Loop time of 0.0250409 on 1 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
8.93627934206 0.319976542343 0.184678853337
|
||||
Force two-norm initial, final = 18864.2 753.682
|
||||
Force max component initial, final = 1617.71 221.622
|
||||
Final line search alpha, max atom move = 0.000384932 0.0853095
|
||||
Iterations, force evaluations = 10 10
|
||||
|
||||
Pair time (%) = 0.0145993 (58.302)
|
||||
Neigh time (%) = 0.00361705 (14.4446)
|
||||
Comm time (%) = 0.000240088 (0.958783)
|
||||
Outpt time (%) = 0.00393724 (15.7233)
|
||||
Other time (%) = 0.00264716 (10.5714)
|
||||
|
||||
Nlocal: 2500 ave 2500 max 2500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 531 ave 531 max 531 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 27582 ave 27582 max 27582 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 27582
|
||||
Ave neighs/atom = 11.0328
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 3.23183 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
40 0 7.767847 0 7.767847 84.925704
|
||||
41 0 3.0582618 0 3.0582618 54.426036
|
||||
42 0 2.3262167 0 2.3262167 49.551755
|
||||
43 0 1.5424972 0 1.5424972 44.209493
|
||||
44 0 1.1584069 0 1.1584069 41.573231
|
||||
45 0 0.64653104 0 0.64653104 37.962296
|
||||
46 0 0.40723134 0 0.40723134 36.303826
|
||||
47 0 0.22801463 0 0.22801463 35.027621
|
||||
48 0 0.083516845 0 0.083516845 34.013608
|
||||
49 0 0.0031254794 0 0.0031254794 33.45763
|
||||
50 0 -0.081313313 0 -0.081313313 32.838812
|
||||
Loop time of 0.0265579 on 1 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
7.76784700214 0.00312547942455 -0.0813133129634
|
||||
Force two-norm initial, final = 17487.9 1815.23
|
||||
Force max component initial, final = 1273.66 876.61
|
||||
Final line search alpha, max atom move = 0.00073525 0.644528
|
||||
Iterations, force evaluations = 10 11
|
||||
|
||||
Pair time (%) = 0.016026 (60.3437)
|
||||
Neigh time (%) = 0.003613 (13.6042)
|
||||
Comm time (%) = 0.000234604 (0.883367)
|
||||
Outpt time (%) = 0.00397921 (14.9831)
|
||||
Other time (%) = 0.0027051 (10.1857)
|
||||
|
||||
Nlocal: 2500 ave 2500 max 2500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 535 ave 535 max 535 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 27865 ave 27865 max 27865 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 27865
|
||||
Ave neighs/atom = 11.146
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 3.23183 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
50 0 7.6174014 0 7.6174014 83.803569
|
||||
51 0 6.2032266 0 6.2032266 74.797688
|
||||
52 0 2.5148735 0 2.5148735 50.744231
|
||||
53 0 1.6582304 0 1.6582304 44.949256
|
||||
54 0 1.1103519 0 1.1103519 41.160347
|
||||
55 0 0.69940704 0 0.69940704 38.296984
|
||||
56 0 0.31006967 0 0.31006967 35.549044
|
||||
57 0 0.081622161 0 0.081622161 33.934922
|
||||
58 0 -0.090832662 0 -0.090832662 32.712284
|
||||
59 0 -0.21786156 0 -0.21786156 31.812246
|
||||
60 0 -0.32169958 0 -0.32169958 31.078298
|
||||
Loop time of 0.0236218 on 1 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
7.6174013995 -0.217861563426 -0.321699583013
|
||||
Force two-norm initial, final = 21782.8 679.792
|
||||
Force max component initial, final = 8739.6 189.661
|
||||
Final line search alpha, max atom move = 0.000489439 0.0928273
|
||||
Iterations, force evaluations = 10 10
|
||||
|
||||
Pair time (%) = 0.0145402 (61.5541)
|
||||
Neigh time (%) = 0.00240993 (10.2022)
|
||||
Comm time (%) = 0.000175714 (0.743866)
|
||||
Outpt time (%) = 0.00391126 (16.5578)
|
||||
Other time (%) = 0.0025847 (10.942)
|
||||
|
||||
Nlocal: 2500 ave 2500 max 2500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 541 ave 541 max 541 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 27986 ave 27986 max 27986 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 27986
|
||||
Ave neighs/atom = 11.1944
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 3.23183 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
60 0 5.8294051 0 5.8294051 71.780312
|
||||
61 0 2.2883695 0 2.2883695 48.754944
|
||||
62 0 0.81882056 0 0.81882056 38.788188
|
||||
63 0 0.50349389 0 0.50349389 36.603591
|
||||
64 0 0.13140705 0 0.13140705 33.961812
|
||||
65 0 -0.085091833 0 -0.085091833 32.438467
|
||||
66 0 -0.28867774 0 -0.28867774 30.97302
|
||||
67 0 -0.42572348 0 -0.42572348 30.002898
|
||||
68 0 -0.52736622 0 -0.52736622 29.258456
|
||||
69 0 -0.66178936 0 -0.66178936 28.29934
|
||||
70 0 -0.72324173 0 -0.72324173 27.862878
|
||||
Loop time of 0.0249891 on 1 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
5.82940513955 -0.661789361841 -0.7232417307
|
||||
Force two-norm initial, final = 15029.7 727.267
|
||||
Force max component initial, final = 1482.04 154.38
|
||||
Final line search alpha, max atom move = 0.000666311 0.102865
|
||||
Iterations, force evaluations = 10 10
|
||||
|
||||
Pair time (%) = 0.0145392 (58.1823)
|
||||
Neigh time (%) = 0.00362301 (14.4983)
|
||||
Comm time (%) = 0.000231981 (0.928329)
|
||||
Outpt time (%) = 0.00396943 (15.8846)
|
||||
Other time (%) = 0.00262547 (10.5064)
|
||||
|
||||
Nlocal: 2500 ave 2500 max 2500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 552 ave 552 max 552 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 28290 ave 28290 max 28290 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 28290
|
||||
Ave neighs/atom = 11.316
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 3.23183 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
70 0 4.9285377 0 4.9285377 65.515598
|
||||
71 0 1.5586603 0 1.5586603 43.561052
|
||||
72 0 0.44697741 0 0.44697741 35.981964
|
||||
73 0 0.069754802 0 0.069754802 33.298965
|
||||
74 0 -0.2107147 0 -0.2107147 31.327263
|
||||
75 0 -0.35830772 0 -0.35830772 30.28328
|
||||
76 0 -0.57195013 0 -0.57195013 28.739001
|
||||
77 0 -0.68409153 0 -0.68409153 27.931128
|
||||
78 0 -0.79228314 0 -0.79228314 27.146502
|
||||
79 0 -0.86504711 0 -0.86504711 26.626848
|
||||
80 0 -0.91680491 0 -0.91680491 26.257842
|
||||
Loop time of 0.0249 on 1 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
4.92853774479 -0.865047109705 -0.916804912211
|
||||
Force two-norm initial, final = 14034.9 476.228
|
||||
Force max component initial, final = 1270.06 91.1396
|
||||
Final line search alpha, max atom move = 0.00036629 0.0333835
|
||||
Iterations, force evaluations = 10 10
|
||||
|
||||
Pair time (%) = 0.0144863 (58.1781)
|
||||
Neigh time (%) = 0.003613 (14.51)
|
||||
Comm time (%) = 0.000246048 (0.988146)
|
||||
Outpt time (%) = 0.00392914 (15.7797)
|
||||
Other time (%) = 0.00262547 (10.5441)
|
||||
|
||||
Nlocal: 2500 ave 2500 max 2500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 551 ave 551 max 551 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 28409 ave 28409 max 28409 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 28409
|
||||
Ave neighs/atom = 11.3636
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 3.23183 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
80 0 4.7702655 0 4.7702655 64.412746
|
||||
81 0 1.4138967 0 1.4138967 42.494974
|
||||
82 0 0.39709508 0 0.39709508 35.562808
|
||||
83 0 0.091357616 0 0.091357616 33.433831
|
||||
84 0 -0.14995689 0 -0.14995689 31.744545
|
||||
85 0 -0.34070771 0 -0.34070771 30.384745
|
||||
86 0 -0.56311713 0 -0.56311713 28.778505
|
||||
87 0 -0.69122357 0 -0.69122357 27.855817
|
||||
88 0 -0.77324301 0 -0.77324301 27.264482
|
||||
89 0 -0.84548243 0 -0.84548243 26.734692
|
||||
90 0 -0.90609547 0 -0.90609547 26.289732
|
||||
Loop time of 0.0249319 on 1 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
4.77026550795 -0.845482429321 -0.906095466828
|
||||
Force two-norm initial, final = 13429.1 828.371
|
||||
Force max component initial, final = 1191.96 285.981
|
||||
Final line search alpha, max atom move = 0.000318774 0.0911633
|
||||
Iterations, force evaluations = 10 10
|
||||
|
||||
Pair time (%) = 0.014478 (58.07)
|
||||
Neigh time (%) = 0.00361109 (14.4838)
|
||||
Comm time (%) = 0.000230074 (0.922809)
|
||||
Outpt time (%) = 0.00393724 (15.792)
|
||||
Other time (%) = 0.00267553 (10.7314)
|
||||
|
||||
Nlocal: 2500 ave 2500 max 2500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 557 ave 557 max 557 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 28482 ave 28482 max 28482 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 28482
|
||||
Ave neighs/atom = 11.3928
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 3.23183 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
90 0 4.6721167 0 4.6721167 63.632364
|
||||
91 0 1.6951784 0 1.6951784 44.238331
|
||||
92 0 0.44841999 0 0.44841999 35.811459
|
||||
93 0 0.10249086 0 0.10249086 33.388633
|
||||
94 0 -0.30440803 0 -0.30440803 30.509055
|
||||
95 0 -0.58377427 0 -0.58377427 28.505707
|
||||
96 0 -0.79655365 0 -0.79655365 26.960847
|
||||
97 0 -0.90735594 0 -0.90735594 26.157017
|
||||
98 0 -0.99343895 0 -0.99343895 25.51798
|
||||
99 0 -1.0302142 0 -1.0302142 25.251301
|
||||
100 0 -1.0696142 0 -1.0696142 24.971979
|
||||
Loop time of 0.0263698 on 1 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
4.67211666559 -1.03021419494 -1.06961424119
|
||||
Force two-norm initial, final = 13689.6 576.187
|
||||
Force max component initial, final = 1523.72 245.904
|
||||
Final line search alpha, max atom move = 0.000449346 0.110496
|
||||
Iterations, force evaluations = 10 11
|
||||
|
||||
Pair time (%) = 0.0158815 (60.2262)
|
||||
Neigh time (%) = 0.00362802 (13.7582)
|
||||
Comm time (%) = 0.000239134 (0.906847)
|
||||
Outpt time (%) = 0.00393391 (14.9182)
|
||||
Other time (%) = 0.00268722 (10.1905)
|
||||
|
||||
Nlocal: 2500 ave 2500 max 2500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 553 ave 553 max 553 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 28522 ave 28522 max 28522 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 28522
|
||||
Ave neighs/atom = 11.4088
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 3.23183 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 0 4.0553768 0 4.0553768 59.538
|
||||
101 0 0.97860768 0 0.97860768 39.398542
|
||||
102 0 0.011581326 0 0.011581326 32.777939
|
||||
103 0 -0.29467441 0 -0.29467441 30.628112
|
||||
104 0 -0.49830972 0 -0.49830972 29.178225
|
||||
105 0 -0.7295283 0 -0.7295283 27.468245
|
||||
106 0 -0.83934397 0 -0.83934397 26.687019
|
||||
107 0 -0.90122046 0 -0.90122046 26.263579
|
||||
108 0 -0.96663619 0 -0.96663619 25.786343
|
||||
109 0 -1.0417159 0 -1.0417159 25.23983
|
||||
110 0 -1.122473 0 -1.122473 24.64702
|
||||
Loop time of 0.0294309 on 1 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
4.05537676723 -1.04171594687 -1.12247296867
|
||||
Force two-norm initial, final = 12331.6 860.308
|
||||
Force max component initial, final = 1058.89 313.708
|
||||
Final line search alpha, max atom move = 0.000932331 0.292479
|
||||
Iterations, force evaluations = 10 13
|
||||
|
||||
Pair time (%) = 0.0187619 (63.749)
|
||||
Neigh time (%) = 0.00360394 (12.2454)
|
||||
Comm time (%) = 0.000266552 (0.905689)
|
||||
Outpt time (%) = 0.0039897 (13.5562)
|
||||
Other time (%) = 0.00280881 (9.54375)
|
||||
|
||||
Nlocal: 2500 ave 2500 max 2500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 550 ave 550 max 550 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 28527 ave 28527 max 28527 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 28527
|
||||
Ave neighs/atom = 11.4108
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 3.23183 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
110 0 4.0088675 0 4.0088675 59.056837
|
||||
111 0 2.2995428 0 2.2995428 47.949107
|
||||
112 0 0.99828672 0 0.99828672 39.337343
|
||||
113 0 0.13527687 0 0.13527687 33.474345
|
||||
114 0 -0.20926445 0 -0.20926445 31.05957
|
||||
115 0 -0.47575259 0 -0.47575259 29.164559
|
||||
116 0 -0.67474214 0 -0.67474214 27.723517
|
||||
117 0 -0.8468153 0 -0.8468153 26.486294
|
||||
118 0 -0.95515511 0 -0.95515511 25.685323
|
||||
119 0 -1.0564735 0 -1.0564735 24.951805
|
||||
120 0 -1.0948823 0 -1.0948823 24.677001
|
||||
Loop time of 0.027849 on 1 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
4.00886751896 -1.05647353137 -1.09488226118
|
||||
Force two-norm initial, final = 12395.7 461.929
|
||||
Force max component initial, final = 2663.69 76.5856
|
||||
Final line search alpha, max atom move = 0.000326804 0.0250284
|
||||
Iterations, force evaluations = 10 12
|
||||
|
||||
Pair time (%) = 0.017323 (62.2035)
|
||||
Neigh time (%) = 0.003613 (12.9735)
|
||||
Comm time (%) = 0.000246763 (0.886077)
|
||||
Outpt time (%) = 0.0039196 (14.0745)
|
||||
Other time (%) = 0.00274658 (9.86242)
|
||||
|
||||
Nlocal: 2500 ave 2500 max 2500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 554 ave 554 max 554 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 28631 ave 28631 max 28631 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 28631
|
||||
Ave neighs/atom = 11.4524
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 3.23183 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
120 0 3.6078219 0 3.6078219 56.132202
|
||||
121 0 1.14077 0 1.14077 40.040613
|
||||
122 0 -0.10482013 0 -0.10482013 31.597603
|
||||
123 0 -0.42488667 0 -0.42488667 29.333621
|
||||
124 0 -0.65936545 0 -0.65936545 27.682524
|
||||
125 0 -0.84075312 0 -0.84075312 26.378534
|
||||
126 0 -0.96129843 0 -0.96129843 25.497027
|
||||
127 0 -1.0968129 0 -1.0968129 24.512431
|
||||
128 0 -1.1694506 0 -1.1694506 23.977989
|
||||
129 0 -1.2126457 0 -1.2126457 23.660862
|
||||
130 0 -1.2583205 0 -1.2583205 23.335303
|
||||
Loop time of 0.0279129 on 1 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
3.60782185256 -1.21264568701 -1.25832049648
|
||||
Force two-norm initial, final = 12338.7 511.335
|
||||
Force max component initial, final = 1518.5 147.585
|
||||
Final line search alpha, max atom move = 0.000294687 0.0434913
|
||||
Iterations, force evaluations = 10 12
|
||||
|
||||
Pair time (%) = 0.0173075 (62.0056)
|
||||
Neigh time (%) = 0.00363278 (13.0147)
|
||||
Comm time (%) = 0.000241041 (0.863549)
|
||||
Outpt time (%) = 0.00393629 (14.1021)
|
||||
Other time (%) = 0.00279522 (10.0141)
|
||||
|
||||
Nlocal: 2500 ave 2500 max 2500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 558 ave 558 max 558 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 28611 ave 28611 max 28611 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 28611
|
||||
Ave neighs/atom = 11.4444
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 3.23183 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
130 0 3.1243455 0 3.1243455 52.793945
|
||||
131 0 0.71565075 0 0.71565075 37.056227
|
||||
132 0 -0.27217454 0 -0.27217454 30.343304
|
||||
133 0 -0.61618257 0 -0.61618257 27.874909
|
||||
134 0 -0.7988002 0 -0.7988002 26.598662
|
||||
135 0 -0.91256484 0 -0.91256484 25.789333
|
||||
136 0 -1.0890032 0 -1.0890032 24.463878
|
||||
137 0 -1.1980686 0 -1.1980686 23.681987
|
||||
138 0 -1.2567103 0 -1.2567103 23.266253
|
||||
139 0 -1.3060322 0 -1.3060322 22.899986
|
||||
140 0 -1.359869 0 -1.359869 22.502063
|
||||
Loop time of 0.0308802 on 1 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
3.12434547963 -1.30603224583 -1.35986897103
|
||||
Force two-norm initial, final = 11522.7 423.596
|
||||
Force max component initial, final = 1304.48 166.359
|
||||
Final line search alpha, max atom move = 0.000640699 0.106586
|
||||
Iterations, force evaluations = 10 14
|
||||
|
||||
Pair time (%) = 0.02019 (65.3817)
|
||||
Neigh time (%) = 0.00362086 (11.7255)
|
||||
Comm time (%) = 0.000261784 (0.847739)
|
||||
Outpt time (%) = 0.00396395 (12.8365)
|
||||
Other time (%) = 0.00284362 (9.20855)
|
||||
|
||||
Nlocal: 2500 ave 2500 max 2500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 560 ave 560 max 560 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 28662 ave 28662 max 28662 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 28662
|
||||
Ave neighs/atom = 11.4648
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 3.23183 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
140 0 2.5370527 0 2.5370527 48.829908
|
||||
141 0 0.17606803 0 0.17606803 33.286136
|
||||
142 0 -0.47155579 0 -0.47155579 28.843352
|
||||
143 0 -0.78220993 0 -0.78220993 26.612272
|
||||
144 0 -0.99344036 0 -0.99344036 25.130357
|
||||
145 0 -1.0847272 0 -1.0847272 24.47808
|
||||
146 0 -1.186227 0 -1.186227 23.697138
|
||||
147 0 -1.2660315 0 -1.2660315 23.115022
|
||||
148 0 -1.3035228 0 -1.3035228 22.861414
|
||||
149 0 -1.3383511 0 -1.3383511 22.607288
|
||||
150 0 -1.3718092 0 -1.3718092 22.359069
|
||||
Loop time of 0.032371 on 1 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
2.53705265492 -1.33835106775 -1.37180924768
|
||||
Force two-norm initial, final = 10219.1 550.71
|
||||
Force max component initial, final = 936.507 270.239
|
||||
Final line search alpha, max atom move = 0.000417128 0.112724
|
||||
Iterations, force evaluations = 10 15
|
||||
|
||||
Pair time (%) = 0.0216274 (66.811)
|
||||
Neigh time (%) = 0.00362229 (11.1899)
|
||||
Comm time (%) = 0.000267029 (0.8249)
|
||||
Outpt time (%) = 0.00395203 (12.2085)
|
||||
Other time (%) = 0.00290227 (8.96563)
|
||||
|
||||
Nlocal: 2500 ave 2500 max 2500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 560 ave 560 max 560 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 28716 ave 28716 max 28716 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 28716
|
||||
Ave neighs/atom = 11.4864
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 3.23183 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
150 0 2.6511871 0 2.6511871 49.579345
|
||||
151 0 0.33433869 0 0.33433869 34.351907
|
||||
152 0 -0.60798579 0 -0.60798579 27.870213
|
||||
153 0 -0.90621268 0 -0.90621268 25.71559
|
||||
154 0 -1.1119344 0 -1.1119344 24.25877
|
||||
155 0 -1.2040479 0 -1.2040479 23.599805
|
||||
156 0 -1.2883766 0 -1.2883766 22.946371
|
||||
157 0 -1.3343075 0 -1.3343075 22.614259
|
||||
158 0 -1.3847759 0 -1.3847759 22.268602
|
||||
159 0 -1.4145217 0 -1.4145217 22.049306
|
||||
160 0 -1.4380243 0 -1.4380243 21.876406
|
||||
Loop time of 0.0337121 on 1 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
2.65118714313 -1.41452169876 -1.4380243142
|
||||
Force two-norm initial, final = 10492.4 416.256
|
||||
Force max component initial, final = 1101.81 185.859
|
||||
Final line search alpha, max atom move = 0.000596367 0.11084
|
||||
Iterations, force evaluations = 10 15
|
||||
|
||||
Pair time (%) = 0.0216587 (64.2459)
|
||||
Neigh time (%) = 0.00483203 (14.3332)
|
||||
Comm time (%) = 0.000329733 (0.978083)
|
||||
Outpt time (%) = 0.00391579 (11.6154)
|
||||
Other time (%) = 0.00297594 (8.8275)
|
||||
|
||||
Nlocal: 2500 ave 2500 max 2500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 562 ave 562 max 562 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 28825 ave 28825 max 28825 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 28825
|
||||
Ave neighs/atom = 11.53
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 3.23183 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
160 0 2.445485 0 2.445485 48.062267
|
||||
161 0 0.13902608 0 0.13902608 32.876214
|
||||
162 0 -0.75396797 0 -0.75396797 26.718868
|
||||
163 0 -1.0071611 0 -1.0071611 24.885772
|
||||
164 0 -1.1819905 0 -1.1819905 23.629123
|
||||
165 0 -1.2798339 0 -1.2798339 22.901472
|
||||
166 0 -1.3806808 0 -1.3806808 22.158356
|
||||
167 0 -1.4560709 0 -1.4560709 21.602465
|
||||
168 0 -1.5015178 0 -1.5015178 21.265259
|
||||
169 0 -1.5465541 0 -1.5465541 20.930655
|
||||
170 0 -1.5820884 0 -1.5820884 20.657365
|
||||
Loop time of 0.023509 on 1 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
2.44548496469 -1.54655408621 -1.58208836572
|
||||
Force two-norm initial, final = 10220.9 661.104
|
||||
Force max component initial, final = 1044.13 354.281
|
||||
Final line search alpha, max atom move = 0.0011882 0.420955
|
||||
Iterations, force evaluations = 10 10
|
||||
|
||||
Pair time (%) = 0.014415 (61.317)
|
||||
Neigh time (%) = 0.00240922 (10.2481)
|
||||
Comm time (%) = 0.000192642 (0.819439)
|
||||
Outpt time (%) = 0.00393844 (16.7529)
|
||||
Other time (%) = 0.0025537 (10.8626)
|
||||
|
||||
Nlocal: 2500 ave 2500 max 2500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 561 ave 561 max 561 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 28706 ave 28706 max 28706 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 28706
|
||||
Ave neighs/atom = 11.4824
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 3.23183 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
170 0 2.5358609 0 2.5358609 48.866435
|
||||
171 0 0.063716631 0 0.063716631 32.5423
|
||||
172 0 -0.53442893 0 -0.53442893 28.41204
|
||||
173 0 -0.80688389 0 -0.80688389 26.509346
|
||||
174 0 -1.0715541 0 -1.0715541 24.564023
|
||||
175 0 -1.2254796 0 -1.2254796 23.462464
|
||||
176 0 -1.3022249 0 -1.3022249 22.903025
|
||||
177 0 -1.3771632 0 -1.3771632 22.333129
|
||||
178 0 -1.4452028 0 -1.4452028 21.833035
|
||||
179 0 -1.4781077 0 -1.4781077 21.596868
|
||||
180 0 -1.5024534 0 -1.5024534 21.415156
|
||||
Loop time of 0.0293849 on 1 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
2.53586089291 -1.47810766266 -1.50245335744
|
||||
Force two-norm initial, final = 9891.64 448.294
|
||||
Force max component initial, final = 808.125 120.102
|
||||
Final line search alpha, max atom move = 0.00131125 0.157484
|
||||
Iterations, force evaluations = 10 13
|
||||
|
||||
Pair time (%) = 0.0187562 (63.8293)
|
||||
Neigh time (%) = 0.00361609 (12.306)
|
||||
Comm time (%) = 0.000254869 (0.86735)
|
||||
Outpt time (%) = 0.00398111 (13.5482)
|
||||
Other time (%) = 0.00277662 (9.44916)
|
||||
|
||||
Nlocal: 2500 ave 2500 max 2500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 567 ave 567 max 567 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 28775 ave 28775 max 28775 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 28775
|
||||
Ave neighs/atom = 11.51
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 3.23183 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
180 0 2.7212223 0 2.7212223 50.026136
|
||||
181 0 0.2721017 0 0.2721017 33.925894
|
||||
182 0 -0.42116779 0 -0.42116779 29.157245
|
||||
183 0 -0.62932201 0 -0.62932201 27.728916
|
||||
184 0 -0.84115646 0 -0.84115646 26.20046
|
||||
185 0 -1.0503044 0 -1.0503044 24.685348
|
||||
186 0 -1.1625169 0 -1.1625169 23.879002
|
||||
187 0 -1.2479996 0 -1.2479996 23.257233
|
||||
188 0 -1.359242 0 -1.359242 22.442562
|
||||
189 0 -1.4157422 0 -1.4157422 22.034518
|
||||
190 0 -1.4675347 0 -1.4675347 21.652723
|
||||
Loop time of 0.024842 on 1 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
2.72122227536 -1.41574216788 -1.46753473448
|
||||
Force two-norm initial, final = 10306.2 415.803
|
||||
Force max component initial, final = 951.75 103.59
|
||||
Final line search alpha, max atom move = 0.00089633 0.0928507
|
||||
Iterations, force evaluations = 10 10
|
||||
|
||||
Pair time (%) = 0.0144215 (58.0527)
|
||||
Neigh time (%) = 0.00360799 (14.5237)
|
||||
Comm time (%) = 0.00022912 (0.922309)
|
||||
Outpt time (%) = 0.00392914 (15.8165)
|
||||
Other time (%) = 0.00265431 (10.6848)
|
||||
|
||||
Nlocal: 2500 ave 2500 max 2500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 570 ave 570 max 570 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 28849 ave 28849 max 28849 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 28849
|
||||
Ave neighs/atom = 11.5396
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 3.23183 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
190 0 2.0041133 0 2.0041133 44.903366
|
||||
191 0 -0.13802828 0 -0.13802828 30.796936
|
||||
192 0 -0.65552855 0 -0.65552855 27.241047
|
||||
193 0 -0.8720148 0 -0.8720148 25.714407
|
||||
194 0 -1.0652883 0 -1.0652883 24.338022
|
||||
195 0 -1.2191873 0 -1.2191873 23.225018
|
||||
196 0 -1.3593543 0 -1.3593543 22.192069
|
||||
197 0 -1.4397147 0 -1.4397147 21.604815
|
||||
198 0 -1.5433079 0 -1.5433079 20.81796
|
||||
199 0 -1.6127297 0 -1.6127297 20.314889
|
||||
200 0 -1.6540467 0 -1.6540467 19.995791
|
||||
Loop time of 0.024853 on 1 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
2.00411330956 -1.61272973671 -1.65404673311
|
||||
Force two-norm initial, final = 9931.07 717.032
|
||||
Force max component initial, final = 976.09 300.507
|
||||
Final line search alpha, max atom move = 0.00121807 0.366038
|
||||
Iterations, force evaluations = 10 10
|
||||
|
||||
Pair time (%) = 0.0144005 (57.9427)
|
||||
Neigh time (%) = 0.00363111 (14.6104)
|
||||
Comm time (%) = 0.000238895 (0.961234)
|
||||
Outpt time (%) = 0.00396919 (15.9707)
|
||||
Other time (%) = 0.00261331 (10.5151)
|
||||
|
||||
Nlocal: 2500 ave 2500 max 2500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 572 ave 572 max 572 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 28888 ave 28888 max 28888 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 28888
|
||||
Ave neighs/atom = 11.5552
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
|
@ -1,978 +0,0 @@
|
|||
LAMMPS (20 Sep 2010)
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style atomic
|
||||
|
||||
read_data data.lammps
|
||||
orthogonal box = (0 0 -0.5) to (50 50 0.5)
|
||||
2 by 2 by 1 processor grid
|
||||
2500 atoms
|
||||
mass * 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.2
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 1.0 1.0
|
||||
pair_coeff 3 3 1.0 1.0
|
||||
pair_coeff 4 4 1.0 1.0
|
||||
pair_coeff 5 5 1.0 1.0
|
||||
pair_coeff 6 6 1.0 1.0
|
||||
pair_coeff 7 7 1.0 1.0
|
||||
pair_coeff 8 8 1.0 1.0
|
||||
pair_coeff 9 9 1.0 1.0
|
||||
pair_coeff 10 10 1.0 1.0
|
||||
pair_coeff 11 11 1.0 1.0
|
||||
pair_coeff 12 12 1.0 1.0
|
||||
pair_coeff 13 13 1.0 1.0
|
||||
pair_coeff 14 14 1.0 1.0
|
||||
pair_coeff 15 15 1.0 1.0
|
||||
pair_coeff 16 16 1.0 1.0
|
||||
pair_coeff 17 17 1.0 1.0
|
||||
pair_coeff 18 18 1.0 1.0
|
||||
pair_coeff 19 19 1.0 1.0
|
||||
pair_coeff 20 20 1.0 1.0
|
||||
pair_coeff 21 21 1.0 1.0
|
||||
pair_coeff 22 22 1.0 1.0
|
||||
pair_coeff 23 23 1.0 1.0
|
||||
pair_coeff 24 24 1.0 1.0
|
||||
pair_coeff 25 25 1.0 1.0
|
||||
pair_coeff 26 26 1.0 1.0
|
||||
pair_coeff 27 27 1.0 1.0
|
||||
pair_coeff 28 28 1.0 1.0
|
||||
pair_coeff 29 29 1.0 1.0
|
||||
pair_coeff 30 30 1.0 1.0
|
||||
pair_coeff 31 31 1.0 1.0
|
||||
pair_coeff 32 32 1.0 1.0
|
||||
pair_coeff 33 33 1.0 1.0
|
||||
pair_coeff 34 34 1.0 1.0
|
||||
pair_coeff 35 35 1.0 1.0
|
||||
pair_coeff 36 36 1.0 1.0
|
||||
pair_coeff 37 37 1.0 1.0
|
||||
pair_coeff 38 38 1.0 1.0
|
||||
pair_coeff 39 39 1.0 1.0
|
||||
pair_coeff 40 40 1.0 1.0
|
||||
pair_coeff 41 41 1.0 1.0
|
||||
pair_coeff 42 42 1.0 1.0
|
||||
pair_coeff 43 43 1.0 1.0
|
||||
pair_coeff 44 44 1.0 1.0
|
||||
pair_coeff 45 45 1.0 1.0
|
||||
pair_coeff 46 46 1.0 1.0
|
||||
pair_coeff 47 47 1.0 1.0
|
||||
pair_coeff 48 48 1.0 1.0
|
||||
pair_coeff 49 49 1.0 1.0
|
||||
pair_coeff 50 50 1.0 1.0
|
||||
pair_coeff 51 51 1.0 1.0
|
||||
pair_coeff 52 52 1.0 1.0
|
||||
pair_coeff 53 53 1.0 1.0
|
||||
pair_coeff 54 54 1.0 1.0
|
||||
pair_coeff 55 55 1.0 1.0
|
||||
pair_coeff 56 56 1.0 1.0
|
||||
pair_coeff 57 57 1.0 1.0
|
||||
pair_coeff 58 58 1.0 1.0
|
||||
pair_coeff 59 59 1.0 1.0
|
||||
pair_coeff 60 60 1.0 1.0
|
||||
pair_coeff 61 61 1.0 1.0
|
||||
pair_coeff 62 62 1.0 1.0
|
||||
pair_coeff 63 63 1.0 1.0
|
||||
pair_coeff 64 64 1.0 1.0
|
||||
pair_coeff 65 65 1.0 1.0
|
||||
pair_coeff 66 66 1.0 1.0
|
||||
pair_coeff 67 67 1.0 1.0
|
||||
pair_coeff 68 68 1.0 1.0
|
||||
pair_coeff 69 69 1.0 1.0
|
||||
pair_coeff 70 70 1.0 1.0
|
||||
pair_coeff 71 71 1.0 1.0
|
||||
pair_coeff 72 72 1.0 1.0
|
||||
pair_coeff 73 73 1.0 1.0
|
||||
pair_coeff 74 74 1.0 1.0
|
||||
pair_coeff 75 75 1.0 1.0
|
||||
pair_coeff 76 76 1.0 1.0
|
||||
pair_coeff 77 77 1.0 1.0
|
||||
pair_coeff 78 78 1.0 1.0
|
||||
pair_coeff 79 79 1.0 1.0
|
||||
pair_coeff 80 80 1.0 1.0
|
||||
pair_coeff 81 81 1.0 1.0
|
||||
pair_coeff 82 82 1.0 1.0
|
||||
pair_coeff 83 83 1.0 1.0
|
||||
pair_coeff 84 84 1.0 1.0
|
||||
pair_coeff 85 85 1.0 1.0
|
||||
pair_coeff 86 86 1.0 1.0
|
||||
pair_coeff 87 87 1.0 1.0
|
||||
pair_coeff 88 88 1.0 1.0
|
||||
pair_coeff 89 89 1.0 1.0
|
||||
pair_coeff 90 90 1.0 1.0
|
||||
pair_coeff 91 91 1.0 1.0
|
||||
pair_coeff 92 92 1.0 1.0
|
||||
pair_coeff 93 93 1.0 1.0
|
||||
pair_coeff 94 94 1.0 1.0
|
||||
pair_coeff 95 95 1.0 1.0
|
||||
pair_coeff 96 96 1.0 1.0
|
||||
pair_coeff 97 97 1.0 1.0
|
||||
pair_coeff 98 98 1.0 1.0
|
||||
pair_coeff 99 99 1.0 1.0
|
||||
pair_coeff 100 100 1.0 1.0
|
||||
|
||||
compute da all displace/atom
|
||||
|
||||
dump 1 all atom 10 dump.md
|
||||
thermo 1
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 2.38041 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 10.131397 0 10.131397 102.99334
|
||||
1 0 3.6579372 0 3.6579372 60.806825
|
||||
2 0 3.0194933 0 3.0194933 56.563578
|
||||
3 0 2.6605525 0 2.6605525 54.146441
|
||||
4 0 2.3447848 0 2.3447848 51.988246
|
||||
5 0 2.1836205 0 2.1836205 50.890593
|
||||
6 0 2.0595616 0 2.0595616 50.04605
|
||||
7 0 1.9519103 0 1.9519103 49.305129
|
||||
8 0 1.8797312 0 1.8797312 48.806422
|
||||
9 0 1.8230663 0 1.8230663 48.416594
|
||||
10 0 1.7618168 0 1.7618168 47.996459
|
||||
Loop time of 0.0110788 on 4 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
10.1313968863 1.82306625671 1.76181675684
|
||||
Force two-norm initial, final = 14853.2 526.892
|
||||
Force max component initial, final = 333.003 154.237
|
||||
Final line search alpha, max atom move = 0.000395826 0.0610509
|
||||
Iterations, force evaluations = 10 13
|
||||
|
||||
Pair time (%) = 0.00475216 (42.894)
|
||||
Neigh time (%) = 0.000601947 (5.43331)
|
||||
Comm time (%) = 0.000704825 (6.3619)
|
||||
Outpt time (%) = 0.00406402 (36.6828)
|
||||
Other time (%) = 0.00095588 (8.62798)
|
||||
|
||||
Nlocal: 625 ave 637 max 614 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Nghost: 275 ave 286 max 263 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Neighs: 6779.25 ave 6929 max 6631 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 27117
|
||||
Ave neighs/atom = 10.8468
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 2.70701 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
10 0 13.855576 0 13.855576 126.15022
|
||||
11 0 5.7386317 0 5.7386317 73.911894
|
||||
12 0 4.0429707 0 4.0429707 62.56527
|
||||
13 0 3.238614 0 3.238614 57.109892
|
||||
14 0 2.4884651 0 2.4884651 51.940745
|
||||
15 0 2.0958214 0 2.0958214 49.224795
|
||||
16 0 1.7591268 0 1.7591268 46.897029
|
||||
17 0 1.5877871 0 1.5877871 45.70491
|
||||
18 0 1.4739685 0 1.4739685 44.914787
|
||||
19 0 1.3756748 0 1.3756748 44.231775
|
||||
20 0 1.2785795 0 1.2785795 43.556465
|
||||
Loop time of 0.00972104 on 4 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
13.8555761196 1.37567476183 1.27857945482
|
||||
Force two-norm initial, final = 24008.6 733.281
|
||||
Force max component initial, final = 1448.98 310.85
|
||||
Final line search alpha, max atom move = 0.000383264 0.119137
|
||||
Iterations, force evaluations = 10 10
|
||||
|
||||
Pair time (%) = 0.00366753 (37.7278)
|
||||
Neigh time (%) = 0.00060153 (6.18792)
|
||||
Comm time (%) = 0.000533044 (5.48341)
|
||||
Outpt time (%) = 0.00406796 (41.8469)
|
||||
Other time (%) = 0.000850976 (8.75395)
|
||||
|
||||
Nlocal: 625 ave 632 max 615 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
Nghost: 275.25 ave 286 max 268 min
|
||||
Histogram: 1 1 0 0 1 0 0 0 0 1
|
||||
Neighs: 6797.25 ave 6867 max 6672 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 1 1
|
||||
|
||||
Total # of neighbors = 27189
|
||||
Ave neighs/atom = 10.8756
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 2.70701 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
20 0 10.453807 0 10.453807 103.11677
|
||||
21 0 4.5433221 0 4.5433221 65.082297
|
||||
22 0 3.5146935 0 3.5146935 58.258548
|
||||
23 0 2.7050903 0 2.7050903 52.787155
|
||||
24 0 2.2715623 0 2.2715623 49.814091
|
||||
25 0 1.8851407 0 1.8851407 47.159818
|
||||
26 0 1.5708258 0 1.5708258 44.974429
|
||||
27 0 1.3890196 0 1.3890196 43.713996
|
||||
28 0 1.1909213 0 1.1909213 42.334449
|
||||
29 0 1.0181817 0 1.0181817 41.121861
|
||||
30 0 0.89407363 0 0.89407363 40.258139
|
||||
Loop time of 0.00972056 on 4 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
10.4538071086 1.01818167882 0.894073631386
|
||||
Force two-norm initial, final = 20855.2 876.637
|
||||
Force max component initial, final = 1585.58 289.452
|
||||
Final line search alpha, max atom move = 0.000300637 0.0870201
|
||||
Iterations, force evaluations = 10 10
|
||||
|
||||
Pair time (%) = 0.0036599 (37.6511)
|
||||
Neigh time (%) = 0.000605106 (6.22501)
|
||||
Comm time (%) = 0.000532508 (5.47816)
|
||||
Outpt time (%) = 0.00407463 (41.9177)
|
||||
Other time (%) = 0.000848413 (8.72802)
|
||||
|
||||
Nlocal: 625 ave 633 max 617 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 276.5 ave 285 max 267 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
Neighs: 6819 ave 6928 max 6722 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 27276
|
||||
Ave neighs/atom = 10.9104
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 2.70701 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
30 0 9.1773214 0 9.1773214 94.19218
|
||||
31 0 3.780095 0 3.780095 59.351334
|
||||
32 0 2.1364679 0 2.1364679 48.310641
|
||||
33 0 1.5981147 0 1.5981147 44.596478
|
||||
34 0 1.1616454 0 1.1616454 41.559729
|
||||
35 0 0.82858726 0 0.82858726 39.203145
|
||||
36 0 0.57784722 0 0.57784722 37.453531
|
||||
37 0 0.42911635 0 0.42911635 36.369814
|
||||
38 0 0.32649469 0 0.32649469 35.641902
|
||||
39 0 0.21091983 0 0.21091983 34.858374
|
||||
40 0 0.13674971 0 0.13674971 34.342788
|
||||
Loop time of 0.0113723 on 4 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
9.17732138819 0.210919834207 0.136749713408
|
||||
Force two-norm initial, final = 19618.6 632.262
|
||||
Force max component initial, final = 1558.39 105.69
|
||||
Final line search alpha, max atom move = 0.000486832 0.0514532
|
||||
Iterations, force evaluations = 10 13
|
||||
|
||||
Pair time (%) = 0.00474131 (41.6916)
|
||||
Neigh time (%) = 0.000910223 (8.00384)
|
||||
Comm time (%) = 0.000718117 (6.3146)
|
||||
Outpt time (%) = 0.00406992 (35.788)
|
||||
Other time (%) = 0.000932753 (8.20195)
|
||||
|
||||
Nlocal: 625 ave 632 max 610 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 0 2
|
||||
Nghost: 279 ave 294 max 271 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Neighs: 6869.75 ave 6965 max 6677 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 2 1
|
||||
|
||||
Total # of neighbors = 27479
|
||||
Ave neighs/atom = 10.9916
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 2.70701 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
40 0 7.1357354 0 7.1357354 80.465664
|
||||
41 0 3.1864291 0 3.1864291 54.920554
|
||||
42 0 1.4411303 0 1.4411303 43.175349
|
||||
43 0 1.0616102 0 1.0616102 40.558071
|
||||
44 0 0.76898007 0 0.76898007 38.515614
|
||||
45 0 0.47634294 0 0.47634294 36.448833
|
||||
46 0 0.26562782 0 0.26562782 34.961948
|
||||
47 0 0.084628043 0 0.084628043 33.672837
|
||||
48 0 -0.075634194 0 -0.075634194 32.547959
|
||||
49 0 -0.21169535 0 -0.21169535 31.582919
|
||||
50 0 -0.32991627 0 -0.32991627 30.759427
|
||||
Loop time of 0.0101295 on 4 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
7.13573543411 -0.211695347593 -0.329916269499
|
||||
Force two-norm initial, final = 16348.9 558.411
|
||||
Force max component initial, final = 1619.91 103.265
|
||||
Final line search alpha, max atom move = 0.000372042 0.038419
|
||||
Iterations, force evaluations = 10 10
|
||||
|
||||
Pair time (%) = 0.00363976 (35.9324)
|
||||
Neigh time (%) = 0.000923395 (9.11594)
|
||||
Comm time (%) = 0.000634491 (6.26383)
|
||||
Outpt time (%) = 0.00405943 (40.0756)
|
||||
Other time (%) = 0.000872374 (8.61225)
|
||||
|
||||
Nlocal: 625 ave 635 max 614 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Nghost: 280.25 ave 290 max 270 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Neighs: 6920.75 ave 7090 max 6722 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
|
||||
Total # of neighbors = 27683
|
||||
Ave neighs/atom = 11.0732
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 2.70701 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
50 0 5.7268723 0 5.7268723 70.877358
|
||||
51 0 2.3773675 0 2.3773675 49.119056
|
||||
52 0 0.80808652 0 0.80808652 38.523549
|
||||
53 0 0.44195199 0 0.44195199 35.94379
|
||||
54 0 0.15030268 0 0.15030268 33.910057
|
||||
55 0 -0.022616619 0 -0.022616619 32.66055
|
||||
56 0 -0.16415793 0 -0.16415793 31.640965
|
||||
57 0 -0.29891652 0 -0.29891652 30.708285
|
||||
58 0 -0.39214086 0 -0.39214086 30.03762
|
||||
59 0 -0.53733622 0 -0.53733622 28.975916
|
||||
60 0 -0.63338854 0 -0.63338854 28.306058
|
||||
Loop time of 0.0101259 on 4 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
5.72687232351 -0.537336224163 -0.633388542189
|
||||
Force two-norm initial, final = 14623.1 1106.47
|
||||
Force max component initial, final = 1563.21 227.768
|
||||
Final line search alpha, max atom move = 0.000202951 0.0462258
|
||||
Iterations, force evaluations = 10 10
|
||||
|
||||
Pair time (%) = 0.00362068 (35.7568)
|
||||
Neigh time (%) = 0.000916481 (9.05088)
|
||||
Comm time (%) = 0.000623763 (6.16009)
|
||||
Outpt time (%) = 0.00407392 (40.2327)
|
||||
Other time (%) = 0.00089103 (8.79953)
|
||||
|
||||
Nlocal: 625 ave 634 max 620 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
Nghost: 282.75 ave 289 max 274 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
Neighs: 6997.75 ave 7188 max 6858 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 27991
|
||||
Ave neighs/atom = 11.1964
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 2.70701 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
60 0 4.8209421 0 4.8209421 64.493854
|
||||
61 0 2.5903199 0 2.5903199 50.078603
|
||||
62 0 0.62828159 0 0.62828159 36.984599
|
||||
63 0 0.28949259 0 0.28949259 34.641614
|
||||
64 0 -0.031290153 0 -0.031290153 32.384853
|
||||
65 0 -0.31225362 0 -0.31225362 30.379734
|
||||
66 0 -0.50896819 0 -0.50896819 28.973548
|
||||
67 0 -0.6583808 0 -0.6583808 27.894862
|
||||
68 0 -0.79610742 0 -0.79610742 26.903809
|
||||
69 0 -0.90468984 0 -0.90468984 26.119699
|
||||
70 0 -0.97482926 0 -0.97482926 25.617752
|
||||
Loop time of 0.0100566 on 4 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
4.82094210064 -0.90468984047 -0.974829264854
|
||||
Force two-norm initial, final = 14460.6 700.095
|
||||
Force max component initial, final = 2632.26 308.176
|
||||
Final line search alpha, max atom move = 0.000565214 0.174185
|
||||
Iterations, force evaluations = 10 10
|
||||
|
||||
Pair time (%) = 0.00361013 (35.8983)
|
||||
Neigh time (%) = 0.000908792 (9.03681)
|
||||
Comm time (%) = 0.000601768 (5.98384)
|
||||
Outpt time (%) = 0.00405914 (40.3631)
|
||||
Other time (%) = 0.000876725 (8.71794)
|
||||
|
||||
Nlocal: 625 ave 635 max 619 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
Nghost: 288 ave 294 max 281 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 7080.5 ave 7261 max 7005 min
|
||||
Histogram: 2 1 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 28322
|
||||
Ave neighs/atom = 11.3288
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 2.70701 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
70 0 4.3980829 0 4.3980829 61.741323
|
||||
71 0 1.1235581 0 1.1235581 40.327809
|
||||
72 0 0.21759714 0 0.21759714 34.129029
|
||||
73 0 -0.081434306 0 -0.081434306 32.015966
|
||||
74 0 -0.31232862 0 -0.31232862 30.394279
|
||||
75 0 -0.52674206 0 -0.52674206 28.841997
|
||||
76 0 -0.73501424 0 -0.73501424 27.343739
|
||||
77 0 -0.84805615 0 -0.84805615 26.519545
|
||||
78 0 -0.93529547 0 -0.93529547 25.886702
|
||||
79 0 -0.99512174 0 -0.99512174 25.451552
|
||||
80 0 -1.0566397 0 -1.0566397 25.00379
|
||||
Loop time of 0.00964552 on 4 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
4.39808292997 -0.995121736021 -1.05663967552
|
||||
Force two-norm initial, final = 12965.9 449.496
|
||||
Force max component initial, final = 1092.61 161.966
|
||||
Final line search alpha, max atom move = 0.000603976 0.0978234
|
||||
Iterations, force evaluations = 10 10
|
||||
|
||||
Pair time (%) = 0.00359595 (37.281)
|
||||
Neigh time (%) = 0.000608981 (6.31361)
|
||||
Comm time (%) = 0.000535309 (5.54982)
|
||||
Outpt time (%) = 0.00404197 (41.9051)
|
||||
Other time (%) = 0.000863314 (8.95041)
|
||||
|
||||
Nlocal: 625 ave 632 max 621 min
|
||||
Histogram: 1 1 1 0 0 0 0 0 0 1
|
||||
Nghost: 288 ave 293 max 286 min
|
||||
Histogram: 2 1 0 0 0 0 0 0 0 1
|
||||
Neighs: 7081.25 ave 7231 max 6981 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 28325
|
||||
Ave neighs/atom = 11.33
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 2.70701 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
80 0 4.0361093 0 4.0361093 59.222435
|
||||
81 0 1.3881798 0 1.3881798 41.953718
|
||||
82 0 0.27963712 0 0.27963712 34.458153
|
||||
83 0 -0.027669726 0 -0.027669726 32.363955
|
||||
84 0 -0.37030062 0 -0.37030062 29.921155
|
||||
85 0 -0.60764833 0 -0.60764833 28.255858
|
||||
86 0 -0.7571808 0 -0.7571808 27.195934
|
||||
87 0 -0.89460643 0 -0.89460643 26.202321
|
||||
88 0 -0.96080854 0 -0.96080854 25.741651
|
||||
89 0 -1.0194781 0 -1.0194781 25.324323
|
||||
90 0 -1.0637943 0 -1.0637943 24.9965
|
||||
Loop time of 0.011281 on 4 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
4.03610925969 -1.01947808117 -1.06379432983
|
||||
Force two-norm initial, final = 12187.6 545.261
|
||||
Force max component initial, final = 1351.69 92.3548
|
||||
Final line search alpha, max atom move = 0.000969229 0.089513
|
||||
Iterations, force evaluations = 10 13
|
||||
|
||||
Pair time (%) = 0.00468087 (41.4934)
|
||||
Neigh time (%) = 0.000908017 (8.04907)
|
||||
Comm time (%) = 0.000690103 (6.11738)
|
||||
Outpt time (%) = 0.00406533 (36.037)
|
||||
Other time (%) = 0.000936687 (8.30322)
|
||||
|
||||
Nlocal: 625 ave 630 max 621 min
|
||||
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||
Nghost: 287 ave 291 max 283 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 7107.5 ave 7201 max 7017 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 28430
|
||||
Ave neighs/atom = 11.372
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 2.70701 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
90 0 3.125718 0 3.125718 52.867181
|
||||
91 0 0.53212967 0 0.53212967 35.875122
|
||||
92 0 -0.34301857 0 -0.34301857 29.831322
|
||||
93 0 -0.58227566 0 -0.58227566 28.151184
|
||||
94 0 -0.79489064 0 -0.79489064 26.623007
|
||||
95 0 -0.97574132 0 -0.97574132 25.298929
|
||||
96 0 -1.0874104 0 -1.0874104 24.482683
|
||||
97 0 -1.1719839 0 -1.1719839 23.862768
|
||||
98 0 -1.2392036 0 -1.2392036 23.370772
|
||||
99 0 -1.2964836 0 -1.2964836 22.943244
|
||||
100 0 -1.3478016 0 -1.3478016 22.567963
|
||||
Loop time of 0.0100085 on 4 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
3.12571795497 -1.29648360341 -1.34780157905
|
||||
Force two-norm initial, final = 11455.2 530.242
|
||||
Force max component initial, final = 1096.07 260.447
|
||||
Final line search alpha, max atom move = 0.00055639 0.14491
|
||||
Iterations, force evaluations = 10 10
|
||||
|
||||
Pair time (%) = 0.00359488 (35.9184)
|
||||
Neigh time (%) = 0.000907004 (9.06238)
|
||||
Comm time (%) = 0.000564218 (5.63741)
|
||||
Outpt time (%) = 0.00406653 (40.6309)
|
||||
Other time (%) = 0.000875831 (8.75091)
|
||||
|
||||
Nlocal: 625 ave 631 max 620 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
Nghost: 290.5 ave 295 max 286 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 7139.5 ave 7236 max 7066 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 28558
|
||||
Ave neighs/atom = 11.4232
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 2.70701 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 0 3.0454477 0 3.0454477 52.211737
|
||||
101 0 0.37762092 0 0.37762092 34.686047
|
||||
102 0 -0.14581755 0 -0.14581755 31.107565
|
||||
103 0 -0.42841021 0 -0.42841021 29.141463
|
||||
104 0 -0.68603979 0 -0.68603979 27.322046
|
||||
105 0 -0.83601254 0 -0.83601254 26.242466
|
||||
106 0 -0.99162456 0 -0.99162456 25.109576
|
||||
107 0 -1.1100134 0 -1.1100134 24.238707
|
||||
108 0 -1.2082157 0 -1.2082157 23.525014
|
||||
109 0 -1.2572245 0 -1.2572245 23.158233
|
||||
110 0 -1.2876903 0 -1.2876903 22.942477
|
||||
Loop time of 0.0104213 on 4 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
3.04544768565 -1.25722445623 -1.28769033314
|
||||
Force two-norm initial, final = 10849.1 693.937
|
||||
Force max component initial, final = 904.387 236.839
|
||||
Final line search alpha, max atom move = 0.000117815 0.027903
|
||||
Iterations, force evaluations = 10 11
|
||||
|
||||
Pair time (%) = 0.00395721 (37.9724)
|
||||
Neigh time (%) = 0.000905097 (8.68508)
|
||||
Comm time (%) = 0.000644565 (6.18508)
|
||||
Outpt time (%) = 0.00403285 (38.6982)
|
||||
Other time (%) = 0.000881553 (8.45916)
|
||||
|
||||
Nlocal: 625 ave 635 max 619 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
Nghost: 293.75 ave 299 max 288 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 7176 ave 7351 max 7047 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 28704
|
||||
Ave neighs/atom = 11.4816
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 2.70701 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
110 0 2.7373476 0 2.7373476 49.916663
|
||||
111 0 0.27920158 0 0.27920158 33.800547
|
||||
112 0 -0.20019322 0 -0.20019322 30.51445
|
||||
113 0 -0.53185019 0 -0.53185019 28.218677
|
||||
114 0 -0.83093001 0 -0.83093001 26.099658
|
||||
115 0 -1.0242231 0 -1.0242231 24.694823
|
||||
116 0 -1.1583232 0 -1.1583232 23.729291
|
||||
117 0 -1.2254882 0 -1.2254882 23.24164
|
||||
118 0 -1.3210175 0 -1.3210175 22.517164
|
||||
119 0 -1.3863132 0 -1.3863132 22.040913
|
||||
120 0 -1.4387351 0 -1.4387351 21.669171
|
||||
Loop time of 0.0104623 on 4 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
2.7373476491 -1.38631322727 -1.43873508821
|
||||
Force two-norm initial, final = 10875.8 508.589
|
||||
Force max component initial, final = 982.141 152.413
|
||||
Final line search alpha, max atom move = 0.000364516 0.0555571
|
||||
Iterations, force evaluations = 10 11
|
||||
|
||||
Pair time (%) = 0.00395113 (37.7655)
|
||||
Neigh time (%) = 0.000912726 (8.72396)
|
||||
Comm time (%) = 0.000642478 (6.1409)
|
||||
Outpt time (%) = 0.0040555 (38.763)
|
||||
Other time (%) = 0.000900447 (8.6066)
|
||||
|
||||
Nlocal: 625 ave 635 max 616 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Nghost: 294.25 ave 298 max 289 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
Neighs: 7165.25 ave 7309 max 7016 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
|
||||
Total # of neighbors = 28661
|
||||
Ave neighs/atom = 11.4644
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 2.70701 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
120 0 2.231579 0 2.231579 46.568479
|
||||
121 0 0.10623671 0 0.10623671 32.582536
|
||||
122 0 -0.57013613 0 -0.57013613 27.925741
|
||||
123 0 -0.82491886 0 -0.82491886 26.137265
|
||||
124 0 -1.032301 0 -1.032301 24.65678
|
||||
125 0 -1.1759783 0 -1.1759783 23.611572
|
||||
126 0 -1.2850499 0 -1.2850499 22.811747
|
||||
127 0 -1.3713102 0 -1.3713102 22.160066
|
||||
128 0 -1.421629 0 -1.421629 21.795582
|
||||
129 0 -1.4557009 0 -1.4557009 21.556374
|
||||
130 0 -1.4891168 0 -1.4891168 21.308053
|
||||
Loop time of 0.0116708 on 4 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
2.23157898725 -1.45570090921 -1.48911681685
|
||||
Force two-norm initial, final = 9946.33 373.99
|
||||
Force max component initial, final = 1003.46 83.0505
|
||||
Final line search alpha, max atom move = 0.000997891 0.0828754
|
||||
Iterations, force evaluations = 10 13
|
||||
|
||||
Pair time (%) = 0.00466818 (39.9989)
|
||||
Neigh time (%) = 0.0012086 (10.3558)
|
||||
Comm time (%) = 0.00076437 (6.54944)
|
||||
Outpt time (%) = 0.00407952 (34.955)
|
||||
Other time (%) = 0.000950098 (8.14084)
|
||||
|
||||
Nlocal: 625 ave 634 max 616 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Nghost: 294 ave 306 max 285 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Neighs: 7190.25 ave 7319 max 7089 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 28761
|
||||
Ave neighs/atom = 11.5044
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 2.70701 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
130 0 2.468581 0 2.468581 48.058148
|
||||
131 0 0.23907579 0 0.23907579 33.424381
|
||||
132 0 -0.57700066 0 -0.57700066 27.834841
|
||||
133 0 -0.78159015 0 -0.78159015 26.389175
|
||||
134 0 -0.96518905 0 -0.96518905 25.087162
|
||||
135 0 -1.1206213 0 -1.1206213 23.938563
|
||||
136 0 -1.2989415 0 -1.2989415 22.649792
|
||||
137 0 -1.3646103 0 -1.3646103 22.169499
|
||||
138 0 -1.404925 0 -1.404925 21.882639
|
||||
139 0 -1.4453211 0 -1.4453211 21.590433
|
||||
140 0 -1.476957 0 -1.476957 21.357542
|
||||
Loop time of 0.0113478 on 4 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
2.46858101287 -1.44532109888 -1.47695704321
|
||||
Force two-norm initial, final = 10339.5 404.157
|
||||
Force max component initial, final = 1066.37 79.792
|
||||
Final line search alpha, max atom move = 0.000516371 0.0412023
|
||||
Iterations, force evaluations = 10 13
|
||||
|
||||
Pair time (%) = 0.00466353 (41.0964)
|
||||
Neigh time (%) = 0.000915468 (8.06738)
|
||||
Comm time (%) = 0.000732958 (6.45905)
|
||||
Outpt time (%) = 0.00408739 (36.0193)
|
||||
Other time (%) = 0.000948429 (8.35785)
|
||||
|
||||
Nlocal: 625 ave 630 max 619 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
Nghost: 297 ave 308 max 291 min
|
||||
Histogram: 1 1 1 0 0 0 0 0 0 1
|
||||
Neighs: 7210.75 ave 7293 max 7157 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 28843
|
||||
Ave neighs/atom = 11.5372
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 2.70701 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
140 0 2.0546282 0 2.0546282 45.130766
|
||||
141 0 0.063378271 0 0.063378271 32.071438
|
||||
142 0 -0.75409628 0 -0.75409628 26.467076
|
||||
143 0 -0.99188685 0 -0.99188685 24.768145
|
||||
144 0 -1.1940141 0 -1.1940141 23.325743
|
||||
145 0 -1.2863947 0 -1.2863947 22.657693
|
||||
146 0 -1.4049088 0 -1.4049088 21.739543
|
||||
147 0 -1.4732876 0 -1.4732876 21.244532
|
||||
148 0 -1.5158202 0 -1.5158202 20.947078
|
||||
149 0 -1.5492971 0 -1.5492971 20.696077
|
||||
150 0 -1.5871773 0 -1.5871773 20.409409
|
||||
Loop time of 0.0121427 on 4 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
2.05462816117 -1.54929713072 -1.58717731498
|
||||
Force two-norm initial, final = 10054.9 460.349
|
||||
Force max component initial, final = 1183.37 112.406
|
||||
Final line search alpha, max atom move = 0.00067079 0.0754006
|
||||
Iterations, force evaluations = 10 15
|
||||
|
||||
Pair time (%) = 0.00539333 (44.4164)
|
||||
Neigh time (%) = 0.000901341 (7.42293)
|
||||
Comm time (%) = 0.000786364 (6.47605)
|
||||
Outpt time (%) = 0.00408238 (33.6202)
|
||||
Other time (%) = 0.000979245 (8.0645)
|
||||
|
||||
Nlocal: 625 ave 627 max 622 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Nghost: 296 ave 303 max 292 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Neighs: 7215.25 ave 7277 max 7165 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 28861
|
||||
Ave neighs/atom = 11.5444
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 2.70701 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
150 0 2.1501435 0 2.1501435 45.854873
|
||||
151 0 0.062697748 0 0.062697748 32.113988
|
||||
152 0 -0.57549777 0 -0.57549777 27.750033
|
||||
153 0 -0.81350196 0 -0.81350196 26.101995
|
||||
154 0 -1.0553818 0 -1.0553818 24.383326
|
||||
155 0 -1.205518 0 -1.205518 23.2918
|
||||
156 0 -1.3021965 0 -1.3021965 22.595323
|
||||
157 0 -1.3787145 0 -1.3787145 22.023536
|
||||
158 0 -1.4667773 0 -1.4667773 21.377314
|
||||
159 0 -1.4990249 0 -1.4990249 21.14571
|
||||
160 0 -1.5341333 0 -1.5341333 20.884655
|
||||
Loop time of 0.00999629 on 4 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
2.15014348714 -1.49902493946 -1.53413332365
|
||||
Force two-norm initial, final = 9686.62 465.976
|
||||
Force max component initial, final = 1025.75 184.146
|
||||
Final line search alpha, max atom move = 0.000606717 0.111725
|
||||
Iterations, force evaluations = 10 10
|
||||
|
||||
Pair time (%) = 0.00359142 (35.9275)
|
||||
Neigh time (%) = 0.000905931 (9.06267)
|
||||
Comm time (%) = 0.000550687 (5.50891)
|
||||
Outpt time (%) = 0.00407612 (40.7763)
|
||||
Other time (%) = 0.000872135 (8.72458)
|
||||
|
||||
Nlocal: 625 ave 626 max 624 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 299.5 ave 310 max 292 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Neighs: 7219.25 ave 7277 max 7155 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 28877
|
||||
Ave neighs/atom = 11.5508
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 2.70701 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
160 0 1.8339319 0 1.8339319 43.573087
|
||||
161 0 -0.15883074 0 -0.15883074 30.485408
|
||||
162 0 -0.88242605 0 -0.88242605 25.479286
|
||||
163 0 -1.1028834 0 -1.1028834 23.930039
|
||||
164 0 -1.3016251 0 -1.3016251 22.476064
|
||||
165 0 -1.4075881 0 -1.4075881 21.708433
|
||||
166 0 -1.4998541 0 -1.4998541 21.023248
|
||||
167 0 -1.5636502 0 -1.5636502 20.550491
|
||||
168 0 -1.6221148 0 -1.6221148 20.112975
|
||||
169 0 -1.6633102 0 -1.6633102 19.808456
|
||||
170 0 -1.6929671 0 -1.6929671 19.579216
|
||||
Loop time of 0.00960529 on 4 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
1.83393187932 -1.66331017868 -1.69296708374
|
||||
Force two-norm initial, final = 9975.74 475.873
|
||||
Force max component initial, final = 1076.81 151.665
|
||||
Final line search alpha, max atom move = 0.00168794 0.256002
|
||||
Iterations, force evaluations = 10 10
|
||||
|
||||
Pair time (%) = 0.00359744 (37.4527)
|
||||
Neigh time (%) = 0.000600696 (6.2538)
|
||||
Comm time (%) = 0.000516534 (5.3776)
|
||||
Outpt time (%) = 0.00404549 (42.1173)
|
||||
Other time (%) = 0.000845134 (8.79863)
|
||||
|
||||
Nlocal: 625 ave 627 max 624 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Nghost: 299 ave 310 max 288 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Neighs: 7226.25 ave 7297 max 7198 min
|
||||
Histogram: 2 1 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 28905
|
||||
Ave neighs/atom = 11.562
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 2.70701 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
170 0 1.5622987 0 1.5622987 41.627713
|
||||
171 0 0.20405372 0 0.20405372 32.73863
|
||||
172 0 -0.87631997 0 -0.87631997 25.414386
|
||||
173 0 -1.1619584 0 -1.1619584 23.352987
|
||||
174 0 -1.353506 0 -1.353506 21.988949
|
||||
175 0 -1.4434669 0 -1.4434669 21.346794
|
||||
176 0 -1.5075839 0 -1.5075839 20.864291
|
||||
177 0 -1.5868121 0 -1.5868121 20.27149
|
||||
178 0 -1.6381464 0 -1.6381464 19.889565
|
||||
179 0 -1.6692179 0 -1.6692179 19.666555
|
||||
180 0 -1.70156 0 -1.70156 19.42945
|
||||
Loop time of 0.0104083 on 4 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
1.56229868243 -1.66921787874 -1.70155998988
|
||||
Force two-norm initial, final = 9429.39 308.746
|
||||
Force max component initial, final = 1781.79 76.8635
|
||||
Final line search alpha, max atom move = 0.000837531 0.0643756
|
||||
Iterations, force evaluations = 10 11
|
||||
|
||||
Pair time (%) = 0.00394958 (37.9463)
|
||||
Neigh time (%) = 0.00091511 (8.79208)
|
||||
Comm time (%) = 0.000590384 (5.67222)
|
||||
Outpt time (%) = 0.00406975 (39.1008)
|
||||
Other time (%) = 0.00088352 (8.48857)
|
||||
|
||||
Nlocal: 625 ave 627 max 622 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 298.75 ave 305 max 293 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Neighs: 7228.75 ave 7301 max 7151 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 28915
|
||||
Ave neighs/atom = 11.566
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 2.70701 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
180 0 1.4799149 0 1.4799149 41.115498
|
||||
181 0 -0.45828563 0 -0.45828563 28.305878
|
||||
182 0 -1.1127382 0 -1.1127382 23.745438
|
||||
183 0 -1.326884 0 -1.326884 22.195474
|
||||
184 0 -1.4902693 0 -1.4902693 21.002247
|
||||
185 0 -1.5727487 0 -1.5727487 20.392828
|
||||
186 0 -1.6421989 0 -1.6421989 19.854484
|
||||
187 0 -1.668478 0 -1.668478 19.66228
|
||||
188 0 -1.7142757 0 -1.7142757 19.337461
|
||||
189 0 -1.7362458 0 -1.7362458 19.174238
|
||||
190 0 -1.7533386 0 -1.7533386 19.045232
|
||||
Loop time of 0.0124404 on 4 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
1.47991489058 -1.73624575112 -1.75333859414
|
||||
Force two-norm initial, final = 9131.13 352.22
|
||||
Force max component initial, final = 915.834 100.035
|
||||
Final line search alpha, max atom move = 0.000889415 0.0889726
|
||||
Iterations, force evaluations = 10 15
|
||||
|
||||
Pair time (%) = 0.00540572 (43.4528)
|
||||
Neigh time (%) = 0.00120753 (9.70649)
|
||||
Comm time (%) = 0.000805736 (6.47674)
|
||||
Outpt time (%) = 0.00404233 (32.4934)
|
||||
Other time (%) = 0.000979125 (7.8705)
|
||||
|
||||
Nlocal: 625 ave 631 max 619 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Nghost: 299.5 ave 307 max 290 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
Neighs: 7246.5 ave 7330 max 7147 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 28986
|
||||
Ave neighs/atom = 11.5944
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
minimize 0.001 0.001 10 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization
|
||||
Memory usage per processor = 2.70701 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
190 0 1.4561992 0 1.4561992 40.970034
|
||||
191 0 -0.12263898 0 -0.12263898 30.588401
|
||||
192 0 -0.96453383 0 -0.96453383 24.824541
|
||||
193 0 -1.1578126 0 -1.1578126 23.461941
|
||||
194 0 -1.3007191 0 -1.3007191 22.433693
|
||||
195 0 -1.4026624 0 -1.4026624 21.70126
|
||||
196 0 -1.4911196 0 -1.4911196 21.053133
|
||||
197 0 -1.5634641 0 -1.5634641 20.530531
|
||||
198 0 -1.5924275 0 -1.5924275 20.314473
|
||||
199 0 -1.6303321 0 -1.6303321 20.023515
|
||||
200 0 -1.6520498 0 -1.6520498 19.869534
|
||||
Loop time of 0.0108462 on 4 procs for 10 steps with 2500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
1.45619920225 -1.63033211038 -1.6520498229
|
||||
Force two-norm initial, final = 8836.39 561.478
|
||||
Force max component initial, final = 1227.95 211.829
|
||||
Final line search alpha, max atom move = 0.000129991 0.0275358
|
||||
Iterations, force evaluations = 10 12
|
||||
|
||||
Pair time (%) = 0.00431436 (39.7777)
|
||||
Neigh time (%) = 0.000909686 (8.38714)
|
||||
Comm time (%) = 0.000643253 (5.93068)
|
||||
Outpt time (%) = 0.00406945 (37.5196)
|
||||
Other time (%) = 0.000909448 (8.38494)
|
||||
|
||||
Nlocal: 625 ave 626 max 623 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 298 ave 306 max 290 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 7246.75 ave 7320 max 7153 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
|
||||
Total # of neighbors = 28987
|
||||
Ave neighs/atom = 11.5948
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
|
@ -1,271 +0,0 @@
|
|||
SPPARKS (26 Aug 2010)
|
||||
# SPPARKS input for coupling MD/MC
|
||||
|
||||
seed 56789
|
||||
|
||||
app_style potts/strain 100
|
||||
|
||||
dimension 2
|
||||
lattice sq/8n 1.0
|
||||
region box block 0 50 0 50 -0.5 0.5
|
||||
create_box box
|
||||
Created box = (0 0 -0.5) to (50 50 0.5)
|
||||
1 by 1 by 1 processor grid
|
||||
create_sites box
|
||||
Creating sites ...
|
||||
2500 sites
|
||||
2500 sites have 8 neighbors
|
||||
set site range 1 100
|
||||
2500 settings made for site
|
||||
set d1 value 0.0
|
||||
2500 settings made for d1
|
||||
|
||||
sector yes
|
||||
solve_style tree
|
||||
|
||||
diag_style energy
|
||||
|
||||
temperature 1.0
|
||||
|
||||
stats 10.0
|
||||
dump 1 10.0 dump.mc
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
0 0 0 0 0 19766
|
||||
10 17929 0 0 0.0776 5324
|
||||
Loop time of 0.077626 on 1 procs
|
||||
|
||||
Solve time (%) = 0.0070138 (9.03537)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.00146031 (1.88122)
|
||||
Outpt time (%) = 0.00415015 (5.34634)
|
||||
App time (%) = 0.0614648 (79.1807)
|
||||
Other time (%) = 0.00353694 (4.55639)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
10 17929 0 0 0 5324
|
||||
20 24582 0 0 0.0279 4750
|
||||
Loop time of 0.027904 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00271416 (9.72676)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000461817 (1.65502)
|
||||
Outpt time (%) = 0.0042181 (15.1165)
|
||||
App time (%) = 0.0191288 (68.5521)
|
||||
Other time (%) = 0.00138116 (4.94967)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
20 24582 0 0 0 4750
|
||||
30 30109 0 0 0.0234 4264
|
||||
Loop time of 0.023375 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00216675 (9.2695)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000342846 (1.46672)
|
||||
Outpt time (%) = 0.00416183 (17.8046)
|
||||
App time (%) = 0.015563 (66.5796)
|
||||
Other time (%) = 0.00114059 (4.87954)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
30 30109 0 0 0 4264
|
||||
40 35032 0 0 0.0208 3880
|
||||
Loop time of 0.020786 on 1 procs
|
||||
|
||||
Solve time (%) = 0.0019896 (9.57182)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000316858 (1.52438)
|
||||
Outpt time (%) = 0.00413609 (19.8984)
|
||||
App time (%) = 0.0132952 (63.962)
|
||||
Other time (%) = 0.00104833 (5.04341)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
40 35032 0 0 0 3880
|
||||
50 39543 0 0 0.0193 3784
|
||||
Loop time of 0.0193491 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00185919 (9.60865)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000333071 (1.72138)
|
||||
Outpt time (%) = 0.00412297 (21.3083)
|
||||
App time (%) = 0.0120728 (62.3946)
|
||||
Other time (%) = 0.000961065 (4.96698)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
50 39543 0 0 0 3784
|
||||
60 43899 0 0 0.0187 3706
|
||||
Loop time of 0.018713 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00176001 (9.40526)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000314474 (1.68051)
|
||||
Outpt time (%) = 0.00413895 (22.118)
|
||||
App time (%) = 0.0116153 (62.0706)
|
||||
Other time (%) = 0.000884295 (4.72556)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
60 43899 0 0 0 3706
|
||||
70 48028 0 0 0.0179 3392
|
||||
Loop time of 0.0178769 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00174618 (9.76781)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000296593 (1.65909)
|
||||
Outpt time (%) = 0.00414801 (23.2032)
|
||||
App time (%) = 0.0108221 (60.5367)
|
||||
Other time (%) = 0.000864029 (4.83322)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
70 48028 0 0 0 3392
|
||||
80 51900 0 0 0.017 3208
|
||||
Loop time of 0.0169971 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00157022 (9.23819)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000290394 (1.70849)
|
||||
Outpt time (%) = 0.00416803 (24.522)
|
||||
App time (%) = 0.0101995 (60.0076)
|
||||
Other time (%) = 0.0007689 (4.52371)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
80 51900 0 0 0 3208
|
||||
90 55450 0 0 0.0159 3162
|
||||
Loop time of 0.0158761 on 1 procs
|
||||
|
||||
Solve time (%) = 0.0014894 (9.38143)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000301123 (1.89671)
|
||||
Outpt time (%) = 0.00413799 (26.0644)
|
||||
App time (%) = 0.00924802 (58.2514)
|
||||
Other time (%) = 0.00069952 (4.40613)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
90 55450 0 0 0 3162
|
||||
100 59009 0 0 0.0158 3038
|
||||
Loop time of 0.0158172 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00142503 (9.00938)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000296831 (1.87664)
|
||||
Outpt time (%) = 0.00412178 (26.0589)
|
||||
App time (%) = 0.00923729 (58.4004)
|
||||
Other time (%) = 0.000736237 (4.65467)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
100 59009 0 0 0 3038
|
||||
110 62454 0 0 0.0155 3066
|
||||
Loop time of 0.015537 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00135612 (8.72834)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000293732 (1.89053)
|
||||
Outpt time (%) = 0.00415182 (26.7221)
|
||||
App time (%) = 0.00904965 (58.2457)
|
||||
Other time (%) = 0.000685692 (4.41328)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
110 62454 0 0 0 3066
|
||||
120 65856 0 0 0.0152 2898
|
||||
Loop time of 0.0152211 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00139046 (9.13505)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000291109 (1.91253)
|
||||
Outpt time (%) = 0.0041492 (27.2595)
|
||||
App time (%) = 0.00871038 (57.2257)
|
||||
Other time (%) = 0.00067997 (4.46728)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
120 65856 0 0 0 2898
|
||||
130 68856 0 0 0.0137 2798
|
||||
Loop time of 0.0137191 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00130701 (9.52695)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000296831 (2.16364)
|
||||
Outpt time (%) = 0.00412989 (30.1032)
|
||||
App time (%) = 0.00742817 (54.1448)
|
||||
Other time (%) = 0.000557184 (4.06138)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
130 68856 0 0 0 2798
|
||||
140 71967 0 0 0.0141 2700
|
||||
Loop time of 0.0141542 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00132799 (9.38232)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000284195 (2.00785)
|
||||
Outpt time (%) = 0.00414681 (29.2974)
|
||||
App time (%) = 0.00777125 (54.9042)
|
||||
Other time (%) = 0.000623941 (4.40817)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
140 71967 0 0 0 2700
|
||||
150 74773 0 0 0.0132 2644
|
||||
Loop time of 0.0131881 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00111961 (8.48956)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000277758 (2.10612)
|
||||
Outpt time (%) = 0.00413394 (31.3459)
|
||||
App time (%) = 0.00711513 (53.951)
|
||||
Other time (%) = 0.000541687 (4.10738)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
150 74773 0 0 0 2644
|
||||
160 77662 0 0 0.0134 2616
|
||||
Loop time of 0.0133891 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00116301 (8.68621)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.00027895 (2.08341)
|
||||
Outpt time (%) = 0.00415397 (31.025)
|
||||
App time (%) = 0.00725079 (54.1544)
|
||||
Other time (%) = 0.000542402 (4.05107)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
160 77662 0 0 0 2616
|
||||
170 80475 0 0 0.0131 2538
|
||||
Loop time of 0.0130939 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00108457 (8.28296)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000279665 (2.13583)
|
||||
Outpt time (%) = 0.00412798 (31.5259)
|
||||
App time (%) = 0.00700951 (53.5324)
|
||||
Other time (%) = 0.000592232 (4.52294)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
170 80475 0 0 0 2538
|
||||
180 83407 0 0 0.0136 2660
|
||||
Loop time of 0.0136199 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00117278 (8.61079)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000262737 (1.92907)
|
||||
Outpt time (%) = 0.00413108 (30.3312)
|
||||
App time (%) = 0.0074532 (54.7229)
|
||||
Other time (%) = 0.0006001 (4.40605)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
180 83407 0 0 0 2660
|
||||
190 86407 0 0 0.0138 2656
|
||||
Loop time of 0.013859 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00119066 (8.59124)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000247717 (1.7874)
|
||||
Outpt time (%) = 0.00414801 (29.93)
|
||||
App time (%) = 0.00767326 (55.3665)
|
||||
Other time (%) = 0.000599384 (4.32486)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
190 86407 0 0 0 2656
|
||||
200 88961 0 0 0.0124 2374
|
||||
Loop time of 0.0124531 on 1 procs
|
||||
|
||||
Solve time (%) = 0.00107932 (8.6671)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000233412 (1.87433)
|
||||
Outpt time (%) = 0.00414777 (33.3072)
|
||||
App time (%) = 0.00648117 (52.0447)
|
||||
Other time (%) = 0.000511408 (4.10668)
|
||||
|
|
@ -1,271 +0,0 @@
|
|||
SPPARKS (26 Aug 2010)
|
||||
# SPPARKS input for coupling MD/MC
|
||||
|
||||
seed 56789
|
||||
|
||||
app_style potts/strain 100
|
||||
|
||||
dimension 2
|
||||
lattice sq/8n 1.0
|
||||
region box block 0 50 0 50 -0.5 0.5
|
||||
create_box box
|
||||
Created box = (0 0 -0.5) to (50 50 0.5)
|
||||
2 by 2 by 1 processor grid
|
||||
create_sites box
|
||||
Creating sites ...
|
||||
2500 sites
|
||||
2500 sites have 8 neighbors
|
||||
set site range 1 100
|
||||
2500 settings made for site
|
||||
set d1 value 0.0
|
||||
2500 settings made for d1
|
||||
|
||||
sector yes
|
||||
solve_style tree
|
||||
|
||||
diag_style energy
|
||||
|
||||
temperature 1.0
|
||||
|
||||
stats 10.0
|
||||
dump 1 10.0 dump.mc
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
0 0 0 0 0 19766
|
||||
10 18695 0 0 0.024 5696
|
||||
Loop time of 0.0240365 on 4 procs
|
||||
|
||||
Solve time (%) = 0.0017997 (7.48737)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.00263286 (10.9536)
|
||||
Outpt time (%) = 0.00416493 (17.3275)
|
||||
App time (%) = 0.0137114 (57.044)
|
||||
Other time (%) = 0.00172764 (7.18756)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
10 18695 0 0 0 5696
|
||||
20 25730 0 0 0.0114 4806
|
||||
Loop time of 0.0113776 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000647247 (5.68877)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.0013088 (11.5033)
|
||||
Outpt time (%) = 0.00417346 (36.6812)
|
||||
App time (%) = 0.0045594 (40.0733)
|
||||
Other time (%) = 0.000688732 (6.05338)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
20 25730 0 0 0 4806
|
||||
30 31377 0 0 0.00985 4308
|
||||
Loop time of 0.00987101 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000525832 (5.32704)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.0012235 (12.3949)
|
||||
Outpt time (%) = 0.00415748 (42.1181)
|
||||
App time (%) = 0.00343758 (34.825)
|
||||
Other time (%) = 0.000526607 (5.33489)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
30 31377 0 0 0 4308
|
||||
40 36311 0 0 0.0092 3840
|
||||
Loop time of 0.00922179 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000474155 (5.14168)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.00114667 (12.4344)
|
||||
Outpt time (%) = 0.00414455 (44.943)
|
||||
App time (%) = 0.00293165 (31.7905)
|
||||
Other time (%) = 0.000524759 (5.69043)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
40 36311 0 0 0 3840
|
||||
50 40886 0 0 0.00891 3534
|
||||
Loop time of 0.0089252 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000433862 (4.86109)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.00113171 (12.68)
|
||||
Outpt time (%) = 0.00413698 (46.3517)
|
||||
App time (%) = 0.00268257 (30.0561)
|
||||
Other time (%) = 0.000540078 (6.05116)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
50 40886 0 0 0 3534
|
||||
60 44888 0 0 0.00831 3306
|
||||
Loop time of 0.00833625 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000383437 (4.59963)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.00106108 (12.7285)
|
||||
Outpt time (%) = 0.00413227 (49.5699)
|
||||
App time (%) = 0.00232393 (27.8774)
|
||||
Other time (%) = 0.000435531 (5.22455)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
60 44888 0 0 0 3306
|
||||
70 48583 0 0 0.00806 3078
|
||||
Loop time of 0.0080772 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000353277 (4.37375)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.00102895 (12.739)
|
||||
Outpt time (%) = 0.0041061 (50.8357)
|
||||
App time (%) = 0.00213838 (26.4742)
|
||||
Other time (%) = 0.000450492 (5.57732)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
70 48583 0 0 0 3078
|
||||
80 52044 0 0 0.00786 2998
|
||||
Loop time of 0.00788343 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000333607 (4.23175)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.00101435 (12.8669)
|
||||
Outpt time (%) = 0.00420028 (53.2799)
|
||||
App time (%) = 0.00198931 (25.234)
|
||||
Other time (%) = 0.000345886 (4.3875)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
80 52044 0 0 0 2998
|
||||
90 55352 0 0 0.0083 3026
|
||||
Loop time of 0.00831437 on 4 procs
|
||||
|
||||
Solve time (%) = 0.00031358 (3.77154)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.00111783 (13.4445)
|
||||
Outpt time (%) = 0.00467652 (56.2462)
|
||||
App time (%) = 0.00188529 (22.6751)
|
||||
Other time (%) = 0.00032115 (3.86259)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
90 55352 0 0 0 3026
|
||||
100 58494 0 0 0.00733 2742
|
||||
Loop time of 0.00735307 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000297189 (4.0417)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000801027 (10.8938)
|
||||
Outpt time (%) = 0.00418043 (56.8529)
|
||||
App time (%) = 0.00179577 (24.422)
|
||||
Other time (%) = 0.000278652 (3.7896)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
100 58494 0 0 0 2742
|
||||
110 61498 0 0 0.00732 2636
|
||||
Loop time of 0.00733691 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000282168 (3.84587)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000877678 (11.9625)
|
||||
Outpt time (%) = 0.00414526 (56.4987)
|
||||
App time (%) = 0.00174332 (23.7609)
|
||||
Other time (%) = 0.000288486 (3.93199)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
110 61498 0 0 0 2636
|
||||
120 64343 0 0 0.00719 2518
|
||||
Loop time of 0.00721735 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000270605 (3.74937)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.00078702 (10.9046)
|
||||
Outpt time (%) = 0.00416625 (57.7254)
|
||||
App time (%) = 0.00162369 (22.497)
|
||||
Other time (%) = 0.000369787 (5.12359)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
120 64343 0 0 0 2518
|
||||
130 66901 0 0 0.00709 2480
|
||||
Loop time of 0.00710845 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000247002 (3.47476)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.00100386 (14.1221)
|
||||
Outpt time (%) = 0.00416774 (58.6307)
|
||||
App time (%) = 0.00143349 (20.166)
|
||||
Other time (%) = 0.00025636 (3.60641)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
130 66901 0 0 0 2480
|
||||
140 69617 0 0 0.00723 2462
|
||||
Loop time of 0.00725645 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000262678 (3.61992)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000848353 (11.691)
|
||||
Outpt time (%) = 0.00418752 (57.7076)
|
||||
App time (%) = 0.00152171 (20.9704)
|
||||
Other time (%) = 0.000436187 (6.01102)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
140 69617 0 0 0 2462
|
||||
150 72516 0 0 0.0077 2368
|
||||
Loop time of 0.00771403 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000279188 (3.61922)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.00115103 (14.9212)
|
||||
Outpt time (%) = 0.00420797 (54.5495)
|
||||
App time (%) = 0.00164241 (21.2911)
|
||||
Other time (%) = 0.000433445 (5.61892)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
150 72516 0 0 0 2368
|
||||
160 75201 0 0 0.00745 2384
|
||||
Loop time of 0.00747746 on 4 procs
|
||||
|
||||
Solve time (%) = 0.00026089 (3.48901)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.00115579 (15.457)
|
||||
Outpt time (%) = 0.00416714 (55.7293)
|
||||
App time (%) = 0.0015164 (20.2796)
|
||||
Other time (%) = 0.000377238 (5.045)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
160 75201 0 0 0 2384
|
||||
170 77794 0 0 0.00709 2286
|
||||
Loop time of 0.00710869 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000261724 (3.68175)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000879705 (12.3751)
|
||||
Outpt time (%) = 0.00419676 (59.0371)
|
||||
App time (%) = 0.00145274 (20.4362)
|
||||
Other time (%) = 0.000317752 (4.46992)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
170 77794 0 0 0 2286
|
||||
180 80320 0 0 0.00723 2186
|
||||
Loop time of 0.00725418 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000241041 (3.32279)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.00100464 (13.8491)
|
||||
Outpt time (%) = 0.00413877 (57.0535)
|
||||
App time (%) = 0.00144053 (19.8579)
|
||||
Other time (%) = 0.000429213 (5.91677)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
180 80320 0 0 0 2186
|
||||
190 82621 0 0 0.00686 2204
|
||||
Loop time of 0.00687295 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000222385 (3.23565)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000860512 (12.5203)
|
||||
Outpt time (%) = 0.00418121 (60.8357)
|
||||
App time (%) = 0.00126499 (18.4053)
|
||||
Other time (%) = 0.000343859 (5.00308)
|
||||
run 10Setting up run ...
|
||||
Time Naccept Nreject Nsweeps CPU Energy
|
||||
190 82621 0 0 0 2204
|
||||
200 84907 0 0 0.00681 2276
|
||||
Loop time of 0.0068413 on 4 procs
|
||||
|
||||
Solve time (%) = 0.000233412 (3.4118)
|
||||
Update time (%) = 0 (0)
|
||||
Comm time (%) = 0.000758171 (11.0823)
|
||||
Outpt time (%) = 0.00421125 (61.5562)
|
||||
App time (%) = 0.00125164 (18.2953)
|
||||
Other time (%) = 0.000386834 (5.65439)
|
||||
|
|
@ -1 +0,0 @@
|
|||
#define SPKPATH /home/sjplimp/spparks
|
||||
|
|
@ -1,42 +0,0 @@
|
|||
# Makefile for coupling library
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
# System-specific settings
|
||||
|
||||
CC = g++
|
||||
CCFLAGS = -g -O -DMPICH_IGNORE_CXX_SEEK
|
||||
DEPFLAGS = -M
|
||||
LINK = g++
|
||||
LINKFLAGS = -g -O
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
|
||||
# Files
|
||||
|
||||
LIB = libcouple.a
|
||||
SRC = $(wildcard *.cpp)
|
||||
INC = $(wildcard *.h)
|
||||
OBJ = $(SRC:.cpp=.o)
|
||||
|
||||
# Targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
|
||||
|
||||
clean:
|
||||
rm $(LIB) *.o *.d
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
|
||||
|
||||
# Individual dependencies
|
||||
|
||||
DEPENDS = $(OBJ:.o=.d)
|
||||
include $(DEPENDS)
|
||||
|
|
@ -1,16 +0,0 @@
|
|||
This directory has a small collection of routines, useful for
|
||||
exchanging data between 2 codes being run together as a coupled
|
||||
application. It is used by the LAMMPS <-> Quest and LAMMPS <->
|
||||
SPPARKS applications in 2 sister directories.
|
||||
|
||||
The library dir has a Makefile (which you may need to edit for your
|
||||
box). If you type
|
||||
|
||||
g++ -f Makefile.g++
|
||||
|
||||
you should create libcouple.a, which the other coupled applications
|
||||
link to.
|
||||
|
||||
Note that the library uses MPI, so the Makefile you use needs to
|
||||
include a path to the MPI include file, if it is not someplace
|
||||
the compiler will find it.
|
||||
|
|
@ -1,42 +0,0 @@
|
|||
#include "mpi.h"
|
||||
#include "stdlib.h"
|
||||
#include "stdio.h"
|
||||
#include "error.h"
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
Error::Error(MPI_Comm caller)
|
||||
{
|
||||
comm = caller;
|
||||
MPI_Comm_rank(comm,&me);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
called by all procs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Error::all(const char *str)
|
||||
{
|
||||
if (me == 0) printf("ERROR: %s\n",str);
|
||||
MPI_Finalize();
|
||||
exit(1);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
called by one proc
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Error::one(const char *str)
|
||||
{
|
||||
printf("ERROR on proc %d: %s\n",me,str);
|
||||
MPI_Abort(comm,1);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
called by one proc
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Error::warning(const char *str)
|
||||
{
|
||||
printf("WARNING: %s\n",str);
|
||||
}
|
||||
|
|
@ -1,19 +0,0 @@
|
|||
#ifndef ERROR_H
|
||||
#define ERROR_H
|
||||
|
||||
#include "mpi.h"
|
||||
|
||||
class Error {
|
||||
public:
|
||||
Error(MPI_Comm);
|
||||
|
||||
void all(const char *);
|
||||
void one(const char *);
|
||||
void warning(const char *);
|
||||
|
||||
private:
|
||||
MPI_Comm comm;
|
||||
int me;
|
||||
};
|
||||
|
||||
#endif
|
||||
|
|
@ -1,48 +0,0 @@
|
|||
#include "stdio.h"
|
||||
#include "string.h"
|
||||
#include "files.h"
|
||||
|
||||
#define MAXLINE 256
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void replace(char *file, char *header, int n, char **lines)
|
||||
{
|
||||
FILE *fpr = fopen(file,"r");
|
||||
FILE *fpw = fopen("tmp.file","w");
|
||||
|
||||
char line[MAXLINE];
|
||||
while (fgets(line,MAXLINE,fpr)) {
|
||||
if (strstr(line,header)) {
|
||||
fprintf(fpw,"%s",line);
|
||||
for (int i = 0; i < n; i++) {
|
||||
fgets(line,MAXLINE,fpr);
|
||||
fprintf(fpw,"%s",lines[i]);
|
||||
}
|
||||
} else fprintf(fpw,"%s",line);
|
||||
}
|
||||
|
||||
fclose(fpr);
|
||||
fclose(fpw);
|
||||
rename("tmp.file",file);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
char **extract(char *file, char *header, int n, char **lines)
|
||||
{
|
||||
FILE *fp = fopen(file,"r");
|
||||
|
||||
char line[MAXLINE];
|
||||
while (fgets(line,MAXLINE,fp)) {
|
||||
if (strstr(line,header)) {
|
||||
for (int i = 0; i < n; i++) {
|
||||
fgets(line,MAXLINE,fp);
|
||||
sprintf(lines[i],"%s",line);
|
||||
}
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
fclose(fp);
|
||||
}
|
||||
|
|
@ -1,2 +0,0 @@
|
|||
void replace(char *, char *, int, char **);
|
||||
char **extract(char *, char *, int, char **);
|
||||
|
|
@ -1,393 +0,0 @@
|
|||
#include "stdio.h"
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "irregular.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
|
||||
|
||||
enum{UNSET,SET};
|
||||
enum{NONE,SAME,VARYING};
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
Irregular::Irregular(MPI_Comm caller)
|
||||
{
|
||||
comm = caller;
|
||||
MPI_Comm_rank(comm,&me);
|
||||
MPI_Comm_size(comm,&nprocs);
|
||||
|
||||
memory = new Memory(comm);
|
||||
error = new Error(comm);
|
||||
|
||||
init();
|
||||
|
||||
patternflag = UNSET;
|
||||
sizestyle = NONE;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
Irregular::~Irregular()
|
||||
{
|
||||
delete memory;
|
||||
delete error;
|
||||
deallocate();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
n = # of datums contributed by this proc
|
||||
proclist = which proc each datum is to be sent to
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Irregular::pattern(int n, int *proclist)
|
||||
{
|
||||
// free any previous irregular info
|
||||
|
||||
deallocate();
|
||||
init();
|
||||
|
||||
patternflag = SET;
|
||||
sizestyle = NONE;
|
||||
|
||||
ndatumsend = n;
|
||||
|
||||
// list = 1 for procs I send to, including self
|
||||
// nrecv = # of messages I receive, not including self
|
||||
// self = 0 if no data for self, 1 if there is
|
||||
|
||||
int *list = new int[nprocs];
|
||||
int *counts = new int[nprocs];
|
||||
|
||||
for (int i = 0; i < nprocs; i++) {
|
||||
list[i] = 0;
|
||||
counts[i] = 1;
|
||||
}
|
||||
|
||||
for (int i = 0; i < n; i++) list[proclist[i]] = 1;
|
||||
MPI_Reduce_scatter(list,&nrecv,counts,MPI_INT,MPI_SUM,comm);
|
||||
|
||||
self = 0;
|
||||
if (list[me]) self = 1;
|
||||
if (self) nrecv--;
|
||||
|
||||
// storage for recv info, not including self
|
||||
|
||||
recvproc = new int[nrecv];
|
||||
recvcount = new int[nrecv];
|
||||
recvsize = new int[nrecv];
|
||||
request = new MPI_Request[nrecv];
|
||||
status = new MPI_Status[nrecv];
|
||||
|
||||
// list = # of datums to send to each proc, including self
|
||||
// nsend = # of messages I send, not including self
|
||||
|
||||
for (int i = 0; i < nprocs; i++) list[i] = 0;
|
||||
for (int i = 0; i < n; i++) list[proclist[i]]++;
|
||||
|
||||
nsend = 0;
|
||||
for (int i = 0; i < nprocs; i++) if (list[i] > 0) nsend++;
|
||||
if (self) nsend--;
|
||||
|
||||
// storage for send info, including self
|
||||
|
||||
sendproc = new int[nsend+self];
|
||||
sendcount = new int[nsend+self];
|
||||
sendsize = new int[nsend+self];
|
||||
sendindices = (int *) memory->smalloc(n*sizeof(int),"sendindices");
|
||||
|
||||
// setup sendprocs and sendcounts, including self
|
||||
// each proc begins with iproc > me, and continues until iproc = me
|
||||
// list ends up with pointer to which send that proc is associated with
|
||||
|
||||
int iproc = me;
|
||||
int isend = 0;
|
||||
for (int i = 0; i < nprocs; i++) {
|
||||
iproc++;
|
||||
if (iproc == nprocs) iproc = 0;
|
||||
if (list[iproc] > 0) {
|
||||
sendproc[isend] = iproc;
|
||||
sendcount[isend] = list[iproc];
|
||||
list[iproc] = isend;
|
||||
isend++;
|
||||
}
|
||||
}
|
||||
|
||||
// post all receives for datum counts
|
||||
|
||||
for (int i = 0; i < nrecv; i++)
|
||||
MPI_Irecv(&recvcount[i],1,MPI_INT,MPI_ANY_SOURCE,0,comm,&request[i]);
|
||||
|
||||
// barrier to insure receives are posted
|
||||
|
||||
MPI_Barrier(comm);
|
||||
|
||||
// send each datum count, packing buf with needed datums
|
||||
|
||||
for (int i = 0; i < nsend; i++)
|
||||
MPI_Send(&sendcount[i],1,MPI_INT,sendproc[i],0,comm);
|
||||
|
||||
// insure all MPI_ANY_SOURCE messages are received
|
||||
// set recvproc
|
||||
|
||||
if (nrecv) MPI_Waitall(nrecv,request,status);
|
||||
for (int i = 0; i < nrecv; i++) recvproc[i] = status[i].MPI_SOURCE;
|
||||
|
||||
// ndatumrecv = total datums received, including self
|
||||
|
||||
ndatumrecv = 0;
|
||||
for (int i = 0; i < nrecv; i++)
|
||||
ndatumrecv += recvcount[i];
|
||||
if (self) ndatumrecv += sendcount[nsend];
|
||||
|
||||
// setup sendindices, including self
|
||||
// counts = offset into sendindices for each proc I send to
|
||||
// let sc0 = sendcount[0], sc1 = sendcount[1], etc
|
||||
// sendindices[0:sc0-1] = indices of datums in 1st message
|
||||
// sendindices[sc0:sc0+sc1-1] = indices of datums in 2nd message, etc
|
||||
|
||||
counts[0] = 0;
|
||||
for (int i = 1; i < nsend+self; i++)
|
||||
counts[i] = counts[i-1] + sendcount[i-1];
|
||||
|
||||
for (int i = 0; i < n; i++) {
|
||||
isend = list[proclist[i]];
|
||||
sendindices[counts[isend]++] = i;
|
||||
}
|
||||
|
||||
// clean up
|
||||
|
||||
delete [] counts;
|
||||
delete [] list;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
n = size of each received datum
|
||||
return total size in bytes of received data on this proc
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int Irregular::size(int n)
|
||||
{
|
||||
if (patternflag == UNSET) error->all("Cannot size without pattern");
|
||||
sizestyle = SAME;
|
||||
|
||||
nsize = n;
|
||||
|
||||
nsendmax = 0;
|
||||
for (int i = 0; i < nsend+self; i++) {
|
||||
sendsize[i] = nsize * sendcount[i];
|
||||
if (i < nsend) nsendmax = MAX(nsendmax,sendsize[i]);
|
||||
}
|
||||
|
||||
for (int i = 0; i < nrecv; i++) recvsize[i] = nsize * recvcount[i];
|
||||
nbytesrecv = nsize * ndatumrecv;
|
||||
|
||||
return nbytesrecv;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
slength,rlength = size of each datum to send and recv
|
||||
soffset = offset into eventual buffer of send data for each datum
|
||||
soffset can be NULL, in which case will build sendoffset from slength
|
||||
return total size in bytes of received data on this proc
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int Irregular::size(int *slength, int *soffset, int *rlength)
|
||||
{
|
||||
if (patternflag == UNSET) error->all("Cannot size without pattern");
|
||||
sizestyle = VARYING;
|
||||
|
||||
// store local copy of pointers to send lengths/offsets
|
||||
// if soffset not provided, create local copy from slength
|
||||
|
||||
sendsizedatum = slength;
|
||||
|
||||
if (soffset == NULL) {
|
||||
sendoffsetflag = 1;
|
||||
sendoffset = (int *) memory->smalloc(ndatumsend*sizeof(int),"sendoffset");
|
||||
|
||||
if (ndatumsend) sendoffset[0] = 0;
|
||||
for (int i = 1; i < ndatumsend; i++)
|
||||
sendoffset[i] = sendoffset[i-1] + sendsizedatum[i-1];
|
||||
|
||||
} else {
|
||||
if (sendoffsetflag) memory->sfree(sendoffset);
|
||||
sendoffsetflag = 0;
|
||||
sendoffset = soffset;
|
||||
}
|
||||
|
||||
nsendmax = 0;
|
||||
int m = 0;
|
||||
for (int i = 0; i < nsend+self; i++) {
|
||||
sendsize[i] = 0;
|
||||
for (int j = 0; j < sendcount[i]; j++)
|
||||
sendsize[i] += sendsizedatum[sendindices[m++]];
|
||||
if (i < nsend) nsendmax = MAX(nsendmax,sendsize[i]);
|
||||
}
|
||||
|
||||
nbytesrecv = 0;
|
||||
m = 0;
|
||||
for (int i = 0; i < nrecv; i++) {
|
||||
recvsize[i] = 0;
|
||||
for (int j = 0; j < recvcount[i]; j++) recvsize[i] += rlength[m++];
|
||||
nbytesrecv += recvsize[i];
|
||||
}
|
||||
if (self) nbytesrecv += sendsize[nsend];
|
||||
|
||||
return nbytesrecv;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
wrapper on 2 versions of exchange
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Irregular::exchange(char *sendbuf, char *recvbuf)
|
||||
{
|
||||
if (sizestyle == SAME) exchange_same(sendbuf,recvbuf);
|
||||
else if (sizestyle == VARYING) exchange_varying(sendbuf,recvbuf);
|
||||
else error->all("Irregular size was not set");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
sendbuf = data to send
|
||||
recvbuf = buffer to recv all data into
|
||||
requires nsize,nsendmax,recvsize,sendsize be setup by size(int)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Irregular::exchange_same(char *sendbuf, char *recvbuf)
|
||||
{
|
||||
// post all receives
|
||||
|
||||
int recvoffset = 0;
|
||||
for (int irecv = 0; irecv < nrecv; irecv++) {
|
||||
MPI_Irecv(&recvbuf[recvoffset],recvsize[irecv],MPI_BYTE,
|
||||
recvproc[irecv],0,comm,&request[irecv]);
|
||||
recvoffset += recvsize[irecv];
|
||||
}
|
||||
|
||||
// malloc buf for largest send
|
||||
|
||||
char *buf = (char *) memory->smalloc(nsendmax,"buf");
|
||||
|
||||
// barrier to insure receives are posted
|
||||
|
||||
MPI_Barrier(comm);
|
||||
|
||||
// send each message, packing buf with needed datums
|
||||
|
||||
int m = 0;
|
||||
for (int isend = 0; isend < nsend; isend++) {
|
||||
int bufoffset = 0;
|
||||
for (int i = 0; i < sendcount[isend]; i++) {
|
||||
memcpy(&buf[bufoffset],&sendbuf[nsize*sendindices[m++]],nsize);
|
||||
bufoffset += nsize;
|
||||
}
|
||||
MPI_Send(buf,sendsize[isend],MPI_BYTE,sendproc[isend],0,comm);
|
||||
}
|
||||
|
||||
// copy self data directly from sendbuf to recvbuf
|
||||
|
||||
if (self)
|
||||
for (int i = 0; i < sendcount[nsend]; i++) {
|
||||
memcpy(&recvbuf[recvoffset],&sendbuf[nsize*sendindices[m++]],nsize);
|
||||
recvoffset += nsize;
|
||||
}
|
||||
|
||||
// free send buffer
|
||||
|
||||
memory->sfree(buf);
|
||||
|
||||
// wait on all incoming messages
|
||||
|
||||
if (nrecv) MPI_Waitall(nrecv,request,status);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
sendbuf = data to send
|
||||
recvbuf = buffer to recv all data into
|
||||
requires nsendmax,recvsize,sendsize,sendoffset,sendsizedatum
|
||||
be setup by size(int *, int *)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Irregular::exchange_varying(char *sendbuf, char *recvbuf)
|
||||
{
|
||||
// post all receives
|
||||
|
||||
int recvoffset = 0;
|
||||
for (int irecv = 0; irecv < nrecv; irecv++) {
|
||||
MPI_Irecv(&recvbuf[recvoffset],recvsize[irecv],MPI_BYTE,
|
||||
recvproc[irecv],0,comm,&request[irecv]);
|
||||
recvoffset += recvsize[irecv];
|
||||
}
|
||||
|
||||
// malloc buf for largest send
|
||||
|
||||
char *buf = (char *) memory->smalloc(nsendmax,"buf");
|
||||
|
||||
// barrier to insure receives are posted
|
||||
|
||||
MPI_Barrier(comm);
|
||||
|
||||
// send each message, packing buf with needed datums
|
||||
|
||||
int index;
|
||||
int m = 0;
|
||||
for (int isend = 0; isend < nsend; isend++) {
|
||||
int bufoffset = 0;
|
||||
for (int i = 0; i < sendcount[isend]; i++) {
|
||||
index = sendindices[m++];
|
||||
memcpy(&buf[bufoffset],&sendbuf[sendoffset[index]],sendsizedatum[index]);
|
||||
bufoffset += sendsizedatum[index];
|
||||
}
|
||||
MPI_Send(buf,sendsize[isend],MPI_BYTE,sendproc[isend],0,comm);
|
||||
}
|
||||
|
||||
// copy self data directly from sendbuf to recvbuf
|
||||
|
||||
if (self)
|
||||
for (int i = 0; i < sendcount[nsend]; i++) {
|
||||
index = sendindices[m++];
|
||||
memcpy(&recvbuf[recvoffset],&sendbuf[sendoffset[index]],
|
||||
sendsizedatum[index]);
|
||||
recvoffset += sendsizedatum[index];
|
||||
}
|
||||
|
||||
// free send buffer
|
||||
|
||||
memory->sfree(buf);
|
||||
|
||||
// wait on all incoming messages
|
||||
|
||||
if (nrecv) MPI_Waitall(nrecv,request,status);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void Irregular::init()
|
||||
{
|
||||
sendoffsetflag = 0;
|
||||
sendproc = sendcount = sendsize = sendindices = NULL;
|
||||
sendoffset = NULL;
|
||||
recvproc = recvcount = recvsize = NULL;
|
||||
request = NULL;
|
||||
status = NULL;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void Irregular::deallocate()
|
||||
{
|
||||
delete [] sendproc;
|
||||
delete [] sendcount;
|
||||
delete [] sendsize;
|
||||
memory->sfree(sendindices);
|
||||
if (sendoffsetflag) memory->sfree(sendoffset);
|
||||
|
||||
delete [] recvproc;
|
||||
delete [] recvcount;
|
||||
delete [] recvsize;
|
||||
|
||||
delete [] request;
|
||||
delete [] status;
|
||||
}
|
||||
|
|
@ -1,58 +0,0 @@
|
|||
#ifndef IRREGULAR_H
|
||||
#define IRREGULAR_H
|
||||
|
||||
#include "mpi.h"
|
||||
|
||||
class Irregular {
|
||||
public:
|
||||
Irregular(MPI_Comm);
|
||||
~Irregular();
|
||||
|
||||
void pattern(int, int *);
|
||||
int size(int);
|
||||
int size(int *, int *, int *);
|
||||
void exchange(char *, char *);
|
||||
|
||||
private:
|
||||
int me,nprocs;
|
||||
|
||||
int patternflag; // UNSET,SET
|
||||
int sizestyle; // NONE,SAME,VARYING
|
||||
|
||||
int self; // 0 = no data to copy to self, 1 = yes
|
||||
|
||||
int ndatumsend; // # of datums to send w/ self
|
||||
int ndatumrecv; // # of datums to recv w/ self
|
||||
int nbytesrecv; // total bytes in received data w/ self
|
||||
int nsend; // # of messages to send w/out self
|
||||
int nrecv; // # of messages to recv w/out self
|
||||
int nsendmax; // # of bytes in largest send message, w/out self
|
||||
|
||||
int *sendproc; // list of procs to send to w/out self
|
||||
int *sendcount; // # of datums to send to each proc w/ self
|
||||
int *sendsize; // # of bytes to send to each proc w/ self
|
||||
int *sendindices; // indices of datums to send to each proc w/ self
|
||||
|
||||
int nsize; // size of every datum in bytes (SAME)
|
||||
int *sendsizedatum; // bytes in each datum to send w/ self (VARYING)
|
||||
int *sendoffset; // byte offset to where each datum starts w/ self
|
||||
int sendoffsetflag; // 1 if allocated sendoffset, 0 if passed in
|
||||
|
||||
int *recvproc; // list of procs to recv from w/out self
|
||||
int *recvcount; // # of datums to recv from each proc w/out self
|
||||
int *recvsize; // # of bytes to recv from each proc w/out self
|
||||
|
||||
MPI_Request *request; // MPI requests for posted recvs
|
||||
MPI_Status *status; // MPI statuses for Waitall
|
||||
MPI_Comm comm; // MPI communicator for all communication
|
||||
|
||||
class Memory *memory;
|
||||
class Error *error;
|
||||
|
||||
void exchange_same(char *, char *);
|
||||
void exchange_varying(char *, char *);
|
||||
void init();
|
||||
void deallocate();
|
||||
};
|
||||
|
||||
#endif
|
||||
|
|
@ -1,249 +0,0 @@
|
|||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "lammps_data_write.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
#define DELTA 4;
|
||||
|
||||
enum{INT,DOUBLE,DOUBLE2};
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
LAMMPSDataWrite::LAMMPSDataWrite(MPI_Comm caller_comm) : Send2One(caller_comm)
|
||||
{
|
||||
outfile = NULL;
|
||||
|
||||
nheader = maxheader = 0;
|
||||
format = NULL;
|
||||
headtype = NULL;
|
||||
ihead = NULL;
|
||||
dhead = NULL;
|
||||
ddhead = NULL;
|
||||
|
||||
nper = maxper = 0;
|
||||
atomtype = NULL;
|
||||
ivec = NULL;
|
||||
dvec = NULL;
|
||||
stride = NULL;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
LAMMPSDataWrite::~LAMMPSDataWrite()
|
||||
{
|
||||
delete [] outfile;
|
||||
|
||||
for (int i = 0; i < nheader; i++) delete [] format[i];
|
||||
memory->sfree(format);
|
||||
memory->sfree(headtype);
|
||||
memory->sfree(ihead);
|
||||
memory->sfree(dhead);
|
||||
memory->destroy_2d_double_array(ddhead);
|
||||
|
||||
memory->sfree(atomtype);
|
||||
memory->sfree(ivec);
|
||||
memory->sfree(dvec);
|
||||
memory->sfree(stride);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void LAMMPSDataWrite::pre()
|
||||
{
|
||||
if (me == 0) {
|
||||
fp = fopen(outfile,"w");
|
||||
if (fp == NULL)
|
||||
error->one("Could not open data_write output file");
|
||||
}
|
||||
|
||||
if (me == 0) {
|
||||
fprintf(fp,"%s","LAMMPS data file\n\n");
|
||||
for (int i = 0; i < nheader; i++)
|
||||
if (headtype[i] == INT) fprintf(fp,format[i],ihead[i]);
|
||||
else if (headtype[i] == DOUBLE) fprintf(fp,format[i],dhead[i]);
|
||||
else if (headtype[i] == DOUBLE2) fprintf(fp,format[i],
|
||||
ddhead[i][0],ddhead[i][1]);
|
||||
fprintf(fp,"\nAtoms\n\n");
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int LAMMPSDataWrite::size()
|
||||
{
|
||||
return nper*nlocal*sizeof(double);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void LAMMPSDataWrite::pack(char *cbuf)
|
||||
{
|
||||
int i,j;
|
||||
|
||||
double *dbuf = (double *) cbuf;
|
||||
|
||||
int m = 0;
|
||||
for (i = 0; i < nlocal; i++)
|
||||
for (j = 0; j < nper; j++) {
|
||||
if (i == 0) {
|
||||
if (atomtype[j] == 0)
|
||||
printf("AT %d %d %p %d\n",
|
||||
atomtype[j],stride[j],ivec[j],ivec[j][0]);
|
||||
else
|
||||
printf("AT %d %d %p %g\n",
|
||||
atomtype[j],stride[j],dvec[j],dvec[j][0]);
|
||||
}
|
||||
if (atomtype[j] == INT) dbuf[m++] = ivec[j][i*stride[j]];
|
||||
else if (atomtype[j] == DOUBLE) dbuf[m++] = dvec[j][i*stride[j]];
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void LAMMPSDataWrite::process(int nbuf, char *cbuf)
|
||||
{
|
||||
int i,j;
|
||||
|
||||
double *dbuf = (double *) cbuf;
|
||||
int n = nbuf/nper/sizeof(double);
|
||||
|
||||
int m = 0;
|
||||
for (i = 0; i < n; i++) {
|
||||
for (j = 0; j < nper; j++) {
|
||||
double dvalue = dbuf[m++];
|
||||
if (atomtype[j] == INT) fprintf(fp,"%d ",static_cast<int> (dvalue));
|
||||
else if (atomtype[j] == DOUBLE) fprintf(fp,"%g ",dvalue);
|
||||
}
|
||||
fprintf(fp,"\n");
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void LAMMPSDataWrite::post()
|
||||
{
|
||||
if (me == 0) fclose(fp);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void LAMMPSDataWrite::file(char *fname)
|
||||
{
|
||||
int n = strlen(fname) + 1;
|
||||
outfile = new char[n];
|
||||
strcpy(outfile,fname);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void LAMMPSDataWrite::header(char *str, int ivalue)
|
||||
{
|
||||
if (nheader == maxheader) grow_header();
|
||||
int n = strlen(str) + 2;
|
||||
format[nheader] = new char[n];
|
||||
strcpy(format[nheader],str);
|
||||
format[nheader][n-2] = '\n';
|
||||
format[nheader][n-1] = '\0';
|
||||
headtype[nheader] = INT;
|
||||
ihead[nheader] = ivalue;
|
||||
nheader++;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void LAMMPSDataWrite::header(char *str, double dvalue)
|
||||
{
|
||||
if (nheader == maxheader) grow_header();
|
||||
int n = strlen(str) + 2;
|
||||
format[nheader] = new char[n];
|
||||
strcpy(format[nheader],str);
|
||||
format[nheader][n-2] = '\n';
|
||||
format[nheader][n-1] = '\0';
|
||||
headtype[nheader] = DOUBLE;
|
||||
dhead[nheader] = dvalue;
|
||||
nheader++;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void LAMMPSDataWrite::header(char *str, double dvalue1, double dvalue2)
|
||||
{
|
||||
if (nheader == maxheader) grow_header();
|
||||
int n = strlen(str) + 2;
|
||||
format[nheader] = new char[n];
|
||||
strcpy(format[nheader],str);
|
||||
format[nheader][n-2] = '\n';
|
||||
format[nheader][n-1] = '\0';
|
||||
headtype[nheader] = DOUBLE2;
|
||||
ddhead[nheader][0] = dvalue1;
|
||||
ddhead[nheader][1] = dvalue2;
|
||||
nheader++;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void LAMMPSDataWrite::atoms(int n)
|
||||
{
|
||||
nlocal = n;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void LAMMPSDataWrite::atoms(int *vec)
|
||||
{
|
||||
if (nper == maxper) grow_peratom();
|
||||
atomtype[nper] = INT;
|
||||
ivec[nper] = vec;
|
||||
stride[nper] = 1;
|
||||
nper++;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void LAMMPSDataWrite::atoms(double *vec)
|
||||
{
|
||||
if (nper == maxper) grow_peratom();
|
||||
atomtype[nper] = DOUBLE;
|
||||
dvec[nper] = vec;
|
||||
stride[nper] = 1;
|
||||
nper++;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void LAMMPSDataWrite::atoms(int n, double **vec)
|
||||
{
|
||||
if (nper+n >= maxper) grow_peratom();
|
||||
for (int i = 0; i < n; i++) {
|
||||
atomtype[nper] = DOUBLE;
|
||||
dvec[nper] = &vec[0][i];
|
||||
stride[nper] = n;
|
||||
nper++;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void LAMMPSDataWrite::grow_header()
|
||||
{
|
||||
int n = maxheader + DELTA;
|
||||
format = (char **) memory->srealloc(format,n*sizeof(char *),"ldw:format");
|
||||
headtype = (int *) memory->srealloc(headtype,n*sizeof(int),"ldw:headtype");
|
||||
ihead = (int *) memory->srealloc(ihead,n*sizeof(int),"ldw:ihead");
|
||||
dhead = (double *) memory->srealloc(dhead,n*sizeof(double),"ldw:dhead");
|
||||
ddhead = memory->grow_2d_double_array(ddhead,n,2,"ldw:ddhead");
|
||||
maxheader = n;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void LAMMPSDataWrite::grow_peratom()
|
||||
{
|
||||
int n = maxper + DELTA;
|
||||
atomtype = (int *) memory->srealloc(atomtype,n*sizeof(int *),"ldw:atomtype");
|
||||
ivec = (int **) memory->srealloc(ivec,n*sizeof(int *),"ldw:ihead");
|
||||
dvec = (double **) memory->srealloc(dvec,n*sizeof(double *),"ldw:dhead");
|
||||
stride = (int *) memory->srealloc(stride,n*sizeof(int *),"ldw:stride");
|
||||
maxper = n;
|
||||
}
|
||||
|
|
@ -1,48 +0,0 @@
|
|||
#ifndef LAMMPS_DATA_WRITE_H
|
||||
#define LAMMPS_DATA_WRITE_H
|
||||
|
||||
#include "send2one.h"
|
||||
#include "stdio.h"
|
||||
|
||||
class LAMMPSDataWrite : public Send2One {
|
||||
public:
|
||||
LAMMPSDataWrite(MPI_Comm);
|
||||
~LAMMPSDataWrite();
|
||||
|
||||
void pre();
|
||||
int size();
|
||||
void pack(char *);
|
||||
void process(int, char *);
|
||||
void post();
|
||||
|
||||
void file(char *);
|
||||
void header(char *, int);
|
||||
void header(char *, double);
|
||||
void header(char *, double, double);
|
||||
void atoms(int);
|
||||
void atoms(int *);
|
||||
void atoms(double *);
|
||||
void atoms(int, double **);
|
||||
|
||||
private:
|
||||
char *outfile;
|
||||
int nlocal;
|
||||
FILE *fp;
|
||||
|
||||
int nheader,maxheader;
|
||||
char **format;
|
||||
int *headtype,*ihead;
|
||||
double *dhead;
|
||||
double **ddhead;
|
||||
|
||||
int nper,maxper;
|
||||
int *atomtype;
|
||||
int **ivec;
|
||||
double **dvec;
|
||||
int *stride;
|
||||
|
||||
void grow_header();
|
||||
void grow_peratom();
|
||||
};
|
||||
|
||||
#endif
|
||||
|
|
@ -1,316 +0,0 @@
|
|||
#include "mpi.h"
|
||||
#include "many2many.h"
|
||||
#include "irregular.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
#include <map>
|
||||
|
||||
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
Many2Many::Many2Many(MPI_Comm caller)
|
||||
{
|
||||
comm = caller;
|
||||
MPI_Comm_rank(comm,&me);
|
||||
MPI_Comm_size(comm,&nprocs);
|
||||
|
||||
memory = new Memory(comm);
|
||||
error = new Error(comm);
|
||||
|
||||
src_own = dest_own = NULL;
|
||||
src_off = dest_off = NULL;
|
||||
src_iwork = dest_iwork = NULL;
|
||||
src_dwork = dest_dwork = NULL;
|
||||
irregular = NULL;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
Many2Many::~Many2Many()
|
||||
{
|
||||
delete memory;
|
||||
delete error;
|
||||
deallocate();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
create a many2many pattern, deallocating any previous pattern
|
||||
each proc will contribute nsrc items with IDs listed in id_src
|
||||
each proc will receive ndest items with IDs listed in id_dest
|
||||
only sets up communication via rendezvous algorithm and Irregular class
|
||||
if id_src does not match id_dest on all procs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Many2Many::setup(int nsrc, int *id_src, int ndest, int *id_dest)
|
||||
{
|
||||
int i,j,isrc,idest,nsend,nrecv;
|
||||
int *proclist,*work;
|
||||
std::map<int,int> hash;
|
||||
std::map<int,int>::iterator loc;
|
||||
|
||||
// free any previous many2many info
|
||||
|
||||
deallocate();
|
||||
|
||||
// allocate on-proc and off-proc index lists
|
||||
|
||||
src_own =
|
||||
(int *) memory->smalloc(nsrc*sizeof(int),"many2many:src_own");
|
||||
dest_own =
|
||||
(int *) memory->smalloc(ndest*sizeof(int),"many2many:dest_own");
|
||||
src_off =
|
||||
(int *) memory->smalloc(nsrc*sizeof(int),"many2many:src_off");
|
||||
dest_off =
|
||||
(int *) memory->smalloc(ndest*sizeof(int),"many2many:dest_off");
|
||||
|
||||
// store destination IDs in hash
|
||||
|
||||
for (int i = 0; i < ndest; i++)
|
||||
hash.insert(std::pair<int,int> (id_dest[i],i));
|
||||
|
||||
// src_own, dest_own = list of IDs in both src and dest
|
||||
// nsrc_off = list of IDs in src owned by other procs
|
||||
|
||||
nown = nsrc_off = 0;
|
||||
nsrc_off = 0;
|
||||
for (i = 0; i < nsrc; i++) {
|
||||
loc = hash.find(id_src[i]);
|
||||
if (loc != hash.end()) {
|
||||
src_own[nown] = i;
|
||||
dest_own[nown] = loc->second;
|
||||
nown++;
|
||||
} else src_off[nsrc_off++] = i;
|
||||
}
|
||||
|
||||
// all done if all procs have one-to-one mapping of src and dest IDs
|
||||
// else figure out irregular comm needed
|
||||
|
||||
int flag = 0;
|
||||
if (nown == nsrc && nown == ndest) flag = 1;
|
||||
int flagall;
|
||||
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_MIN,comm);
|
||||
if (flagall) return;
|
||||
|
||||
// ndest_off = list of IDs in dest owned by other procs
|
||||
|
||||
work = (int *) memory->smalloc(ndest*sizeof(int),"many2many:work");
|
||||
|
||||
for (i = 0; i < ndest; i++) work[i] = 0;
|
||||
for (i = 0; i < nown; i++) work[dest_own[i]] = 1;
|
||||
|
||||
ndest_off = 0;
|
||||
for (i = 0; i < ndest; i++)
|
||||
if (work[i] == 0) dest_off[ndest_off++] = i;
|
||||
|
||||
memory->sfree(work);
|
||||
|
||||
// realloc off-proc arrays to smaller size
|
||||
|
||||
src_off = (int *)
|
||||
memory->srealloc(src_off,nsrc_off*sizeof(int),"many2many:src_off");
|
||||
dest_off = (int *)
|
||||
memory->srealloc(dest_off,ndest_off*sizeof(int),"many2many:dest_off");
|
||||
|
||||
// send off-proc src and dest Datums to 3rd-party proc via irregular comm
|
||||
// proc = ID % nprocs
|
||||
|
||||
nsend = nsrc_off + ndest_off;
|
||||
proclist = new int[nsend];
|
||||
Datum1 *send1 = new Datum1[nsend];
|
||||
|
||||
for (i = 0; i < nsrc_off; i++) {
|
||||
proclist[i] = id_src[src_off[i]] % nprocs;
|
||||
send1[i].id = id_src[src_off[i]];
|
||||
send1[i].proc = me;
|
||||
send1[i].index = src_off[i];
|
||||
}
|
||||
for (i = 0, j = nsrc_off; i < ndest_off; i++, j++) {
|
||||
proclist[j] = id_dest[dest_off[i]] % nprocs;
|
||||
send1[j].id = -id_dest[dest_off[i]];
|
||||
send1[j].proc = me;
|
||||
send1[j].index = dest_off[i];
|
||||
}
|
||||
|
||||
irregular = new Irregular(comm);
|
||||
irregular->pattern(nsend,proclist);
|
||||
nrecv = irregular->size(sizeof(Datum1)) / sizeof(Datum1);
|
||||
Datum1 *recv1 = new Datum1[nrecv];
|
||||
irregular->exchange((char *) send1, (char *) recv1);
|
||||
delete irregular;
|
||||
delete [] proclist;
|
||||
|
||||
// as 3rd-party proc, now have matching pairs of off-proc IDs
|
||||
// store src IDs (which are positive) in hash
|
||||
// loop over dest IDs (which are negative) to find matches
|
||||
// send match info back to src procs via a 2nd irregular comm
|
||||
|
||||
nsend = nrecv/2;
|
||||
proclist = new int[nsend];
|
||||
Datum2 *send2 = new Datum2[nsend];
|
||||
nsend = 0;
|
||||
|
||||
hash.clear();
|
||||
for (isrc = 0; isrc < nrecv; isrc++)
|
||||
if (recv1[isrc].id > 0)
|
||||
hash.insert(std::pair<int,int> (recv1[isrc].id,isrc));
|
||||
|
||||
for (idest = 0; idest < nrecv; idest++)
|
||||
if (recv1[idest].id < 0) {
|
||||
loc = hash.find(-recv1[idest].id);
|
||||
if (loc != hash.end()) {
|
||||
isrc = loc->second;
|
||||
proclist[nsend] = recv1[isrc].proc;
|
||||
send2[nsend].slocal = recv1[isrc].index;
|
||||
send2[nsend].dlocal = recv1[idest].index;
|
||||
send2[nsend].dproc = recv1[idest].proc;
|
||||
nsend++;
|
||||
} else error->one("Did not receive matching src/dest ID");
|
||||
}
|
||||
|
||||
irregular = new Irregular(comm);
|
||||
irregular->pattern(nsend,proclist);
|
||||
nrecv = irregular->size(sizeof(Datum2)) / sizeof(Datum2);
|
||||
Datum2 *recv2 = new Datum2[nrecv];
|
||||
irregular->exchange((char *) send2, (char *) recv2);
|
||||
delete irregular;
|
||||
delete [] proclist;
|
||||
|
||||
// use list of received src->dest Datums to build final irregular commm
|
||||
// irregular comm will communicate off-proc info from src to dest directly
|
||||
// work = local indices of dest IDs to send initially
|
||||
|
||||
nsend = nrecv;
|
||||
proclist = new int[nsend];
|
||||
work = new int[nsend];
|
||||
|
||||
for (i = 0; i < nrecv; i++) {
|
||||
src_off[i] = recv2[i].slocal;
|
||||
work[i] = recv2[i].dlocal;
|
||||
proclist[i] = recv2[i].dproc;
|
||||
}
|
||||
|
||||
irregular = new Irregular(comm);
|
||||
irregular->pattern(nsend,proclist);
|
||||
|
||||
// send receiver's local indices
|
||||
// receiver stores them as indirection list in dest_off
|
||||
|
||||
nrecv = irregular->size(sizeof(int)) / sizeof(int);
|
||||
irregular->exchange((char *) work, (char *) dest_off);
|
||||
|
||||
delete [] proclist;
|
||||
delete [] work;
|
||||
|
||||
// create work arrays for data exchange of int/double data
|
||||
|
||||
src_iwork =
|
||||
(int *) memory->smalloc(nsrc_off*sizeof(int),"many2many:src_iwork");
|
||||
dest_iwork =
|
||||
(int *) memory->smalloc(ndest_off*sizeof(int),"many2many:dest_iwork");
|
||||
src_dwork =
|
||||
(double *) memory->smalloc(nsrc_off*sizeof(double),"many2many:src_dwork");
|
||||
dest_dwork =
|
||||
(double *) memory->smalloc(ndest_off*sizeof(double),
|
||||
"many2many:dest_dwork");
|
||||
|
||||
// clean up
|
||||
|
||||
delete [] send1;
|
||||
delete [] recv1;
|
||||
delete [] send2;
|
||||
delete [] recv2;
|
||||
|
||||
// debug checks for full coverage of srd/dest - can delete eventually
|
||||
|
||||
work = new int[MAX(nsrc,ndest)];
|
||||
|
||||
for (i = 0; i < nsrc; i++) work[i] = 0;
|
||||
for (i = 0; i < nown; i++) work[src_own[i]]++;
|
||||
for (i = 0; i < nsrc_off; i++) work[src_off[i]]++;
|
||||
for (i = 0; i < nsrc; i++)
|
||||
if (work[i] != 1) {
|
||||
char str[128];
|
||||
sprintf(str,"BAD SRC %d: %d %d\n",me,i,work[i]);
|
||||
error->one(str);
|
||||
}
|
||||
|
||||
for (i = 0; i < ndest; i++) work[i] = 0;
|
||||
for (i = 0; i < nown; i++) work[dest_own[i]]++;
|
||||
for (i = 0; i < ndest_off; i++) work[dest_off[i]]++;
|
||||
for (i = 0; i < ndest; i++)
|
||||
if (work[i] != 1) {
|
||||
char str[128];
|
||||
sprintf(str,"BAD DEST %d: %d %d\n",me,i,work[i]);
|
||||
error->one(str);
|
||||
}
|
||||
|
||||
delete [] work;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
transfer one src entity to dest entity, matched by IDs in create()
|
||||
operates on an int vector
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Many2Many::exchange(int *src, int *dest)
|
||||
{
|
||||
int i;
|
||||
|
||||
// copy on-proc info
|
||||
|
||||
for (i = 0; i < nown; i++)
|
||||
dest[dest_own[i]] = src[src_own[i]];
|
||||
|
||||
// communicate off-proc info
|
||||
// user src_off and dest_off to pack/unpack data
|
||||
|
||||
if (irregular) {
|
||||
int nrecv = irregular->size(sizeof(int)) / sizeof(int);
|
||||
for (i = 0; i < nsrc_off; i++) src_iwork[i] = src[src_off[i]];
|
||||
irregular->exchange((char *) src_iwork, (char *) dest_iwork);
|
||||
for (i = 0; i < ndest_off; i++) dest[dest_off[i]] = dest_iwork[i];
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
transfer one src entity to dest entity, matched by IDs in create()
|
||||
operates on a double vector
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Many2Many::exchange(double *src, double *dest)
|
||||
{
|
||||
int i;
|
||||
|
||||
// copy on-proc info
|
||||
|
||||
for (int i = 0; i < nown; i++)
|
||||
dest[dest_own[i]] = src[src_own[i]];
|
||||
|
||||
// communicate off-proc info
|
||||
// user src_off and dest_off to pack/unpack data
|
||||
|
||||
if (irregular) {
|
||||
int nrecv = irregular->size(sizeof(double)) / sizeof(double);
|
||||
for (i = 0; i < nsrc_off; i++) src_dwork[i] = src[src_off[i]];
|
||||
irregular->exchange((char *) src_dwork, (char *) dest_dwork);
|
||||
for (i = 0; i < ndest_off; i++) dest[dest_off[i]] = dest_dwork[i];
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void Many2Many::deallocate()
|
||||
{
|
||||
memory->sfree(src_own);
|
||||
memory->sfree(dest_own);
|
||||
memory->sfree(src_off);
|
||||
memory->sfree(dest_off);
|
||||
memory->sfree(src_iwork);
|
||||
memory->sfree(dest_iwork);
|
||||
memory->sfree(src_dwork);
|
||||
memory->sfree(dest_dwork);
|
||||
|
||||
delete irregular;
|
||||
}
|
||||
|
|
@ -1,47 +0,0 @@
|
|||
#ifndef MANY2MANY_H
|
||||
#define MANY2MANY_H
|
||||
|
||||
#include "mpi.h"
|
||||
|
||||
class Many2Many {
|
||||
public:
|
||||
Many2Many(MPI_Comm);
|
||||
~Many2Many();
|
||||
|
||||
void setup(int, int *, int, int *);
|
||||
void exchange(int *, int *);
|
||||
void exchange(double *, double *);
|
||||
|
||||
protected:
|
||||
int me,nprocs;
|
||||
MPI_Comm comm;
|
||||
class Memory *memory;
|
||||
class Error *error;
|
||||
|
||||
int nown; // # of IDs common to src and dest
|
||||
int nsrc_off,ndest_off; // # of off-processor IDs
|
||||
|
||||
int *src_own,*dest_own; // indices of the owned IDs
|
||||
int *src_off,*dest_off; // indices of the off-proc IDs
|
||||
|
||||
int *src_iwork,*dest_iwork; // work arrays for comm of ints
|
||||
double *src_dwork,*dest_dwork; // work arrays for comm of doubles
|
||||
|
||||
class Irregular *irregular; // irregular comm from src->dest
|
||||
|
||||
struct Datum1 {
|
||||
int id; // src or dest global ID
|
||||
int proc; // owning proc
|
||||
int index; // local index on owning proc
|
||||
};
|
||||
|
||||
struct Datum2 {
|
||||
int slocal; // local index of src ID on sending proc
|
||||
int dlocal; // local index of dest ID on receiving proc
|
||||
int dproc; // receiving proc
|
||||
};
|
||||
|
||||
void deallocate();
|
||||
};
|
||||
|
||||
#endif
|
||||
|
|
@ -1,103 +0,0 @@
|
|||
#include "mpi.h"
|
||||
#include "stdio.h"
|
||||
#include "stdlib.h"
|
||||
#include "many2one.h"
|
||||
#include "memory.h"
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
Many2One::Many2One(MPI_Comm caller_comm)
|
||||
{
|
||||
comm = caller_comm;
|
||||
MPI_Comm_rank(comm,&me);
|
||||
MPI_Comm_size(comm,&nprocs);
|
||||
|
||||
memory = new Memory(comm);
|
||||
|
||||
if (me == 0) {
|
||||
counts = new int[nprocs];
|
||||
multicounts = new int[nprocs];
|
||||
displs = new int[nprocs];
|
||||
multidispls = new int[nprocs];
|
||||
} else counts = multicounts = displs = multidispls = NULL;
|
||||
|
||||
idall = NULL;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
Many2One::~Many2One()
|
||||
{
|
||||
delete memory;
|
||||
|
||||
delete [] counts;
|
||||
delete [] multicounts;
|
||||
delete [] displs;
|
||||
delete [] multidispls;
|
||||
|
||||
memory->sfree(idall);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void Many2One::setup(int nsrc_in, int *id, int ndest)
|
||||
{
|
||||
nsrc = nsrc_in;
|
||||
MPI_Allreduce(&nsrc,&nall,1,MPI_INT,MPI_SUM,comm);
|
||||
MPI_Gather(&nsrc,1,MPI_INT,counts,1,MPI_INT,0,comm);
|
||||
|
||||
if (me == 0) {
|
||||
displs[0] = 0;
|
||||
for (int i = 1; i < nprocs; i++)
|
||||
displs[i] = displs[i-1] + counts[i-1];
|
||||
}
|
||||
|
||||
// gather IDs into idall
|
||||
|
||||
idall = NULL;
|
||||
if (me == 0)
|
||||
idall = (int *) memory->smalloc(nall*sizeof(int),"many2one:idall");
|
||||
MPI_Gatherv(id,nsrc,MPI_INT,idall,counts,displs,MPI_INT,0,comm);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void Many2One::gather(double *src, int n, double *dest)
|
||||
{
|
||||
int i,j,ii,jj,m;
|
||||
|
||||
if (me == 0)
|
||||
for (int i = 0; i < nprocs; i++) {
|
||||
multicounts[i] = n*counts[i];
|
||||
multidispls[i] = n*displs[i];
|
||||
}
|
||||
|
||||
// allgather src into desttmp
|
||||
|
||||
double *desttmp = NULL;
|
||||
if (me == 0)
|
||||
desttmp = (double *) memory->smalloc(n*nall*sizeof(double),
|
||||
"many2one:idsttmp");
|
||||
MPI_Gatherv(src,n*nsrc,MPI_DOUBLE,desttmp,multicounts,multidispls,
|
||||
MPI_DOUBLE,0,comm);
|
||||
|
||||
// use idall to move datums from desttmp to dest
|
||||
|
||||
if (me == 0) {
|
||||
if (n == 1)
|
||||
for (i = 0; i < nall; i++) {
|
||||
j = idall[i] - 1;
|
||||
dest[j] = desttmp[i];
|
||||
}
|
||||
else
|
||||
for (i = 0; i < nall; i++) {
|
||||
j = idall[i] - 1;
|
||||
ii = n*i;
|
||||
jj = n*j;
|
||||
for (m = 0; m < n; m++)
|
||||
dest[jj++] = desttmp[ii++];
|
||||
}
|
||||
}
|
||||
|
||||
memory->sfree(desttmp);
|
||||
}
|
||||
|
|
@ -1,25 +0,0 @@
|
|||
#ifndef MANY2ONE_H
|
||||
#define MANY2ONE_H
|
||||
|
||||
#include "mpi.h"
|
||||
|
||||
class Many2One {
|
||||
public:
|
||||
Many2One(MPI_Comm);
|
||||
~Many2One();
|
||||
|
||||
void setup(int, int *, int);
|
||||
void gather(double *, int, double *);
|
||||
|
||||
protected:
|
||||
int me,nprocs;
|
||||
MPI_Comm comm;
|
||||
class Memory *memory;
|
||||
|
||||
int nsrc,nall;
|
||||
int *counts,*multicounts;
|
||||
int *displs,*multidispls;
|
||||
int *idall;
|
||||
};
|
||||
|
||||
#endif
|
||||
|
|
@ -1,120 +0,0 @@
|
|||
#include "mpi.h"
|
||||
#include "stdlib.h"
|
||||
#include "stdio.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
Memory::Memory(MPI_Comm comm)
|
||||
{
|
||||
error = new Error(comm);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
Memory::~Memory()
|
||||
{
|
||||
delete error;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
safe malloc
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void *Memory::smalloc(int n, const char *name)
|
||||
{
|
||||
if (n == 0) return NULL;
|
||||
void *ptr = malloc(n);
|
||||
if (ptr == NULL) {
|
||||
char str[128];
|
||||
sprintf(str,"Failed to allocate %d bytes for array %s",n,name);
|
||||
error->one(str);
|
||||
}
|
||||
return ptr;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
safe free
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Memory::sfree(void *ptr)
|
||||
{
|
||||
if (ptr == NULL) return;
|
||||
free(ptr);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
safe realloc
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void *Memory::srealloc(void *ptr, int n, const char *name)
|
||||
{
|
||||
if (n == 0) {
|
||||
sfree(ptr);
|
||||
return NULL;
|
||||
}
|
||||
|
||||
ptr = realloc(ptr,n);
|
||||
if (ptr == NULL) {
|
||||
char str[128];
|
||||
sprintf(str,"Failed to reallocate %d bytes for array %s",n,name);
|
||||
error->one(str);
|
||||
}
|
||||
return ptr;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
create a 2d double array
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double **Memory::create_2d_double_array(int n1, int n2, const char *name)
|
||||
|
||||
{
|
||||
double *data = (double *) smalloc(n1*n2*sizeof(double),name);
|
||||
double **array = (double **) smalloc(n1*sizeof(double *),name);
|
||||
|
||||
int n = 0;
|
||||
for (int i = 0; i < n1; i++) {
|
||||
array[i] = &data[n];
|
||||
n += n2;
|
||||
}
|
||||
|
||||
return array;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
grow or shrink 1st dim of a 2d double array
|
||||
last dim must stay the same
|
||||
if either dim is 0, return NULL
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double **Memory::grow_2d_double_array(double **array,
|
||||
int n1, int n2, const char *name)
|
||||
|
||||
{
|
||||
if (array == NULL) return create_2d_double_array(n1,n2,name);
|
||||
|
||||
double *data = (double *) srealloc(array[0],n1*n2*sizeof(double),name);
|
||||
array = (double **) srealloc(array,n1*sizeof(double *),name);
|
||||
|
||||
int n = 0;
|
||||
for (int i = 0; i < n1; i++) {
|
||||
array[i] = &data[n];
|
||||
n += n2;
|
||||
}
|
||||
|
||||
return array;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
free a 2d double array
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Memory::destroy_2d_double_array(double **array)
|
||||
|
||||
{
|
||||
if (array == NULL) return;
|
||||
sfree(array[0]);
|
||||
sfree(array);
|
||||
}
|
||||
|
|
@ -1,23 +0,0 @@
|
|||
#ifndef MEMORY_H
|
||||
#define MEMORY_H
|
||||
|
||||
#include "mpi.h"
|
||||
|
||||
class Memory {
|
||||
public:
|
||||
Memory(MPI_Comm);
|
||||
~Memory();
|
||||
|
||||
void *smalloc(int n, const char *);
|
||||
void sfree(void *);
|
||||
void *srealloc(void *, int n, const char *name);
|
||||
|
||||
double **create_2d_double_array(int, int, const char *);
|
||||
double **grow_2d_double_array(double **, int, int, const char *);
|
||||
void destroy_2d_double_array(double **);
|
||||
|
||||
private:
|
||||
class Error *error;
|
||||
};
|
||||
|
||||
#endif
|
||||
|
|
@ -1,76 +0,0 @@
|
|||
#include "mpi.h"
|
||||
#include "one2many.h"
|
||||
#include "memory.h"
|
||||
|
||||
#include <map>
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
One2Many::One2Many(MPI_Comm caller_comm)
|
||||
{
|
||||
comm = caller_comm;
|
||||
MPI_Comm_rank(comm,&me);
|
||||
MPI_Comm_size(comm,&nprocs);
|
||||
|
||||
memory = new Memory(comm);
|
||||
hash = new std::map<int,int>();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
One2Many::~One2Many()
|
||||
{
|
||||
delete memory;
|
||||
delete hash;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void One2Many::setup(int nsrc_in, int ndest, int *id)
|
||||
{
|
||||
nsrc = nsrc_in;
|
||||
|
||||
// store my local IDs in hash
|
||||
|
||||
hash->clear();
|
||||
for (int i = 0; i < ndest; i++)
|
||||
hash->insert(std::pair<int,int> (id[i],i));
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void One2Many::scatter(double *src, int n, double *dest)
|
||||
{
|
||||
int i,j,k,m;
|
||||
|
||||
// allocate src on procs that don't have it
|
||||
|
||||
int flag = 0;
|
||||
if (src == NULL) {
|
||||
src = (double *) memory->smalloc(n*nsrc*sizeof(double),"one2many:src");
|
||||
flag = 1;
|
||||
}
|
||||
|
||||
// broadcast src from 0 to other procs
|
||||
|
||||
MPI_Bcast(src,n*nsrc,MPI_DOUBLE,0,comm);
|
||||
|
||||
// each proc loops over entire src
|
||||
// if I own the global ID, copy src values into dest
|
||||
|
||||
std::map<int,int>::iterator loc;
|
||||
for (m = 1; m <= nsrc; m++) {
|
||||
loc = hash->find(m);
|
||||
if (loc == hash->end()) continue;
|
||||
i = n*loc->second;
|
||||
j = 3*(m-1);
|
||||
if (n == 1) dest[i] = src[j];
|
||||
else
|
||||
for (k = 0; k < n; k++)
|
||||
dest[i++] = src[j++];
|
||||
}
|
||||
|
||||
// free locally allocated src
|
||||
|
||||
if (flag) memory->sfree(src);
|
||||
}
|
||||
|
|
@ -1,24 +0,0 @@
|
|||
#ifndef ONE2MANY_H
|
||||
#define ONE2MANY_H
|
||||
|
||||
#include "mpi.h"
|
||||
|
||||
#include <map>
|
||||
|
||||
class One2Many {
|
||||
public:
|
||||
One2Many(MPI_Comm);
|
||||
~One2Many();
|
||||
|
||||
void setup(int, int, int *);
|
||||
void scatter(double *, int, double *);
|
||||
|
||||
protected:
|
||||
int me,nprocs;
|
||||
MPI_Comm comm;
|
||||
class Memory *memory;
|
||||
std::map<int,int> *hash;
|
||||
int nsrc;
|
||||
};
|
||||
|
||||
#endif
|
||||
|
|
@ -1,83 +0,0 @@
|
|||
#include "mpi.h"
|
||||
#include "stdlib.h"
|
||||
#include "stdio.h"
|
||||
#include "send2one.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
Send2One::Send2One(MPI_Comm caller_comm)
|
||||
{
|
||||
comm = caller_comm;
|
||||
MPI_Comm_rank(comm,&me);
|
||||
MPI_Comm_size(comm,&nprocs);
|
||||
|
||||
memory = new Memory(comm);
|
||||
error = new Error(comm);
|
||||
|
||||
buf = NULL;
|
||||
maxbuf = 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
Send2One::~Send2One()
|
||||
{
|
||||
delete memory;
|
||||
delete error;
|
||||
memory->sfree(buf);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void Send2One::execute()
|
||||
{
|
||||
int nme,nmax,nsize,ping;
|
||||
MPI_Status status;
|
||||
MPI_Request request;
|
||||
|
||||
// pre-processing before ping loop
|
||||
|
||||
pre();
|
||||
|
||||
// nme = size of data I contribute, in bytes
|
||||
// nmax = max size of data on any proc, in bytes
|
||||
// reallocate buf if necessary
|
||||
|
||||
nme = size();
|
||||
MPI_Allreduce(&nme,&nmax,1,MPI_INT,MPI_MAX,comm);
|
||||
|
||||
if (nmax > maxbuf) {
|
||||
maxbuf = nmax;
|
||||
memory->sfree(buf);
|
||||
buf = (char *) memory->smalloc(maxbuf,"foo:buf");
|
||||
}
|
||||
|
||||
// pack my data into buf
|
||||
|
||||
pack(buf);
|
||||
|
||||
// proc 0 pings each proc, receives its data
|
||||
// all other procs wait for ping, send their data to proc 0
|
||||
// invoke process() to work with data
|
||||
|
||||
if (me == 0) {
|
||||
for (int iproc = 0; iproc < nprocs; iproc++) {
|
||||
if (iproc) {
|
||||
MPI_Irecv(buf,maxbuf,MPI_CHAR,iproc,0,comm,&request);
|
||||
MPI_Send(&ping,0,MPI_INT,iproc,0,comm);
|
||||
MPI_Wait(&request,&status);
|
||||
MPI_Get_count(&status,MPI_CHAR,&nsize);
|
||||
} else nsize = nme;
|
||||
|
||||
process(nsize,buf);
|
||||
}
|
||||
|
||||
} else {
|
||||
MPI_Recv(&ping,0,MPI_INT,0,0,comm,&status);
|
||||
MPI_Rsend(buf,nme,MPI_CHAR,0,0,comm);
|
||||
}
|
||||
|
||||
post();
|
||||
}
|
||||
|
|
@ -1,29 +0,0 @@
|
|||
#ifndef SEND2ONE_H
|
||||
#define SEND2ONE_H
|
||||
|
||||
#include "mpi.h"
|
||||
|
||||
class Send2One {
|
||||
public:
|
||||
Send2One(MPI_Comm);
|
||||
virtual ~Send2One();
|
||||
|
||||
void execute();
|
||||
|
||||
protected:
|
||||
int me,nprocs;
|
||||
MPI_Comm comm;
|
||||
class Memory *memory;
|
||||
class Error *error;
|
||||
|
||||
int maxbuf;
|
||||
char *buf;
|
||||
|
||||
virtual void pre() = 0;
|
||||
virtual int size() = 0;
|
||||
virtual void pack(char *) = 0;
|
||||
virtual void process(int, char *) = 0;
|
||||
virtual void post() = 0;
|
||||
};
|
||||
|
||||
#endif
|
||||
|
|
@ -1,78 +0,0 @@
|
|||
This directory has a simple C, C++, and Fortran 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.cpp is the C++ driver
|
||||
simple.c is the C driver
|
||||
simple.f90 is the Fortran driver
|
||||
libfwrapper.c is the Fortran-to-C wrapper
|
||||
|
||||
The 3 codes do the same thing, so you can compare them to see how to
|
||||
drive LAMMPS in this manner. The C driver is similar in spirit to what
|
||||
one could use to write a scripting language interface. The Fortran
|
||||
driver in addition requires a wrapper library that interfaces the C
|
||||
interface of the LAMMPS library to Fortran and also translates the MPI
|
||||
communicator from Fortran to C.
|
||||
|
||||
You can then build either driver code with a compile line something
|
||||
like this, which includes paths to the LAMMPS library interface, MPI,
|
||||
and FFTW (assuming you built LAMMPS as a library with its PPPM
|
||||
solver).
|
||||
|
||||
This builds the C++ driver with the LAMMPS library using a C++ compiler:
|
||||
|
||||
g++ -I/home/sjplimp/lammps/src -c simple.cpp
|
||||
g++ -L/home/sjplimp/lammps/src simple.o \
|
||||
-llmp_g++ -lfftw -lmpich -lmpl -lpthread -o simpleCC
|
||||
|
||||
This builds the C driver with the LAMMPS library using a C compiler:
|
||||
|
||||
gcc -I/home/sjplimp/lammps/src -c simple.c
|
||||
gcc -L/home/sjplimp/lammps/src simple.o \
|
||||
-llmp_g++ -lfftw -lmpich -lmpl -lpthread -lstdc++ -o simpleC
|
||||
|
||||
This builds the Fortran wrapper and driver with the LAMMPS library
|
||||
using a Fortran and C compiler:
|
||||
|
||||
cp ../fortran/libfwrapper.c .
|
||||
gcc -I/home/sjplimp/lammps/src -c libfwrapper.c
|
||||
gfortran -I/home/sjplimp/lammps/src -c simple.f90
|
||||
gfortran -L/home/sjplimp/lammps/src simple.o libfwrapper.o \
|
||||
-llmp_g++ -lfftw -lfmpich -lmpich -lpthread -lstdc++ -o simpleF
|
||||
|
||||
You then run simpleCC, simpleC, or simpleF on a parallel machine
|
||||
on some number of processors Q with 2 arguments:
|
||||
|
||||
mpirun -np Q simpleCC P in.lj
|
||||
|
||||
P is the number of procs you want LAMMPS to run on (must be <= Q) and
|
||||
in.lj is a LAMMPS input script.
|
||||
|
||||
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. You could add any functions you wish to this file to
|
||||
manipulate LAMMPS data however you wish.
|
||||
|
||||
The Fortran driver is using the same C-style routines, but requires an
|
||||
additional wrapper to make them Fortran callable. Only a subset of the
|
||||
library functions are currently wrapped, but it should be clear how to
|
||||
extend the wrapper if desired.
|
||||
|
||||
The C++ driver does the same thing, except that it instantiates LAMMPS
|
||||
as an object first. Some of the functions in src/library.cpp can be
|
||||
invoked directly as methods within appropriate LAMMPS classes, which
|
||||
is what the driver does. Any public LAMMPS class method could be
|
||||
called from the driver this way. However the get/put functions are
|
||||
only implemented in src/library.cpp, so the C++ driver calls them as
|
||||
C-style functions.
|
||||
|
|
@ -1,24 +0,0 @@
|
|||
# 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
|
||||
|
||||
run 10
|
||||
|
||||
|
|
@ -1,124 +0,0 @@
|
|||
LAMMPS (20 Sep 2010)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
|
||||
|
||||
units lj
|
||||
|
||||
atom_style atomic
|
||||
|
||||
atom_modify map array
|
||||
|
||||
|
||||
|
||||
lattice fcc 0.8442
|
||||
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 4 0 4 0 4
|
||||
|
||||
create_box 1 box
|
||||
|
||||
Created orthogonal box = (0 0 0) to (6.71838 6.71838 6.71838)
|
||||
1 by 1 by 1 processor grid
|
||||
create_atoms 1 box
|
||||
|
||||
Created 256 atoms
|
||||
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
|
||||
|
||||
|
||||
|
||||
run 10
|
||||
|
||||
Memory usage per processor = 1.50139 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 0.00370193 on 1 procs for 10 steps with 256 atoms
|
||||
|
||||
Pair time (%) = 0.00340414 (91.9559)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000165701 (4.47607)
|
||||
Outpt time (%) = 2.31266e-05 (0.624718)
|
||||
Other time (%) = 0.000108957 (2.94326)
|
||||
|
||||
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 = 0
|
||||
|
||||
|
||||
run 10
|
||||
Memory usage per processor = 1.50139 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 0.00365806 on 1 procs for 10 steps with 256 atoms
|
||||
|
||||
Pair time (%) = 0.0033741 (92.2375)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000161886 (4.42547)
|
||||
Outpt time (%) = 1.09673e-05 (0.299811)
|
||||
Other time (%) = 0.000111103 (3.03722)
|
||||
|
||||
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 = 0
|
||||
run 1
|
||||
Memory usage per processor = 1.50139 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 0.000490904 on 1 procs for 1 steps with 256 atoms
|
||||
|
||||
Pair time (%) = 0.000452042 (92.0835)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 1.69277e-05 (3.44828)
|
||||
Outpt time (%) = 1.00136e-05 (2.03983)
|
||||
Other time (%) = 1.19209e-05 (2.42836)
|
||||
|
||||
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 = 0
|
||||
|
|
@ -1,124 +0,0 @@
|
|||
LAMMPS (20 Sep 2010)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
|
||||
|
||||
units lj
|
||||
|
||||
atom_style atomic
|
||||
|
||||
atom_modify map array
|
||||
|
||||
|
||||
|
||||
lattice fcc 0.8442
|
||||
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 4 0 4 0 4
|
||||
|
||||
create_box 1 box
|
||||
|
||||
Created orthogonal box = (0 0 0) to (6.71838 6.71838 6.71838)
|
||||
1 by 2 by 2 processor grid
|
||||
create_atoms 1 box
|
||||
|
||||
Created 256 atoms
|
||||
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
|
||||
|
||||
|
||||
|
||||
run 10
|
||||
|
||||
Memory usage per processor = 1.48354 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 0.00202775 on 4 procs for 10 steps with 256 atoms
|
||||
|
||||
Pair time (%) = 0.00085938 (42.381)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.00108671 (53.592)
|
||||
Outpt time (%) = 2.79546e-05 (1.3786)
|
||||
Other time (%) = 5.37038e-05 (2.64844)
|
||||
|
||||
Nlocal: 64 ave 64 max 64 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 843 ave 843 max 843 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2496 ave 2496 max 2496 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9984
|
||||
Ave neighs/atom = 39
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
run 10
|
||||
Memory usage per processor = 1.48354 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 0.00224167 on 4 procs for 10 steps with 256 atoms
|
||||
|
||||
Pair time (%) = 0.000862718 (38.4855)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.00127524 (56.888)
|
||||
Outpt time (%) = 5.19753e-05 (2.31859)
|
||||
Other time (%) = 5.17368e-05 (2.30796)
|
||||
|
||||
Nlocal: 64 ave 69 max 59 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Nghost: 843 ave 848 max 838 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Neighs: 2488 ave 2745 max 2319 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 9952
|
||||
Ave neighs/atom = 38.875
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
run 1
|
||||
Memory usage per processor = 1.48354 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 0.000325441 on 4 procs for 1 steps with 256 atoms
|
||||
|
||||
Pair time (%) = 0.000120759 (37.1062)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000165045 (50.7143)
|
||||
Outpt time (%) = 2.86698e-05 (8.80952)
|
||||
Other time (%) = 1.09673e-05 (3.36996)
|
||||
|
||||
Nlocal: 64 ave 70 max 58 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 843 ave 849 max 837 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Neighs: 2426.25 ave 2704 max 2229 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 9705
|
||||
Ave neighs/atom = 37.9102
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
|
@ -1,116 +0,0 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
www.cs.sandia.gov/~sjplimp/lammps.html
|
||||
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* c_driver = simple example of how an umbrella program
|
||||
can invoke LAMMPS as a library on some subset of procs
|
||||
Syntax: c_driver P in.lammps
|
||||
P = # of procs to run LAMMPS on
|
||||
must be <= # of procs the driver code itself runs on
|
||||
in.lammps = LAMMPS input script
|
||||
See README for compilation instructions */
|
||||
|
||||
#include "stdio.h"
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "mpi.h"
|
||||
#include "library.h" /* this is a LAMMPS include file */
|
||||
|
||||
int main(int narg, char **arg)
|
||||
{
|
||||
/* setup MPI and various communicators
|
||||
driver runs on all procs in MPI_COMM_WORLD
|
||||
comm_lammps only has 1st P procs (could be all or any subset) */
|
||||
|
||||
MPI_Init(&narg,&arg);
|
||||
|
||||
if (narg != 3) {
|
||||
printf("Syntax: c_driver P in.lammps\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
int me,nprocs;
|
||||
MPI_Comm_rank(MPI_COMM_WORLD,&me);
|
||||
MPI_Comm_size(MPI_COMM_WORLD,&nprocs);
|
||||
|
||||
int nprocs_lammps = atoi(arg[1]);
|
||||
if (nprocs_lammps > nprocs) {
|
||||
if (me == 0)
|
||||
printf("ERROR: LAMMPS cannot use more procs than available\n");
|
||||
MPI_Abort(MPI_COMM_WORLD,1);
|
||||
}
|
||||
|
||||
int lammps;
|
||||
if (me < nprocs_lammps) lammps = 1;
|
||||
else lammps = MPI_UNDEFINED;
|
||||
MPI_Comm comm_lammps;
|
||||
MPI_Comm_split(MPI_COMM_WORLD,lammps,0,&comm_lammps);
|
||||
|
||||
/* open LAMMPS input script */
|
||||
|
||||
FILE *fp;
|
||||
if (me == 0) {
|
||||
fp = fopen(arg[2],"r");
|
||||
if (fp == NULL) {
|
||||
printf("ERROR: Could not open LAMMPS input script\n");
|
||||
MPI_Abort(MPI_COMM_WORLD,1);
|
||||
}
|
||||
}
|
||||
|
||||
/* run the input script thru LAMMPS one line at a time until end-of-file
|
||||
driver proc 0 reads a line, Bcasts it to all procs
|
||||
(could just send it to proc 0 of comm_lammps and let it Bcast)
|
||||
all LAMMPS procs call lammps_command() on the line */
|
||||
|
||||
void *ptr;
|
||||
if (lammps == 1) lammps_open(0,NULL,comm_lammps,&ptr);
|
||||
|
||||
int n;
|
||||
char line[1024];
|
||||
while (1) {
|
||||
if (me == 0) {
|
||||
if (fgets(line,1024,fp) == NULL) n = 0;
|
||||
else n = strlen(line) + 1;
|
||||
if (n == 0) fclose(fp);
|
||||
}
|
||||
MPI_Bcast(&n,1,MPI_INT,0,MPI_COMM_WORLD);
|
||||
if (n == 0) break;
|
||||
MPI_Bcast(line,n,MPI_CHAR,0,MPI_COMM_WORLD);
|
||||
if (lammps == 1) lammps_command(ptr,line);
|
||||
}
|
||||
|
||||
/* run 10 more steps
|
||||
get coords from LAMMPS
|
||||
change coords of 1st atom
|
||||
put coords back into LAMMPS
|
||||
run a single step with changed coords */
|
||||
|
||||
if (lammps == 1) {
|
||||
lammps_command(ptr,"run 10");
|
||||
|
||||
int natoms = lammps_get_natoms(ptr);
|
||||
double *x = (double *) malloc(3*natoms*sizeof(double));
|
||||
lammps_get_coords(ptr,x);
|
||||
double epsilon = 0.1;
|
||||
x[0] += epsilon;
|
||||
lammps_put_coords(ptr,x);
|
||||
free(x);
|
||||
|
||||
lammps_command(ptr,"run 1");
|
||||
}
|
||||
|
||||
if (lammps == 1) lammps_close(ptr);
|
||||
|
||||
/* close down MPI */
|
||||
|
||||
MPI_Finalize();
|
||||
}
|
||||
|
|
@ -1,121 +0,0 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
www.cs.sandia.gov/~sjplimp/lammps.html
|
||||
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
// c++_driver = simple example of how an umbrella program
|
||||
// can invoke LAMMPS as a library on some subset of procs
|
||||
// Syntax: c++_driver P in.lammps
|
||||
// P = # of procs to run LAMMPS on
|
||||
// must be <= # of procs the driver code itself runs on
|
||||
// in.lammps = LAMMPS input script
|
||||
// See README for compilation instructions
|
||||
|
||||
#include "stdio.h"
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "mpi.h"
|
||||
#include "lammps.h" // these are LAMMPS include files
|
||||
#include "input.h"
|
||||
#include "atom.h"
|
||||
#include "library.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
int main(int narg, char **arg)
|
||||
{
|
||||
// setup MPI and various communicators
|
||||
// driver runs on all procs in MPI_COMM_WORLD
|
||||
// comm_lammps only has 1st P procs (could be all or any subset)
|
||||
|
||||
MPI_Init(&narg,&arg);
|
||||
|
||||
if (narg != 3) {
|
||||
printf("Syntax: c++_driver P in.lammps\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
int me,nprocs;
|
||||
MPI_Comm_rank(MPI_COMM_WORLD,&me);
|
||||
MPI_Comm_size(MPI_COMM_WORLD,&nprocs);
|
||||
|
||||
int nprocs_lammps = atoi(arg[1]);
|
||||
if (nprocs_lammps > nprocs) {
|
||||
if (me == 0)
|
||||
printf("ERROR: LAMMPS cannot use more procs than available\n");
|
||||
MPI_Abort(MPI_COMM_WORLD,1);
|
||||
}
|
||||
|
||||
int lammps;
|
||||
if (me < nprocs_lammps) lammps = 1;
|
||||
else lammps = MPI_UNDEFINED;
|
||||
MPI_Comm comm_lammps;
|
||||
MPI_Comm_split(MPI_COMM_WORLD,lammps,0,&comm_lammps);
|
||||
|
||||
// open LAMMPS input script
|
||||
|
||||
FILE *fp;
|
||||
if (me == 0) {
|
||||
fp = fopen(arg[2],"r");
|
||||
if (fp == NULL) {
|
||||
printf("ERROR: Could not open LAMMPS input script\n");
|
||||
MPI_Abort(MPI_COMM_WORLD,1);
|
||||
}
|
||||
}
|
||||
|
||||
// run the input script thru LAMMPS one line at a time until end-of-file
|
||||
// driver proc 0 reads a line, Bcasts it to all procs
|
||||
// (could just send it to proc 0 of comm_lammps and let it Bcast)
|
||||
// all LAMMPS procs call input->one() on the line
|
||||
|
||||
LAMMPS *lmp;
|
||||
if (lammps == 1) lmp = new LAMMPS(0,NULL,comm_lammps);
|
||||
|
||||
int n;
|
||||
char line[1024];
|
||||
while (1) {
|
||||
if (me == 0) {
|
||||
if (fgets(line,1024,fp) == NULL) n = 0;
|
||||
else n = strlen(line) + 1;
|
||||
if (n == 0) fclose(fp);
|
||||
}
|
||||
MPI_Bcast(&n,1,MPI_INT,0,MPI_COMM_WORLD);
|
||||
if (n == 0) break;
|
||||
MPI_Bcast(line,n,MPI_CHAR,0,MPI_COMM_WORLD);
|
||||
if (lammps == 1) lmp->input->one(line);
|
||||
}
|
||||
|
||||
// run 10 more steps
|
||||
// get coords from LAMMPS
|
||||
// change coords of 1st atom
|
||||
// put coords back into LAMMPS
|
||||
// run a single step with changed coords
|
||||
|
||||
if (lammps == 1) {
|
||||
lmp->input->one("run 10");
|
||||
|
||||
int natoms = static_cast<int> (lmp->atom->natoms);
|
||||
double *x = new double[3*natoms];
|
||||
lammps_get_coords(lmp,x); // no LAMMPS class function for this
|
||||
double epsilon = 0.1;
|
||||
x[0] += epsilon;
|
||||
lammps_put_coords(lmp,x); // no LAMMPS class function for this
|
||||
delete [] x;
|
||||
|
||||
lmp->input->one("run 1");
|
||||
}
|
||||
|
||||
if (lammps == 1) delete lmp;
|
||||
|
||||
// close down MPI
|
||||
|
||||
MPI_Finalize();
|
||||
}
|
||||
|
|
@ -1,135 +0,0 @@
|
|||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
! www.cs.sandia.gov/~sjplimp/lammps.html
|
||||
! Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
!
|
||||
! 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.
|
||||
|
||||
! f_driver = simple example of how an umbrella program
|
||||
! can invoke LAMMPS as a library on some subset of procs
|
||||
! Syntax: f_driver P in.lammps
|
||||
! P = # of procs to run LAMMPS on
|
||||
! must be <= # of procs the driver code itself runs on
|
||||
! in.lammps = LAMMPS input script
|
||||
! See README for compilation instructions
|
||||
|
||||
PROGRAM f_driver
|
||||
IMPLICIT NONE
|
||||
INCLUDE 'mpif.h'
|
||||
|
||||
INTEGER, PARAMETER :: fp=20
|
||||
INTEGER :: n, narg, ierr, me, nprocs, natoms
|
||||
INTEGER :: lammps, nprocs_lammps, comm_lammps
|
||||
INTEGER (kind=8) :: ptr
|
||||
|
||||
REAL (kind=8), ALLOCATABLE :: x(:)
|
||||
REAL (kind=8), PARAMETER :: epsilon=0.1
|
||||
|
||||
CHARACTER (len=64) :: arg
|
||||
CHARACTER (len=1024) :: line
|
||||
|
||||
! setup MPI and various communicators
|
||||
! driver runs on all procs in MPI_COMM_WORLD
|
||||
! comm_lammps only has 1st P procs (could be all or any subset)
|
||||
|
||||
CALL mpi_init(ierr)
|
||||
|
||||
narg = command_argument_count()
|
||||
|
||||
IF (narg /= 2) THEN
|
||||
PRINT *, 'Syntax: f_driver P in.lammps'
|
||||
CALL mpi_abort(MPI_COMM_WORLD,1,ierr)
|
||||
END IF
|
||||
|
||||
CALL mpi_comm_rank(MPI_COMM_WORLD,me,ierr);
|
||||
CALL mpi_comm_size(MPI_COMM_WORLD,nprocs,ierr);
|
||||
|
||||
CALL get_command_argument(1,arg)
|
||||
READ (arg,'(I10)') nprocs_lammps
|
||||
|
||||
IF (nprocs_lammps > nprocs) THEN
|
||||
IF (me == 0) THEN
|
||||
PRINT *, 'ERROR: LAMMPS cannot use more procs than available'
|
||||
CALL mpi_abort(MPI_COMM_WORLD,2,ierr)
|
||||
END IF
|
||||
END IF
|
||||
|
||||
lammps = 0
|
||||
IF (me < nprocs_lammps) THEN
|
||||
lammps = 1
|
||||
ELSE
|
||||
lammps = MPI_UNDEFINED
|
||||
END IF
|
||||
|
||||
CALL mpi_comm_split(MPI_COMM_WORLD,lammps,0,comm_lammps,ierr)
|
||||
|
||||
! open LAMMPS input script on rank zero
|
||||
|
||||
CALL get_command_argument(2,arg)
|
||||
OPEN(UNIT=fp, FILE=arg, ACTION='READ', STATUS='OLD', IOSTAT=ierr)
|
||||
IF (ierr /= 0) THEN
|
||||
PRINT *, 'ERROR: Could not open LAMMPS input script'
|
||||
CALL mpi_abort(MPI_COMM_WORLD,3,ierr);
|
||||
END IF
|
||||
|
||||
! run the input script thru LAMMPS one line at a time until end-of-file
|
||||
! driver proc 0 reads a line, Bcasts it to all procs
|
||||
! (could just send it to proc 0 of comm_lammps and let it Bcast)
|
||||
! all LAMMPS procs call lammps_command() on the line */
|
||||
|
||||
IF (lammps == 1) CALL lammps_open(comm_lammps,ptr)
|
||||
|
||||
n = 0
|
||||
DO
|
||||
IF (me == 0) THEN
|
||||
READ (UNIT=fp, FMT='(A)', IOSTAT=ierr) line
|
||||
n = 0
|
||||
IF (ierr == 0) THEN
|
||||
n = LEN(TRIM(line))
|
||||
IF (n == 0 ) THEN
|
||||
line = ' '
|
||||
n = 1
|
||||
END IF
|
||||
END IF
|
||||
END IF
|
||||
CALL mpi_bcast(n,1,MPI_INTEGER,0,MPI_COMM_WORLD,ierr)
|
||||
IF (n == 0) EXIT
|
||||
CALL mpi_bcast(line,n,MPI_CHARACTER,0,MPI_COMM_WORLD,ierr)
|
||||
IF (lammps == 1) CALL lammps_command(ptr,line,n)
|
||||
END DO
|
||||
CLOSE(UNIT=fp)
|
||||
|
||||
! run 10 more steps
|
||||
! get coords from LAMMPS
|
||||
! change coords of 1st atom
|
||||
! put coords back into LAMMPS
|
||||
! run a single step with changed coords */
|
||||
|
||||
IF (lammps == 1) THEN
|
||||
CALL lammps_command(ptr,'run 10',6)
|
||||
|
||||
CALL lammps_get_natoms(ptr,natoms)
|
||||
ALLOCATE(x(3*natoms))
|
||||
|
||||
CALL lammps_get_coords(ptr,x)
|
||||
x(1) = x(1) + epsilon
|
||||
CALL lammps_put_coords(ptr,x)
|
||||
|
||||
DEALLOCATE(x)
|
||||
|
||||
CALL lammps_command(ptr,'run 1',5);
|
||||
END IF
|
||||
|
||||
! free LAMMPS object
|
||||
|
||||
IF (lammps == 1) CALL lammps_close(ptr);
|
||||
|
||||
! close down MPI
|
||||
|
||||
CALL mpi_finalize(ierr)
|
||||
|
||||
END PROGRAM f_driver
|
||||
|
|
@ -11,19 +11,22 @@
|
|||
This section describes how to build and use LAMMPS via a Python
|
||||
interface.
|
||||
|
||||
11.1 "Extending Python with a serial version of LAMMPS"_#py_1
|
||||
11.2 "Creating a shared MPI library"_#py_2
|
||||
11.3 "Extending Python with a parallel version of LAMMPS"_#py_3
|
||||
11.4 "Extending Python with MPI"_#py_4
|
||||
11.5 "Testing the Python-LAMMPS interface"_#py_5
|
||||
11.6 "Using LAMMPS from Python"_#py_6
|
||||
11.7 "Example Python scripts that use LAMMPS"_#py_7 :ul
|
||||
11.1 "Setting necessary environment variables"_#py_1
|
||||
11.2 "Building LAMMPS as a shared library"_#py_2
|
||||
11.3 "Extending Python with MPI"_#py_3
|
||||
11.4 "Testing the Python-LAMMPS interface"_#py_4
|
||||
11.5 "Using LAMMPS from Python"_#py_5
|
||||
11.6 "Example Python scripts that use LAMMPS"_#py_6 :ul
|
||||
|
||||
The LAMMPS distribution includes some Python code in its python
|
||||
directory which wraps the library interface to LAMMPS. This makes it
|
||||
is possible to run LAMMPS, invoke LAMMPS commands or give it an input
|
||||
script, extract LAMMPS results, an modify internal LAMMPS variables,
|
||||
either from a Python script or interactively from a Python prompt.
|
||||
The LAMMPS distribution includes the file python/lammps.py which wraps
|
||||
the library interface to LAMMPS. This file makes it is possible to
|
||||
run LAMMPS, invoke LAMMPS commands or give it an input script, extract
|
||||
LAMMPS results, an modify internal LAMMPS variables, either from a
|
||||
Python script or interactively from a Python prompt. You can do the
|
||||
former in serial or parallel. Running Python interactively in
|
||||
parallel does not generally work, unless you have a package installed
|
||||
that extends your Python to enable multiple instances of Python to
|
||||
read what you type.
|
||||
|
||||
"Python"_http://www.python.org is a powerful scripting and programming
|
||||
language which can be used to wrap software like LAMMPS and other
|
||||
|
|
@ -37,75 +40,116 @@ section"_Section_howto.html#howto_19 for a description of the library
|
|||
interface provided in src/library.cpp and src/library.h and how to
|
||||
extend it for your needs. As described below, that interface is what
|
||||
is exposed to Python. It is designed to be easy to add functions to.
|
||||
This has the effect of extending the Python inteface as well. See
|
||||
details below.
|
||||
This can easily extend the Python inteface as well. See details
|
||||
below.
|
||||
|
||||
By using the Python interface LAMMPS can also be coupled with a GUI or
|
||||
visualization tools that display graphs or animations in real time as
|
||||
LAMMPS runs. Examples of such scripts are inlcluded in the python
|
||||
directory.
|
||||
By using the Python interface, LAMMPS can also be coupled with a GUI
|
||||
or other visualization tools that display graphs or animations in real
|
||||
time as LAMMPS runs. Examples of such scripts are inlcluded in the
|
||||
python directory.
|
||||
|
||||
Two advantages of using Python are how concise the language is and
|
||||
Two advantages of using Python are how concise the language is, and
|
||||
that it can be run interactively, enabling rapid development and
|
||||
debugging of programs. If you use it to mostly invoke costly
|
||||
operations within LAMMPS, such as running a simulation for a
|
||||
reasonable number of timesteps, then the overhead cost of invoking
|
||||
LAMMPS thru Python will be negligible.
|
||||
|
||||
Before using LAMMPS from a Python script, the Python on your machine
|
||||
must be "extended" to include an interface to the LAMMPS library. If
|
||||
your Python script will invoke MPI operations, you will also need to
|
||||
extend your Python with an interface to MPI itself.
|
||||
Before using LAMMPS from a Python script, you have to do two things.
|
||||
You need to set two environment variables. And you need to build
|
||||
LAMMPS as a dynamic shared library, so it can be loaded by Python.
|
||||
Both these steps are discussed below.
|
||||
|
||||
Thus you should first decide how you intend to use LAMMPS from Python.
|
||||
There are 3 options:
|
||||
The Python wrapper for LAMMPS uses the amazing and magical (to me)
|
||||
"ctypes" package in Python, which auto-generates the interface code
|
||||
needed between Python and a set of C interface routines for a library.
|
||||
Ctypes is part of standard Python for versions 2.5 and later. You can
|
||||
check which version of Python you have installed, by simply typing
|
||||
"python" at a shell prompt.
|
||||
|
||||
(1) Use LAMMPS on a single processor running Python.
|
||||
:line
|
||||
:line
|
||||
|
||||
(2) Use LAMMPS in parallel, where each processor runs Python, but your
|
||||
Python program does not use MPI.
|
||||
11.1 Setting necessary environment variables :link(py_1),h4
|
||||
|
||||
(3) Use LAMMPS in parallel, where each processor runs Python, and your
|
||||
Python script also makes MPI calls through a Python/MPI interface.
|
||||
For Python to use the LAMMPS interface, it needs to find two files.
|
||||
The paths to these files need to be added to two environment variables
|
||||
that Python checks.
|
||||
|
||||
Note that for (2) and (3) you will not be able to use Python
|
||||
interactively by typing commands and getting a response. This is
|
||||
because you will have multiple instances of Python running (e.g. on a
|
||||
parallel machine) and they cannot all read what you type.
|
||||
The first is the environment variable PYTHONPATH. It needs
|
||||
to include the directory where the python/lammps.py file is.
|
||||
|
||||
For the csh or tcsh shells, you could add something like this to your
|
||||
~/.cshrc file:
|
||||
|
||||
setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python :pre
|
||||
|
||||
The second is the environment variable LD_LIBRARY_PATH, which is used
|
||||
by the operating system to find dynamic shared libraries when it loads
|
||||
them. It needs to include the directory where the shared LAMMPS
|
||||
library will be. Normally this is the LAMMPS src dir, as explained in
|
||||
the following section.
|
||||
|
||||
For the csh or tcsh shells, you could add something like this to your
|
||||
~/.cshrc file:
|
||||
|
||||
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src :pre
|
||||
|
||||
Note that a LAMMPS build may depend on several auxiliary libraries,
|
||||
which are specied in your low-level src/Makefile.foo file. For
|
||||
example, an MPI library, the FFTW library, a JPEG library, etc.
|
||||
Depending on what LAMMPS packages you have installed, you may
|
||||
pre-build additional libraries in the lib directories, which are linked
|
||||
to in your LAMMPS build.
|
||||
|
||||
As discussed below, in you are including those options in LAMMPS, all
|
||||
of the auxiliary libraries have to be available as shared libraries
|
||||
for Python to successfully load LAMMPS. If they are not in default
|
||||
places where the operating system can find them, then you also have to
|
||||
add their paths to the LD_LIBRARY_PATH environment variable.
|
||||
|
||||
For example, if you are using the dummy MPI library provided in
|
||||
src/STUBS, you need to add something like this to your ~/.cshrc file:
|
||||
|
||||
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src/STUBS :pre
|
||||
|
||||
If you are using the LAMMPS USER-ATC package, you need to add
|
||||
something like this to your ~/.cshrc file:
|
||||
|
||||
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/lib/atc :pre
|
||||
|
||||
:line
|
||||
|
||||
11.2 Building LAMMPS as a shared library :link(py_2),h4
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
A shared library is one that is dynamically loadable, which is what
|
||||
Python requires. On Linux this is a library file that ends in ".so",
|
||||
not ".a". Such a shared library is normally not built if you
|
||||
installed MPI yourself, but it is easy to do. Here is how to do it
|
||||
for "MPICH"_mpich, a popular open-source version of MPI, distributed
|
||||
by Argonne National Labs. From within the mpich directory, type
|
||||
|
||||
:link(mpich,http://www-unix.mcs.anl.gov/mpi)
|
||||
|
||||
./configure --enable-shared
|
||||
make
|
||||
make install :pre
|
||||
|
||||
You may need to use "sudo make install" in place of the last line.
|
||||
The end result should be the file libmpich.so in /usr/local/lib.
|
||||
|
||||
Working in mode (1) does not require your machine to have MPI
|
||||
installed. You should extend your Python with a serial version of
|
||||
LAMMPS and the dummy MPI library provided with LAMMPS. See
|
||||
instructions below on how to do this.
|
||||
|
||||
Working in mode (2) requires your machine to have an MPI library
|
||||
installed, but your Python does not need to be extended with MPI
|
||||
itself. The MPI library must be a shared library (e.g. a *.so file on
|
||||
Linux) which is not typically created when MPI is built/installed.
|
||||
See instruction below on how to do this. You should extend your
|
||||
Python with the a parallel versionn of LAMMPS which will use the
|
||||
shared MPI system library. See instructions below on how to do this.
|
||||
|
||||
Working in mode (3) requires your machine to have MPI installed (as a
|
||||
shared library as in (2)). You must also extend your Python with a
|
||||
parallel version of LAMMPS (same as in (2)) and with MPI itself, via
|
||||
one of several available Python/MPI packages. See instructions below
|
||||
on how to do the latter task.
|
||||
|
||||
Several of the following sub-sections cover the rest of the Python
|
||||
setup discussion. The next to last sub-section describes the Python
|
||||
syntax used to invoke LAMMPS. The last sub-section describes example
|
||||
Python scripts included in the python directory.
|
||||
|
||||
Before proceeding, there are 2 items to note.
|
||||
|
||||
(1) The provided Python wrapper for LAMMPS uses the amazing and
|
||||
magical (to me) "ctypes" package in Python, which auto-generates the
|
||||
interface code needed between Python and a set of C interface routines
|
||||
for a library. Ctypes is part of standard Python for versions 2.5 and
|
||||
later. You can check which version of Python you have installed, by
|
||||
simply typing "python" at a shell prompt.
|
||||
|
||||
(2) Any library wrapped by Python, including LAMMPS, must be built as
|
||||
a shared library (e.g. a *.so file on Linux and not a *.a file). The
|
||||
python/setup_serial.py and setup.py scripts do this build for LAMMPS
|
||||
|
|
@ -131,63 +175,6 @@ will also require you to edit the python/setup_serial.py or setup.py
|
|||
scripts to enable Python to access those libraries when it builds the
|
||||
LAMMPS wrapper.
|
||||
|
||||
:line
|
||||
:line
|
||||
|
||||
11.1 Extending Python with a serial version of LAMMPS :link(py_1),h4
|
||||
|
||||
From the python directory in the LAMMPS distribution, type
|
||||
|
||||
python setup_serial.py build :pre
|
||||
|
||||
and then one of these commands:
|
||||
|
||||
sudo python setup_serial.py install
|
||||
python setup_serial.py install --home=~/foo :pre
|
||||
|
||||
The "build" command should compile all the needed LAMMPS files,
|
||||
including its dummy MPI library. The first "install" command will put
|
||||
the needed files in your Python's site-packages sub-directory, so that
|
||||
Python can load them. For example, if you installed Python yourself
|
||||
on a Linux machine, it would typically be somewhere like
|
||||
/usr/local/lib/python2.5/site-packages. Installing Python packages
|
||||
this way often requires you to be able to write to the Python
|
||||
directories, which may require root priveleges, hence the "sudo"
|
||||
prefix. If this is not the case, you can drop the "sudo". If you use
|
||||
the "sudo" prefix and you have installed Python yourself, you should
|
||||
make sure that root uses the same Python as the one you did the
|
||||
"install" in. E.g. these 2 commands may do the install in different
|
||||
Python versions:
|
||||
|
||||
python setup_serial.py install --home=~/foo
|
||||
python /usr/local/bin/python/setup_serial.py install --home=~/foo :pre
|
||||
|
||||
Alternatively, you can install the LAMMPS files (or any other Python
|
||||
packages) in your own user space. The second "install" command does
|
||||
this, where you should replace "foo" with your directory of choice.
|
||||
|
||||
If these commands are successful, a {lammps.py} and
|
||||
{_lammps_serial.so} file will be put in the appropriate directory.
|
||||
|
||||
:line
|
||||
|
||||
11.2 Creating a shared MPI library :link(py_2),h4
|
||||
|
||||
A shared library is one that is dynamically loadable, which is what
|
||||
Python requires. On Linux this is a library file that ends in ".so",
|
||||
not ".a". Such a shared library is normally not built if you
|
||||
installed MPI yourself, but it is easy to do. Here is how to do it
|
||||
for "MPICH"_mpich, a popular open-source version of MPI, distributed
|
||||
by Argonne National Labs. From within the mpich directory, type
|
||||
|
||||
:link(mpich,http://www-unix.mcs.anl.gov/mpi)
|
||||
|
||||
./configure --enable-shared
|
||||
make
|
||||
make install :pre
|
||||
|
||||
You may need to use "sudo make install" in place of the last line.
|
||||
The end result should be the file libmpich.so in /usr/local/lib.
|
||||
|
||||
IMPORTANT NOTE: If the file libmpich.a already exists in your
|
||||
installation directory (e.g. /usr/local/lib), you will now have both a
|
||||
|
|
@ -200,47 +187,16 @@ this happens, it means you will need to remove the file
|
|||
/usr/local/lib/libmich.so before building LAMMPS again as a
|
||||
stand-alone code.
|
||||
|
||||
:line
|
||||
11.3 Extending Python with MPI :link(py_3),h4
|
||||
|
||||
11.3 Extending Python with a parallel version of LAMMPS :link(py_3),h4
|
||||
|
||||
From the python directory, type
|
||||
|
||||
python setup.py build :pre
|
||||
If
|
||||
your Python script will run in parallel and you want to be able to
|
||||
invoke MPI calls directly from Python, you will also need to extend
|
||||
your Python with an interface to MPI.
|
||||
|
||||
and then one of these commands:
|
||||
|
||||
sudo python setup.py install
|
||||
python setup.py install --home=~/foo :pre
|
||||
|
||||
The "build" command should compile all the needed LAMMPS C++ files,
|
||||
which will require MPI to be installed on your system. This means it
|
||||
must find both the header file mpi.h and a shared library file,
|
||||
e.g. libmpich.so if the MPICH version of MPI is installed. See the
|
||||
preceding section for how to create a shared library version of MPI if
|
||||
it does not exist. You may need to adjust the "include_dirs" and
|
||||
"library_dirs" and "libraries" fields in python/setup.py to
|
||||
insure the Python build finds all the files it needs.
|
||||
|
||||
The first "install" command will put the needed files in your Python's
|
||||
site-packages sub-directory, so that Python can load them. For
|
||||
example, if you installed Python yourself on a Linux machine, it would
|
||||
typically be somewhere like /usr/local/lib/python2.5/site-packages.
|
||||
Installing Python packages this way often requires you to be able to
|
||||
write to the Python directories, which may require root priveleges,
|
||||
hence the "sudo" prefix. If this is not the case, you can drop the
|
||||
"sudo".
|
||||
|
||||
Alternatively, you can install the LAMMPS files (or any other Python
|
||||
packages) in your own user space. The second "install" command does
|
||||
this, where you should replace "foo" with your directory of choice.
|
||||
|
||||
If these commands are successful, a {lammps.py} and {_lammps.so} file
|
||||
will be put in the appropriate directory.
|
||||
|
||||
:line
|
||||
|
||||
11.4 Extending Python with MPI :link(py_4),h4
|
||||
|
||||
There are several Python packages available that purport to wrap MPI
|
||||
as a library and allow MPI functions to be called from Python.
|
||||
|
|
@ -315,37 +271,16 @@ and see one line of output for each processor you ran on.
|
|||
|
||||
:line
|
||||
|
||||
11.5 Testing the Python-LAMMPS interface :link(py_5),h4
|
||||
11.4 Testing the Python-LAMMPS interface :link(py_4),h4
|
||||
|
||||
Before using LAMMPS in a Python program, one more step is needed. The
|
||||
interface to LAMMPS is via the Python ctypes package, which loads the
|
||||
shared LAMMPS library via a CDLL() call, which in turn is a wrapper on
|
||||
the C-library dlopen(). This command is different than a normal
|
||||
Python "import" and needs to be able to find the LAMMPS shared
|
||||
library, which is either in the Python site-packages directory or in a
|
||||
local directory you specified in the "python setup.py install"
|
||||
command, as described above.
|
||||
|
||||
The simplest way to do this is add a line like this to your
|
||||
.cshrc or other shell start-up file.
|
||||
|
||||
setenv LD_LIBRARY_PATH
|
||||
$\{LD_LIBRARY_PATH\}:/usr/local/lib/python2.5/site-packages :pre
|
||||
|
||||
and then execute the shell file to insure the path has been updated.
|
||||
This will extend the path that dlopen() uses to look for shared
|
||||
libraries.
|
||||
|
||||
To test if the serial LAMMPS library has been successfully installed
|
||||
(mode 1 above), launch Python and type
|
||||
To test if LAMMPS is now callable from Python, launch Python and type:
|
||||
|
||||
>>> from lammps import lammps
|
||||
>>> lmp = lammps() :pre
|
||||
|
||||
If you get no errors, you're ready to use serial LAMMPS from Python.
|
||||
If you get no errors, you're ready to use LAMMPS from Python.
|
||||
|
||||
|
||||
If you built LAMMPS for parallel use (mode 2 or 3 above), launch
|
||||
Python in parallel:
|
||||
|
||||
% mpirun -np 4 python test.script :pre
|
||||
|
||||
|
|
@ -368,15 +303,6 @@ see if the LAMMPS run says it ran on P processors or if you get output
|
|||
from P duplicated 1-processor runs written to the screen. In the
|
||||
latter case, Pypar is not working correctly.
|
||||
|
||||
Note that this line:
|
||||
|
||||
from lammps import lammps :pre
|
||||
|
||||
will import either the serial or parallel version of the LAMMPS
|
||||
library, as wrapped by lammps.py. But if you installed both via
|
||||
setup_serial.py and setup.py, it will always import the parallel
|
||||
version, since it attempts that first.
|
||||
|
||||
Note that if your Python script imports the Pypar package (as above),
|
||||
so that it can use MPI calls directly, then Pypar initializes MPI for
|
||||
you. Thus the last line of your Python script should be
|
||||
|
|
@ -408,7 +334,7 @@ Python on a single processor, not in parallel.
|
|||
:line
|
||||
:line
|
||||
|
||||
11.6 Using LAMMPS from Python :link(py_6),h4
|
||||
11.5 Using LAMMPS from Python :link(py_5),h4
|
||||
|
||||
The Python interface to LAMMPS consists of a Python "lammps" module,
|
||||
the source code for which is in python/lammps.py, which creates a
|
||||
|
|
@ -599,7 +525,7 @@ Python script. Isn't ctypes amazing? :l,ule
|
|||
:line
|
||||
:line
|
||||
|
||||
11.7 Example Python scripts that use LAMMPS :link(py_7),h4
|
||||
11.6 Example Python scripts that use LAMMPS :link(py_6),h4
|
||||
|
||||
These are the Python scripts included as demos in the python/examples
|
||||
directory of the LAMMPS distribution, to illustrate the kinds of
|
||||
|
|
|
|||
Loading…
Reference in New Issue