ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge pull request #778 from athomps/fix_gcmc_segfault_fix

Browse Source 
Fixed recent segfault in fix gcmc and added mcmoves keyword
This commit is contained in:
Steve Plimpton
2018-02-02 14:40:14 -07:00
committed by GitHub
parent 2913d3da60 9bb7f1ddf6
commit 553b3ff69a
3 changed files with 229 additions and 160 deletions
Download Patch File Download Diff File Expand all files Collapse all files

134
doc/src/fix_gcmc.txt
View File

@ -26,16 +26,20 @@ zero or more keyword/value pairs may be appended to args :l
keyword = {mol}, {region}, {maxangle}, {pressure}, {fugacity_coeff}, {full_energy}, {charge}, {group}, {grouptype}, {intra_energy}, {tfac_insert}, or {overlap_cutoff}
{mol} value = template-ID
template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
{mcmoves} values = Patomtrans Pmoltrans Pmolrotate
Patomtrans = proportion of atom translation MC moves
Pmoltrans = proportion of molecule translation MC moves
Pmolrotate = proportion of molecule rotation MC moves
{rigid} value = fix-ID
fix-ID = ID of "fix rigid/small"_fix_rigid.html command
{shake} value = fix-ID
fix-ID = ID of "fix shake"_fix_shake.html command
{region} value = region-ID
region-ID = ID of region where MC moves are allowed
region-ID = ID of region where GCMC exchanges and MC moves are allowed
{maxangle} value = maximum molecular rotation angle (degrees)
{pressure} value = pressure of the gas reservoir (pressure units)
{fugacity_coeff} value = fugacity coefficient of the gas reservoir (unitless)
{full_energy} = compute the entire system energy when performing MC moves
{full_energy} = compute the entire system energy when performing GCMC exchanges and MC moves
{charge} value = charge of inserted atoms (charge units)
{group} value = group-ID
group-ID = group-ID for inserted atoms (string)
@ -56,34 +60,42 @@ fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk :pre
[Description:]
This fix performs grand canonical Monte Carlo (GCMC) exchanges of
atoms or molecules of the given type with an imaginary ideal gas
atoms or molecules with an imaginary ideal gas
reservoir at the specified T and chemical potential (mu) as discussed
in "(Frenkel)"_#Frenkel. If used with the "fix nvt"_fix_nh.html
in "(Frenkel)"_#Frenkel. It also
attempts Monte Carlo (MC) moves (translations and molecule
rotations) within the simulation cell or
region. If used with the "fix nvt"_fix_nh.html
command, simulations in the grand canonical ensemble (muVT, constant
chemical potential, constant volume, and constant temperature) can be
performed. Specific uses include computing isotherms in microporous
materials, or computing vapor-liquid coexistence curves.
Every N timesteps the fix attempts a number of GCMC exchanges
(insertions or deletions) of gas atoms or molecules of the given type
between the simulation cell and the imaginary reservoir. It also
attempts a number of Monte Carlo moves (translations and molecule
rotations) of gas of the given type within the simulation cell or
region. The average number of attempted GCMC exchanges is X. The
average number of attempted MC moves is M. M should typically be
Every N timesteps the fix attempts both GCMC exchanges
(insertions or deletions) and MC moves of gas atoms or molecules.
On those timesteps, the average number of attempted GCMC exchanges is X,
while the average number of attempted MC moves is M.
For GCMC exchanges of either molecular or atomic gasses,
these exchanges can be either deletions or insertions,
with equal probability.
The possible choices for MC moves are translation of an atom,
translation of a molecule, and rotation of a molecule.
The relative amounts of each are determined by the optional
{mcmoves} keyword (see below).
The default behavior is as follows.
If the {mol} keyword is used, only molecule translations
and molecule rotations are performed with equal probability.
Conversely, if the {mol} keyword is not used, only atom
translations are performed.
M should typically be
chosen to be approximately equal to the expected number of gas atoms
or molecules of the given type within the simulation cell or region,
which will result in roughly one MC translation per atom or molecule
which will result in roughly one MC move per atom or molecule
per MC cycle.
For MC moves of molecular gasses, rotations and translations are each
attempted with 50% probability. For MC moves of atomic gasses,
translations are attempted 100% of the time. For MC exchanges of
either molecular or atomic gasses, deletions and insertions are each
attempted with 50% probability.
All inserted particles are always assigned to two groups: the default
group "all" and the group specified in the fix gcmc command (which can
All inserted particles are always added to two groups: the default
group "all" and the fix group specified in the fix command (which can
also be "all"). In addition, particles are also added to any groups
specified by the {group} and {grouptype} keywords. If inserted
particles are individual atoms, they are assigned the atom type given
@ -92,9 +104,9 @@ effect and must be set to zero. Instead, the type of each atom in the
inserted molecule is specified in the file read by the
"molecule"_molecule.html command.
This fix cannot be used to perform MC insertions of gas atoms or
molecules other than the exchanged type, but MC deletions,
translations, and rotations can be performed on any atom/molecule in
This fix cannot be used to perform GCMC insertions of gas atoms or
molecules other than the exchanged type, but GCMC deletions,
and MC translations, and rotations can be performed on any atom/molecule in
the fix group. All atoms in the simulation cell can be moved using
regular time integration translations, e.g. via "fix nvt"_fix_nh.html,
resulting in a hybrid GCMC+MD simulation. A smaller-than-usual
@ -150,8 +162,8 @@ about this point.
Individual atoms are inserted, unless the {mol} keyword is used. It
specifies a {template-ID} previously defined using the
"molecule"_molecule.html command, which reads a file that defines the
molecule. The coordinates, atom types, charges, etc, as well as any
bond/angle/etc and special neighbor information for the molecule can
molecule. The coordinates, atom types, charges, etc., as well as any
bonding and special neighbor information for the molecule can
be specified in the molecule file. See the "molecule"_molecule.html
command for details. The only settings required to be in this file
are the coordinates and types of atoms in the molecule.
@ -162,7 +174,7 @@ error when it tries to find bonded neighbors. LAMMPS will warn you if
any of the atoms eligible for deletion have a non-zero molecule ID,
but does not check for this at the time of deletion.
If you wish to insert molecules via the {mol} keyword, that will be
If you wish to insert molecules using the {mol} keyword that will be
treated as rigid bodies, use the {rigid} keyword, specifying as its
value the ID of a separate "fix rigid/small"_fix_rigid.html command
which also appears in your input script.
@ -178,6 +190,15 @@ their bonds or angles constrained via SHAKE, use the {shake} keyword,
specifying as its value the ID of a separate "fix
shake"_fix_shake.html command which also appears in your input script.
Optionally, users may specify the relative amounts of different MC
moves using the {mcmoves} keyword. The values {Patomtrans},
{Pmoltrans}, {Pmolrotate} specify the average proportion of
atom translations, molecule translations, and molecule rotations,
respectively. The values must be non-negative integers or real
numbers, with at least one non-zero value. For example, (10,30,0)
would result in 25% of the MC moves being atomic translations, 75%
molecular translations, and no molecular rotations.
Optionally, users may specify the maximum rotation angle for molecular
rotations using the {maxangle} keyword and specifying the angle in
degrees. Rotations are performed by generating a random point on the
@ -188,19 +209,19 @@ to the unit vector defined by the point on the unit sphere. The same
procedure is used for randomly rotating molecules when they are
inserted, except that the maximum angle is 360 degrees.
Note that fix GCMC does not use configurational bias MC or any other
Note that fix gcmc does not use configurational bias MC or any other
kind of sampling of intramolecular degrees of freedom. Inserted
molecules can have different orientations, but they will all have the
same intramolecular configuration, which was specified in the molecule
command input.
For atomic gasses, inserted atoms have the specified atom type, but
deleted atoms are any atoms that have been inserted or that belong to
the user-specified fix group. For molecular gasses, exchanged
deleted atoms are any atoms that have been inserted or that already
belong to the fix group. For molecular gasses, exchanged
molecules use the same atom types as in the template molecule supplied
by the user. In both cases, exchanged atoms/molecules are assigned to
two groups: the default group "all" and the group specified in the fix
gcmc command (which can also be "all").
two groups: the default group "all" and the fix group
(which can also be "all").
The chemical potential is a user-specified input parameter defined
as:
@ -241,13 +262,16 @@ which case the user-specified chemical potential is ignored. The user
may also specify the fugacity coefficient phi using the
{fugacity_coeff} keyword, which defaults to unity.
The {full_energy} option means that fix GCMC will compute the total
potential energy of the entire simulated system. The total system
energy before and after the proposed GCMC move is then used in the
The {full_energy} option means that the fix calculates the total
potential energy of the entire simulated system, instead of just
the energy of the part that is changed. The total system
energy before and after the proposed GCMC exchange or MC move
is then used in the
Metropolis criterion to determine whether or not to accept the
proposed GCMC move. By default, this option is off, in which case only
partial energies are computed to determine the difference in energy
that would be caused by the proposed GCMC move.
proposed change. By default, this option is off,
in which case only
partial energies are computed to determine the energy difference
due to the proposed change.
The {full_energy} option is needed for systems with complicated
potential energy calculations, including the following:
@ -263,10 +287,11 @@ In these cases, LAMMPS will automatically apply the {full_energy}
keyword and issue a warning message.
When the {mol} keyword is used, the {full_energy} option also includes
the intramolecular energy of inserted and deleted molecules. If this
the intramolecular energy of inserted and deleted molecules, whereas
this energy is not included when {full_energy} is not used. If this
is not desired, the {intra_energy} keyword can be used to define an
amount of energy that is subtracted from the final energy when a
molecule is inserted, and added to the initial energy when a molecule
molecule is inserted, and subtracted from the initial energy when a molecule
is deleted. For molecules that have a non-zero intramolecular energy,
this will ensure roughly the same behavior whether or not the
{full_energy} option is used.
@ -291,7 +316,8 @@ include: "efield"_fix_efield.html, "gravity"_fix_gravity.html,
"temp/berendsen"_fix_temp_berendsen.html,
"temp/rescale"_fix_temp_rescale.html, and "wall fixes"_fix_wall.html.
For that energy to be included in the total potential energy of the
system (the quantity used when performing GCMC moves), you MUST enable
system (the quantity used when performing GCMC exchange and MC moves),
you MUST enable
the "fix_modify"_fix_modify.html {energy} option for that fix. The
doc pages for individual "fix"_fix.html commands specify if this
should be done.
@ -305,9 +331,14 @@ about simulating non-neutral systems with kspace on.
Use of this fix typically will cause the number of atoms to fluctuate,
therefore, you will want to use the
"compute_modify"_compute_modify.html command to insure that the
"compute_modify dynamic/dof"_compute_modify.html command to insure that the
current number of atoms is used as a normalizing factor each time
temperature is computed. Here is the necessary command:
temperature is computed. A simple example of this is:
compute_modify thermo_temp dynamic yes :pre
A more complicated example is listed earlier on this page
in the context of NVT dynamics.
NOTE: If the density of the cell is initially very small or zero, and
increases to a much larger density after a period of equilibration,
@ -327,17 +358,9 @@ assigning an infinite positive energy to all new configurations that
place any pair of atoms closer than the specified overlap cutoff
distance.
compute_modify thermo_temp dynamic yes :pre
If LJ units are used, note that a value of 0.18292026 is used by this
fix as the reduced value for Planck's constant. This value was
derived from LJ parameters for argon, where h* = h/sqrt(sigma^2 *
epsilon * mass), sigma = 3.429 angstroms, epsilon/k = 121.85 K, and
mass = 39.948 amu.
The {group} keyword assigns all inserted atoms to the
The {group} keyword adds all inserted atoms to the
"group"_group.html of the group-ID value. The {grouptype} keyword
assigns all inserted atoms of the specified type to the
adds all inserted atoms of the specified type to the
"group"_group.html of the group-ID value.
[Restart, fix_modify, output, run start/stop, minimize info:]
@ -384,7 +407,8 @@ Can be run in parallel, but aspects of the GCMC part will not scale
well in parallel. Only usable for 3D simulations.
When using fix gcmc in combination with fix shake or fix rigid,
only gcmc exchange moves are supported.
only GCMC exchange moves are supported, so the argument
{M} must be zero.
Note that very lengthy simulations involving insertions/deletions of
billions of gas molecules may run out of atom or molecule IDs and
@ -409,7 +433,9 @@ the user for each subsequent fix gcmc command.
[Default:]
The option defaults are mol = no, maxangle = 10, overlap_cutoff = 0.0,
fugacity_coeff = 1, and full_energy = no,
fugacity_coeff = 1.0, intra_energy = 0.0, tfac_insert = 1.0.
(Patomtrans, Pmoltrans, Pmolrotate) = (1, 0, 0) for mol = no and
(0, 1, 1) for mol = yes. full_energy = no,
except for the situations where full_energy is required, as
listed above.