forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9982 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
e56c4a1358
commit
2ab555de25
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@ -54,7 +54,7 @@ packages, more details are provided.
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<TR ALIGN="center"><TD >KIM</TD><TD > openKIM potentials</TD><TD > Smirichinski & Elliot & Tadmor (3)</TD><TD > <A HREF = "pair_kim.html">pair_style kim</A></TD><TD > kim</TD><TD > lib/kim</TD></TR>
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<TR ALIGN="center"><TD >KSPACE</TD><TD > long-range Coulombic solvers</TD><TD > -</TD><TD > <A HREF = "kspace_style.html">kspace_style</A></TD><TD > peptide</TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >MANYBODY</TD><TD > many-body potentials</TD><TD > -</TD><TD > <A HREF = "pair_tersoff.html">pair_style tersoff</A></TD><TD > shear</TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >MEAM</TD><TD > modified EAM potential</TD><TD > Greg Wagner (Sandia)</TD><TD > <A HREF = "pair_meam.html">pair_style meam</A></TD><TD > meam</TD><TD > lib/meam</TD></TR>
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<TR ALIGN="center"><TD >MEAM</TD><TD > modified EAM potential</TD><TD > Greg Wagner (Sandia)</TD><TD > <A HREF = "pair_meam.html">pair_style meam</A></TD><TD > meam</TD><TD > KIM</TD></TR>
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<TR ALIGN="center"><TD >MC</TD><TD > Monte Carlo options</TD><TD > -</TD><TD > <A HREF = "fix_gcmc.html">fix gcmc</A></TD><TD > -</TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >MOLECULE</TD><TD > molecular system force fields</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_3">Section_howto</A></TD><TD > peptide</TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >OPT</TD><TD > optimized pair potentials</TD><TD > Fischer & Richie & Natoli (2)</TD><TD > <A HREF = "Section_accelerate.html#acc_4">Section accelerate</A></TD><TD > -</TD><TD > -</TD></TR>
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@ -65,6 +65,7 @@ packages, more details are provided.
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<TR ALIGN="center"><TD >RIGID</TD><TD > rigid bodies</TD><TD > -</TD><TD > <A HREF = "fix_rigid.html">fix rigid</A></TD><TD > rigid</TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >SHOCK</TD><TD > shock loading methods</TD><TD > -</TD><TD > <A HREF = "fix_msst.html">fix msst</A></TD><TD > -</TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >SRD</TD><TD > stochastic rotation dynamics</TD><TD > -</TD><TD > <A HREF = "fix_srd.html">fix srd</A></TD><TD > srd</TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >VORONOI</TD><TD > Voronoi tesselations</TD><TD > Daniel Schwen (LANL)</TD><TD > <A HREF = "compute_voronoi_atom.html">compute voronoi/atom</A></TD><TD > -</TD><TD > Voro++</TD></TR>
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<TR ALIGN="center"><TD >XTC</TD><TD > dumps in XTC format</TD><TD > -</TD><TD > <A HREF = "dump.html">dump</A></TD><TD > -</TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >
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</TD></TR></TABLE></DIV>
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@ -90,7 +91,16 @@ command implemented as part of the package.
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the distribution which has an input script that uses the package.
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E.g. "peptide" refers to the examples/peptide directory.
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</P>
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<P>The "Library" column lists an external library which must be built first and which LAMMPS links to when it is built. These are in the lib directory of the distribution. <A HREF = "Section_start.html#start_3_3">This section</A> of the manual gives details on the 2-step build process with external libraries.
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<P>The "Library" column lists an external library which must be built
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first and which LAMMPS links to when it is built. If it is listed as
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lib/package, then the code for the library is under the lib directory
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of the LAMMPS distribution. See the lib/package/README file for info
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on how to build the library. If it is not listed as lib/package, then
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it is a third-party library not included in the LAMMPS distribution.
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See the src/package/Makefile.lammps file for info on where to download
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the library. <A HREF = "Section_start.html#start_3_3">Section start</A> of the
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manual also gives details on how to build LAMMPS with both kinds of
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auxiliary libraries.
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</P>
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<HR>
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@ -102,14 +112,14 @@ E.g. "peptide" refers to the examples/peptide directory.
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</P>
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR ALIGN="center"><TD >Package</TD><TD > Description</TD><TD > Author(s)</TD><TD > Doc page</TD><TD > Example</TD><TD > Pic/movie</TD><TD > Library</TD></TR>
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<TR ALIGN="center"><TD >USER-MISC</TD><TD > single-file contributions</TD><TD > USER-MISC/README</TD><TD > USER-MISC/README</TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >USER-ATC</TD><TD > atom-to-continuum coupling</TD><TD > Jones & Templeton & Zimmerman (2)</TD><TD > <A HREF = "fix_atc.html">fix atc</A></TD><TD > USER/atc</TD><TD > <A HREF = "http://lammps.sandia.gov/pictures.html#atc">atc</A></TD><TD > lib/atc</TD></TR>
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<TR ALIGN="center"><TD >USER-AWPMD</TD><TD > wave-packet MD</TD><TD > Ilya Valuev (JIHT)</TD><TD > <A HREF = "pair_awpmd.html">pair_style awpmd/cut</A></TD><TD > USER/awpmd</TD><TD > -</TD><TD > lib/awpmd</TD></TR>
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<TR ALIGN="center"><TD >USER-CG-CMM</TD><TD > coarse-graining model</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "pair_sdk.html">pair_style lj/sdk</A></TD><TD > USER/cg-cmm</TD><TD > <A HREF = "http://lammps.sandia.gov/pictures.html#cg">cg</A></TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >USER-COLVARS</TD><TD > collective variables</TD><TD > Fiorin & Henin & Kohlmeyer (3)</TD><TD > <A HREF = "fix_colvars.html">fix colvars</A></TD><TD > USER/colvars</TD><TD > <A HREF = "colvars">colvars</A></TD><TD > lib/colvars</TD></TR>
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<TR ALIGN="center"><TD >USER-CUDA</TD><TD > NVIDIA GPU styles</TD><TD > Christian Trott (U Tech Ilmenau)</TD><TD > <A HREF = "Section_accelerate.html#acc_7">Section accelerate</A></TD><TD > USER/cuda</TD><TD > -</TD><TD > lib/cuda</TD></TR>
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<TR ALIGN="center"><TD >USER-EFF</TD><TD > electron force field</TD><TD > Andres Jaramillo-Botero (Caltech)</TD><TD > <A HREF = "pair_eff.html">pair_style eff/cut</A></TD><TD > USER/eff</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#eff">eff</A></TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >USER-MOLFILE</TD><TD > <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> molfile plug-ins</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "dump_molfile.html">dump molfile</A></TD><TD > -</TD><TD > -</TD><TD > lib/molfile</TD></TR>
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<TR ALIGN="center"><TD >USER-MISC</TD><TD > single-file contributions</TD><TD > USER-MISC/README</TD><TD > USER-MISC/README</TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >USER-MOLFILE</TD><TD > <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> molfile plug-ins</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "dump_molfile.html">dump molfile</A></TD><TD > -</TD><TD > -</TD><TD > VMD-MOLFILE</TD></TR>
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<TR ALIGN="center"><TD >USER-OMP</TD><TD > OpenMP threaded styles</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "Section_accelerate.html#acc_5">Section accelerate</A></TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >USER-REAXC</TD><TD > C version of ReaxFF</TD><TD > Metin Aktulga (LBNL)</TD><TD > <A HREF = "pair_reax_c.html">pair_style reaxc</A></TD><TD > reax</TD><TD > -</TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >USER-SPH</TD><TD > smoothed particle hydrodynamics</TD><TD > Georg Ganzenmuller (EMI)</TD><TD > <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">userguide.pdf</A></TD><TD > USER/sph</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#sph">sph</A></TD><TD > -</TD></TR>
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@ -129,6 +139,11 @@ E.g. "peptide" refers to the examples/peptide directory.
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<P>The "Authors" column lists a name(s) if a specific person is
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responible for creating and maintaining the package.
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</P>
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<P>If the Library is not listed as lib/package, then it is a third-party
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library not included in the LAMMPS distribution. See the
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src/package/Makefile.lammps file for info on where to download the
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library from.
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</P>
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<P>(2) The ATC package was created by Reese Jones, Jeremy Templeton, and
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Jon Zimmerman (Sandia).
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</P>
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@ -147,13 +162,18 @@ E.g. "peptide" refers to the examples/peptide directory. USER/cuda
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refers to the examples/USER/cuda directory.
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</P>
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<P>The "Library" column lists an external library which must be built
|
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first and which LAMMPS links to when it is built. These are in the
|
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lib directory of the distribution. <A HREF = "Section_start.html#start_3_3">This
|
||||
section</A> of the manual gives details on
|
||||
the 2-step build process with external libraries.
|
||||
first and which LAMMPS links to when it is built. If it is listed as
|
||||
lib/package, then the code for the library is under the lib directory
|
||||
of the LAMMPS distribution. See the lib/package/README file for info
|
||||
on how to build the library. If it is not listed as lib/package, then
|
||||
it is a third-party library not included in the LAMMPS distribution.
|
||||
See the src/package/Makefile.lammps file for info on where to download
|
||||
the library. <A HREF = "Section_start.html#start_3_3">Section start</A> of the
|
||||
manual also gives details on how to build LAMMPS with both kinds of
|
||||
auxiliary libraries.
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</P>
|
||||
<P>More details on each package, from the USER-blah/README file
|
||||
is given below.
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||||
<P>More details on each package, from the USER-*/README file is given
|
||||
below.
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||||
</P>
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<HR>
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|
|
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@ -49,7 +49,7 @@ GRANULAR, granular systems, -, "Section_howto"_Section_howto.html#howto_6, pour,
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KIM, openKIM potentials, Smirichinski & Elliot & Tadmor (3), "pair_style kim"_pair_kim.html, kim, lib/kim
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KSPACE, long-range Coulombic solvers, -, "kspace_style"_kspace_style.html, peptide, -
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MANYBODY, many-body potentials, -, "pair_style tersoff"_pair_tersoff.html, shear, -
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MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, lib/meam
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MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, KIM
|
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MC, Monte Carlo options, -, "fix gcmc"_fix_gcmc.html, -, -
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MOLECULE, molecular system force fields, -, "Section_howto"_Section_howto.html#howto_3, peptide, -
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OPT, optimized pair potentials, Fischer & Richie & Natoli (2), "Section accelerate"_Section_accelerate.html#acc_4, -, -
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||||
|
|
@ -60,6 +60,7 @@ REPLICA, multi-replica methods, -, "Section_howto"_Section_howto.html#howto_5, t
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RIGID, rigid bodies, -, "fix rigid"_fix_rigid.html, rigid, -
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||||
SHOCK, shock loading methods, -, "fix msst"_fix_msst.html, -, -
|
||||
SRD, stochastic rotation dynamics, -, "fix srd"_fix_srd.html, srd, -
|
||||
VORONOI, Voronoi tesselations, Daniel Schwen (LANL), "compute voronoi/atom"_compute_voronoi_atom.html, -, Voro++
|
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XTC, dumps in XTC format, -, "dump"_dump.html, -, -
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||||
:tb(ea=c)
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|
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|
|
@ -84,7 +85,16 @@ The "Example" column is a sub-directory in the examples directory of
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the distribution which has an input script that uses the package.
|
||||
E.g. "peptide" refers to the examples/peptide directory.
|
||||
|
||||
The "Library" column lists an external library which must be built first and which LAMMPS links to when it is built. These are in the lib directory of the distribution. "This section"_Section_start.html#start_3_3 of the manual gives details on the 2-step build process with external libraries.
|
||||
The "Library" column lists an external library which must be built
|
||||
first and which LAMMPS links to when it is built. If it is listed as
|
||||
lib/package, then the code for the library is under the lib directory
|
||||
of the LAMMPS distribution. See the lib/package/README file for info
|
||||
on how to build the library. If it is not listed as lib/package, then
|
||||
it is a third-party library not included in the LAMMPS distribution.
|
||||
See the src/package/Makefile.lammps file for info on where to download
|
||||
the library. "Section start"_Section_start.html#start_3_3 of the
|
||||
manual also gives details on how to build LAMMPS with both kinds of
|
||||
auxiliary libraries.
|
||||
|
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:line
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:line
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|
|
@ -94,14 +104,14 @@ The "Library" column lists an external library which must be built first and whi
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The current list of user-contributed packages is as follows:
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Package, Description, Author(s), Doc page, Example, Pic/movie, Library
|
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USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
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USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (2), "fix atc"_fix_atc.html, USER/atc, "atc"_atc, lib/atc
|
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USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, -, lib/awpmd
|
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USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cg-cmm, "cg"_cg, -
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USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (3), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
|
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USER-CUDA, NVIDIA GPU styles, Christian Trott (U Tech Ilmenau), "Section accelerate"_Section_accelerate.html#acc_7, USER/cuda, -, lib/cuda
|
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USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
|
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USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, lib/molfile
|
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USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
|
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USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE
|
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USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section accelerate"_Section_accelerate.html#acc_5, -, -, -
|
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USER-REAXC, C version of ReaxFF, Metin Aktulga (LBNL), "pair_style reaxc"_pair_reax_c.html, reax, -, -
|
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USER-SPH, smoothed particle hydrodynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_USER/sph/SPH_LAMMPS_userguide.pdf, USER/sph, "sph"_sph, -
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|
|
@ -116,6 +126,11 @@ USER-SPH, smoothed particle hydrodynamics, Georg Ganzenmuller (EMI), "userguide.
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The "Authors" column lists a name(s) if a specific person is
|
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responible for creating and maintaining the package.
|
||||
|
||||
If the Library is not listed as lib/package, then it is a third-party
|
||||
library not included in the LAMMPS distribution. See the
|
||||
src/package/Makefile.lammps file for info on where to download the
|
||||
library from.
|
||||
|
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(2) The ATC package was created by Reese Jones, Jeremy Templeton, and
|
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Jon Zimmerman (Sandia).
|
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|
||||
|
|
@ -134,13 +149,18 @@ E.g. "peptide" refers to the examples/peptide directory. USER/cuda
|
|||
refers to the examples/USER/cuda directory.
|
||||
|
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The "Library" column lists an external library which must be built
|
||||
first and which LAMMPS links to when it is built. These are in the
|
||||
lib directory of the distribution. "This
|
||||
section"_Section_start.html#start_3_3 of the manual gives details on
|
||||
the 2-step build process with external libraries.
|
||||
first and which LAMMPS links to when it is built. If it is listed as
|
||||
lib/package, then the code for the library is under the lib directory
|
||||
of the LAMMPS distribution. See the lib/package/README file for info
|
||||
on how to build the library. If it is not listed as lib/package, then
|
||||
it is a third-party library not included in the LAMMPS distribution.
|
||||
See the src/package/Makefile.lammps file for info on where to download
|
||||
the library. "Section start"_Section_start.html#start_3_3 of the
|
||||
manual also gives details on how to build LAMMPS with both kinds of
|
||||
auxiliary libraries.
|
||||
|
||||
More details on each package, from the USER-blah/README file
|
||||
is given below.
|
||||
More details on each package, from the USER-*/README file is given
|
||||
below.
|
||||
|
||||
:line
|
||||
|
||||
|
|
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|
|
@ -433,7 +433,7 @@ Obj_target where it stores the system-specific *.o files.
|
|||
</P>
|
||||
<P>(2) Cleaning up.
|
||||
</P>
|
||||
<P>Typing "make clean-all" or "make clean-foo" will delete *.o object
|
||||
<P>Typing "make clean-all" or "make clean-machine" will delete *.o object
|
||||
files created when LAMMPS is built, for either all builds or for a
|
||||
particular machine.
|
||||
</P>
|
||||
|
|
@ -566,6 +566,9 @@ get help. Information on how to submit additions you make to LAMMPS
|
|||
as a user-contributed package is given in <A HREF = "Section_modify.html#mod_15">this
|
||||
section</A> of the documentation.
|
||||
</P>
|
||||
<P>Some packages (both standard and user) require additional libraries.
|
||||
See more details below.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<A NAME = "start_3_2"></A><B><I>Including/excluding packages:</I></B>
|
||||
|
|
@ -636,82 +639,59 @@ type "make package" to see all of the package-related make options.
|
|||
<A NAME = "start_3_3"></A><B><I>Packages that require extra libraries:</I></B>
|
||||
|
||||
<P>A few of the standard and user packages require additional auxiliary
|
||||
libraries to be compiled first. If you get a LAMMPS build error about
|
||||
a missing library, this is likely the reason. The source code or
|
||||
hooks to these libraries is included in the LAMMPS distribution under
|
||||
the "lib" directory. Look at the lib/README file for a list of these
|
||||
or see <A HREF = "Section_packages.html">Section_packages</A> of the doc pages.
|
||||
libraries. They must be compiled first, before LAMMPS is built. If
|
||||
you get a LAMMPS build error about a missing library, this is likely
|
||||
the reason. See the <A HREF = "Section_packages.html">Section_packages</A> doc page
|
||||
for a list of packages that have auxiliary libraries.
|
||||
</P>
|
||||
<P>Each lib directory has a README file (e.g. lib/reax/README) with
|
||||
instructions on how to build that library. Typically this is done
|
||||
in this manner:
|
||||
<P>Code for some of these auxiliary libraries is included in the LAMMPS
|
||||
distribution under the lib directory. Examples are the USER-ATC and
|
||||
MEAM packages. Some auxiliary libraries are not included with LAMMPS;
|
||||
to use the associated package you must download and install the
|
||||
auxiliary library yourself. Examples are the KIM and VORONOI and
|
||||
USER-MOLFILE packages.
|
||||
</P>
|
||||
<P>For libraries with provided source code, each lib directory has a
|
||||
README file (e.g. lib/reax/README) with instructions on how to build
|
||||
that library. Typically this is done by typing something like:
|
||||
</P>
|
||||
<PRE>make -f Makefile.g++
|
||||
</PRE>
|
||||
<P>in the appropriate directory, e.g. in lib/reax. However, some of the
|
||||
libraries do not build this way. Again, see the libary README file
|
||||
for details.
|
||||
<P>If one of the provided Makefiles is not
|
||||
appropriate for your system you will need to edit or add one.
|
||||
Note that all the Makefiles have a setting for EXTRAMAKE at
|
||||
the top that names a Makefile.lammps.* file.
|
||||
</P>
|
||||
<P>If you are building the library, you will need to use a Makefile that
|
||||
is a match for your system. If one of the provided Makefiles is not
|
||||
appropriate for your system you will need to edit or add one. For
|
||||
example, in the case of Fortran-based libraries, your system must have
|
||||
a Fortran compiler, the settings for which will need to be listed in
|
||||
the Makefile.
|
||||
<P>If successful, this will produce 2 files in the lib directory:
|
||||
</P>
|
||||
<P>When you have built one of these libraries, there are 2 things to
|
||||
check:
|
||||
<PRE>libpackage.a
|
||||
Makefile.lammps
|
||||
</PRE>
|
||||
<P>The Makefile.lammps file is a copy of the EXTRAMAKE file specified
|
||||
in the Makefile you used.
|
||||
</P>
|
||||
<P>(1) The file libname.a should now exist in lib/name.
|
||||
E.g. lib/reax/libreax.a. This is the library file LAMMPS will link
|
||||
against. One exception is the lib/cuda library which produces the
|
||||
file liblammpscuda.a, because there is already a system library
|
||||
libcuda.a.
|
||||
<P>You MUST insure that the settings in Makefile.lammps are appropriate
|
||||
for your system. If they are not, the LAMMPS build will fail.
|
||||
</P>
|
||||
<P>(2) The file Makefile.lammps should exist in lib/name. E.g.
|
||||
lib/cuda/Makefile.lammps. This file may be auto-generated by the
|
||||
build of the library, or you may need to make a copy of the
|
||||
appropriate provided file (e.g. lib/meam/Makefile.lammps.gfortran).
|
||||
Either way you should insure that the settings in this file are
|
||||
appropriate for your system.
|
||||
<P>As explained in the lib/package/README files, they are used to specify
|
||||
additional system libraries and their locations so that LAMMPS can
|
||||
build with the auxiliary library. For example, if the MEAM or REAX
|
||||
packages are used, the auxiliary libraries consist of F90 code, build
|
||||
with a F90 complier. To link that library with LAMMPS (a C++ code)
|
||||
via whatever C++ compiler LAMMPS is built with, typically requires
|
||||
additional Fortran-to-C libraries be included in the link. Another
|
||||
example are the BLAS and LAPACK libraries needed to use the USER-ATC
|
||||
or USER-AWPMD packages.
|
||||
</P>
|
||||
<P>There are typically 3 settings in the Makefile.lammps file (unless
|
||||
some are blank or not needed): a SYSINC, SYSPATH, and SYSLIB setting,
|
||||
specific to this package. These are settings the LAMMPS build will
|
||||
import when compiling the LAMMPS package files (not the library
|
||||
files), and linking to the auxiliary library. They typically list any
|
||||
other system libraries needed to support the package and where to find
|
||||
them. An example is the BLAS and LAPACK libraries needed by the
|
||||
USER-ATC package. Or the system libraries that support calling
|
||||
Fortran from C++, as the MEAM and REAX packages do.
|
||||
</P>
|
||||
<P>(3) One exception to these rules is the lib/linalg directory, which is
|
||||
simply BLAS and LAPACK files used by the USER-ATC package (and
|
||||
possibly other packages in the future). If you do not have these
|
||||
libraries on your system, you can use one of the Makefiles in this
|
||||
directory (which you may need to modify) to build a dummy BLAS and
|
||||
LAPACK library. It can then be included in the
|
||||
lib/atc/Makefile.lammps file as part of the SYSPATH and SYSLIB lines
|
||||
so that LAMMPS will build properly with the USER-ATC package.
|
||||
</P>
|
||||
<P>Note that if the Makefile.lammps settings are not correct for your
|
||||
box, the LAMMPS build will likely fail.
|
||||
</P>
|
||||
<P>There are also a few packages, like KIM and USER-MOLFILE, that use
|
||||
additional auxiliary libraries which are not provided with LAMMPS. In
|
||||
these cases, there is no corresponding sub-directory under the lib
|
||||
directory. You are expected to download and install these libraries
|
||||
yourself before building LAMMPS with the package installed, if they
|
||||
are not already on your system.
|
||||
</P>
|
||||
<P>However there is still a Makefile.lammps file with settings used when
|
||||
building LAMMPS with the package installed, as in (2) above. Is is
|
||||
found in the package directory itself, e.g. src/KIM/Makefile.lammps.
|
||||
This file contains the same 3 settings described above for SYSINC,
|
||||
SYSPATH, and SYSLIB. The Makefile.lammps file contains instructions
|
||||
on how to specify these settings for your system. You need to specify
|
||||
the settings before building LAMMPS with one of those packages
|
||||
installed, else the LAMMPS build will likely fail.
|
||||
<P>For libraries without provided source code, see the
|
||||
src/package/Makefile.lammps file for information on where to find the
|
||||
library and how to build it. E.g. the file src/KIM/Makefile.lammps.
|
||||
This file serves the same purpose as the lib/package/Makefile.lammps
|
||||
file described above. It has settings needed when LAMMPS is built to
|
||||
link with the auxiliary library. Again, you MUST insure that the
|
||||
settings in src/package/Makefile.lammps are appropriate for your
|
||||
system and where you installed the auxiliary library. If they are
|
||||
not, the LAMMPS build will fail.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
|
|
|
|||
|
|
@ -427,7 +427,7 @@ Obj_target where it stores the system-specific *.o files.
|
|||
|
||||
(2) Cleaning up.
|
||||
|
||||
Typing "make clean-all" or "make clean-foo" will delete *.o object
|
||||
Typing "make clean-all" or "make clean-machine" will delete *.o object
|
||||
files created when LAMMPS is built, for either all builds or for a
|
||||
particular machine.
|
||||
|
||||
|
|
@ -560,6 +560,9 @@ get help. Information on how to submit additions you make to LAMMPS
|
|||
as a user-contributed package is given in "this
|
||||
section"_Section_modify.html#mod_15 of the documentation.
|
||||
|
||||
Some packages (both standard and user) require additional libraries.
|
||||
See more details below.
|
||||
|
||||
:line
|
||||
|
||||
[{Including/excluding packages:}] :link(start_3_2)
|
||||
|
|
@ -630,82 +633,59 @@ type "make package" to see all of the package-related make options.
|
|||
[{Packages that require extra libraries:}] :link(start_3_3)
|
||||
|
||||
A few of the standard and user packages require additional auxiliary
|
||||
libraries to be compiled first. If you get a LAMMPS build error about
|
||||
a missing library, this is likely the reason. The source code or
|
||||
hooks to these libraries is included in the LAMMPS distribution under
|
||||
the "lib" directory. Look at the lib/README file for a list of these
|
||||
or see "Section_packages"_Section_packages.html of the doc pages.
|
||||
libraries. They must be compiled first, before LAMMPS is built. If
|
||||
you get a LAMMPS build error about a missing library, this is likely
|
||||
the reason. See the "Section_packages"_Section_packages.html doc page
|
||||
for a list of packages that have auxiliary libraries.
|
||||
|
||||
Each lib directory has a README file (e.g. lib/reax/README) with
|
||||
instructions on how to build that library. Typically this is done
|
||||
in this manner:
|
||||
Code for some of these auxiliary libraries is included in the LAMMPS
|
||||
distribution under the lib directory. Examples are the USER-ATC and
|
||||
MEAM packages. Some auxiliary libraries are not included with LAMMPS;
|
||||
to use the associated package you must download and install the
|
||||
auxiliary library yourself. Examples are the KIM and VORONOI and
|
||||
USER-MOLFILE packages.
|
||||
|
||||
For libraries with provided source code, each lib directory has a
|
||||
README file (e.g. lib/reax/README) with instructions on how to build
|
||||
that library. Typically this is done by typing something like:
|
||||
|
||||
make -f Makefile.g++ :pre
|
||||
|
||||
in the appropriate directory, e.g. in lib/reax. However, some of the
|
||||
libraries do not build this way. Again, see the libary README file
|
||||
for details.
|
||||
If one of the provided Makefiles is not
|
||||
appropriate for your system you will need to edit or add one.
|
||||
Note that all the Makefiles have a setting for EXTRAMAKE at
|
||||
the top that names a Makefile.lammps.* file.
|
||||
|
||||
If you are building the library, you will need to use a Makefile that
|
||||
is a match for your system. If one of the provided Makefiles is not
|
||||
appropriate for your system you will need to edit or add one. For
|
||||
example, in the case of Fortran-based libraries, your system must have
|
||||
a Fortran compiler, the settings for which will need to be listed in
|
||||
the Makefile.
|
||||
If successful, this will produce 2 files in the lib directory:
|
||||
|
||||
When you have built one of these libraries, there are 2 things to
|
||||
check:
|
||||
libpackage.a
|
||||
Makefile.lammps :pre
|
||||
|
||||
(1) The file libname.a should now exist in lib/name.
|
||||
E.g. lib/reax/libreax.a. This is the library file LAMMPS will link
|
||||
against. One exception is the lib/cuda library which produces the
|
||||
file liblammpscuda.a, because there is already a system library
|
||||
libcuda.a.
|
||||
The Makefile.lammps file is a copy of the EXTRAMAKE file specified
|
||||
in the Makefile you used.
|
||||
|
||||
(2) The file Makefile.lammps should exist in lib/name. E.g.
|
||||
lib/cuda/Makefile.lammps. This file may be auto-generated by the
|
||||
build of the library, or you may need to make a copy of the
|
||||
appropriate provided file (e.g. lib/meam/Makefile.lammps.gfortran).
|
||||
Either way you should insure that the settings in this file are
|
||||
appropriate for your system.
|
||||
You MUST insure that the settings in Makefile.lammps are appropriate
|
||||
for your system. If they are not, the LAMMPS build will fail.
|
||||
|
||||
There are typically 3 settings in the Makefile.lammps file (unless
|
||||
some are blank or not needed): a SYSINC, SYSPATH, and SYSLIB setting,
|
||||
specific to this package. These are settings the LAMMPS build will
|
||||
import when compiling the LAMMPS package files (not the library
|
||||
files), and linking to the auxiliary library. They typically list any
|
||||
other system libraries needed to support the package and where to find
|
||||
them. An example is the BLAS and LAPACK libraries needed by the
|
||||
USER-ATC package. Or the system libraries that support calling
|
||||
Fortran from C++, as the MEAM and REAX packages do.
|
||||
As explained in the lib/package/README files, they are used to specify
|
||||
additional system libraries and their locations so that LAMMPS can
|
||||
build with the auxiliary library. For example, if the MEAM or REAX
|
||||
packages are used, the auxiliary libraries consist of F90 code, build
|
||||
with a F90 complier. To link that library with LAMMPS (a C++ code)
|
||||
via whatever C++ compiler LAMMPS is built with, typically requires
|
||||
additional Fortran-to-C libraries be included in the link. Another
|
||||
example are the BLAS and LAPACK libraries needed to use the USER-ATC
|
||||
or USER-AWPMD packages.
|
||||
|
||||
(3) One exception to these rules is the lib/linalg directory, which is
|
||||
simply BLAS and LAPACK files used by the USER-ATC package (and
|
||||
possibly other packages in the future). If you do not have these
|
||||
libraries on your system, you can use one of the Makefiles in this
|
||||
directory (which you may need to modify) to build a dummy BLAS and
|
||||
LAPACK library. It can then be included in the
|
||||
lib/atc/Makefile.lammps file as part of the SYSPATH and SYSLIB lines
|
||||
so that LAMMPS will build properly with the USER-ATC package.
|
||||
|
||||
Note that if the Makefile.lammps settings are not correct for your
|
||||
box, the LAMMPS build will likely fail.
|
||||
|
||||
There are also a few packages, like KIM and USER-MOLFILE, that use
|
||||
additional auxiliary libraries which are not provided with LAMMPS. In
|
||||
these cases, there is no corresponding sub-directory under the lib
|
||||
directory. You are expected to download and install these libraries
|
||||
yourself before building LAMMPS with the package installed, if they
|
||||
are not already on your system.
|
||||
|
||||
However there is still a Makefile.lammps file with settings used when
|
||||
building LAMMPS with the package installed, as in (2) above. Is is
|
||||
found in the package directory itself, e.g. src/KIM/Makefile.lammps.
|
||||
This file contains the same 3 settings described above for SYSINC,
|
||||
SYSPATH, and SYSLIB. The Makefile.lammps file contains instructions
|
||||
on how to specify these settings for your system. You need to specify
|
||||
the settings before building LAMMPS with one of those packages
|
||||
installed, else the LAMMPS build will likely fail.
|
||||
For libraries without provided source code, see the
|
||||
src/package/Makefile.lammps file for information on where to find the
|
||||
library and how to build it. E.g. the file src/KIM/Makefile.lammps.
|
||||
This file serves the same purpose as the lib/package/Makefile.lammps
|
||||
file described above. It has settings needed when LAMMPS is built to
|
||||
link with the auxiliary library. Again, you MUST insure that the
|
||||
settings in src/package/Makefile.lammps are appropriate for your
|
||||
system and where you installed the auxiliary library. If they are
|
||||
not, the LAMMPS build will fail.
|
||||
|
||||
:line
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue