Merge branch 'master' into lammps-icms
This commit is contained in:
Axel Kohlmeyer
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@ -609,14 +609,14 @@ distribution.
|
||||
<TR><TD >gui.py</TD><TD > GUI go/stop/temperature-slider to control LAMMPS</TD></TR>
|
||||
<TR><TD >plot.py</TD><TD > real-time temeperature plot with GnuPlot via Pizza.py</TD></TR>
|
||||
<TR><TD >viz_tool.py</TD><TD > real-time viz via some viz package</TD></TR>
|
||||
<TR><TD >vizplotgui_tool.py</TD><TD > combination of viz.py and plot.py and gui.py
|
||||
<TR><TD >vizplotgui_tool.py</TD><TD > combination of viz_tool.py and plot.py and gui.py
|
||||
</TD></TR></TABLE></DIV>
|
||||
|
||||
<HR>
|
||||
|
||||
<P>For the viz_tool.py and vizplotgui_tool.py commands, replace "tool"
|
||||
with "gl" or "atomeye" or "pymol", depending on what visualization
|
||||
package you have installed. We hope to add a VMD option soon.
|
||||
with "gl" or "atomeye" or "pymol" or "vmd", depending on what
|
||||
visualization package you have installed.
|
||||
</P>
|
||||
<P>Note that for GL, you need to be able to run the Pizza.py GL tool,
|
||||
which is included in the pizza sub-directory. See the <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py doc
|
||||
@ -624,7 +624,7 @@ pages</A> for more info:
|
||||
</P>
|
||||
|
||||
|
||||
<P>Note that for AtomEye, you need version 3, and their is a line in the
|
||||
<P>Note that for AtomEye, you need version 3, and there is a line in the
|
||||
scripts that specifies the path and name of the executable. See the
|
||||
AtomEye WWW pages <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">here</A> or <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html">here</A> for more details:
|
||||
</P>
|
||||
@ -652,6 +652,10 @@ http://sourceforge.net/scm/?type=svn&group_id=4546
|
||||
|
||||
<P>The latter link is to the open-source version.
|
||||
</P>
|
||||
<P>Note that for VMD, you need a fairly current version (1.8.7 works for
|
||||
me) and there are some lines in the pizza/vmd.py script for 4 PIZZA
|
||||
variables that have to match the VMD installation on your system.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>See the python/README file for instructions on how to run them and the
|
||||
@ -666,4 +670,6 @@ different visualization package options. Click to see larger images:
|
||||
|
||||
<A HREF = "JPG/screenshot_pymol.jpg"><IMG SRC = "JPG/screenshot_pymol_small.jpg"></A>
|
||||
|
||||
<A HREF = "JPG/screenshot_vmd.jpg"><IMG SRC = "JPG/screenshot_vmd_small.jpg"></A>
|
||||
|
||||
</HTML>
|
||||
|
||||
@ -602,13 +602,13 @@ simple.py, mimic operation of couple/simple/simple.cpp in Python,
|
||||
gui.py, GUI go/stop/temperature-slider to control LAMMPS,
|
||||
plot.py, real-time temeperature plot with GnuPlot via Pizza.py,
|
||||
viz_tool.py, real-time viz via some viz package,
|
||||
vizplotgui_tool.py, combination of viz.py and plot.py and gui.py :tb(c=2)
|
||||
vizplotgui_tool.py, combination of viz_tool.py and plot.py and gui.py :tb(c=2)
|
||||
|
||||
:line
|
||||
|
||||
For the viz_tool.py and vizplotgui_tool.py commands, replace "tool"
|
||||
with "gl" or "atomeye" or "pymol", depending on what visualization
|
||||
package you have installed. We hope to add a VMD option soon.
|
||||
with "gl" or "atomeye" or "pymol" or "vmd", depending on what
|
||||
visualization package you have installed.
|
||||
|
||||
Note that for GL, you need to be able to run the Pizza.py GL tool,
|
||||
which is included in the pizza sub-directory. See the "Pizza.py doc
|
||||
@ -616,7 +616,7 @@ pages"_pizza for more info:
|
||||
|
||||
:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
|
||||
|
||||
Note that for AtomEye, you need version 3, and their is a line in the
|
||||
Note that for AtomEye, you need version 3, and there is a line in the
|
||||
scripts that specifies the path and name of the executable. See the
|
||||
AtomEye WWW pages "here"_atomeye or "here"_atomeye3 for more details:
|
||||
|
||||
@ -642,6 +642,10 @@ http://sourceforge.net/scm/?type=svn&group_id=4546 :pre
|
||||
|
||||
The latter link is to the open-source version.
|
||||
|
||||
Note that for VMD, you need a fairly current version (1.8.7 works for
|
||||
me) and there are some lines in the pizza/vmd.py script for 4 PIZZA
|
||||
variables that have to match the VMD installation on your system.
|
||||
|
||||
:line
|
||||
|
||||
See the python/README file for instructions on how to run them and the
|
||||
@ -653,4 +657,4 @@ different visualization package options. Click to see larger images:
|
||||
:image(JPG/screenshot_gl_small.jpg,JPG/screenshot_gl.jpg)
|
||||
:image(JPG/screenshot_atomeye_small.jpg,JPG/screenshot_atomeye.jpg)
|
||||
:image(JPG/screenshot_pymol_small.jpg,JPG/screenshot_pymol.jpg)
|
||||
|
||||
:image(JPG/screenshot_vmd_small.jpg,JPG/screenshot_vmd.jpg)
|
||||
|
||||
@ -379,8 +379,8 @@ and barostatting to the system's potential energy as part of
|
||||
</P>
|
||||
<P>These fixes compute a global scalar and a global vector of quantities,
|
||||
which can be accessed by various <A HREF = "Section_howto.html#4_15">output
|
||||
commands</A>. The scalar values calculated by
|
||||
this fix are "extensive"; the vector values are "intensive".
|
||||
commands</A>. The scalar value calculated by
|
||||
these fixes is "extensive"; the vector values are "intensive".
|
||||
</P>
|
||||
<P>The scalar is the cumulative energy change due to the fix.
|
||||
</P>
|
||||
|
||||
@ -371,8 +371,8 @@ and barostatting to the system's potential energy as part of
|
||||
|
||||
These fixes compute a global scalar and a global vector of quantities,
|
||||
which can be accessed by various "output
|
||||
commands"_Section_howto.html#4_15. The scalar values calculated by
|
||||
this fix are "extensive"; the vector values are "intensive".
|
||||
commands"_Section_howto.html#4_15. The scalar value calculated by
|
||||
these fixes is "extensive"; the vector values are "intensive".
|
||||
|
||||
The scalar is the cumulative energy change due to the fix.
|
||||
|
||||
@ -433,7 +433,6 @@ limiting factor for numerical stability. Both
|
||||
factorizations are time-reversible and can be shown to preserve the phase
|
||||
space measure of the underlying non-Hamiltonian equations of motion.
|
||||
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
Non-periodic dimensions cannot be barostatted. {Z}, {xz}, and {yz},
|
||||
|
||||
@ -272,21 +272,28 @@ for info on how to re-specify a fix in an input script that reads a
|
||||
restart file, so that the operation of the fix continues in an
|
||||
uninterrupted fashion.
|
||||
</P>
|
||||
<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to these
|
||||
fixes.
|
||||
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by the
|
||||
rigid/nvt fix to add the energy change induced by the thermostatting
|
||||
to the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
|
||||
output</A>.
|
||||
</P>
|
||||
<P>These fixes compute a global array of values which can be accessed by
|
||||
various <A HREF = "Section_howto.html#4_15">output commands</A>. The number of rows
|
||||
in the array is equal to the number of rigid bodies. The number of
|
||||
columns is 15. Thus for each rigid body, 12 values are stored: the
|
||||
xyz coords of the center of mass (COM), the xyz components of the COM
|
||||
velocity, the xyz components of the force acting on the COM, the xyz
|
||||
components of the torque acting on the COM, and the xyz image flags of
|
||||
the COM, which have the same meaning as image flags for atom positions
|
||||
(see the "dump" command). The force and torque values in the array
|
||||
are not affected by the <I>force</I> and <I>torque</I> keywords in the fix rigid
|
||||
command; they reflect values before any changes are made by those
|
||||
keywords.
|
||||
<P>The rigid/nvt fix computes a global scalar which can be accessed by
|
||||
various <A HREF = "Section_howto.html#4_15">output commands</A>. The scalar value
|
||||
calculated by the rigid/nvt fix is "extensive". The scalar is the
|
||||
cumulative energy change due to the thermostatting the fix performs.
|
||||
</P>
|
||||
<P>All of these fixes compute a global array of values which can be
|
||||
accessed by various <A HREF = "Section_howto.html#4_15">output commands</A>. The
|
||||
number of rows in the array is equal to the number of rigid bodies.
|
||||
The number of columns is 15. Thus for each rigid body, 12 values are
|
||||
stored: the xyz coords of the center of mass (COM), the xyz components
|
||||
of the COM velocity, the xyz components of the force acting on the
|
||||
COM, the xyz components of the torque acting on the COM, and the xyz
|
||||
image flags of the COM, which have the same meaning as image flags for
|
||||
atom positions (see the "dump" command). The force and torque values
|
||||
in the array are not affected by the <I>force</I> and <I>torque</I> keywords in
|
||||
the fix rigid command; they reflect values before any changes are made
|
||||
by those keywords.
|
||||
</P>
|
||||
<P>The ordering of the rigid bodies (by row in the array) is as follows.
|
||||
For the <I>single</I> keyword there is just one rigid body. For the
|
||||
|
||||
@ -261,21 +261,28 @@ for info on how to re-specify a fix in an input script that reads a
|
||||
restart file, so that the operation of the fix continues in an
|
||||
uninterrupted fashion.
|
||||
|
||||
None of the "fix_modify"_fix_modify.html options are relevant to these
|
||||
fixes.
|
||||
The "fix_modify"_fix_modify.html {energy} option is supported by the
|
||||
rigid/nvt fix to add the energy change induced by the thermostatting
|
||||
to the system's potential energy as part of "thermodynamic
|
||||
output"_thermo_style.html.
|
||||
|
||||
These fixes compute a global array of values which can be accessed by
|
||||
various "output commands"_Section_howto.html#4_15. The number of rows
|
||||
in the array is equal to the number of rigid bodies. The number of
|
||||
columns is 15. Thus for each rigid body, 12 values are stored: the
|
||||
xyz coords of the center of mass (COM), the xyz components of the COM
|
||||
velocity, the xyz components of the force acting on the COM, the xyz
|
||||
components of the torque acting on the COM, and the xyz image flags of
|
||||
the COM, which have the same meaning as image flags for atom positions
|
||||
(see the "dump" command). The force and torque values in the array
|
||||
are not affected by the {force} and {torque} keywords in the fix rigid
|
||||
command; they reflect values before any changes are made by those
|
||||
keywords.
|
||||
The rigid/nvt fix computes a global scalar which can be accessed by
|
||||
various "output commands"_Section_howto.html#4_15. The scalar value
|
||||
calculated by the rigid/nvt fix is "extensive". The scalar is the
|
||||
cumulative energy change due to the thermostatting the fix performs.
|
||||
|
||||
All of these fixes compute a global array of values which can be
|
||||
accessed by various "output commands"_Section_howto.html#4_15. The
|
||||
number of rows in the array is equal to the number of rigid bodies.
|
||||
The number of columns is 15. Thus for each rigid body, 12 values are
|
||||
stored: the xyz coords of the center of mass (COM), the xyz components
|
||||
of the COM velocity, the xyz components of the force acting on the
|
||||
COM, the xyz components of the torque acting on the COM, and the xyz
|
||||
image flags of the COM, which have the same meaning as image flags for
|
||||
atom positions (see the "dump" command). The force and torque values
|
||||
in the array are not affected by the {force} and {torque} keywords in
|
||||
the fix rigid command; they reflect values before any changes are made
|
||||
by those keywords.
|
||||
|
||||
The ordering of the rigid bodies (by row in the array) is as follows.
|
||||
For the {single} keyword there is just one rigid body. For the
|
||||
|
||||
@ -52,11 +52,13 @@
|
||||
group functions = count(group), mass(group), charge(group),
|
||||
xcm(group,dim), vcm(group,dim), fcm(group,dim),
|
||||
bound(group,xmin), gyration(group), ke(group),
|
||||
angmom(group,dim),inertia(group,dimdim),omega(group,dim)
|
||||
angmom(group,dim), torque(group,dim),
|
||||
inertia(group,dimdim), omega(group,dim)
|
||||
region functions = count(group,region), mass(group,region), charge(group,region),
|
||||
xcm(group,dim,region), vcm(group,dim,region), fcm(group,dim,region),
|
||||
bound(group,xmin,region), gyration(group,region), ke(group,reigon),
|
||||
angmom(group,dim,region), inertia(group,dimdim,region),omega(group,dim,region)
|
||||
angmom(group,dim,region), torque(group,dim,region),
|
||||
inertia(group,dimdim,region), omega(group,dim,region)
|
||||
special functions = sum(x), min(x), max(x), ave(x), trap(x), gmask(x), rmask(x), grmask(x,y)
|
||||
atom value = mass[i], type[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i]
|
||||
atom vector = mass, type, x, y, z, vx, vy, vz, fx, fy, fz
|
||||
@ -274,8 +276,8 @@ references to other variables.
|
||||
<TR><TD >Thermo keywords</TD><TD > vol, pe, ebond, etc</TD></TR>
|
||||
<TR><TD >Math operators</TD><TD > (), -x, x+y, x-y, x*y, x/y, x^y, x==y, x!=y, x<y, x<=y, x>y, x>=y, x&&y, x||y, !x</TD></TR>
|
||||
<TR><TD >Math functions</TD><TD > sqrt(x), exp(x), ln(x), log(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ramp(x,y), stagger(x,y), logfreq(x,y,z), vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)</TD></TR>
|
||||
<TR><TD >Group functions</TD><TD > count(ID), mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), fcm(ID,dim), bound(ID,dir), gyration(ID), ke(ID), angmom(ID,dim), inertia(ID,dimdim), omega(ID,dim)</TD></TR>
|
||||
<TR><TD >Region functions</TD><TD > count(ID,IDR), mass(ID,IDR), charge(ID,IDR), xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR), bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), angmom(ID,dim,IDR), inertia(ID,dimdim,IDR), omega(ID,dim,IDR)</TD></TR>
|
||||
<TR><TD >Group functions</TD><TD > count(ID), mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), fcm(ID,dim), bound(ID,dir), gyration(ID), ke(ID), angmom(ID,dim), torque(ID,dim), inertia(ID,dimdim), omega(ID,dim)</TD></TR>
|
||||
<TR><TD >Region functions</TD><TD > count(ID,IDR), mass(ID,IDR), charge(ID,IDR), xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR), bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), angmom(ID,dim,IDR), torque(ID,dim,IDR), inertia(ID,dimdim,IDR), omega(ID,dim,IDR)</TD></TR>
|
||||
<TR><TD >Special functions</TD><TD > sum(x), min(x), max(x), ave(x), trap(x), gmask(x), rmask(x), grmask(x,y)</TD></TR>
|
||||
<TR><TD >Atom values</TD><TD > mass[i], type[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i]</TD></TR>
|
||||
<TR><TD >Atom vectors</TD><TD > mass, type, x, y, z, vx, vy, vz, fx, fy, fz</TD></TR>
|
||||
@ -476,10 +478,12 @@ the min/max of a particular coordinate for all atoms in the group.
|
||||
Gyration() computes the radius-of-gyration of the group of atoms. See
|
||||
the <A HREF = "compute_gyration.html">compute gyration</A> command for a definition
|
||||
of the formula. Angmom() returns components of the angular momentum
|
||||
of the group of atoms around its center of mass. Inertia() returns
|
||||
one of 6 components of the inertia tensor of the group of atoms around
|
||||
its center of mass. Omega() returns components of the angular
|
||||
velocity of the group of atoms around its center of mass.
|
||||
of the group of atoms around its center of mass. Torque() returns
|
||||
components of the torque on the group of atoms around its center of
|
||||
mass, based on current forces on the atoms. Inertia() returns one of
|
||||
6 components of the inertia tensor of the group of atoms around its
|
||||
center of mass. Omega() returns components of the angular velocity of
|
||||
the group of atoms around its center of mass.
|
||||
</P>
|
||||
<P>Region functions are specified exactly the same way as group functions
|
||||
except they take an extra argument which is the region ID. The
|
||||
|
||||
@ -47,11 +47,13 @@ style = {delete} or {index} or {loop} or {world} or {universe} or {uloop} or {st
|
||||
group functions = count(group), mass(group), charge(group),
|
||||
xcm(group,dim), vcm(group,dim), fcm(group,dim),
|
||||
bound(group,xmin), gyration(group), ke(group),
|
||||
angmom(group,dim),inertia(group,dimdim),omega(group,dim)
|
||||
angmom(group,dim), torque(group,dim),
|
||||
inertia(group,dimdim), omega(group,dim)
|
||||
region functions = count(group,region), mass(group,region), charge(group,region),
|
||||
xcm(group,dim,region), vcm(group,dim,region), fcm(group,dim,region),
|
||||
bound(group,xmin,region), gyration(group,region), ke(group,reigon),
|
||||
angmom(group,dim,region), inertia(group,dimdim,region),omega(group,dim,region)
|
||||
angmom(group,dim,region), torque(group,dim,region),
|
||||
inertia(group,dimdim,region), omega(group,dim,region)
|
||||
special functions = sum(x), min(x), max(x), ave(x), trap(x), gmask(x), rmask(x), grmask(x,y)
|
||||
atom value = mass\[i\], type\[i\], x\[i\], y\[i\], z\[i\], vx\[i\], vy\[i\], vz\[i\], fx\[i\], fy\[i\], fz\[i\]
|
||||
atom vector = mass, type, x, y, z, vx, vy, vz, fx, fy, fz
|
||||
@ -269,12 +271,13 @@ Math operators: (), -x, x+y, x-y, x*y, x/y, x^y, x==y, x!=y, x<y, x<=y, x>y, x>=
|
||||
Math functions: sqrt(x), exp(x), ln(x), log(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ramp(x,y), stagger(x,y), logfreq(x,y,z), vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)
|
||||
Group functions: count(ID), mass(ID), charge(ID), xcm(ID,dim), \
|
||||
vcm(ID,dim), fcm(ID,dim), bound(ID,dir), \
|
||||
gyration(ID), ke(ID), angmom(ID,dim), \
|
||||
gyration(ID), ke(ID), angmom(ID,dim), torque(ID,dim), \
|
||||
inertia(ID,dimdim), omega(ID,dim)
|
||||
Region functions: count(ID,IDR), mass(ID,IDR), charge(ID,IDR), \
|
||||
xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR), \
|
||||
bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), \
|
||||
angmom(ID,dim,IDR), inertia(ID,dimdim,IDR), omega(ID,dim,IDR)
|
||||
angmom(ID,dim,IDR), torque(ID,dim,IDR), \
|
||||
inertia(ID,dimdim,IDR), omega(ID,dim,IDR)
|
||||
Special functions: sum(x), min(x), max(x), ave(x), trap(x), gmask(x), rmask(x), grmask(x,y)
|
||||
Atom values: mass\[i\], type\[i\], x\[i\], y\[i\], z\[i\], \
|
||||
vx\[i\], vy\[i\], vz\[i\], fx\[i\], fy\[i\], fz\[i\]
|
||||
@ -475,10 +478,12 @@ the min/max of a particular coordinate for all atoms in the group.
|
||||
Gyration() computes the radius-of-gyration of the group of atoms. See
|
||||
the "compute gyration"_compute_gyration.html command for a definition
|
||||
of the formula. Angmom() returns components of the angular momentum
|
||||
of the group of atoms around its center of mass. Inertia() returns
|
||||
one of 6 components of the inertia tensor of the group of atoms around
|
||||
its center of mass. Omega() returns components of the angular
|
||||
velocity of the group of atoms around its center of mass.
|
||||
of the group of atoms around its center of mass. Torque() returns
|
||||
components of the torque on the group of atoms around its center of
|
||||
mass, based on current forces on the atoms. Inertia() returns one of
|
||||
6 components of the inertia tensor of the group of atoms around its
|
||||
center of mass. Omega() returns components of the angular velocity of
|
||||
the group of atoms around its center of mass.
|
||||
|
||||
Region functions are specified exactly the same way as group functions
|
||||
except they take an extra argument which is the region ID. The
|
||||
|
||||
@ -1,13 +1,20 @@
|
||||
# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html
|
||||
# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
#
|
||||
# Minimalistic VMD embedding for Pizza.py
|
||||
#
|
||||
# This class will replace the VMD startup script,
|
||||
# open a pipe to the executable, and feed it Tcl
|
||||
# command lines one at a time.
|
||||
#
|
||||
# (c) 2010 Axel Kohlmeyer <akohlmey@gmail.com>
|
||||
# Copyright (2005) 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.
|
||||
|
||||
oneline = "Control VMD from python."
|
||||
# vmd tool
|
||||
|
||||
# Minimalistic VMD embedding for Pizza.py
|
||||
# (c) 2010 Axel Kohlmeyer <akohlmey@gmail.com>
|
||||
# This class will replace the VMD startup script,
|
||||
# open a pipe to the executable,
|
||||
# and feed it Tcl command lines one at a time
|
||||
|
||||
oneline = "Control VMD from python"
|
||||
|
||||
docstr = """
|
||||
v = vmd() start up VMD
|
||||
@ -30,6 +37,9 @@ v.enter() enter interactive shell
|
||||
v.debug([True|False]) display generated VMD script commands?
|
||||
"""
|
||||
|
||||
# History
|
||||
# 11/10, Axel Kohlmeyer (Temple U): original version
|
||||
|
||||
# Imports and external programs
|
||||
|
||||
import types, os
|
||||
@ -42,12 +52,14 @@ except: PIZZA_VMDDIR = "/usr/local/lib/vmd"
|
||||
try: from DEFAULTS import PIZZA_VMDDEV
|
||||
except: PIZZA_VMDDEV = "win"
|
||||
try: from DEFAULTS import PIZZA_VMDARCH
|
||||
except: PIZZA_VMDARCH = "LINUXAMD64"
|
||||
except: PIZZA_VMDARCH = "LINUX"
|
||||
|
||||
try: import pexpect
|
||||
except:
|
||||
print "pexpect from http://pypi.python.org/pypi/pexpect/ is required for vmd module"
|
||||
print "pexpect from http://pypi.python.org/pypi/pexpect", \
|
||||
"is required for vmd tool"
|
||||
raise
|
||||
|
||||
# Class definition
|
||||
|
||||
class vmd:
|
||||
|
||||
@ -1,9 +1,9 @@
|
||||
#!/usr/local/bin/python -i
|
||||
# preceeding line should have path for Python on your machine
|
||||
|
||||
# viz.py
|
||||
# Purpose: viz running LAMMPS simulation via GL tool in Pizza.py
|
||||
# Syntax: viz.py in.lammps Nfreq Nsteps
|
||||
# viz_atomeye.py
|
||||
# Purpose: viz running LAMMPS simulation via AtomEye
|
||||
# Syntax: viz_atomeye.py in.lammps Nfreq Nsteps
|
||||
# in.lammps = LAMMPS input script
|
||||
# Nfreq = dump and viz shapshot every this many steps
|
||||
# Nsteps = run for this many steps
|
||||
@ -11,14 +11,15 @@
|
||||
import sys,os
|
||||
|
||||
# set this to point to AtomEye version 3 executable
|
||||
|
||||
ATOMEYE3 = "/home/sjplimp/tools/atomeye3/A3.i686-20060530"
|
||||
# first line if want AtomEye output to screen, 2nd line to file
|
||||
#ATOMEYE3 = "/home/sjplimp/tools/atomeye3/A3.i686-20060530"
|
||||
ATOMEYE3 = "/home/sjplimp/tools/atomeye3/A3.i686-20060530 > atomeye.out"
|
||||
|
||||
# parse command line
|
||||
|
||||
argv = sys.argv
|
||||
if len(argv) != 4:
|
||||
print "Syntax: viz.py in.lammps Nfreq Nsteps"
|
||||
print "Syntax: viz_atomeye.py in.lammps Nfreq Nsteps"
|
||||
sys.exit()
|
||||
|
||||
infile = sys.argv[1]
|
||||
|
||||
@ -1,9 +1,9 @@
|
||||
#!/usr/local/bin/python -i
|
||||
# preceeding line should have path for Python on your machine
|
||||
|
||||
# viz.py
|
||||
# viz_gl.py
|
||||
# Purpose: viz running LAMMPS simulation via GL tool in Pizza.py
|
||||
# Syntax: viz.py in.lammps Nfreq Nsteps
|
||||
# Syntax: viz_gl.py in.lammps Nfreq Nsteps
|
||||
# in.lammps = LAMMPS input script
|
||||
# Nfreq = dump and viz shapshot every this many steps
|
||||
# Nsteps = run for this many steps
|
||||
@ -15,7 +15,7 @@ sys.path.append("./pizza")
|
||||
|
||||
argv = sys.argv
|
||||
if len(argv) != 4:
|
||||
print "Syntax: viz.py in.lammps Nfreq Nsteps"
|
||||
print "Syntax: viz_gl.py in.lammps Nfreq Nsteps"
|
||||
sys.exit()
|
||||
|
||||
infile = sys.argv[1]
|
||||
|
||||
@ -81,9 +81,9 @@ lmp.command("run 0 pre no post yes")
|
||||
if me == 0:
|
||||
v.flush()
|
||||
# uncomment the following, if you want to work with the viz some more.
|
||||
v('menu main on')
|
||||
# print "type quit to terminate."
|
||||
v.enter()
|
||||
#v('menu main on')
|
||||
#print "type quit to terminate."
|
||||
#v.enter()
|
||||
#v.stop()
|
||||
|
||||
# uncomment if running in parallel via Pypar
|
||||
|
||||
@ -1,9 +1,9 @@
|
||||
#!/usr/local/bin/python -i
|
||||
# preceeding line should have path for Python on your machine
|
||||
|
||||
# vizplotgui.py
|
||||
# Purpose: viz running LAMMPS simulation with plot and GUI
|
||||
# Syntax: vizplotgui.py in.lammps Nfreq compute-ID
|
||||
# vizplotgui_atomeye.py
|
||||
# Purpose: viz running LAMMPS simulation via AtomEye with plot and GUI
|
||||
# Syntax: vizplotgui_atomeye.py in.lammps Nfreq compute-ID
|
||||
# in.lammps = LAMMPS input script
|
||||
# Nfreq = plot data point and viz shapshot every this many steps
|
||||
# compute-ID = ID of compute that calculates temperature
|
||||
@ -15,6 +15,7 @@
|
||||
import sys,os,time
|
||||
sys.path.append("./pizza")
|
||||
|
||||
# set this to point to AtomEye version 3 executable
|
||||
# first line if want AtomEye output to screen, 2nd line to file
|
||||
#ATOMEYE3 = "/home/sjplimp/tools/atomeye3/A3.i686-20060530"
|
||||
ATOMEYE3 = "/home/sjplimp/tools/atomeye3/A3.i686-20060530 > atomeye.out"
|
||||
@ -49,7 +50,7 @@ def update(ntimestep):
|
||||
|
||||
argv = sys.argv
|
||||
if len(argv) != 4:
|
||||
print "Syntax: vizplotgui.py in.lammps Nfreq compute-ID"
|
||||
print "Syntax: vizplotgui_atomeye.py in.lammps Nfreq compute-ID"
|
||||
sys.exit()
|
||||
|
||||
infile = sys.argv[1]
|
||||
@ -85,7 +86,7 @@ breakflag = 0
|
||||
runflag = 0
|
||||
temptarget = 1.0
|
||||
|
||||
# wrapper on GL window via Pizza.py gl tool
|
||||
# wrapper on AtomEye
|
||||
# just proc 0 handles reading of dump file and viz
|
||||
|
||||
if me == 0:
|
||||
|
||||
@ -1,9 +1,9 @@
|
||||
#!/usr/local/bin/python -i
|
||||
# preceeding line should have path for Python on your machine
|
||||
|
||||
# vizplotgui.py
|
||||
# Purpose: viz running LAMMPS simulation with plot and GUI
|
||||
# Syntax: vizplotgui.py in.lammps Nfreq compute-ID
|
||||
# vizplotgui_gl.py
|
||||
# Purpose: viz running LAMMPS simulation via GL tool with plot and GUI
|
||||
# Syntax: vizplotgui_gl.py in.lammps Nfreq compute-ID
|
||||
# in.lammps = LAMMPS input script
|
||||
# Nfreq = plot data point and viz shapshot every this many steps
|
||||
# compute-ID = ID of compute that calculates temperature
|
||||
@ -46,7 +46,7 @@ def update(ntimestep):
|
||||
|
||||
argv = sys.argv
|
||||
if len(argv) != 4:
|
||||
print "Syntax: vizplotgui.py in.lammps Nfreq compute-ID"
|
||||
print "Syntax: vizplotgui_gl.py in.lammps Nfreq compute-ID"
|
||||
sys.exit()
|
||||
|
||||
infile = sys.argv[1]
|
||||
|
||||
@ -2,7 +2,7 @@
|
||||
# preceeding line should have path for Python on your machine
|
||||
|
||||
# vizplotgui_pymol.py
|
||||
# Purpose: viz running LAMMPS simulation with plot and GUI
|
||||
# Purpose: viz running LAMMPS simulation via PyMol with plot and GUI
|
||||
# Syntax: vizplotgui_pymol.py in.lammps Nfreq compute-ID
|
||||
# in.lammps = LAMMPS input script
|
||||
# Nfreq = plot data point and viz shapshot every this many steps
|
||||
@ -48,7 +48,7 @@ def update(ntimestep):
|
||||
|
||||
argv = sys.argv
|
||||
if len(argv) != 4:
|
||||
print "Syntax: vizplotgui.py in.lammps Nfreq compute-ID"
|
||||
print "Syntax: vizplotgui_pymol.py in.lammps Nfreq compute-ID"
|
||||
sys.exit()
|
||||
|
||||
infile = sys.argv[1]
|
||||
|
||||
173
python/examples/vizplotgui_vmd.py
Executable file
173
python/examples/vizplotgui_vmd.py
Executable file
@ -0,0 +1,173 @@
|
||||
#!/usr/local/bin/python -i
|
||||
# preceeding line should have path for Python on your machine
|
||||
|
||||
# vizplotgui_vmd.py
|
||||
# Purpose: viz running LAMMPS simulation via VMD with plot and GUI
|
||||
# Syntax: vizplotgui_vmd.py in.lammps Nfreq compute-ID
|
||||
# in.lammps = LAMMPS input script
|
||||
# Nfreq = plot data point and viz shapshot every this many steps
|
||||
# compute-ID = ID of compute that calculates temperature
|
||||
# (or any other scalar quantity)
|
||||
|
||||
# IMPORTANT: this script cannot yet be run in parallel via Pypar,
|
||||
# because I can't seem to do a MPI-style broadcast in Pypar
|
||||
|
||||
import sys,time
|
||||
sys.path.append("./pizza")
|
||||
|
||||
# methods called by GUI
|
||||
|
||||
def run():
|
||||
global runflag
|
||||
runflag = 1
|
||||
def stop():
|
||||
global runflag
|
||||
runflag = 0
|
||||
def settemp(value):
|
||||
global temptarget
|
||||
temptarget = slider.get()
|
||||
def quit():
|
||||
global breakflag
|
||||
breakflag = 1
|
||||
|
||||
# method called by timestep loop every Nfreq steps
|
||||
# read dump snapshot and viz it, update plot with compute value
|
||||
|
||||
def update(ntimestep):
|
||||
d.next()
|
||||
d.unscale()
|
||||
p.single(ntimestep)
|
||||
v.append('tmp.pdb','pdb')
|
||||
value = lmp.extract_compute(compute,0,0)
|
||||
xaxis.append(ntimestep)
|
||||
yaxis.append(value)
|
||||
gn.plot(xaxis,yaxis)
|
||||
|
||||
# parse command line
|
||||
|
||||
argv = sys.argv
|
||||
if len(argv) != 4:
|
||||
print "Syntax: vizplotgui_vmd.py in.lammps Nfreq compute-ID"
|
||||
sys.exit()
|
||||
|
||||
infile = sys.argv[1]
|
||||
nfreq = int(sys.argv[2])
|
||||
compute = sys.argv[3]
|
||||
|
||||
me = 0
|
||||
# uncomment if running in parallel via Pypar
|
||||
#import pypar
|
||||
#me = pypar.rank()
|
||||
#nprocs = pypar.size()
|
||||
|
||||
from lammps import lammps
|
||||
lmp = lammps()
|
||||
|
||||
# run infile all at once
|
||||
# assumed to have no run command in it
|
||||
# dump a file in native LAMMPS dump format for Pizza.py dump tool
|
||||
|
||||
lmp.file(infile)
|
||||
lmp.command("thermo %d" % nfreq)
|
||||
lmp.command("dump python all atom %d tmp.dump" % nfreq)
|
||||
|
||||
# initial 0-step run to generate initial 1-point plot, dump file, and image
|
||||
|
||||
lmp.command("run 0 pre yes post no")
|
||||
value = lmp.extract_compute(compute,0,0)
|
||||
ntimestep = 0
|
||||
xaxis = [ntimestep]
|
||||
yaxis = [value]
|
||||
|
||||
breakflag = 0
|
||||
runflag = 0
|
||||
temptarget = 1.0
|
||||
|
||||
# wrapper on VMD window via Pizza.py vmd tool
|
||||
# just proc 0 handles reading of dump file and viz
|
||||
|
||||
if me == 0:
|
||||
from vmd import vmd
|
||||
v = vmd()
|
||||
v('menu main off')
|
||||
v.rep('VDW')
|
||||
|
||||
from dump import dump
|
||||
from pdbfile import pdbfile
|
||||
|
||||
d = dump('tmp.dump',0)
|
||||
p = pdbfile(d)
|
||||
d.next()
|
||||
d.unscale()
|
||||
p.single(ntimestep)
|
||||
v.new('tmp.pdb','pdb')
|
||||
|
||||
# display GUI with run/stop buttons and slider for temperature
|
||||
|
||||
if me == 0:
|
||||
from Tkinter import *
|
||||
tkroot = Tk()
|
||||
tkroot.withdraw()
|
||||
root = Toplevel(tkroot)
|
||||
root.title("LAMMPS GUI")
|
||||
|
||||
frame = Frame(root)
|
||||
Button(frame,text="Run",command=run).pack(side=LEFT)
|
||||
Button(frame,text="Stop",command=stop).pack(side=LEFT)
|
||||
slider = Scale(frame,from_=0.0,to=5.0,resolution=0.1,
|
||||
orient=HORIZONTAL,label="Temperature")
|
||||
slider.bind('<ButtonRelease-1>',settemp)
|
||||
slider.set(temptarget)
|
||||
slider.pack(side=LEFT)
|
||||
Button(frame,text="Quit",command=quit).pack(side=RIGHT)
|
||||
frame.pack()
|
||||
tkroot.update()
|
||||
|
||||
# wrapper on GnuPlot via Pizza.py gnu tool
|
||||
|
||||
if me == 0:
|
||||
from gnu import gnu
|
||||
gn = gnu()
|
||||
gn.plot(xaxis,yaxis)
|
||||
gn.title(compute,"Timestep","Temperature")
|
||||
|
||||
# endless loop, checking status of GUI settings every Nfreq steps
|
||||
# run with pre yes/no and post yes/no depending on go/stop status
|
||||
# re-invoke fix langevin with new seed when temperature slider changes
|
||||
# after re-invoke of fix langevin, run with pre yes
|
||||
|
||||
running = 0
|
||||
temp = temptarget
|
||||
seed = 12345
|
||||
|
||||
lmp.command("fix 2 all langevin %g %g 0.1 %d" % (temp,temp,seed))
|
||||
|
||||
while 1:
|
||||
if me == 0: tkroot.update()
|
||||
if temp != temptarget:
|
||||
temp = temptarget
|
||||
seed += me+1
|
||||
lmp.command("fix 2 all langevin %g %g 0.1 12345" % (temp,temp))
|
||||
running = 0
|
||||
if runflag and running:
|
||||
lmp.command("run %d pre no post no" % nfreq)
|
||||
ntimestep += nfreq
|
||||
if me == 0: update(ntimestep)
|
||||
elif runflag and not running:
|
||||
lmp.command("run %d pre yes post no" % nfreq)
|
||||
ntimestep += nfreq
|
||||
if me == 0: update(ntimestep)
|
||||
elif not runflag and running:
|
||||
lmp.command("run %d pre no post yes" % nfreq)
|
||||
ntimestep += nfreq
|
||||
if me == 0: update(ntimestep)
|
||||
if breakflag: break
|
||||
if runflag: running = 1
|
||||
else: running = 0
|
||||
time.sleep(0.01)
|
||||
|
||||
lmp.command("run 0 pre no post yes")
|
||||
|
||||
# uncomment if running in parallel via Pypar
|
||||
#print "Proc %d out of %d procs has" % (me,nprocs), lmp
|
||||
#pypar.finalize()
|
||||
@ -275,6 +275,8 @@ void PairCoulLong::init_style()
|
||||
|
||||
double PairCoulLong::init_one(int i, int j)
|
||||
{
|
||||
scale[j][i] = scale[i][j];
|
||||
|
||||
return cut_coul;
|
||||
}
|
||||
|
||||
|
||||
@ -12,7 +12,7 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Axel Kohlmeyer (U Penn), akohlmey at cmm.chem.upenn.edu
|
||||
Contributing author: Axel Kohlmeyer (Temple U), akohlmey at gmail.com
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "math.h"
|
||||
|
||||
@ -132,6 +132,7 @@ void FixNEB::min_setup(int vflag)
|
||||
void FixNEB::min_post_force(int vflag)
|
||||
{
|
||||
MPI_Status status;
|
||||
MPI_Request request;
|
||||
double vprev,vnext,vmax,vmin;
|
||||
double delx,dely,delz;
|
||||
double delta1[3],delta2[3];
|
||||
@ -141,10 +142,21 @@ void FixNEB::min_post_force(int vflag)
|
||||
|
||||
veng = pe->compute_scalar();
|
||||
|
||||
if (ireplica < nreplica-1)
|
||||
if (ireplica == 0)
|
||||
MPI_Send(&veng,1,MPI_DOUBLE,procnext,0,uworld);
|
||||
else if (ireplica == nreplica-1) {
|
||||
MPI_Irecv(&vprev,1,MPI_DOUBLE,procprev,0,uworld,&request);
|
||||
MPI_Wait(&request,&status);
|
||||
} else
|
||||
MPI_Sendrecv(&veng,1,MPI_DOUBLE,procnext,0,
|
||||
&vprev,1,MPI_DOUBLE,procprev,0,uworld,&status);
|
||||
if (ireplica > 0)
|
||||
|
||||
if (ireplica == 0) {
|
||||
MPI_Irecv(&vnext,1,MPI_DOUBLE,procnext,0,uworld,&request);
|
||||
MPI_Wait(&request,&status);
|
||||
} else if (ireplica == nreplica-1)
|
||||
MPI_Send(&veng,1,MPI_DOUBLE,procprev,0,uworld);
|
||||
else
|
||||
MPI_Sendrecv(&veng,1,MPI_DOUBLE,procprev,0,
|
||||
&vnext,1,MPI_DOUBLE,procnext,0,uworld,&status);
|
||||
|
||||
@ -157,10 +169,21 @@ void FixNEB::min_post_force(int vflag)
|
||||
int nlocal = atom->nlocal;
|
||||
if (nlocal != natoms) error->one("Atom count changed in fix neb");
|
||||
|
||||
if (ireplica < nreplica-1)
|
||||
if (ireplica == 0)
|
||||
MPI_Send(x[0],3*nlocal,MPI_DOUBLE,procnext,0,uworld);
|
||||
else if (ireplica == nreplica-1) {
|
||||
MPI_Irecv(xprev[0],3*nlocal,MPI_DOUBLE,procprev,0,uworld,&request);
|
||||
MPI_Wait(&request,&status);
|
||||
} else
|
||||
MPI_Sendrecv(x[0],3*nlocal,MPI_DOUBLE,procnext,0,
|
||||
xprev[0],3*nlocal,MPI_DOUBLE,procprev,0,uworld,&status);
|
||||
if (ireplica > 0)
|
||||
|
||||
if (ireplica == 0) {
|
||||
MPI_Irecv(xnext[0],3*nlocal,MPI_DOUBLE,procnext,0,uworld,&request);
|
||||
MPI_Wait(&request,&status);
|
||||
} else if (ireplica == nreplica-1)
|
||||
MPI_Send(x[0],3*nlocal,MPI_DOUBLE,procprev,0,uworld);
|
||||
else
|
||||
MPI_Sendrecv(x[0],3*nlocal,MPI_DOUBLE,procprev,0,
|
||||
xnext[0],3*nlocal,MPI_DOUBLE,procnext,0,uworld,&status);
|
||||
|
||||
|
||||
@ -383,12 +383,13 @@ void NEB::print_status()
|
||||
for (int i = 1; i < nreplica; i++)
|
||||
rdist[i] = rdist[i-1] + all[i][1];
|
||||
double endpt = rdist[nreplica-1] = rdist[nreplica-2] + all[nreplica-2][2];
|
||||
if (endpt > 0.0)
|
||||
for (int i = 1; i < nreplica; i++)
|
||||
rdist[i] /= endpt;
|
||||
|
||||
// look up GradV for the initial, final, and climbing replicas
|
||||
// These are identical to fnorm2, but better to be safe we
|
||||
// take them straight from fix_neb
|
||||
// these should be identical to fnorm2
|
||||
// but to be safe take them straight from fix neb
|
||||
|
||||
double gradvnorm0, gradvnorm1, gradvnormc;
|
||||
|
||||
|
||||
@ -13,7 +13,7 @@
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Common parameters for the CMM coarse grained MD potentials.
|
||||
Contributing author: Axel Kohlmeyer <akohlmey@gmail.com>
|
||||
Contributing author: Axel Kohlmeyer (Temple U) <akohlmey@gmail.com>
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef LMP_CG_CMM_PARMS_H
|
||||
|
||||
@ -1416,6 +1416,13 @@ double FixNH::compute_vector(int n)
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixNH::reset_target(double t_new)
|
||||
{
|
||||
t_start = t_stop = t_new;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixNH::reset_dt()
|
||||
{
|
||||
dtv = update->dt;
|
||||
|
||||
@ -34,6 +34,7 @@ class FixNH : public Fix {
|
||||
void write_restart(FILE *);
|
||||
void restart(char *);
|
||||
int modify_param(int, char **);
|
||||
void reset_target(double);
|
||||
void reset_dt();
|
||||
|
||||
protected:
|
||||
|
||||
@ -28,7 +28,7 @@ class FixRigid : public Fix {
|
||||
public:
|
||||
FixRigid(class LAMMPS *, int, char **);
|
||||
virtual ~FixRigid();
|
||||
int setmask();
|
||||
virtual int setmask();
|
||||
virtual void init();
|
||||
virtual void setup(int);
|
||||
virtual void initial_integrate(int);
|
||||
|
||||
@ -42,7 +42,9 @@ FixRigidNVT::FixRigidNVT(LAMMPS *lmp, int narg, char **arg) :
|
||||
{
|
||||
// other settings are made by FixRigid parent
|
||||
|
||||
scalar_flag = 1;
|
||||
restart_global = 1;
|
||||
extscalar = 1;
|
||||
|
||||
// error checking
|
||||
// convert input period to frequency
|
||||
@ -86,6 +88,20 @@ FixRigidNVT::~FixRigidNVT()
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixRigidNVT::setmask()
|
||||
{
|
||||
int mask = 0;
|
||||
mask |= INITIAL_INTEGRATE;
|
||||
mask |= FINAL_INTEGRATE;
|
||||
mask |= PRE_NEIGHBOR;
|
||||
mask |= THERMO_ENERGY;
|
||||
mask |= INITIAL_INTEGRATE_RESPA;
|
||||
mask |= FINAL_INTEGRATE_RESPA;
|
||||
return mask;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixRigidNVT::init()
|
||||
{
|
||||
FixRigid::init();
|
||||
@ -105,6 +121,8 @@ void FixRigidNVT::init()
|
||||
for (int k = 0; k < domain->dimension; k++)
|
||||
if (fabs(inertia[ibody][k]) < 1e-6) nf_r--;
|
||||
|
||||
// see Table 1 in Kamberaj et al
|
||||
|
||||
if (t_order == 3) {
|
||||
w[0] = 1.0 / (2.0 - pow(2.0, 1.0/3.0));
|
||||
w[1] = 1.0 - 2.0*w[0];
|
||||
@ -200,12 +218,12 @@ void FixRigidNVT::initial_integrate(int vflag)
|
||||
xcm[ibody][1] += dtv * vcm[ibody][1];
|
||||
xcm[ibody][2] += dtv * vcm[ibody][2];
|
||||
|
||||
// step 1.3 - apply torque (body coords) to quaternion momentum
|
||||
|
||||
torque[ibody][0] *= tflag[ibody][0];
|
||||
torque[ibody][1] *= tflag[ibody][1];
|
||||
torque[ibody][2] *= tflag[ibody][2];
|
||||
|
||||
// step 1.3 - apply torque (body coords) to quaternion momentum
|
||||
|
||||
matvec_rows(ex_space[ibody],ey_space[ibody],ez_space[ibody],
|
||||
torque[ibody],tbody);
|
||||
quatvec(quat[ibody],tbody,fquat);
|
||||
@ -219,7 +237,7 @@ void FixRigidNVT::initial_integrate(int vflag)
|
||||
conjqm[ibody][2] *= scale_r;
|
||||
conjqm[ibody][3] *= scale_r;
|
||||
|
||||
// step 1.4 to 1.13 - use no_squish rotate to update p and q
|
||||
// step 1.4 to 1.8 - use no_squish rotate to update p (i.e. conjqm) and q
|
||||
|
||||
no_squish_rotate(3,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
|
||||
no_squish_rotate(2,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
|
||||
@ -227,7 +245,7 @@ void FixRigidNVT::initial_integrate(int vflag)
|
||||
no_squish_rotate(2,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
|
||||
no_squish_rotate(3,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
|
||||
|
||||
// update the exyz_space
|
||||
// update the exyz_space from new quaternion
|
||||
// transform p back to angmom
|
||||
// update angular velocity
|
||||
|
||||
@ -271,7 +289,7 @@ void FixRigidNVT::final_integrate()
|
||||
double tmp,scale_t,scale_r,akin_t,akin_r;
|
||||
double dtfm,xy,xz,yz;
|
||||
|
||||
// intialize velocity scale for translation and rotation
|
||||
// compute velocity scales for translation and rotation
|
||||
|
||||
tmp = -1.0 * dtq * eta_dot_t[0];
|
||||
scale_t = exp(tmp);
|
||||
@ -360,7 +378,7 @@ void FixRigidNVT::final_integrate()
|
||||
torque[ibody][1] = all[ibody][4];
|
||||
torque[ibody][2] = all[ibody][5];
|
||||
|
||||
// update vcm by 1/2 step
|
||||
// 2.5-2.6 update vcm by 1/2 step
|
||||
|
||||
dtfm = dtf / masstotal[ibody];
|
||||
vcm[ibody][0] *= scale_t;
|
||||
@ -370,22 +388,31 @@ void FixRigidNVT::final_integrate()
|
||||
vcm[ibody][1] += dtfm * fcm[ibody][1] * fflag[ibody][1];
|
||||
vcm[ibody][2] += dtfm * fcm[ibody][2] * fflag[ibody][2];
|
||||
|
||||
// update conjqm, then transform to angmom, set velocity again
|
||||
// virial is already setup from initial_integrate
|
||||
// 2.1-2.4 update conjqm, angular momentum and angular velocity
|
||||
// apply body torque flags
|
||||
|
||||
torque[ibody][0] *= tflag[ibody][0];
|
||||
torque[ibody][1] *= tflag[ibody][1];
|
||||
torque[ibody][2] *= tflag[ibody][2];
|
||||
|
||||
// convert torque to the body frame
|
||||
|
||||
matvec_rows(ex_space[ibody],ey_space[ibody],ez_space[ibody],
|
||||
torque[ibody],tbody);
|
||||
|
||||
// compute "force" for quaternion
|
||||
|
||||
quatvec(quat[ibody],tbody,fquat);
|
||||
|
||||
// update the conjugate quaternion momentum (conjqm)
|
||||
|
||||
conjqm[ibody][0] = scale_r * conjqm[ibody][0] + dtf2 * fquat[0];
|
||||
conjqm[ibody][1] = scale_r * conjqm[ibody][1] + dtf2 * fquat[1];
|
||||
conjqm[ibody][2] = scale_r * conjqm[ibody][2] + dtf2 * fquat[2];
|
||||
conjqm[ibody][3] = scale_r * conjqm[ibody][3] + dtf2 * fquat[3];
|
||||
|
||||
// compute angular momentum in the body frame then convert to the space-fixed frame
|
||||
|
||||
invquatvec(quat[ibody],conjqm[ibody],mbody);
|
||||
matvec_cols(ex_space[ibody],ey_space[ibody],ez_space[ibody],
|
||||
mbody,angmom[ibody]);
|
||||
@ -394,6 +421,8 @@ void FixRigidNVT::final_integrate()
|
||||
angmom[ibody][1] *= 0.5;
|
||||
angmom[ibody][2] *= 0.5;
|
||||
|
||||
// compute new angular velocity
|
||||
|
||||
omega_from_angmom(angmom[ibody],ex_space[ibody],ey_space[ibody],
|
||||
ez_space[ibody],inertia[ibody],omega[ibody]);
|
||||
}
|
||||
@ -535,6 +564,76 @@ void FixRigidNVT::write_restart(FILE *fp)
|
||||
delete list;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute kinetic energy in the extended Hamiltonian
|
||||
conserved quantity = sum of returned energy and potential energy
|
||||
-----------------------------------------------------------------------*/
|
||||
|
||||
double FixRigidNVT::compute_scalar()
|
||||
{
|
||||
int i,k,ibody;
|
||||
double kt = boltz * t_target;
|
||||
double energy,ke_t,ke_q,tmp,Pkq[4];
|
||||
|
||||
// compute the kinetic parts of H_NVE in Kameraj et al (JCP 2005, pp 224114)
|
||||
|
||||
// translational kinetic energy
|
||||
|
||||
ke_t = 0.0;
|
||||
for (ibody = 0; ibody < nbody; ibody++)
|
||||
ke_t += 0.5 * masstotal[ibody] * (vcm[ibody][0]*vcm[ibody][0] +
|
||||
vcm[ibody][1]*vcm[ibody][1] +
|
||||
vcm[ibody][2]*vcm[ibody][2]);
|
||||
|
||||
// rotational kinetic energy
|
||||
|
||||
ke_q = 0.0;
|
||||
for (ibody = 0; ibody < nbody; ibody++) {
|
||||
for (k = 1; k < 4; k++) {
|
||||
if (k == 1) {
|
||||
Pkq[0] = -quat[ibody][1];
|
||||
Pkq[1] = quat[ibody][0];
|
||||
Pkq[2] = quat[ibody][3];
|
||||
Pkq[3] = -quat[ibody][2];
|
||||
} else if (k == 2) {
|
||||
Pkq[0] = -quat[ibody][2];
|
||||
Pkq[1] = -quat[ibody][3];
|
||||
Pkq[2] = quat[ibody][0];
|
||||
Pkq[3] = quat[ibody][1];
|
||||
} else if (k == 3) {
|
||||
Pkq[0] = -quat[ibody][3];
|
||||
Pkq[1] = quat[ibody][2];
|
||||
Pkq[2] = -quat[ibody][1];
|
||||
Pkq[3] = quat[ibody][0];
|
||||
}
|
||||
|
||||
tmp = conjqm[ibody][0]*Pkq[0] + conjqm[ibody][1]*Pkq[1] +
|
||||
conjqm[ibody][2]*Pkq[2] + conjqm[ibody][3]*Pkq[3];
|
||||
tmp *= tmp;
|
||||
|
||||
if (fabs(inertia[ibody][k-1]) < 1e-6) tmp = 0.0;
|
||||
else tmp /= (8.0 * inertia[ibody][k-1]);
|
||||
ke_q += tmp;
|
||||
}
|
||||
}
|
||||
|
||||
energy = ke_t + ke_q;
|
||||
|
||||
// thermostat chain energy: from equation 12 in Kameraj et al (JCP 2005)
|
||||
|
||||
energy += kt * (nf_t * eta_t[0] + nf_r * eta_r[0]);
|
||||
|
||||
for (i = 1; i < t_chain; i++)
|
||||
energy += kt * (eta_t[i] + eta_r[i]);
|
||||
|
||||
for (i = 0; i < t_chain; i++) {
|
||||
energy += 0.5 * q_t[i] * (eta_dot_t[i] * eta_dot_t[i]);
|
||||
energy += 0.5 * q_r[i] * (eta_dot_r[i] * eta_dot_r[i]);
|
||||
}
|
||||
|
||||
return energy;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
use state info from restart file to restart the Fix
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
@ -28,10 +28,12 @@ class FixRigidNVT : public FixRigid {
|
||||
public:
|
||||
FixRigidNVT(class LAMMPS *, int, char **);
|
||||
virtual ~FixRigidNVT();
|
||||
virtual int setmask();
|
||||
virtual void init();
|
||||
virtual void setup(int);
|
||||
virtual void initial_integrate(int);
|
||||
virtual void final_integrate();
|
||||
virtual double compute_scalar();
|
||||
virtual void write_restart(FILE *);
|
||||
virtual void restart(char *);
|
||||
virtual void reset_target(double);
|
||||
|
||||
@ -1240,6 +1240,87 @@ void Group::angmom(int igroup, double *cm, double *lmom, int iregion)
|
||||
MPI_Allreduce(p,lmom,3,MPI_DOUBLE,MPI_SUM,world);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute the torque T (tq) on group
|
||||
around center-of-mass cm
|
||||
must unwrap atoms to compute T correctly
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Group::torque(int igroup, double *cm, double *tq)
|
||||
{
|
||||
int groupbit = bitmask[igroup];
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int *mask = atom->mask;
|
||||
int *image = atom->image;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
int xbox,ybox,zbox;
|
||||
double dx,dy,dz;
|
||||
double xprd = domain->xprd;
|
||||
double yprd = domain->yprd;
|
||||
double zprd = domain->zprd;
|
||||
double tlocal[3];
|
||||
tlocal[0] = tlocal[1] = tlocal[2] = 0.0;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
xbox = (image[i] & 1023) - 512;
|
||||
ybox = (image[i] >> 10 & 1023) - 512;
|
||||
zbox = (image[i] >> 20) - 512;
|
||||
dx = (x[i][0] + xbox*xprd) - cm[0];
|
||||
dy = (x[i][1] + ybox*yprd) - cm[1];
|
||||
dz = (x[i][2] + zbox*zprd) - cm[2];
|
||||
tlocal[0] += dy*f[i][2] - dz*f[i][1];
|
||||
tlocal[1] += dz*f[i][0] - dx*f[i][2];
|
||||
tlocal[2] += dx*f[i][1] - dy*f[i][0];
|
||||
}
|
||||
|
||||
MPI_Allreduce(tlocal,tq,3,MPI_DOUBLE,MPI_SUM,world);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute the torque T (tq) on group of atoms in region
|
||||
around center-of-mass cm
|
||||
must unwrap atoms to compute T correctly
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Group::torque(int igroup, double *cm, double *tq, int iregion)
|
||||
{
|
||||
int groupbit = bitmask[igroup];
|
||||
Region *region = domain->regions[iregion];
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int *mask = atom->mask;
|
||||
int *image = atom->image;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
int xbox,ybox,zbox;
|
||||
double dx,dy,dz;
|
||||
double xprd = domain->xprd;
|
||||
double yprd = domain->yprd;
|
||||
double zprd = domain->zprd;
|
||||
double tlocal[3];
|
||||
tlocal[0] = tlocal[1] = tlocal[2] = 0.0;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
|
||||
xbox = (image[i] & 1023) - 512;
|
||||
ybox = (image[i] >> 10 & 1023) - 512;
|
||||
zbox = (image[i] >> 20) - 512;
|
||||
dx = (x[i][0] + xbox*xprd) - cm[0];
|
||||
dy = (x[i][1] + ybox*yprd) - cm[1];
|
||||
dz = (x[i][2] + zbox*zprd) - cm[2];
|
||||
tlocal[0] += dy*f[i][2] - dz*f[i][1];
|
||||
tlocal[1] += dz*f[i][0] - dx*f[i][2];
|
||||
tlocal[2] += dx*f[i][1] - dy*f[i][0];
|
||||
}
|
||||
|
||||
MPI_Allreduce(tlocal,tq,3,MPI_DOUBLE,MPI_SUM,world);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute moment of inertia tensor around center-of-mass cm of group
|
||||
must unwrap atoms to compute itensor correctly
|
||||
|
||||
@ -54,6 +54,8 @@ class Group : protected Pointers {
|
||||
double gyration(int, double, double *, int);
|
||||
void angmom(int, double *, double *); // angular momentum of group
|
||||
void angmom(int, double *, double *, int);
|
||||
void torque(int, double *, double *); // torque on group
|
||||
void torque(int, double *, double *, int);
|
||||
void inertia(int, double *, double [3][3]); // inertia tensor
|
||||
void inertia(int, double *, double [3][3], int);
|
||||
void omega(double *, double [3][3], double *); // angular velocity
|
||||
|
||||
@ -219,6 +219,8 @@ double PairCoulCut::init_one(int i, int j)
|
||||
if (setflag[i][j] == 0)
|
||||
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
|
||||
|
||||
scale[j][i] = scale[i][j];
|
||||
|
||||
return cut[i][j];
|
||||
}
|
||||
|
||||
|
||||
@ -2423,8 +2423,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
|
||||
customize by adding a group function with optional region arg:
|
||||
count(group),mass(group),charge(group),
|
||||
xcm(group,dim),vcm(group,dim),fcm(group,dim),
|
||||
bound(group,xmin),gyration(group),ke(group),angmom(group),
|
||||
inertia(group,dim),omega(group,dim)
|
||||
bound(group,xmin),gyration(group),ke(group),angmom(group,dim),
|
||||
torque(group,dim),inertia(group,dim),omega(group,dim)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int Variable::group_function(char *word, char *contents, Tree **tree,
|
||||
@ -2438,7 +2438,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
|
||||
strcmp(word,"vcm") && strcmp(word,"fcm") &&
|
||||
strcmp(word,"bound") && strcmp(word,"gyration") &&
|
||||
strcmp(word,"ke") && strcmp(word,"angmom") &&
|
||||
strcmp(word,"inertia") && strcmp(word,"omega"))
|
||||
strcmp(word,"torque") && strcmp(word,"inertia") &&
|
||||
strcmp(word,"omega"))
|
||||
return 0;
|
||||
|
||||
// parse contents for arg1,arg2,arg3 separated by commas
|
||||
@ -2588,6 +2589,24 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
|
||||
else if (strcmp(arg2,"z") == 0) value = lmom[2];
|
||||
else error->all("Invalid group function in variable formula");
|
||||
|
||||
} else if (strcmp(word,"torque") == 0) {
|
||||
atom->check_mass();
|
||||
double xcm[3],tq[3];
|
||||
if (narg == 2) {
|
||||
double masstotal = group->mass(igroup);
|
||||
group->xcm(igroup,masstotal,xcm);
|
||||
group->torque(igroup,xcm,tq);
|
||||
} else if (narg == 3) {
|
||||
int iregion = region_function(arg3);
|
||||
double masstotal = group->mass(igroup,iregion);
|
||||
group->xcm(igroup,masstotal,xcm,iregion);
|
||||
group->torque(igroup,xcm,tq,iregion);
|
||||
} else error->all("Invalid group function in variable formula");
|
||||
if (strcmp(arg2,"x") == 0) value = tq[0];
|
||||
else if (strcmp(arg2,"y") == 0) value = tq[1];
|
||||
else if (strcmp(arg2,"z") == 0) value = tq[2];
|
||||
else error->all("Invalid group function in variable formula");
|
||||
|
||||
} else if (strcmp(word,"inertia") == 0) {
|
||||
atom->check_mass();
|
||||
double xcm[3],inertia[3][3];
|
||||
|
||||
@ -1 +1 @@
|
||||
#define LAMMPS_VERSION "23 Nov 2010"
|
||||
#define LAMMPS_VERSION "1 Dec 2010"
|
||||
|
||||
@ -75,7 +75,7 @@ class Data {
|
||||
|
||||
char *atom_style;
|
||||
int style_angle,style_atomic,style_bond,style_charge,style_dipole;
|
||||
int style_dpd,style_ellipsoid,style_full,style_granular;
|
||||
int style_ellipsoid,style_full,style_granular;
|
||||
int style_hybrid,style_molecular,style_peri;
|
||||
|
||||
int natoms,nbonds,nangles,ndihedrals,nimpropers;
|
||||
@ -204,7 +204,6 @@ class Data {
|
||||
void write_atom_bond(FILE *, int, int, int, int);
|
||||
void write_atom_charge(FILE *, int, int, int, int);
|
||||
void write_atom_dipole(FILE *, int, int, int, int);
|
||||
void write_atom_dpd(FILE *, int, int, int, int);
|
||||
void write_atom_ellipsoid(FILE *, int, int, int, int);
|
||||
void write_atom_full(FILE *, int, int, int, int);
|
||||
void write_atom_granular(FILE *, int, int, int, int);
|
||||
@ -216,7 +215,6 @@ class Data {
|
||||
void write_atom_bond_extra(FILE *, int);
|
||||
void write_atom_charge_extra(FILE *, int);
|
||||
void write_atom_dipole_extra(FILE *, int);
|
||||
void write_atom_dpd_extra(FILE *, int);
|
||||
void write_atom_ellipsoid_extra(FILE *, int);
|
||||
void write_atom_full_extra(FILE *, int);
|
||||
void write_atom_granular_extra(FILE *, int);
|
||||
@ -228,7 +226,6 @@ class Data {
|
||||
void write_vel_bond(FILE *, int);
|
||||
void write_vel_charge(FILE *, int);
|
||||
void write_vel_dipole(FILE *, int);
|
||||
void write_vel_dpd(FILE *, int);
|
||||
void write_vel_ellipsoid(FILE *, int);
|
||||
void write_vel_full(FILE *, int);
|
||||
void write_vel_granular(FILE *, int);
|
||||
@ -240,7 +237,6 @@ class Data {
|
||||
void write_vel_bond_extra(FILE *, int);
|
||||
void write_vel_charge_extra(FILE *, int);
|
||||
void write_vel_dipole_extra(FILE *, int);
|
||||
void write_vel_dpd_extra(FILE *, int);
|
||||
void write_vel_ellipsoid_extra(FILE *, int);
|
||||
void write_vel_full_extra(FILE *, int);
|
||||
void write_vel_granular_extra(FILE *, int);
|
||||
@ -270,7 +266,6 @@ void allocate_atomic(Data &data);
|
||||
void allocate_bond(Data &data);
|
||||
void allocate_charge(Data &data);
|
||||
void allocate_dipole(Data &data);
|
||||
void allocate_dpd(Data &data);
|
||||
void allocate_ellipsoid(Data &data);
|
||||
void allocate_full(Data &data);
|
||||
void allocate_granular(Data &data);
|
||||
@ -282,7 +277,6 @@ int atom_atomic(double *, Data &, int);
|
||||
int atom_bond(double *, Data &, int);
|
||||
int atom_charge(double *, Data &, int);
|
||||
int atom_dipole(double *, Data &, int);
|
||||
int atom_dpd(double *, Data &, int);
|
||||
int atom_ellipsoid(double *, Data &, int);
|
||||
int atom_full(double *, Data &, int);
|
||||
int atom_granular(double *, Data &, int);
|
||||
@ -464,7 +458,7 @@ void header(FILE *fp, Data &data)
|
||||
|
||||
else if (flag == ATOM_STYLE) {
|
||||
data.style_angle = data.style_atomic = data.style_bond =
|
||||
data.style_charge = data.style_dipole = data.style_dpd =
|
||||
data.style_charge = data.style_dipole =
|
||||
data.style_ellipsoid = data.style_full = data.style_granular =
|
||||
data.style_hybrid = data.style_molecular = data.style_peri = 0;
|
||||
|
||||
@ -538,7 +532,6 @@ void set_style(char *name, Data &data, int flag)
|
||||
else if (strcmp(name,"bond") == 0) data.style_bond = flag;
|
||||
else if (strcmp(name,"charge") == 0) data.style_charge = flag;
|
||||
else if (strcmp(name,"dipole") == 0) data.style_dipole = flag;
|
||||
else if (strcmp(name,"dpd") == 0) data.style_dpd = flag;
|
||||
else if (strcmp(name,"ellipsoid") == 0) data.style_ellipsoid = flag;
|
||||
else if (strcmp(name,"full") == 0) data.style_full = flag;
|
||||
else if (strcmp(name,"granular") == 0) data.style_granular = flag;
|
||||
@ -712,7 +705,6 @@ int atom(double *buf, Data &data)
|
||||
if (data.style_bond) allocate_bond(data);
|
||||
if (data.style_charge) allocate_charge(data);
|
||||
if (data.style_dipole) allocate_dipole(data);
|
||||
if (data.style_dpd) allocate_dpd(data);
|
||||
if (data.style_ellipsoid) allocate_ellipsoid(data);
|
||||
if (data.style_full) allocate_full(data);
|
||||
if (data.style_granular) allocate_granular(data);
|
||||
@ -735,7 +727,6 @@ int atom(double *buf, Data &data)
|
||||
if (k == data.style_bond) m += atom_bond(&buf[m],data,iatoms);
|
||||
if (k == data.style_charge) m += atom_charge(&buf[m],data,iatoms);
|
||||
if (k == data.style_dipole) m += atom_dipole(&buf[m],data,iatoms);
|
||||
if (k == data.style_dpd) m += atom_dpd(&buf[m],data,iatoms);
|
||||
if (k == data.style_ellipsoid) m += atom_ellipsoid(&buf[m],data,iatoms);
|
||||
if (k == data.style_full) m += atom_full(&buf[m],data,iatoms);
|
||||
if (k == data.style_granular) m += atom_granular(&buf[m],data,iatoms);
|
||||
@ -892,23 +883,6 @@ int atom_dipole(double *buf, Data &data, int iatoms)
|
||||
return m;
|
||||
}
|
||||
|
||||
int atom_dpd(double *buf, Data &data, int iatoms)
|
||||
{
|
||||
int m = 1;
|
||||
data.x[iatoms] = buf[m++];
|
||||
data.y[iatoms] = buf[m++];
|
||||
data.z[iatoms] = buf[m++];
|
||||
data.tag[iatoms] = static_cast<int> (buf[m++]);
|
||||
data.type[iatoms] = static_cast<int> (buf[m++]);
|
||||
data.mask[iatoms] = static_cast<int> (buf[m++]);
|
||||
data.image[iatoms] = static_cast<int> (buf[m++]);
|
||||
data.vx[iatoms] = buf[m++];
|
||||
data.vy[iatoms] = buf[m++];
|
||||
data.vz[iatoms] = buf[m++];
|
||||
|
||||
return m;
|
||||
}
|
||||
|
||||
int atom_ellipsoid(double *buf, Data &data, int iatoms)
|
||||
{
|
||||
int m = 1;
|
||||
@ -1187,8 +1161,6 @@ void allocate_dipole(Data &data)
|
||||
data.muz = new double[data.natoms];
|
||||
}
|
||||
|
||||
void allocate_dpd(Data &data) {}
|
||||
|
||||
void allocate_full(Data &data)
|
||||
{
|
||||
data.q = new double[data.natoms];
|
||||
@ -3362,7 +3334,6 @@ void Data::write(FILE *fp, FILE *fp2)
|
||||
if (style_bond) write_atom_bond(fp,i,ix,iy,iz);
|
||||
if (style_charge) write_atom_charge(fp,i,ix,iy,iz);
|
||||
if (style_dipole) write_atom_dipole(fp,i,ix,iy,iz);
|
||||
if (style_dpd) write_atom_dpd(fp,i,ix,iy,iz);
|
||||
if (style_ellipsoid) write_atom_ellipsoid(fp,i,ix,iy,iz);
|
||||
if (style_full) write_atom_full(fp,i,ix,iy,iz);
|
||||
if (style_granular) write_atom_granular(fp,i,ix,iy,iz);
|
||||
@ -3379,7 +3350,6 @@ void Data::write(FILE *fp, FILE *fp2)
|
||||
if (k == style_bond) write_atom_bond_extra(fp,i);
|
||||
if (k == style_charge) write_atom_charge_extra(fp,i);
|
||||
if (k == style_dipole) write_atom_dipole_extra(fp,i);
|
||||
if (k == style_dpd) write_atom_dpd_extra(fp,i);
|
||||
if (k == style_ellipsoid) write_atom_ellipsoid_extra(fp,i);
|
||||
if (k == style_full) write_atom_full_extra(fp,i);
|
||||
if (k == style_granular) write_atom_granular_extra(fp,i);
|
||||
@ -3401,7 +3371,6 @@ void Data::write(FILE *fp, FILE *fp2)
|
||||
if (style_bond) write_vel_bond(fp,i);
|
||||
if (style_charge) write_vel_charge(fp,i);
|
||||
if (style_dipole) write_vel_dipole(fp,i);
|
||||
if (style_dpd) write_vel_dpd(fp,i);
|
||||
if (style_ellipsoid) write_vel_ellipsoid(fp,i);
|
||||
if (style_full) write_vel_full(fp,i);
|
||||
if (style_granular) write_vel_granular(fp,i);
|
||||
@ -3417,7 +3386,6 @@ void Data::write(FILE *fp, FILE *fp2)
|
||||
if (k == style_bond) write_vel_bond_extra(fp,i);
|
||||
if (k == style_charge) write_vel_charge_extra(fp,i);
|
||||
if (k == style_dipole) write_vel_dipole_extra(fp,i);
|
||||
if (k == style_dpd) write_vel_dpd_extra(fp,i);
|
||||
if (k == style_ellipsoid) write_vel_ellipsoid_extra(fp,i);
|
||||
if (k == style_full) write_vel_full_extra(fp,i);
|
||||
if (k == style_granular) write_vel_granular_extra(fp,i);
|
||||
@ -3494,12 +3462,6 @@ void Data::write_atom_dipole(FILE *fp, int i, int ix, int iy, int iz)
|
||||
tag[i],type[i],q[i],x[i],y[i],z[i],mux[i],muy[i],muz[i],ix,iy,iz);
|
||||
}
|
||||
|
||||
void Data::write_atom_dpd(FILE *fp, int i, int ix, int iy, int iz)
|
||||
{
|
||||
fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %d %d %d",
|
||||
tag[i],type[i],x[i],y[i],z[i],ix,iy,iz);
|
||||
}
|
||||
|
||||
void Data::write_atom_ellipsoid(FILE *fp, int i, int ix, int iy, int iz)
|
||||
{
|
||||
fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d",
|
||||
@ -3558,8 +3520,6 @@ void Data::write_atom_dipole_extra(FILE *fp, int i)
|
||||
fprintf(fp," %-1.16e %-1.16e %-1.16e %-1.16e",q[i],mux[i],muy[i],muz[i]);
|
||||
}
|
||||
|
||||
void Data::write_atom_dpd_extra(FILE *fp, int i) {}
|
||||
|
||||
void Data::write_atom_ellipsoid_extra(FILE *fp, int i)
|
||||
{
|
||||
fprintf(fp," %-1.16e %-1.16e %-1.16e %-1.16e",quatw[i],quati[i],quatj[i],quatk[i]);
|
||||
@ -3615,11 +3575,6 @@ void Data::write_vel_dipole(FILE *fp, int i)
|
||||
fprintf(fp,"%d %-1.16e %-1.16e %-1.16e",tag[i],vx[i],vy[i],vz[i]);
|
||||
}
|
||||
|
||||
void Data::write_vel_dpd(FILE *fp, int i)
|
||||
{
|
||||
fprintf(fp,"%d %-1.16e %-1.16e %-1.16e",tag[i],vx[i],vy[i],vz[i]);
|
||||
}
|
||||
|
||||
void Data::write_vel_ellipsoid(FILE *fp, int i)
|
||||
{
|
||||
fprintf(fp,"%d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e",
|
||||
@ -3657,7 +3612,6 @@ void Data::write_vel_atomic_extra(FILE *fp, int i) {}
|
||||
void Data::write_vel_bond_extra(FILE *fp, int i) {}
|
||||
void Data::write_vel_charge_extra(FILE *fp, int i) {}
|
||||
void Data::write_vel_dipole_extra(FILE *fp, int i) {}
|
||||
void Data::write_vel_dpd_extra(FILE *fp, int i) {}
|
||||
|
||||
void Data::write_vel_ellipsoid_extra(FILE *fp, int i)
|
||||
{
|
||||
|
||||
@ -18,3 +18,14 @@ in the syntax file (lammps.vim). You can easily add new ones.
|
||||
|
||||
Gerolf Ziegenhain <gerolf@ziegenhain.com> 2007
|
||||
|
||||
---------------
|
||||
|
||||
updated by Sam Bateman, 11/2010
|
||||
|
||||
Sam Bateman
|
||||
Naval Research Laboratory
|
||||
Code 7434
|
||||
1005 Balch Blvd.
|
||||
Stennis Space Center, MS 39529
|
||||
Phone: (228) 688-4328
|
||||
Email: sam.bateman@nrlssc.navy.mil
|
||||
|
||||
@ -1,20 +1,20 @@
|
||||
" Vim syntax file
|
||||
" Language: Lammps Simulation Script File
|
||||
" Maintainer: Gerolf Ziegenhain <gerolf@ziegenhain.com>
|
||||
" Updates: Axel Kohlmeyer <akohlmey@gmail.com>
|
||||
" Latest Revision: 2010-06-06
|
||||
" Updates: Axel Kohlmeyer <akohlmey@gmail.com>, Sam Bateman <sam.bateman@nrlssc.navy.mil>
|
||||
" Latest Revision: 2010-11-25
|
||||
|
||||
syn clear
|
||||
|
||||
syn keyword lammpsOutput log write_restart dump undump thermo thermo_modify thermo_style print
|
||||
syn keyword lammpsRead include read read_restart read_data
|
||||
syn keyword lammpsLattice boundary units atom_style lattice region create_box create_atoms dielectric
|
||||
syn keyword lammpsLattice delete_atoms change_box dimension newton replicate
|
||||
syn keyword lammpsParticle pair_coeff pair_style pair_modify mass angle_coeff angle_style atom_modify
|
||||
syn keyword lammpsParticle atom_style bond_coeff bond_style delete_bonds kspace_style kspace_modify
|
||||
syn keyword lammpsParticle dihedral_style dihedral_coeff improper_style improper_coeff
|
||||
syn keyword lammpsSetup min_style fix_modify run_style timestep neighbor fix unfix communicate
|
||||
syn keyword lammpsSetup neigh_modify reset_timestep velocity
|
||||
syn keyword lammpsLattice delete_atoms change_box dimension replicate
|
||||
syn keyword lammpsParticle pair_coeff pair_style pair_modify mass velocity angle_coeff angle_style
|
||||
syn keyword lammpsParticle atom_modify atom_style bond_coeff bond_style delete_bonds kspace_style
|
||||
syn keyword lammpsParticle kspace_modify dihedral_style dihedral_coeff improper_style improper_coeff
|
||||
syn keyword lammpsSetup min_style fix_modify run_style timestep neighbor neigh_modify fix unfix
|
||||
syn keyword lammpsSetup communicate newton nthreads processors reset_timestep
|
||||
syn keyword lammpsRun minimize run
|
||||
syn keyword lammpsDefine variable group
|
||||
|
||||
@ -22,7 +22,9 @@ syn keyword lammpsRepeat jump next loop
|
||||
|
||||
syn keyword lammpsOperator equal add sub mult div
|
||||
|
||||
syn keyword lammpsConditional if then else
|
||||
syn keyword lammpsConditional if then elif else
|
||||
|
||||
syn keyword lammpsSpecial EDGE NULL
|
||||
|
||||
syn region lammpsString start=+'+ end=+'+ oneline
|
||||
syn region lammpsString start=+"+ end=+"+ oneline
|
||||
@ -34,7 +36,7 @@ syn match lammpsFloat "\<[0-9]\+[edED][-+]\=[0-9]\+[ij]\=\>"
|
||||
|
||||
syn match lammpsComment "#.*$"
|
||||
|
||||
syn match lammpsVariable "\$\({[a-zA-Z0-9]\+}\)"
|
||||
syn match lammpsVariable "\$\({[a-zA-Z0-9_]\+}\)"
|
||||
syn match lammpsVariable "\$[A-Za-z]"
|
||||
|
||||
if !exists("did_lammps_syntax_inits")
|
||||
@ -55,6 +57,7 @@ if !exists("did_lammps_syntax_inits")
|
||||
hi link lammpsVariable Identifier
|
||||
hi link lammpsConditional Conditional
|
||||
hi link lammpsOperator Operator
|
||||
hi link lammpsSpecial Number
|
||||
endif
|
||||
|
||||
let b:current_syntax = "lammps"
|
||||
|
||||
Reference in New Issue
Block a user