modernize a couple examples/COUPLE apps
This commit is contained in:
Steve Plimpton
@ -33,7 +33,6 @@ These are the sub-directories included in this directory:
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simple simple example of driver code calling LAMMPS as a lib
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multiple example of driver code calling multiple instances of LAMMPS
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plugin example for loading LAMMPS at runtime from a shared library
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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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@ -1,47 +0,0 @@
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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 -llammps_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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@ -1,70 +0,0 @@
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IMPORTANT NOTE: This example has not been updated since 2014,
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so it is not likely to work anymore out of the box. There have
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been changes to LAMMPS and its library interface that would need
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to be applied. Please see the manual for the documentation of
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the library interface.
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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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make -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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@ -1,20 +0,0 @@
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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 pf/callback 1 1
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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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@ -1,270 +0,0 @@
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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 <cstdio>
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#include <cstdlib>
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#include <cstring>
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#include "stdint.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 *, bigint, 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 available 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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// this could also be done thru Python, using a ctypes callback
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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, bigint ntimestep,
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int nlocal, 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 boxxy = *((double *) lammps_extract_global(info->lmp,"xy"));
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double boxxz = *((double *) lammps_extract_global(info->lmp,"xz"));
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double boxyz = *((double *) lammps_extract_global(info->lmp,"yz"));
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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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double xy = boxxy/ANGSTROM_per_BOHR;
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double xz = boxxz/ANGSTROM_per_BOHR;
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double yz = boxyz/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",xy,yprd,0.0);
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sprintf(boxlines[2],"%g %g %g\n",xz,yz,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");
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xlines = new char*[natoms];
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for (i = 0; i < natoms; i++) xlines[i] = new char[128];
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}
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if (info->me == 0) lmp2qst->gather(&x[0][0],3,&xquest[0][0]);
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else lmp2qst->gather(&x[0][0],3,NULL);
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if (info->me == 0) {
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for (i = 0; i < natoms; i++) {
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xquest[i][0] /= ANGSTROM_per_BOHR;
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xquest[i][1] /= ANGSTROM_per_BOHR;
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xquest[i][2] /= ANGSTROM_per_BOHR;
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}
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for (i = 0; i < natoms; i++) {
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sprintf(xlines[i],"%d %d %g %g %g\n",i+1,1,
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xquest[i][0],xquest[i][1],xquest[i][2]);
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}
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}
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// one-processor tasks:
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// whack all lcao.* files
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// cp quest_input to lcao.in
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// replace atom coords section of lcao.in with new atom coords
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// run Quest on one proc, save screen output to file
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// flines = atom forces extracted from Quest screen file
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// fquest = atom forces
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// convert Quest Ryd/bohr to LAMMPS eV/Angstrom
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char **flines = NULL;
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double **fquest = NULL;
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if (info->me == 0) {
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fquest = info->memory->create_2d_double_array(natoms,3,"lmpqst:fquest");
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flines = new char*[natoms];
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for (i = 0; i < natoms; i++) flines[i] = new char[128];
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}
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if (info->me == 0) {
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system("rm lcao.*");
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sprintf(str,"cp %s lcao.in",info->quest_input);
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system(str);
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sprintf(str,"cp %s lcao.x",QUOTE(QUEST));
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system(str);
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replace("lcao.in","primitive lattice vectors",3,boxlines);
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replace("lcao.in","atom, type, position vector",natoms,xlines);
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system("lcao.x > lcao.screen");
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extract("lcao.screen","atom x force "
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"y force z force",natoms,flines);
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int itmp;
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for (i = 0; i < natoms; i++)
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sscanf(flines[i],"%d %lg %lg %lg",&itmp,
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&fquest[i][0],&fquest[i][1],&fquest[i][2]);
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for (i = 0; i < natoms; i++) {
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fquest[i][0] *= EV_per_RYDBERG / ANGSTROM_per_BOHR;
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fquest[i][1] *= EV_per_RYDBERG / ANGSTROM_per_BOHR;
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fquest[i][2] *= EV_per_RYDBERG / ANGSTROM_per_BOHR;
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}
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}
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// convert fquest on one proc into f for atoms on each proc
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One2Many *qst2lmp = new One2Many(MPI_COMM_WORLD);
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qst2lmp->setup(natoms,nlocal,id);
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double *fvec = NULL;
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if (f) fvec = &f[0][0];
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if (info->me == 0) qst2lmp->scatter(&fquest[0][0],3,fvec);
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else qst2lmp->scatter(NULL,3,fvec);
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// clean up
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// some data only exists on proc 0
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delete lmp2qst;
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delete qst2lmp;
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info->memory->destroy_2d_double_array(xquest);
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info->memory->destroy_2d_double_array(fquest);
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if (boxlines) {
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for (i = 0; i < 3; i++) delete [] boxlines[i];
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delete [] boxlines;
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}
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if (xlines) {
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for (i = 0; i < natoms; i++) delete [] xlines[i];
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delete [] xlines;
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}
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if (flines) {
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for (i = 0; i < natoms; i++) delete [] flines[i];
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delete [] flines;
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}
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}
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@ -1,58 +0,0 @@
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LAMMPS (20 Sep 2010)
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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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Lattice spacing in x,y,z = 5.43 5.43 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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Created orthogonal box = (0 0 0) to (5.43 5.43 5.43)
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1 by 1 by 1 processor grid
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create_atoms 1 box
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Created 8 atoms
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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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run 10
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Memory usage per processor = 1.25982 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 300 0 0 0.2714463 1810.9378
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1 298.22165 0 0 0.26983722 1800.2029
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2 293.2839 0 0 0.26536943 1770.3964
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3 286.18537 0 0 0.25894654 1727.5464
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4 277.61576 0 0 0.25119258 1675.8163
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5 267.3325 0 0 0.24188807 1613.7418
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6 254.94702 0 0 0.23068142 1538.9774
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7 240.91176 0 0 0.21798202 1454.2541
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8 226.27996 0 0 0.20474287 1365.9298
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9 212.1059 0 0 0.19191788 1280.3687
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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
|
||||
@ -4,13 +4,13 @@ SHELL = /bin/sh
|
||||
|
||||
# System-specific settings
|
||||
|
||||
LAMMPS = /home/sjplimp/lammps
|
||||
SPPARKS = /home/sjplimp/spparks
|
||||
LAMMPS = /home/sjplimp/lammps/git/src
|
||||
SPPARKS = /home/sjplimp/spparks/git/src
|
||||
|
||||
CC = g++
|
||||
CC = mpicxx
|
||||
CCFLAGS = -g -O -DMPICH_IGNORE_CXX_SEEK -I../library
|
||||
DEPFLAGS = -M
|
||||
LINK = g++
|
||||
LINK = mpicxx
|
||||
LINKFLAGS = -g -O -L../library -L${LAMMPS}/src -L${SPPARKS}/src
|
||||
USRLIB = -lcouple -llmp_g++ -lspk_g++
|
||||
SYSLIB = -lfftw -lmpich -lpthread
|
||||
@ -1 +1 @@
|
||||
#define LMPPATH /home/sjplimp/lammps
|
||||
#define LMPPATH /home/sjplimp/lammps/git
|
||||
|
||||
@ -20,10 +20,10 @@
|
||||
#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 "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)
|
||||
@ -32,7 +32,7 @@
|
||||
#include QUOTE(LMPPATH/src/modify.h)
|
||||
#include QUOTE(LMPPATH/src/compute.h)
|
||||
|
||||
using namespace SPPARKS_NS;
|
||||
//using namespace SPPARKS_NS;
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -83,28 +83,28 @@ int main(int narg, char **arg)
|
||||
double **xyz;
|
||||
double *strain;
|
||||
|
||||
dimension = *((int *) spparks_extract(spk,"dimension"));
|
||||
nglobal = *((int *) spparks_extract(spk,"nglobal"));
|
||||
nlocal_spparks = *((int *) spparks_extract(spk,"nlocal"));
|
||||
dimension = *((int *) spparks_extract(spk,(char *) "dimension"));
|
||||
nglobal = *((int *) spparks_extract(spk,(char *) "nglobal"));
|
||||
nlocal_spparks = *((int *) spparks_extract(spk,(char *) "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"));
|
||||
boxxlo = *((double *) spparks_extract(spk,(char *) "boxxlo"));
|
||||
boxxhi = *((double *) spparks_extract(spk,(char *) "boxxhi"));
|
||||
boxylo = *((double *) spparks_extract(spk,(char *) "boxylo"));
|
||||
boxyhi = *((double *) spparks_extract(spk,(char *) "boxyhi"));
|
||||
if (dimension == 3) {
|
||||
boxzlo = *((double *) spparks_extract(spk,"boxzlo"));
|
||||
boxzhi = *((double *) spparks_extract(spk,"boxzhi"));
|
||||
boxzlo = *((double *) spparks_extract(spk,(char *) "boxzlo"));
|
||||
boxzhi = *((double *) spparks_extract(spk,(char *) "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");
|
||||
id_spparks = (int *) spparks_extract(spk,(char *) "id");
|
||||
spins = (int *) spparks_extract(spk,(char *) "site");
|
||||
xyz = (double **) spparks_extract(spk,(char *) "xyz");
|
||||
|
||||
nspins = *((int *) spparks_extract(spk,"nspins"));
|
||||
strain = (double *) spparks_extract(spk,"strain");
|
||||
nspins = *((int *) spparks_extract(spk,(char *) "nspins"));
|
||||
strain = (double *) spparks_extract(spk,(char *) "strain");
|
||||
|
||||
// write a LAMMPS input script using SPPARKS params
|
||||
|
||||
@ -114,7 +114,7 @@ int main(int narg, char **arg)
|
||||
|
||||
fprintf(fp,"units lj\n");
|
||||
sprintf(str,"dimension %d\n",dimension);
|
||||
fprintf(fp,str);
|
||||
fprintf(fp,"%s",str);
|
||||
fprintf(fp,"atom_style atomic\n\n");
|
||||
|
||||
fprintf(fp,"read_data data.lammps\n");
|
||||
@ -124,7 +124,7 @@ int main(int narg, char **arg)
|
||||
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,"%s",str);
|
||||
}
|
||||
fprintf(fp,"\n");
|
||||
|
||||
@ -138,12 +138,12 @@ int main(int narg, char **arg)
|
||||
// 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->file((char *) "data.lammps");
|
||||
lwd->header((char *) "%d atoms",nglobal);
|
||||
lwd->header((char *) "%d atom types",nspins);
|
||||
lwd->header((char *) "%g %g xlo xhi",boxxlo,boxxhi);
|
||||
lwd->header((char *) "%g %g ylo yhi",boxylo,boxyhi);
|
||||
lwd->header((char *) "%g %g zlo zhi",boxzlo,boxzhi);
|
||||
lwd->atoms(nlocal_spparks);
|
||||
lwd->atoms(id_spparks);
|
||||
lwd->atoms(spins);
|
||||
|
||||
@ -1 +1 @@
|
||||
#define SPKPATH /home/sjplimp/spparks
|
||||
#define SPKPATH /home/sjplimp/spparks/git
|
||||
|
||||
@ -6,7 +6,7 @@ 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++
|
||||
g++ -f Makefile.mpi
|
||||
|
||||
you should create libcouple.a, which the other coupled applications
|
||||
link to.
|
||||
|
||||
@ -1,11 +1,11 @@
|
||||
#include <mpi.h>
|
||||
#include <cstdio>
|
||||
#include <cstdlib>
|
||||
#include "error.h"
|
||||
#include "errorlib.h"
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
Error::Error(MPI_Comm caller)
|
||||
ErrorLib::ErrorLib(MPI_Comm caller)
|
||||
{
|
||||
comm = caller;
|
||||
MPI_Comm_rank(comm,&me);
|
||||
@ -15,7 +15,7 @@ Error::Error(MPI_Comm caller)
|
||||
called by all procs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Error::all(const char *str)
|
||||
void ErrorLib::all(const char *str)
|
||||
{
|
||||
if (me == 0) printf("ERROR: %s\n",str);
|
||||
MPI_Finalize();
|
||||
@ -26,7 +26,7 @@ void Error::all(const char *str)
|
||||
called by one proc
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Error::one(const char *str)
|
||||
void ErrorLib::one(const char *str)
|
||||
{
|
||||
printf("ERROR on proc %d: %s\n",me,str);
|
||||
MPI_Abort(comm,1);
|
||||
@ -36,7 +36,7 @@ void Error::one(const char *str)
|
||||
called by one proc
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Error::warning(const char *str)
|
||||
void ErrorLib::warning(const char *str)
|
||||
{
|
||||
printf("WARNING: %s\n",str);
|
||||
}
|
||||
@ -1,11 +1,11 @@
|
||||
#ifndef ERROR_H
|
||||
#define ERROR_H
|
||||
#ifndef ERRORLIB_H
|
||||
#define ERRORLIB_H
|
||||
|
||||
#include <mpi.h>
|
||||
|
||||
class Error {
|
||||
class ErrorLib {
|
||||
public:
|
||||
Error(MPI_Comm);
|
||||
ErrorLib(MPI_Comm);
|
||||
|
||||
void all(const char *);
|
||||
void one(const char *);
|
||||
@ -29,7 +29,7 @@ void replace(char *file, char *header, int n, char **lines)
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
char **extract(char *file, char *header, int n, char **lines)
|
||||
void extract(char *file, char *header, int n, char **lines)
|
||||
{
|
||||
FILE *fp = fopen(file,"r");
|
||||
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
#ifndef FILES_H
|
||||
#define FILES_H
|
||||
void replace(char *, char *, int, char **);
|
||||
char **extract(char *, char *, int, char **);
|
||||
void extract(char *, char *, int, char **);
|
||||
#endif
|
||||
|
||||
@ -3,7 +3,7 @@
|
||||
#include <cstring>
|
||||
#include "irregular.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "errorlib.h"
|
||||
|
||||
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
|
||||
|
||||
@ -19,7 +19,7 @@ Irregular::Irregular(MPI_Comm caller)
|
||||
MPI_Comm_size(comm,&nprocs);
|
||||
|
||||
memory = new Memory(comm);
|
||||
error = new Error(comm);
|
||||
error = new ErrorLib(comm);
|
||||
|
||||
init();
|
||||
|
||||
|
||||
@ -47,7 +47,7 @@ class Irregular {
|
||||
MPI_Comm comm; // MPI communicator for all communication
|
||||
|
||||
class Memory *memory;
|
||||
class Error *error;
|
||||
class ErrorLib *error;
|
||||
|
||||
void exchange_same(char *, char *);
|
||||
void exchange_varying(char *, char *);
|
||||
|
||||
@ -4,7 +4,7 @@
|
||||
#include "many2many.h"
|
||||
#include "irregular.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "errorlib.h"
|
||||
|
||||
#include <map>
|
||||
|
||||
@ -19,7 +19,7 @@ Many2Many::Many2Many(MPI_Comm caller)
|
||||
MPI_Comm_size(comm,&nprocs);
|
||||
|
||||
memory = new Memory(comm);
|
||||
error = new Error(comm);
|
||||
error = new ErrorLib(comm);
|
||||
|
||||
src_own = dest_own = NULL;
|
||||
src_off = dest_off = NULL;
|
||||
|
||||
@ -16,7 +16,7 @@ class Many2Many {
|
||||
int me,nprocs;
|
||||
MPI_Comm comm;
|
||||
class Memory *memory;
|
||||
class Error *error;
|
||||
class ErrorLib *error;
|
||||
|
||||
int nown; // # of IDs common to src and dest
|
||||
int nsrc_off,ndest_off; // # of off-processor IDs
|
||||
|
||||
@ -2,13 +2,13 @@
|
||||
#include <cstdlib>
|
||||
#include <cstdio>
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "errorlib.h"
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
Memory::Memory(MPI_Comm comm)
|
||||
{
|
||||
error = new Error(comm);
|
||||
error = new ErrorLib(comm);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -17,7 +17,7 @@ class Memory {
|
||||
void destroy_2d_double_array(double **);
|
||||
|
||||
private:
|
||||
class Error *error;
|
||||
class ErrorLib *error;
|
||||
};
|
||||
|
||||
#endif
|
||||
|
||||
@ -3,7 +3,7 @@
|
||||
#include <cstdio>
|
||||
#include "send2one.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "errorlib.h"
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -14,7 +14,7 @@ Send2One::Send2One(MPI_Comm caller_comm)
|
||||
MPI_Comm_size(comm,&nprocs);
|
||||
|
||||
memory = new Memory(comm);
|
||||
error = new Error(comm);
|
||||
error = new ErrorLib(comm);
|
||||
|
||||
buf = NULL;
|
||||
maxbuf = 0;
|
||||
|
||||
@ -14,7 +14,7 @@ class Send2One {
|
||||
int me,nprocs;
|
||||
MPI_Comm comm;
|
||||
class Memory *memory;
|
||||
class Error *error;
|
||||
class ErrorLib *error;
|
||||
|
||||
int maxbuf;
|
||||
char *buf;
|
||||
|
||||
Reference in New Issue
Block a user