Merge branch 'develop' into fix-pair-dump-skip
This commit is contained in:
Axel Kohlmeyer
@ -1373,7 +1373,7 @@ Bibliography
|
||||
Zhu, Tajkhorshid, and Schulten, Biophys. J. 83, 154 (2002).
|
||||
|
||||
**(Ziegler)**
|
||||
J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter," Volume 1, Pergamon, 1985.
|
||||
J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter", Volume 1, Pergamon, 1985.
|
||||
|
||||
**(Zimmerman2004)**
|
||||
Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004),12:S319.
|
||||
|
||||
@ -276,7 +276,7 @@ the barostat as outlined in:
|
||||
|
||||
N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
|
||||
accurately describe the structure, pressure, and compressibility of
|
||||
molecular liquids," J. Chem. Phys. 143, 243148 (2015).
|
||||
molecular liquids", J. Chem. Phys. 143, 243148 (2015).
|
||||
|
||||
**Authors:** Nicholas J. H. Dunn and Michael R. DeLyser (The
|
||||
Pennsylvania State University)
|
||||
|
||||
@ -495,7 +495,7 @@ run:
|
||||
write_dump group-ID dumpstyle dumpfile arg1 arg2 ...
|
||||
|
||||
Note that the specified restartfile and dumpfile names may contain
|
||||
wild-card characters ("\*","%") as explained on the
|
||||
wild-card characters ("\*" or "%") as explained on the
|
||||
:doc:`read_restart <read_restart>` and :doc:`write_dump <write_dump>` doc
|
||||
pages. The use of "%" means that a parallel restart file and/or
|
||||
parallel dump file can be read and/or written. Note that a filename
|
||||
|
||||
@ -536,6 +536,6 @@ supported.
|
||||
References
|
||||
""""""""""
|
||||
|
||||
* Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann.
|
||||
* Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS", in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann.
|
||||
* Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. `Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. <http://dl.acm.org/citation.cfm?id=3014915>`_ 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95).
|
||||
* Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101.
|
||||
|
||||
@ -78,7 +78,7 @@ These values can be accessed by any command that uses global array
|
||||
values from a compute as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The array values are "intensive." The array values will be in
|
||||
The array values are "intensive". The array values will be in
|
||||
mass-velocity-distance :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -182,7 +182,7 @@ by any command that uses global values from a compute as input. See
|
||||
the :doc:`Howto output <Howto_output>` doc page for an overview of
|
||||
LAMMPS output options.
|
||||
|
||||
The array values calculated by this compute are all "extensive."
|
||||
The array values calculated by this compute are all "extensive".
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
@ -49,7 +49,7 @@ accessed by indices 1--3 by any command that uses global vector values
|
||||
from a compute as input. See the :doc:`Howto output <Howto_output>` doc
|
||||
page for an overview of LAMMPS output options.
|
||||
|
||||
The vector values are "intensive." The vector values will be in
|
||||
The vector values are "intensive". The vector values will be in
|
||||
distance :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -77,7 +77,7 @@ values can be accessed by any command that uses global array values
|
||||
from a compute as input. See the :doc:`Howto output <Howto_output>` doc
|
||||
page for an overview of LAMMPS output options.
|
||||
|
||||
The array values are "intensive." The array values will be in
|
||||
The array values are "intensive". The array values will be in
|
||||
distance :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -54,7 +54,7 @@ the computed dipole moment and a global vector of length 3 with the
|
||||
dipole vector. See the :doc:`Howto output <Howto_output>` page for
|
||||
an overview of LAMMPS output options.
|
||||
|
||||
The computed values are "intensive." The array values will be in
|
||||
The computed values are "intensive". The array values will be in
|
||||
dipole units (i.e., charge :doc:`units <units>` times distance
|
||||
:doc:`units <units>`).
|
||||
|
||||
|
||||
@ -86,7 +86,7 @@ chunk. These values can be accessed by any command that uses global
|
||||
array values from a compute as input. See the :doc:`Howto output
|
||||
<Howto_output>` page for an overview of LAMMPS output options.
|
||||
|
||||
The array values are "intensive." The array values will be in
|
||||
The array values are "intensive". The array values will be in
|
||||
dipole units (i.e., charge :doc:`units <units>` times distance
|
||||
:doc:`units <units>`).
|
||||
|
||||
|
||||
@ -48,7 +48,7 @@ used by any command that uses a global scalar value from a compute as
|
||||
input. See the :doc:`Howto output <Howto_output>` page for an
|
||||
overview of LAMMPS output options.
|
||||
|
||||
The scalar value calculated by this compute is "extensive." The
|
||||
The scalar value calculated by this compute is "extensive". The
|
||||
scalar value will be in energy :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -48,7 +48,7 @@ of all the rigid bodies). This value can be used by any command that
|
||||
uses a global scalar value from a compute as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The scalar value calculated by this compute is "extensive." The
|
||||
The scalar value calculated by this compute is "extensive". The
|
||||
scalar value will be in energy :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -44,7 +44,7 @@ used by any command that uses a global scalar value from a compute as
|
||||
input. See the :doc:`Howto output <Howto_output>` page for an
|
||||
overview of LAMMPS output options.
|
||||
|
||||
The scalar value calculated by this compute is "extensive." The
|
||||
The scalar value calculated by this compute is "extensive". The
|
||||
scalar value will be in energy :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -40,7 +40,7 @@ further than the threshold distance.
|
||||
If the system is undergoing significant center-of-mass motion,
|
||||
due to thermal motion, an external force, or an initial net momentum,
|
||||
then this compute will not be able to distinguish that motion from
|
||||
local atom displacements and may generate "false positives."
|
||||
local atom displacements and may generate "false positives".
|
||||
|
||||
Output info
|
||||
"""""""""""
|
||||
@ -50,7 +50,7 @@ used by any command that uses a global scalar value from a compute as
|
||||
input. See the :doc:`Howto output <Howto_output>` page for an
|
||||
overview of LAMMPS output options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
scalar value will be a 0 or 1 as explained above.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -299,7 +299,7 @@ These output results can be used by any command that uses a global
|
||||
scalar or vector from a compute as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options. For example, the computed values can be averaged using :doc:`fix ave/time <fix_ave_time>`.
|
||||
|
||||
The values calculated by this compute are "extensive."
|
||||
The values calculated by this compute are "extensive".
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
@ -140,7 +140,7 @@ vector values from a compute as input. See the
|
||||
options.
|
||||
|
||||
Both the scalar and vector values calculated by this compute are
|
||||
"extensive." The scalar value will be in energy :doc:`units <units>`.
|
||||
"extensive". The scalar value will be in energy :doc:`units <units>`.
|
||||
The vector values will be in force :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -69,7 +69,7 @@ vector values from a compute as input. See the :doc:`Howto output <Howto_output
|
||||
options.
|
||||
|
||||
The scalar and vector values calculated by this compute are
|
||||
"intensive." The scalar and vector values will be in distance and
|
||||
"intensive". The scalar and vector values will be in distance and
|
||||
distance\ :math:`^2` :doc:`units <units>`, respectively.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -78,7 +78,7 @@ vector values from a compute as input. See the
|
||||
options.
|
||||
|
||||
The vector values calculated by this compute are
|
||||
"intensive." The first five vector values will be in
|
||||
"intensive". The first five vector values will be in
|
||||
distance\ :math:`2` :doc:`units <units>` while the sixth one is dimensionless.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -80,7 +80,7 @@ See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
|
||||
output options.
|
||||
|
||||
The array calculated by this compute is
|
||||
"intensive." The first five columns will be in
|
||||
"intensive". The first five columns will be in
|
||||
distance\ :math:`^2` :doc:`units <units>` while the sixth one is dimensionless.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -142,14 +142,14 @@ command that uses global vector values from a compute as input.
|
||||
See the :doc:`Howto output <Howto_output>` documentation for an overview of
|
||||
LAMMPS output options.
|
||||
|
||||
The vector values calculated by this compute are "extensive," meaning
|
||||
The vector values calculated by this compute are "extensive", meaning
|
||||
they scale with the number of atoms in the simulation. They can be
|
||||
divided by the appropriate volume to get a flux, which would then be
|
||||
an "intensive" value, meaning independent of the number of atoms in
|
||||
the simulation. Note that if the compute is "all," then the
|
||||
appropriate volume to divide by is the simulation box volume.
|
||||
However, if a sub-group is used, it should be the volume containing
|
||||
those atoms.
|
||||
divided by the appropriate volume to get a flux, which would then be an
|
||||
"intensive" value, meaning independent of the number of atoms in the
|
||||
simulation. Note that if the compute group is "all", then the
|
||||
appropriate volume to divide by is the simulation box volume. However,
|
||||
if a group with a subset of atoms is used, it should be the volume
|
||||
containing those atoms.
|
||||
|
||||
The vector values will be in energy\*velocity :doc:`units <units>`. Once
|
||||
divided by a volume the units will be that of flux, namely
|
||||
|
||||
@ -172,7 +172,7 @@ requested as arguments to the command (the potential energy, pressure and/or hea
|
||||
capacity). The elements of the vector can be accessed by indices 1--n by any
|
||||
command that uses global vector values as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output options.
|
||||
|
||||
The vector values calculated by this compute are "extensive." The
|
||||
The vector values calculated by this compute are "extensive". The
|
||||
scalar value will be in energy :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -84,7 +84,7 @@ by any command that uses global array values from a compute as input. See the
|
||||
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The array values are "intensive." The array values will be in
|
||||
The array values are "intensive". The array values will be in
|
||||
mass\*distance\ :math:`^2` :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -52,7 +52,7 @@ can be used by any command that uses a global scalar value from a
|
||||
compute as input. See the :doc:`Howto output <Howto_output>` doc page
|
||||
for an overview of LAMMPS output options.
|
||||
|
||||
The scalar value calculated by this compute is "extensive." The
|
||||
The scalar value calculated by this compute is "extensive". The
|
||||
scalar value will be in energy :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -48,7 +48,7 @@ global scalar value from a compute as input. See the
|
||||
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The scalar value calculated by this compute is "extensive." The
|
||||
The scalar value calculated by this compute is "extensive". The
|
||||
scalar value will be in energy :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -37,7 +37,7 @@ length 3. This value can be used by any command that uses a global
|
||||
vector value from a compute as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The vector value calculated by this compute is "extensive." The vector
|
||||
The vector value calculated by this compute is "extensive". The vector
|
||||
value will be in mass\*velocity :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -105,7 +105,7 @@ accessed by indices 1--4 by any command that uses global vector values
|
||||
from a compute as input. See the :doc:`Howto output <Howto_output>` doc
|
||||
page for an overview of LAMMPS output options.
|
||||
|
||||
The vector values are "intensive." The vector values will be in
|
||||
The vector values are "intensive". The vector values will be in
|
||||
distance\ :math:`^2` :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -121,7 +121,7 @@ These values can be accessed by any command that uses global array values from
|
||||
a compute as input. See the :doc:`Howto output <Howto_output>` page for an
|
||||
overview of LAMMPS output options.
|
||||
|
||||
The array values are "intensive." The array values will be in
|
||||
The array values are "intensive". The array values will be in
|
||||
distance\ :math:`^2` :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -67,7 +67,7 @@ accessed by indices 1--3 by any command that uses global vector values
|
||||
from a compute as input. See the :doc:`Howto output <Howto_output>` doc
|
||||
page for an overview of LAMMPS output options.
|
||||
|
||||
The vector values are "intensive." The first vector value will be in
|
||||
The vector values are "intensive". The first vector value will be in
|
||||
distance\ :math:`^2` :doc:`units <units>`, the second is in
|
||||
distance\ :math:`^4` units, and the third is dimensionless.
|
||||
|
||||
|
||||
@ -84,7 +84,7 @@ These values can be accessed by any command that uses global array
|
||||
values from a compute as input. See the :doc:`Howto output <Howto_output>`
|
||||
page for an overview of LAMMPS output options.
|
||||
|
||||
The array values are "intensive." The array values will be in
|
||||
The array values are "intensive". The array values will be in
|
||||
velocity/distance :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -27,7 +27,7 @@ Description
|
||||
"""""""""""
|
||||
|
||||
Define a computation that calculates the potential energy of the
|
||||
entire system of atoms. The specified group must be "all." See the
|
||||
entire system of atoms. The specified group must be "all". See the
|
||||
:doc:`compute pe/atom <compute_pe_atom>` command if you want per-atom
|
||||
energies. These per-atom values could be summed for a group of atoms
|
||||
via the :doc:`compute reduce <compute_reduce>` command.
|
||||
@ -73,7 +73,7 @@ value can be used by any command that uses a global scalar value from
|
||||
a compute as input. See the :doc:`Howto output <Howto_output>` doc page
|
||||
for an overview of LAMMPS output options.
|
||||
|
||||
The scalar value calculated by this compute is "extensive." The
|
||||
The scalar value calculated by this compute is "extensive". The
|
||||
scalar value will be in energy :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -73,5 +73,5 @@ none
|
||||
.. _Mitchell:
|
||||
|
||||
**(Mitchell)** Mitchell, "A non-local, ordinary-state-based
|
||||
viscoelasticity model for peridynamics," Sandia National Lab Report,
|
||||
viscoelasticity model for peridynamics", Sandia National Lab Report,
|
||||
8064:1-28 (2011).
|
||||
|
||||
@ -29,7 +29,7 @@ Description
|
||||
"""""""""""
|
||||
|
||||
Define a computation that calculates the pressure of the entire system
|
||||
of atoms. The specified group must be "all." See the
|
||||
of atoms. The specified group must be "all". See the
|
||||
:doc:`compute stress/atom <compute_stress_atom>` command if you want per-atom
|
||||
pressure (stress). These per-atom values could be summed for a group
|
||||
of atoms via the :doc:`compute reduce <compute_reduce>` command.
|
||||
@ -115,7 +115,7 @@ LAMMPS starts up, as if this command were in the input script:
|
||||
compute thermo_press all pressure thermo_temp
|
||||
|
||||
where thermo_temp is the ID of a similarly defined compute of style
|
||||
"temp." See the :doc:`thermo_style <thermo_style>` command for more details.
|
||||
"temp". See the :doc:`thermo_style <thermo_style>` command for more details.
|
||||
|
||||
----------
|
||||
|
||||
@ -137,7 +137,7 @@ The ordering of values in the symmetric pressure tensor is as follows:
|
||||
:math:`p_{xz},` :math:`p_{yz}.`
|
||||
|
||||
The scalar and vector values calculated by this compute are
|
||||
"intensive." The scalar and vector values will be in pressure
|
||||
"intensive". The scalar and vector values will be in pressure
|
||||
:doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -110,7 +110,7 @@ accessed by any command that uses global values from a compute as
|
||||
input. See the :doc:`Howto output <Howto_output>` page for an
|
||||
overview of LAMMPS output options.
|
||||
|
||||
The vector or array values are "intensive." The values will be
|
||||
The vector or array values are "intensive". The values will be
|
||||
unitless or in the units discussed above.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -164,7 +164,7 @@ the type of the bond, from 1 to Nbtypes = # of bond types. The number
|
||||
of bond types is defined in the data file read by the
|
||||
:doc:`read_data <read_data>` command.
|
||||
|
||||
The attributes that start with "a," "d," and "i" refer to similar values
|
||||
The attributes that start with "a", "d", and "i" refer to similar values
|
||||
for :doc:`angles <angle_style>`, :doc:`dihedrals <dihedral_style>`, and
|
||||
:doc:`impropers <improper_style>`.
|
||||
|
||||
|
||||
@ -166,7 +166,7 @@ by any command that uses a global values from a compute as input. See
|
||||
the :doc:`Howto output <Howto_output>` page for an overview of
|
||||
LAMMPS output options.
|
||||
|
||||
The array values calculated by this compute are all "intensive."
|
||||
The array values calculated by this compute are all "intensive".
|
||||
|
||||
The first column of array values will be in distance
|
||||
:doc:`units <units>`. The :math:`g(r)` columns of array values are normalized
|
||||
|
||||
@ -128,7 +128,7 @@ inputs to this fix by using the
|
||||
:doc:`compute property/atom <compute_property_atom>` command and then specifying
|
||||
an input value from that compute.
|
||||
|
||||
If a value begins with "c\_," a compute ID must follow which has been
|
||||
If a value begins with "c\_", a compute ID must follow which has been
|
||||
previously defined in the input script. Computes can generate
|
||||
per-atom or local quantities. See the individual
|
||||
:doc:`compute <compute>` page for details. If no bracketed integer
|
||||
@ -139,7 +139,7 @@ compute styles and :doc:`add them to LAMMPS <Modify>`. See the
|
||||
discussion above for how :math:`I` can be specified with a wildcard asterisk
|
||||
to effectively specify multiple values.
|
||||
|
||||
If a value begins with "f\_," a fix ID must follow which has been
|
||||
If a value begins with "f\_", a fix ID must follow which has been
|
||||
previously defined in the input script. Fixes can generate per-atom
|
||||
or local quantities. See the individual :doc:`fix <fix>` page for
|
||||
details. Note that some fixes only produce their values on certain
|
||||
@ -152,7 +152,7 @@ is used. Users can also write code for their own fix style and
|
||||
:math:`I` can be specified with a wildcard asterisk to effectively specify
|
||||
multiple values.
|
||||
|
||||
If a value begins with "v\_," a variable name must follow which has
|
||||
If a value begins with "v\_", a variable name must follow which has
|
||||
been previously defined in the input script. It must be an
|
||||
:doc:`atom-style variable <variable>`. Atom-style variables can
|
||||
reference thermodynamic keywords and various per-atom attributes, or
|
||||
@ -197,7 +197,7 @@ global vector of values, the length of which is equal to the number of
|
||||
inputs specified.
|
||||
|
||||
As discussed below, for the *sum*, *sumabs*, and *sumsq* modes, the value(s)
|
||||
produced by this compute are all "extensive," meaning their value
|
||||
produced by this compute are all "extensive", meaning their value
|
||||
scales linearly with the number of atoms involved. If normalized
|
||||
values are desired, this compute can be accessed by the
|
||||
:doc:`thermo_style custom <thermo_style>` command with
|
||||
@ -218,9 +218,9 @@ compute as input. See the :doc:`Howto output <Howto_output>` doc page
|
||||
for an overview of LAMMPS output options.
|
||||
|
||||
All the scalar or vector values calculated by this compute are
|
||||
"intensive," except when the *sum*, *sumabs*, or *sumsq* modes are used on
|
||||
"intensive", except when the *sum*, *sumabs*, or *sumsq* modes are used on
|
||||
per-atom or local vectors, in which case the calculated values are
|
||||
"extensive."
|
||||
"extensive".
|
||||
|
||||
The scalar or vector values will be in whatever :doc:`units <units>` the
|
||||
quantities being reduced are in.
|
||||
|
||||
@ -102,7 +102,7 @@ The commands below can be added to the examples/in.micelle script.
|
||||
|
||||
Imagine a collection of polymer chains or small molecules with
|
||||
hydrophobic end groups. All the hydrophobic (HP) atoms are assigned
|
||||
to a group called "phobic."
|
||||
to a group called "phobic".
|
||||
|
||||
These commands will assign a unique cluster ID to all HP atoms within
|
||||
a specified distance of each other. A cluster will contain all HP
|
||||
|
||||
@ -114,7 +114,7 @@ This array can be output with :doc:`fix ave/time <fix_ave_time>`,
|
||||
compute p all stress/cartesian x 0.1
|
||||
fix 2 all ave/time 100 1 100 c_p[*] file dump_p.out mode vector
|
||||
|
||||
The values calculated by this compute are "intensive." The stress
|
||||
The values calculated by this compute are "intensive". The stress
|
||||
values will be in pressure :doc:`units <units>`. The number density
|
||||
values are in inverse volume :doc:`units <units>`.
|
||||
|
||||
|
||||
@ -182,7 +182,7 @@ Output info
|
||||
from individual atoms in both groups).
|
||||
|
||||
Both the scalar and vector values calculated by this compute are
|
||||
"extensive."
|
||||
"extensive".
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
@ -91,7 +91,7 @@ vector values from a compute as input. See the
|
||||
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`. The
|
||||
|
||||
@ -134,8 +134,8 @@ vector values from a compute as input.
|
||||
See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
|
||||
output options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
vector values are "extensive."
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`. The
|
||||
vector values will be in energy :doc:`units <units>`.
|
||||
|
||||
@ -117,8 +117,8 @@ vector values from a compute as input.
|
||||
See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
|
||||
output options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
vector values are "extensive."
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`.
|
||||
The vector values will be in energy :doc:`units <units>`.
|
||||
|
||||
@ -242,8 +242,8 @@ can be accessed by any command that uses global array values from a
|
||||
compute as input. Again, see the :doc:`Howto output <Howto_output>` doc
|
||||
page for an overview of LAMMPS output options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
vector values are "extensive." The array values are "intensive."
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive". The array values are "intensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`. The
|
||||
vector values will be in energy :doc:`units <units>`. The array values
|
||||
|
||||
@ -87,8 +87,8 @@ vector values from a compute as input. See the
|
||||
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
vector values are "extensive."
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`.
|
||||
The vector values will be in energy :doc:`units <units>`.
|
||||
|
||||
@ -101,8 +101,8 @@ vector of length 6 (KE tensor), which can be accessed by indices 1--6.
|
||||
These values can be used by any command that uses global scalar or
|
||||
vector values from a compute as input.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
vector values are "extensive."
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`. The
|
||||
vector values will be in energy :doc:`units <units>`.
|
||||
|
||||
@ -134,7 +134,7 @@ vector values from a compute as input. See the
|
||||
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`.
|
||||
|
||||
@ -53,8 +53,8 @@ vector values from a compute as input. See the
|
||||
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
vector values are "extensive."
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`. The
|
||||
vector values will be in energy :doc:`units <units>`.
|
||||
|
||||
@ -67,8 +67,8 @@ vector values from a compute as input. See the
|
||||
options.
|
||||
|
||||
Both the scalar value and the first two values of the vector
|
||||
calculated by this compute are "intensive." The other four vector values
|
||||
are "extensive."
|
||||
calculated by this compute are "intensive". The other four vector values
|
||||
are "extensive".
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
@ -88,9 +88,9 @@ thermostatting.
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
The scalar value calculated by this compute is "intensive," meaning it
|
||||
The scalar value calculated by this compute is "intensive", meaning it
|
||||
is independent of the number of atoms in the simulation. The vector
|
||||
values are "extensive," meaning they scale with the number of atoms in
|
||||
values are "extensive", meaning they scale with the number of atoms in
|
||||
the simulation.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -94,8 +94,8 @@ vector values from a compute as input.
|
||||
See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
|
||||
output options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
vector values are "extensive."
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`. The
|
||||
vector values will be in energy :doc:`units <units>`.
|
||||
|
||||
@ -183,8 +183,8 @@ vector or array values from a compute as input. See the
|
||||
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
vector values are "extensive." The array values are "intensive."
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive". The array values are "intensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`. The
|
||||
vector values will be in energy :doc:`units <units>`. The first column
|
||||
|
||||
@ -106,8 +106,8 @@ vector values from a compute as input. See the
|
||||
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
vector values are "extensive."
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`. The
|
||||
vector values will be in energy :doc:`units <units>`.
|
||||
|
||||
@ -99,8 +99,8 @@ vector values from a compute as input. See the
|
||||
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
vector values are "extensive."
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`.
|
||||
The vector values will be in energy :doc:`units <units>`.
|
||||
|
||||
@ -46,8 +46,8 @@ vector values from a compute as input. See the
|
||||
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
vector values are "extensive."
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`. The
|
||||
vector values will be in energy :doc:`units <units>`.
|
||||
|
||||
@ -86,8 +86,8 @@ vector values from a compute as input. See the
|
||||
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
vector values are "extensive."
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`. The
|
||||
vector values will be in energy :doc:`units <units>`.
|
||||
|
||||
@ -122,8 +122,8 @@ vector values from a compute as input.
|
||||
See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
|
||||
output options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
vector values are "extensive."
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`. The
|
||||
vector values will be in energy :doc:`units <units>`.
|
||||
|
||||
@ -125,7 +125,7 @@ value can be used by any command that uses a global scalar value from
|
||||
a compute as input. See the :doc:`Howto output <Howto_output>` doc page
|
||||
for an overview of LAMMPS output options.
|
||||
|
||||
The scalar value calculated by this compute is "extensive."
|
||||
The scalar value calculated by this compute is "extensive".
|
||||
|
||||
The scalar value will be in energy :doc:`units <units>`.
|
||||
|
||||
|
||||
@ -83,7 +83,7 @@ array values from a compute as input.
|
||||
See the :doc:`Howto output <Howto_output>` doc page
|
||||
for an overview of LAMMPS output options.
|
||||
|
||||
The array values are "intensive." The array values will be in
|
||||
The array values are "intensive". The array values will be in
|
||||
force-distance :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -66,7 +66,7 @@ accessed by indices 1--4 by any command that uses global vector values
|
||||
from a compute as input. See the :doc:`Howto output <Howto_output>` doc
|
||||
page for an overview of LAMMPS output options.
|
||||
|
||||
The vector values are "intensive." The vector values will be in
|
||||
The vector values are "intensive". The vector values will be in
|
||||
velocity\ :math:`^2` :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -69,7 +69,7 @@ each chunk. These values can be accessed by any command that uses global array
|
||||
values from a compute as input. See the :doc:`Howto output <Howto_output>`
|
||||
page for an overview of LAMMPS output options.
|
||||
|
||||
The array values are "intensive." The array values will be in
|
||||
The array values are "intensive". The array values will be in
|
||||
velocity :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -134,9 +134,9 @@ These values can be used by any command that uses global scalar or
|
||||
vector values from a compute as input.
|
||||
See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
first six elements of vector values are "extensive,"
|
||||
and the seventh element of vector values is "intensive."
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
first six elements of vector values are "extensive",
|
||||
and the seventh element of vector values is "intensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`.
|
||||
The first six elements of vector values will be in energy :doc:`units <units>`.
|
||||
|
||||
@ -198,7 +198,7 @@ Voronoi volume, the second is the neighbor count, as described above
|
||||
(read above for the output data in case the *occupation* keyword is
|
||||
specified). These values can be accessed by any command that uses
|
||||
per-atom values from a compute as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options. If the *peratom* keyword is set to "no," the per-atom array
|
||||
options. If the *peratom* keyword is set to "no", the per-atom array
|
||||
is still created, but it is not accessible.
|
||||
|
||||
If the *edge_histo* keyword is used, then this compute generates a
|
||||
|
||||
@ -219,7 +219,7 @@ The array can be accessed by any command that uses global values from
|
||||
a compute as input. See the :doc:`Howto output <Howto_output>` doc page
|
||||
for an overview of LAMMPS output options.
|
||||
|
||||
All array values calculated by this compute are "intensive."
|
||||
All array values calculated by this compute are "intensive".
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
@ -95,7 +95,7 @@ typically created via the :doc:`create_box <create_box>` command.
|
||||
Before using this command, a lattice must also be defined using the
|
||||
:doc:`lattice <lattice>` command, unless you specify the *single* style
|
||||
with units = box or the *random* style. For the remainder of this doc
|
||||
page, a created atom or molecule is referred to as a "particle."
|
||||
page, a created atom or molecule is referred to as a "particle".
|
||||
|
||||
If created particles are individual atoms, they are assigned the
|
||||
specified atom *type*, though this can be altered via the *basis*
|
||||
@ -352,7 +352,7 @@ As an example, these commands can be used in a 2d simulation, to
|
||||
create a sinusoidal surface. Note that the surface is "rough" due to
|
||||
individual lattice points being "above" or "below" the mathematical
|
||||
expression for the sinusoidal curve. If a finer lattice were used,
|
||||
the sinusoid would appear to be "smoother." Also note the use of the
|
||||
the sinusoid would appear to be "smoother". Also note the use of the
|
||||
"xlat" and "ylat" :doc:`thermo_style <thermo_style>` keywords, which
|
||||
converts lattice spacings to distance.
|
||||
|
||||
|
||||
233
doc/src/dump.rst
233
doc/src/dump.rst
@ -224,30 +224,29 @@ page for details.
|
||||
|
||||
The *atom/gz*, *cfg/gz*, *custom/gz*, *local/gz*, and *xyz/gz* styles
|
||||
are identical in command syntax to the corresponding styles without
|
||||
"gz," however, they generate compressed files using the zlib
|
||||
"gz", however, they generate compressed files using the zlib
|
||||
library. Thus the filename suffix ".gz" is mandatory. This is an
|
||||
alternative approach to writing compressed files via a pipe, as done
|
||||
by the regular dump styles, which may be required on clusters where
|
||||
the interface to the high-speed network disallows using the fork()
|
||||
library call (which is needed for a pipe). For the remainder of this
|
||||
page, you should thus consider the *atom* and *atom/gz* styles
|
||||
(etc.) to be inter-changeable, with the exception of the required
|
||||
filename suffix.
|
||||
alternative approach to writing compressed files via a pipe, as done by
|
||||
the regular dump styles, which may be required on clusters where the
|
||||
interface to the high-speed network disallows using the fork() library
|
||||
call (which is needed for a pipe). For the remainder of this page, you
|
||||
should thus consider the *atom* and *atom/gz* styles (etc.) to be
|
||||
inter-changeable, with the exception of the required filename suffix.
|
||||
|
||||
Similarly, the *atom/zstd*, *cfg/zstd*, *custom/zstd*, *local/zstd*,
|
||||
and *xyz/zstd* styles are identical to the gz styles, but use the Zstd
|
||||
Similarly, the *atom/zstd*, *cfg/zstd*, *custom/zstd*, *local/zstd*, and
|
||||
*xyz/zstd* styles are identical to the gz styles, but use the Zstd
|
||||
compression library instead and require the ".zst" suffix. See the
|
||||
:doc:`dump_modify <dump_modify>` page for details on how to control
|
||||
the compression level in both variants.
|
||||
:doc:`dump_modify <dump_modify>` page for details on how to control the
|
||||
compression level in both variants.
|
||||
|
||||
As explained below, the *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and
|
||||
*xyz/mpiio* styles are identical in command syntax and in the format
|
||||
of the dump files they create, to the corresponding styles without
|
||||
"mpiio," except the single dump file they produce is written in
|
||||
parallel via the MPI-IO library. For the remainder of this page,
|
||||
you should thus consider the *atom* and *atom/mpiio* styles (etc.) to
|
||||
be inter-changeable. The one exception is how the filename is
|
||||
specified for the MPI-IO styles, as explained below.
|
||||
*xyz/mpiio* styles are identical in command syntax and in the format of
|
||||
the dump files they create, to the corresponding styles without "mpiio",
|
||||
except the single dump file they produce is written in parallel via the
|
||||
MPI-IO library. For the remainder of this page, you should thus
|
||||
consider the *atom* and *atom/mpiio* styles (etc.) to be
|
||||
inter-changeable. The one exception is how the filename is specified
|
||||
for the MPI-IO styles, as explained below.
|
||||
|
||||
.. warning::
|
||||
|
||||
@ -434,7 +433,7 @@ Below is an example for a YAML format dump created by the following commands.
|
||||
dump out all yaml 100 dump.yaml id type x y z vx vy vz ix iy iz
|
||||
dump_modify out time yes units yes thermo yes format 1 %5d format "% 10.6e"
|
||||
|
||||
The tags "time," "units," and "thermo" are optional and enabled by the
|
||||
The tags "time", "units", and "thermo" are optional and enabled by the
|
||||
dump_modify command. The list under the "box" tag has three lines for
|
||||
orthogonal boxes and four lines for triclinic boxes, where the first three are
|
||||
the box boundaries and the fourth the three tilt factors (:math:`xy`,
|
||||
@ -553,15 +552,14 @@ package installed, viz.,
|
||||
make yes-mpiio # installs the MPIIO package
|
||||
make mpi # build LAMMPS for your platform
|
||||
|
||||
Second, use a dump filename which contains ".mpiio." Note that it
|
||||
does not have to end in ".mpiio," just contain those characters.
|
||||
Unlike MPI-IO restart files, which must be both written and read using
|
||||
MPI-IO, the dump files produced by these MPI-IO styles are identical
|
||||
in format to the files produced by their non-MPI-IO style
|
||||
counterparts. This means you can write a dump file using MPI-IO and
|
||||
use the :doc:`read_dump <read_dump>` command or perform other
|
||||
post-processing, just as if the dump file was not written using
|
||||
MPI-IO.
|
||||
Second, use a dump filename which contains ".mpiio". Note that it does
|
||||
not have to end in ".mpiio", just contain those characters. Unlike
|
||||
MPI-IO restart files, which must be both written and read using MPI-IO,
|
||||
the dump files produced by these MPI-IO styles are identical in format
|
||||
to the files produced by their non-MPI-IO style counterparts. This
|
||||
means you can write a dump file using MPI-IO and use the :doc:`read_dump
|
||||
<read_dump>` command or perform other post-processing, just as if the
|
||||
dump file was not written using MPI-IO.
|
||||
|
||||
.. warning::
|
||||
|
||||
@ -570,37 +568,40 @@ MPI-IO.
|
||||
|
||||
Note that MPI-IO dump files are one large file which all processors
|
||||
write to. You thus cannot use the "%" wildcard character described
|
||||
above in the filename since that specifies generation of multiple
|
||||
files. You can use the ".bin" or ".lammpsbin" suffix described below in an
|
||||
MPI-IO dump file; again this file will be written in parallel and have the
|
||||
same binary format as if it were written without MPI-IO.
|
||||
above in the filename since that specifies generation of multiple files.
|
||||
You can use the ".bin" or ".lammpsbin" suffix described below in an
|
||||
MPI-IO dump file; again this file will be written in parallel and have
|
||||
the same binary format as if it were written without MPI-IO.
|
||||
|
||||
If the filename ends with ".bin" or ".lammpsbin," the dump file (or files, if
|
||||
"\*" or "%" is also used) is written in binary format. A binary dump file
|
||||
will be about the same size as a text version, but will typically
|
||||
write out much faster. Of course, when post-processing, you will need
|
||||
to convert it back to text format (see the :ref:`binary2txt tool <binary>`) or
|
||||
write your own code to read the binary file. The format of the binary file can
|
||||
be understood by looking at the :file:`tools/binary2txt.cpp` file. This option
|
||||
is only available for the *atom* and *custom* styles.
|
||||
If the filename ends with ".bin" or ".lammpsbin", the dump file (or
|
||||
files, if "\*" or "%" is also used) is written in binary format. A
|
||||
binary dump file will be about the same size as a text version, but will
|
||||
typically write out much faster. Of course, when post-processing, you
|
||||
will need to convert it back to text format (see the :ref:`binary2txt
|
||||
tool <binary>`) or write your own code to read the binary file. The
|
||||
format of the binary file can be understood by looking at the
|
||||
:file:`tools/binary2txt.cpp` file. This option is only available for
|
||||
the *atom* and *custom* styles.
|
||||
|
||||
If the filename ends with ".gz," the dump file (or files, if "\*" or "%"
|
||||
is also used) is written in gzipped format. A gzipped dump file will be about
|
||||
:math:`3\times` smaller than the text version, but will also take longer
|
||||
to write. This option is not available for the *dcd* and *xtc* styles.
|
||||
If the filename ends with ".gz", the dump file (or files, if "\*" or "%"
|
||||
is also used) is written in gzipped format. A gzipped dump file will be
|
||||
about :math:`3\times` smaller than the text version, but will also take
|
||||
longer to write. This option is not available for the *dcd* and *xtc*
|
||||
styles.
|
||||
|
||||
----------
|
||||
|
||||
Note that in the discussion which follows, for styles which can
|
||||
reference values from a compute or fix or custom atom property, like
|
||||
the *custom*\ , *cfg*\ , or *local* styles, the bracketed index :math:`i` can
|
||||
be specified using a wildcard asterisk with the index to effectively
|
||||
specify multiple values. This takes the form "\*" or "\*n" or "m\*"
|
||||
or "m\*n." If :math:`N` is the number of columns in the array, then an
|
||||
asterisk with no numeric values means all column indices from 1 to :math:`N`.
|
||||
A leading asterisk means all indices from 1 to n (inclusive). A
|
||||
trailing asterisk means all indices from m to :math:`N` (inclusive). A middle
|
||||
asterisk means all indices from m to n (inclusive).
|
||||
reference values from a compute or fix or custom atom property, like the
|
||||
*custom*\ , *cfg*\ , or *local* styles, the bracketed index :math:`i`
|
||||
can be specified using a wildcard asterisk with the index to effectively
|
||||
specify multiple values. This takes the form "\*" or "\*n" or "m\*" or
|
||||
"m\*n". If :math:`N` is the number of columns in the array, then an
|
||||
asterisk with no numeric values means all column indices from 1 to
|
||||
:math:`N`. A leading asterisk means all indices from 1 to n
|
||||
(inclusive). A trailing asterisk means all indices from m to :math:`N`
|
||||
(inclusive). A middle asterisk means all indices from m to n
|
||||
(inclusive).
|
||||
|
||||
Using a wildcard is the same as if the individual columns of the array
|
||||
had been listed one by one. For example, these two dump commands are
|
||||
@ -679,37 +680,38 @@ The *id*, *mol*, *proc*, *procp1*, *type*, *element*, *mass*, *vx*,
|
||||
|
||||
*Id* is the atom ID. *Mol* is the molecule ID, included in the data
|
||||
file for molecular systems. *Proc* is the ID of the processor (0 to
|
||||
:math:`N_\text{procs}-1`) that currently owns the atom.
|
||||
*Procp1* is the proc ID+1, which can be convenient in place of a *type*
|
||||
attribute (1 to :math:`N_\text{types}`) for coloring atoms in a visualization
|
||||
program. *Type* is the atom type (1 to :math:`N_\text{types}`). *Element* is
|
||||
typically the chemical name of an element, which you must assign to each type
|
||||
via the :doc:`dump_modify element <dump_modify>` command. More generally, it
|
||||
can be any string you wish to associated with an atom type. *Mass* is the atom
|
||||
mass. The quantities *vx*, *vy*, *vz*, *fx*, *fy*, *fz*, and *q* are components
|
||||
of atom velocity and force and atomic charge.
|
||||
:math:`N_\text{procs}-1`) that currently owns the atom. *Procp1* is the
|
||||
proc ID+1, which can be convenient in place of a *type* attribute (1 to
|
||||
:math:`N_\text{types}`) for coloring atoms in a visualization program.
|
||||
*Type* is the atom type (1 to :math:`N_\text{types}`). *Element* is
|
||||
typically the chemical name of an element, which you must assign to each
|
||||
type via the :doc:`dump_modify element <dump_modify>` command. More
|
||||
generally, it can be any string you wish to associated with an atom
|
||||
type. *Mass* is the atom mass. The quantities *vx*, *vy*, *vz*, *fx*,
|
||||
*fy*, *fz*, and *q* are components of atom velocity and force and atomic
|
||||
charge.
|
||||
|
||||
There are several options for outputting atom coordinates. The *x*,
|
||||
*y*, and *z* attributes write atom coordinates "unscaled," in the
|
||||
*y*, and *z* attributes write atom coordinates "unscaled", in the
|
||||
appropriate distance :doc:`units <units>` (:math:`\mathrm{\mathring A}`,
|
||||
:math:`\sigma`, etc.). Use *xs*, *ys*, and *zs* if you want the coordinates
|
||||
"scaled" to the box size so that each value is 0.0 to 1.0. If the simulation
|
||||
box is triclinic (tilted), then all atom coords will still be between 0.0 and
|
||||
1.0. The actual unscaled :math:`(x,y,z)` coordinate is
|
||||
:math:`x_s a + y_s b + z_s c`, where :math:`(a,b,c)` are the non-orthogonal
|
||||
vectors of the simulation box edges, as discussed on the
|
||||
:doc:`Howto triclinic <Howto_triclinic>` page.
|
||||
:math:`\sigma`, etc.). Use *xs*, *ys*, and *zs* if you want the
|
||||
coordinates "scaled" to the box size so that each value is 0.0 to 1.0.
|
||||
If the simulation box is triclinic (tilted), then all atom coords will
|
||||
still be between 0.0 and 1.0. The actual unscaled :math:`(x,y,z)`
|
||||
coordinate is :math:`x_s a + y_s b + z_s c`, where :math:`(a,b,c)` are
|
||||
the non-orthogonal vectors of the simulation box edges, as discussed on
|
||||
the :doc:`Howto triclinic <Howto_triclinic>` page.
|
||||
|
||||
Use *xu*, *yu*, and *zu* if you want the coordinates "unwrapped" by the
|
||||
image flags for each atom. Unwrapped means that if the atom has
|
||||
passed through a periodic boundary one or more times, the value is
|
||||
printed for what the coordinate would be if it had not been wrapped
|
||||
back into the periodic box. Note that using *xu*, *yu*, and *zu* means
|
||||
that the coordinate values may be far outside the box bounds printed
|
||||
with the snapshot. Using *xsu*, *ysu*, and *zsu* is similar to using
|
||||
*xu*, *yu*, and *zu*, except that the unwrapped coordinates are scaled by
|
||||
the box size. Atoms that have passed through a periodic boundary will
|
||||
have the corresponding coordinate increased or decreased by 1.0.
|
||||
image flags for each atom. Unwrapped means that if the atom has passed
|
||||
through a periodic boundary one or more times, the value is printed for
|
||||
what the coordinate would be if it had not been wrapped back into the
|
||||
periodic box. Note that using *xu*, *yu*, and *zu* means that the
|
||||
coordinate values may be far outside the box bounds printed with the
|
||||
snapshot. Using *xsu*, *ysu*, and *zsu* is similar to using *xu*, *yu*,
|
||||
and *zu*, except that the unwrapped coordinates are scaled by the box
|
||||
size. Atoms that have passed through a periodic boundary will have the
|
||||
corresponding coordinate increased or decreased by 1.0.
|
||||
|
||||
The image flags can be printed directly using the *ix*, *iy*, and *iz*
|
||||
attributes. For periodic dimensions, they specify which image of the
|
||||
@ -721,8 +723,8 @@ periodic boundaries during the simulation.
|
||||
|
||||
The *mux*, *muy*, and *muz* attributes are specific to dipolar systems
|
||||
defined with an atom style of *dipole*\ . They give the orientation of
|
||||
the atom's point dipole moment. The *mu* attribute gives the
|
||||
magnitude of the atom's dipole moment.
|
||||
the atom's point dipole moment. The *mu* attribute gives the magnitude
|
||||
of the atom's dipole moment.
|
||||
|
||||
The *radius* and *diameter* attributes are specific to spherical
|
||||
particles that have a finite size, such as those defined with an atom
|
||||
@ -736,17 +738,17 @@ The *angmomx*, *angmomy*, and *angmomz* attributes are specific to
|
||||
finite-size aspherical particles that have an angular momentum. Only
|
||||
the *ellipsoid* atom style defines this quantity.
|
||||
|
||||
The *tqx*, *tqy*, and *tqz* attributes are for finite-size particles that
|
||||
can sustain a rotational torque due to interactions with other
|
||||
The *tqx*, *tqy*, and *tqz* attributes are for finite-size particles
|
||||
that can sustain a rotational torque due to interactions with other
|
||||
particles.
|
||||
|
||||
The *c_ID* and *c_ID[I]* attributes allow per-atom vectors or arrays
|
||||
calculated by a :doc:`compute <compute>` to be output. The ID in the
|
||||
attribute should be replaced by the actual ID of the compute that has
|
||||
been defined previously in the input script. See the
|
||||
:doc:`compute <compute>` command for details. There are computes for
|
||||
calculating the per-atom energy, stress, centro-symmetry parameter,
|
||||
and coordination number of individual atoms.
|
||||
been defined previously in the input script. See the :doc:`compute
|
||||
<compute>` command for details. There are computes for calculating the
|
||||
per-atom energy, stress, centro-symmetry parameter, and coordination
|
||||
number of individual atoms.
|
||||
|
||||
Note that computes which calculate global or local quantities, as
|
||||
opposed to per-atom quantities, cannot be output in a dump custom
|
||||
@ -754,39 +756,39 @@ command. Instead, global quantities can be output by the
|
||||
:doc:`thermo_style custom <thermo_style>` command, and local quantities
|
||||
can be output by the dump local command.
|
||||
|
||||
If *c_ID* is used as a attribute, then the per-atom vector calculated
|
||||
by the compute is printed. If *c_ID[i]* is used, then :math:`i` must be in
|
||||
the range from 1 to :math:`M`, which will print the :math:`i`\ th column of the
|
||||
per-atom array with :math:`M` columns calculated by the compute. See the
|
||||
discussion above for how :math:`i` can be specified with a wildcard asterisk to
|
||||
effectively specify multiple values.
|
||||
If *c_ID* is used as a attribute, then the per-atom vector calculated by
|
||||
the compute is printed. If *c_ID[i]* is used, then :math:`i` must be in
|
||||
the range from 1 to :math:`M`, which will print the :math:`i`\ th column
|
||||
of the per-atom array with :math:`M` columns calculated by the compute.
|
||||
See the discussion above for how :math:`i` can be specified with a
|
||||
wildcard asterisk to effectively specify multiple values.
|
||||
|
||||
The *f_ID* and *f_ID[I]* attributes allow vector or array per-atom
|
||||
quantities calculated by a :doc:`fix <fix>` to be output. The ID in
|
||||
the attribute should be replaced by the actual ID of the fix that has
|
||||
been defined previously in the input script. The :doc:`fix ave/atom
|
||||
quantities calculated by a :doc:`fix <fix>` to be output. The ID in the
|
||||
attribute should be replaced by the actual ID of the fix that has been
|
||||
defined previously in the input script. The :doc:`fix ave/atom
|
||||
<fix_ave_atom>` command is one that calculates per-atom quantities.
|
||||
Since it can time-average per-atom quantities produced by any
|
||||
:doc:`compute <compute>`, :doc:`fix <fix>`, or atom-style
|
||||
:doc:`variable <variable>`, this allows those time-averaged results to
|
||||
be written to a dump file.
|
||||
:doc:`compute <compute>`, :doc:`fix <fix>`, or atom-style :doc:`variable
|
||||
<variable>`, this allows those time-averaged results to be written to a
|
||||
dump file.
|
||||
|
||||
If *f_ID* is used as a attribute, then the per-atom vector calculated
|
||||
by the fix is printed. If *f_ID[i]* is used, then :math:`i` must be in the
|
||||
range from 1 to :math:`M`, which will print the :math:`i`\ th column of the
|
||||
per-atom array with :math:`M` columns calculated by the fix. See the
|
||||
discussion above for how :math:`i` can be specified with a wildcard asterisk
|
||||
to effectively specify multiple values.
|
||||
If *f_ID* is used as a attribute, then the per-atom vector calculated by
|
||||
the fix is printed. If *f_ID[i]* is used, then :math:`i` must be in the
|
||||
range from 1 to :math:`M`, which will print the :math:`i`\ th column of
|
||||
the per-atom array with :math:`M` columns calculated by the fix. See
|
||||
the discussion above for how :math:`i` can be specified with a wildcard
|
||||
asterisk to effectively specify multiple values.
|
||||
|
||||
The *v_name* attribute allows per-atom vectors calculated by a
|
||||
:doc:`variable <variable>` to be output. The name in the attribute
|
||||
should be replaced by the actual name of the variable that has been
|
||||
defined previously in the input script. Only an atom-style variable
|
||||
can be referenced, since it is the only style that generates per-atom
|
||||
defined previously in the input script. Only an atom-style variable can
|
||||
be referenced, since it is the only style that generates per-atom
|
||||
values. Variables of style *atom* can reference individual atom
|
||||
attributes, per-atom attributes, thermodynamic keywords, or invoke
|
||||
other computes, fixes, or variables when they are evaluated, so this
|
||||
is a very general means of creating quantities to output to a dump file.
|
||||
attributes, per-atom attributes, thermodynamic keywords, or invoke other
|
||||
computes, fixes, or variables when they are evaluated, so this is a very
|
||||
general means of creating quantities to output to a dump file.
|
||||
|
||||
The *i_name*, *d_name*, *i2_name*, *d2_name* attributes refer to
|
||||
per-atom integer and floating-point vectors or arrays that have been
|
||||
@ -794,10 +796,11 @@ added via the :doc:`fix property/atom <fix_property_atom>` command.
|
||||
When that command is used specific names are given to each attribute
|
||||
which are the "name" portion of these keywords. For arrays *i2_name*
|
||||
and *d2_name*, the column of the array must also be included following
|
||||
the name in brackets (e.g., d2_xyz[i], i2_mySpin[i], where :math:`i` is in the
|
||||
range from 1 to :math:`M`, where :math:`M` is the number of columns in the
|
||||
custom array). See the discussion above for how :math:`i` can be specified with
|
||||
a wildcard asterisk to effectively specify multiple values.
|
||||
the name in brackets (e.g., d2_xyz[i], i2_mySpin[i], where :math:`i` is
|
||||
in the range from 1 to :math:`M`, where :math:`M` is the number of
|
||||
columns in the custom array). See the discussion above for how :math:`i`
|
||||
can be specified with a wildcard asterisk to effectively specify
|
||||
multiple values.
|
||||
|
||||
See the :doc:`Modify <Modify>` page for information on how to add
|
||||
new compute and fix styles to LAMMPS to calculate per-atom quantities
|
||||
|
||||
@ -196,8 +196,8 @@ Only atoms in the specified group are rendered in the image. The
|
||||
alter what atoms are included in the image.
|
||||
The filename suffix determines whether a JPEG, PNG, or PPM file is
|
||||
created with the *image* dump style. If the suffix is ".jpg" or
|
||||
".jpeg," then a `JPEG format <jpeg_format_>`_ file is created, if the
|
||||
suffix is ".png," then a `PNG format <png_format_>`_ is created, else
|
||||
".jpeg", then a `JPEG format <jpeg_format_>`_ file is created, if the
|
||||
suffix is ".png", then a `PNG format <png_format_>`_ is created, else
|
||||
a `PPM (aka NETPBM) format <ppm_format_>`_ file is created.
|
||||
The JPEG and PNG files are binary; PPM has a text mode header followed
|
||||
by binary data. JPEG images have lossy compression, PNG has lossless
|
||||
@ -261,7 +261,7 @@ atoms rendered in the image. They can be any atom attribute defined
|
||||
for the :doc:`dump custom <dump>` command, including *type* and
|
||||
*element*\ . This includes per-atom quantities calculated by a
|
||||
:doc:`compute <compute>`, :doc:`fix <fix>`, or :doc:`variable <variable>`,
|
||||
which are prefixed by "c\_," "f\_," or "v\_," respectively. Note that the
|
||||
which are prefixed by "c\_", "f\_", or "v\_", respectively. Note that the
|
||||
*diameter* setting can be overridden with a numeric value applied to
|
||||
all atoms by the optional *adiam* keyword.
|
||||
|
||||
@ -297,18 +297,18 @@ and sizes used by the `AtomEye <atomeye_>`_ visualization package.
|
||||
If other atom attributes are used for the *color* or *diameter*
|
||||
settings, they are interpreted in the following way.
|
||||
|
||||
If "vx," for example, is used as the *color* setting, then the color
|
||||
If "vx", for example, is used as the *color* setting, then the color
|
||||
of the atom will depend on the x-component of its velocity. The
|
||||
association of a per-atom value with a specific color is determined by
|
||||
a "color map," which can be specified via the dump_modify command, as
|
||||
a "color map", which can be specified via the dump_modify command, as
|
||||
described below. The basic idea is that the atom-attribute will be
|
||||
within a range of values, and every value within the range is mapped
|
||||
to a specific color. Depending on how the color map is defined, that
|
||||
mapping can take place via interpolation so that a value of -3.2 is
|
||||
halfway between "red" and "blue," or discretely so that the value of
|
||||
halfway between "red" and "blue", or discretely so that the value of
|
||||
-3.2 is "orange".
|
||||
|
||||
If "vx," for example, is used as the *diameter* setting, then the atom
|
||||
If "vx", for example, is used as the *diameter* setting, then the atom
|
||||
will be rendered using the x-component of its velocity as the
|
||||
diameter. If the per-atom value <= 0.0, them the atom will not be
|
||||
drawn. Note that finite-size spherical particles, as defined by
|
||||
@ -792,14 +792,14 @@ increasing values. Note that numeric values can be specified either
|
||||
as absolute numbers or as fractions (0.0 to 1.0) of the range,
|
||||
depending on the "a" or "f" in the style setting for the color map.
|
||||
|
||||
Here is how the entries are used to determine the color of an
|
||||
individual atom, given the value :math:`X` of its atom attribute.
|
||||
:math:`X` will fall between 2 of the entry values. The color of the atom is
|
||||
linearly interpolated (in each of the RGB values) between the 2 colors
|
||||
associated with those entries. For example, if :math:`X = -5.0` and the two
|
||||
surrounding entries are "red" at :math:`-10.0` and "blue" at :math:`0.0`,
|
||||
then the atom's color will be halfway between "red" and "blue," which happens
|
||||
to be "purple."
|
||||
Here is how the entries are used to determine the color of an individual
|
||||
atom, given the value :math:`X` of its atom attribute. :math:`X` will
|
||||
fall between 2 of the entry values. The color of the atom is linearly
|
||||
interpolated (in each of the RGB values) between the 2 colors associated
|
||||
with those entries. For example, if :math:`X = -5.0` and the two
|
||||
surrounding entries are "red" at :math:`-10.0` and "blue" at
|
||||
:math:`0.0`, then the atom's color will be halfway between "red" and
|
||||
"blue", which happens to be "purple".
|
||||
|
||||
For discrete color maps, each entry has a *lo* and *hi* value and a
|
||||
*color*\ . The *lo* and *hi* settings are either numbers within the
|
||||
@ -807,19 +807,18 @@ range of values or *lo* can be *min* or *hi* can be *max*\ . The *lo*
|
||||
and *hi* settings of the last entry must be *min* and *max*\ . Other
|
||||
entries can have any *lo* and *hi* values and the sub-ranges of
|
||||
different values can overlap. Note that numeric *lo* and *hi* values
|
||||
can be specified either as absolute numbers or as fractions (0.0 to
|
||||
1.0) of the range, depending on the "a" or "f" in the style setting
|
||||
for the color map.
|
||||
can be specified either as absolute numbers or as fractions (0.0 to 1.0)
|
||||
of the range, depending on the "a" or "f" in the style setting for the
|
||||
color map.
|
||||
|
||||
Here is how the entries are used to determine the color of an
|
||||
individual atom, given the value X of its atom attribute. The entries
|
||||
are scanned from first to last. The first time that *lo* <= X <=
|
||||
*hi*, X is assigned the color associated with that entry. You can
|
||||
think of the last entry as assigning a default color (since it will
|
||||
always be matched by X), and the earlier entries as colors that
|
||||
override the default. Also note that no interpolation of a color RGB
|
||||
is done. All atoms will be drawn with one of the colors in the list
|
||||
of entries.
|
||||
Here is how the entries are used to determine the color of an individual
|
||||
atom, given the value X of its atom attribute. The entries are scanned
|
||||
from first to last. The first time that *lo* <= X <= *hi*, X is
|
||||
assigned the color associated with that entry. You can think of the
|
||||
last entry as assigning a default color (since it will always be matched
|
||||
by X), and the earlier entries as colors that override the default.
|
||||
Also note that no interpolation of a color RGB is done. All atoms will
|
||||
be drawn with one of the colors in the list of entries.
|
||||
|
||||
For sequential color maps, each entry has only a *color*\ . Here is how
|
||||
the entries are used to determine the color of an individual atom,
|
||||
@ -867,7 +866,7 @@ that bonds of each type will be drawn in the image.
|
||||
The specified *type* should be an integer from 1 to :math:`N`, where :math:`N`
|
||||
is the number of bond types. A wildcard asterisk can be used in place of or
|
||||
in conjunction with the *type* argument to specify a range of bond
|
||||
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N`
|
||||
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n". If :math:`N`
|
||||
is the number of bond types, then an asterisk with no numerical values
|
||||
means all types from 1 to :math:`N`. A leading asterisk means all types from
|
||||
1 to n (inclusive). A trailing asterisk means all types from m to :math:`N`
|
||||
|
||||
@ -122,7 +122,7 @@ The *pstyle* argument is the name of the pair style. If
|
||||
sub-styles using the same pair style, then *pstyle* should be specified
|
||||
as "style:N", where :math:`N` is which instance of the pair style you wish to
|
||||
adapt (e.g., the first or second). For example, *pstyle* could be
|
||||
specified as "soft" or "lubricate" or "lj/cut:1" or "lj/cut:2." The
|
||||
specified as "soft" or "lubricate" or "lj/cut:1" or "lj/cut:2". The
|
||||
*pparam* argument is the name of the parameter to change. This is the
|
||||
current list of pair styles and parameters that can be varied by this
|
||||
fix. See the doc pages for individual pair styles and their energy
|
||||
@ -245,7 +245,7 @@ the coefficients for the symmetric :math:`J,I` interaction to the same values.
|
||||
|
||||
A wild-card asterisk can be used in place of or in conjunction with
|
||||
the :math:`I,J` arguments to set the coefficients for multiple pairs of atom
|
||||
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N`
|
||||
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n". If :math:`N`
|
||||
is the number of atom types, then an asterisk with no numeric values
|
||||
means all types from 1 to :math:`N`. A leading asterisk means all types from
|
||||
1 to n (inclusive). A trailing asterisk means all types from m to :math:`N`
|
||||
@ -260,17 +260,17 @@ values defined (via the :doc:`pair_coeff <pair_coeff>` command) for
|
||||
that sub-style.
|
||||
|
||||
The *v_name* argument for keyword *pair* is the name of an
|
||||
:doc:`equal-style variable <variable>` which will be evaluated each
|
||||
time this fix is invoked to set the parameter to a new value. It
|
||||
should be specified as v_name, where name is the variable name.
|
||||
Equal-style variables can specify formulas with various mathematical
|
||||
functions, and include :doc:`thermo_style <thermo_style>` command
|
||||
keywords for the simulation box parameters and timestep and elapsed
|
||||
time. Thus it is easy to specify parameters that change as a function
|
||||
of time or span consecutive runs in a continuous fashion. For the
|
||||
latter, see the *start* and *stop* keywords of the :doc:`run <run>`
|
||||
command and the *elaplong* keyword of :doc:`thermo_style custom
|
||||
<thermo_style>` for details.
|
||||
:doc:`equal-style variable <variable>` which will be evaluated each time
|
||||
this fix is invoked to set the parameter to a new value. It should be
|
||||
specified as v_name, where name is the variable name. Equal-style
|
||||
variables can specify formulas with various mathematical functions, and
|
||||
include :doc:`thermo_style <thermo_style>` command keywords for the
|
||||
simulation box parameters and timestep and elapsed time. Thus it is
|
||||
easy to specify parameters that change as a function of time or span
|
||||
consecutive runs in a continuous fashion. For the latter, see the
|
||||
*start* and *stop* keywords of the :doc:`run <run>` command and the
|
||||
*elaplong* keyword of :doc:`thermo_style custom <thermo_style>` for
|
||||
details.
|
||||
|
||||
For example, these commands would change the prefactor coefficient of
|
||||
the :doc:`pair_style soft <pair_soft>` potential from 10.0 to 30.0 in a
|
||||
@ -288,13 +288,14 @@ a bond coefficient over time, very similar to how the *pair* keyword
|
||||
operates. The only difference is that now a bond coefficient for a
|
||||
given bond type is adapted.
|
||||
|
||||
A wild-card asterisk can be used in place of or in conjunction with
|
||||
the bond type argument to set the coefficients for multiple bond
|
||||
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N`
|
||||
is the number of bond types, then an asterisk with no numeric values
|
||||
means all types from 1 to :math:`N`. A leading asterisk means all types from
|
||||
1 to n (inclusive). A trailing asterisk means all types from m to :math:`N`
|
||||
(inclusive). A middle asterisk means all types from m to n (inclusive).
|
||||
A wild-card asterisk can be used in place of or in conjunction with the
|
||||
bond type argument to set the coefficients for multiple bond types.
|
||||
This takes the form "\*" or "\*n" or "m\*" or "m\*n". If :math:`N` is
|
||||
the number of bond types, then an asterisk with no numeric values means
|
||||
all types from 1 to :math:`N`. A leading asterisk means all types from
|
||||
1 to n (inclusive). A trailing asterisk means all types from m to
|
||||
:math:`N` (inclusive). A middle asterisk means all types from m to n
|
||||
(inclusive).
|
||||
|
||||
Currently *bond* does not support bond_style hybrid nor bond_style
|
||||
hybrid/overlay as bond styles. The bond styles that currently work
|
||||
@ -323,13 +324,14 @@ an angle coefficient over time, very similar to how the *pair* keyword
|
||||
operates. The only difference is that now an angle coefficient for a
|
||||
given angle type is adapted.
|
||||
|
||||
A wild-card asterisk can be used in place of or in conjunction with
|
||||
the angle type argument to set the coefficients for multiple angle
|
||||
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N`
|
||||
is the number of angle types, then an asterisk with no numeric values
|
||||
means all types from 1 to :math:`N`. A leading asterisk means all types from
|
||||
1 to n (inclusive). A trailing asterisk means all types from m to :math:`N`
|
||||
(inclusive). A middle asterisk means all types from m to n (inclusive).
|
||||
A wild-card asterisk can be used in place of or in conjunction with the
|
||||
angle type argument to set the coefficients for multiple angle types.
|
||||
This takes the form "\*" or "\*n" or "m\*" or "m\*n". If :math:`N` is
|
||||
the number of angle types, then an asterisk with no numeric values means
|
||||
all types from 1 to :math:`N`. A leading asterisk means all types from
|
||||
1 to n (inclusive). A trailing asterisk means all types from m to
|
||||
:math:`N` (inclusive). A middle asterisk means all types from m to n
|
||||
(inclusive).
|
||||
|
||||
Currently *angle* does not support angle_style hybrid nor angle_style
|
||||
hybrid/overlay as angle styles. The angle styles that currently work
|
||||
|
||||
@ -115,7 +115,7 @@ overrides the parameters.
|
||||
|
||||
The *pstyle* argument is the name of the pair style. If :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is used, *pstyle* should be
|
||||
a sub-style name. For example, *pstyle* could be specified as "soft"
|
||||
or "lubricate." The *pparam* argument is the name of the parameter to
|
||||
or "lubricate". The *pparam* argument is the name of the parameter to
|
||||
change. This is the current list of pair styles and parameters that
|
||||
can be varied by this fix. See the doc pages for individual pair
|
||||
styles and their energy formulas for the meaning of these parameters:
|
||||
@ -209,7 +209,7 @@ the coefficients for the symmetric J,I interaction to the same values.
|
||||
|
||||
A wild-card asterisk can be used in place of or in conjunction with
|
||||
the :math:`I,J` arguments to set the coefficients for multiple pairs of atom
|
||||
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N` is
|
||||
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n". If :math:`N` is
|
||||
the number of atom types, then an asterisk with no numeric values means
|
||||
all types from 1 to :math:`N`. A leading asterisk means all types from 1 to n
|
||||
(inclusive). A trailing asterisk means all types from m to :math:`N`
|
||||
|
||||
@ -153,7 +153,7 @@ which can be accessed by various :doc:`output commands
|
||||
<Howto_output>`. The scalar is the potential energy discussed above.
|
||||
The vector is the total force on the group of atoms before the forces
|
||||
on individual atoms are changed by the fix. The scalar and vector
|
||||
values calculated by this fix are "extensive."
|
||||
values calculated by this fix are "extensive".
|
||||
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command.
|
||||
|
||||
@ -75,7 +75,7 @@ accessed by various :doc:`output commands <Howto_output>`. The scalar
|
||||
is the potential energy discussed above. The vector is the total
|
||||
torque on the group of atoms before the forces on individual atoms are
|
||||
changed by the fix. The scalar and vector values calculated by this
|
||||
fix are "extensive."
|
||||
fix are "extensive".
|
||||
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command.
|
||||
|
||||
@ -124,7 +124,7 @@ setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
|
||||
This fix computes a global scalar which can be accessed by various
|
||||
:doc:`output commands <Howto_output>`. The scalar is the potential
|
||||
energy discussed above. The scalar value calculated by this fix is
|
||||
"extensive."
|
||||
"extensive".
|
||||
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command.
|
||||
|
||||
@ -138,7 +138,7 @@ setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
|
||||
This fix computes a global scalar which can be accessed by various
|
||||
:doc:`output commands <Howto_output>`. The scalar is the potential
|
||||
energy discussed above. The scalar value calculated by this fix is
|
||||
"extensive."
|
||||
"extensive".
|
||||
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command.
|
||||
|
||||
@ -135,7 +135,7 @@ fix are listed below.
|
||||
|
||||
This fix computes a global scalar which can be accessed by various
|
||||
:doc:`output commands <Howto_output>`. The scalar is the energy
|
||||
discussed in the previous paragraph. The scalar value is "extensive."
|
||||
discussed in the previous paragraph. The scalar value is "extensive".
|
||||
|
||||
No parameter of this fix can be used with the
|
||||
*start/stop* keywords of the :doc:`run <run>` command. This fix is not
|
||||
|
||||
@ -167,7 +167,7 @@ the following global cumulative quantities:
|
||||
* 1 = swap attempts
|
||||
* 2 = swap accepts
|
||||
|
||||
The vector values calculated by this fix are "extensive."
|
||||
The vector values calculated by this fix are "extensive".
|
||||
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command. This fix is not invoked during
|
||||
|
||||
@ -70,7 +70,7 @@ per-atom vectors.
|
||||
Note that for values from a compute or fix, the bracketed index I can
|
||||
be specified using a wildcard asterisk with the index to effectively
|
||||
specify multiple values. This takes the form "\*" or "\*n" or "m\*" or
|
||||
"m\*n." If :math:`N` is the size of the vector (for *mode* = scalar) or the
|
||||
"m\*n". If :math:`N` is the size of the vector (for *mode* = scalar) or the
|
||||
number of columns in the array (for *mode* = vector), then an asterisk
|
||||
with no numeric values means all indices from 1 to :math:`N`. A leading
|
||||
asterisk means all indices from 1 to n (inclusive). A trailing
|
||||
@ -127,7 +127,7 @@ specifying an input value from that compute.
|
||||
:doc:`compute property/atom <compute_property_atom>`
|
||||
command via its *xu*, *yu*, and *zu* attributes.
|
||||
|
||||
If a value begins with "c\_," a compute ID must follow which has been
|
||||
If a value begins with "c\_", a compute ID must follow which has been
|
||||
previously defined in the input script. If no bracketed term is
|
||||
appended, the per-atom vector calculated by the compute is used. If a
|
||||
bracketed term containing an index :math:`I` is appended, the
|
||||
@ -137,7 +137,7 @@ used. Users can also write code for their own compute styles and
|
||||
:math:`I` can be specified with a wildcard asterisk to effectively specify
|
||||
multiple values.
|
||||
|
||||
If a value begins with "f\_," a fix ID must follow which has been previously
|
||||
If a value begins with "f\_", a fix ID must follow which has been previously
|
||||
defined in the input script. If no bracketed term is appended, the per-atom
|
||||
vector calculated by the fix is used. If a bracketed term containing an index
|
||||
:math:`I` is appended, the :math:`I^\text{th}` column of the per-atom array
|
||||
@ -148,7 +148,7 @@ and :doc:`add them to LAMMPS <Modify>`. See the discussion above for how
|
||||
:math:`I` can be specified with a wildcard asterisk to effectively specify
|
||||
multiple values.
|
||||
|
||||
If a value begins with "v\_," a variable name must follow which has
|
||||
If a value begins with "v\_", a variable name must follow which has
|
||||
been previously defined in the input script as an
|
||||
:doc:`atom-style variable <variable>`. Variables of style *atom* can reference
|
||||
thermodynamic keywords or invoke other computes, fixes, or variables
|
||||
|
||||
@ -288,7 +288,7 @@ together as one set of atoms to calculate their temperature. The
|
||||
compute allows the center-of-mass velocity of each chunk to be
|
||||
subtracted before calculating the temperature; this fix does not.
|
||||
|
||||
If a value begins with "c\_," a compute ID must follow which has been
|
||||
If a value begins with "c\_", a compute ID must follow which has been
|
||||
previously defined in the input script. If no bracketed integer is
|
||||
appended, the per-atom vector calculated by the compute is used. If a
|
||||
bracketed integer is appended, the Ith column of the per-atom array
|
||||
@ -297,7 +297,7 @@ their own compute styles and :doc:`add them to LAMMPS <Modify>`.
|
||||
See the discussion above for how I can be specified with a wildcard
|
||||
asterisk to effectively specify multiple values.
|
||||
|
||||
If a value begins with "f\_," a fix ID must follow which has been
|
||||
If a value begins with "f\_", a fix ID must follow which has been
|
||||
previously defined in the input script. If no bracketed integer is
|
||||
appended, the per-atom vector calculated by the fix is used. If a
|
||||
bracketed integer is appended, the Ith column of the per-atom array
|
||||
@ -308,7 +308,7 @@ their own fix styles and :doc:`add them to LAMMPS <Modify>`. See the
|
||||
discussion above for how I can be specified with a wildcard asterisk
|
||||
to effectively specify multiple values.
|
||||
|
||||
If a value begins with "v\_," a variable name must follow which has
|
||||
If a value begins with "v\_", a variable name must follow which has
|
||||
been previously defined in the input script. Variables of style
|
||||
*atom* can reference thermodynamic keywords and various per-atom
|
||||
attributes, or invoke other computes, fixes, or variables when they
|
||||
@ -348,7 +348,7 @@ at each sampling step.
|
||||
|
||||
If the *norm* setting is *none*, a similar computation as for the
|
||||
*sample* setting is done, except the individual "average sample
|
||||
values" are "summed sample values." A summed sample value is simply
|
||||
values" are "summed sample values". A summed sample value is simply
|
||||
the chunk value summed over atoms in the sample, without dividing by
|
||||
the number of atoms in the sample. The output value for the chunk on
|
||||
the :math:`N_\text{freq}` timesteps is the average of the
|
||||
@ -494,21 +494,21 @@ relevant to this fix.
|
||||
|
||||
This fix computes a global array of values which can be accessed by
|
||||
various :doc:`output commands <Howto_output>`. The values can only be
|
||||
accessed on timesteps that are multiples of :math:`N_\text{freq}`, since that
|
||||
is when averaging is performed. The global array has # of rows = the number
|
||||
of chunks :math:`N_\text{chunk}`, as calculated by the specified
|
||||
:doc:`compute chunk/atom <compute_chunk_atom>` command. The # of columns is
|
||||
:math:`M+1+N_\text{values}`, where :math:`M \in \{1,\dotsc,4\}`,
|
||||
depending on whether the optional
|
||||
columns for OrigID and CoordN are used, as explained above. Following
|
||||
the optional columns, the next column contains the count of atoms in
|
||||
the chunk, and the remaining columns are the Nvalue quantities. When
|
||||
the array is accessed with a row :math:`I` that exceeds the current number of
|
||||
chunks, than a 0.0 is returned by the fix instead of an error, since
|
||||
the number of chunks can vary as a simulation runs depending on how
|
||||
that value is computed by the compute chunk/atom command.
|
||||
accessed on timesteps that are multiples of :math:`N_\text{freq}`, since
|
||||
that is when averaging is performed. The global array has # of rows =
|
||||
the number of chunks :math:`N_\text{chunk}`, as calculated by the
|
||||
specified :doc:`compute chunk/atom <compute_chunk_atom>` command. The #
|
||||
of columns is :math:`M+1+N_\text{values}`, where :math:`M \in
|
||||
\{1,\dotsc,4\}`, depending on whether the optional columns for OrigID
|
||||
and CoordN are used, as explained above. Following the optional
|
||||
columns, the next column contains the count of atoms in the chunk, and
|
||||
the remaining columns are the Nvalue quantities. When the array is
|
||||
accessed with a row :math:`I` that exceeds the current number of chunks,
|
||||
than a 0.0 is returned by the fix instead of an error, since the number
|
||||
of chunks can vary as a simulation runs depending on how that value is
|
||||
computed by the compute chunk/atom command.
|
||||
|
||||
The array values calculated by this fix are treated as "intensive,"
|
||||
The array values calculated by this fix are treated as "intensive",
|
||||
since they are typically already normalized by the count of atoms in
|
||||
each chunk.
|
||||
|
||||
|
||||
@ -189,7 +189,7 @@ Also, if the *ave* keyword is set to *one* which is the default, then
|
||||
|
||||
----------
|
||||
|
||||
If a value begins with "c\_," a compute ID must follow which has been
|
||||
If a value begins with "c\_", a compute ID must follow which has been
|
||||
previously defined in the input script. If no bracketed term is
|
||||
appended, the global scalar calculated by the compute is used. If a
|
||||
bracketed term is appended, the :math:`I^\text{th}` element of the global
|
||||
@ -206,7 +206,7 @@ or :doc:`fix temp/rescale <fix_temp_rescale>`. See the doc pages for
|
||||
these commands which give the IDs of these computes. Users can also
|
||||
write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
|
||||
|
||||
If a value begins with "f\_," a fix ID must follow which has been
|
||||
If a value begins with "f\_", a fix ID must follow which has been
|
||||
previously defined in the input script. If no bracketed term is
|
||||
appended, the global scalar calculated by the fix is used. If a
|
||||
bracketed term is appended, the :math:`I^\text{th}` element of the global
|
||||
@ -219,7 +219,7 @@ which must be compatible with :math:`N_\text{every}`, else an error will
|
||||
result. Users can also write code for their own fix styles and
|
||||
:doc:`add them to LAMMPS <Modify>`.
|
||||
|
||||
If a value begins with "v\_," a variable name must follow which has been
|
||||
If a value begins with "v\_", a variable name must follow which has been
|
||||
previously defined in the input script. Only equal-style or vector-style
|
||||
variables can be referenced; the latter requires a bracketed term to specify
|
||||
the :math:`I^\text{th}` element of the vector calculated by the variable.
|
||||
|
||||
@ -193,7 +193,7 @@ inputs to this fix by using the
|
||||
:doc:`compute property/atom <compute_property_atom>` command and then
|
||||
specifying an input value from that compute.
|
||||
|
||||
If a value begins with "c\_," a compute ID must follow which has been
|
||||
If a value begins with "c\_", a compute ID must follow which has been
|
||||
previously defined in the input script. If *mode* = scalar, then if
|
||||
no bracketed term is appended, the global scalar calculated by the
|
||||
compute is used. If a bracketed term is appended, the Ith element of
|
||||
@ -215,7 +215,7 @@ these commands which give the IDs of these computes. Users can also
|
||||
write code for their own compute styles and
|
||||
:doc:`add them to LAMMPS <Modify>`.
|
||||
|
||||
If a value begins with "f\_," a fix ID must follow which has been
|
||||
If a value begins with "f\_", a fix ID must follow which has been
|
||||
previously defined in the input script. If *mode* = scalar, then if
|
||||
no bracketed term is appended, the global scalar calculated by the fix
|
||||
is used. If a bracketed term is appended, the Ith element of the
|
||||
@ -232,7 +232,7 @@ which must be compatible with :math:`N_\text{every}`, else an error will
|
||||
result. Users can also write code for their own fix styles and
|
||||
:doc:`add them to LAMMPS <Modify>`.
|
||||
|
||||
If a value begins with "v\_," a variable name must follow which has
|
||||
If a value begins with "v\_", a variable name must follow which has
|
||||
been previously defined in the input script. If *mode* = scalar, then
|
||||
only equal-style or vector-style variables can be used, which both
|
||||
produce global values. In this mode, a vector-style variable requires
|
||||
|
||||
@ -358,11 +358,11 @@ of rows = length of the input vectors and # of columns = number of
|
||||
inputs.
|
||||
|
||||
If the fix produces a scalar or vector, then the scalar and each
|
||||
element of the vector can be either "intensive" or "extensive,"
|
||||
element of the vector can be either "intensive" or "extensive",
|
||||
depending on whether the values contributing to the scalar or vector
|
||||
element are "intensive" or "extensive." If the fix produces an array,
|
||||
element are "intensive" or "extensive". If the fix produces an array,
|
||||
then all elements in the array must be the same, either "intensive" or
|
||||
"extensive." If a compute or fix provides the value being time
|
||||
"extensive". If a compute or fix provides the value being time
|
||||
averaged, then the compute or fix determines whether the value is
|
||||
intensive or extensive; see the page for that compute or fix for
|
||||
further info. Values produced by a variable are treated as intensive.
|
||||
|
||||
@ -361,7 +361,7 @@ The "SQUARES" section lists the node IDs of the four vertices in a
|
||||
rectangle for each processor (1 to 4).
|
||||
|
||||
For a 3d problem, the syntax is similar but with eight vertices listed for
|
||||
each processor instead of four, and "SQUARES" replaced by "CUBES."
|
||||
each processor instead of four, and "SQUARES" replaced by "CUBES".
|
||||
|
||||
----------
|
||||
|
||||
@ -387,7 +387,7 @@ number of particles (or total weight) per processor.
|
||||
|
||||
These quantities can be accessed by various
|
||||
:doc:`output commands <Howto_output>`. The scalar and vector values calculated
|
||||
by this fix are "intensive."
|
||||
by this fix are "intensive".
|
||||
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command. This fix is not invoked during
|
||||
|
||||
@ -8,18 +8,27 @@ Syntax
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
fix ID group-ID latte peID
|
||||
fix ID group-ID latte keyword value ...
|
||||
|
||||
* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||
* latte = style name of this fix command
|
||||
* peID = NULL or ID of compute used to calculate per-atom energy
|
||||
* zero or more keyword/value pairs may be appended
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
keyword = *coulomb* or *exclude*
|
||||
*coulomb* value = peID
|
||||
peID = ID of compute used to calculate per-atom energy
|
||||
*exclude* value = fixID
|
||||
fixID = ID of fix which potentially excludes atoms before calling LATTE
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix dftb all latte NULL
|
||||
fix dftb all latte
|
||||
fix dftb all exclude GCMC
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
@ -48,10 +57,41 @@ found in examples/latte.
|
||||
|
||||
A step-by-step tutorial can be followed at: `LAMMPS-LATTE tutorial <https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS>`_
|
||||
|
||||
The *peID* argument is not yet supported by fix latte, so it must be
|
||||
specified as NULL. Eventually it will be used to enable LAMMPS to
|
||||
calculate a Coulomb potential as an alternative to LATTE performing
|
||||
the calculation.
|
||||
Currently, LAMMPS must be run in serial or as a single MPI task, to
|
||||
use this fix. This is because the version of the LATTE library LAMMPS
|
||||
uses does not support MPI. On the LAMMPS size, this is typically not
|
||||
a bottleneck, since LATTE will be doing 99% or more of the work to
|
||||
compute quantum-accurate forces. On the LATTE side, the LATTE library
|
||||
does support threaded parallelism via OpenMP. You must build the
|
||||
LATTE library with OpenMP support, then set the OMP_NUM_THREADS
|
||||
environment variable before performing a LAMMPS + LATTE simulation to
|
||||
tell LATTE how many threads to invoke.
|
||||
|
||||
.. note::
|
||||
|
||||
NEB calculations can be done using this fix using multiple
|
||||
replicas and running LAMMPS in parallel. However, each replica must
|
||||
be run on a single MPI task. For details, see the :doc:`neb <neb>`
|
||||
command page and the :doc:`-partition command-line switch <Run_options>`
|
||||
|
||||
----------
|
||||
|
||||
The *coulomb* argument is not yet supported by fix latte (as of Sept
|
||||
2022). Eventually it will be used to enable LAMMPS to calculate a
|
||||
Coulomb potential as an alternative to LATTE performing the
|
||||
calculation.
|
||||
|
||||
The *exclude* argument allows this fix to work in tandem with another
|
||||
fix which may decide to delete one or more atoms of molecules. The
|
||||
specified fixID is the ID of the other fix.
|
||||
|
||||
The one current example of such a fix is the :doc:`fix gcmc
|
||||
<fix_gcmc>` command which performs Monte Carlo insertions and
|
||||
deletions. If a trial deletion is performed, then LAMMPS needs to
|
||||
only pass LATTE the atoms which remain. Fix gcmc does not actually
|
||||
remove any atoms until after the new energy is computed (in this case
|
||||
by LATTE), and a Monte Carlo accept/reject decision is made for the
|
||||
trial deletion.
|
||||
|
||||
----------
|
||||
|
||||
@ -153,18 +193,8 @@ use this fix.
|
||||
|
||||
LATTE does not currently compute per-atom energy or per-atom virial
|
||||
contributions. So they will not show up as part of the calculations
|
||||
performed by the :doc:`compute pe/atom <compute_pe_atom>` or :doc:`compute stress/atom <compute_stress_atom>` commands.
|
||||
|
||||
Currently, LAMMPS must be run in serial or as a single MPI task, to
|
||||
use this fix. This is typically not a bottleneck, since LATTE will be
|
||||
doing 99% or more of the work to compute quantum-accurate forces.
|
||||
|
||||
.. note::
|
||||
|
||||
NEB calculations can be done using this fix using multiple
|
||||
replicas and running LAMMPS in parallel. However, each replica must
|
||||
be run on a single MPI task. For details, see the :doc:`neb <neb>`
|
||||
command page and the :doc:`-partition command-line switch <Run_options>`
|
||||
performed by the :doc:`compute pe/atom <compute_pe_atom>` or
|
||||
:doc:`compute stress/atom <compute_stress_atom>` commands.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
@ -318,7 +318,7 @@ Restrictions
|
||||
""""""""""""
|
||||
|
||||
There can be no more than 32 groups defined at one time, including
|
||||
"all."
|
||||
"all".
|
||||
|
||||
The parent group of a dynamic group cannot itself be a dynamic group.
|
||||
|
||||
|
||||
@ -981,7 +981,7 @@ In the last example, "new-property.edn" and
|
||||
"/home/mary/marys-kim-properties/dissociation-energy.edn" are the names of files
|
||||
that contain user-defined (local) property definitions.
|
||||
|
||||
A KIM property instance takes the form of a "map," i.e. a set of key-value
|
||||
A KIM property instance takes the form of a "map", i.e. a set of key-value
|
||||
pairs akin to Perl's hash, Python's dictionary, or Java's Hashtable. It
|
||||
consists of a set of property key names, each of which is referred to here by
|
||||
the *key_name* argument, that are defined as part of the relevant KIM Property
|
||||
|
||||
@ -69,13 +69,13 @@ there is a label defined for *every* numeric type within a given
|
||||
type-kind in order to write out the type label section for that
|
||||
type-kind.
|
||||
|
||||
The *clear* option resets the labelmap and thus discards all previous
|
||||
The *clear* option resets the label map and thus discards all previous
|
||||
settings.
|
||||
|
||||
The *write* option takes a filename as argument and writes the current
|
||||
label mappings to a file as labelmap commands, so the file can be copied
|
||||
into a new LAMMPS input file or read in using the :doc:`include
|
||||
<include>` command.
|
||||
label mappings to a file as a sequence of *labelmap* commands, so the
|
||||
file can be copied into a new LAMMPS input file or read in using the
|
||||
:doc:`include <include>` command.
|
||||
|
||||
----------
|
||||
|
||||
@ -86,7 +86,7 @@ This command must come after the simulation box is defined by a
|
||||
:doc:`read_data <read_data>`, :doc:`read_restart <read_restart>`, or
|
||||
:doc:`create_box <create_box>` command.
|
||||
|
||||
Labelmaps are currently not supported when using the KOKKOS package.
|
||||
Label maps are currently not supported when using the KOKKOS package.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
@ -140,4 +140,4 @@ none
|
||||
.. _Ziegler:
|
||||
|
||||
**(Ziegler)** J.F. Ziegler, J. P. Biersack and U. Littmark, "The
|
||||
Stopping and Range of Ions in Matter," Volume 1, Pergamon, 1985.
|
||||
Stopping and Range of Ions in Matter", Volume 1, Pergamon, 1985.
|
||||
|
||||
@ -1519,7 +1519,7 @@ To read gzipped data files, you must compile LAMMPS with the
|
||||
-DLAMMPS_GZIP option. See the :doc:`Build settings <Build_settings>`
|
||||
doc page for details.
|
||||
|
||||
Labelmaps are currently not supported when using the KOKKOS package.
|
||||
Label maps are currently not supported when using the KOKKOS package.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
@ -12,7 +12,7 @@ Syntax
|
||||
restart N root keyword value ...
|
||||
restart N file1 file2 keyword value ...
|
||||
|
||||
* N = write a restart file on timesteps which are multipls of N
|
||||
* N = write a restart file on timesteps which are multiples of N
|
||||
* N can be a variable (see below)
|
||||
* root = filename to which timestep # is appended
|
||||
* file1,file2 = two full filenames, toggle between them when writing file
|
||||
|
||||
@ -1,35 +1,35 @@
|
||||
# Simple water model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
||||
|
||||
read_data data.graphene
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 0.0 87287 loop geom
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all box/relax iso 0.0 vmax 0.001
|
||||
|
||||
fix 2 all latte NULL
|
||||
fix 2 all latte
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom etotal
|
||||
@ -9,7 +9,7 @@ read_data data.water
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
@ -17,7 +17,7 @@ neigh_modify every 1 delay 0 check yes
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all latte NULL
|
||||
fix 2 all latte
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
@ -44,7 +44,7 @@ read_data data.ch4
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
@ -53,7 +53,7 @@ timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all latte NULL
|
||||
fix 2 all latte
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
@ -1,40 +0,0 @@
|
||||
# simple sucrose model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
||||
|
||||
read_data data.sucrose
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all latte NULL
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
# dynamics
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
@ -1,35 +1,35 @@
|
||||
# simple sucrose model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
||||
|
||||
read_data data.sucrose
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 0.0 87287 loop geom
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all latte NULL
|
||||
fix 2 all latte
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
@ -37,4 +37,4 @@ thermo_style custom step temp pe etotal press
|
||||
# dynamics
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
run 100
|
||||
|
||||
@ -1,40 +0,0 @@
|
||||
# simple water model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
||||
|
||||
read_data data.water
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all latte NULL
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
# dynamics
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
@ -1,35 +1,35 @@
|
||||
# simple water model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
||||
|
||||
read_data data.water
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 0.0 87287 loop geom
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all latte NULL
|
||||
fix 2 all latte
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
@ -37,4 +37,4 @@ thermo_style custom step temp pe etotal press
|
||||
# dynamics
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
run 100
|
||||
|
||||
@ -1,35 +1,35 @@
|
||||
# simple water model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
||||
|
||||
read_data data.water
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 0.0 87287 loop geom
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all latte NULL
|
||||
fix 2 all latte
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
179
examples/latte/log.13Sep22.latte.graphene.boxrelax.g++.1
Normal file
179
examples/latte/log.13Sep22.latte.graphene.boxrelax.g++.1
Normal file
@ -0,0 +1,179 @@
|
||||
LAMMPS (3 Aug 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Simple water model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
||||
|
||||
read_data data.graphene
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (10 8 20) with tilt (4.8985872e-16 1.2246468e-15 1.2246468e-15)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
32 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all box/relax iso 0.0 vmax 0.001
|
||||
|
||||
fix 2 all latte
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom etotal
|
||||
|
||||
# minimization
|
||||
|
||||
thermo 1
|
||||
fix 3 all print 1 "Total Energy ="
|
||||
min_style cg
|
||||
min_modify dmax 0.1
|
||||
min_modify line quadratic
|
||||
minimize 1.0e-4 1.0e-4 10000 10000
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 11 9 20
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton/tri
|
||||
stencil: half/bin/3d/tri
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.03 | 7.03 | 7.03 Mbytes
|
||||
TotEng
|
||||
-247.46002
|
||||
-247.67224
|
||||
-247.87937
|
||||
-248.08148
|
||||
-248.27865
|
||||
-248.47096
|
||||
-248.65851
|
||||
-248.84137
|
||||
-249.01964
|
||||
-249.19342
|
||||
-249.36281
|
||||
-249.52791
|
||||
-249.68883
|
||||
-249.8457
|
||||
-249.99865
|
||||
-250.1478
|
||||
-250.29332
|
||||
-250.43535
|
||||
-250.57409
|
||||
-250.70972
|
||||
-250.84247
|
||||
-250.97258
|
||||
-251.10035
|
||||
-251.2261
|
||||
-251.35021
|
||||
-251.47314
|
||||
-251.59543
|
||||
-251.71776
|
||||
-251.84096
|
||||
-251.9661
|
||||
-252.09459
|
||||
-252.22833
|
||||
-252.37003
|
||||
-252.52371
|
||||
-252.69578
|
||||
-252.89752
|
||||
-253.15197
|
||||
-253.52044
|
||||
-254.31418
|
||||
-255.6175
|
||||
-256.8162
|
||||
-258.1227
|
||||
-259.38401
|
||||
-260.74831
|
||||
-262.03991
|
||||
-263.5463
|
||||
-264.70486
|
||||
-267.69143
|
||||
-267.88682
|
||||
-269.0352
|
||||
-270.602
|
||||
-270.65395
|
||||
-270.7429
|
||||
-271.55831
|
||||
-271.81159
|
||||
-271.87447
|
||||
-273.03096
|
||||
-273.23109
|
||||
-273.27869
|
||||
-273.34621
|
||||
-273.4082
|
||||
-273.45599
|
||||
-273.53849
|
||||
-273.57478
|
||||
-273.71381
|
||||
-273.74092
|
||||
Loop time of 20.5496 on 1 procs for 65 steps with 32 atoms
|
||||
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-247.460020562055 -273.713813242259 -273.740918498854
|
||||
Force two-norm initial, final = 201.60784 9.4927634
|
||||
Force max component initial, final = 188.92406 2.4327308
|
||||
Final line search alpha, max atom move = 0.00022885545 0.0005567437
|
||||
Iterations, force evaluations = 65 65
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.7869e-05 | 7.7869e-05 | 7.7869e-05 | 0.0 | 0.00
|
||||
Bond | 3.531e-06 | 3.531e-06 | 3.531e-06 | 0.0 | 0.00
|
||||
Neigh | 1.3988e-05 | 1.3988e-05 | 1.3988e-05 | 0.0 | 0.00
|
||||
Comm | 0.00014355 | 0.00014355 | 0.00014355 | 0.0 | 0.00
|
||||
Output | 0.00071475 | 0.00071475 | 0.00071475 | 0.0 | 0.00
|
||||
Modify | 20.547 | 20.547 | 20.547 | 0.0 | 99.99
|
||||
Other | | 0.001683 | | | 0.01
|
||||
|
||||
Nlocal: 32 ave 32 max 32 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 100 ave 100 max 100 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 48 ave 48 max 48 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 48
|
||||
Ave neighs/atom = 1.5
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:20
|
||||
189
examples/latte/log.13Sep22.latte.multiple.g++.1
Normal file
189
examples/latte/log.13Sep22.latte.multiple.g++.1
Normal file
@ -0,0 +1,189 @@
|
||||
LAMMPS (3 Aug 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
||||
|
||||
read_data data.water
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (6.267 6.267 6.267)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
24 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all latte
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
# dynamics
|
||||
|
||||
thermo 10
|
||||
run 10
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.88 | 5.88 | 5.88 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 0 -104.95596 -104.95596 48235.442
|
||||
10 336.53107 -105.96027 -104.95977 97996.851
|
||||
Loop time of 0.334108 on 1 procs for 10 steps with 24 atoms
|
||||
|
||||
Performance: 0.646 ns/day, 37.123 hours/ns, 29.930 timesteps/s
|
||||
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.714e-06 | 3.714e-06 | 3.714e-06 | 0.0 | 0.00
|
||||
Bond | 5.02e-07 | 5.02e-07 | 5.02e-07 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 1.1209e-05 | 1.1209e-05 | 1.1209e-05 | 0.0 | 0.00
|
||||
Output | 2.3638e-05 | 2.3638e-05 | 2.3638e-05 | 0.0 | 0.01
|
||||
Modify | 0.33404 | 0.33404 | 0.33404 | 0.0 | 99.98
|
||||
Other | | 2.795e-05 | | | 0.01
|
||||
|
||||
Nlocal: 24 ave 24 max 24 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 71 ave 71 max 71 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 37 ave 37 max 37 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 37
|
||||
Ave neighs/atom = 1.5416667
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
# Clear up previus calculation
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
# simple CH4 molecule with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
||||
|
||||
read_data data.ch4
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (19.523 12.758 11.692) with tilt (0 0 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
5 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.007 seconds
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all latte
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
# dynamics
|
||||
|
||||
thermo 10
|
||||
run 10
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 20 13 12
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton/tri
|
||||
stencil: half/bin/3d/tri
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.902 | 5.902 | 5.902 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 0 -23.980353 -23.980353 348.02716
|
||||
10 19.123149 -23.990297 -23.98041 18.774332
|
||||
Loop time of 0.0121573 on 1 procs for 10 steps with 5 atoms
|
||||
|
||||
Performance: 17.767 ns/day, 1.351 hours/ns, 822.549 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 | 1.224e-06 | 1.224e-06 | 1.224e-06 | 0.0 | 0.01
|
||||
Bond | 2.93e-07 | 2.93e-07 | 2.93e-07 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 3.845e-06 | 3.845e-06 | 3.845e-06 | 0.0 | 0.03
|
||||
Output | 8.633e-06 | 8.633e-06 | 8.633e-06 | 0.0 | 0.07
|
||||
Modify | 0.012132 | 0.012132 | 0.012132 | 0.0 | 99.80
|
||||
Other | | 1.089e-05 | | | 0.09
|
||||
|
||||
Nlocal: 5 ave 5 max 5 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 7 ave 7 max 7 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 10 ave 10 max 10 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 10
|
||||
Ave neighs/atom = 2
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
112
examples/latte/log.13Sep22.latte.sucrose.md.g++.1
Normal file
112
examples/latte/log.13Sep22.latte.sucrose.md.g++.1
Normal file
@ -0,0 +1,112 @@
|
||||
LAMMPS (3 Aug 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# simple sucrose model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
||||
|
||||
read_data data.sucrose
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (17.203 18.009 21.643)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
45 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all latte
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
# dynamics
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 18 19 22
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.93 | 5.93 | 5.93 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 0 -251.26617 -251.26617 16.617233
|
||||
10 0.025263738 -251.26631 -251.26617 8.0576369
|
||||
20 0.034232485 -251.26636 -251.26617 1.6672772
|
||||
30 0.059079585 -251.2665 -251.26617 11.058355
|
||||
40 0.055499785 -251.26648 -251.26617 14.837599
|
||||
50 0.058499496 -251.2665 -251.26617 6.7180488
|
||||
60 0.071094531 -251.26657 -251.26617 6.6131215
|
||||
70 0.084309398 -251.26665 -251.26617 12.372502
|
||||
80 0.1089929 -251.26679 -251.26617 8.8352747
|
||||
90 0.11378255 -251.26681 -251.26617 5.1175071
|
||||
100 0.13003967 -251.26691 -251.26617 8.2429118
|
||||
Loop time of 14.4456 on 1 procs for 100 steps with 45 atoms
|
||||
|
||||
Performance: 0.150 ns/day, 160.507 hours/ns, 6.923 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 | 7.5758e-05 | 7.5758e-05 | 7.5758e-05 | 0.0 | 0.00
|
||||
Bond | 6.748e-06 | 6.748e-06 | 6.748e-06 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 9.0137e-05 | 9.0137e-05 | 9.0137e-05 | 0.0 | 0.00
|
||||
Output | 0.00025976 | 0.00025976 | 0.00025976 | 0.0 | 0.00
|
||||
Modify | 14.445 | 14.445 | 14.445 | 0.0 | 99.99
|
||||
Other | | 0.0005283 | | | 0.00
|
||||
|
||||
Nlocal: 45 ave 45 max 45 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 59 ave 59 max 59 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 59
|
||||
Ave neighs/atom = 1.3111111
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:14
|
||||
112
examples/latte/log.13Sep22.latte.water.md.g++.1
Normal file
112
examples/latte/log.13Sep22.latte.water.md.g++.1
Normal file
@ -0,0 +1,112 @@
|
||||
LAMMPS (3 Aug 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# simple water model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
||||
|
||||
read_data data.water
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (6.267 6.267 6.267)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
24 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all latte
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
# dynamics
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.88 | 5.88 | 5.88 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 0 -104.95596 -104.95596 48235.442
|
||||
10 336.53107 -105.96027 -104.95977 97996.851
|
||||
20 529.06408 -106.53023 -104.95733 131519.85
|
||||
30 753.62603 -107.19952 -104.959 49296.66
|
||||
40 716.65648 -107.08803 -104.95742 28307.121
|
||||
50 824.04392 -107.40823 -104.95836 102167.59
|
||||
60 933.56146 -107.73479 -104.95933 92508.517
|
||||
70 851.18489 -107.48767 -104.95711 13993.262
|
||||
80 999.8028 -107.93147 -104.95907 36700.736
|
||||
90 998.77488 -107.9257 -104.95636 107233.54
|
||||
100 1281.4438 -108.76963 -104.95992 49702.386
|
||||
Loop time of 3.14578 on 1 procs for 100 steps with 24 atoms
|
||||
|
||||
Performance: 0.687 ns/day, 34.953 hours/ns, 31.789 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 | 3.0818e-05 | 3.0818e-05 | 3.0818e-05 | 0.0 | 0.00
|
||||
Bond | 4.704e-06 | 4.704e-06 | 4.704e-06 | 0.0 | 0.00
|
||||
Neigh | 1.8668e-05 | 1.8668e-05 | 1.8668e-05 | 0.0 | 0.00
|
||||
Comm | 0.00010831 | 0.00010831 | 0.00010831 | 0.0 | 0.00
|
||||
Output | 0.00021087 | 0.00021087 | 0.00021087 | 0.0 | 0.01
|
||||
Modify | 3.1452 | 3.1452 | 3.1452 | 0.0 | 99.98
|
||||
Other | | 0.0002339 | | | 0.01
|
||||
|
||||
Nlocal: 24 ave 24 max 24 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 77 ave 77 max 77 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 31 ave 31 max 31 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 31
|
||||
Ave neighs/atom = 1.2916667
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
122
examples/latte/log.13Sep22.latte.water.min.g++.1
Normal file
122
examples/latte/log.13Sep22.latte.water.min.g++.1
Normal file
@ -0,0 +1,122 @@
|
||||
LAMMPS (3 Aug 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# simple water model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
||||
|
||||
read_data data.water
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (6.267 6.267 6.267)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
24 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all latte
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
# minimization
|
||||
|
||||
thermo 10
|
||||
|
||||
min_style fire
|
||||
minimize 1.0e-4 1.0e-4 500 500
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Parameters for fire:
|
||||
dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback
|
||||
0.1 20 1.1 0.5 0.25 0.99 10 0.02 eulerimplicit yes
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.88 | 5.88 | 5.88 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 0 -104.95596 -104.95596 48235.442
|
||||
10 853.69689 -106.31143 -103.7734 79191.444
|
||||
20 1112.0893 -107.2723 -103.96607 82675.468
|
||||
30 1897.6249 -108.36769 -102.72608 71447.508
|
||||
40 3068.3491 -110.06452 -100.94237 47627.967
|
||||
50 3.730935 -110.16042 -110.14932 5913.0643
|
||||
60 28.603141 -110.18885 -110.10381 5778.8586
|
||||
66 54.717686 -110.21503 -110.05236 5739.5831
|
||||
Loop time of 2.48723 on 1 procs for 66 steps with 24 atoms
|
||||
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-104.955957263186 -110.209885831179 -110.215033825672
|
||||
Force two-norm initial, final = 19.119006 0.51695213
|
||||
Force max component initial, final = 11.775801 0.1663917
|
||||
Final line search alpha, max atom move = 0 0
|
||||
Iterations, force evaluations = 66 69
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.7159e-05 | 2.7159e-05 | 2.7159e-05 | 0.0 | 0.00
|
||||
Bond | 3.124e-06 | 3.124e-06 | 3.124e-06 | 0.0 | 0.00
|
||||
Neigh | 1.0201e-05 | 1.0201e-05 | 1.0201e-05 | 0.0 | 0.00
|
||||
Comm | 0.000109 | 0.000109 | 0.000109 | 0.0 | 0.00
|
||||
Output | 0.00010568 | 0.00010568 | 0.00010568 | 0.0 | 0.00
|
||||
Modify | 2.4866 | 2.4866 | 2.4866 | 0.0 | 99.98
|
||||
Other | | 0.0003552 | | | 0.01
|
||||
|
||||
Nlocal: 24 ave 24 max 24 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 75 ave 75 max 75 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 33 ave 33 max 33 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 33
|
||||
Ave neighs/atom = 1.375
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
@ -1,406 +0,0 @@
|
||||
The log file for latte_lib
|
||||
|
||||
CONTROL{ }
|
||||
|
||||
WARNING: variable JobName= is missing. I will use a default value instead ...
|
||||
WARNING: variable PARAMPATH= is missing. I will use a default value instead ...
|
||||
WARNING: variable DEBUGON= is missing. I will use a default value instead ...
|
||||
WARNING: variable FERMIM= is missing. I will use a default value instead ...
|
||||
WARNING: variable CGORLIB= is missing. I will use a default value instead ...
|
||||
WARNING: variable NORECS= is missing. I will use a default value instead ...
|
||||
WARNING: variable VDWON= is missing. I will use a default value instead ...
|
||||
WARNING: variable ORDERNMOL= is missing. I will use a default value instead ...
|
||||
WARNING: variable LCNON= is missing. I will use a default value instead ...
|
||||
WARNING: variable LCNITER= is missing. I will use a default value instead ...
|
||||
WARNING: variable MDON= is missing. I will use a default value instead ...
|
||||
WARNING: variable PBCON= is missing. I will use a default value instead ...
|
||||
WARNING: variable RESTART= is missing. I will use a default value instead ...
|
||||
WARNING: variable NGPU= is missing. I will use a default value instead ...
|
||||
WARNING: variable COMPFORCE= is missing. I will use a default value instead ...
|
||||
WARNING: variable DOSFIT= is missing. I will use a default value instead ...
|
||||
WARNING: variable INTS2FIT= is missing. I will use a default value instead ...
|
||||
WARNING: variable NFITSTEP= is missing. I will use a default value instead ...
|
||||
WARNING: variable QFIT= is missing. I will use a default value instead ...
|
||||
WARNING: variable PPFITON= is missing. I will use a default value instead ...
|
||||
WARNING: variable ALLFITON= is missing. I will use a default value instead ...
|
||||
WARNING: variable PPSTEP= is missing. I will use a default value instead ...
|
||||
WARNING: variable BISTEP= is missing. I will use a default value instead ...
|
||||
WARNING: variable PP2FIT= is missing. I will use a default value instead ...
|
||||
WARNING: variable BINT2FIT= is missing. I will use a default value instead ...
|
||||
WARNING: variable PPNMOL= is missing. I will use a default value instead ...
|
||||
WARNING: variable PPNGEOM= is missing. I will use a default value instead ...
|
||||
WARNING: variable PARREP= is missing. I will use a default value instead ...
|
||||
WARNING: variable VERBOSE= is missing. I will use a default value instead ...
|
||||
WARNING: variable MIXER= is missing. I will use a default value instead ...
|
||||
WARNING: variable RESTARTLIB= is missing. I will use a default value instead ...
|
||||
WARNING: variable CGTOL= is missing. I will use a default value instead ...
|
||||
WARNING: variable ELEC_ETOL= is missing. I will use a default value instead ...
|
||||
WARNING: variable COULACC= is missing. I will use a default value instead ...
|
||||
WARNING: variable COULCUT= is missing. I will use a default value instead ...
|
||||
WARNING: variable COULR1= is missing. I will use a default value instead ...
|
||||
WARNING: variable CHTOL= is missing. I will use a default value instead ...
|
||||
WARNING: variable BETA= is missing. I will use a default value instead ...
|
||||
WARNING: variable MCSIGMA= is missing. I will use a default value instead ...
|
||||
WARNING: variable PPBETA= is missing. I will use a default value instead ...
|
||||
WARNING: variable PPSIGMA= is missing. I will use a default value instead ...
|
||||
WARNING: variable ER= is missing. I will use a default value instead ...
|
||||
WARNING: variable INITIALIZED= is missing. I will use a default value instead ...
|
||||
|
||||
|
||||
############### Parameters used for this run ################
|
||||
CONTROL{
|
||||
xControl= 1
|
||||
DEBUGON= 0
|
||||
FERMIM= 6
|
||||
CGORLIB= 1
|
||||
NORECS= 1
|
||||
ENTROPYKIND= 1
|
||||
PPOTON= 1
|
||||
VDWON= 0
|
||||
SPINON= 0
|
||||
ELECTRO= 1
|
||||
ELECMETH= 0
|
||||
MAXSCF= 450
|
||||
MINSP2ITER= 22
|
||||
FULLQCONV= 1
|
||||
QITER= 3
|
||||
ORDERNMOL= 0
|
||||
SPARSEON= 1
|
||||
THRESHOLDON= 1
|
||||
FILLINSTOP= 100
|
||||
BLKSZ= 4
|
||||
MSPARSE= 1500
|
||||
LCNON= 0
|
||||
LCNITER= 4
|
||||
RELAX= 0
|
||||
MAXITER= 100000
|
||||
MDON= 1
|
||||
PBCON= 1
|
||||
RESTART= 0
|
||||
CHARGE= 0
|
||||
XBO= 1
|
||||
XBODISON= 1
|
||||
XBODISORDER= 5
|
||||
NGPU= 2
|
||||
KON= 0
|
||||
COMPFORCE= 1
|
||||
DOSFIT= 0
|
||||
INTS2FIT= 1
|
||||
NFITSTEP= 5000
|
||||
QFIT= 0
|
||||
PPFITON= 0
|
||||
ALLFITON= 0
|
||||
PPSTEP= 500
|
||||
BISTEP= 500
|
||||
PP2FIT= 2
|
||||
BINT2FIT= 6
|
||||
PPNMOL= 10
|
||||
PPNGEOM= 200
|
||||
PARREP= 0
|
||||
VERBOSE= 0
|
||||
MIXER= 0
|
||||
RESTARTLIB= 0
|
||||
CGTOL= 9.9999999747524271E-007
|
||||
KBT= 0.0000000000000000
|
||||
SPINTOL= 1.0000000000000000E-004
|
||||
ELEC_ETOL= 1.0000000474974513E-003
|
||||
ELEC_QTOL= 1.0000000000000000E-008
|
||||
COULACC= 9.9999999747524271E-007
|
||||
COULCUT= -500.00000000000000
|
||||
COULR1= 500.00000000000000
|
||||
BREAKTOL= 9.9999999999999995E-007
|
||||
QMIX= 0.25000000000000000
|
||||
SPINMIX= 0.25000000000000000
|
||||
MDMIX= 0.25000000000000000
|
||||
NUMTHRESH= 9.9999999999999995E-007
|
||||
CHTOL= 9.9999997764825821E-003
|
||||
SKIN= 1.0000000000000000
|
||||
RLXFTOL= 9.9999999999999995E-008
|
||||
BETA= 1000.0000000000000
|
||||
MCSIGMA= 0.20000000298023224
|
||||
PPBETA= 1000.0000000000000
|
||||
PPSIGMA= 9.9999997764825821E-003
|
||||
ER= 1.0000000000000000
|
||||
JobName=MyJob
|
||||
BASISTYPE=NONORTHO
|
||||
SP2CONV=REL
|
||||
RELAXTYPE=SD
|
||||
PARAMPATH=./TBparam
|
||||
COORDSFILE=./coords.dat
|
||||
INITIALIZED= F
|
||||
}
|
||||
|
||||
./TBparam/electrons.dat
|
||||
MDCONTROL{ }
|
||||
|
||||
WARNING: variable RNDIST= is missing. I will use a default value instead ...
|
||||
WARNING: variable SEEDINIT= is missing. I will use a default value instead ...
|
||||
WARNING: variable NPTTYPE= is missing. I will use a default value instead ...
|
||||
WARNING: variable UDNEIGH= is missing. I will use a default value instead ...
|
||||
WARNING: variable DUMPFREQ= is missing. I will use a default value instead ...
|
||||
WARNING: variable RSFREQ= is missing. I will use a default value instead ...
|
||||
WARNING: variable WRTFREQ= is missing. I will use a default value instead ...
|
||||
WARNING: variable TOINITTEMP5= is missing. I will use a default value instead ...
|
||||
WARNING: variable THERMPER= is missing. I will use a default value instead ...
|
||||
WARNING: variable THERMRUN= is missing. I will use a default value instead ...
|
||||
WARNING: variable NVTON= is missing. I will use a default value instead ...
|
||||
WARNING: variable NPTON= is missing. I will use a default value instead ...
|
||||
WARNING: variable AVEPER= is missing. I will use a default value instead ...
|
||||
WARNING: variable SEED= is missing. I will use a default value instead ...
|
||||
WARNING: variable SHOCKON= is missing. I will use a default value instead ...
|
||||
WARNING: variable SHOCKSTART= is missing. I will use a default value instead ...
|
||||
WARNING: variable SHOCKDIR= is missing. I will use a default value instead ...
|
||||
WARNING: variable MDADAPT= is missing. I will use a default value instead ...
|
||||
WARNING: variable GETHUG= is missing. I will use a default value instead ...
|
||||
WARNING: variable RSLEVEL= is missing. I will use a default value instead ...
|
||||
WARNING: variable DT= is missing. I will use a default value instead ...
|
||||
WARNING: variable TEMPERATURE= is missing. I will use a default value instead ...
|
||||
WARNING: variable FRICTION= is missing. I will use a default value instead ...
|
||||
WARNING: variable PTARGET= is missing. I will use a default value instead ...
|
||||
WARNING: variable UPARTICLE= is missing. I will use a default value instead ...
|
||||
WARNING: variable USHOCK= is missing. I will use a default value instead ...
|
||||
WARNING: variable C0= is missing. I will use a default value instead ...
|
||||
WARNING: variable E0= is missing. I will use a default value instead ...
|
||||
WARNING: variable V0= is missing. I will use a default value instead ...
|
||||
WARNING: variable P0= is missing. I will use a default value instead ...
|
||||
WARNING: variable DUMMY= is missing. I will use a default value instead ...
|
||||
|
||||
|
||||
############### Parameters used for this run ################
|
||||
MDCONTROL{
|
||||
MAXITER= -1
|
||||
UDNEIGH= 1
|
||||
DUMPFREQ= 250
|
||||
RSFREQ= 500
|
||||
WRTFREQ= 25
|
||||
TOINITTEMP5= 1
|
||||
THERMPER= 500
|
||||
THERMRUN= 50000
|
||||
NVTON= 0
|
||||
NPTON= 0
|
||||
AVEPER= 1000
|
||||
SEED= 54
|
||||
SHOCKON= 0
|
||||
SHOCKSTART= 100000
|
||||
SHOCKDIR= 1
|
||||
MDADAPT= 0
|
||||
GETHUG= 0
|
||||
RSLEVEL= 0
|
||||
DT= 0.25000000000000000
|
||||
TEMPERATURE= 300.00000000000000
|
||||
FRICTION= 1000.0000000000000
|
||||
PTARGET= 0.0000000000000000
|
||||
UPARTICLE= 500.00000000000000
|
||||
USHOCK= -4590.0000000000000
|
||||
C0= 1300.0000000000000
|
||||
E0= -795.72497558593750
|
||||
V0= 896.98486328125000
|
||||
P0= 8.3149001002311707E-002
|
||||
RNDIST=GAUSSIAN
|
||||
SEEDINIT=UNIFORM
|
||||
NPTTYPE=ISO
|
||||
DUMMY= F
|
||||
}
|
||||
|
||||
LIBCALLS 0
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15165627147849 13.850829743067372 0.0000000000000000 3.9653384620309846
|
||||
LIBCALLS 1
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15142147081917 13.850596160685321 0.0000000000000000 3.9653428217526296
|
||||
LIBCALLS 2
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15072431717670 13.849902902335046 0.0000000000000000 3.9653556077235628
|
||||
LIBCALLS 3
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14958682134301 13.848772166382796 0.0000000000000000 3.9653762812719782
|
||||
LIBCALLS 4
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14804481054080 13.847240065975685 0.0000000000000000 3.9654039257311324
|
||||
LIBCALLS 5
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14614669298459 13.845355347298943 0.0000000000000000 3.9654372593625880
|
||||
LIBCALLS 6
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14395200541782 13.843177681164811 0.0000000000000000 3.9654747563744728
|
||||
LIBCALLS 7
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14152950027858 13.840775605612510 0.0000000000000000 3.9655146828204026
|
||||
LIBCALLS 8
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13895477239572 13.838224210058369 0.0000000000000000 3.9655551214573213
|
||||
LIBCALLS 9
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13630808318862 13.835602658269416 0.0000000000000000 3.9655940696401335
|
||||
LIBCALLS 10
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13367156672246 13.832991646694552 0.0000000000000000 3.9656294961085377
|
||||
LIBCALLS 11
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13112695791978 13.830470890853416 0.0000000000000000 3.9656594331001127
|
||||
LIBCALLS 12
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12875304084571 13.828116721514562 0.0000000000000000 3.9656820468287637
|
||||
LIBCALLS 13
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12662314462005 13.825999860613845 0.0000000000000000 3.9656956633599689
|
||||
LIBCALLS 14
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12480303363179 13.824183432931337 0.0000000000000000 3.9656988576578489
|
||||
LIBCALLS 15
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12334906554690 13.822721254684298 0.0000000000000000 3.9656905013961525
|
||||
LIBCALLS 16
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12230649281338 13.821656427050725 0.0000000000000000 3.9656697961568699
|
||||
LIBCALLS 17
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12170820445976 13.821020251989051 0.0000000000000000 3.9656362957330207
|
||||
LIBCALLS 18
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12157378544725 13.820831478957400 0.0000000000000000 3.9655899465557289
|
||||
LIBCALLS 19
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12190902409918 13.821095885466233 0.0000000000000000 3.9655310732858191
|
||||
LIBCALLS 20
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12270578464654 13.821806190548854 0.0000000000000000 3.9654603894825375
|
||||
LIBCALLS 21
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12394226924755 13.822942298269552 0.0000000000000000 3.9653789701528157
|
||||
LIBCALLS 22
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12558369933174 13.824471866833779 0.0000000000000000 3.9652882392864672
|
||||
LIBCALLS 23
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12758334335854 13.826351196916939 0.0000000000000000 3.9651899208403507
|
||||
LIBCALLS 24
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12988392857540 13.828526429544008 0.0000000000000000 3.9650859962581815
|
||||
LIBCALLS 25
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13241933900565 13.830935038404082 0.0000000000000000 3.9649786471076300
|
||||
LIBCALLS 26
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13511663668885 13.833507593821677 0.0000000000000000 3.9648702062183578
|
||||
LIBCALLS 27
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13789821166085 13.836169765592846 0.0000000000000000 3.9647630647732250
|
||||
LIBCALLS 28
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14068416314257 13.838844520440762 0.0000000000000000 3.9646596094056243
|
||||
LIBCALLS 29
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14339478125902 13.841454456993119 0.0000000000000000 3.9645621614306648
|
||||
LIBCALLS 30
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14595299166797 13.843924209084781 0.0000000000000000 3.9644728862209537
|
||||
LIBCALLS 31
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14828672908391 13.846182838096166 0.0000000000000000 3.9643937231592781
|
||||
LIBCALLS 32
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15033121417270 13.848166127650318 0.0000000000000000 3.9643263326484774
|
||||
LIBCALLS 33
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15203097820654 13.849818691045462 0.0000000000000000 3.9642720350529470
|
||||
LIBCALLS 34
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15334158494318 13.851095804201121 0.0000000000000000 3.9642317563508436
|
||||
LIBCALLS 35
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15423101277941 13.851964884709183 0.0000000000000000 3.9642060118064197
|
||||
LIBCALLS 36
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15468060067406 13.852406550643760 0.0000000000000000 3.9641948735126151
|
||||
LIBCALLS 37
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15468556770435 13.852415210893483 0.0000000000000000 3.9641979705462513
|
||||
LIBCALLS 38
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15425506702360 13.851999160128511 0.0000000000000000 3.9642145018322728
|
||||
LIBCALLS 39
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15341177086162 13.851180175004831 0.0000000000000000 3.9642432622019754
|
||||
LIBCALLS 40
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15219100341108 13.849992631968849 0.0000000000000000 3.9642826797086155
|
||||
LIBCALLS 41
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15063948253476 13.848482189284203 0.0000000000000000 3.9643308764467280
|
||||
LIBCALLS 42
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14881366363778 13.846704095034502 0.0000000000000000 3.9643857194231229
|
||||
LIBCALLS 43
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14677783841711 13.844721197666447 0.0000000000000000 3.9644449063996254
|
||||
LIBCALLS 44
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14460195130079 13.842601745208173 0.0000000000000000 3.9645060327113080
|
||||
LIBCALLS 45
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14235930197236 13.840417063344470 0.0000000000000000 3.9645666751650537
|
||||
LIBCALLS 46
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14012416839108 13.838239201362184 0.0000000000000000 3.9646244709241216
|
||||
LIBCALLS 47
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13796944534135 13.836138629087953 0.0000000000000000 3.9646771958199687
|
||||
LIBCALLS 48
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13596436459642 13.834182058508610 0.0000000000000000 3.9647228360374207
|
||||
LIBCALLS 49
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13417236277201 13.832430452024822 0.0000000000000000 3.9647596471475066
|
||||
LIBCALLS 50
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13264918465853 13.830937266579358 0.0000000000000000 3.9647862263274365
|
||||
LIBCALLS 51
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13144121811348 13.829746970164395 0.0000000000000000 3.9648015300858930
|
||||
LIBCALLS 52
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13058418584075 13.828893856279002 0.0000000000000000 3.9648049379175174
|
||||
LIBCALLS 53
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13010212355317 13.828401171909800 0.0000000000000000 3.9647962482159476
|
||||
LIBCALLS 54
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13000675986638 13.828280567696357 0.0000000000000000 3.9647757005033171
|
||||
LIBCALLS 55
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13029725443062 13.828531873218640 0.0000000000000000 3.9647439679967813
|
||||
LIBCALLS 56
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13096031859556 13.829143196581525 0.0000000000000000 3.9647021412055241
|
||||
LIBCALLS 57
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13197071275096 13.830091344339912 0.0000000000000000 3.9646517009757813
|
||||
LIBCALLS 58
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13329208290526 13.831342554670950 0.0000000000000000 3.9645944691057076
|
||||
LIBCALLS 59
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13487817952188 13.832853532802908 0.0000000000000000 3.9645325717081379
|
||||
LIBCALLS 60
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13667431785007 13.834572772174083 0.0000000000000000 3.9644683636269380
|
||||
LIBCALLS 61
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13861917436014 13.836442137716100 0.0000000000000000 3.9644043716683206
|
||||
LIBCALLS 62
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14064674344610 13.838398678492441 0.0000000000000000 3.9643432117931376
|
||||
LIBCALLS 63
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14268847880851 13.840376626541268 0.0000000000000000 3.9642875107994442
|
||||
LIBCALLS 64
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14467552446979 13.842309527587247 0.0000000000000000 3.9642398279114381
|
||||
LIBCALLS 65
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14654097615647 13.844132438475109 0.0000000000000000 3.9642025589783412
|
||||
LIBCALLS 66
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14822207995957 13.845784117078871 0.0000000000000000 3.9641778771678413
|
||||
LIBCALLS 67
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14966231911774 13.847209123749478 0.0000000000000000 3.9641676470155103
|
||||
LIBCALLS 68
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15081329445576 13.848359751049152 0.0000000000000000 3.9641733618391299
|
||||
LIBCALLS 69
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15163634076458 13.849197700537186 0.0000000000000000 3.9641960937768981
|
||||
LIBCALLS 70
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15210380659516 13.849695432596437 0.0000000000000000 3.9642364336978391
|
||||
LIBCALLS 71
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15219997215792 13.849837127658775 0.0000000000000000 3.9642944914660605
|
||||
LIBCALLS 72
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15192153900722 13.849619213627008 0.0000000000000000 3.9643698667021590
|
||||
LIBCALLS 73
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15127769530471 13.849050434626310 0.0000000000000000 3.9644616585289247
|
||||
LIBCALLS 74
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15028974592457 13.848151458176057 0.0000000000000000 3.9645684873567908
|
||||
LIBCALLS 75
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14899032381624 13.846954040343237 0.0000000000000000 3.9646885325372980
|
||||
LIBCALLS 76
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14742221364327 13.845499789571511 0.0000000000000000 3.9648195821504211
|
||||
LIBCALLS 77
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14563684020112 13.843838588134755 0.0000000000000000 3.9649591055666282
|
||||
LIBCALLS 78
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14369246883172 13.842026744273829 0.0000000000000000 3.9651043223068876
|
||||
LIBCALLS 79
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14165219754119 13.840124957235691 0.0000000000000000 3.9652522794782556
|
||||
LIBCALLS 80
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13958181195608 13.838196181062383 0.0000000000000000 3.9653999492835532
|
||||
LIBCALLS 81
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13754757713065 13.836303471774007 0.0000000000000000 3.9655443071963385
|
||||
LIBCALLS 82
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13561405478509 13.834507896249461 0.0000000000000000 3.9656824354232736
|
||||
LIBCALLS 83
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13384198639028 13.832866571528193 0.0000000000000000 3.9658115908515681
|
||||
LIBCALLS 84
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13228634940748 13.831430891696755 0.0000000000000000 3.9659292903699495
|
||||
LIBCALLS 85
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13099461122306 13.830244986101496 0.0000000000000000 3.9660333724384569
|
||||
LIBCALLS 86
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13000526350720 13.829344440260281 0.0000000000000000 3.9661220782532145
|
||||
LIBCALLS 87
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12934661713206 13.828755299191645 0.0000000000000000 3.9661940662588862
|
||||
LIBCALLS 88
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12903595764971 13.828493364127572 0.0000000000000000 3.9662484623936765
|
||||
LIBCALLS 89
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12907904533250 13.828563786156602 0.0000000000000000 3.9662848954537067
|
||||
LIBCALLS 90
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12946994320248 13.828960955791626 0.0000000000000000 3.9663034756730777
|
||||
LIBCALLS 91
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13019123489619 13.829668684955367 0.0000000000000000 3.9663048073711558
|
||||
LIBCALLS 92
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13121457766835 13.830660675785223 0.0000000000000000 3.9662899643566578
|
||||
LIBCALLS 93
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13250159637499 13.831901269302985 0.0000000000000000 3.9662604605307470
|
||||
LIBCALLS 94
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13400508153813 13.833346464674193 0.0000000000000000 3.9662181906403653
|
||||
LIBCALLS 95
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13567049003717 13.834945196074795 0.0000000000000000 3.9661653991148187
|
||||
LIBCALLS 96
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13743766487022 13.836640848231452 0.0000000000000000 3.9661045863001441
|
||||
LIBCALLS 97
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13924277096038 13.838372983906890 0.0000000000000000 3.9660384593805307
|
||||
LIBCALLS 98
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14102036682124 13.840079246589914 0.0000000000000000 3.9659698320311318
|
||||
LIBCALLS 99
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14270555407057 13.841697390518378 0.0000000000000000 3.9659015537535014
|
||||
LIBCALLS 100
|
||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14423615166146 13.843167378892108 0.0000000000000000 3.9658364191978137
|
||||
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Reference in New Issue
Block a user