Merge pull request #482 from akohlmey/add-pair-python
Add python pair style for implementing simple pairwise additive potentials in python
This commit is contained in:
sjplimp
@ -157,6 +157,8 @@ doc page for its python-style variables for more info, including
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examples of Python code you can write for both pure Python operations
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and callbacks to LAMMPS. See "fix python"_fix_python.html to learn about
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possibilities to execute Python code during each time step.
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Through the "python pair style"_pair_python.html it is also possible
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to define potential functions as python code.
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To run pure Python code from LAMMPS, you only need to build LAMMPS
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with the PYTHON package installed:
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@ -237,6 +237,7 @@ fix_pour.html
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fix_press_berendsen.html
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fix_print.html
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fix_property_atom.html
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fix_python.html
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fix_qbmsst.html
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fix_qeq.html
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fix_qeq_comb.html
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@ -468,6 +469,7 @@ pair_oxdna.html
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pair_oxdna2.html
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pair_peri.html
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pair_polymorphic.html
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pair_python.html
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pair_quip.html
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pair_reax.html
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pair_reaxc.html
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212
doc/src/pair_python.txt
Normal file
212
doc/src/pair_python.txt
Normal file
@ -0,0 +1,212 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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pair_style python command :h3
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[Syntax:]
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pair_style python cutoff :pre
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cutoff = global cutoff for interactions in python potential classes
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[Examples:]
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pair_style python 2.5
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pair_coeff * * py_pot.LJCutMelt lj :pre
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pair_style hybrid/overlay coul/long 12.0 python 12.0
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pair_coeff * * coul/long
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pair_coeff * * python py_pot.LJCutSPCE OW NULL :pre
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[Description:]
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The {python} pair style provides a way to define pairwise additive
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potential functions as python script code that is loaded into LAMMPS
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from a python file which must contain specific python class definitions.
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This allows to rapidly evaluate different potential functions without
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having to modify and recompile LAMMPS. Due to python being an
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interpreted language, however, the performance of this pair style is
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going to be significantly slower (often between 20x and 100x) than
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corresponding compiled code. This penalty can be significantly reduced
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through generating tabulations from the python code through the
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"pair_write"_pair_write.html command, which is supported by this style.
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Only a single pair_coeff command is used with the {python} pair style
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which specifies a python class inside a python module or file that
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LAMMPS will look up in the current directory, the folder pointed to by
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the LAMMPS_POTENTIALS environment variable or somewhere in your python
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path. A single python module can hold multiple python pair class
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definitions. The class definitions itself have to follow specific rules
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that are explained below.
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Atom types in the python class are specified through symbolic constants,
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typically strings. These are mapped to LAMMPS atom types by specifying
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N additional arguments after the class name in the pair_coeff command,
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where N must be the number of currently defined atom types:
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As an example, imagine a file {py_pot.py} has a python potential class
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names {LJCutMelt} with parameters and potential functions for a two
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Lennard-Jones atom types labeled as 'LJ1' and 'LJ2'. In your LAMMPS
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input and you would have defined 3 atom types, out of which the first
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two are supposed to be using the 'LJ1' parameters and the third
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the 'LJ2' parameters, then you would use the following pair_coeff
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command:
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pair_coeff * * py_pot.LJCutMelt LJ1 LJ1 LJ2 :pre
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The first two arguments [must] be * * so as to span all LAMMPS atom types.
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The first two LJ1 arguments map LAMMPS atom types 1 and 2 to the LJ1
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atom type in the LJCutMelt class of the py_pot.py file. The final LJ2
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argument maps LAMMPS atom type 3 to the LJ2 atom type the python file.
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If a mapping value is specified as NULL, the mapping is not performed,
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any pair interaction with this atom type will be skipped. This can be
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used when a {python} potential is used as part of the {hybrid} or
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{hybrid/overlay} pair style. The NULL values are then placeholders for
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atom types that will be used with other potentials.
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:line
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The python potential file has to start with the following code:
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from __future__ import print_function
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class LAMMPSPairPotential(object):
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def __init__(self):
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self.pmap=dict()
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self.units='lj'
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def map_coeff(self,name,ltype):
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self.pmap\[ltype\]=name
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def check_units(self,units):
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if (units != self.units):
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raise Exception("Conflicting units: %s vs. %s" % (self.units,units))
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:pre
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Any classes with definitions of specific potentials have to be derived
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from this class and should be initialize in a similar fashion to the
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example given below. NOTE: The class constructor has to set up a data
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structure containing the potential parameters supported by this class.
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It should also define a variable {self.units} containing a string
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matching one of the options of LAMMPS' "units"_units.html command, which
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is used to verify, that the potential definition in the python class and
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in the LAMMPS input match. Example for a single type Lennard-Jones
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potential class {LJCutMelt} in reducted units, which defines an atom
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type {lj} for which the parameters epsilon and sigma are both 1.0:
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class LJCutMelt(LAMMPSPairPotential):
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def __init__(self):
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super(LJCutMelt,self).__init__()
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# set coeffs: 48*eps*sig**12, 24*eps*sig**6,
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# 4*eps*sig**12, 4*eps*sig**6
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self.units = 'lj'
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self.coeff = {'lj' : {'lj' : (48.0,24.0,4.0,4.0)}}
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:pre
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The class also has to provide two methods for the computation of the
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potential energy and forces, which have be named {compute_force},
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and {compute_energy}, which both take 3 numerical arguments:
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rsq = the square of the distance between a pair of atoms (float) :li
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itype = the (numerical) type of the first atom :li
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jtype = the (numerical) type of the second atom :ul
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This functions need to compute the force and the energy, respectively,
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and use the result as return value. The functions need to use the
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{pmap} dictionary to convert the LAMMPS atom type number to the symbolic
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value of the internal potential parameter data structure. Following
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the {LJCutMelt} example, here are the two functions:
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def compute_force(self,rsq,itype,jtype):
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coeff = self.coeff\[self.pmap\[itype\]\]\[self.pmap\[jtype\]\]
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r2inv = 1.0/rsq
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r6inv = r2inv*r2inv*r2inv
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lj1 = coeff\[0\]
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lj2 = coeff\[1\]
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return (r6inv * (lj1*r6inv - lj2))*r2inv :pre
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def compute_energy(self,rsq,itype,jtype):
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coeff = self.coeff\[self.pmap\[itype\]\]\[self.pmap\[jtype\]\]
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r2inv = 1.0/rsq
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r6inv = r2inv*r2inv*r2inv
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lj3 = coeff\[2\]
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lj4 = coeff\[3\]
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return (r6inv * (lj3*r6inv - lj4)) :pre
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IMPORTANT NOTE: for consistency with the C++ pair styles in LAMMPS,
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the {compute_force} function follows the conventions of the Pair::single()
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methods and does not return the full force, but the force scaled by
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the distance between the two atoms, so this value only needs to be
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multiplied by delta x, delta y, and delta z to conveniently obtain
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the three components of the force vector between these two atoms.
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:line
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IMPORTANT NOTE: The evaluation of scripted python code will slow down
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the computation pair-wise interactions quite significantly. However,
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this can be largely worked around through using the python pair style
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not for the actual simulation, but to generate tabulated potentials
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on the fly using the "pair_write"_pair_write.html command. Please
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see below for an example LAMMPS input of how to build a table file:
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pair_style python 2.5
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pair_coeff * * py_pot.LJCutMelt lj
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shell rm -f melt.table
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pair_write 1 1 2000 rsq 0.01 2.5 lj1_lj2.table lj :pre
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Note, that it is strong recommended to try to [delete] the potential
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table file before generating it. Since the {pair_write} command will
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always append to a table file, which pair style table will use the first
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match. Thus when changing the potential function in the python class,
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the table pair style will still read the old variant.
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After switching the pair style to {table}, the potential tables need
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to be assigned to the LAMMPS atom types like this:
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pair_style table linear 2000
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pair_coeff 1 1 melt.table lj :pre
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This can also be done for more complex systems. Please see the
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{examples/python} folders for a few more examples.
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:line
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[Mixing, shift, table, tail correction, restart, rRESPA info]:
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Mixing of potential parameters has to be handled inside the provided
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python module. The python pair style simply assumes that force and
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energy computation can be correctly performed for all pairs of atom
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types as they are mapped to the atom type labels inside the python
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potential class.
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This pair style does not support the "pair_modify"_pair_modify.html
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shift, table, and tail options.
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This pair style does not write its information to "binary restart
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files"_restart.html, since it is stored in potential files. Thus, you
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need to re-specify the pair_style and pair_coeff commands in an input
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script that reads a restart file.
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This pair style can only be used via the {pair} keyword of the
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"run_style respa"_run_style.html command. It does not support the
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{inner}, {middle}, {outer} keywords.
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:line
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[Restrictions:]
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This pair style is part of the PYTHON package. It is only enabled
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if LAMMPS was built with that package. See
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the "Making LAMMPS"_Section_start.html#start_3 section for more info.
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[Related commands:]
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"pair_coeff"_pair_coeff.html, "pair_write"_pair_write.html,
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"pair style table"_pair_table.html
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[Default:] none
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@ -72,6 +72,7 @@ Pair Styles :h1
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pair_oxdna2
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pair_peri
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pair_polymorphic
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pair_python
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pair_quip
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pair_reax
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pair_reaxc
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41
examples/python/README.pair_python
Normal file
41
examples/python/README.pair_python
Normal file
@ -0,0 +1,41 @@
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This folder contains several LAMMPS input scripts and a python module
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file py_pot.py to demonstrate the use of the pair style python.
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in.pair_python_melt:
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This is a version of the melt example using the python pair style. The first
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part of the output should have identical energies, temperature and pressure
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than the melt example. The following two sections then demonstrate how to
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restart with pair style python from a restart file and a data file.
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in.pair_python_hybrid:
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This versions shows how to mix regular pair styles with a python pair style.
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However, in this case both potentials are the same, so the energies and
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pressure in the output should be identical to that of the previous example.
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in.pair_python_spce:
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This input shows a simulation of small bulk water system with the SPC/E
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water potential. Since the python pair style does not support computing
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coulomb contributions, pair style hybrid/overload is used to combine
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the python style containing the Lennard-Jones part with the long-range coulomb.
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Same as for the previous example, it also showcases restarting.
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in.pair_python_table:
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This input demonstrates the use of using the python pair style to build
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a table file for use with pair style table. This will run much faster
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than the python pair style. This example tabulates the melt example from
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above. Note that tabulation is approximative, so the output will only
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agree with the melt result to some degree.
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in.pair_python_coulomb:
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This is another tabulation example, this time for the SPC/E water example
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with cutoff coulomb interactions.
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Please note, that tabulating long-range coulomb has a systematic error in
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forces and energies for all systems with bonds, angle and dihedrals.
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In this case, this will only affect the energies, since the water molecules
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are held rigid with fix shake. To enable long-range coulomb the coul/cut
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style needs to be replaced with coul/long, a suitable kspace style added
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and the pppm keyword added to the table pair style definition.
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in.pair_python_long:
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The final example shows how to combine long-range coulomb with tabulation
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for only the short range interactions via pair style hybrid/overlay.
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9029
examples/python/data.spce
Normal file
9029
examples/python/data.spce
Normal file
File diff suppressed because it is too large
Load Diff
42
examples/python/in.pair_python_coulomb
Normal file
42
examples/python/in.pair_python_coulomb
Normal file
@ -0,0 +1,42 @@
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units real
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atom_style full
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read_data data.spce
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pair_style hybrid/overlay coul/cut 12.0 python 12.0
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pair_coeff * * coul/cut
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pair_coeff * * python py_pot.LJCutSPCE OW NULL
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bond_style harmonic
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angle_style harmonic
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dihedral_style none
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improper_style none
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bond_coeff 1 1000.00 1.000
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angle_coeff 1 100.0 109.47
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special_bonds lj/coul 0.0 0.0 1.0
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neighbor 2.0 bin
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fix 1 all shake 0.0001 20 0 b 1 a 1
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fix 2 all nvt temp 300.0 300.0 100.0
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# create combined lj/coul table for all atom types
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# generate tabulated potential from python variant
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pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472
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pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236
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pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236
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# switch to tabulated potential
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pair_style table linear 2000 pppm
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pair_coeff 1 1 spce.table OW-OW
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pair_coeff 1 2 spce.table OW-HW
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pair_coeff 2 2 spce.table HW-HW
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thermo 10
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run 100
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shell rm spce.table
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63
examples/python/in.pair_python_hybrid
Normal file
63
examples/python/in.pair_python_hybrid
Normal file
@ -0,0 +1,63 @@
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# 3d Lennard-Jones hybrid
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units lj
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atom_style atomic
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lattice fcc 0.8442
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region box block 0 10 0 10 0 10
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create_box 2 box
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create_atoms 1 box
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mass * 1.0
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region half block -0.1 4.9 0 10 0 10
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set region half type 2
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velocity all create 3.0 87287
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pair_style hybrid lj/cut 2.5 python 2.5
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pair_coeff * * python py_pot.LJCutMelt lj NULL
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pair_coeff * 2 lj/cut 1.0 1.0
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neighbor 0.3 bin
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neigh_modify every 20 delay 0 check no
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fix 1 all nve
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thermo 50
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run 250
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write_data hybrid.data
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write_restart hybrid.restart
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clear
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read_restart hybrid.restart
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pair_style hybrid lj/cut 2.5 python 2.5
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pair_coeff * * python py_pot.LJCutMelt lj NULL
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pair_coeff * 2 lj/cut 1.0 1.0
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fix 1 all nve
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thermo 50
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run 250
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clear
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units lj
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atom_style atomic
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read_data hybrid.data
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pair_style hybrid lj/cut 2.5 python 2.5
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pair_coeff * * python py_pot.LJCutMelt lj NULL
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pair_coeff * 2 lj/cut 1.0 1.0
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neighbor 0.3 bin
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neigh_modify every 20 delay 0 check no
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fix 1 all nve
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thermo 50
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run 250
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shell rm hybrid.data hybrid.restart
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38
examples/python/in.pair_python_long
Normal file
38
examples/python/in.pair_python_long
Normal file
@ -0,0 +1,38 @@
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units real
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atom_style full
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read_data data.spce
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pair_style python 12.0
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pair_coeff * * py_pot.LJCutSPCE OW HW
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bond_style harmonic
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angle_style harmonic
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dihedral_style none
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improper_style none
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bond_coeff 1 1000.00 1.000
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angle_coeff 1 100.0 109.47
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special_bonds lj/coul 0.0 0.0 1.0
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neighbor 2.0 bin
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fix 1 all shake 0.0001 20 0 b 1 a 1
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fix 2 all nvt temp 300.0 300.0 100.0
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# create only lj/cut table for the oxygen atoms from python
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shell rm -f spce.table
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pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW
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# switch to tabulated potential with long-range coulomb as overlay
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pair_style hybrid/overlay coul/long 12.0 table linear 2000
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kspace_style pppm 1.0e-6
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pair_coeff * * coul/long
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pair_coeff 1 1 table spce.table OW-OW
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thermo 10
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run 100
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shell rm spce.table
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58
examples/python/in.pair_python_melt
Normal file
58
examples/python/in.pair_python_melt
Normal file
@ -0,0 +1,58 @@
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# 3d Lennard-Jones melt
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units lj
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atom_style atomic
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||||
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lattice fcc 0.8442
|
||||
region box block 0 10 0 10 0 10
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||||
create_box 1 box
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||||
create_atoms 1 box
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mass * 1.0
|
||||
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style python 2.5
|
||||
pair_coeff * * py_pot.LJCutMelt lj
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
|
||||
write_data melt.data
|
||||
write_restart melt.restart
|
||||
|
||||
clear
|
||||
|
||||
read_restart melt.restart
|
||||
|
||||
pair_style python 2.5
|
||||
pair_coeff * * py_pot.LJCutMelt lj
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
|
||||
clear
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data melt.data
|
||||
|
||||
pair_style python 2.5
|
||||
pair_coeff * * py_pot.LJCutMelt lj
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
|
||||
shell rm melt.data melt.restart
|
||||
28
examples/python/in.pair_python_spce
Normal file
28
examples/python/in.pair_python_spce
Normal file
@ -0,0 +1,28 @@
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
read_data data.spce
|
||||
|
||||
pair_style hybrid/overlay coul/long 12.0 python 12.0
|
||||
kspace_style pppm 1.0e-6
|
||||
|
||||
pair_coeff * * coul/long
|
||||
pair_coeff * * python py_pot.LJCutSPCE OW NULL
|
||||
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
bond_coeff 1 1000.00 1.000
|
||||
angle_coeff 1 100.0 109.47
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 1.0
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
fix 1 all shake 0.0001 20 0 b 1 a 1
|
||||
fix 2 all nvt temp 300.0 300.0 100.0
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
32
examples/python/in.pair_python_table
Normal file
32
examples/python/in.pair_python_table
Normal file
@ -0,0 +1,32 @@
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style python 2.5
|
||||
pair_coeff * * py_pot.LJCutMelt lj
|
||||
|
||||
# generate tabulated potential from python variant
|
||||
pair_write 1 1 2000 rsq 0.01 2.5 lj_1_1.table LJ
|
||||
|
||||
pair_style table linear 2000
|
||||
pair_coeff 1 1 lj_1_1.table LJ
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
|
||||
shell rm lj_1_1.table
|
||||
|
||||
178
examples/python/log.4May17.pair_python_coulomb.1
Normal file
178
examples/python/log.4May17.pair_python_coulomb.1
Normal file
@ -0,0 +1,178 @@
|
||||
LAMMPS (4 May 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
read_data data.spce
|
||||
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
4500 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
3000 bonds
|
||||
reading angles ...
|
||||
1500 angles
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
pair_style hybrid/overlay python 12.0 coul/long 12.0
|
||||
kspace_style pppm 1.0e-6
|
||||
|
||||
pair_coeff * * coul/long
|
||||
pair_coeff * * python potentials.LJCutSPCE OW NULL
|
||||
|
||||
pair_modify table 0
|
||||
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
bond_coeff 1 1000.00 1.000
|
||||
angle_coeff 1 100.0 109.47
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 1.0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
fix 1 all shake 0.0001 20 0 b 1 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
1500 = # of frozen angles
|
||||
fix 2 all nvt temp 300.0 300.0 100.0
|
||||
|
||||
# create combined lj/coul table for all atom types
|
||||
# generate tabulated potential from python variant
|
||||
pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472
|
||||
PPPM initialization ...
|
||||
WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.279652
|
||||
grid = 40 40 40
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000394206
|
||||
estimated relative force accuracy = 1.18714e-06
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 103823 64000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair python, perpetual, skip from (2)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236
|
||||
PPPM initialization ...
|
||||
WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.279652
|
||||
grid = 40 40 40
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000394206
|
||||
estimated relative force accuracy = 1.18714e-06
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 103823 64000
|
||||
pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236
|
||||
PPPM initialization ...
|
||||
WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.279652
|
||||
grid = 40 40 40
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000394206
|
||||
estimated relative force accuracy = 1.18714e-06
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 103823 64000
|
||||
|
||||
# switch to tabulated potential
|
||||
pair_style table linear 2000 pppm
|
||||
pair_coeff 1 1 spce.table OW-OW
|
||||
pair_coeff 1 2 spce.table OW-HW
|
||||
pair_coeff 2 2 spce.table HW-HW
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.279652
|
||||
grid = 40 40 40
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000394674
|
||||
estimated relative force accuracy = 1.18855e-06
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 103823 64000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 35.26 | 35.26 | 35.26 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -100272.97 0 -100272.97 -1282.0708
|
||||
10 120.61568 -101350.63 0 -100272.39 -4077.5051
|
||||
20 136.11379 -101465.43 0 -100248.65 -5136.5677
|
||||
30 137.01602 -101455.3 0 -100230.46 -5347.8311
|
||||
40 153.424 -101582.46 0 -100210.93 -5223.1676
|
||||
50 167.73654 -101686.24 0 -100186.77 -4468.6687
|
||||
60 163.11642 -101618.16 0 -100159.99 -3291.7815
|
||||
70 169.64512 -101647.89 0 -100131.35 -2611.638
|
||||
80 182.9979 -101737.01 0 -100101.11 -2390.6293
|
||||
90 191.33873 -101778.71 0 -100068.24 -2239.386
|
||||
100 194.7458 -101775.84 0 -100034.92 -1951.9128
|
||||
Loop time of 7.60221 on 1 procs for 100 steps with 4500 atoms
|
||||
|
||||
Performance: 1.137 ns/day, 21.117 hours/ns, 13.154 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.7401 | 5.7401 | 5.7401 | 0.0 | 75.51
|
||||
Bond | 0.00017881 | 0.00017881 | 0.00017881 | 0.0 | 0.00
|
||||
Kspace | 1.5387 | 1.5387 | 1.5387 | 0.0 | 20.24
|
||||
Neigh | 0.2299 | 0.2299 | 0.2299 | 0.0 | 3.02
|
||||
Comm | 0.024311 | 0.024311 | 0.024311 | 0.0 | 0.32
|
||||
Output | 0.00057936 | 0.00057936 | 0.00057936 | 0.0 | 0.01
|
||||
Modify | 0.063158 | 0.063158 | 0.063158 | 0.0 | 0.83
|
||||
Other | | 0.005243 | | | 0.07
|
||||
|
||||
Nlocal: 4500 ave 4500 max 4500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 21216 ave 21216 max 21216 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2.60177e+06 ave 2.60177e+06 max 2.60177e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2601766
|
||||
Ave neighs/atom = 578.17
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
shell rm spce.table
|
||||
|
||||
Total wall time: 0:00:07
|
||||
138
examples/python/log.4May17.pair_python_coulomb.g++.1
Normal file
138
examples/python/log.4May17.pair_python_coulomb.g++.1
Normal file
@ -0,0 +1,138 @@
|
||||
LAMMPS (4 May 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
read_data data.spce
|
||||
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
4500 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
3000 bonds
|
||||
reading angles ...
|
||||
1500 angles
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
pair_style hybrid/overlay coul/cut 12.0 python 12.0
|
||||
|
||||
pair_coeff * * coul/cut
|
||||
pair_coeff * * python py_pot.LJCutSPCE OW NULL
|
||||
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
bond_coeff 1 1000.00 1.000
|
||||
angle_coeff 1 100.0 109.47
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 1.0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
fix 1 all shake 0.0001 20 0 b 1 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
1500 = # of frozen angles
|
||||
fix 2 all nvt temp 300.0 300.0 100.0
|
||||
|
||||
# create combined lj/coul table for all atom types
|
||||
# generate tabulated potential from python variant
|
||||
pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair coul/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair python, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236
|
||||
pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236
|
||||
|
||||
# switch to tabulated potential
|
||||
pair_style table linear 2000 pppm
|
||||
pair_coeff 1 1 spce.table OW-OW
|
||||
pair_coeff 1 2 spce.table OW-HW
|
||||
pair_coeff 2 2 spce.table HW-HW
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 25.08 | 25.08 | 25.08 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -18284.922 0 -18284.922 -2080.7739
|
||||
10 146.83806 -19552.072 0 -18239.421 -4865.31
|
||||
20 183.15761 -18706.872 0 -17069.543 -4865.6695
|
||||
30 205.96203 -18901.541 0 -17060.354 -4454.8634
|
||||
40 241.62768 -18323.117 0 -16163.099 -3269.1475
|
||||
50 265.98384 -19883.562 0 -17505.813 -2788.5194
|
||||
60 274.01897 -21320.575 0 -18870.996 -2387.0708
|
||||
70 288.7601 -19849.269 0 -17267.913 -1235.818
|
||||
80 300.64724 -20958.602 0 -18270.981 -1714.7988
|
||||
90 304.19113 -21580.4 0 -18861.099 -2144.1614
|
||||
100 304.22027 -21239.014 0 -18519.452 -2092.6759
|
||||
Loop time of 6.01861 on 1 procs for 100 steps with 4500 atoms
|
||||
|
||||
Performance: 1.436 ns/day, 16.718 hours/ns, 16.615 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.698 | 5.698 | 5.698 | 0.0 | 94.67
|
||||
Bond | 0.0001626 | 0.0001626 | 0.0001626 | 0.0 | 0.00
|
||||
Neigh | 0.23235 | 0.23235 | 0.23235 | 0.0 | 3.86
|
||||
Comm | 0.018961 | 0.018961 | 0.018961 | 0.0 | 0.32
|
||||
Output | 0.00058126 | 0.00058126 | 0.00058126 | 0.0 | 0.01
|
||||
Modify | 0.063452 | 0.063452 | 0.063452 | 0.0 | 1.05
|
||||
Other | | 0.005146 | | | 0.09
|
||||
|
||||
Nlocal: 4500 ave 4500 max 4500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 21285 ave 21285 max 21285 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2.59766e+06 ave 2.59766e+06 max 2.59766e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2597662
|
||||
Ave neighs/atom = 577.258
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
shell rm spce.table
|
||||
|
||||
Total wall time: 0:00:06
|
||||
138
examples/python/log.4May17.pair_python_coulomb.g++.4
Normal file
138
examples/python/log.4May17.pair_python_coulomb.g++.4
Normal file
@ -0,0 +1,138 @@
|
||||
LAMMPS (4 May 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
read_data data.spce
|
||||
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
4500 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
3000 bonds
|
||||
reading angles ...
|
||||
1500 angles
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
pair_style hybrid/overlay coul/cut 12.0 python 12.0
|
||||
|
||||
pair_coeff * * coul/cut
|
||||
pair_coeff * * python py_pot.LJCutSPCE OW NULL
|
||||
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
bond_coeff 1 1000.00 1.000
|
||||
angle_coeff 1 100.0 109.47
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 1.0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
fix 1 all shake 0.0001 20 0 b 1 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
1500 = # of frozen angles
|
||||
fix 2 all nvt temp 300.0 300.0 100.0
|
||||
|
||||
# create combined lj/coul table for all atom types
|
||||
# generate tabulated potential from python variant
|
||||
pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair coul/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair python, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236
|
||||
pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236
|
||||
|
||||
# switch to tabulated potential
|
||||
pair_style table linear 2000 pppm
|
||||
pair_coeff 1 1 spce.table OW-OW
|
||||
pair_coeff 1 2 spce.table OW-HW
|
||||
pair_coeff 2 2 spce.table HW-HW
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.962 | 9.963 | 9.963 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -18284.922 0 -18284.922 -2080.7739
|
||||
10 146.83806 -19552.072 0 -18239.421 -4865.31
|
||||
20 183.15761 -18706.872 0 -17069.543 -4865.6695
|
||||
30 205.96203 -18901.541 0 -17060.354 -4454.8634
|
||||
40 241.62768 -18323.117 0 -16163.099 -3269.1475
|
||||
50 265.98384 -19883.562 0 -17505.813 -2788.5194
|
||||
60 274.01897 -21320.575 0 -18870.996 -2387.0708
|
||||
70 288.7601 -19849.269 0 -17267.913 -1235.818
|
||||
80 300.64724 -20958.602 0 -18270.981 -1714.7988
|
||||
90 304.19113 -21580.4 0 -18861.099 -2144.1614
|
||||
100 304.22027 -21239.014 0 -18519.452 -2092.6759
|
||||
Loop time of 1.7361 on 4 procs for 100 steps with 4500 atoms
|
||||
|
||||
Performance: 4.977 ns/day, 4.823 hours/ns, 57.600 timesteps/s
|
||||
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.4424 | 1.5149 | 1.6066 | 5.3 | 87.26
|
||||
Bond | 8.9407e-05 | 0.00010258 | 0.00012374 | 0.0 | 0.01
|
||||
Neigh | 0.064205 | 0.064241 | 0.064295 | 0.0 | 3.70
|
||||
Comm | 0.023643 | 0.1155 | 0.18821 | 19.2 | 6.65
|
||||
Output | 0.00038004 | 0.00042355 | 0.00054145 | 0.0 | 0.02
|
||||
Modify | 0.037507 | 0.037787 | 0.038042 | 0.1 | 2.18
|
||||
Other | | 0.003148 | | | 0.18
|
||||
|
||||
Nlocal: 1125 ave 1162 max 1098 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Nghost: 12267.8 ave 12302 max 12238 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Neighs: 649416 ave 681458 max 630541 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 2597662
|
||||
Ave neighs/atom = 577.258
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
shell rm spce.table
|
||||
|
||||
Total wall time: 0:00:01
|
||||
250
examples/python/log.4May17.pair_python_hybrid.g++.1
Normal file
250
examples/python/log.4May17.pair_python_hybrid.g++.1
Normal file
@ -0,0 +1,250 @@
|
||||
LAMMPS (4 May 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 3d Lennard-Jones hybrid
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4000 atoms
|
||||
mass * 1.0
|
||||
region half block -0.1 4.9 0 10 0 10
|
||||
set region half type 2
|
||||
2000 settings made for type
|
||||
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style hybrid lj/cut 2.5 python 2.5
|
||||
pair_coeff * * python py_pot.LJCutMelt lj NULL
|
||||
pair_coeff * 2 lj/cut 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
Neighbor list info ...
|
||||
update every 20 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 12 12 12
|
||||
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||
(1) pair lj/cut, perpetual, skip from (3)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair python, perpetual, skip from (3)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) neighbor class addition, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.446 | 4.446 | 4.446 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 3 -6.7733681 0 -2.2744931 -3.7033504
|
||||
50 1.6758903 -4.7955425 0 -2.2823355 5.670064
|
||||
100 1.6458363 -4.7492704 0 -2.2811332 5.8691042
|
||||
150 1.6324555 -4.7286791 0 -2.280608 5.9589514
|
||||
200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
|
||||
250 1.6275257 -4.7224992 0 -2.281821 5.9567365
|
||||
Loop time of 10.0384 on 1 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 10758.705 tau/day, 24.904 timesteps/s
|
||||
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 9.913 | 9.913 | 9.913 | 0.0 | 98.75
|
||||
Neigh | 0.095569 | 0.095569 | 0.095569 | 0.0 | 0.95
|
||||
Comm | 0.012686 | 0.012686 | 0.012686 | 0.0 | 0.13
|
||||
Output | 0.00027537 | 0.00027537 | 0.00027537 | 0.0 | 0.00
|
||||
Modify | 0.01386 | 0.01386 | 0.01386 | 0.0 | 0.14
|
||||
Other | | 0.003027 | | | 0.03
|
||||
|
||||
Nlocal: 4000 ave 4000 max 4000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5499 ave 5499 max 5499 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 85978 ave 85978 max 85978 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 85978
|
||||
Ave neighs/atom = 21.4945
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds not checked
|
||||
|
||||
write_data hybrid.data
|
||||
write_restart hybrid.restart
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
read_restart hybrid.restart
|
||||
orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
4000 atoms
|
||||
|
||||
pair_style hybrid lj/cut 2.5 python 2.5
|
||||
pair_coeff * * python py_pot.LJCutMelt lj NULL
|
||||
pair_coeff * 2 lj/cut 1.0 1.0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 12 12 12
|
||||
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||
(1) pair lj/cut, perpetual, skip from (3)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair python, perpetual, skip from (3)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) neighbor class addition, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.245 | 4.245 | 4.245 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
250 1.6275257 -4.7224992 0 -2.281821 5.9567365
|
||||
300 1.645592 -4.7496711 0 -2.2819002 5.8734193
|
||||
350 1.6514972 -4.7580756 0 -2.2814491 5.810167
|
||||
400 1.6540555 -4.7622999 0 -2.281837 5.8200413
|
||||
450 1.6264734 -4.7200865 0 -2.2809863 5.9546991
|
||||
500 1.6366891 -4.7350979 0 -2.2806781 5.9369284
|
||||
Loop time of 10.0803 on 1 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 10713.932 tau/day, 24.801 timesteps/s
|
||||
98.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 9.8479 | 9.8479 | 9.8479 | 0.0 | 97.69
|
||||
Neigh | 0.20002 | 0.20002 | 0.20002 | 0.0 | 1.98
|
||||
Comm | 0.01437 | 0.01437 | 0.01437 | 0.0 | 0.14
|
||||
Output | 0.00024033 | 0.00024033 | 0.00024033 | 0.0 | 0.00
|
||||
Modify | 0.013422 | 0.013422 | 0.013422 | 0.0 | 0.13
|
||||
Other | | 0.004348 | | | 0.04
|
||||
|
||||
Nlocal: 4000 ave 4000 max 4000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5472 ave 5472 max 5472 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 86930 ave 86930 max 86930 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 86930
|
||||
Ave neighs/atom = 21.7325
|
||||
Neighbor list builds = 25
|
||||
Dangerous builds = 25
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data hybrid.data
|
||||
orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
4000 atoms
|
||||
reading velocities ...
|
||||
4000 velocities
|
||||
|
||||
pair_style hybrid lj/cut 2.5 python 2.5
|
||||
pair_coeff * * python py_pot.LJCutMelt lj NULL
|
||||
pair_coeff * 2 lj/cut 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
Neighbor list info ...
|
||||
update every 20 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 12 12 12
|
||||
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||
(1) pair lj/cut, perpetual, skip from (3)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair python, perpetual, skip from (3)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) neighbor class addition, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.745 | 3.745 | 3.745 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.6275257 -4.7224992 0 -2.281821 5.9567365
|
||||
50 1.6454666 -4.7497515 0 -2.2821686 5.8729175
|
||||
100 1.6512008 -4.7582693 0 -2.2820874 5.8090548
|
||||
150 1.6537193 -4.7627023 0 -2.2827434 5.8177704
|
||||
200 1.6258731 -4.7205017 0 -2.2823017 5.952511
|
||||
250 1.6370862 -4.7373176 0 -2.2823022 5.925807
|
||||
Loop time of 9.93686 on 1 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 10868.626 tau/day, 25.159 timesteps/s
|
||||
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 9.8119 | 9.8119 | 9.8119 | 0.0 | 98.74
|
||||
Neigh | 0.096041 | 0.096041 | 0.096041 | 0.0 | 0.97
|
||||
Comm | 0.01243 | 0.01243 | 0.01243 | 0.0 | 0.13
|
||||
Output | 0.00028133 | 0.00028133 | 0.00028133 | 0.0 | 0.00
|
||||
Modify | 0.013261 | 0.013261 | 0.013261 | 0.0 | 0.13
|
||||
Other | | 0.002994 | | | 0.03
|
||||
|
||||
Nlocal: 4000 ave 4000 max 4000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5487 ave 5487 max 5487 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 86831 ave 86831 max 86831 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 86831
|
||||
Ave neighs/atom = 21.7078
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds not checked
|
||||
|
||||
shell rm hybrid.data hybrid.restart
|
||||
Total wall time: 0:00:30
|
||||
250
examples/python/log.4May17.pair_python_hybrid.g++.4
Normal file
250
examples/python/log.4May17.pair_python_hybrid.g++.4
Normal file
@ -0,0 +1,250 @@
|
||||
LAMMPS (4 May 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 3d Lennard-Jones hybrid
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4000 atoms
|
||||
mass * 1.0
|
||||
region half block -0.1 4.9 0 10 0 10
|
||||
set region half type 2
|
||||
2000 settings made for type
|
||||
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style hybrid lj/cut 2.5 python 2.5
|
||||
pair_coeff * * python py_pot.LJCutMelt lj NULL
|
||||
pair_coeff * 2 lj/cut 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
Neighbor list info ...
|
||||
update every 20 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 12 12 12
|
||||
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||
(1) pair lj/cut, perpetual, skip from (3)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair python, perpetual, skip from (3)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) neighbor class addition, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.953 | 3.953 | 3.953 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 3 -6.7733681 0 -2.2744931 -3.7033504
|
||||
50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
|
||||
100 1.6503357 -4.756014 0 -2.2811293 5.8050524
|
||||
150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
|
||||
200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
|
||||
250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
|
||||
Loop time of 2.71748 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 39742.745 tau/day, 91.997 timesteps/s
|
||||
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.4777 | 2.5639 | 2.6253 | 3.9 | 94.35
|
||||
Neigh | 0.024626 | 0.025331 | 0.02598 | 0.3 | 0.93
|
||||
Comm | 0.061933 | 0.12297 | 0.20987 | 18.0 | 4.53
|
||||
Output | 0.00026131 | 0.00027591 | 0.00031352 | 0.0 | 0.01
|
||||
Modify | 0.0036087 | 0.0036573 | 0.0037553 | 0.1 | 0.13
|
||||
Other | | 0.001337 | | | 0.05
|
||||
|
||||
Nlocal: 1000 ave 1010 max 982 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 2703.75 ave 2713 max 2689 min
|
||||
Histogram: 1 0 0 0 0 0 0 2 0 1
|
||||
Neighs: 21469.8 ave 22167 max 20546 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
|
||||
Total # of neighbors = 85879
|
||||
Ave neighs/atom = 21.4698
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds not checked
|
||||
|
||||
write_data hybrid.data
|
||||
write_restart hybrid.restart
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
read_restart hybrid.restart
|
||||
orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
4000 atoms
|
||||
|
||||
pair_style hybrid lj/cut 2.5 python 2.5
|
||||
pair_coeff * * python py_pot.LJCutMelt lj NULL
|
||||
pair_coeff * 2 lj/cut 1.0 1.0
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 12 12 12
|
||||
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||
(1) pair lj/cut, perpetual, skip from (3)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair python, perpetual, skip from (3)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) neighbor class addition, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.612 | 3.612 | 3.612 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
250 1.6323462 -4.7292062 0 -2.2812991 5.9762168
|
||||
300 1.6451788 -4.7488091 0 -2.2816578 5.8375485
|
||||
350 1.6171909 -4.7064928 0 -2.2813129 6.0094235
|
||||
400 1.6388136 -4.7387093 0 -2.2811035 5.9331084
|
||||
450 1.6431295 -4.7452215 0 -2.2811435 5.8929898
|
||||
500 1.643316 -4.7454222 0 -2.2810644 5.8454817
|
||||
Loop time of 2.75827 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 39155.038 tau/day, 90.637 timesteps/s
|
||||
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.3631 | 2.5412 | 2.6672 | 7.2 | 92.13
|
||||
Neigh | 0.050358 | 0.052316 | 0.053312 | 0.5 | 1.90
|
||||
Comm | 0.032793 | 0.15893 | 0.33904 | 29.1 | 5.76
|
||||
Output | 0.00018525 | 0.00020212 | 0.00024509 | 0.0 | 0.01
|
||||
Modify | 0.0034482 | 0.0035321 | 0.0036578 | 0.1 | 0.13
|
||||
Other | | 0.002039 | | | 0.07
|
||||
|
||||
Nlocal: 1000 ave 1012 max 983 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Nghost: 2699 ave 2706 max 2693 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
Neighs: 21802 ave 22700 max 21236 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 87208
|
||||
Ave neighs/atom = 21.802
|
||||
Neighbor list builds = 25
|
||||
Dangerous builds = 25
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data hybrid.data
|
||||
orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
4000 atoms
|
||||
reading velocities ...
|
||||
4000 velocities
|
||||
|
||||
pair_style hybrid lj/cut 2.5 python 2.5
|
||||
pair_coeff * * python py_pot.LJCutMelt lj NULL
|
||||
pair_coeff * 2 lj/cut 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
Neighbor list info ...
|
||||
update every 20 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 12 12 12
|
||||
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||
(1) pair lj/cut, perpetual, skip from (3)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair python, perpetual, skip from (3)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) neighbor class addition, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.112 | 3.112 | 3.112 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.6323462 -4.7292062 0 -2.2812991 5.9762168
|
||||
50 1.6450626 -4.7488948 0 -2.2819177 5.8370409
|
||||
100 1.6169004 -4.7066969 0 -2.2819526 6.0082546
|
||||
150 1.6384234 -4.7389689 0 -2.2819482 5.9315273
|
||||
200 1.6428814 -4.7460743 0 -2.2823683 5.8888228
|
||||
250 1.6432631 -4.7466603 0 -2.2823818 5.8398819
|
||||
Loop time of 2.71936 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 39715.257 tau/day, 91.933 timesteps/s
|
||||
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.3769 | 2.5432 | 2.6447 | 6.6 | 93.52
|
||||
Neigh | 0.024088 | 0.025093 | 0.025748 | 0.4 | 0.92
|
||||
Comm | 0.044614 | 0.14598 | 0.31339 | 27.5 | 5.37
|
||||
Output | 0.00026488 | 0.00028872 | 0.00034189 | 0.0 | 0.01
|
||||
Modify | 0.0034099 | 0.0035709 | 0.0036535 | 0.2 | 0.13
|
||||
Other | | 0.001215 | | | 0.04
|
||||
|
||||
Nlocal: 1000 ave 1013 max 989 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Nghost: 2695.5 ave 2706 max 2682 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 21792 ave 22490 max 21457 min
|
||||
Histogram: 2 0 1 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 87168
|
||||
Ave neighs/atom = 21.792
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds not checked
|
||||
|
||||
shell rm hybrid.data hybrid.restart
|
||||
Total wall time: 0:00:08
|
||||
146
examples/python/log.4May17.pair_python_long.g++.1
Normal file
146
examples/python/log.4May17.pair_python_long.g++.1
Normal file
@ -0,0 +1,146 @@
|
||||
LAMMPS (4 May 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
read_data data.spce
|
||||
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
4500 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
3000 bonds
|
||||
reading angles ...
|
||||
1500 angles
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
pair_style python 12.0
|
||||
pair_coeff * * py_pot.LJCutSPCE OW HW
|
||||
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
bond_coeff 1 1000.00 1.000
|
||||
angle_coeff 1 100.0 109.47
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 1.0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
fix 1 all shake 0.0001 20 0 b 1 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
1500 = # of frozen angles
|
||||
fix 2 all nvt temp 300.0 300.0 100.0
|
||||
|
||||
# create only lj/cut table for the oxygen atoms from python
|
||||
shell rm -f spce.table
|
||||
WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285)
|
||||
WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285)
|
||||
pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair python, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
|
||||
# switch to tabulated potential with long-range coulomb as overlay
|
||||
pair_style hybrid/overlay coul/long 12.0 table linear 2000
|
||||
kspace_style pppm 1.0e-6
|
||||
pair_coeff * * coul/long
|
||||
pair_coeff 1 1 table spce.table OW-OW
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.279652
|
||||
grid = 40 40 40
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000394674
|
||||
estimated relative force accuracy = 1.18855e-06
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 103823 64000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair table, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 36.47 | 36.47 | 36.47 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -16690.032 0 -16690.032 -1268.9538
|
||||
10 120.58553 -17767.504 0 -16689.536 -4063.8589
|
||||
20 136.11736 -17882.557 0 -16665.742 -5124.6758
|
||||
30 137.00764 -17872.318 0 -16647.545 -5337.2022
|
||||
40 153.38868 -17999.269 0 -16628.059 -5213.6001
|
||||
50 167.70342 -18103.06 0 -16603.883 -4460.6632
|
||||
60 163.07134 -18034.856 0 -16577.088 -3285.0037
|
||||
70 169.59286 -18064.636 0 -16548.57 -2606.407
|
||||
80 182.92893 -18153.499 0 -16518.215 -2385.5152
|
||||
90 191.2793 -18195.356 0 -16485.425 -2235.3701
|
||||
100 194.68587 -18192.458 0 -16452.073 -1948.3746
|
||||
Loop time of 7.90705 on 1 procs for 100 steps with 4500 atoms
|
||||
|
||||
Performance: 1.093 ns/day, 21.964 hours/ns, 12.647 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 6.0343 | 6.0343 | 6.0343 | 0.0 | 76.32
|
||||
Bond | 0.00019622 | 0.00019622 | 0.00019622 | 0.0 | 0.00
|
||||
Kspace | 1.5311 | 1.5311 | 1.5311 | 0.0 | 19.36
|
||||
Neigh | 0.246 | 0.246 | 0.246 | 0.0 | 3.11
|
||||
Comm | 0.023937 | 0.023937 | 0.023937 | 0.0 | 0.30
|
||||
Output | 0.00060368 | 0.00060368 | 0.00060368 | 0.0 | 0.01
|
||||
Modify | 0.065543 | 0.065543 | 0.065543 | 0.0 | 0.83
|
||||
Other | | 0.005364 | | | 0.07
|
||||
|
||||
Nlocal: 4500 ave 4500 max 4500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 21216 ave 21216 max 21216 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2.60177e+06 ave 2.60177e+06 max 2.60177e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2601769
|
||||
Ave neighs/atom = 578.171
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
shell rm spce.table
|
||||
|
||||
Total wall time: 0:00:08
|
||||
146
examples/python/log.4May17.pair_python_long.g++.4
Normal file
146
examples/python/log.4May17.pair_python_long.g++.4
Normal file
@ -0,0 +1,146 @@
|
||||
LAMMPS (4 May 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
read_data data.spce
|
||||
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
4500 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
3000 bonds
|
||||
reading angles ...
|
||||
1500 angles
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
pair_style python 12.0
|
||||
pair_coeff * * py_pot.LJCutSPCE OW HW
|
||||
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
bond_coeff 1 1000.00 1.000
|
||||
angle_coeff 1 100.0 109.47
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 1.0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
fix 1 all shake 0.0001 20 0 b 1 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
1500 = # of frozen angles
|
||||
fix 2 all nvt temp 300.0 300.0 100.0
|
||||
|
||||
# create only lj/cut table for the oxygen atoms from python
|
||||
shell rm -f spce.table
|
||||
WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285)
|
||||
WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285)
|
||||
pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair python, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
|
||||
# switch to tabulated potential with long-range coulomb as overlay
|
||||
pair_style hybrid/overlay coul/long 12.0 table linear 2000
|
||||
kspace_style pppm 1.0e-6
|
||||
pair_coeff * * coul/long
|
||||
pair_coeff 1 1 table spce.table OW-OW
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.279652
|
||||
grid = 40 40 40
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000394674
|
||||
estimated relative force accuracy = 1.18855e-06
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 34263 16000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair table, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 13.45 | 13.45 | 13.45 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -16690.032 0 -16690.032 -1268.9538
|
||||
10 120.58553 -17767.504 0 -16689.536 -4063.8589
|
||||
20 136.11736 -17882.557 0 -16665.742 -5124.6758
|
||||
30 137.00764 -17872.318 0 -16647.545 -5337.2022
|
||||
40 153.38868 -17999.269 0 -16628.059 -5213.6001
|
||||
50 167.70342 -18103.06 0 -16603.883 -4460.6632
|
||||
60 163.07134 -18034.856 0 -16577.088 -3285.0037
|
||||
70 169.59286 -18064.636 0 -16548.57 -2606.407
|
||||
80 182.92893 -18153.499 0 -16518.215 -2385.5152
|
||||
90 191.2793 -18195.356 0 -16485.425 -2235.3701
|
||||
100 194.68587 -18192.458 0 -16452.073 -1948.3746
|
||||
Loop time of 2.36748 on 4 procs for 100 steps with 4500 atoms
|
||||
|
||||
Performance: 3.649 ns/day, 6.576 hours/ns, 42.239 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.5309 | 1.5977 | 1.6926 | 4.7 | 67.49
|
||||
Bond | 9.9182e-05 | 0.00012749 | 0.00016403 | 0.0 | 0.01
|
||||
Kspace | 0.52158 | 0.61232 | 0.67676 | 7.3 | 25.86
|
||||
Neigh | 0.066937 | 0.06702 | 0.067093 | 0.0 | 2.83
|
||||
Comm | 0.035882 | 0.039862 | 0.042244 | 1.2 | 1.68
|
||||
Output | 0.0004003 | 0.00044602 | 0.00057578 | 0.0 | 0.02
|
||||
Modify | 0.046088 | 0.046227 | 0.046315 | 0.0 | 1.95
|
||||
Other | | 0.003775 | | | 0.16
|
||||
|
||||
Nlocal: 1125 ave 1154 max 1092 min
|
||||
Histogram: 1 0 0 0 1 0 0 1 0 1
|
||||
Nghost: 12256.2 ave 12296 max 12213 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Neighs: 650442 ave 678831 max 626373 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 2601769
|
||||
Ave neighs/atom = 578.171
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
shell rm spce.table
|
||||
|
||||
Total wall time: 0:00:02
|
||||
214
examples/python/log.4May17.pair_python_melt.g++.1
Normal file
214
examples/python/log.4May17.pair_python_melt.g++.1
Normal file
@ -0,0 +1,214 @@
|
||||
LAMMPS (4 May 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4000 atoms
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style python 2.5
|
||||
pair_coeff * * py_pot.LJCutMelt lj
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
Neighbor list info ...
|
||||
update every 20 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 12 12 12
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair python, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.184 | 3.184 | 3.184 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 3 -6.7733681 0 -2.2744931 -3.7033504
|
||||
50 1.6758903 -4.7955425 0 -2.2823355 5.670064
|
||||
100 1.6458363 -4.7492704 0 -2.2811332 5.8691042
|
||||
150 1.6324555 -4.7286791 0 -2.280608 5.9589514
|
||||
200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
|
||||
250 1.6275257 -4.7224992 0 -2.281821 5.9567365
|
||||
Loop time of 20.9283 on 1 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 5160.475 tau/day, 11.946 timesteps/s
|
||||
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 20.809 | 20.809 | 20.809 | 0.0 | 99.43
|
||||
Neigh | 0.088638 | 0.088638 | 0.088638 | 0.0 | 0.42
|
||||
Comm | 0.013424 | 0.013424 | 0.013424 | 0.0 | 0.06
|
||||
Output | 0.0002737 | 0.0002737 | 0.0002737 | 0.0 | 0.00
|
||||
Modify | 0.014334 | 0.014334 | 0.014334 | 0.0 | 0.07
|
||||
Other | | 0.003089 | | | 0.01
|
||||
|
||||
Nlocal: 4000 ave 4000 max 4000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5499 ave 5499 max 5499 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 151513 ave 151513 max 151513 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 151513
|
||||
Ave neighs/atom = 37.8783
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds not checked
|
||||
|
||||
write_data melt.data
|
||||
write_restart melt.restart
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
read_restart melt.restart
|
||||
orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
4000 atoms
|
||||
|
||||
pair_style python 2.5
|
||||
pair_coeff * * py_pot.LJCutMelt lj
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 12 12 12
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair python, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.36 | 3.36 | 3.36 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
250 1.6275257 -4.7224992 0 -2.281821 5.9567365
|
||||
300 1.645592 -4.7496711 0 -2.2819002 5.8734193
|
||||
350 1.6514972 -4.7580756 0 -2.2814491 5.810167
|
||||
400 1.6540555 -4.7622999 0 -2.281837 5.8200413
|
||||
450 1.6264734 -4.7200865 0 -2.2809863 5.9546991
|
||||
500 1.6366891 -4.7350979 0 -2.2806781 5.9369284
|
||||
Loop time of 21.1422 on 1 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 5108.279 tau/day, 11.825 timesteps/s
|
||||
98.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 20.925 | 20.925 | 20.925 | 0.0 | 98.97
|
||||
Neigh | 0.18452 | 0.18452 | 0.18452 | 0.0 | 0.87
|
||||
Comm | 0.014836 | 0.014836 | 0.014836 | 0.0 | 0.07
|
||||
Output | 0.00027108 | 0.00027108 | 0.00027108 | 0.0 | 0.00
|
||||
Modify | 0.01366 | 0.01366 | 0.01366 | 0.0 | 0.06
|
||||
Other | | 0.004355 | | | 0.02
|
||||
|
||||
Nlocal: 4000 ave 4000 max 4000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5472 ave 5472 max 5472 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 151513 ave 151513 max 151513 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 151513
|
||||
Ave neighs/atom = 37.8783
|
||||
Neighbor list builds = 25
|
||||
Dangerous builds = 25
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data melt.data
|
||||
orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
4000 atoms
|
||||
reading velocities ...
|
||||
4000 velocities
|
||||
|
||||
pair_style python 2.5
|
||||
pair_coeff * * py_pot.LJCutMelt lj
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
Neighbor list info ...
|
||||
update every 20 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 12 12 12
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair python, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.86 | 2.86 | 2.86 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.6275257 -4.7224992 0 -2.281821 5.9567365
|
||||
50 1.6454666 -4.7497515 0 -2.2821686 5.8729175
|
||||
100 1.6512008 -4.7582693 0 -2.2820874 5.8090548
|
||||
150 1.6537193 -4.7627023 0 -2.2827434 5.8177704
|
||||
200 1.6258731 -4.7205017 0 -2.2823017 5.952511
|
||||
250 1.6370862 -4.7373176 0 -2.2823022 5.925807
|
||||
Loop time of 21.1026 on 1 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 5117.845 tau/day, 11.847 timesteps/s
|
||||
98.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 20.984 | 20.984 | 20.984 | 0.0 | 99.44
|
||||
Neigh | 0.088639 | 0.088639 | 0.088639 | 0.0 | 0.42
|
||||
Comm | 0.012881 | 0.012881 | 0.012881 | 0.0 | 0.06
|
||||
Output | 0.00028563 | 0.00028563 | 0.00028563 | 0.0 | 0.00
|
||||
Modify | 0.013523 | 0.013523 | 0.013523 | 0.0 | 0.06
|
||||
Other | | 0.003033 | | | 0.01
|
||||
|
||||
Nlocal: 4000 ave 4000 max 4000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5487 ave 5487 max 5487 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 151490 ave 151490 max 151490 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 151490
|
||||
Ave neighs/atom = 37.8725
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds not checked
|
||||
|
||||
shell rm melt.data melt.restart
|
||||
Total wall time: 0:01:05
|
||||
214
examples/python/log.4May17.pair_python_melt.g++.4
Normal file
214
examples/python/log.4May17.pair_python_melt.g++.4
Normal file
@ -0,0 +1,214 @@
|
||||
LAMMPS (4 May 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4000 atoms
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style python 2.5
|
||||
pair_coeff * * py_pot.LJCutMelt lj
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
Neighbor list info ...
|
||||
update every 20 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 12 12 12
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair python, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.69 | 2.69 | 2.69 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 3 -6.7733681 0 -2.2744931 -3.7033504
|
||||
50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
|
||||
100 1.6503357 -4.756014 0 -2.2811293 5.8050524
|
||||
150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
|
||||
200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
|
||||
250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
|
||||
Loop time of 5.65922 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 19083.895 tau/day, 44.176 timesteps/s
|
||||
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.4529 | 5.5207 | 5.5575 | 1.7 | 97.55
|
||||
Neigh | 0.023164 | 0.023376 | 0.023883 | 0.2 | 0.41
|
||||
Comm | 0.073318 | 0.1099 | 0.17804 | 12.2 | 1.94
|
||||
Output | 0.00023365 | 0.00026143 | 0.00030684 | 0.0 | 0.00
|
||||
Modify | 0.0036483 | 0.0037143 | 0.003896 | 0.2 | 0.07
|
||||
Other | | 0.001274 | | | 0.02
|
||||
|
||||
Nlocal: 1000 ave 1010 max 982 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 2703.75 ave 2713 max 2689 min
|
||||
Histogram: 1 0 0 0 0 0 0 2 0 1
|
||||
Neighs: 37915.5 ave 39239 max 36193 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
|
||||
Total # of neighbors = 151662
|
||||
Ave neighs/atom = 37.9155
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds not checked
|
||||
|
||||
write_data melt.data
|
||||
write_restart melt.restart
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
read_restart melt.restart
|
||||
orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
4000 atoms
|
||||
|
||||
pair_style python 2.5
|
||||
pair_coeff * * py_pot.LJCutMelt lj
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 12 12 12
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair python, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.815 | 2.816 | 2.816 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
250 1.6323462 -4.7292062 0 -2.2812991 5.9762168
|
||||
300 1.6451788 -4.7488091 0 -2.2816578 5.8375485
|
||||
350 1.6171909 -4.7064928 0 -2.2813129 6.0094235
|
||||
400 1.6388136 -4.7387093 0 -2.2811035 5.9331084
|
||||
450 1.6431295 -4.7452215 0 -2.2811435 5.8929898
|
||||
500 1.643316 -4.7454222 0 -2.2810644 5.8454817
|
||||
Loop time of 5.70169 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 18941.760 tau/day, 43.847 timesteps/s
|
||||
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.3919 | 5.4905 | 5.6136 | 3.7 | 96.30
|
||||
Neigh | 0.046791 | 0.047817 | 0.048795 | 0.3 | 0.84
|
||||
Comm | 0.034221 | 0.1575 | 0.25635 | 22.1 | 2.76
|
||||
Output | 0.00020409 | 0.00023448 | 0.00026131 | 0.0 | 0.00
|
||||
Modify | 0.0035028 | 0.0035674 | 0.0036926 | 0.1 | 0.06
|
||||
Other | | 0.002079 | | | 0.04
|
||||
|
||||
Nlocal: 1000 ave 1012 max 983 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Nghost: 2699 ave 2706 max 2693 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
Neighs: 37930.8 ave 39292 max 36264 min
|
||||
Histogram: 1 0 0 0 1 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 151723
|
||||
Ave neighs/atom = 37.9308
|
||||
Neighbor list builds = 25
|
||||
Dangerous builds = 25
|
||||
|
||||
clear
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
read_data melt.data
|
||||
orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
4000 atoms
|
||||
reading velocities ...
|
||||
4000 velocities
|
||||
|
||||
pair_style python 2.5
|
||||
pair_coeff * * py_pot.LJCutMelt lj
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
Neighbor list info ...
|
||||
update every 20 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 12 12 12
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair python, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.315 | 2.316 | 2.316 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.6323462 -4.7292062 0 -2.2812991 5.9762168
|
||||
50 1.6450626 -4.7488948 0 -2.2819177 5.8370409
|
||||
100 1.6169004 -4.7066969 0 -2.2819526 6.0082546
|
||||
150 1.6384234 -4.7389689 0 -2.2819482 5.9315273
|
||||
200 1.6428814 -4.7460743 0 -2.2823683 5.8888228
|
||||
250 1.6432631 -4.7466603 0 -2.2823818 5.8398819
|
||||
Loop time of 5.69568 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 18961.751 tau/day, 43.893 timesteps/s
|
||||
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.4041 | 5.5245 | 5.6139 | 3.2 | 96.99
|
||||
Neigh | 0.022658 | 0.022986 | 0.023398 | 0.2 | 0.40
|
||||
Comm | 0.053521 | 0.14309 | 0.26385 | 20.2 | 2.51
|
||||
Output | 0.00027037 | 0.00029504 | 0.00033665 | 0.0 | 0.01
|
||||
Modify | 0.0035288 | 0.0035585 | 0.0035827 | 0.0 | 0.06
|
||||
Other | | 0.001275 | | | 0.02
|
||||
|
||||
Nlocal: 1000 ave 1013 max 989 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Nghost: 2695.5 ave 2706 max 2682 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 37927.2 ave 39002 max 36400 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 151709
|
||||
Ave neighs/atom = 37.9273
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds not checked
|
||||
|
||||
shell rm melt.data melt.restart
|
||||
Total wall time: 0:00:17
|
||||
122
examples/python/log.4May17.pair_python_spce.g++.1
Normal file
122
examples/python/log.4May17.pair_python_spce.g++.1
Normal file
@ -0,0 +1,122 @@
|
||||
LAMMPS (4 May 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
read_data data.spce
|
||||
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
4500 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
3000 bonds
|
||||
reading angles ...
|
||||
1500 angles
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
pair_style hybrid/overlay coul/long 12.0 python 12.0
|
||||
kspace_style pppm 1.0e-6
|
||||
|
||||
pair_coeff * * coul/long
|
||||
pair_coeff * * python py_pot.LJCutSPCE OW NULL
|
||||
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
bond_coeff 1 1000.00 1.000
|
||||
angle_coeff 1 100.0 109.47
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 1.0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
fix 1 all shake 0.0001 20 0 b 1 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
1500 = # of frozen angles
|
||||
fix 2 all nvt temp 300.0 300.0 100.0
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.279652
|
||||
grid = 40 40 40
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000394674
|
||||
estimated relative force accuracy = 1.18855e-06
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 103823 64000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair python, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 41.05 | 41.05 | 41.05 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -16692.369 0 -16692.369 -1289.222
|
||||
10 120.56861 -17769.719 0 -16691.902 -4082.7098
|
||||
20 136.08014 -17884.591 0 -16668.109 -5140.7824
|
||||
30 136.97316 -17874.351 0 -16649.887 -5351.3571
|
||||
40 153.37285 -18001.493 0 -16630.424 -5227.0601
|
||||
50 167.70414 -18105.435 0 -16606.252 -4473.2089
|
||||
60 163.08253 -18037.29 0 -16579.422 -3295.8963
|
||||
70 169.60395 -18067.078 0 -16550.912 -2615.7026
|
||||
80 182.94811 -18155.978 0 -16520.523 -2393.3156
|
||||
90 191.29902 -18197.887 0 -16487.779 -2242.7104
|
||||
100 194.70949 -18195.021 0 -16454.425 -1955.2916
|
||||
Loop time of 23.5385 on 1 procs for 100 steps with 4500 atoms
|
||||
|
||||
Performance: 0.367 ns/day, 65.385 hours/ns, 4.248 timesteps/s
|
||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 21.642 | 21.642 | 21.642 | 0.0 | 91.94
|
||||
Bond | 0.00021696 | 0.00021696 | 0.00021696 | 0.0 | 0.00
|
||||
Kspace | 1.5436 | 1.5436 | 1.5436 | 0.0 | 6.56
|
||||
Neigh | 0.25623 | 0.25623 | 0.25623 | 0.0 | 1.09
|
||||
Comm | 0.024325 | 0.024325 | 0.024325 | 0.0 | 0.10
|
||||
Output | 0.00064301 | 0.00064301 | 0.00064301 | 0.0 | 0.00
|
||||
Modify | 0.065919 | 0.065919 | 0.065919 | 0.0 | 0.28
|
||||
Other | | 0.005401 | | | 0.02
|
||||
|
||||
Nlocal: 4500 ave 4500 max 4500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 21216 ave 21216 max 21216 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2.60176e+06 ave 2.60176e+06 max 2.60176e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2601762
|
||||
Ave neighs/atom = 578.169
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:24
|
||||
122
examples/python/log.4May17.pair_python_spce.g++.4
Normal file
122
examples/python/log.4May17.pair_python_spce.g++.4
Normal file
@ -0,0 +1,122 @@
|
||||
LAMMPS (4 May 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
read_data data.spce
|
||||
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
4500 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
3000 bonds
|
||||
reading angles ...
|
||||
1500 angles
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
pair_style hybrid/overlay coul/long 12.0 python 12.0
|
||||
kspace_style pppm 1.0e-6
|
||||
|
||||
pair_coeff * * coul/long
|
||||
pair_coeff * * python py_pot.LJCutSPCE OW NULL
|
||||
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
bond_coeff 1 1000.00 1.000
|
||||
angle_coeff 1 100.0 109.47
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 1.0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
fix 1 all shake 0.0001 20 0 b 1 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
1500 = # of frozen angles
|
||||
fix 2 all nvt temp 300.0 300.0 100.0
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.279652
|
||||
grid = 40 40 40
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000394674
|
||||
estimated relative force accuracy = 1.18855e-06
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 34263 16000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair python, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 14.59 | 14.59 | 14.59 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -16692.369 0 -16692.369 -1289.222
|
||||
10 120.56861 -17769.719 0 -16691.902 -4082.7098
|
||||
20 136.08014 -17884.591 0 -16668.109 -5140.7824
|
||||
30 136.97316 -17874.351 0 -16649.887 -5351.3571
|
||||
40 153.37285 -18001.493 0 -16630.424 -5227.0601
|
||||
50 167.70414 -18105.435 0 -16606.252 -4473.2089
|
||||
60 163.08253 -18037.29 0 -16579.422 -3295.8963
|
||||
70 169.60395 -18067.078 0 -16550.912 -2615.7026
|
||||
80 182.94811 -18155.978 0 -16520.523 -2393.3156
|
||||
90 191.29902 -18197.887 0 -16487.779 -2242.7104
|
||||
100 194.70949 -18195.021 0 -16454.425 -1955.2916
|
||||
Loop time of 6.4942 on 4 procs for 100 steps with 4500 atoms
|
||||
|
||||
Performance: 1.330 ns/day, 18.039 hours/ns, 15.398 timesteps/s
|
||||
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.4084 | 5.572 | 5.8013 | 7.2 | 85.80
|
||||
Bond | 0.00012994 | 0.0001421 | 0.00016356 | 0.0 | 0.00
|
||||
Kspace | 0.52942 | 0.75773 | 0.92078 | 19.5 | 11.67
|
||||
Neigh | 0.071055 | 0.07116 | 0.071278 | 0.0 | 1.10
|
||||
Comm | 0.040311 | 0.041255 | 0.041817 | 0.3 | 0.64
|
||||
Output | 0.00040603 | 0.00048071 | 0.00058675 | 0.0 | 0.01
|
||||
Modify | 0.047507 | 0.047629 | 0.047772 | 0.1 | 0.73
|
||||
Other | | 0.003771 | | | 0.06
|
||||
|
||||
Nlocal: 1125 ave 1154 max 1092 min
|
||||
Histogram: 1 0 0 0 1 0 0 1 0 1
|
||||
Nghost: 12256.2 ave 12296 max 12213 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Neighs: 650440 ave 678828 max 626375 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 2601762
|
||||
Ave neighs/atom = 578.169
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:06
|
||||
99
examples/python/log.4May17.pair_python_table.g++.1
Normal file
99
examples/python/log.4May17.pair_python_table.g++.1
Normal file
@ -0,0 +1,99 @@
|
||||
LAMMPS (4 May 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4000 atoms
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style python 2.5
|
||||
pair_coeff * * py_pot.LJCutMelt lj
|
||||
|
||||
# generate tabulated potential from python variant
|
||||
pair_write 1 1 2000 rsq 0.01 2.5 lj_1_1.table LJ
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 12 12 12
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair python, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
|
||||
pair_style table linear 2000
|
||||
pair_coeff 1 1 lj_1_1.table LJ
|
||||
WARNING: 2 of 2000 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (../pair_table.cpp:476)
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
Neighbor list info ...
|
||||
update every 20 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 12 12 12
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.184 | 3.184 | 3.184 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 3 -6.7733629 0 -2.2744879 -3.7032813
|
||||
50 1.6758731 -4.7953067 0 -2.2821255 5.6706553
|
||||
100 1.6458118 -4.7490281 0 -2.2809276 5.8697466
|
||||
150 1.632425 -4.7284533 0 -2.2804279 5.9595684
|
||||
200 1.6631578 -4.7749889 0 -2.2808759 5.7365839
|
||||
250 1.6277062 -4.7224727 0 -2.2815238 5.9572913
|
||||
Loop time of 0.996739 on 1 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 108353.298 tau/day, 250.818 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.87985 | 0.87985 | 0.87985 | 0.0 | 88.27
|
||||
Neigh | 0.08799 | 0.08799 | 0.08799 | 0.0 | 8.83
|
||||
Comm | 0.012301 | 0.012301 | 0.012301 | 0.0 | 1.23
|
||||
Output | 0.00013161 | 0.00013161 | 0.00013161 | 0.0 | 0.01
|
||||
Modify | 0.013656 | 0.013656 | 0.013656 | 0.0 | 1.37
|
||||
Other | | 0.002808 | | | 0.28
|
||||
|
||||
Nlocal: 4000 ave 4000 max 4000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5500 ave 5500 max 5500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 151496 ave 151496 max 151496 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 151496
|
||||
Ave neighs/atom = 37.874
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds not checked
|
||||
|
||||
shell rm lj_1_1.table
|
||||
|
||||
Total wall time: 0:00:01
|
||||
99
examples/python/log.4May17.pair_python_table.g++.4
Normal file
99
examples/python/log.4May17.pair_python_table.g++.4
Normal file
@ -0,0 +1,99 @@
|
||||
LAMMPS (4 May 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4000 atoms
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style python 2.5
|
||||
pair_coeff * * py_pot.LJCutMelt lj
|
||||
|
||||
# generate tabulated potential from python variant
|
||||
pair_write 1 1 2000 rsq 0.01 2.5 lj_1_1.table LJ
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 12 12 12
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair python, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
|
||||
pair_style table linear 2000
|
||||
pair_coeff 1 1 lj_1_1.table LJ
|
||||
WARNING: 2 of 2000 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (../pair_table.cpp:476)
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
Neighbor list info ...
|
||||
update every 20 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 12 12 12
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.69 | 2.69 | 2.69 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 3 -6.7733629 0 -2.2744879 -3.7032813
|
||||
50 1.675395 -4.7945736 0 -2.2821094 5.6620623
|
||||
100 1.6503067 -4.7558145 0 -2.2809733 5.8055967
|
||||
150 1.6595852 -4.7697199 0 -2.2809644 5.7837898
|
||||
200 1.6371471 -4.7363942 0 -2.2812874 5.924977
|
||||
250 1.6315623 -4.7278268 0 -2.2810951 5.9807196
|
||||
Loop time of 0.291846 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
Performance: 370058.286 tau/day, 856.616 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.22586 | 0.23364 | 0.24085 | 1.3 | 80.06
|
||||
Neigh | 0.022808 | 0.023235 | 0.023602 | 0.2 | 7.96
|
||||
Comm | 0.022573 | 0.030065 | 0.038092 | 3.9 | 10.30
|
||||
Output | 0.00013423 | 0.00014067 | 0.00015759 | 0.0 | 0.05
|
||||
Modify | 0.0035079 | 0.0035501 | 0.0036008 | 0.1 | 1.22
|
||||
Other | | 0.001211 | | | 0.42
|
||||
|
||||
Nlocal: 1000 ave 1010 max 981 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 2703 ave 2715 max 2688 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
Neighs: 37915.2 ave 39191 max 36151 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
|
||||
Total # of neighbors = 151661
|
||||
Ave neighs/atom = 37.9153
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds not checked
|
||||
|
||||
shell rm lj_1_1.table
|
||||
|
||||
Total wall time: 0:00:00
|
||||
65
examples/python/py_pot.py
Normal file
65
examples/python/py_pot.py
Normal file
@ -0,0 +1,65 @@
|
||||
from __future__ import print_function
|
||||
|
||||
class LAMMPSPairPotential(object):
|
||||
def __init__(self):
|
||||
self.pmap=dict()
|
||||
self.units='lj'
|
||||
def map_coeff(self,name,ltype):
|
||||
self.pmap[ltype]=name
|
||||
def check_units(self,units):
|
||||
if (units != self.units):
|
||||
raise Exception("Conflicting units: %s vs. %s" % (self.units,units))
|
||||
|
||||
class LJCutMelt(LAMMPSPairPotential):
|
||||
def __init__(self):
|
||||
super(LJCutMelt,self).__init__()
|
||||
# set coeffs: 48*eps*sig**12, 24*eps*sig**6,
|
||||
# 4*eps*sig**12, 4*eps*sig**6
|
||||
self.units = 'lj'
|
||||
self.coeff = {'lj' : {'lj' : (48.0,24.0,4.0,4.0)}}
|
||||
|
||||
def compute_force(self,rsq,itype,jtype):
|
||||
coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]]
|
||||
r2inv = 1.0/rsq
|
||||
r6inv = r2inv*r2inv*r2inv
|
||||
lj1 = coeff[0]
|
||||
lj2 = coeff[1]
|
||||
return (r6inv * (lj1*r6inv - lj2))*r2inv
|
||||
|
||||
def compute_energy(self,rsq,itype,jtype):
|
||||
coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]]
|
||||
r2inv = 1.0/rsq
|
||||
r6inv = r2inv*r2inv*r2inv
|
||||
lj3 = coeff[2]
|
||||
lj4 = coeff[3]
|
||||
return (r6inv * (lj3*r6inv - lj4))
|
||||
|
||||
|
||||
class LJCutSPCE(LAMMPSPairPotential):
|
||||
def __init__(self):
|
||||
super(LJCutSPCE,self).__init__()
|
||||
self.units='real'
|
||||
# SPCE oxygen LJ parameters in real units
|
||||
eps=0.15535
|
||||
sig=3.166
|
||||
self.coeff = {'OW' : {'OW' : (48.0*eps*sig**12,24.0*eps*sig**6,
|
||||
4.0*eps*sig**12, 4.0*eps*sig**6),
|
||||
'HW' : (0.0,0.0, 0.0,0.0)},
|
||||
'HW' : {'OW' : (0.0,0.0, 0.0,0.0),
|
||||
'HW' : (0.0,0.0, 0.0,0.0)}}
|
||||
|
||||
def compute_force(self,rsq,itype,jtype):
|
||||
coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]]
|
||||
r2inv = 1.0/rsq
|
||||
r6inv = r2inv*r2inv*r2inv
|
||||
lj1 = coeff[0]
|
||||
lj2 = coeff[1]
|
||||
return (r6inv * (lj1*r6inv - lj2))*r2inv
|
||||
|
||||
def compute_energy(self,rsq,itype,jtype):
|
||||
coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]]
|
||||
r2inv = 1.0/rsq
|
||||
r6inv = r2inv*r2inv*r2inv
|
||||
lj3 = coeff[2]
|
||||
lj4 = coeff[3]
|
||||
return (r6inv * (lj3*r6inv - lj4))
|
||||
3
src/.gitignore
vendored
3
src/.gitignore
vendored
@ -852,8 +852,11 @@
|
||||
/prd.h
|
||||
/python_impl.cpp
|
||||
/python_impl.h
|
||||
/python_compat.h
|
||||
/fix_python.cpp
|
||||
/fix_python.h
|
||||
/pair_python.cpp
|
||||
/pair_python.h
|
||||
/reader_molfile.cpp
|
||||
/reader_molfile.h
|
||||
/reaxc_allocate.cpp
|
||||
|
||||
@ -11,6 +11,11 @@
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Richard Berger (Temple U)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <Python.h>
|
||||
#include <stdio.h>
|
||||
#include <string.h>
|
||||
#include "fix_python.h"
|
||||
@ -20,17 +25,11 @@
|
||||
#include "respa.h"
|
||||
#include "error.h"
|
||||
#include "python.h"
|
||||
#include "python_compat.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
|
||||
// Wrap API changes between Python 2 and 3 using macros
|
||||
#if PY_MAJOR_VERSION == 2
|
||||
#define PY_VOID_POINTER(X) PyCObject_FromVoidPtr((void *) X, NULL)
|
||||
#elif PY_MAJOR_VERSION == 3
|
||||
#define PY_VOID_POINTER(X) PyCapsule_New((void *) X, NULL, NULL)
|
||||
#endif
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixPython::FixPython(LAMMPS *lmp, int narg, char **arg) :
|
||||
@ -87,7 +86,7 @@ void FixPython::end_of_step()
|
||||
PyObject * ptr = PY_VOID_POINTER(lmp);
|
||||
PyObject * arglist = Py_BuildValue("(O)", ptr);
|
||||
|
||||
PyObject * result = PyEval_CallObject(pFunc, arglist);
|
||||
PyObject * result = PyEval_CallObject((PyObject*)pFunc, arglist);
|
||||
Py_DECREF(arglist);
|
||||
|
||||
PyGILState_Release(gstate);
|
||||
@ -104,7 +103,7 @@ void FixPython::post_force(int vflag)
|
||||
PyObject * ptr = PY_VOID_POINTER(lmp);
|
||||
PyObject * arglist = Py_BuildValue("(Oi)", ptr, vflag);
|
||||
|
||||
PyObject * result = PyEval_CallObject(pFunc, arglist);
|
||||
PyObject * result = PyEval_CallObject((PyObject*)pFunc, arglist);
|
||||
Py_DECREF(arglist);
|
||||
|
||||
PyGILState_Release(gstate);
|
||||
|
||||
@ -21,7 +21,6 @@ FixStyle(python,FixPython)
|
||||
#define LMP_FIX_PYTHON_H
|
||||
|
||||
#include "fix.h"
|
||||
#include <Python.h>
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
@ -34,7 +33,7 @@ class FixPython : public Fix {
|
||||
virtual void post_force(int);
|
||||
|
||||
private:
|
||||
PyObject * pFunc;
|
||||
void * pFunc;
|
||||
int selected_callback;
|
||||
};
|
||||
|
||||
|
||||
483
src/PYTHON/pair_python.cpp
Normal file
483
src/PYTHON/pair_python.cpp
Normal file
@ -0,0 +1,483 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing authors: Axel Kohlmeyer and Richard Berger (Temple U)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <Python.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include "pair_python.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "update.h"
|
||||
#include "neigh_list.h"
|
||||
#include "python.h"
|
||||
#include "error.h"
|
||||
#include "python_compat.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairPython::PairPython(LAMMPS *lmp) : Pair(lmp) {
|
||||
respa_enable = 0;
|
||||
single_enable = 1;
|
||||
writedata = 0;
|
||||
restartinfo = 0;
|
||||
one_coeff = 1;
|
||||
reinitflag = 0;
|
||||
|
||||
py_potential = NULL;
|
||||
skip_types = NULL;
|
||||
|
||||
python->init();
|
||||
|
||||
// add current directory to PYTHONPATH
|
||||
PyObject * py_path = PySys_GetObject((char *)"path");
|
||||
PyList_Append(py_path, PY_STRING_FROM_STRING("."));
|
||||
|
||||
// if LAMMPS_POTENTIALS environment variable is set, add it to PYTHONPATH as well
|
||||
const char * potentials_path = getenv("LAMMPS_POTENTIALS");
|
||||
if (potentials_path != NULL) {
|
||||
PyList_Append(py_path, PY_STRING_FROM_STRING(potentials_path));
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairPython::~PairPython()
|
||||
{
|
||||
if (py_potential) Py_DECREF((PyObject*) py_potential);
|
||||
delete[] skip_types;
|
||||
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairPython::compute(int eflag, int vflag)
|
||||
{
|
||||
int i,j,ii,jj,inum,jnum,itype,jtype;
|
||||
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
|
||||
double rsq,factor_lj;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
double *special_lj = force->special_lj;
|
||||
int newton_pair = force->newton_pair;
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// prepare access to compute_force and compute_energy functions
|
||||
|
||||
PyGILState_STATE gstate = PyGILState_Ensure();
|
||||
PyObject *py_pair_instance = (PyObject *) py_potential;
|
||||
PyObject *py_compute_force = PyObject_GetAttrString(py_pair_instance,"compute_force");
|
||||
if (!py_compute_force) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Could not find 'compute_force' method'");
|
||||
}
|
||||
if (!PyCallable_Check(py_compute_force)) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Python 'compute_force' is not callable");
|
||||
}
|
||||
|
||||
PyObject *py_compute_energy = PyObject_GetAttrString(py_pair_instance,"compute_energy");
|
||||
if (!py_compute_energy) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Could not find 'compute_energy' method'");
|
||||
}
|
||||
if (!PyCallable_Check(py_compute_energy)) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Python 'compute_energy' is not callable");
|
||||
}
|
||||
|
||||
PyObject *py_compute_args = PyTuple_New(3);
|
||||
if (!py_compute_args) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Could not create tuple for 'compute' function arguments");
|
||||
}
|
||||
|
||||
PyObject *py_rsq, *py_itype, *py_jtype, *py_value;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
py_itype = PY_INT_FROM_LONG(itype);
|
||||
PyTuple_SetItem(py_compute_args,1,py_itype);
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
jtype = type[j];
|
||||
|
||||
// with hybrid/overlay we might get called for skipped types
|
||||
if (skip_types[itype] || skip_types[jtype]) continue;
|
||||
|
||||
py_jtype = PY_INT_FROM_LONG(jtype);
|
||||
PyTuple_SetItem(py_compute_args,2,py_jtype);
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
py_rsq = PyFloat_FromDouble(rsq);
|
||||
PyTuple_SetItem(py_compute_args,0,py_rsq);
|
||||
py_value = PyObject_CallObject(py_compute_force,py_compute_args);
|
||||
if (!py_value) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Calling 'compute_force' function failed");
|
||||
}
|
||||
fpair = factor_lj*PyFloat_AsDouble(py_value);
|
||||
|
||||
f[i][0] += delx*fpair;
|
||||
f[i][1] += dely*fpair;
|
||||
f[i][2] += delz*fpair;
|
||||
if (newton_pair || j < nlocal) {
|
||||
f[j][0] -= delx*fpair;
|
||||
f[j][1] -= dely*fpair;
|
||||
f[j][2] -= delz*fpair;
|
||||
}
|
||||
|
||||
if (eflag) {
|
||||
py_value = PyObject_CallObject(py_compute_energy,py_compute_args);
|
||||
evdwl = factor_lj*PyFloat_AsDouble(py_value);
|
||||
} else evdwl = 0.0;
|
||||
|
||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,
|
||||
evdwl,0.0,fpair,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
Py_DECREF(py_compute_args);
|
||||
PyGILState_Release(gstate);
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairPython::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
||||
memory->create(setflag,n+1,n+1,"pair:setflag");
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
setflag[i][j] = 0;
|
||||
|
||||
memory->create(cutsq,n+1,n+1,"pair:cutsq");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairPython::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 1)
|
||||
error->all(FLERR,"Illegal pair_style command");
|
||||
|
||||
cut_global = force->numeric(FLERR,arg[0]);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for all type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairPython::coeff(int narg, char **arg)
|
||||
{
|
||||
const int ntypes = atom->ntypes;
|
||||
|
||||
if (narg != 3+ntypes)
|
||||
error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
|
||||
if (!allocated) allocate();
|
||||
|
||||
// make sure I,J args are * *
|
||||
|
||||
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
|
||||
error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
|
||||
// check if python potential file exists and source it
|
||||
char * full_cls_name = arg[2];
|
||||
char * lastpos = strrchr(full_cls_name, '.');
|
||||
|
||||
if (lastpos == NULL) {
|
||||
error->all(FLERR,"Python pair style requires fully qualified class name");
|
||||
}
|
||||
|
||||
size_t module_name_length = strlen(full_cls_name) - strlen(lastpos);
|
||||
size_t cls_name_length = strlen(lastpos)-1;
|
||||
|
||||
char * module_name = new char[module_name_length+1];
|
||||
char * cls_name = new char[cls_name_length+1];
|
||||
strncpy(module_name, full_cls_name, module_name_length);
|
||||
module_name[module_name_length] = 0;
|
||||
|
||||
strcpy(cls_name, lastpos+1);
|
||||
|
||||
PyGILState_STATE gstate = PyGILState_Ensure();
|
||||
|
||||
PyObject * pModule = PyImport_ImportModule(module_name);
|
||||
if (!pModule) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Loading python pair style module failure");
|
||||
}
|
||||
|
||||
// create LAMMPS atom type to potential file type mapping in python class
|
||||
// by calling 'lammps_pair_style.map_coeff(name,type)'
|
||||
|
||||
PyObject *py_pair_type = PyObject_GetAttrString(pModule, cls_name);
|
||||
if (!py_pair_type) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Could not find pair style class in module'");
|
||||
}
|
||||
|
||||
delete [] module_name;
|
||||
delete [] cls_name;
|
||||
|
||||
PyObject * py_pair_instance = PyObject_CallObject(py_pair_type, NULL);
|
||||
if (!py_pair_instance) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Could not instantiate instance of pair style class'");
|
||||
}
|
||||
|
||||
py_potential = (void *) py_pair_instance;
|
||||
|
||||
PyObject *py_check_units = PyObject_GetAttrString(py_pair_instance,"check_units");
|
||||
if (!py_check_units) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Could not find 'check_units' method'");
|
||||
}
|
||||
if (!PyCallable_Check(py_check_units)) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Python 'check_units' is not callable");
|
||||
}
|
||||
PyObject *py_units_args = PyTuple_New(1);
|
||||
if (!py_units_args) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Could not create tuple for 'check_units' function arguments");
|
||||
}
|
||||
|
||||
PyObject *py_name = PY_STRING_FROM_STRING(update->unit_style);
|
||||
PyTuple_SetItem(py_units_args,0,py_name);
|
||||
PyObject *py_value = PyObject_CallObject(py_check_units,py_units_args);
|
||||
if (!py_value) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Calling 'check_units' function failed");
|
||||
}
|
||||
Py_DECREF(py_units_args);
|
||||
|
||||
|
||||
PyObject *py_map_coeff = PyObject_GetAttrString(py_pair_instance,"map_coeff");
|
||||
if (!py_map_coeff) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Could not find 'map_coeff' method'");
|
||||
}
|
||||
if (!PyCallable_Check(py_map_coeff)) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Python 'map_coeff' is not callable");
|
||||
}
|
||||
|
||||
PyObject *py_map_args = PyTuple_New(2);
|
||||
if (!py_map_args) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Could not create tuple for 'map_coeff' function arguments");
|
||||
}
|
||||
|
||||
delete[] skip_types;
|
||||
skip_types = new int[ntypes+1];
|
||||
skip_types[0] = 1;
|
||||
for (int i = 1; i <= ntypes ; i++) {
|
||||
if (strcmp(arg[2+i],"NULL") == 0) {
|
||||
skip_types[i] = 1;
|
||||
continue;
|
||||
} else skip_types[i] = 0;
|
||||
PyObject *py_type = PY_INT_FROM_LONG(i);
|
||||
py_name = PY_STRING_FROM_STRING(arg[2+i]);
|
||||
PyTuple_SetItem(py_map_args,0,py_name);
|
||||
PyTuple_SetItem(py_map_args,1,py_type);
|
||||
py_value = PyObject_CallObject(py_map_coeff,py_map_args);
|
||||
if (!py_value) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Calling 'map_coeff' function failed");
|
||||
}
|
||||
|
||||
for (int j = i; j <= ntypes ; j++) {
|
||||
setflag[i][j] = 1;
|
||||
cutsq[i][j] = cut_global*cut_global;
|
||||
}
|
||||
}
|
||||
Py_DECREF(py_map_args);
|
||||
PyGILState_Release(gstate);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairPython::init_one(int, int)
|
||||
{
|
||||
return cut_global;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairPython::single(int i, int j, int itype, int jtype, double rsq,
|
||||
double factor_coul, double factor_lj,
|
||||
double &fforce)
|
||||
{
|
||||
// with hybrid/overlay we might get called for skipped types
|
||||
if (skip_types[itype] || skip_types[jtype]) {
|
||||
fforce = 0.0;
|
||||
return 0.0;
|
||||
}
|
||||
|
||||
// prepare access to compute_force and compute_energy functions
|
||||
|
||||
PyGILState_STATE gstate = PyGILState_Ensure();
|
||||
PyObject *py_pair_instance = (PyObject *) py_potential;
|
||||
PyObject *py_compute_force
|
||||
= PyObject_GetAttrString(py_pair_instance,"compute_force");
|
||||
if (!py_compute_force) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Could not find 'compute_force' method'");
|
||||
}
|
||||
if (!PyCallable_Check(py_compute_force)) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Python 'compute_force' is not callable");
|
||||
}
|
||||
|
||||
PyObject *py_compute_energy
|
||||
= PyObject_GetAttrString(py_pair_instance,"compute_energy");
|
||||
if (!py_compute_energy) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Could not find 'compute_energy' method'");
|
||||
}
|
||||
if (!PyCallable_Check(py_compute_energy)) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Python 'compute_energy' is not callable");
|
||||
}
|
||||
|
||||
PyObject *py_rsq, *py_itype, *py_jtype, *py_value;
|
||||
PyObject *py_compute_args = PyTuple_New(3);
|
||||
if (!py_compute_args) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Could not create tuple for 'compute' function arguments");
|
||||
}
|
||||
|
||||
py_itype = PY_INT_FROM_LONG(itype);
|
||||
PyTuple_SetItem(py_compute_args,1,py_itype);
|
||||
py_jtype = PY_INT_FROM_LONG(jtype);
|
||||
PyTuple_SetItem(py_compute_args,2,py_jtype);
|
||||
py_rsq = PyFloat_FromDouble(rsq);
|
||||
PyTuple_SetItem(py_compute_args,0,py_rsq);
|
||||
|
||||
py_value = PyObject_CallObject(py_compute_force,py_compute_args);
|
||||
if (!py_value) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Calling 'compute_force' function failed");
|
||||
}
|
||||
fforce = factor_lj*PyFloat_AsDouble(py_value);
|
||||
|
||||
py_value = PyObject_CallObject(py_compute_energy,py_compute_args);
|
||||
if (!py_value) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Calling 'compute_energy' function failed");
|
||||
}
|
||||
double evdwl = factor_lj*PyFloat_AsDouble(py_value);
|
||||
|
||||
Py_DECREF(py_compute_args);
|
||||
PyGILState_Release(gstate);
|
||||
|
||||
return evdwl;
|
||||
}
|
||||
77
src/PYTHON/pair_python.h
Normal file
77
src/PYTHON/pair_python.h
Normal file
@ -0,0 +1,77 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
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.
|
||||
|
||||
Pair zero is a dummy pair interaction useful for requiring a
|
||||
force cutoff distance in the absense of pair-interactions or
|
||||
with hybrid/overlay if a larger force cutoff distance is required.
|
||||
|
||||
This can be used in conjunction with bond/create to create bonds
|
||||
that are longer than the cutoff of a given force field, or to
|
||||
calculate radial distribution functions for models without
|
||||
pair interactions.
|
||||
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(python,PairPython)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_PYTHON_H
|
||||
#define LMP_PAIR_PYTHON_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairPython : public Pair {
|
||||
public:
|
||||
PairPython(class LAMMPS *);
|
||||
virtual ~PairPython();
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
double init_one(int, int);
|
||||
double single(int, int, int, int, double, double, double, double &);
|
||||
|
||||
protected:
|
||||
double cut_global;
|
||||
void * py_potential;
|
||||
int * skip_types;
|
||||
|
||||
virtual void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Incorrect args for pair coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
E: Pair cutoff < Respa interior cutoff
|
||||
|
||||
One or more pairwise cutoffs are too short to use with the specified
|
||||
rRESPA cutoffs.
|
||||
|
||||
*/
|
||||
33
src/PYTHON/python_compat.h
Normal file
33
src/PYTHON/python_compat.h
Normal file
@ -0,0 +1,33 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef LMP_PYTHON_COMPAT_H
|
||||
#define LMP_PYTHON_COMPAT_H
|
||||
|
||||
// Wrap API changes between Python 2 and 3 using macros
|
||||
#if PY_MAJOR_VERSION == 2
|
||||
#define PY_INT_FROM_LONG(X) PyInt_FromLong(X)
|
||||
#define PY_INT_AS_LONG(X) PyInt_AsLong(X)
|
||||
#define PY_STRING_FROM_STRING(X) PyString_FromString(X)
|
||||
#define PY_VOID_POINTER(X) PyCObject_FromVoidPtr((void *) X, NULL)
|
||||
#define PY_STRING_AS_STRING(X) PyString_AsString(X)
|
||||
|
||||
#elif PY_MAJOR_VERSION == 3
|
||||
#define PY_INT_FROM_LONG(X) PyLong_FromLong(X)
|
||||
#define PY_INT_AS_LONG(X) PyLong_AsLong(X)
|
||||
#define PY_STRING_FROM_STRING(X) PyUnicode_FromString(X)
|
||||
#define PY_VOID_POINTER(X) PyCapsule_New((void *) X, NULL, NULL)
|
||||
#define PY_STRING_AS_STRING(X) PyUnicode_AsUTF8(X)
|
||||
#endif
|
||||
|
||||
#endif
|
||||
@ -11,6 +11,10 @@
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Richard Berger and Axel Kohlmeyer (Temple U)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <Python.h>
|
||||
#include "python.h"
|
||||
#include "force.h"
|
||||
@ -18,6 +22,7 @@
|
||||
#include "variable.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "python_compat.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
@ -25,21 +30,6 @@ enum{NONE,INT,DOUBLE,STRING,PTR};
|
||||
|
||||
#define VALUELENGTH 64 // also in variable.cpp
|
||||
|
||||
// Wrap API changes between Python 2 and 3 using macros
|
||||
#if PY_MAJOR_VERSION == 2
|
||||
#define PY_INT_FROM_LONG(X) PyInt_FromLong(X)
|
||||
#define PY_INT_AS_LONG(X) PyInt_AsLong(X)
|
||||
#define PY_STRING_FROM_STRING(X) PyString_FromString(X)
|
||||
#define PY_VOID_POINTER(X) PyCObject_FromVoidPtr((void *) X, NULL)
|
||||
#define PY_STRING_AS_STRING(X) PyString_AsString(X)
|
||||
|
||||
#elif PY_MAJOR_VERSION == 3
|
||||
#define PY_INT_FROM_LONG(X) PyLong_FromLong(X)
|
||||
#define PY_INT_AS_LONG(X) PyLong_AsLong(X)
|
||||
#define PY_STRING_FROM_STRING(X) PyUnicode_FromString(X)
|
||||
#define PY_VOID_POINTER(X) PyCapsule_New((void *) X, NULL, NULL)
|
||||
#define PY_STRING_AS_STRING(X) PyUnicode_AsUTF8(X)
|
||||
#endif
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -51,7 +41,7 @@ PythonImpl::PythonImpl(LAMMPS *lmp) : Pointers(lmp)
|
||||
pfuncs = NULL;
|
||||
|
||||
// one-time initialization of Python interpreter
|
||||
// pymain stores pointer to main module
|
||||
// pyMain stores pointer to main module
|
||||
external_interpreter = Py_IsInitialized();
|
||||
|
||||
Py_Initialize();
|
||||
@ -63,7 +53,6 @@ PythonImpl::PythonImpl(LAMMPS *lmp) : Pointers(lmp)
|
||||
if (!pModule) error->all(FLERR,"Could not initialize embedded Python");
|
||||
|
||||
pyMain = (void *) pModule;
|
||||
|
||||
PyGILState_Release(gstate);
|
||||
}
|
||||
|
||||
|
||||
Reference in New Issue
Block a user