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Installation of lammps-6Jan13 - 12Jan13 on OS X 10.8 (Mountain Lion)

Installation of lammps-6Jan13 - 12Jan13 on OS X 10.8 (Mountain Lion)

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Published by Fumihiro Chiba

Installation of lammps-6Jan13, 8Jan13, 11Jan13 and 12Jan13 on Mac OS X 10.8 without CUDA and molfile packages.

Installation of lammps-6Jan13, 8Jan13, 11Jan13 and 12Jan13 on Mac OS X 10.8 without CUDA and molfile packages.

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Categories:Types, Research
Published by: Fumihiro Chiba on Jan 04, 2013
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09/17/2013

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Installation of LAMMPS-6Jan13 – 12Jan13on OS X 10.8 (Mountain Lion)chibaf12 January 2013
LAMMPS Molecular Dynamics Simulatorhttp://lammps.sandia.gov/Copyright (2003) Sandia Corporation.
LAMMPS is a software for molecular (and particles) dynamics.It can be installed on Mac OS X with several steps.On multi-core Mac, lammps is installed with fftw 3.x and OpenMPI.This document corresponds tolammps-6Jan13,8Jan13,11Jan13and 12Jan13.Remark: for lammps-6Jan13, 8Jan13 and 11Jan13, the followingattached file (http://sourceforge.net/mailarchive/forum.php?thread_name=CADTmJ6FC4RJq1cAnqKDybB7cOdtjGroLG4r8muc%3DXXgqWUWYsg%40mail.gmail.com&forum_name=lammps-users) should be replacedwith src/input.cpp.Remark: a package user-molfile was added on lammps-14Jun12.But this document doesn't describe installation of the package.Remark: a packageUSER-COLVARSwas added on lammps-27May12.Remark: built without CUDA package.Remark: OS X 10.6 or later is necessary for GPU/OpenCL package.SeeRecent LAMMPS Newsfor recent lammps updates.(1) OS X 10.8.x (mountain lion) is employed with MacBook Core2Duo(late 2009).(2) if you employ xcode 4.4 or later, you need to install commandline tools for it.(3) downloading gfortran fromhttp://hpc.sf.net:
gfortran-mlion.tar.gz for os x 10.8.x
instruction:(A) $ gunzip gfortran-mlion.tar.gz(B) $ sudo tar -xf gfortrn-mlion.tar -C /(3') you can also obtain gfortran from:Tools - R for Mac OS X -developer's page - GNU Fortan for Xcode(4.1) installation of OpenMPI 1.6.xdownloading OpenMPI from
extracting tar file (double clicking tar.gz file) and:$ ./configure$ make all$ make check$ sudo make install(4.2) installation of FFTWwe employ FFTW version 3.x # 29 February 2012http://www.fftw.org/download.htmlextracting tar file (double clicking tar.gz file) and:$ ./configure$ make all$ make check
 
$ sudo make install(5) installingOpenKIM(Open Knowledge base Interatomic Model)download KIM API fromhttps://openkim.org/kim_api#download#We employed version 1.1.1 or later.Extract the file and On Terminal$ export KIM_DIR=”the path to openkim” # ending with “/”# example: KIM_DIR = /Users/foo/openkim-api-v1.1.1/$ cd $KIM_DIM$ make examples$ make(6) Downloading Lammpsthe latest version is obtained from below:http://lammps.sandia.gov/download.html#tarold versions are obtained from below:http://lammps.sandia.gov/tars/(7) building LAMMPS
Remark: in Makefile, tab is used for spacing.
(A) build libraries: awpmd, atc, meam, poem, reax, gpu, colvars.
at awpmd:
modification of Makefile.lammps:
user-awpmd_SYSINC user-awpmd_SYSLIB = -framework vecLib # use apple lapack and blasuser-awpmd_SYSPATH
$ make -f Makefile.openmpi
at atc:
 modification of Matrix.cpp:#include "DenseMatrix.h"#include "Solver.h"
#include "SparseMatrix.h"
// added on 28 september 2011
#include "DiagonalMatrix.h"
// added on 28 september 2011modification of Makefile.lammps:user-awpmd_SYSINC =user-awpmd_SYSLIB =
-framework vecLib
# use apple lapack and blasuser-awpmd_SYSPATH =$ make -f Makefile.g++
at meam:
 modification of Makefile.lammps:
meam_SYSINC = meam_SYSLIB = -lgfortran# for gfortranmeam_SYSPATH = 
$ make -f Makefile.gfortran
at poems:
 $ make -f Makefile.g++
at reax:
$ make -f Makefile.gfortran
at gpu (OpenCL)
modification of Makefile.lammps:
 
gpu_SYSINC = gpu_SYSLIB = -framework OpenCL# use apple opencl frameworkgpu_SYSPATH = 
$ make -f Makefile.mac_opencl
at colvars
$ make -f Makefile.g++(B) at
src/MAKE
:modification of Makefile.openmpiCC = mpic++CCFLAGS = -O2 \-funroll-loops -fstrict-aliasing -Wall -W -Wno-uninitialized
-fopenmp
# use openmpDEPFLAGS = -MLINK = mpic++LINKFLAGS = -O
-lgfortran -framework vecLib -lgomp #
for gfortran and openmp; use apple framework for lapack and blas..............
# FFT library, OPTIONAL# see discussion in doc/Section_start.html#2_2 (step 6)# can be left blank to use provided KISS FFT library # INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings# PATH = path for FFT library # LIB = name of FFT library FFT_INC = -DFFT_FFTW3
# use fftw 3.x
FFT_PATH = FFT_LIB = -lfftw3
# use fftw 3.x(C) generating makefile at src directory$ make yes-all
Installing package asphereInstalling package class2Installing package colloid Installing package dipoleInstalling package fld Installing package gpuInstalling package granular Installing package kimInstalling package kspaceInstalling package manybody Installing package mcInstalling package meamInstalling package moleculeInstalling package optInstalling package periInstalling package poemsInstalling package reax Installing package replicaInstalling package rigid Installing package shockInstalling package srd Installing package xtcInstalling package user-miscInstalling package user-atcInstalling package user-awpmd Installing package user-cg-cmm

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