git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@645 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
4
README
4
README
@ -1,4 +1,4 @@
|
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This is the LAMMPS (12 Feb 2007) software package.
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This is the LAMMPS (22 June 2007) software package.
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LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
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Simulator.
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@ -21,7 +21,7 @@ at sjplimp@sandia.gov. The LAMMPS WWW Site at
|
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www.cs.sandia.gov/~sjplimp/lammps.html has more information about the
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code and its uses.
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The LAMMPS (12 Feb 2007) distribution includes the following files
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The LAMMPS (22 June 2007) distribution includes the following files
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and directories:
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README this file
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@ -13,7 +13,7 @@
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<CENTER><H3>LAMMPS Documentation
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</H3></CENTER>
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<CENTER>(12 Feb 2007 version of LAMMPS)
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<CENTER>(22 June 2007 version of LAMMPS)
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</CENTER>
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<P>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
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Simulator.
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BIN
doc/Manual.pdf
BIN
doc/Manual.pdf
Binary file not shown.
@ -10,7 +10,7 @@
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|
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LAMMPS Documentation :c,h3
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(12 Feb 2007 version of LAMMPS) :c
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(22 June 2007 version of LAMMPS) :c
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LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
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Simulator.
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@ -407,8 +407,11 @@ description:
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|
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<HR>
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<P>Kspace solvers. All of these solver styles are discussed as part of
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the <A HREF = "kspace_style.html">kspace_style</A> command:
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<P>Improper_style potentials.
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</P>
|
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<P>Kspace solvers. See the <A HREF = "kspace_style.html">kspace_style</A> command for
|
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an overview of Kspace solvers. Click on the style itself for a full
|
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description:
|
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</P>
|
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<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
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<TR ALIGN="center"><TD WIDTH="100"><A HREF = "kspace_style.html">ewald</A></TD><TD WIDTH="100"><A HREF = "kspace_style.html">pppm</A></TD><TD WIDTH="100"><A HREF = "kspace_style.html">pppm/tip4p</A>
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|
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@ -560,8 +560,11 @@ description:
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|
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:line
|
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|
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Kspace solvers. All of these solver styles are discussed as part of
|
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the "kspace_style"_kspace_style.html command:
|
||||
Improper_style potentials.
|
||||
|
||||
Kspace solvers. See the "kspace_style"_kspace_style.html command for
|
||||
an overview of Kspace solvers. Click on the style itself for a full
|
||||
description:
|
||||
|
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"ewald"_kspace_style.html,
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"pppm"_kspace_style.html,
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|
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@ -3058,6 +3058,15 @@ lattice must first be defined via the lattice command.
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<DD>If scale = lattice (the default) for the velocity set or velocity ramp
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command, then a lattice must first be defined via the lattice command.
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<DT><I>Using fix nvt/sllod with inconsistent fix deform remap option</I>
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<DD>Fix nvt/sllod requires that deforming atoms have a velocity profile
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provided by "remap v" as a fix deform option.
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|
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<DT><I>Using fix nvt/sllod with no fix deform defined</I>
|
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|
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<DD>Self-explanatory.
|
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|
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<DT><I>Variable compute ID does not compute scalar info</I>
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|
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<DD>The specified compute ID does not compute a scalar quantity
|
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@ -3360,15 +3369,6 @@ by "remap v" or "remap none" as a fix deform option.
|
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|
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<DD>Self-explanatory.
|
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|
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<DT><I>Using fix nvt/sllod with inconsistent fix deform remap option</I>
|
||||
|
||||
<DD>Fix nvt/sllod assumes deforming atoms have a velocity profile
|
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provided by "remap v" as a fix deform option.
|
||||
|
||||
<DT><I>Using fix nvt/sllod with no fix deform defined</I>
|
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|
||||
<DD>Self-explanatory.
|
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|
||||
<DT><I>Using pair tail corrections with nonperiodic system</I>
|
||||
|
||||
<DD>This is probably a bogus thing to do, since tail corrections are
|
||||
|
||||
@ -3055,6 +3055,15 @@ lattice must first be defined via the lattice command. :dd
|
||||
If scale = lattice (the default) for the velocity set or velocity ramp
|
||||
command, then a lattice must first be defined via the lattice command. :dd
|
||||
|
||||
{Using fix nvt/sllod with inconsistent fix deform remap option} :dt
|
||||
|
||||
Fix nvt/sllod requires that deforming atoms have a velocity profile
|
||||
provided by "remap v" as a fix deform option. :dd
|
||||
|
||||
{Using fix nvt/sllod with no fix deform defined} :dt
|
||||
|
||||
Self-explanatory. :dd
|
||||
|
||||
{Variable compute ID does not compute scalar info} :dt
|
||||
|
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The specified compute ID does not compute a scalar quantity
|
||||
@ -3357,15 +3366,6 @@ by "remap v" or "remap none" as a fix deform option. :dd
|
||||
|
||||
Self-explanatory. :dd
|
||||
|
||||
{Using fix nvt/sllod with inconsistent fix deform remap option} :dt
|
||||
|
||||
Fix nvt/sllod assumes deforming atoms have a velocity profile
|
||||
provided by "remap v" as a fix deform option. :dd
|
||||
|
||||
{Using fix nvt/sllod with no fix deform defined} :dt
|
||||
|
||||
Self-explanatory. :dd
|
||||
|
||||
{Using pair tail corrections with nonperiodic system} :dt
|
||||
|
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This is probably a bogus thing to do, since tail corrections are
|
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|
||||
@ -23,20 +23,26 @@ the directories to compare your answers to. E.g. a log file like
|
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log.crack.foo.P means it ran on P processors of machine "foo".
|
||||
</P>
|
||||
<P>The dump files produced by the example runs can be animated using the
|
||||
xmovie tool described in the <A HREF = "Section_tools.html">Tools section</A>. MPEG
|
||||
versions of most of the xmovie animations are also viewable from the
|
||||
Examples page of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>.
|
||||
xmovie tool described in the <A HREF = "Section_tools.html">Additional Tools</A>
|
||||
section of the LAMMPS documentation. Animations of many of these
|
||||
examples can be viewed on the Movies section of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW
|
||||
Site</A>.
|
||||
</P>
|
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<P>These are the sample problems in the examples sub-directories:
|
||||
</P>
|
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<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
|
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<TR><TD >crack</TD><TD > crack propagation in a 2d solid</TD></TR>
|
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<TR><TD >flow</TD><TD > Couette and Poiseuille flow in a 2d channel</TD></TR>
|
||||
<TR><TD >colloid</TD><TD > big colloid particles in a small particle solvent, 2d system</TD></TR>
|
||||
<TR><TD >crack</TD><TD > crack propagation in a 2d solid</TD></TR>
|
||||
<TR><TD >dipole</TD><TD > point dipolar particles, 2d system</TD></TR>
|
||||
<TR><TD >ellipse</TD><TD > ellipsoidal particles in spherical solvent, 2d system</TD></TR>
|
||||
<TR><TD >flow</TD><TD > Couette and Poisseuille flow in a 2d channel</TD></TR>
|
||||
<TR><TD >friction</TD><TD > frictional contact of spherical asperities between 2d surfaces</TD></TR>
|
||||
<TR><TD >indent</TD><TD > spherical indenter into a 2d solid</TD></TR>
|
||||
<TR><TD >melt</TD><TD > rapid melt of 3d LJ system</TD></TR>
|
||||
<TR><TD >indent</TD><TD > spherical indenter into a 2d solid</TD></TR>
|
||||
<TR><TD >meam</TD><TD > MEAM test for SiC and shear (same as shear examples)</TD></TR>
|
||||
<TR><TD >melt</TD><TD > rapid melt of 3d LJ system</TD></TR>
|
||||
<TR><TD >micelle</TD><TD > self-assembly of small lipid-like molecules into 2d bilayers</TD></TR>
|
||||
<TR><TD >min</TD><TD > energy minimization of 2d LJ melt</TD></TR>
|
||||
<TR><TD >min</TD><TD > energy minimization of 2d LJ melt</TD></TR>
|
||||
<TR><TD >nemd</TD><TD > non-equilibrium MD of 2d sheared system</TD></TR>
|
||||
<TR><TD >obstacle</TD><TD > flow around two voids in a 2d channel</TD></TR>
|
||||
<TR><TD >peptide</TD><TD > dynamics of a small solvated peptide chain (5-mer)</TD></TR>
|
||||
<TR><TD >pour</TD><TD > pouring of granular particles into a 3d box, then chute flow</TD></TR>
|
||||
|
||||
@ -20,19 +20,25 @@ the directories to compare your answers to. E.g. a log file like
|
||||
log.crack.foo.P means it ran on P processors of machine "foo".
|
||||
|
||||
The dump files produced by the example runs can be animated using the
|
||||
xmovie tool described in the "Tools section"_Section_tools.html. MPEG
|
||||
versions of most of the xmovie animations are also viewable from the
|
||||
Examples page of the "LAMMPS WWW Site"_lws.
|
||||
xmovie tool described in the "Additional Tools"_Section_tools.html
|
||||
section of the LAMMPS documentation. Animations of many of these
|
||||
examples can be viewed on the Movies section of the "LAMMPS WWW
|
||||
Site"_lws.
|
||||
|
||||
These are the sample problems in the examples sub-directories:
|
||||
|
||||
crack: crack propagation in a 2d solid
|
||||
flow: Couette and Poiseuille flow in a 2d channel
|
||||
colloid: big colloid particles in a small particle solvent, 2d system
|
||||
crack: crack propagation in a 2d solid
|
||||
dipole: point dipolar particles, 2d system
|
||||
ellipse: ellipsoidal particles in spherical solvent, 2d system
|
||||
flow: Couette and Poisseuille flow in a 2d channel
|
||||
friction: frictional contact of spherical asperities between 2d surfaces
|
||||
indent: spherical indenter into a 2d solid
|
||||
melt: rapid melt of 3d LJ system
|
||||
indent: spherical indenter into a 2d solid
|
||||
meam: MEAM test for SiC and shear (same as shear examples)
|
||||
melt: rapid melt of 3d LJ system
|
||||
micelle: self-assembly of small lipid-like molecules into 2d bilayers
|
||||
min: energy minimization of 2d LJ melt
|
||||
min: energy minimization of 2d LJ melt
|
||||
nemd: non-equilibrium MD of 2d sheared system
|
||||
obstacle: flow around two voids in a 2d channel
|
||||
peptide: dynamics of a small solvated peptide chain (5-mer)
|
||||
pour: pouring of granular particles into a 3d box, then chute flow
|
||||
|
||||
@ -33,11 +33,11 @@ time or interest; others are just a lot of work!
|
||||
</P>
|
||||
<UL><LI>Monte Carlo bond-swapping for polymers (was in Fortran LAMMPS)
|
||||
<LI>torsional shear boundary conditions and temperature calculation
|
||||
<LI>NPT with changing box shape (Parinello-Rahman)
|
||||
<LI>bond creation potentials
|
||||
<LI>point dipole force fields
|
||||
<LI>long-range point dipole solver
|
||||
<LI>REBO bond-order potential
|
||||
<LI>ReaxFF force field from Bill Goddard's group
|
||||
<LI>Parinello-Rahman non-rectilinear simulation box
|
||||
<LI>ReaxFF force field from Bill Goddard's group
|
||||
</UL>
|
||||
<HR>
|
||||
|
||||
|
||||
@ -30,11 +30,11 @@ time or interest; others are just a lot of work!
|
||||
|
||||
Monte Carlo bond-swapping for polymers (was in Fortran LAMMPS)
|
||||
torsional shear boundary conditions and temperature calculation
|
||||
NPT with changing box shape (Parinello-Rahman)
|
||||
bond creation potentials
|
||||
point dipole force fields
|
||||
long-range point dipole solver
|
||||
REBO bond-order potential
|
||||
ReaxFF force field from Bill Goddard's group
|
||||
Parinello-Rahman non-rectilinear simulation box :ul
|
||||
ReaxFF force field from Bill Goddard's group :ul
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -109,6 +109,8 @@ LAMMPS.
|
||||
<LI> metals
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||||
<LI> granular materials
|
||||
<LI> coarse-grained mesoscale models
|
||||
<LI> ellipsoidal particles
|
||||
<LI> point dipolar particles
|
||||
<LI> hybrid systems
|
||||
</UL>
|
||||
<H4>Force fields:
|
||||
@ -118,12 +120,15 @@ LAMMPS.
|
||||
<A HREF = "improper_style.html">improper style</A>, <A HREF = "kspace_style.html">kspace style</A>
|
||||
commands)
|
||||
</P>
|
||||
<UL><LI> pairwise potentials: Lennard-Jones, Coulombic, Buckingham, Morse, Yukawa, frictional granular, Debye, soft, DPD, class 2 (COMPASS), tabulated, hybrid
|
||||
<LI> manybody potentials: EAM, Finnis/Sinclair, modified EAM (MEAM), Stillinger-Weber, Tersoff
|
||||
<LI> bond potentials: harmonic, FENE, Morse, nonlinear, class 2, quartic (breakable), hybrid
|
||||
<LI> angle potentials: harmonic, CHARMM, cosine, cosine/squared, class 2 (COMPASS), hybrid
|
||||
<LI> dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, class 2 (COMPASS), OPLS, hybrid
|
||||
<LI> improper potentials: harmonic, cvff, class 2 (COMPASS), hybrid
|
||||
<UL><LI> pairwise potentials: Lennard-Jones, Buckingham, Morse, Yukawa, Debye, soft, class 2 (COMPASS), tabulated
|
||||
<LI> charged pairwise potentials: Coulombic, point-dipole
|
||||
<LI> manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), Stillinger-Weber, Tersoff
|
||||
<LI> coarse-grain potentials: granular, DPD, GayBerne, colloidal
|
||||
<LI> bond potentials: harmonic, FENE, Morse, nonlinear, class 2, quartic (breakable)
|
||||
<LI> angle potentials: harmonic, CHARMM, cosine, cosine/squared, class 2 (COMPASS)
|
||||
<LI> dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, class 2 (COMPASS), OPLS
|
||||
<LI> improper potentials: harmonic, cvff, class 2 (COMPASS)
|
||||
<LI> hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used
|
||||
<LI> polymer potentials: all-atom, united-atom, bead-spring, breakable
|
||||
<LI> water potentials: TIP3P, TIP4P, SPC
|
||||
<LI> long-range Coulombics: Ewald, PPPM (similar to particle-mesh Ewald)
|
||||
@ -144,10 +149,12 @@ commands)
|
||||
</H4>
|
||||
<P>(<A HREF = "fix.html">fix</A> command)
|
||||
</P>
|
||||
<UL><LI> constant NVE, NVT, NPT, NPH integrators
|
||||
<UL><LI> 2d or 3d systems
|
||||
<LI> orthogonal or triclinic simulation domains
|
||||
<LI> constant NVE, NVT, NPT, NPH integrators
|
||||
<LI> thermostatting options for groups and geometric regions of atoms
|
||||
<LI> pressure control via Nose/Hoover barostatting in 1 to 3 dimensions
|
||||
<LI> volume rescaling
|
||||
<LI> simulation box deformation (tensile and shear)
|
||||
<LI> altered motion via velocity and force constraints
|
||||
<LI> harmonic (umbrella) constraint forces
|
||||
<LI> dragging of atoms to new positions
|
||||
@ -155,6 +162,7 @@ commands)
|
||||
<LI> SHAKE bond and angle constraints
|
||||
<LI> wall constraints of various kinds
|
||||
<LI> targeted molecular dynamics (TMD) constraints
|
||||
<LI> non-equilibrium molecular dynamics (NEMD)
|
||||
<LI> gravity
|
||||
</UL>
|
||||
<H4>Integrators:
|
||||
@ -172,10 +180,12 @@ commands)
|
||||
</H4>
|
||||
<P>(<A HREF = "dump.html">dump</A>, <A HREF = "restart.html">restart</A> commands)
|
||||
</P>
|
||||
<UL><LI> binary restart files
|
||||
<LI> text dump files of atom coords, velocities, other per-atom attributes
|
||||
<LI> atom snapshots in native, XYZ, XTC, DCD formats
|
||||
<LI> per-atom energy, stress, centro-symmetry parameter
|
||||
<UL><LI> log file of thermodynanmic info
|
||||
<LI> text dump files of atom coords, velocities, other per-atom quantities
|
||||
<LI> binary restart files
|
||||
<LI> per-atom energy, stress, centro-symmetry parameter
|
||||
<LI> user-defined system-wide (log file) or per-atom (dump file) calculations
|
||||
<LI> atom snapshots in native, XYZ, XTC, DCD formats
|
||||
</UL>
|
||||
<H4>Pre- and post-processing:
|
||||
</H4>
|
||||
@ -230,14 +240,14 @@ to all atoms and bonds. LAMMPS will not build molecular systems and
|
||||
assign force-field parameters for you.
|
||||
</P>
|
||||
<P>For atomic systems LAMMPS provides a <A HREF = "create_atoms.html">create_atoms</A>
|
||||
command which places atoms on solid-state lattices (fcc, bcc, etc).
|
||||
Assigning small numbers of force field coefficients can be done via
|
||||
the <A HREF = "pair_coeff.html">pair coeff</A>, <A HREF = "bond_coeff.html">bond coeff</A>, <A HREF = "angle_coeff.html">angle
|
||||
coeff</A>, etc commands. For molecular systems or more
|
||||
complicated simulation geometries, users typically use another code as
|
||||
a builder and convert its output to LAMMPS input format, or write
|
||||
their own code to generate atom coordinate and molecular topology for
|
||||
LAMMPS to read in.
|
||||
command which places atoms on solid-state lattices (fcc, bcc,
|
||||
user-defined, etc). Assigning small numbers of force field
|
||||
coefficients can be done via the <A HREF = "pair_coeff.html">pair coeff</A>, <A HREF = "bond_coeff.html">bond
|
||||
coeff</A>, <A HREF = "angle_coeff.html">angle coeff</A>, etc commands.
|
||||
For molecular systems or more complicated simulation geometries, users
|
||||
typically use another code as a builder and convert its output to
|
||||
LAMMPS input format, or write their own code to generate atom
|
||||
coordinate and molecular topology for LAMMPS to read in.
|
||||
</P>
|
||||
<P>For complicated molecular systems (e.g. a protein), a multitude of
|
||||
topology information and hundreds of force-field coefficients must
|
||||
@ -251,12 +261,13 @@ section</A> can assist in this process.
|
||||
post-process these files with their own analysis tools or re-format
|
||||
them for input into other programs, including visualization packages.
|
||||
If you are convinced you need to compute something on-the-fly as
|
||||
LAMMPS runs, see <A HREF = "Section_modify.html">this section</A> for a discussion of how you
|
||||
can use the <A HREF = "dump.html">dump</A> and <A HREF = "fix.html">fix</A> commands to print out
|
||||
data of your choosing. Keep in mind that complicated computations can
|
||||
slow down the molecular dynamics timestepping, particularly if the
|
||||
computations are not parallel, so it is often better to leave such
|
||||
analysis to post-processing codes.
|
||||
LAMMPS runs, see <A HREF = "Section_modify.html">this section</A> for a discussion
|
||||
of how you can use the <A HREF = "dump.html">dump</A> and <A HREF = "compute.html">compute</A> and
|
||||
<A HREF = "fix.html">fix</A> commands to print out data of your choosing. Keep in
|
||||
mind that complicated computations can slow down the molecular
|
||||
dynamics timestepping, particularly if the computations are not
|
||||
parallel, so it is often better to leave such analysis to
|
||||
post-processing codes.
|
||||
</P>
|
||||
<P>A very simple (yet fast) visualizer is provided with the LAMMPS
|
||||
package - see the <A HREF = "Section_tools.html#xmovie">xmovie</A> tool in <A HREF = "Section_tools.html">this
|
||||
@ -265,10 +276,11 @@ atomic coordinates and animates them. We find it very useful for
|
||||
debugging purposes. For high-quality visualization we recommend the
|
||||
following packages:
|
||||
</P>
|
||||
<UL><LI><A HREF = "http://www.bmsc.washington.edu/raster3d/raster3d.html">Raster3d</A>
|
||||
<LI><A HREF = "http://www.openrasmol.org">RasMol</A>
|
||||
<LI><A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A>
|
||||
<LI><A HREF = "http://164.107.79.177/Archive/Graphics/A">AtomEye</A>
|
||||
<UL><LI><A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A>
|
||||
<LI><A HREF = "http://164.107.79.177/Archive/Graphics/A">AtomEye</A>
|
||||
<LI><A HREF = "http://pymol.sourceforge.net">PyMol</A>
|
||||
<LI><A HREF = "http://www.bmsc.washington.edu/raster3d/raster3d.html">Raster3d</A>
|
||||
<LI><A HREF = "http://www.openrasmol.org">RasMol</A>
|
||||
</UL>
|
||||
<P>Other features that LAMMPS does not yet (and may never) support are
|
||||
discussed in <A HREF = "Section_history.html">this section</A>.
|
||||
@ -441,55 +453,68 @@ features in LAMMPS:
|
||||
</P>
|
||||
|
||||
|
||||
Ewald and PPPM solvers: Roy Pollock (LLNL)
|
||||
rRESPA: Mark Stevens & Paul Crozier (Sandia)
|
||||
NVT/NPT integrators: Mark Stevens (Sandia)
|
||||
class 2 force fields: Eric Simon (Cray)
|
||||
HTFN energy minimizer: Todd Plantenga (Sandia)
|
||||
msi2lmp tool: Steve Lustig (Dupont), Mike Peachey & John Carpenter (Cray)
|
||||
CHARMM force fields: Paul Crozier (Sandia)
|
||||
2d Ewald/PPPM: Paul Crozier (Sandia)
|
||||
granular force fields and BC: Leo Silbert & Gary Grest (Sandia)
|
||||
multi-harmonic dihedral potential: Mathias Putz (Sandia)
|
||||
EAM potentials: Stephen Foiles (Sandia)
|
||||
parallel tempering: Mark Sears (Sandia)
|
||||
lmp2cfg and lmp2traj tools: Ara Kooser, Jeff Greathouse, Andrey Kalinichev (Sandia)
|
||||
FFT support for SGI SCLS (Altix): Jim Shepherd (Ga Tech)
|
||||
targeted molecular dynamics (TMD): Paul Crozier (Sandia), Christian Burisch (Bochum University, Germany)
|
||||
force tables for long-range Coulombics: Paul Crozier (Sandia)
|
||||
radial distribution functions: Paul Crozier & Jeff Greathouse (Sandia)
|
||||
Morse bond potential: Jeff Greathouse (Sandia)
|
||||
CHARMM <-> LAMMPS tool: Pieter in't Veld and Paul Crozier (Sandia)
|
||||
AMBER <-> LAMMPS tool: Keir Novik (Univ College London) and Vikas Varshney (U Akron)
|
||||
electric field fix: Christina Payne (Vanderbilt U)
|
||||
cylindrical indenter fix: Ravi Agrawal (Northwestern U)
|
||||
compressed dump files: Erik Luijten (U Illinois)
|
||||
thermodynamics enhanced by fix quantities: Aidan Thompson (Sandia)
|
||||
uniaxial strain fix: Carsten Svaneborg (Max Planck Institute)
|
||||
TIP4P potential (4-site water): Ahmed Ismail and Amalie Frischknecht (Sandia)
|
||||
dissipative particle dynamics (DPD) potentials: Kurt Smith (U Pitt) and Frank van Swol (Sandia)
|
||||
Finnis/Sinclair EAM: Tim Lau (MIT)
|
||||
helix dihedral potential : Naveen Michaud-Agrawal (Johns Hopkins U) and Mark Stevens (Sandia)
|
||||
cosine/squared angle potential : Naveen Michaud-Agrawal (Johns Hopkins U)
|
||||
EAM CoAl and AlCu potentials : Kwang-Reoul Lee (KIST, Korea)
|
||||
self spring fix : Naveen Michaud-Agrawal (Johns Hopkins U)
|
||||
radius-of-gyration spring fix : Naveen Michaud-Agrawal (Johns Hopkins U) and Paul Crozier (Sandia)
|
||||
lj/smooth pair potential : Craig Maloney (UCSB)
|
||||
grain boundary orientation fix : Koenraad Janssens and David Olmsted (SNL)
|
||||
DCD and XTC dump styles: Naveen Michaud-Agrawal (Johns Hopkins U)
|
||||
breakable bond quartic potential: Chris Lorenz and Mark Stevens (SNL)
|
||||
faster pair hybrid potential: James Fischer (High Performance Technologies, Inc), Vincent Natoli and David Richie (Stone Ridge Technology)
|
||||
POEMS coupled rigid body integrator: Rudranarayan Mukherjee (RPI)
|
||||
OPLS dihedral potential: Mark Stevens (Sandia)
|
||||
multi-letter variable names : Naveen Michaud-Agrawal (Johns Hopkins U)
|
||||
fix momentum and recenter : Naveen Michaud-Agrawal (Johns Hopkins U)
|
||||
LJ tail corrections for energy/pressure : Paul Crozier (Sandia)
|
||||
region prism : Pieter in't Veld (Sandia)
|
||||
Stillinger-Weber and Tersoff potentials : Aidan Thompson (Sandia)
|
||||
fix wall/lj126 : Mark Stevens (Sandia)
|
||||
optimized pair potentials for lj/cut, charmm/long, eam, morse : James Fischer (High Performance Tech), David Richie and Vincent Natol (Stone Ridge Technologies)
|
||||
MEAM potential : Greg Wagner (Sandia)
|
||||
fix ave/time and fix ave/spatial : Pieter in 't Veld (Sandia)
|
||||
thermo_extract tool: Vikas Varshney (Wright Patterson AFB)
|
||||
triclinic (non-orthogonal) simulation domains : Pieter in 't Veld (Sandia)
|
||||
MATLAB post-processing scripts : Arun Subramaniyan (Purdue)
|
||||
neighbor multi and communicate multi : Pieter in 't Veld (Sandia)
|
||||
fix heat : Paul Crozier and Ed Webb (Sandia)
|
||||
colloid potentials : Pieter in 't Veld (Sandia)
|
||||
ellipsoidal particles : Mike Brown (Sandia)
|
||||
GayBerne potential : Mike Brown (Sandia)
|
||||
tensile and shear box deformations
|
||||
|
||||
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
|
||||
<TR><TD >Ewald and PPPM solvers</TD><TD > Roy Pollock (LLNL)</TD></TR>
|
||||
<TR><TD >rRESPA</TD><TD > Mark Stevens & Paul Crozier (Sandia)</TD></TR>
|
||||
<TR><TD >NVT/NPT integrators</TD><TD > Mark Stevens (Sandia)</TD></TR>
|
||||
<TR><TD >class 2 force fields</TD><TD > Eric Simon (Cray)</TD></TR>
|
||||
<TR><TD >HTFN energy minimizer</TD><TD > Todd Plantenga (Sandia)</TD></TR>
|
||||
<TR><TD >msi2lmp tool</TD><TD > Steve Lustig (Dupont), Mike Peachey & John Carpenter (Cray)</TD></TR>
|
||||
<TR><TD >CHARMM force fields</TD><TD > Paul Crozier (Sandia)</TD></TR>
|
||||
<TR><TD >2d Ewald/PPPM</TD><TD > Paul Crozier (Sandia)</TD></TR>
|
||||
<TR><TD >granular force fields and BC</TD><TD > Leo Silbert & Gary Grest (Sandia)</TD></TR>
|
||||
<TR><TD >multi-harmonic dihedral potential</TD><TD > Mathias Putz (Sandia)</TD></TR>
|
||||
<TR><TD >EAM potentials</TD><TD > Stephen Foiles (Sandia)</TD></TR>
|
||||
<TR><TD >parallel tempering</TD><TD > Mark Sears (Sandia)</TD></TR>
|
||||
<TR><TD >lmp2cfg and lmp2traj tools</TD><TD > Ara Kooser, Jeff Greathouse, Andrey Kalinichev (Sandia)</TD></TR>
|
||||
<TR><TD >FFT support for SGI SCLS (Altix)</TD><TD > Jim Shepherd (Ga Tech)</TD></TR>
|
||||
<TR><TD >targeted molecular dynamics (TMD)</TD><TD > Paul Crozier (Sandia), Christian Burisch (Bochum University, Germany)</TD></TR>
|
||||
<TR><TD >force tables for long-range Coulombics</TD><TD > Paul Crozier (Sandia)</TD></TR>
|
||||
<TR><TD >radial distribution functions</TD><TD > Paul Crozier & Jeff Greathouse (Sandia)</TD></TR>
|
||||
<TR><TD >Morse bond potential</TD><TD > Jeff Greathouse (Sandia)</TD></TR>
|
||||
<TR><TD >CHARMM <-> LAMMPS tool</TD><TD > Pieter in't Veld and Paul Crozier (Sandia)</TD></TR>
|
||||
<TR><TD >AMBER <-> LAMMPS tool</TD><TD > Keir Novik (Univ College London) and Vikas Varshney (U Akron)</TD></TR>
|
||||
<TR><TD >electric field fix</TD><TD > Christina Payne (Vanderbilt U)</TD></TR>
|
||||
<TR><TD >cylindrical indenter fix</TD><TD > Ravi Agrawal (Northwestern U)</TD></TR>
|
||||
<TR><TD >compressed dump files</TD><TD > Erik Luijten (U Illinois)</TD></TR>
|
||||
<TR><TD >thermodynamics enhanced by fix quantities</TD><TD > Aidan Thompson (Sandia)</TD></TR>
|
||||
<TR><TD >uniaxial strain fix</TD><TD > Carsten Svaneborg (Max Planck Institute)</TD></TR>
|
||||
<TR><TD >TIP4P potential (4-site water)</TD><TD > Ahmed Ismail and Amalie Frischknecht (Sandia)</TD></TR>
|
||||
<TR><TD >dissipative particle dynamics (DPD) potentials</TD><TD > Kurt Smith (U Pitt) and Frank van Swol (Sandia)</TD></TR>
|
||||
<TR><TD >Finnis/Sinclair EAM</TD><TD > Tim Lau (MIT)</TD></TR>
|
||||
<TR><TD >helix dihedral potential </TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U) and Mark Stevens (Sandia)</TD></TR>
|
||||
<TR><TD >cosine/squared angle potential </TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U)</TD></TR>
|
||||
<TR><TD >EAM CoAl and AlCu potentials </TD><TD > Kwang-Reoul Lee (KIST, Korea)</TD></TR>
|
||||
<TR><TD >self spring fix </TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U)</TD></TR>
|
||||
<TR><TD >radius-of-gyration spring fix </TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U) and Paul Crozier (Sandia)</TD></TR>
|
||||
<TR><TD >lj/smooth pair potential </TD><TD > Craig Maloney (UCSB) </TD></TR>
|
||||
<TR><TD >grain boundary orientation fix </TD><TD > Koenraad Janssens and David Olmsted (SNL)</TD></TR>
|
||||
<TR><TD >DCD and XTC dump styles</TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U)</TD></TR>
|
||||
<TR><TD >breakable bond quartic potential</TD><TD > Chris Lorenz and Mark Stevens (SNL)</TD></TR>
|
||||
<TR><TD >faster pair hybrid potential</TD><TD > James Fischer (High Performance Technologies, Inc), Vincent Natoli and David Richie (Stone Ridge Technology)</TD></TR>
|
||||
<TR><TD >POEMS coupled rigid body integrator</TD><TD > Rudranarayan Mukherjee (RPI)</TD></TR>
|
||||
<TR><TD >OPLS dihedral potential</TD><TD > Mark Stevens (Sandia)</TD></TR>
|
||||
<TR><TD >multi-letter variable names </TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U)</TD></TR>
|
||||
<TR><TD >fix momentum and recenter </TD><TD > Naveen Michaud-Agrawal (Johns Hopkins U)</TD></TR>
|
||||
<TR><TD >LJ tail corrections for energy/pressure </TD><TD > Paul Crozier (Sandia)</TD></TR>
|
||||
<TR><TD >region prism </TD><TD > Pieter in't Veld (Sandia)</TD></TR>
|
||||
<TR><TD >Stillinger-Weber and Tersoff potentials </TD><TD > Aidan Thompson (Sandia)</TD></TR>
|
||||
<TR><TD >fix wall/lj126 </TD><TD > Mark Stevens (Sandia)</TD></TR>
|
||||
<TR><TD >optimized pair potentials for lj/cut, charmm/long, eam, morse </TD><TD > James Fischer (High Performance Tech), David Richie and Vincent Natol (Stone Ridge Technologies)</TD></TR>
|
||||
<TR><TD >MEAM potential </TD><TD > Greg Wagner (Sandia)
|
||||
<TR><TD >NEMD SLLOD integration </TD><TD > Pieter in 't Veld (Sandia)</TD></TR>
|
||||
<TR><TD >pymol_asphere viz tool </TD><TD > Mike Brown (Sandia)
|
||||
</TD></TR></TABLE></DIV>
|
||||
|
||||
<P>Other CRADA partners involved in the design and testing of LAMMPS were
|
||||
|
||||
@ -105,6 +105,8 @@ Kinds of systems LAMMPS can simulate: :h4
|
||||
metals
|
||||
granular materials
|
||||
coarse-grained mesoscale models
|
||||
ellipsoidal particles
|
||||
point dipolar particles
|
||||
hybrid systems :ul
|
||||
|
||||
Force fields: :h4
|
||||
@ -113,18 +115,21 @@ Force fields: :h4
|
||||
"improper style"_improper_style.html, "kspace style"_kspace_style.html
|
||||
commands)
|
||||
|
||||
pairwise potentials: Lennard-Jones, Coulombic, Buckingham, Morse, \
|
||||
Yukawa, frictional granular, Debye, soft, DPD, class 2 (COMPASS), \
|
||||
tabulated, hybrid
|
||||
manybody potentials: EAM, Finnis/Sinclair, modified EAM (MEAM), \
|
||||
pairwise potentials: Lennard-Jones, Buckingham, Morse, \
|
||||
Yukawa, Debye, soft, class 2 (COMPASS), tabulated
|
||||
charged pairwise potentials: Coulombic, point-dipole
|
||||
manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \
|
||||
Stillinger-Weber, Tersoff
|
||||
coarse-grain potentials: granular, DPD, GayBerne, colloidal
|
||||
bond potentials: harmonic, FENE, Morse, nonlinear, class 2, \
|
||||
quartic (breakable), hybrid
|
||||
quartic (breakable)
|
||||
angle potentials: harmonic, CHARMM, cosine, cosine/squared, \
|
||||
class 2 (COMPASS), hybrid
|
||||
class 2 (COMPASS)
|
||||
dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, \
|
||||
class 2 (COMPASS), OPLS, hybrid
|
||||
improper potentials: harmonic, cvff, class 2 (COMPASS), hybrid
|
||||
class 2 (COMPASS), OPLS
|
||||
improper potentials: harmonic, cvff, class 2 (COMPASS)
|
||||
hybrid potentials: multiple pair, bond, angle, dihedral, improper \
|
||||
potentials can be used
|
||||
polymer potentials: all-atom, united-atom, bead-spring, breakable
|
||||
water potentials: TIP3P, TIP4P, SPC
|
||||
long-range Coulombics: Ewald, PPPM (similar to particle-mesh Ewald)
|
||||
@ -143,18 +148,19 @@ Creation of atoms: :h4
|
||||
Ensembles, constraints, and boundary conditions: :h4
|
||||
("fix"_fix.html command)
|
||||
|
||||
2d or 3d systems
|
||||
orthogonal or non-orthogonal (triclinic symmetry) simulation domains
|
||||
constant NVE, NVT, NPT, NPH integrators
|
||||
thermostatting options for groups and geometric regions of atoms
|
||||
pressure control via Nose/Hoover barostatting in 1 to 3 dimensions
|
||||
volume rescaling
|
||||
altered motion via velocity and force constraints
|
||||
simulation box deformation (tensile and shear)
|
||||
harmonic (umbrella) constraint forces
|
||||
dragging of atoms to new positions
|
||||
independent or coupled rigid body integration
|
||||
SHAKE bond and angle constraints
|
||||
wall constraints of various kinds
|
||||
walls of various kinds
|
||||
targeted molecular dynamics (TMD) constraints
|
||||
gravity :ul
|
||||
non-equilibrium molecular dynamics (NEMD)
|
||||
variety of additional boundary conditions and constraints :ul
|
||||
|
||||
Integrators: :h4
|
||||
("run"_run.html, "run_style"_run_style.html, "temper"_temper.html commands)
|
||||
@ -164,15 +170,17 @@ Integrators: :h4
|
||||
energy minimization via conjugate gradient relaxation
|
||||
rRESPA hierarchical timestepping
|
||||
parallel tempering (replica exchange)
|
||||
multiple independent simulations simultaneously :ul
|
||||
run multiple independent simulations simultaneously :ul
|
||||
|
||||
Output: :h4
|
||||
("dump"_dump.html, "restart"_restart.html commands)
|
||||
|
||||
log file of thermodynanmic info
|
||||
text dump files of atom coords, velocities, other per-atom quantities
|
||||
binary restart files
|
||||
text dump files of atom coords, velocities, other per-atom attributes
|
||||
atom snapshots in native, XYZ, XTC, DCD formats
|
||||
per-atom energy, stress, centro-symmetry parameter :ul
|
||||
per-atom energy, stress, centro-symmetry parameter
|
||||
user-defined system-wide (log file) or per-atom (dump file) calculations
|
||||
atom snapshots in native, XYZ, XTC, DCD formats :ul
|
||||
|
||||
Pre- and post-processing: :h4
|
||||
|
||||
@ -226,14 +234,14 @@ to all atoms and bonds. LAMMPS will not build molecular systems and
|
||||
assign force-field parameters for you.
|
||||
|
||||
For atomic systems LAMMPS provides a "create_atoms"_create_atoms.html
|
||||
command which places atoms on solid-state lattices (fcc, bcc, etc).
|
||||
Assigning small numbers of force field coefficients can be done via
|
||||
the "pair coeff"_pair_coeff.html, "bond coeff"_bond_coeff.html, "angle
|
||||
coeff"_angle_coeff.html, etc commands. For molecular systems or more
|
||||
complicated simulation geometries, users typically use another code as
|
||||
a builder and convert its output to LAMMPS input format, or write
|
||||
their own code to generate atom coordinate and molecular topology for
|
||||
LAMMPS to read in.
|
||||
command which places atoms on solid-state lattices (fcc, bcc,
|
||||
user-defined, etc). Assigning small numbers of force field
|
||||
coefficients can be done via the "pair coeff"_pair_coeff.html, "bond
|
||||
coeff"_bond_coeff.html, "angle coeff"_angle_coeff.html, etc commands.
|
||||
For molecular systems or more complicated simulation geometries, users
|
||||
typically use another code as a builder and convert its output to
|
||||
LAMMPS input format, or write their own code to generate atom
|
||||
coordinate and molecular topology for LAMMPS to read in.
|
||||
|
||||
For complicated molecular systems (e.g. a protein), a multitude of
|
||||
topology information and hundreds of force-field coefficients must
|
||||
@ -247,12 +255,13 @@ Similarly, LAMMPS creates output files in a simple format. Most users
|
||||
post-process these files with their own analysis tools or re-format
|
||||
them for input into other programs, including visualization packages.
|
||||
If you are convinced you need to compute something on-the-fly as
|
||||
LAMMPS runs, see "this section"_Section_modify.html for a discussion of how you
|
||||
can use the "dump"_dump.html and "fix"_fix.html commands to print out
|
||||
data of your choosing. Keep in mind that complicated computations can
|
||||
slow down the molecular dynamics timestepping, particularly if the
|
||||
computations are not parallel, so it is often better to leave such
|
||||
analysis to post-processing codes.
|
||||
LAMMPS runs, see "this section"_Section_modify.html for a discussion
|
||||
of how you can use the "dump"_dump.html and "compute"_compute.html and
|
||||
"fix"_fix.html commands to print out data of your choosing. Keep in
|
||||
mind that complicated computations can slow down the molecular
|
||||
dynamics timestepping, particularly if the computations are not
|
||||
parallel, so it is often better to leave such analysis to
|
||||
post-processing codes.
|
||||
|
||||
A very simple (yet fast) visualizer is provided with the LAMMPS
|
||||
package - see the "xmovie"_Section_tools.html#xmovie tool in "this
|
||||
@ -261,10 +270,11 @@ atomic coordinates and animates them. We find it very useful for
|
||||
debugging purposes. For high-quality visualization we recommend the
|
||||
following packages:
|
||||
|
||||
"Raster3d"_http://www.bmsc.washington.edu/raster3d/raster3d.html
|
||||
"RasMol"_http://www.openrasmol.org
|
||||
"VMD"_http://www.ks.uiuc.edu/Research/vmd
|
||||
"AtomEye"_http://164.107.79.177/Archive/Graphics/A :ul
|
||||
"AtomEye"_http://164.107.79.177/Archive/Graphics/A
|
||||
"PyMol"_http://pymol.sourceforge.net
|
||||
"Raster3d"_http://www.bmsc.washington.edu/raster3d/raster3d.html
|
||||
"RasMol"_http://www.openrasmol.org :ul
|
||||
|
||||
Other features that LAMMPS does not yet (and may never) support are
|
||||
discussed in "this section"_Section_history.html.
|
||||
@ -479,7 +489,19 @@ region prism : Pieter in't Veld (Sandia)
|
||||
Stillinger-Weber and Tersoff potentials : Aidan Thompson (Sandia)
|
||||
fix wall/lj126 : Mark Stevens (Sandia)
|
||||
optimized pair potentials for lj/cut, charmm/long, eam, morse : James Fischer (High Performance Tech), David Richie and Vincent Natol (Stone Ridge Technologies)
|
||||
MEAM potential : Greg Wagner (Sandia) :tb(s=:)
|
||||
MEAM potential : Greg Wagner (Sandia)
|
||||
fix ave/time and fix ave/spatial : Pieter in 't Veld (Sandia)
|
||||
thermo_extract tool: Vikas Varshney (Wright Patterson AFB)
|
||||
triclinic (non-orthogonal) simulation domains : Pieter in 't Veld (Sandia)
|
||||
MATLAB post-processing scripts : Arun Subramaniyan (Purdue)
|
||||
neighbor multi and communicate multi : Pieter in 't Veld (Sandia)
|
||||
fix heat : Paul Crozier and Ed Webb (Sandia)
|
||||
colloid potentials : Pieter in 't Veld (Sandia)
|
||||
ellipsoidal particles : Mike Brown (Sandia)
|
||||
GayBerne potential : Mike Brown (Sandia)
|
||||
tensile and shear box deformations :
|
||||
NEMD SLLOD integration : Pieter in 't Veld (Sandia)
|
||||
pymol_asphere viz tool : Mike Brown (Sandia) :tb(s=:)
|
||||
|
||||
Other CRADA partners involved in the design and testing of LAMMPS were
|
||||
|
||||
|
||||
@ -274,9 +274,10 @@ can see the list of packages by typing "make package". The current
|
||||
list of packages is as follows:
|
||||
</P>
|
||||
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
|
||||
<TR><TD >asphere </TD><TD > aspherical particles</TD></TR>
|
||||
<TR><TD >asphere </TD><TD > aspherical particles and force fields</TD></TR>
|
||||
<TR><TD >class2 </TD><TD > class 2 force fields</TD></TR>
|
||||
<TR><TD >colloid </TD><TD > colloidal particle force fields</TD></TR>
|
||||
<TR><TD >dipole </TD><TD > point dipole particles and force fields</TD></TR>
|
||||
<TR><TD >dpd </TD><TD > dissipative particle dynamics (DPD) force field</TD></TR>
|
||||
<TR><TD >granular </TD><TD > force fields and boundary conditions for granular systems</TD></TR>
|
||||
<TR><TD >kspace </TD><TD > long-range Ewald and particle-mesh (PPPM) solvers</TD></TR>
|
||||
|
||||
@ -268,9 +268,10 @@ fields for molecular systems or granular systems are in packages. You
|
||||
can see the list of packages by typing "make package". The current
|
||||
list of packages is as follows:
|
||||
|
||||
asphere : aspherical particles
|
||||
asphere : aspherical particles and force fields
|
||||
class2 : class 2 force fields
|
||||
colloid : colloidal particle force fields
|
||||
dipole : point dipole particles and force fields
|
||||
dpd : dissipative particle dynamics (DPD) force field
|
||||
granular : force fields and boundary conditions for granular systems
|
||||
kspace : long-range Ewald and particle-mesh (PPPM) solvers
|
||||
|
||||
@ -54,7 +54,7 @@ own sub-directories with their own Makefiles.
|
||||
<LI><A HREF = "#matlab">matlab</A>
|
||||
<LI><A HREF = "#micelle">micelle2d</A>
|
||||
<LI><A HREF = "#msi">msi2lmp</A>
|
||||
<LI><A HREF = "#replicate">replicate</A>
|
||||
<LI><A HREF = "#pymol">pymol_asphere</A>
|
||||
<LI><A HREF = "#restart">restart2data</A>
|
||||
<LI><A HREF = "#thermo_extract">thermo_extract</A>
|
||||
<LI><A HREF = "#xmovie">xmovie</A>
|
||||
@ -227,17 +227,20 @@ experiment with it yourself.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<H4><A NAME = "replicate"></A>replicate tool
|
||||
<H4><A NAME = "pymol"></A>pymol_asphere tool
|
||||
</H4>
|
||||
<P>The file replicate.c takes a LAMMPS data file and replicates it into a
|
||||
larger system. The syntax for running the tool is
|
||||
<P>The pymol_asphere sub-directory contains a tool for converting a
|
||||
LAMMPS dump file that contains orientation info for ellipsoidal
|
||||
particles into an input file for the <A HREF = "http://pymol.sourceforge.net">PyMol visualization
|
||||
package</A>.
|
||||
</P>
|
||||
<PRE>replicate <B>options</B> < infile > outfile
|
||||
</PRE>
|
||||
<P>See the top of the replicate.c file for a discussion of the options.
|
||||
This tool is used by some of the <A HREF = "Section_perf.html">LAMMPS benchmarks</A>
|
||||
for creating larger systems to run scaled-size problems on multiple
|
||||
processors.
|
||||
|
||||
|
||||
<P>Specifically, the tool triangulates the ellipsoids so they can be
|
||||
viewed as true ellipsoidal particles within PyMol. See the README and
|
||||
examples directory within pymol_asphere for more information.
|
||||
</P>
|
||||
<P>This tool was written by Mike Brown at Sandia.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
|
||||
@ -50,7 +50,7 @@ own sub-directories with their own Makefiles.
|
||||
"matlab"_#matlab
|
||||
"micelle2d"_#micelle
|
||||
"msi2lmp"_#msi
|
||||
"replicate"_#replicate
|
||||
"pymol_asphere"_#pymol
|
||||
"restart2data"_#restart
|
||||
"thermo_extract"_#thermo_extract
|
||||
"xmovie"_#xmovie :ul
|
||||
@ -223,17 +223,20 @@ experiment with it yourself.
|
||||
|
||||
:line
|
||||
|
||||
replicate tool :h4,link(replicate)
|
||||
pymol_asphere tool :h4,link(pymol)
|
||||
|
||||
The file replicate.c takes a LAMMPS data file and replicates it into a
|
||||
larger system. The syntax for running the tool is
|
||||
The pymol_asphere sub-directory contains a tool for converting a
|
||||
LAMMPS dump file that contains orientation info for ellipsoidal
|
||||
particles into an input file for the "PyMol visualization
|
||||
package"_pymol.
|
||||
|
||||
replicate [options] < infile > outfile :pre
|
||||
:link(pymol,http://pymol.sourceforge.net)
|
||||
|
||||
See the top of the replicate.c file for a discussion of the options.
|
||||
This tool is used by some of the "LAMMPS benchmarks"_Section_perf.html
|
||||
for creating larger systems to run scaled-size problems on multiple
|
||||
processors.
|
||||
Specifically, the tool triangulates the ellipsoids so they can be
|
||||
viewed as true ellipsoidal particles within PyMol. See the README and
|
||||
examples directory within pymol_asphere for more information.
|
||||
|
||||
This tool was written by Mike Brown at Sandia.
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -20,7 +20,7 @@
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>compute myTemp all temp/deform myDeform
|
||||
<PRE>compute myTemp all temp/deform
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
|
||||
@ -17,7 +17,7 @@ temp/deform = style name of this compute command :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute myTemp all temp/deform myDeform :pre
|
||||
compute myTemp all temp/deform :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
|
||||
@ -61,10 +61,10 @@ remapping either atom coordinates or velocities to the changing
|
||||
simulation box. To use fix nvt/sllod, fix deform should NOT remap
|
||||
atom positions, because fix nvt/sllod adjusts the atom positions and
|
||||
velocities to create a velocity profile that matches the changing box
|
||||
size/shape. Fix deform SHOUDLD remap atom velocities when atoms cross
|
||||
size/shape. Fix deform SHOULD remap atom velocities when atoms cross
|
||||
periodic boundaries since that is consistent with maintaining the
|
||||
velocity profile created by fix nvt/sllod. LAMMPS will warn you if
|
||||
this setting is not consistent.
|
||||
velocity profile created by fix nvt/sllod. LAMMPS will give an
|
||||
error if this setting is not consistent.
|
||||
</P>
|
||||
<P>The SLLOD equations of motion coupled to a Nose/Hoover thermostat are
|
||||
discussed in <A HREF = "#Tuckerman">(Tuckerman)</A> (eqs 4 and 5), which is what is
|
||||
|
||||
@ -52,10 +52,10 @@ remapping either atom coordinates or velocities to the changing
|
||||
simulation box. To use fix nvt/sllod, fix deform should NOT remap
|
||||
atom positions, because fix nvt/sllod adjusts the atom positions and
|
||||
velocities to create a velocity profile that matches the changing box
|
||||
size/shape. Fix deform SHOUDLD remap atom velocities when atoms cross
|
||||
size/shape. Fix deform SHOULD remap atom velocities when atoms cross
|
||||
periodic boundaries since that is consistent with maintaining the
|
||||
velocity profile created by fix nvt/sllod. LAMMPS will warn you if
|
||||
this setting is not consistent.
|
||||
velocity profile created by fix nvt/sllod. LAMMPS will give an
|
||||
error if this setting is not consistent.
|
||||
|
||||
The SLLOD equations of motion coupled to a Nose/Hoover thermostat are
|
||||
discussed in "(Tuckerman)"_#Tuckerman (eqs 4 and 5), which is what is
|
||||
|
||||
42
doc/set.html
42
doc/set.html
@ -21,7 +21,7 @@
|
||||
|
||||
<LI>one or more keyword/value pairs may be appended to the args
|
||||
|
||||
<LI>keyword = <I>type</I> or <I>type/fraction</I> or <I>mol</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>vx</I> or <I>vy</I> or <I>vz</I> or <I>charge</I> or <I>dipole</I> or <I>dipole/random</I> or <I>quat</I> or <I>quat/random</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I>
|
||||
<LI>keyword = <I>type</I> or <I>type/fraction</I> or <I>mol</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>vx</I> or <I>vy</I> or <I>vz</I> or <I>charge</I> or <I>dipole</I> or <I>dipole/random</I> or <I>quat/random</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I>
|
||||
|
||||
<PRE> <I>type</I> value = atom type
|
||||
<I>type/fraction</I> values = type fraction seed
|
||||
@ -36,8 +36,9 @@
|
||||
x,y,z = orientation of dipole moment vector
|
||||
<I>dipole/random</I> value = seed
|
||||
seed = random # seed (8 digits or less) for dipole moment orientations
|
||||
<I>quat</I> values = w i j k
|
||||
w,i,j,k = quaternion components (see below)
|
||||
<I>quat</I> values = a b c theta
|
||||
a,b,c = unit vector to rotate particle around via right-hand rule
|
||||
theta = rotation angle in degrees
|
||||
<I>quat/random</I> value = seed
|
||||
seed = random # seed (8 digits or less) for quaternion orientations
|
||||
<I>bond</I> value = bond type for all bonds between selected atoms
|
||||
@ -110,27 +111,30 @@ set by the <A HREF = "dipole.html">dipole</A> command.
|
||||
</P>
|
||||
<P>Keyword <I>dipole/random</I> randomizes the orientation of the dipole
|
||||
moment vectors of the selected atoms. The magnitude of the dipole
|
||||
moment for each atom is set by the <A HREF = "dipole.html">dipole</A> command.
|
||||
Random numbers are used in such a way that the orientation of a
|
||||
particular atom is the same, regardless of how many processors are
|
||||
being used.
|
||||
moment for each atom is set by the <A HREF = "dipole.html">dipole</A> command. For
|
||||
2d systems, the z component of the orientation is set to 0.0. Random
|
||||
numbers are used in such a way that the orientation of a particular
|
||||
atom is the same, regardless of how many processors are being used.
|
||||
</P>
|
||||
<P>Keyword <I>quat</I> uses the specified values as components of a quaternion
|
||||
(4-vector) to set the orientation of the selected atoms. Note that
|
||||
the <A HREF = "shape.html">shape</A> command is used to specify the aspect ratios of
|
||||
an ellipsoidal particle, which is oriented by default with its x-axis
|
||||
along the simulation box's x-axis, and similarly for y and z. If this
|
||||
body is rotated (via the right-hand rule) by an angle theta around a
|
||||
unit vector (a,b,c), then the quaternion that represents its new
|
||||
orientation is given by (cos(theta/2), a*sin(theta/2), b*sin(theta/2),
|
||||
c*sin(theta/2)). These 4 components are the arguments w,i,j,k to the
|
||||
<I>quat</I> keyword. LAMMPS normalizes the quaternion in case (a,b,c) was
|
||||
not a unit vector.
|
||||
<P>Keyword <I>quat</I> uses the specified values to create a quaternion
|
||||
(4-vector) that represents the orientation of the selected atoms.
|
||||
Note that the <A HREF = "shape.html">shape</A> command is used to specify the aspect
|
||||
ratios of an ellipsoidal particle, which is oriented by default with
|
||||
its x-axis along the simulation box's x-axis, and similarly for y and
|
||||
z. If this body is rotated (via the right-hand rule) by an angle
|
||||
theta around a unit rotation vector (a,b,c), then the quaternion that
|
||||
represents its new orientation is given by (cos(theta/2),
|
||||
a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). The theta and a,b,c
|
||||
values are the arguments to the <I>quat</I> keyword. LAMMPS normalizes the
|
||||
quaternion in case (a,b,c) was not specified as a unit vector. For 2d
|
||||
systems, the a,b,c values are ignored, since a rotation vector of
|
||||
(0,0,1) is the only valid choice.
|
||||
</P>
|
||||
<P>Keyword <I>quat/random</I> randomizes the orientation of the quaternion of
|
||||
the selected atoms. Random numbers are used in such a way that the
|
||||
orientation of a particular atom is the same, regardless of how many
|
||||
processors are being used.
|
||||
processors are being used. For 2d systems, only orientations in the
|
||||
xy plane are generated.
|
||||
</P>
|
||||
<P>For the <I>dipole</I> and <I>quat</I> keywords, the <A HREF = "atom_style.html">atom style</A>
|
||||
being used must support the use of dipoles or quaternions.
|
||||
|
||||
43
doc/set.txt
43
doc/set.txt
@ -17,8 +17,7 @@ ID = atom ID or group ID or region ID :l
|
||||
one or more keyword/value pairs may be appended to the args :l
|
||||
keyword = {type} or {type/fraction} or {mol} or \
|
||||
{x} or {y} or {z} or {vx} or {vy} or {vz} or \
|
||||
{charge} or {dipole} or {dipole/random} or \
|
||||
{quat} or {quat/random} or \
|
||||
{charge} or {dipole} or {dipole/random} or {quat/random} or \
|
||||
{bond} or {angle} or {dihedral} or {improper} :l
|
||||
{type} value = atom type
|
||||
{type/fraction} values = type fraction seed
|
||||
@ -33,8 +32,9 @@ keyword = {type} or {type/fraction} or {mol} or \
|
||||
x,y,z = orientation of dipole moment vector
|
||||
{dipole/random} value = seed
|
||||
seed = random # seed (8 digits or less) for dipole moment orientations
|
||||
{quat} values = w i j k
|
||||
w,i,j,k = quaternion components (see below)
|
||||
{quat} values = a b c theta
|
||||
a,b,c = unit vector to rotate particle around via right-hand rule
|
||||
theta = rotation angle in degrees
|
||||
{quat/random} value = seed
|
||||
seed = random # seed (8 digits or less) for quaternion orientations
|
||||
{bond} value = bond type for all bonds between selected atoms
|
||||
@ -106,27 +106,30 @@ set by the "dipole"_dipole.html command.
|
||||
|
||||
Keyword {dipole/random} randomizes the orientation of the dipole
|
||||
moment vectors of the selected atoms. The magnitude of the dipole
|
||||
moment for each atom is set by the "dipole"_dipole.html command.
|
||||
Random numbers are used in such a way that the orientation of a
|
||||
particular atom is the same, regardless of how many processors are
|
||||
being used.
|
||||
moment for each atom is set by the "dipole"_dipole.html command. For
|
||||
2d systems, the z component of the orientation is set to 0.0. Random
|
||||
numbers are used in such a way that the orientation of a particular
|
||||
atom is the same, regardless of how many processors are being used.
|
||||
|
||||
Keyword {quat} uses the specified values as components of a quaternion
|
||||
(4-vector) to set the orientation of the selected atoms. Note that
|
||||
the "shape"_shape.html command is used to specify the aspect ratios of
|
||||
an ellipsoidal particle, which is oriented by default with its x-axis
|
||||
along the simulation box's x-axis, and similarly for y and z. If this
|
||||
body is rotated (via the right-hand rule) by an angle theta around a
|
||||
unit vector (a,b,c), then the quaternion that represents its new
|
||||
orientation is given by (cos(theta/2), a*sin(theta/2), b*sin(theta/2),
|
||||
c*sin(theta/2)). These 4 components are the arguments w,i,j,k to the
|
||||
{quat} keyword. LAMMPS normalizes the quaternion in case (a,b,c) was
|
||||
not a unit vector.
|
||||
Keyword {quat} uses the specified values to create a quaternion
|
||||
(4-vector) that represents the orientation of the selected atoms.
|
||||
Note that the "shape"_shape.html command is used to specify the aspect
|
||||
ratios of an ellipsoidal particle, which is oriented by default with
|
||||
its x-axis along the simulation box's x-axis, and similarly for y and
|
||||
z. If this body is rotated (via the right-hand rule) by an angle
|
||||
theta around a unit rotation vector (a,b,c), then the quaternion that
|
||||
represents its new orientation is given by (cos(theta/2),
|
||||
a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). The theta and a,b,c
|
||||
values are the arguments to the {quat} keyword. LAMMPS normalizes the
|
||||
quaternion in case (a,b,c) was not specified as a unit vector. For 2d
|
||||
systems, the a,b,c values are ignored, since a rotation vector of
|
||||
(0,0,1) is the only valid choice.
|
||||
|
||||
Keyword {quat/random} randomizes the orientation of the quaternion of
|
||||
the selected atoms. Random numbers are used in such a way that the
|
||||
orientation of a particular atom is the same, regardless of how many
|
||||
processors are being used.
|
||||
processors are being used. For 2d systems, only orientations in the
|
||||
xy plane are generated.
|
||||
|
||||
For the {dipole} and {quat} keywords, the "atom style"_atom_style.html
|
||||
being used must support the use of dipoles or quaternions.
|
||||
|
||||
@ -18,14 +18,18 @@ See the Errors section of the LAMMPS documentation for more
|
||||
discussion.
|
||||
|
||||
The dump files produced by the example runs can be animated using the
|
||||
xmovie tool described in the Examples section of the LAMMPS
|
||||
documentation. MPEG versions of most of the xmovie animations are
|
||||
also viewable from the Examples section of the LAMMPS WWW Site.
|
||||
xmovie tool described in the "Additional Tools" section of the LAMMPS
|
||||
documentation. Animations of many of these examples can be viewed on
|
||||
the Movies section of the LAMMPS WWW Site.
|
||||
|
||||
These are the sample problems in the various sub-directories:
|
||||
|
||||
couple: illustration of how to link to LAMMPS as a library
|
||||
couple: code example of how to link to LAMMPS as a library
|
||||
|
||||
colloid: big colloid particles in a small particle solvent, 2d system
|
||||
crack: crack propagation in a 2d solid
|
||||
dipole: point dipolar particles, 2d system
|
||||
ellipse: ellipsoidal particles in spherical solvent, 2d system
|
||||
flow: Couette and Poisseuille flow in a 2d channel
|
||||
friction: frictional contact of spherical asperities between 2d surfaces
|
||||
indent: spherical indenter into a 2d solid
|
||||
@ -33,6 +37,7 @@ meam: MEAM test for SiC and shear (same as shear examples)
|
||||
melt: rapid melt of 3d LJ system
|
||||
micelle: self-assembly of small lipid-like molecules into 2d bilayers
|
||||
min: energy minimization of 2d LJ melt
|
||||
nemd: non-equilibrium MD of 2d sheared system
|
||||
obstacle: flow around two voids in a 2d channel
|
||||
peptide: dynamics of a small solvated peptide chain (5-mer)
|
||||
pour: pouring of granular particles into a 3d box, then chute flow
|
||||
|
||||
@ -7,7 +7,7 @@ atom_modify map array
|
||||
lattice fcc 0.8442
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
create_atoms 1
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
@ -12,7 +12,7 @@ neigh_modify delay 5
|
||||
lattice hex 0.93
|
||||
region box block 0 100 0 40 -0.25 0.25
|
||||
create_box 5 box
|
||||
create_atoms 1
|
||||
create_atoms 1 box
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
@ -48,8 +48,8 @@ set group upper type 5
|
||||
|
||||
compute new mobile temp
|
||||
velocity mobile create 0.01 887723 temp new
|
||||
velocity upper set 0.0 0.02 0.0
|
||||
velocity mobile ramp vy 0.0 0.02 y 1.25 38.75 sum yes
|
||||
velocity upper set 0.0 0.3 0.0
|
||||
velocity mobile ramp vy 0.0 0.3 y 1.25 38.75 sum yes
|
||||
|
||||
# fixes
|
||||
|
||||
@ -59,9 +59,9 @@ fix 2 boundary setforce NULL 0.0 0.0
|
||||
# run
|
||||
|
||||
timestep 0.003
|
||||
thermo 1000
|
||||
thermo 200
|
||||
thermo_modify temp new
|
||||
|
||||
neigh_modify exclude type 2 3
|
||||
dump 1 all atom 250 dump.crack
|
||||
run 50000
|
||||
dump 1 all atom 500 dump.crack
|
||||
run 5000
|
||||
|
||||
@ -12,7 +12,7 @@ neigh_modify delay 5
|
||||
lattice hex 0.7
|
||||
region box block 0 20 0 10 -0.25 0.25
|
||||
create_box 3 box
|
||||
create_atoms 1
|
||||
create_atoms 1 box
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
|
||||
@ -12,7 +12,7 @@ neigh_modify delay 5
|
||||
lattice hex 0.7
|
||||
region box block 0 20 0 10 -0.25 0.25
|
||||
create_box 3 box
|
||||
create_atoms 1
|
||||
create_atoms 1 box
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
|
||||
@ -76,5 +76,5 @@ timestep 0.0025
|
||||
thermo 1000
|
||||
thermo_modify temp new
|
||||
|
||||
dump 1 all atom 100 dump.friction
|
||||
dump 1 all atom 500 dump.friction
|
||||
run 20000
|
||||
|
||||
@ -12,7 +12,7 @@ neigh_modify delay 5
|
||||
lattice hex 0.9
|
||||
region box block 0 20 0 10 -0.25 0.25
|
||||
create_box 2 box
|
||||
create_atoms 1
|
||||
create_atoms 1 box
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
|
||||
@ -12,7 +12,7 @@ neigh_modify delay 5
|
||||
lattice hex 0.9
|
||||
region box block 0 20 0 10 -0.25 0.25
|
||||
create_box 2 box
|
||||
create_atoms 1
|
||||
create_atoms 1 box
|
||||
|
||||
mass * 1.0
|
||||
|
||||
@ -40,7 +40,7 @@ fix 5 all enforce2d
|
||||
|
||||
thermo 10
|
||||
|
||||
dump 1 all atom 10 dump.indent.min
|
||||
dump 1 all atom 10 dump.indent
|
||||
dump_modify 1 scale no
|
||||
|
||||
minimize 1.0e-6 1000 1000
|
||||
|
||||
@ -8,7 +8,7 @@ atom_style atomic
|
||||
read_data data.meam
|
||||
|
||||
pair_style meam
|
||||
pair_coeff * * library.meam Si C sic.meam Si C
|
||||
pair_coeff * * library.meam Si C SiC.meam Si C
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 10
|
||||
|
||||
@ -10,10 +10,10 @@ create_box 3 box
|
||||
|
||||
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 &
|
||||
origin 0.5 0 0
|
||||
create_atoms 1
|
||||
create_atoms 1 box
|
||||
|
||||
pair_style meam
|
||||
pair_coeff * * library.meam Ni4 ni.meam Ni4 Ni4 Ni4
|
||||
pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
@ -62,7 +62,7 @@ unfix 3
|
||||
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
|
||||
fix_modify 3 temp new2d
|
||||
|
||||
dump 1 all atom 10 dump.meam.shear
|
||||
dump 1 all atom 100 dump.meam
|
||||
thermo 100
|
||||
thermo_modify temp new2d
|
||||
|
||||
|
||||
@ -4,9 +4,9 @@ units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 20 0 20 0 20
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
create_atoms 1
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 3.0 87287
|
||||
@ -19,7 +19,7 @@ neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
dump id all atom 10 dump.melt
|
||||
dump id all atom 50 dump.melt
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
|
||||
@ -54,7 +54,7 @@ pair_coeff 2 3 1.0 0.88 1.12246
|
||||
pair_coeff 2 4 1.0 0.75 1.12246
|
||||
|
||||
thermo 1000
|
||||
dump 1 all atom 250 dump.micelle
|
||||
dump 1 all atom 500 dump.micelle
|
||||
|
||||
reset_timestep 0
|
||||
run 60000
|
||||
|
||||
@ -7,7 +7,7 @@ atom_style atomic
|
||||
lattice sq2 0.8442
|
||||
region box block 0 20 0 20 -0.1 0.1
|
||||
create_box 1 box
|
||||
create_atoms 1
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 5.0 87287 loop geom
|
||||
|
||||
@ -12,7 +12,7 @@ neigh_modify delay 5
|
||||
lattice hex 0.7
|
||||
region box block 0 40 0 10 -0.25 0.25
|
||||
create_box 3 box
|
||||
create_atoms 1
|
||||
create_atoms 1 box
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
|
||||
@ -30,7 +30,7 @@ thermo 1000
|
||||
thermo_modify lost ignore
|
||||
compute_modify thermo_temp dynamic yes
|
||||
|
||||
dump id all atom 125 dump.pour
|
||||
dump id all atom 1000 dump.pour
|
||||
run 25000
|
||||
|
||||
unfix ins
|
||||
|
||||
@ -2,7 +2,7 @@
|
||||
|
||||
dimension 2
|
||||
atom_style granular
|
||||
boundary p fm p
|
||||
boundary f fm p
|
||||
newton off
|
||||
|
||||
region reg block 0 100 0 50 -0.5 0.5 units box
|
||||
@ -35,5 +35,5 @@ thermo 1000
|
||||
thermo_modify lost ignore
|
||||
compute_modify thermo_temp dynamic yes
|
||||
|
||||
dump id all atom 100 dump.pour
|
||||
dump id all atom 250 dump.pour
|
||||
run 25000
|
||||
|
||||
@ -10,10 +10,10 @@ create_box 3 box
|
||||
|
||||
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 &
|
||||
origin 0.5 0 0
|
||||
create_atoms 1
|
||||
create_atoms 1 box
|
||||
|
||||
pair_style eam
|
||||
pair_coeff * * niu3.eam
|
||||
pair_coeff * * Ni_u3.eam
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
@ -62,7 +62,7 @@ unfix 3
|
||||
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
|
||||
fix_modify 3 temp new2d
|
||||
|
||||
dump 1 all atom 10 dump.shear
|
||||
dump 1 all atom 100 dump.shear
|
||||
thermo 100
|
||||
thermo_modify temp new2d
|
||||
|
||||
|
||||
@ -10,10 +10,10 @@ create_box 3 box
|
||||
|
||||
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 &
|
||||
origin 0.5 0 0
|
||||
create_atoms 1
|
||||
create_atoms 1 box
|
||||
|
||||
pair_style eam
|
||||
pair_coeff * * niu3.eam
|
||||
pair_coeff * * Ni_u3.eam
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
@ -62,7 +62,7 @@ unfix 3
|
||||
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
|
||||
fix_modify 3 temp new2d
|
||||
|
||||
dump 1 all atom 10 dump.shear
|
||||
dump 1 all atom 100 dump.shear
|
||||
thermo 100
|
||||
thermo_modify temp new2d
|
||||
|
||||
|
||||
@ -399,6 +399,8 @@ double PairEAM::init_one(int i, int j)
|
||||
} else if (setfl) cutmax = setfl->cut;
|
||||
else if (fs) cutmax = fs->cut;
|
||||
|
||||
cutforcesq = cutmax*cutmax;
|
||||
|
||||
return cutmax;
|
||||
}
|
||||
|
||||
@ -412,8 +414,6 @@ void PairEAM::init_style()
|
||||
|
||||
file2array();
|
||||
array2spline();
|
||||
|
||||
cutforcesq = cutmax*cutmax;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
||||
@ -7,9 +7,9 @@ SHELL = /bin/sh
|
||||
ROOT = lmp
|
||||
EXE = lib$(ROOT)_$@.a
|
||||
|
||||
SRC = angle.cpp angle_charmm.cpp angle_class2.cpp angle_cosine.cpp angle_cosine_squared.cpp angle_harmonic.cpp angle_hybrid.cpp atom.cpp atom_vec.cpp atom_vec_angle.cpp atom_vec_atomic.cpp atom_vec_bond.cpp atom_vec_charge.cpp atom_vec_dpd.cpp atom_vec_ellipsoid.cpp atom_vec_full.cpp atom_vec_granular.cpp atom_vec_hybrid.cpp atom_vec_molecular.cpp bond.cpp bond_class2.cpp bond_fene.cpp bond_fene_expand.cpp bond_harmonic.cpp bond_hybrid.cpp bond_morse.cpp bond_nonlinear.cpp bond_quartic.cpp comm.cpp compute.cpp compute_centro_atom.cpp compute_coord_atom.cpp compute_epair_atom.cpp compute_etotal_atom.cpp compute_ke_atom.cpp compute_pressure.cpp compute_rotate_dipole.cpp compute_rotate_gran.cpp compute_stress_atom.cpp compute_temp.cpp compute_temp_asphere.cpp compute_temp_partial.cpp compute_temp_ramp.cpp compute_temp_region.cpp compute_variable.cpp compute_variable_atom.cpp create_atoms.cpp create_box.cpp delete_atoms.cpp delete_bonds.cpp dihedral.cpp dihedral_charmm.cpp dihedral_class2.cpp dihedral_harmonic.cpp dihedral_helix.cpp dihedral_hybrid.cpp dihedral_multi_harmonic.cpp dihedral_opls.cpp displace_atoms.cpp domain.cpp dump.cpp dump_atom.cpp dump_bond.cpp dump_custom.cpp dump_dcd.cpp dump_xtc.cpp dump_xyz.cpp error.cpp ewald.cpp fft3d.cpp fft3d_wrap.cpp finish.cpp fix.cpp fix_add_force.cpp fix_ave_force.cpp fix_ave_spatial.cpp fix_ave_time.cpp fix_com.cpp fix_deposit.cpp fix_drag.cpp fix_efield.cpp fix_enforce2d.cpp fix_freeze.cpp fix_gran_diag.cpp fix_gravity.cpp fix_gyration.cpp fix_heat.cpp fix_indent.cpp fix_langevin.cpp fix_line_force.cpp fix_minimize.cpp fix_momentum.cpp fix_msd.cpp fix_nph.cpp fix_npt.cpp fix_npt_asphere.cpp fix_nve.cpp fix_nve_asphere.cpp fix_nve_gran.cpp fix_nve_noforce.cpp fix_nvt.cpp fix_nvt_asphere.cpp fix_orient_fcc.cpp fix_plane_force.cpp fix_pour.cpp fix_print.cpp fix_rdf.cpp fix_recenter.cpp fix_respa.cpp fix_rigid.cpp fix_set_force.cpp fix_shake.cpp fix_shear_history.cpp fix_spring.cpp fix_spring_rg.cpp fix_spring_self.cpp fix_temp_rescale.cpp fix_tmd.cpp fix_uniaxial.cpp fix_viscous.cpp fix_volume_rescale.cpp fix_wall_gran.cpp fix_wall_lj126.cpp fix_wall_lj93.cpp fix_wall_reflect.cpp fix_wiggle.cpp force.cpp group.cpp improper.cpp improper_class2.cpp improper_cvff.cpp improper_harmonic.cpp improper_hybrid.cpp input.cpp kspace.cpp lammps.cpp lattice.cpp library.cpp memory.cpp min.cpp min_cg.cpp min_cg_fr.cpp min_sd.cpp minimize.cpp modify.cpp neigh_bond.cpp neigh_full.cpp neigh_gran.cpp neigh_half.cpp neigh_respa.cpp neigh_stencil.cpp neighbor.cpp output.cpp pack.cpp pair.cpp pair_airebo.cpp pair_buck.cpp pair_buck_coul_cut.cpp pair_buck_coul_long.cpp pair_dpd.cpp pair_eam.cpp pair_eam_alloy.cpp pair_eam_alloy_opt.cpp pair_eam_fs.cpp pair_eam_fs_opt.cpp pair_eam_opt.cpp pair_gayberne.cpp pair_gran_hertzian.cpp pair_gran_history.cpp pair_gran_no_history.cpp pair_hybrid.cpp pair_lj_charmm_coul_charmm.cpp pair_lj_charmm_coul_charmm_implicit.cpp pair_lj_charmm_coul_long.cpp pair_lj_charmm_coul_long_opt.cpp pair_lj_class2.cpp pair_lj_class2_coul_cut.cpp pair_lj_class2_coul_long.cpp pair_lj_cut.cpp pair_lj_cut_coul_cut.cpp pair_lj_cut_coul_debye.cpp pair_lj_cut_coul_long.cpp pair_lj_cut_coul_long_tip4p.cpp pair_lj_cut_opt.cpp pair_lj_expand.cpp pair_lj_smooth.cpp pair_morse.cpp pair_morse_opt.cpp pair_soft.cpp pair_sw.cpp pair_table.cpp pair_tersoff.cpp pair_yukawa.cpp pppm.cpp pppm_tip4p.cpp random_mars.cpp random_park.cpp read_data.cpp read_restart.cpp region.cpp region_block.cpp region_cylinder.cpp region_intersect.cpp region_prism.cpp region_sphere.cpp region_union.cpp remap.cpp remap_wrap.cpp replicate.cpp respa.cpp run.cpp set.cpp shell.cpp special.cpp temper.cpp thermo.cpp timer.cpp universe.cpp update.cpp variable.cpp velocity.cpp verlet.cpp write_restart.cpp
|
||||
SRC = angle.cpp angle_charmm.cpp angle_class2.cpp angle_cosine.cpp angle_cosine_squared.cpp angle_harmonic.cpp angle_hybrid.cpp atom.cpp atom_vec.cpp atom_vec_angle.cpp atom_vec_atomic.cpp atom_vec_bond.cpp atom_vec_charge.cpp atom_vec_dipole.cpp atom_vec_dpd.cpp atom_vec_ellipsoid.cpp atom_vec_full.cpp atom_vec_granular.cpp atom_vec_hybrid.cpp atom_vec_molecular.cpp bond.cpp bond_class2.cpp bond_fene.cpp bond_fene_expand.cpp bond_harmonic.cpp bond_hybrid.cpp bond_morse.cpp bond_nonlinear.cpp bond_quartic.cpp comm.cpp compute.cpp compute_centro_atom.cpp compute_coord_atom.cpp compute_epair_atom.cpp compute_etotal_atom.cpp compute_ke_atom.cpp compute_pressure.cpp compute_rotate_dipole.cpp compute_rotate_gran.cpp compute_stress_atom.cpp compute_temp.cpp compute_temp_asphere.cpp compute_temp_deform.cpp compute_temp_dipole.cpp compute_temp_partial.cpp compute_temp_ramp.cpp compute_temp_region.cpp compute_variable.cpp compute_variable_atom.cpp create_atoms.cpp create_box.cpp delete_atoms.cpp delete_bonds.cpp dihedral.cpp dihedral_charmm.cpp dihedral_class2.cpp dihedral_harmonic.cpp dihedral_helix.cpp dihedral_hybrid.cpp dihedral_multi_harmonic.cpp dihedral_opls.cpp displace_atoms.cpp domain.cpp dump.cpp dump_atom.cpp dump_bond.cpp dump_custom.cpp dump_dcd.cpp dump_xtc.cpp dump_xyz.cpp error.cpp ewald.cpp fft3d.cpp fft3d_wrap.cpp finish.cpp fix.cpp fix_add_force.cpp fix_ave_force.cpp fix_ave_spatial.cpp fix_ave_time.cpp fix_com.cpp fix_deform.cpp fix_deposit.cpp fix_drag.cpp fix_efield.cpp fix_enforce2d.cpp fix_freeze.cpp fix_gran_diag.cpp fix_gravity.cpp fix_gyration.cpp fix_heat.cpp fix_indent.cpp fix_langevin.cpp fix_line_force.cpp fix_minimize.cpp fix_momentum.cpp fix_msd.cpp fix_nph.cpp fix_npt.cpp fix_npt_asphere.cpp fix_nve.cpp fix_nve_asphere.cpp fix_nve_dipole.cpp fix_nve_gran.cpp fix_nve_noforce.cpp fix_nvt.cpp fix_nvt_asphere.cpp fix_nvt_sllod.cpp fix_orient_fcc.cpp fix_plane_force.cpp fix_poems.cpp fix_pour.cpp fix_print.cpp fix_rdf.cpp fix_recenter.cpp fix_respa.cpp fix_rigid.cpp fix_set_force.cpp fix_shake.cpp fix_shear_history.cpp fix_spring.cpp fix_spring_rg.cpp fix_spring_self.cpp fix_temp_rescale.cpp fix_tmd.cpp fix_viscous.cpp fix_wall_gran.cpp fix_wall_lj126.cpp fix_wall_lj93.cpp fix_wall_reflect.cpp fix_wiggle.cpp force.cpp group.cpp improper.cpp improper_class2.cpp improper_cvff.cpp improper_harmonic.cpp improper_hybrid.cpp input.cpp kspace.cpp lammps.cpp lattice.cpp library.cpp memory.cpp min.cpp min_cg.cpp min_cg_fr.cpp min_sd.cpp minimize.cpp modify.cpp neigh_bond.cpp neigh_full.cpp neigh_gran.cpp neigh_half.cpp neigh_respa.cpp neigh_stencil.cpp neighbor.cpp output.cpp pack.cpp pair.cpp pair_buck.cpp pair_buck_coul_cut.cpp pair_buck_coul_long.cpp pair_colloid.cpp pair_dipole_cut.cpp pair_dpd.cpp pair_eam.cpp pair_eam_alloy.cpp pair_eam_alloy_opt.cpp pair_eam_fs.cpp pair_eam_fs_opt.cpp pair_eam_opt.cpp pair_gayberne.cpp pair_gran_hertzian.cpp pair_gran_history.cpp pair_gran_no_history.cpp pair_hybrid.cpp pair_lj_charmm_coul_charmm.cpp pair_lj_charmm_coul_charmm_implicit.cpp pair_lj_charmm_coul_long.cpp pair_lj_charmm_coul_long_opt.cpp pair_lj_class2.cpp pair_lj_class2_coul_cut.cpp pair_lj_class2_coul_long.cpp pair_lj_cut.cpp pair_lj_cut_coul_cut.cpp pair_lj_cut_coul_debye.cpp pair_lj_cut_coul_long.cpp pair_lj_cut_coul_long_tip4p.cpp pair_lj_cut_opt.cpp pair_lj_expand.cpp pair_lj_smooth.cpp pair_meam.cpp pair_morse.cpp pair_morse_opt.cpp pair_soft.cpp pair_sw.cpp pair_table.cpp pair_tersoff.cpp pair_yukawa.cpp pppm.cpp pppm_tip4p.cpp random_mars.cpp random_park.cpp read_data.cpp read_restart.cpp region.cpp region_block.cpp region_cylinder.cpp region_intersect.cpp region_prism.cpp region_sphere.cpp region_union.cpp remap.cpp remap_wrap.cpp replicate.cpp respa.cpp run.cpp set.cpp shell.cpp special.cpp temper.cpp thermo.cpp timer.cpp universe.cpp update.cpp variable.cpp velocity.cpp verlet.cpp write_restart.cpp
|
||||
|
||||
INC = angle.h angle_charmm.h angle_class2.h angle_cosine.h angle_cosine_squared.h angle_harmonic.h angle_hybrid.h atom.h atom_vec.h atom_vec_angle.h atom_vec_atomic.h atom_vec_bond.h atom_vec_charge.h atom_vec_dpd.h atom_vec_ellipsoid.h atom_vec_full.h atom_vec_granular.h atom_vec_hybrid.h atom_vec_molecular.h bond.h bond_class2.h bond_fene.h bond_fene_expand.h bond_harmonic.h bond_hybrid.h bond_morse.h bond_nonlinear.h bond_quartic.h comm.h compute.h compute_centro_atom.h compute_coord_atom.h compute_epair_atom.h compute_etotal_atom.h compute_ke_atom.h compute_pressure.h compute_rotate_dipole.h compute_rotate_gran.h compute_stress_atom.h compute_temp.h compute_temp_asphere.h compute_temp_partial.h compute_temp_ramp.h compute_temp_region.h compute_variable.h compute_variable_atom.h create_atoms.h create_box.h delete_atoms.h delete_bonds.h dihedral.h dihedral_charmm.h dihedral_class2.h dihedral_harmonic.h dihedral_helix.h dihedral_hybrid.h dihedral_multi_harmonic.h dihedral_opls.h displace_atoms.h domain.h dump.h dump_atom.h dump_bond.h dump_custom.h dump_dcd.h dump_xtc.h dump_xyz.h error.h ewald.h fft3d.h fft3d_wrap.h finish.h fix.h fix_add_force.h fix_ave_force.h fix_ave_spatial.h fix_ave_time.h fix_com.h fix_deposit.h fix_drag.h fix_efield.h fix_enforce2d.h fix_freeze.h fix_gran_diag.h fix_gravity.h fix_gyration.h fix_heat.h fix_indent.h fix_langevin.h fix_line_force.h fix_minimize.h fix_momentum.h fix_msd.h fix_nph.h fix_npt.h fix_npt_asphere.h fix_nve.h fix_nve_asphere.h fix_nve_gran.h fix_nve_noforce.h fix_nvt.h fix_nvt_asphere.h fix_orient_fcc.h fix_plane_force.h fix_pour.h fix_print.h fix_rdf.h fix_recenter.h fix_respa.h fix_rigid.h fix_set_force.h fix_shake.h fix_shear_history.h fix_spring.h fix_spring_rg.h fix_spring_self.h fix_temp_rescale.h fix_tmd.h fix_uniaxial.h fix_viscous.h fix_volume_rescale.h fix_wall_gran.h fix_wall_lj126.h fix_wall_lj93.h fix_wall_reflect.h fix_wiggle.h force.h group.h improper.h improper_class2.h improper_cvff.h improper_harmonic.h improper_hybrid.h input.h integrate.h kspace.h lammps.h lattice.h library.h math_extra.h matho.h memory.h min.h min_cg.h min_cg_fr.h min_sd.h minimize.h modify.h neighbor.h output.h pack.h pair.h pair_airebo.h pair_buck.h pair_buck_coul_cut.h pair_buck_coul_long.h pair_dpd.h pair_eam.h pair_eam_alloy.h pair_eam_alloy_opt.h pair_eam_fs.h pair_eam_fs_opt.h pair_eam_opt.h pair_gayberne.h pair_gran_hertzian.h pair_gran_history.h pair_gran_no_history.h pair_hybrid.h pair_lj_charmm_coul_charmm.h pair_lj_charmm_coul_charmm_implicit.h pair_lj_charmm_coul_long.h pair_lj_charmm_coul_long_opt.h pair_lj_class2.h pair_lj_class2_coul_cut.h pair_lj_class2_coul_long.h pair_lj_cut.h pair_lj_cut_coul_cut.h pair_lj_cut_coul_debye.h pair_lj_cut_coul_long.h pair_lj_cut_coul_long_tip4p.h pair_lj_cut_opt.h pair_lj_expand.h pair_lj_smooth.h pair_morse.h pair_morse_opt.h pair_soft.h pair_sw.h pair_table.h pair_tersoff.h pair_yukawa.h pointers.h pppm.h pppm_tip4p.h random_mars.h random_park.h read_data.h read_restart.h region.h region_block.h region_cylinder.h region_intersect.h region_prism.h region_sphere.h region_union.h remap.h remap_wrap.h replicate.h respa.h run.h set.h shell.h special.h style.h style_asphere.h style_class2.h style_dpd.h style_granular.h style_kspace.h style_manybody.h style_meam.h style_molecule.h style_opt.h style_poems.h style_user.h style_xtc.h temper.h thermo.h timer.h universe.h update.h variable.h vector.h velocity.h verlet.h write_restart.h
|
||||
INC = angle.h angle_charmm.h angle_class2.h angle_cosine.h angle_cosine_squared.h angle_harmonic.h angle_hybrid.h atom.h atom_vec.h atom_vec_angle.h atom_vec_atomic.h atom_vec_bond.h atom_vec_charge.h atom_vec_dipole.h atom_vec_dpd.h atom_vec_ellipsoid.h atom_vec_full.h atom_vec_granular.h atom_vec_hybrid.h atom_vec_molecular.h bond.h bond_class2.h bond_fene.h bond_fene_expand.h bond_harmonic.h bond_hybrid.h bond_morse.h bond_nonlinear.h bond_quartic.h comm.h compute.h compute_centro_atom.h compute_coord_atom.h compute_epair_atom.h compute_etotal_atom.h compute_ke_atom.h compute_pressure.h compute_rotate_dipole.h compute_rotate_gran.h compute_stress_atom.h compute_temp.h compute_temp_asphere.h compute_temp_deform.h compute_temp_dipole.h compute_temp_partial.h compute_temp_ramp.h compute_temp_region.h compute_variable.h compute_variable_atom.h create_atoms.h create_box.h delete_atoms.h delete_bonds.h dihedral.h dihedral_charmm.h dihedral_class2.h dihedral_harmonic.h dihedral_helix.h dihedral_hybrid.h dihedral_multi_harmonic.h dihedral_opls.h displace_atoms.h domain.h dump.h dump_atom.h dump_bond.h dump_custom.h dump_dcd.h dump_xtc.h dump_xyz.h error.h ewald.h fft3d.h fft3d_wrap.h finish.h fix.h fix_add_force.h fix_ave_force.h fix_ave_spatial.h fix_ave_time.h fix_com.h fix_deform.h fix_deposit.h fix_drag.h fix_efield.h fix_enforce2d.h fix_freeze.h fix_gran_diag.h fix_gravity.h fix_gyration.h fix_heat.h fix_indent.h fix_langevin.h fix_line_force.h fix_minimize.h fix_momentum.h fix_msd.h fix_nph.h fix_npt.h fix_npt_asphere.h fix_nve.h fix_nve_asphere.h fix_nve_dipole.h fix_nve_gran.h fix_nve_noforce.h fix_nvt.h fix_nvt_asphere.h fix_nvt_sllod.h fix_orient_fcc.h fix_plane_force.h fix_poems.h fix_pour.h fix_print.h fix_rdf.h fix_recenter.h fix_respa.h fix_rigid.h fix_set_force.h fix_shake.h fix_shear_history.h fix_spring.h fix_spring_rg.h fix_spring_self.h fix_temp_rescale.h fix_tmd.h fix_viscous.h fix_wall_gran.h fix_wall_lj126.h fix_wall_lj93.h fix_wall_reflect.h fix_wiggle.h force.h group.h improper.h improper_class2.h improper_cvff.h improper_harmonic.h improper_hybrid.h input.h integrate.h kspace.h lammps.h lattice.h library.h math_extra.h memory.h min.h min_cg.h min_cg_fr.h min_sd.h minimize.h modify.h neighbor.h output.h pack.h pair.h pair_buck.h pair_buck_coul_cut.h pair_buck_coul_long.h pair_colloid.h pair_dipole_cut.h pair_dpd.h pair_eam.h pair_eam_alloy.h pair_eam_alloy_opt.h pair_eam_fs.h pair_eam_fs_opt.h pair_eam_opt.h pair_gayberne.h pair_gran_hertzian.h pair_gran_history.h pair_gran_no_history.h pair_hybrid.h pair_lj_charmm_coul_charmm.h pair_lj_charmm_coul_charmm_implicit.h pair_lj_charmm_coul_long.h pair_lj_charmm_coul_long_opt.h pair_lj_class2.h pair_lj_class2_coul_cut.h pair_lj_class2_coul_long.h pair_lj_cut.h pair_lj_cut_coul_cut.h pair_lj_cut_coul_debye.h pair_lj_cut_coul_long.h pair_lj_cut_coul_long_tip4p.h pair_lj_cut_opt.h pair_lj_expand.h pair_lj_smooth.h pair_meam.h pair_morse.h pair_morse_opt.h pair_soft.h pair_sw.h pair_table.h pair_tersoff.h pair_yukawa.h pointers.h pppm.h pppm_tip4p.h random_mars.h random_park.h read_data.h read_restart.h region.h region_block.h region_cylinder.h region_intersect.h region_prism.h region_sphere.h region_union.h remap.h remap_wrap.h replicate.h respa.h run.h set.h shell.h special.h style.h style_asphere.h style_class2.h style_colloid.h style_dipole.h style_dpd.h style_granular.h style_kspace.h style_manybody.h style_meam.h style_molecule.h style_opt.h style_poems.h style_user.h style_xtc.h temper.h thermo.h timer.h universe.h update.h variable.h velocity.h verlet.h write_restart.h
|
||||
|
||||
OBJ = $(SRC:.cpp=.o)
|
||||
|
||||
|
||||
@ -7,9 +7,9 @@ SHELL = /bin/sh
|
||||
ROOT = lmp
|
||||
EXE = $(ROOT)_$@
|
||||
|
||||
SRC = angle.cpp angle_charmm.cpp angle_cosine.cpp angle_cosine_squared.cpp angle_harmonic.cpp angle_hybrid.cpp atom.cpp atom_vec.cpp atom_vec_angle.cpp atom_vec_atomic.cpp atom_vec_bond.cpp atom_vec_charge.cpp atom_vec_full.cpp atom_vec_hybrid.cpp atom_vec_molecular.cpp bond.cpp bond_fene.cpp bond_fene_expand.cpp bond_harmonic.cpp bond_hybrid.cpp bond_morse.cpp bond_nonlinear.cpp bond_quartic.cpp comm.cpp compute.cpp compute_centro_atom.cpp compute_epair_atom.cpp compute_etotal_atom.cpp compute_ke_atom.cpp compute_pressure.cpp compute_rotate_dipole.cpp compute_rotate_gran.cpp compute_stress_atom.cpp compute_temp.cpp compute_temp_partial.cpp compute_temp_ramp.cpp compute_temp_region.cpp create_atoms.cpp create_box.cpp delete_atoms.cpp delete_bonds.cpp dihedral.cpp dihedral_charmm.cpp dihedral_harmonic.cpp dihedral_helix.cpp dihedral_hybrid.cpp dihedral_multi_harmonic.cpp dihedral_opls.cpp displace_atoms.cpp domain.cpp dump.cpp dump_atom.cpp dump_bond.cpp dump_custom.cpp dump_dcd.cpp dump_xyz.cpp error.cpp ewald.cpp fft3d.cpp fft3d_wrap.cpp finish.cpp fix.cpp fix_add_force.cpp fix_ave_force.cpp fix_com.cpp fix_deposit.cpp fix_drag.cpp fix_efield.cpp fix_enforce2d.cpp fix_gravity.cpp fix_gyration.cpp fix_indent.cpp fix_langevin.cpp fix_line_force.cpp fix_minimize.cpp fix_momentum.cpp fix_msd.cpp fix_nph.cpp fix_npt.cpp fix_nve.cpp fix_nvt.cpp fix_orient_fcc.cpp fix_plane_force.cpp fix_print.cpp fix_rdf.cpp fix_recenter.cpp fix_respa.cpp fix_rigid.cpp fix_set_force.cpp fix_shake.cpp fix_shear_history.cpp fix_spring.cpp fix_spring_rg.cpp fix_spring_self.cpp fix_temp_rescale.cpp fix_tmd.cpp fix_uniaxial.cpp fix_viscous.cpp fix_volume_rescale.cpp fix_wall_lj126.cpp fix_wall_lj93.cpp fix_wall_reflect.cpp fix_wiggle.cpp force.cpp group.cpp improper.cpp improper_cvff.cpp improper_harmonic.cpp improper_hybrid.cpp input.cpp kspace.cpp lammps.cpp lattice.cpp library.cpp main.cpp memory.cpp min.cpp min_cg.cpp min_cg_fr.cpp min_sd.cpp minimize.cpp modify.cpp neigh_bond.cpp neigh_full.cpp neigh_gran.cpp neigh_half.cpp neigh_respa.cpp neighbor.cpp output.cpp pack.cpp pair.cpp pair_buck.cpp pair_buck_coul_cut.cpp pair_buck_coul_long.cpp pair_eam.cpp pair_eam_alloy.cpp pair_eam_fs.cpp pair_hybrid.cpp pair_lj_charmm_coul_charmm.cpp pair_lj_charmm_coul_charmm_implicit.cpp pair_lj_charmm_coul_long.cpp pair_lj_cut.cpp pair_lj_cut_coul_cut.cpp pair_lj_cut_coul_debye.cpp pair_lj_cut_coul_long.cpp pair_lj_cut_coul_long_tip4p.cpp pair_lj_expand.cpp pair_lj_smooth.cpp pair_morse.cpp pair_soft.cpp pair_sw.cpp pair_table.cpp pair_tersoff.cpp pair_yukawa.cpp pppm.cpp pppm_tip4p.cpp random_mars.cpp random_park.cpp read_data.cpp read_restart.cpp region.cpp region_block.cpp region_cylinder.cpp region_intersect.cpp region_prism.cpp region_sphere.cpp region_union.cpp remap.cpp remap_wrap.cpp replicate.cpp respa.cpp run.cpp set.cpp shell.cpp special.cpp temper.cpp thermo.cpp timer.cpp universe.cpp update.cpp variable.cpp velocity.cpp verlet.cpp write_restart.cpp
|
||||
SRC = angle.cpp angle_charmm.cpp angle_class2.cpp angle_cosine.cpp angle_cosine_squared.cpp angle_harmonic.cpp angle_hybrid.cpp atom.cpp atom_vec.cpp atom_vec_angle.cpp atom_vec_atomic.cpp atom_vec_bond.cpp atom_vec_charge.cpp atom_vec_dipole.cpp atom_vec_dpd.cpp atom_vec_ellipsoid.cpp atom_vec_full.cpp atom_vec_granular.cpp atom_vec_hybrid.cpp atom_vec_molecular.cpp bond.cpp bond_class2.cpp bond_fene.cpp bond_fene_expand.cpp bond_harmonic.cpp bond_hybrid.cpp bond_morse.cpp bond_nonlinear.cpp bond_quartic.cpp comm.cpp compute.cpp compute_centro_atom.cpp compute_coord_atom.cpp compute_epair_atom.cpp compute_etotal_atom.cpp compute_ke_atom.cpp compute_pressure.cpp compute_rotate_dipole.cpp compute_rotate_gran.cpp compute_stress_atom.cpp compute_temp.cpp compute_temp_asphere.cpp compute_temp_deform.cpp compute_temp_dipole.cpp compute_temp_partial.cpp compute_temp_ramp.cpp compute_temp_region.cpp compute_variable.cpp compute_variable_atom.cpp create_atoms.cpp create_box.cpp delete_atoms.cpp delete_bonds.cpp dihedral.cpp dihedral_charmm.cpp dihedral_class2.cpp dihedral_harmonic.cpp dihedral_helix.cpp dihedral_hybrid.cpp dihedral_multi_harmonic.cpp dihedral_opls.cpp displace_atoms.cpp domain.cpp dump.cpp dump_atom.cpp dump_bond.cpp dump_custom.cpp dump_dcd.cpp dump_xtc.cpp dump_xyz.cpp error.cpp ewald.cpp fft3d.cpp fft3d_wrap.cpp finish.cpp fix.cpp fix_add_force.cpp fix_ave_force.cpp fix_ave_spatial.cpp fix_ave_time.cpp fix_com.cpp fix_deform.cpp fix_deposit.cpp fix_drag.cpp fix_efield.cpp fix_enforce2d.cpp fix_freeze.cpp fix_gran_diag.cpp fix_gravity.cpp fix_gyration.cpp fix_heat.cpp fix_indent.cpp fix_langevin.cpp fix_line_force.cpp fix_minimize.cpp fix_momentum.cpp fix_msd.cpp fix_nph.cpp fix_npt.cpp fix_npt_asphere.cpp fix_nve.cpp fix_nve_asphere.cpp fix_nve_dipole.cpp fix_nve_gran.cpp fix_nve_noforce.cpp fix_nvt.cpp fix_nvt_asphere.cpp fix_nvt_sllod.cpp fix_orient_fcc.cpp fix_plane_force.cpp fix_poems.cpp fix_pour.cpp fix_print.cpp fix_rdf.cpp fix_recenter.cpp fix_respa.cpp fix_rigid.cpp fix_set_force.cpp fix_shake.cpp fix_shear_history.cpp fix_spring.cpp fix_spring_rg.cpp fix_spring_self.cpp fix_temp_rescale.cpp fix_tmd.cpp fix_viscous.cpp fix_wall_gran.cpp fix_wall_lj126.cpp fix_wall_lj93.cpp fix_wall_reflect.cpp fix_wiggle.cpp force.cpp group.cpp improper.cpp improper_class2.cpp improper_cvff.cpp improper_harmonic.cpp improper_hybrid.cpp input.cpp kspace.cpp lammps.cpp lattice.cpp library.cpp main.cpp memory.cpp min.cpp min_cg.cpp min_cg_fr.cpp min_sd.cpp minimize.cpp modify.cpp neigh_bond.cpp neigh_full.cpp neigh_gran.cpp neigh_half.cpp neigh_respa.cpp neigh_stencil.cpp neighbor.cpp output.cpp pack.cpp pair.cpp pair_buck.cpp pair_buck_coul_cut.cpp pair_buck_coul_long.cpp pair_colloid.cpp pair_dipole_cut.cpp pair_dpd.cpp pair_eam.cpp pair_eam_alloy.cpp pair_eam_alloy_opt.cpp pair_eam_fs.cpp pair_eam_fs_opt.cpp pair_eam_opt.cpp pair_gayberne.cpp pair_gran_hertzian.cpp pair_gran_history.cpp pair_gran_no_history.cpp pair_hybrid.cpp pair_lj_charmm_coul_charmm.cpp pair_lj_charmm_coul_charmm_implicit.cpp pair_lj_charmm_coul_long.cpp pair_lj_charmm_coul_long_opt.cpp pair_lj_class2.cpp pair_lj_class2_coul_cut.cpp pair_lj_class2_coul_long.cpp pair_lj_cut.cpp pair_lj_cut_coul_cut.cpp pair_lj_cut_coul_debye.cpp pair_lj_cut_coul_long.cpp pair_lj_cut_coul_long_tip4p.cpp pair_lj_cut_opt.cpp pair_lj_expand.cpp pair_lj_smooth.cpp pair_meam.cpp pair_morse.cpp pair_morse_opt.cpp pair_soft.cpp pair_sw.cpp pair_table.cpp pair_tersoff.cpp pair_yukawa.cpp pppm.cpp pppm_tip4p.cpp random_mars.cpp random_park.cpp read_data.cpp read_restart.cpp region.cpp region_block.cpp region_cylinder.cpp region_intersect.cpp region_prism.cpp region_sphere.cpp region_union.cpp remap.cpp remap_wrap.cpp replicate.cpp respa.cpp run.cpp set.cpp shell.cpp special.cpp temper.cpp thermo.cpp timer.cpp universe.cpp update.cpp variable.cpp velocity.cpp verlet.cpp write_restart.cpp
|
||||
|
||||
INC = angle.h angle_charmm.h angle_cosine.h angle_cosine_squared.h angle_harmonic.h angle_hybrid.h atom.h atom_vec.h atom_vec_angle.h atom_vec_atomic.h atom_vec_bond.h atom_vec_charge.h atom_vec_full.h atom_vec_hybrid.h atom_vec_molecular.h bond.h bond_fene.h bond_fene_expand.h bond_harmonic.h bond_hybrid.h bond_morse.h bond_nonlinear.h bond_quartic.h comm.h compute.h compute_centro_atom.h compute_epair_atom.h compute_etotal_atom.h compute_ke_atom.h compute_pressure.h compute_rotate_dipole.h compute_rotate_gran.h compute_stress_atom.h compute_temp.h compute_temp_partial.h compute_temp_ramp.h compute_temp_region.h create_atoms.h create_box.h delete_atoms.h delete_bonds.h dihedral.h dihedral_charmm.h dihedral_harmonic.h dihedral_helix.h dihedral_hybrid.h dihedral_multi_harmonic.h dihedral_opls.h displace_atoms.h domain.h dump.h dump_atom.h dump_bond.h dump_custom.h dump_dcd.h dump_xyz.h error.h ewald.h fft3d.h fft3d_wrap.h finish.h fix.h fix_add_force.h fix_ave_force.h fix_com.h fix_deposit.h fix_drag.h fix_efield.h fix_enforce2d.h fix_gravity.h fix_gyration.h fix_indent.h fix_langevin.h fix_line_force.h fix_minimize.h fix_momentum.h fix_msd.h fix_nph.h fix_npt.h fix_nve.h fix_nvt.h fix_orient_fcc.h fix_plane_force.h fix_print.h fix_rdf.h fix_recenter.h fix_respa.h fix_rigid.h fix_set_force.h fix_shake.h fix_shear_history.h fix_spring.h fix_spring_rg.h fix_spring_self.h fix_temp_rescale.h fix_tmd.h fix_uniaxial.h fix_viscous.h fix_volume_rescale.h fix_wall_lj126.h fix_wall_lj93.h fix_wall_reflect.h fix_wiggle.h force.h group.h improper.h improper_cvff.h improper_harmonic.h improper_hybrid.h input.h integrate.h kspace.h lammps.h lattice.h library.h memory.h min.h min_cg.h min_cg_fr.h min_sd.h minimize.h modify.h neighbor.h output.h pack.h pair.h pair_buck.h pair_buck_coul_cut.h pair_buck_coul_long.h pair_eam.h pair_eam_alloy.h pair_eam_fs.h pair_hybrid.h pair_lj_charmm_coul_charmm.h pair_lj_charmm_coul_charmm_implicit.h pair_lj_charmm_coul_long.h pair_lj_cut.h pair_lj_cut_coul_cut.h pair_lj_cut_coul_debye.h pair_lj_cut_coul_long.h pair_lj_cut_coul_long_tip4p.h pair_lj_expand.h pair_lj_smooth.h pair_morse.h pair_soft.h pair_sw.h pair_table.h pair_tersoff.h pair_yukawa.h pointers.h pppm.h pppm_tip4p.h random_mars.h random_park.h read_data.h read_restart.h region.h region_block.h region_cylinder.h region_intersect.h region_prism.h region_sphere.h region_union.h remap.h remap_wrap.h replicate.h respa.h run.h set.h shell.h special.h style.h style_class2.h style_dpd.h style_granular.h style_kspace.h style_manybody.h style_meam.h style_molecule.h style_opt.h style_poems.h style_user.h style_xtc.h temper.h thermo.h timer.h universe.h update.h variable.h velocity.h verlet.h write_restart.h
|
||||
INC = angle.h angle_charmm.h angle_class2.h angle_cosine.h angle_cosine_squared.h angle_harmonic.h angle_hybrid.h atom.h atom_vec.h atom_vec_angle.h atom_vec_atomic.h atom_vec_bond.h atom_vec_charge.h atom_vec_dipole.h atom_vec_dpd.h atom_vec_ellipsoid.h atom_vec_full.h atom_vec_granular.h atom_vec_hybrid.h atom_vec_molecular.h bond.h bond_class2.h bond_fene.h bond_fene_expand.h bond_harmonic.h bond_hybrid.h bond_morse.h bond_nonlinear.h bond_quartic.h comm.h compute.h compute_centro_atom.h compute_coord_atom.h compute_epair_atom.h compute_etotal_atom.h compute_ke_atom.h compute_pressure.h compute_rotate_dipole.h compute_rotate_gran.h compute_stress_atom.h compute_temp.h compute_temp_asphere.h compute_temp_deform.h compute_temp_dipole.h compute_temp_partial.h compute_temp_ramp.h compute_temp_region.h compute_variable.h compute_variable_atom.h create_atoms.h create_box.h delete_atoms.h delete_bonds.h dihedral.h dihedral_charmm.h dihedral_class2.h dihedral_harmonic.h dihedral_helix.h dihedral_hybrid.h dihedral_multi_harmonic.h dihedral_opls.h displace_atoms.h domain.h dump.h dump_atom.h dump_bond.h dump_custom.h dump_dcd.h dump_xtc.h dump_xyz.h error.h ewald.h fft3d.h fft3d_wrap.h finish.h fix.h fix_add_force.h fix_ave_force.h fix_ave_spatial.h fix_ave_time.h fix_com.h fix_deform.h fix_deposit.h fix_drag.h fix_efield.h fix_enforce2d.h fix_freeze.h fix_gran_diag.h fix_gravity.h fix_gyration.h fix_heat.h fix_indent.h fix_langevin.h fix_line_force.h fix_minimize.h fix_momentum.h fix_msd.h fix_nph.h fix_npt.h fix_npt_asphere.h fix_nve.h fix_nve_asphere.h fix_nve_dipole.h fix_nve_gran.h fix_nve_noforce.h fix_nvt.h fix_nvt_asphere.h fix_nvt_sllod.h fix_orient_fcc.h fix_plane_force.h fix_poems.h fix_pour.h fix_print.h fix_rdf.h fix_recenter.h fix_respa.h fix_rigid.h fix_set_force.h fix_shake.h fix_shear_history.h fix_spring.h fix_spring_rg.h fix_spring_self.h fix_temp_rescale.h fix_tmd.h fix_viscous.h fix_wall_gran.h fix_wall_lj126.h fix_wall_lj93.h fix_wall_reflect.h fix_wiggle.h force.h group.h improper.h improper_class2.h improper_cvff.h improper_harmonic.h improper_hybrid.h input.h integrate.h kspace.h lammps.h lattice.h library.h math_extra.h memory.h min.h min_cg.h min_cg_fr.h min_sd.h minimize.h modify.h neighbor.h output.h pack.h pair.h pair_buck.h pair_buck_coul_cut.h pair_buck_coul_long.h pair_colloid.h pair_dipole_cut.h pair_dpd.h pair_eam.h pair_eam_alloy.h pair_eam_alloy_opt.h pair_eam_fs.h pair_eam_fs_opt.h pair_eam_opt.h pair_gayberne.h pair_gran_hertzian.h pair_gran_history.h pair_gran_no_history.h pair_hybrid.h pair_lj_charmm_coul_charmm.h pair_lj_charmm_coul_charmm_implicit.h pair_lj_charmm_coul_long.h pair_lj_charmm_coul_long_opt.h pair_lj_class2.h pair_lj_class2_coul_cut.h pair_lj_class2_coul_long.h pair_lj_cut.h pair_lj_cut_coul_cut.h pair_lj_cut_coul_debye.h pair_lj_cut_coul_long.h pair_lj_cut_coul_long_tip4p.h pair_lj_cut_opt.h pair_lj_expand.h pair_lj_smooth.h pair_meam.h pair_morse.h pair_morse_opt.h pair_soft.h pair_sw.h pair_table.h pair_tersoff.h pair_yukawa.h pointers.h pppm.h pppm_tip4p.h random_mars.h random_park.h read_data.h read_restart.h region.h region_block.h region_cylinder.h region_intersect.h region_prism.h region_sphere.h region_union.h remap.h remap_wrap.h replicate.h respa.h run.h set.h shell.h special.h style.h style_asphere.h style_class2.h style_colloid.h style_dipole.h style_dpd.h style_granular.h style_kspace.h style_manybody.h style_meam.h style_molecule.h style_opt.h style_poems.h style_user.h style_xtc.h temper.h thermo.h timer.h universe.h update.h variable.h velocity.h verlet.h write_restart.h
|
||||
|
||||
OBJ = $(SRC:.cpp=.o)
|
||||
|
||||
|
||||
@ -56,8 +56,8 @@ void CreateAtoms::command(int narg, char **arg)
|
||||
} else if (strcmp(arg[1],"region") == 0) {
|
||||
style = REGION;
|
||||
if (narg < 3) error->all("Illegal create_atoms command");
|
||||
int iregion = domain->find_region(arg[2]);
|
||||
if (iregion == -1) error->all("Create_atoms region ID does not exist");
|
||||
nregion = domain->find_region(arg[2]);
|
||||
if (nregion == -1) error->all("Create_atoms region ID does not exist");
|
||||
iarg = 3;;
|
||||
} else if (strcmp(arg[1],"single") == 0) {
|
||||
style = SINGLE;
|
||||
@ -315,7 +315,7 @@ void CreateAtoms::add_many()
|
||||
// if a region was specified, test if atom is in it
|
||||
|
||||
if (style == REGION)
|
||||
if (!domain->regions[iregion]->match(x[0],x[1],x[2])) continue;
|
||||
if (!domain->regions[nregion]->match(x[0],x[1],x[2])) continue;
|
||||
|
||||
// test if atom is in my subbox
|
||||
|
||||
|
||||
@ -24,7 +24,7 @@ class CreateAtoms : protected Pointers {
|
||||
void command(int, char **);
|
||||
|
||||
private:
|
||||
int itype,style,iregion,nbasis;
|
||||
int itype,style,nregion,nbasis;
|
||||
int *basistype;
|
||||
double xone[3];
|
||||
|
||||
|
||||
@ -441,6 +441,7 @@ void FixAveSpatial::end_of_step()
|
||||
for (i = 0; i < nvalues; i++) fprintf(fp," %g",values_total[m][i]);
|
||||
fprintf(fp,"\n");
|
||||
}
|
||||
fflush(fp);
|
||||
}
|
||||
|
||||
nsum = 0;
|
||||
|
||||
@ -156,6 +156,7 @@ void FixAveTime::end_of_step()
|
||||
if (vflag)
|
||||
for (i = 0; i < size_vector; i++) fprintf(fp," %g",vector[i]/nsum);
|
||||
fprintf(fp,"\n");
|
||||
fflush(fp);
|
||||
}
|
||||
|
||||
nsum = 0;
|
||||
|
||||
@ -23,7 +23,6 @@
|
||||
#include "atom.h"
|
||||
#include "force.h"
|
||||
#include "domain.h"
|
||||
#include "comm.h"
|
||||
#include "group.h"
|
||||
#include "update.h"
|
||||
#include "respa.h"
|
||||
@ -53,13 +52,12 @@ void FixNVTSlodd::init()
|
||||
int i;
|
||||
for (i = 0; i < modify->nfix; i++)
|
||||
if (strcmp(modify->fix[i]->style,"deform") == 0) {
|
||||
if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP &&
|
||||
comm->me == 0)
|
||||
error->warning("Using fix nvt/sllod with inconsistent fix deform remap option");
|
||||
if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP)
|
||||
error->all("Using fix nvt/sllod with inconsistent fix deform remap option");
|
||||
break;
|
||||
}
|
||||
if (i == modify->nfix && comm->me == 0)
|
||||
error->warning("Using fix nvt/sllod with no fix deform defined");
|
||||
if (i == modify->nfix)
|
||||
error->all("Using fix nvt/sllod with no fix deform defined");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -253,7 +253,7 @@ void MathExtra::mldivide3(const double m[3][3], const double *v, double *ans,
|
||||
}
|
||||
}
|
||||
|
||||
while (aug[p][i] == 0 && p < 3) p++;
|
||||
while (aug[p][i] == 0.0 && p < 3) p++;
|
||||
|
||||
if (p == 3) error->all("Bad matrix inversion in MathExtra::mldivide3");
|
||||
else
|
||||
@ -270,7 +270,7 @@ void MathExtra::mldivide3(const double m[3][3], const double *v, double *ans,
|
||||
}
|
||||
}
|
||||
|
||||
if (aug[2][2] == 0)
|
||||
if (aug[2][2] == 0.0)
|
||||
error->all("Bad matrix inversion in MathExtra::mldivide3");
|
||||
|
||||
// back substitution
|
||||
|
||||
@ -0,0 +1,20 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PairInclude
|
||||
#include "pair_meam.h"
|
||||
#endif
|
||||
|
||||
#ifdef PairClass
|
||||
PairStyle(meam,PairMEAM)
|
||||
#endif
|
||||
|
||||
@ -0,0 +1,20 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FixInclude
|
||||
#include "fix_poems.h"
|
||||
#endif
|
||||
|
||||
#ifdef FixClass
|
||||
FixStyle(poems,FixPOEMS)
|
||||
#endif
|
||||
|
||||
@ -26,7 +26,7 @@ using namespace LAMMPS_NS;
|
||||
|
||||
Universe::Universe(LAMMPS *lmp, MPI_Comm communicator) : Pointers(lmp)
|
||||
{
|
||||
version = "12 Feb 2007";
|
||||
version = "22 June 2007";
|
||||
|
||||
uworld = communicator;
|
||||
MPI_Comm_rank(uworld,&me);
|
||||
|
||||
47
tools/README
47
tools/README
@ -2,40 +2,33 @@ LAMMPS pre- and post-processing tools
|
||||
|
||||
This directory contains several stand-alone tools for creating LAMMPS
|
||||
input files and massaging LAMMPS output data. Instructions on how to
|
||||
use the tools are discussed in the Tools section of the LAMMPS
|
||||
documentation. The source files in this directory have additional
|
||||
comments that may be useful at the top of the code. The packages that
|
||||
reside in their own sub-directories have README files of their own
|
||||
that you want to look at.
|
||||
use the tools are discussed in the "Additional Tools" section of the
|
||||
LAMMPS documentation.
|
||||
|
||||
You will need to compile each of these tools if you wish to use them.
|
||||
Building LAMMPS itself (in the src dir) does not build these tools.
|
||||
Tools that are single source files in this directory have additional
|
||||
comments that may be useful at the top of the source file. Tools that
|
||||
reside in their own sub-directories have README files you should look
|
||||
at.
|
||||
|
||||
These are the included tools:
|
||||
|
||||
binary2txt convert a LAMMPS dump file from binary to ASCII text
|
||||
replicate replicate a LAMMPS data file in one or more dimensions
|
||||
restart2data convert a binary restart file to an input data file
|
||||
data2xmovie convert a data file to a snapshot that xmovie can viz
|
||||
chain create a data file of bead-spring chains
|
||||
micelle2d create a data file of small lipid chains in solvent
|
||||
|
||||
xmovie a quick/simple viz package that displays 2d projections
|
||||
of 3d LAMMPS snapshots
|
||||
|
||||
amber2lammps python scripts for using AMBER to setup LAMMPS input
|
||||
binary2txt convert a LAMMPS dump file from binary to ASCII text
|
||||
ch2lmp convert CHARMM files to LAMMPS input
|
||||
chain create a data file of bead-spring chains
|
||||
data2xmovie convert a data file to a snapshot that xmovie can viz
|
||||
lmp2arc convert LAMMPS output to Accelrys Insight format
|
||||
for analysis
|
||||
lmp2cfg convert LAMMPS output to CFG files that can be
|
||||
read by AtomEye visualizer
|
||||
lmp2cfg convert LAMMPS output to CFG files for AtomEye viz
|
||||
lmp2traj convert LAMMPS output to contour, density profiles
|
||||
msi2lmp use the Accelrys Insight (nee MSI/Biosym Discover)
|
||||
code to setup LAMMPS input
|
||||
micelle2d create a data file of small lipid chains in solvent
|
||||
msi2lmp use Accelrys Insight code to setup LAMMPS input
|
||||
pymol_asphere convert LAMMPS output of ellipsoids to PyMol format
|
||||
restart2data convert a binary restart file to an input data file
|
||||
xmovie a quick/simple viz package (2d projections of 3d)
|
||||
|
||||
The set of tools are single C, C++, or Fortran files. A Makefile for
|
||||
building them is included in this directory, but you will have to edit
|
||||
it for the compilers and paths on your system.
|
||||
For tools that are single C, C++, or Fortran files, a Makefile for
|
||||
building them is included in this directory. You may need to edit it
|
||||
for the compilers and paths on your system.
|
||||
|
||||
The other tools are in their own sub-directories, and each has its own
|
||||
README file on how to build and use it.
|
||||
For tools in their own sub-directories, see their README file for info
|
||||
on how to build and use it.
|
||||
|
||||
@ -366,7 +366,7 @@ main (int argc, char **argv)
|
||||
|
||||
void header(FILE *fp, Data &data)
|
||||
{
|
||||
char *version = "12 Feb 2007";
|
||||
char *version = "22 June 2007";
|
||||
|
||||
data.triclinic = 0;
|
||||
|
||||
|
||||
Reference in New Issue
Block a user