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# Conflicts:
#	doc/src/Build_development.rst
This commit is contained in:
Axel Kohlmeyer
2020-03-18 20:59:16 -04:00
parent a569027a14 164bf1b60e
commit 2714fad178
449 changed files with 86628 additions and 730 deletions
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2
cmake/Modules/Packages/USER-NETCDF.cmake
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@ -1,6 +1,6 @@
if(PKG_USER-NETCDF)
# USER-NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.
# NetCDF library enables dump sytle "netcdf", while PNetCDF enables dump style "netcdf/mpiio"
# NetCDF library enables dump style "netcdf", while PNetCDF enables dump style "netcdf/mpiio"
find_package(NetCDF)
if(NETCDF_FOUND)
find_package(PNetCDF)

4
cmake/README.md
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@ -217,7 +217,7 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
</tr>
<tr>
<td><code>CMAKE_VERBOSE_MAKEFILE</code></td>
<td>Enable verbose output from Makefile builds (useful for debugging), the same can be achived by adding `VERBOSE=1` to the `make` call.</td>
<td>Enable verbose output from Makefile builds (useful for debugging), the same can be achieved by adding `VERBOSE=1` to the `make` call.</td>
<td>
<dl>
<dt><code>off</code> (default)</dt>
@ -576,7 +576,7 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
Several fixes and a pair style that have Monte Carlo (MC) or MC-like
attributes. These include fixes for creating, breaking, and swapping bonds,
for performing atomic swaps, and performing grand-canonical MC (GCMC) in
conjuction with dynamics.
conjunction with dynamics.
</td>
<td>
<dl>

2
doc/msi2lmp.1
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@ -31,7 +31,7 @@ of benzene, you have to provide the files 'benzene.car' and 'benzene.mdf'
in the current working directory.
.B msi2lmp
will then read and process those files according to its remaining settings.
All other settins are optional and have defaults as listed.
All other settings are optional and have defaults as listed.
.TP
\fB\-c <I,1,II,2,O,0>\fR, \fB\-class <I,1,II,2,O,0>\fR
The \-c or \-class option selects the force field class, i.e which pair

2
doc/src/2001/README.html
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@ -10,7 +10,7 @@ LAMMPS</H2>
LAMMPS = Large-scale Atomic/Molecular Massively Parallel Simulator</P>
<P>
This is the documentation for the LAMMPS 2001 version, written in F90,
which has been superceded by more current versions. See the <A
which has been superseded by more current versions. See the <A
HREF="http://www.cs.sandia.gov/~sjplimp/lammps.html">LAMMPS WWW
Site</A> for more information.
<P>

2
doc/src/2001/basics.html
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@ -47,7 +47,7 @@ directories: </P>
<P>
The src directory contains the F90 and C source files for LAMMPS as
well as several sample Makefiles for different machines. To make LAMMPS
for a specfic machine, you simply type</P>
for a specific machine, you simply type</P>
<P>
make machine</P>
<P>

6
doc/src/2001/input_commands.html
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@ -1079,7 +1079,7 @@ for style aveforce, average force on the group of fixed atoms is computed,
to new total value -> has effect of applying same force to entire group
of atoms
thermostatting constraints (rescale, hoover/drag, langevin) cannot be used in
conjuction with global &quot;temp control&quot;, since they conflict and will
conjunction with global &quot;temp control&quot;, since they conflict and will
cause atom velocities to be reset twice
thermostatting constraints (rescale, hoover/drag, langevin) cannot be used
when performing a minimization
@ -1089,7 +1089,7 @@ meaning of rescale and Langevin thermostatting coefficients is same as in
&quot;temp control&quot; command
for rescale style, it can be used as a coarse temperature rescaler,
for example &quot;rescale 200.0 300.0 100 10.0 1.0&quot; will ramp the temperature
up during the simulation, resetting it to the target temperatue as needed
up during the simulation, resetting it to the target temperature as needed
for rescale style, it can be used to create an instantaneous
drag force that slowly rescales the temperature without oscillation,
for example &quot;rescale 300.0 300.0 1 0.0 0.0001&quot; will force (or keep)
@ -1952,7 +1952,7 @@ for rescale style, the amount of rescaling is contfolled by the fractional
to halfway between the current and target temperature
for rescale style, it can be used as a coarse temperature rescaler,
for example "rescale 200.0 300.0 100 10.0 1.0" will ramp the temperature
up during the simulation, resetting it to the target temperatue as needed
up during the simulation, resetting it to the target temperature as needed
for rescale style, it can be used to create an instantaneous
drag force that slowly rescales the temperature without oscillation,
for example "rescale 300.0 300.0 1 0.0 0.0001" will force (or keep)

2
doc/src/99/README.html
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@ -10,7 +10,7 @@ LAMMPS</H2>
LAMMPS = Large-scale Atomic/Molecular Massively Parallel Simulator</P>
<P>
This is the documentation for the LAMMPS 99 version, written in F77,
which has been superceded by more current versions. See the <A
which has been superseded by more current versions. See the <A
HREF="http://www.cs.sandia.gov/~sjplimp/lammps.html">LAMMPS WWW
Site</A> for more information.
<P>

2
doc/src/99/basics.html
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@ -45,7 +45,7 @@ directories: </P>
<P>
The src directory contains the F77 and C source files for LAMMPS as
well as several sample Makefiles for different machines. To make LAMMPS
for a specfic machine, you simply type</P>
for a specific machine, you simply type</P>
<P>
make machine</P>
<P>

4
doc/src/99/input_commands.html
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@ -430,7 +430,7 @@ accuracy criterion effectively determines how many k-space vectors are used
for PPPM, accuracy criterion determines mesh spacing (see &quot;particle mesh&quot;
command)
for PPPM, must be running on power-of-2 number of processors for FFTs
must use periodic boundary conditions in conjuction with Ewald and PPPM
must use periodic boundary conditions in conjunction with Ewald and PPPM
cannot use any styles other than none with nonbond style = lj/shift or
nonbond style = soft
Coulomb style = smooth should be used with nonbond style = lj/switch,
@ -772,7 +772,7 @@ for style aveforce, average force on the group of fixed atoms is computed,
to new total value -&gt; has effect of applying same force to entire group
of atoms
thermostatting constraints (rescale, langevin, nose/hoover) cannot be used in
conjuction with global &quot;temp control&quot;, since they conflict and will
conjunction with global &quot;temp control&quot;, since they conflict and will
cause atom velocities to be reset twice
if multiple Langevin constraints are specified the Marsaglia RNG will
only use the last RNG seed specified for initialization

2
doc/src/Build_development.rst
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@ -49,7 +49,7 @@ setting the ``CMAKE_TUNE_FLAGS`` variable during configuration. Examples:
.. code-block:: bash
-D CMAKE_TUNE_FLAGS=-fsanitize=address # enable address sanitizer / memory leak checker
-D CMAKE_TUNE_FLAGS=-fsanitize=undefined # enable undefined behaviour sanitizer
-D CMAKE_TUNE_FLAGS=-fsanitize=undefined # enable undefined behavior sanitizer
-D CMAKE_TUNE_FLAGS=-fsanitize=thread # enable thread sanitizer
.. _valgrind: https://valgrind.org

2
doc/src/Commands_pair.rst
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@ -77,6 +77,8 @@ OPT.
* :doc:`coul/long/cs (g) <pair_cs>`
* :doc:`coul/long/soft (o) <pair_fep_soft>`
* :doc:`coul/msm (o) <pair_coul>`
* :doc:`coul/slater/cut <pair_coul_slater>`
* :doc:`coul/slater/long <pair_coul_slater>`
* :doc:`coul/shield <pair_coul_shield>`
* :doc:`coul/streitz <pair_coul>`
* :doc:`coul/wolf (ko) <pair_coul>`

11
doc/src/Errors_messages.rst
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@ -4724,6 +4724,12 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Invalid Masses section in molecule file*
Self-explanatory.
*Invalid molecule ID in molecule file*
Molecule ID must be a non-zero positive integer.
*Invalid Molecules section in molecule file*
Self-explanatory.
*Invalid REAX atom type*
There is a mis-match between LAMMPS atom types and the elements
listed in the ReaxFF force field file.
@ -4790,6 +4796,9 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
Atom IDs must be positive integers and within range of defined
atoms.
*Invalid atom ID in Fragments section of molecule file*
Self-explanatory.
*Invalid atom ID in Impropers section of data file*
Atom IDs must be positive integers and within range of defined
atoms.
@ -7666,7 +7675,7 @@ keyword to allow for additional bonds to be formed
Keywords that refer to time (such as cpu, elapsed) do not
make sense in between runs.
*Threshhold for an atom property that isn't allocated*
*Threshold for an atom property that isn't allocated*
A dump threshold has been requested on a quantity that is
not defined by the atom style used in this simulation.

2
doc/src/USER/atc/man_boundary.html
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@ -32,7 +32,7 @@ examples</a></h4>
<p><code> fix_modify AtC boundary type ghost_atoms </code> </p>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Command to define the atoms that represent the ficticious boundary internal to the FE mesh. For fully overlapped MD/FE domains with periodic boundary conditions no boundary atoms should be defined. </p>
<p>Command to define the atoms that represent the fictitious boundary internal to the FE mesh. For fully overlapped MD/FE domains with periodic boundary conditions no boundary atoms should be defined. </p>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<h4><a class="anchor" id="default">

2
doc/src/USER/atc/man_hardy_gradients.html
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@ -38,7 +38,7 @@ examples</a></h4>
</p>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Requests calculation and ouput of gradients of the fields from the transfer class. These gradients will be with regard to spatial or material coordinate for eulerian or lagrangian analysis, respectively, as specified by atom_element_map (see <a class="el" href="man_atom_element_map.html">fix_modify AtC atom_element_map</a> ) </p>
<p>Requests calculation and output of gradients of the fields from the transfer class. These gradients will be with regard to spatial or material coordinate for eulerian or lagrangian analysis, respectively, as specified by atom_element_map (see <a class="el" href="man_atom_element_map.html">fix_modify AtC atom_element_map</a> ) </p>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>

2
doc/src/USER/atc/man_hardy_rates.html
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@ -38,7 +38,7 @@ examples</a></h4>
</p>
<h4><a class="anchor" id="description">
description</a></h4>
<p>Requests calculation and ouput of rates (time derivatives) of the fields from the transfer class. For eulerian analysis (see <a class="el" href="man_atom_element_map.html">fix_modify AtC atom_element_map</a> ), these rates are the partial time derivatives of the nodal fields, not the full (material) time derivatives. <br/>
<p>Requests calculation and output of rates (time derivatives) of the fields from the transfer class. For eulerian analysis (see <a class="el" href="man_atom_element_map.html">fix_modify AtC atom_element_map</a> ), these rates are the partial time derivatives of the nodal fields, not the full (material) time derivatives. <br/>
</p>
<h4><a class="anchor" id="restrictions">
restrictions</a></h4>

24
doc/src/molecule.rst
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@ -60,6 +60,7 @@ templates include:
* :doc:`fix rigid/small <fix_rigid>`
* :doc:`fix shake <fix_shake>`
* :doc:`fix gcmc <fix_gcmc>`
* :doc:`fix bond/react <fix_bond_react>`
* :doc:`create_atoms <create_atoms>`
* :doc:`atom_style template <atom_style>`
@ -144,6 +145,7 @@ appear if the value(s) are different than the default.
* Na *angles* = # of angles Na in molecule, default = 0
* Nd *dihedrals* = # of dihedrals Nd in molecule, default = 0
* Ni *impropers* = # of impropers Ni in molecule, default = 0
* Nf *fragments* = # of fragments in molecule, default = 0
* Mtotal *mass* = total mass of molecule
* Xc Yc Zc *com* = coordinates of center-of-mass of molecule
* Ixx Iyy Izz Ixy Ixz Iyz *inertia* = 6 components of inertia tensor of molecule
@ -166,7 +168,7 @@ internally.
These are the allowed section keywords for the body of the file.
* *Coords, Types, Charges, Diameters, Masses* = atom-property sections
* *Coords, Types, Molecules, Fragments, Charges, Diameters, Masses* = atom-property sections
* *Bonds, Angles, Dihedrals, Impropers* = molecular topology sections
* *Special Bond Counts, Special Bonds* = special neighbor info
* *Shake Flags, Shake Atoms, Shake Bond Types* = SHAKE info
@ -223,6 +225,26 @@ listed in order from 1 to Nlines, but LAMMPS does not check for this.
----------
*Molecules* section:
* one line per atom
* line syntax: ID molecule-ID
* molecule-ID = molecule ID of atom
----------
*Fragments* section:
* one line per fragment
* line syntax: ID a b c d ...
* a,b,c,d,... = IDs of atoms in fragment
The ID of a fragment can only contain alphanumeric characters and
underscores. The atom IDs should be values from 1 to Natoms, where
Natoms = # of atoms in the molecule.
----------
*Charges* section:
* one line per atom

121
doc/src/pair_coul_slater.rst Normal file
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@ -0,0 +1,121 @@
.. index:: pair_style coul/slater
pair_style coul/slater/cut command
==================================
pair_style coul/slater/long command
===================================
Syntax
""""""
.. code-block:: LAMMPS
pair_style coul/slater/cut lamda cutoff
pair_style coul/slater/long lamda cutoff
lamda = decay length of the charge (distance units)
cutoff = cutoff (distance units)
Examples
""""""""
.. code-block:: LAMMPS
pair_style coul/slater/cut 1.0 3.5
pair_coeff * *
pair_coeff 2 2 2.5
pair_style coul/slater/long 1.0 12.0
pair_coeff * *
pair_coeff 1 1 5.0
Description
"""""""""""
Styles *coul/slater* compute electrostatic interactions in mesoscopic models
which employ potentials without explicit excluded-volume interactions.
The goal is to prevent artificial ionic pair formation by including a charge
distribution in the Coulomb potential, following the formulation of
:ref:`(Melchor) <Melchor>`:
.. math::
E = \frac{Cq_iq_j}{\epsilon r} \left( 1- \left( 1 + \frac{r_{ij}}{\lambda} exp\left( -2r_{ij}/\lambda \right) \right) \right) \qquad r < r_c
where :math:`r_c` is the cutoff distance and :math:`\lambda` is the decay length of the charge.
C is the same Coulomb conversion factor as in the pair\_styles coul/cut and coul/long. In this way the Coulomb
interaction between ions is corrected at small distances r.
For the *coul/slater/cut* style, the potential energy for distances larger than the cutoff is zero,
while for the *coul/slater/long*, the long-range interactions are computed either by the Ewald or the PPPM technique.
Phenomena that can be captured at a mesoscopic level using this type of electrostatic
interactions include the formation of polyelectrolyte-surfactant aggregates,
charge stabilization of colloidal suspensions, and the formation of
complexes driven by charged species in biological systems. :ref:`(Vaiwala) <Vaiwala>`.
The cutoff distance is optional. If it is not used,
the default global value specified in the pair_style command is used.
For each pair of atom types, a specific cutoff distance can be defined via the :doc:`pair_coeff <pair_coeff>` command as in the example
above, or in the data file or restart files read by the
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands:
* :math:`r_c` (distance units)
The global decay length of the charge (:math:`\lambda`) specified in the pair\_style command is used for all pairs.
----------
**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
For atom type pairs I,J and I != J, the cutoff distance for the
*coul/slater* styles can be mixed. The default mix value is *geometric*\ .
See the "pair\_modify" command for details.
The :doc:`pair_modify <pair_modify>` shift and table options are not relevant
for these pair styles.
These pair styles do not support the :doc:`pair_modify <pair_modify>`
tail option for adding long-range tail corrections to energy and
pressure.
These pair styles write their information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. It does not support the
*inner*\ , *middle*\ , *outer* keywords.
Restrictions
""""""""""""
The *coul/slater/long* style requires the long-range solvers included in the KSPACE package.
These styles are part of the "USER-MISC" package. They are only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`, :doc:`pair_style, hybrid/overlay <pair_hybrid>`, :doc:`kspace_style <kspace_style>`
**Default:** none
----------
.. _Melchor:
**(Melchor)** Gonzalez-Melchor, Mayoral, Velázquez, and Alejandre, J Chem Phys, 125, 224107 (2006).
.. _Vaiwala:
**(Vaiwala)** Vaiwala, Jadhav, and Thaokar, J Chem Phys, 146, 124904 (2017).

9
doc/utils/sphinx-config/false_positives.txt
View File

@ -1027,6 +1027,7 @@ Gmask
gneb
GNEB
Goldfarb
Gonzalez-Melchor
googlemail
Gordan
GPa
@ -1290,6 +1291,7 @@ Izvekov
izz
Izz
Jacobsen
Jadhav
jagreat
Jalalvand
james
@ -1663,6 +1665,7 @@ maxwell
Maxwellian
maxX
Mayergoyz
Mayoral
mbt
Mbytes
MBytes
@ -1691,6 +1694,7 @@ mediumvioletred
Mees
Mehl
Mei
Melchor
Meloni
Melrose
Mem
@ -2260,6 +2264,7 @@ polyA
polybond
polydisperse
polydispersity
polyelectrolyte
polyhedra
popen
Popov
@ -2768,6 +2773,7 @@ superset
supersphere
Supinski
Surblys
surfactant
surfactants
Suter
Sutmann
@ -2830,6 +2836,7 @@ tfmc
tfMC
th
Thakkar
Thaokar
thb
thei
Theodorou
@ -3024,6 +3031,7 @@ uwo
Uzdin
vacf
Vaid
Vaiwala
valent
Valeriu
valgrind
@ -3052,6 +3060,7 @@ Vectorization
vectorized
Vegt
vel
Velázquez
Verlag
verlet
Verlet

2
examples/COUPLE/lammps_nwchem/planewave/nwchem_lammps.out
View File

@ -1845,7 +1845,7 @@ Translation force removed: ( -0.00000 -0.00000 -0.00000)
Outputing formatted_stress_filename: ./W.vpp2
Outputting formatted_stress_filename: ./W.vpp2
======================

2
examples/COUPLE/lammps_quest/lmpqst.cpp
View File

@ -84,7 +84,7 @@ int main(int narg, char **arg)
lmp->input->file(lammps_input);
// make info avaiable to callback function
// make info available to callback function
Info info;
info.me = me;

4
examples/UNITS/README
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@ -27,7 +27,7 @@ The real and metal scripts each have a set of variables at the top
which define scale factors for converting quantities like distance,
energy, pressure from reduced LJ units to real or metal units. Once
these are defined the rest of the input script is very similar to the
LJ script. The approprate scale factor is applied to every input.
LJ script. The appropriate scale factor is applied to every input.
Output quantities are printed in both the native real/metal units and
unscaled back to LJ units. So that you can see the outputs are the
same if you examine the log files. Comments about this comparison
@ -49,6 +49,6 @@ identical input script in an alternate set of units. Where
"identical" means it runs the same simulation in a statistical sense.
You can find the full set of scale factors LAMMPS uses internally for
different unit systems it supports, at the top of the src/udpate.cpp
different unit systems it supports, at the top of the src/update.cpp
file. A couple of those values are used in the real and metal
scripts.

4
examples/USER/atc/README
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@ -68,7 +68,7 @@ elastic:
in.cnt_electrostatic2 - Mechanical response of CNT with self-consistent charge density and electric field
in.cnt_fixed_charge - Mechancial response of CNT with fixed atomic charges in an electric field
in.eam_energy - Quasi-static/quasi-1D coupling and transfer extraction of energy density for EAM gold
in.electron_density - Mechanical response of differnt CNT models with a self-consistent electron density and electric field
in.electron_density - Mechanical response of different CNT models with a self-consistent electron density and electric field
in.electrostatic_bending_dos - Quasi-static bending of a CNT using a quantum density of states model for electron density
in.no_atoms - FE solution of a box subject to an initial displacement condition
in.no_atoms_cb - FE solution of a box subject to an initial displacement condition with a Cauchy-Born material model
@ -149,7 +149,7 @@ elastic:
in.cnt_electrostatic2 - Mechanical response of CNT with self-consistent charge density and electric field
in.cnt_fixed_charge - Mechancial response of CNT with fixed atomic charges in an electric field
in.eam_energy - Quasi-static/quasi-1D coupling and transfer extraction of energy density for EAM gold
in.electron_density - Mechanical response of differnt CNT models with a self-consistent electron density and electric field
in.electron_density - Mechanical response of different CNT models with a self-consistent electron density and electric field
in.electrostatic_bending_dos - Quasi-static bending of a CNT using a quantum density of states model for electron density
in.no_atoms - FE solution of a box subject to an initial displacement condition
in.no_atoms_cb - FE solution of a box subject to an initial displacement condition with a Cauchy-Born material model

2
examples/USER/atc/fluids/in.bar1d_fluids
View File

@ -85,7 +85,7 @@ fix_modify AtC control localized_lambda on
fix_modify AtC filter type exponential
fix_modify AtC filter scale 1000.0
fix_modify AtC filter on
# ouput commands
# output commands
fix_modify AtC output bar1d_fluidsFE 100 text
#undump D1
#dump D2 all atom 200 dump.bar1d

2
examples/USER/atc/fluids/in.conducting_interface
View File

@ -1,6 +1,6 @@
# simulation of negatively charge liquid argon-positively charged solid/frozen argon
# MAKE this conducting_interface then interface (major difference: non-uniform grid)
# START with extrinsic charges on both and then use an instrinsic charge density for frozen
# START with extrinsic charges on both and then use an intrinsic charge density for frozen
echo both
units real
atom_style full

2
examples/USER/atc/fluids/in.dielectric_interface
View File

@ -1,6 +1,6 @@
# simulation of negatively charge liquid argon-positively charged solid/frozen argon
# MAKE this dielectric_interface then interface (major difference: non-uniform grid)
# START with extrinsic charges on both and then use an instrinsic charge density for frozen
# START with extrinsic charges on both and then use an intrinsic charge density for frozen
echo both
units real
atom_style full

2
examples/USER/atc/fluids/in.shear_flow
View File

@ -75,7 +75,7 @@ fix_modify AtC control localized_lambda on
#fix_modify AtC filter scale 1000.0
#fix_modify AtC filter on
# ouput commands
# output commands
fix_modify AtC output shear_flowFE 100 text #binary
#undump D1
#dump D1 all custom 100 shear_flow.dmp id type xs ys zs vx vy vz

2
examples/USER/atc/fluids/in.shear_no_atoms
View File

@ -25,7 +25,7 @@ fix_modify AtC reset_time
fix_modify AtC fix velocity y rbc 0.1
fix_modify AtC fix velocity y lbc 0.
# ouput commands
# output commands
fix_modify AtC output shear_no_atomsFE 200 text binary
# set-up non-equilibrium IC
thermo 100

2
examples/USER/atc/thermal/bar1d.screen
View File

@ -239,7 +239,7 @@ fix_modify AtC output bar1dFE 100 text binary
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
# ouput command
# output command
#dump D1 all atom 1000 dump.bar1d
# run with FE
reset_timestep 0

2
examples/USER/atc/thermal/in.bar1d
View File

@ -71,7 +71,7 @@ thermo 1
run 100
# set up output, should be before a "run"
fix_modify AtC output bar1dFE 100 text binary
# ouput command
# output command
#dump D1 all atom 1000 dump.bar1d
# run with FE
reset_timestep 0

2
examples/USER/atc/thermal/in.bar1d_all_atoms
View File

@ -93,7 +93,7 @@ fix_modify AtC fix_flux temperature lbndy 0.0000000001
fix_modify AtC fix_flux temperature rbndy -0.0000000001
# set up output, should be before a "run"
fix_modify AtC output bar1d_all_atomsFE 200 text binary
# ouput command
# output command
#dump D1 all atom 1000 dump.bar1d
# run with FE
reset_timestep 0

2
examples/USER/atc/thermal/in.bar1d_combined
View File

@ -79,7 +79,7 @@ thermo 100
# set up output, should be before a "run"
fix_modify AtC output bar1d_combinedFE 100 text
# ouput command
# output command
#dump D1 all atom 100 dump.bar1d_combined
# run with FE
reset_timestep 0

2
examples/USER/atc/thermal/in.bar1d_flux
View File

@ -71,7 +71,7 @@ fix_modify AtC fix temperature rbc 20.
run 100
# set up output, should be before a "run"
fix_modify AtC output bar1d_fluxFE 100 text binary
# ouput command
# output command
#dump D1 all atom 1000 dump.bar1d
# run with FE
reset_timestep 0

2
examples/USER/atc/thermal/in.bar1d_frac_step
View File

@ -72,7 +72,7 @@ fix_modify AtC filter scale 1000.0
fix_modify AtC filter on
# set up output, should be before a "run"
fix_modify AtC output bar1d_frac_stepFE 200 text
# ouput command
# output command
#dump D1 all atom 1000 dump.bar1d
# run with FE
reset_timestep 0

2
examples/USER/cgdna/README
View File

@ -46,7 +46,7 @@ moment of inertia set to the value used in the standalone implementation
of oxDNA (M = I = 1). The masses can be set directly in the input and
data file, whereas the moment of inertia is set via the diameter of the
ellipsoid in the data file and has a value of 3.16227766.
The change of mass and moment of inertia allows direct comparision of
The change of mass and moment of inertia allows direct comparison of
trajectory data or time-dependent observables on a per-timestep basis.
As mentioned above, the stacking and hydrogen-bonding interactions

16
examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py
View File

@ -105,7 +105,7 @@ EXCL_RC2 = 0.335388426126
EXCL_RC3 = 0.52329943261
"""
Define auxillary variables for the construction of a helix
Define auxiliary variables for the construction of a helix
"""
# center of the double strand
COM_CENTRE_DS = POS_BASE + 0.2
@ -127,7 +127,7 @@ number_to_base = {1 : 'A', 2 : 'C', 3 : 'G', 4 : 'T'}
base_to_number = {'A' : 1, 'a' : 1, 'C' : 2, 'c' : 2,
'G' : 3, 'g' : 3, 'T' : 4, 't' : 4}
# auxillary arrays
# auxiliary arrays
positions = []
a1s = []
a3s = []
@ -373,7 +373,7 @@ def generate_strand(bp, sequence=None, start_pos=np.array([0, 0, 0]), \
# if not provided switch off random orientation
if perp is None or perp is False:
v1 = np.random.random_sample(3)
# comment in to suppress randomised base vector
# comment in to suppress randomized base vector
v1 = [1,0,0]
v1 -= dir * (np.dot(dir, v1))
v1 /= np.sqrt(sum(v1*v1))
@ -551,7 +551,7 @@ def read_strands(filename):
smallest_n_bases = n_g
if smallest_n_bases < N_BASE_TYPES:
print('## Not enough occurances of base types in the sequence for ' + str(N_BASE_TYPES))
print('## Not enough occurrences of base types in the sequence for ' + str(N_BASE_TYPES))
print('## unique base types, switching to ' + str(smallest_n_bases) + ' unique types')
else:
smallest_n_bases = N_BASE_TYPES
@ -644,12 +644,12 @@ def read_strands(filename):
# generate random position of the first nucleotide
com = box_offset + np.random.random_sample(3) * box
# comment out to randomise
# comment out to randomize
com = [0,0,0]
# generate the random direction of the helix
axis = np.random.random_sample(3)
# comment out to randomise
# comment out to randomize
axis = [0,0,1]
axis /= np.sqrt(np.dot(axis, axis))
@ -702,12 +702,12 @@ def read_strands(filename):
# generate random position of the first nucleotide
com = box_offset + np.random.random_sample(3) * box
# comment out to randomise
# comment out to randomize
com = [-30,0,0]
# generate the random direction of the helix
axis = np.random.random_sample(3)
# comment out to randomise
# comment out to randomize
axis = [0,0,1]
axis /= np.sqrt(np.dot(axis, axis))

4
examples/USER/cgdna/util/generate.py
View File

@ -81,7 +81,7 @@ EXCL_RC2 = 0.335388426126
EXCL_RC3 = 0.52329943261
"""
Define auxillary variables for the construction of a helix
Define auxiliary variables for the construction of a helix
"""
# center of the double strand
CM_CENTER_DS = POS_BASE + 0.2
@ -103,7 +103,7 @@ number_to_base = {1 : 'A', 2 : 'C', 3 : 'G', 4 : 'T'}
base_to_number = {'A' : 1, 'a' : 1, 'C' : 2, 'c' : 2,
'G' : 3, 'g' : 3, 'T' : 4, 't' : 4}
# auxillary arrays
# auxiliary arrays
positions = []
a1s = []
a3s = []

2
examples/USER/diffraction/README
View File

@ -1,4 +1,4 @@
This is a simple example of showing the computation of virutal x-ray
This is a simple example of showing the computation of virtual x-ray
and electron diffraction patterns for Ni.
In addition to the LAMMPS output, a simple visualizaiton of the electron

2
examples/USER/eff/Li-dendritic/README
View File

@ -1,2 +1,2 @@
Shows the formation of lithium dendrites during the minimization of a volume expanded lithium cell with particle positions remaped to fit the cell.
Shows the formation of lithium dendrites during the minimization of a volume expanded lithium cell with particle positions remapped to fit the cell.
This depicts the process of electrode replating in lithium batteries, which leads to failure (short-circuit).

2
examples/USER/lb/fourspheres/in.fourspheres_default_gamma
View File

@ -1,5 +1,5 @@
#===========================================================================#
# Sytem of 2 pairs of rigid particles moving towards one another. #
# System of 2 pairs of rigid particles moving towards one another. #
# At each timestep, the hydrodynamic force acting on one of these four #
# rigid particles is printed to the screen. #
# #

2
examples/USER/lb/fourspheres/in.fourspheres_set_gamma
View File

@ -1,5 +1,5 @@
#===========================================================================#
# Sytem of 2 pairs of rigid particles moving towards one another. #
# System of 2 pairs of rigid particles moving towards one another. #
# At each timestep, the hydrodynamic force acting on one of these four #
# rigid particles is printed to the screen. #
# #

2
examples/USER/manifold/diffusion/plot_msd.gpl
View File

@ -47,7 +47,7 @@ set object 1 rectangle from graph 0,0 to graph 1,1 fillcolor rgb "white" behind
unset key
set grid front
set title 'Short time behaviour' offset 0,-0.8
set title 'Short time behavior' offset 0,-0.8
set ylabel ''
set xrange[0:10]
set yrange[0:40]

2
examples/USER/misc/ees/README
View File

@ -5,7 +5,7 @@ Here one may find simple examples showing how "fix wall/ess" and "fix wall/regio
This input uses "Data_region" to setup a system of three particles colliding with a
cubic region which its walls interact with particle with EES potential. To find out details
of how to set parameters of "fix wall/region/ees" see documentaion.
of how to set parameters of "fix wall/region/ees" see documentation.
--in.fix_wall

2
examples/USER/misc/hma/README
View File

@ -15,7 +15,7 @@ Averages of the potential energy (#3 and #4) agree although #4 (HMA) is more pre
Averages of the pressure (#5 and #6) agree once the ideal gas
contribution is included; #6 (HMA) is more precise.
The heat capacity can be computed from colume #3 (convential) as
The heat capacity can be computed from colume #3 (conventional) as
Cv = Var(#3)/(k T^2)
With HMA, the heat capacity can be computed from column #4 and #7 as

6020
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60
examples/USER/misc/slater/in.slater Normal file
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@ -0,0 +1,60 @@
# Bulk polyelectrolyte as described in section IV of J. Chem. Phys. 125, 224107 (2006)
boundary p p p
units lj
atom_style charge
region my_sim_box block 0.0 10.0 0.0 10.0 0.0 10.0
create_box 3 my_sim_box
create_atoms 1 random 2804 100 my_sim_box
create_atoms 2 random 98 200 my_sim_box
create_atoms 3 random 98 300 my_sim_box
set type 2 charge -1.0
set type 3 charge 1.0
comm_modify mode single vel yes
mass 1 1.0
mass 2 1.0
mass 3 1.0
pair_style hybrid/overlay dpd 1.0 1.0 245455 coul/slater/long 0.929 3.0
pair_coeff * * dpd 25.0 4.5
pair_coeff * * coul/slater/long
kspace_style ewald 0.00001
dielectric 1.0
neighbor 2.0 bin
neigh_modify every 1 delay 0 check no once no
timestep 0.02
fix 2 all nve
thermo 10
thermo_style custom step spcpu temp press etotal pe ke ecoul elong evdwl
thermo_modify line one
run 100000
write_data data.after_equilibration
compute RDF_1_1 all rdf 50 1 1 cutoff 3.0
compute RDF_1_2 all rdf 50 1 2 cutoff 3.0
compute RDF_1_3 all rdf 50 1 3 cutoff 3.0
compute RDF_2_2 all rdf 50 2 2 cutoff 3.0
compute RDF_2_3 all rdf 50 2 3 cutoff 3.0
compute RDF_3_3 all rdf 50 3 3 cutoff 3.0
fix 11 all ave/time 50 1 50 c_RDF_1_1[*] file tmp_1_1.rdf mode vector
fix 12 all ave/time 50 1 50 c_RDF_1_2[*] file tmp_1_2.rdf mode vector
fix 13 all ave/time 50 1 50 c_RDF_1_3[*] file tmp_1_3.rdf mode vector
fix 14 all ave/time 50 1 50 c_RDF_2_2[*] file tmp_2_2.rdf mode vector
fix 15 all ave/time 50 1 50 c_RDF_2_3[*] file tmp_2_3.rdf mode vector
fix 16 all ave/time 50 1 50 c_RDF_3_3[*] file tmp_3_3.rdf mode vector
run 10000
write_data data.after_production_run

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2
examples/USER/plumed/reference/p.log
View File

@ -48,7 +48,7 @@ PLUMED: [1] The PLUMED consortium, Nat. Methods 16, 670 (2019)
PLUMED: [2] Tribello, Bonomi, Branduardi, Camilloni, and Bussi, Comput. Phys. Commun. 185, 604 (2014)
PLUMED: Please read and cite where appropriate!
PLUMED: Finished setup
PLUMED: Cycles Total Average Minumum Maximum
PLUMED: Cycles Total Average Minimum Maximum
PLUMED: 1 0.010018 0.010018 0.010018 0.010018
PLUMED: 1 Prepare dependencies 102 0.000241 0.000002 0.000001 0.000003
PLUMED: 2 Sharing data 102 0.002132 0.000021 0.000006 0.000151

2
examples/USER/qtb/methane_qbmsst/methane_qtb.mod
View File

@ -48,7 +48,7 @@ neigh_modify every 10 delay 0 check no
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
#Initilization
#Initialization
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
#Setup output

2
examples/USER/qtb/methane_qtb/methane_qtb.in
View File

@ -54,7 +54,7 @@ neigh_modify every 10 delay 0 check no
## This part equilibrates liquid methane to a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
#Initilization
#Initialization
velocity all create ${temperature} 93 dist gaussian sum no mom yes rot yes loop all
#Setup output

2
examples/USER/quip/in.molecular
View File

@ -17,7 +17,7 @@ pair_style hybrid/overlay lj/cut 8.0 quip
special_bonds lj/coul 0.999999999 0.999999999 0.999999999
# Intermolecular: OPLS (JACS 118 (45), p. 11225 (1996))
# Coulomb interactions ommitted for simplicity
# Coulomb interactions omitted for simplicity
pair_coeff 1 1 lj/cut 0.0028619844 3.5 # CT
pair_coeff 2 2 lj/cut 0.0013009018 2.5 # HC
pair_coeff 1 2 lj/cut 0.0019295487 2.95

2
examples/USER/quip/log.24Jul17.molecular.g++.1
View File

@ -39,7 +39,7 @@ special_bonds lj/coul 0.999999999 0.999999999 0.999999999
4 = max # of special neighbors
# Intermolecular: OPLS (JACS 118 (45), p. 11225 (1996))
# Coulomb interactions ommitted for simplicity
# Coulomb interactions omitted for simplicity
pair_coeff 1 1 lj/cut 0.0028619844 3.5 # CT
pair_coeff 2 2 lj/cut 0.0013009018 2.5 # HC
pair_coeff 1 2 lj/cut 0.0019295487 2.95

2
examples/USER/quip/log.24Jul17.molecular.g++.4
View File

@ -39,7 +39,7 @@ special_bonds lj/coul 0.999999999 0.999999999 0.999999999
4 = max # of special neighbors
# Intermolecular: OPLS (JACS 118 (45), p. 11225 (1996))
# Coulomb interactions ommitted for simplicity
# Coulomb interactions omitted for simplicity
pair_coeff 1 1 lj/cut 0.0028619844 3.5 # CT
pair_coeff 2 2 lj/cut 0.0013009018 2.5 # HC
pair_coeff 1 2 lj/cut 0.0019295487 2.95

4
examples/USER/smd/aluminum_strip_pull/aluminum_strip_pull.lmp
View File

@ -2,7 +2,7 @@
#
# TLSPH example: elongate a 2d strip of aluminum py pulling its ends apart
#
# unit sytem: GPa / mm / ms
# unit system: GPa / mm / ms
#
####################################################################################################
@ -18,7 +18,7 @@ variable q2 equal 0.0 # standard artificial viscosity quadratic coeffici
variable hg equal 10.0 # hourglass control coefficient
variable cp equal 1.0 # heat capacity of material -- not used here
variable JC_A equal 0.3241 # Johnson Cook arameters
variable JC_A equal 0.3241 # Johnson Cook parameters
variable JC_B equal 0.1138
variable JC_N equal 0.42
variable JC_C equal 0 #0.002

4
examples/USER/smd/fluid_structure_interaction/fluid_structure_interaction.lmp
View File

@ -4,7 +4,7 @@
#
# A column of water is placed in a container and allowed to collapse unter the
# influence of gravity. Several solid objects are also placed in the container.
# The water flow pushes the solid objects around until the sytem comes to halt due to
# The water flow pushes the solid objects around until the system comes to halt due to
# viscous damping. The solid objects have a lower mass density than water and finally float on
# the water surface.
#
@ -12,7 +12,7 @@
# Total Lagrangian formalism. Contact forces between container, solid bodies, and water prevent
# mutual penetration of these physical entities.
#
# unit sytem: GPa / mm / ms
# unit system: GPa / mm / ms
#
####################################################################################################

2
examples/USER/smd/funnel_flow/funnel_flow.lmp
View File

@ -5,7 +5,7 @@
# The boundary dump file (see below) can be converted into VTK format using the conversion
# tool dump2vtk_tris from the tools/smd directory.
#
# unit sytem: GPa / mm / ms
# unit system: GPa / mm / ms
#
####################################################################################################

2
examples/USER/smd/rubber_rings_3d/rubber_rings_3d.lmp
View File

@ -3,7 +3,7 @@
#
# TLSPH example: Two rubber rings impact each other.
#
# unit sytem: GPa / mm / ms
# unit system: GPa / mm / ms
#
####################################################################################################

2
examples/USER/smd/rubber_strip_pull/rubber_strip_pull.lmp
View File

@ -2,7 +2,7 @@
#
# TLSPH example: elongate a 2d strip of a linear elastic material py pulling its ends apart
#
# unit sytem: GPa / mm / ms
# unit system: GPa / mm / ms
#
####################################################################################################

2
examples/USER/tally/in.pe
View File

@ -37,7 +37,7 @@ group hyd type 2
compute epa oxy group/group hyd pair yes kspace no boundary no
# tally pairwise energy between all oygen and all hydrogen
compute c1 oxy pe/tally hyd
# tally pairwise energy beween all atoms to compare with globals
# tally pairwise energy between all atoms to compare with globals
compute c2 all pe/tally all
# collect per atom energies
compute c3 all pe/atom pair

2
examples/USER/tally/log.12Jun17.pe.1
View File

@ -89,7 +89,7 @@ group hyd type 2
compute epa oxy group/group hyd pair yes kspace no boundary no
# tally pairwise energy between all oygen and all hydrogen
compute c1 oxy pe/tally hyd
# tally pairwise energy beween all atoms to compare with globals
# tally pairwise energy between all atoms to compare with globals
compute c2 all pe/tally all
# collect per atom energies
compute c3 all pe/atom pair

2
examples/USER/tally/log.12Jun17.pe.4
View File

@ -89,7 +89,7 @@ group hyd type 2
compute epa oxy group/group hyd pair yes kspace no boundary no
# tally pairwise energy between all oygen and all hydrogen
compute c1 oxy pe/tally hyd
# tally pairwise energy beween all atoms to compare with globals
# tally pairwise energy between all atoms to compare with globals
compute c2 all pe/tally all
# collect per atom energies
compute c3 all pe/atom pair

6
examples/hugoniostat/in.hugoniostat
View File

@ -67,7 +67,7 @@ fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0 drag 0.0 tchain 1 pchain
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
# Add fix energy to ouput etotal
# Add fix energy to output etotal
fix_modify myhug energy yes
@ -115,7 +115,7 @@ fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 drag 200.0 tchain 1 pchain
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
# Add fix energy to ouput etotal
# Add fix energy to output etotal
fix_modify myhug energy yes
@ -153,7 +153,7 @@ fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
# Add fix energy to ouput etotal
# Add fix energy to output etotal
fix_modify myhug energy yes

6
examples/hugoniostat/log.27Nov18.hugoniostat.g++.1
View File

@ -129,7 +129,7 @@ fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0 drag 0.0 tchain 1 pchain
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
# Add fix energy to ouput etotal
# Add fix energy to output etotal
fix_modify myhug energy yes
@ -232,7 +232,7 @@ fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 drag 200.0 tchain 1 pchain
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
# Add fix energy to ouput etotal
# Add fix energy to output etotal
fix_modify myhug energy yes
@ -327,7 +327,7 @@ fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
# Add fix energy to ouput etotal
# Add fix energy to output etotal
fix_modify myhug energy yes

6
examples/hugoniostat/log.27Nov18.hugoniostat.g++.4
View File

@ -129,7 +129,7 @@ fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0 drag 0.0 tchain 1 pchain
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
# Add fix energy to ouput etotal
# Add fix energy to output etotal
fix_modify myhug energy yes
@ -232,7 +232,7 @@ fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 drag 200.0 tchain 1 pchain
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
# Add fix energy to ouput etotal
# Add fix energy to output etotal
fix_modify myhug energy yes
@ -327,7 +327,7 @@ fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0
fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
# Add fix energy to ouput etotal
# Add fix energy to output etotal
fix_modify myhug energy yes

2
examples/reax/HNS/README.txt
View File

@ -17,7 +17,7 @@ Questions: Mitchell Wood, mitwood@sandia.gov
The type of simulation is set by the 'fix' commands, dynamic charges are controlled with 'fix qeq' and the integration style is given as 'fix nve' here.
More information about each of the individual commands can be found online at lammps.sandia.gov in the user manual section.
*There are four free varaibles in this file, three of which control the size of the simulation and the last will dictate how many MD time steps are taken.
*There are four free variables in this file, three of which control the size of the simulation and the last will dictate how many MD time steps are taken.
*The size of the system is controlled by the 'replicate' command given the values of $x, $y and $z.
*The number of timesteps taken is controlled by the 'run' command given the value of $t

2
lib/atc/ATC_Coupling.cpp
View File

@ -625,7 +625,7 @@ namespace ATC {
/*! \page man_consistent_fe_initialization fix_modify AtC consistent_fe_initialization
\section syntax
fix_modify AtC consistent_fe_initialization <on | off>
- <on|off> = switch to activiate/deactiviate the intial setting of FE intrinsic field to match the projected MD field
- <on|off> = switch to activiate/deactiviate the initial setting of FE intrinsic field to match the projected MD field
\section examples
<TT> fix_modify atc consistent_fe_initialization on </TT>
\section description

2
lib/atc/ATC_Coupling.h
View File

@ -227,7 +227,7 @@ namespace ATC {
void set_mass_mat_time_filter(FieldName thisField,TimeFilterManager::FilterIntegrationType filterIntegrationType);
/** return referece to ExtrinsicModelManager */
/** return reference to ExtrinsicModelManager */
ExtrinsicModelManager & extrinsic_model_manager()
{ return extrinsicModelManager_; }
/** access to time integrator */

2
lib/atc/ATC_CouplingEnergy.cpp
View File

@ -364,7 +364,7 @@ namespace ATC {
(_tiIt_->second)->post_process();
}
// auxilliary data
// auxiliary data
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
(_tiIt_->second)->output(outputData);
}

2
lib/atc/ATC_CouplingMass.cpp
View File

@ -221,7 +221,7 @@ namespace ATC {
(_tiIt_->second)->post_process();
}
// auxilliary data
// auxiliary data
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
(_tiIt_->second)->output(outputData);
}

2
lib/atc/ATC_CouplingMomentum.cpp
View File

@ -325,7 +325,7 @@ namespace ATC {
(_tiIt_->second)->post_process();
}
// auxilliary data
// auxiliary data
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
(_tiIt_->second)->output(outputData);
}

2
lib/atc/ATC_CouplingMomentumEnergy.cpp
View File

@ -446,7 +446,7 @@ namespace ATC {
(_tiIt_->second)->post_process();
}
// auxilliary data
// auxiliary data
for (_tiIt_ = timeIntegrators_.begin(); _tiIt_ != timeIntegrators_.end(); ++_tiIt_) {
(_tiIt_->second)->output(outputData);

4
lib/atc/ATC_Method.cpp
View File

@ -693,12 +693,12 @@ pecified
/*! \page man_boundary fix_modify AtC boundary
\section syntax
fix_modify AtC boundary type <atom-type-id>
- <atom-type-id> = type id for atoms that represent a ficticious
- <atom-type-id> = type id for atoms that represent a fictitious
boundary internal to the FE mesh
\section examples
<TT> fix_modify AtC boundary type ghost_atoms </TT>
\section description
Command to define the atoms that represent the ficticious
Command to define the atoms that represent the fictitious
boundary internal to the FE mesh. For fully overlapped MD/FE
domains with periodic boundary conditions no boundary atoms should
be defined.

8
lib/atc/ATC_Transfer.cpp
View File

@ -148,7 +148,7 @@ namespace ATC {
}
if (!initialized_ || ATC::LammpsInterface::instance()->atoms_sorted() || resetKernelFunction_) {
// initialize kernel funciton matrix N_Ia
// initialize kernel function matrix N_Ia
if (! kernelOnTheFly_) {
try{
if (!moleculeIds_.empty()) compute_kernel_matrix_molecule(); //KKM add
@ -654,7 +654,7 @@ namespace ATC {
<TT> fix_modify AtC gradients add temperature velocity stress </TT> \n
<TT> fix_modify AtC gradients delete velocity </TT> \n
\section description
Requests calculation and ouput of gradients of the fields from the
Requests calculation and output of gradients of the fields from the
transfer class. These gradients will be with regard to spatial or material
coordinate for eulerian or lagrangian analysis, respectively, as specified by
atom_element_map (see \ref man_atom_element_map )
@ -698,7 +698,7 @@ namespace ATC {
<TT> fix_modify AtC rates add temperature velocity stress </TT> \n
<TT> fix_modify AtC rates delete stress </TT> \n
\section description
Requests calculation and ouput of rates (time derivatives) of the fields from the
Requests calculation and output of rates (time derivatives) of the fields from the
transfer class. For eulerian analysis (see \ref man_atom_element_map ), these rates
are the partial time derivatives of the nodal fields, not the full (material) time
derivatives. \n
@ -865,7 +865,7 @@ namespace ATC {
}
//-------------------------------------------------------------------
// called at the begining of second half timestep
// called at the beginning of second half timestep
// REFACTOR move this to post_neighbor
void ATC_Transfer::pre_final_integrate()
{

2
lib/atc/AtomToMoleculeTransfer.h
View File

@ -217,7 +217,7 @@ namespace ATC {
/** reference to shape function matrix */
SPAR_MAN * shapeFunction_;
/** persistant workspace */
/** persistent workspace */
mutable DENS_MAT _workspace_;

2
lib/atc/AtomicRegulator.h
View File

@ -585,7 +585,7 @@ namespace ATC {
protected:
/** lumped version of the matrix governing lamda */
/** lumped version of the matrix governing lambda */
DIAG_MAT lumpedMatrix_;
/** set of regulated nodes */

2
lib/atc/CbPotential.h
View File

@ -7,7 +7,7 @@ namespace ATC
enum Interaction{PAIRWISE=1, EAM=2, THREE_BDY=4, ANGLE_BND=8};
//! Booleans that enable types of terms the potential uses.
struct Interactions {
//! Enables up to 3 interaction types. (order independant)
//! Enables up to 3 interaction types. (order independent)
Interactions(int a=0, int b=0, int c=0);
bool pairwise; //!< Pairwise interaction terms exist.
bool embedding; //!< Embedding interaction terms (EAM) exist.

4
lib/atc/ChargeRegulator.cpp
View File

@ -214,7 +214,7 @@ namespace ATC {
qV2e_ = lammpsInterface_->qv2e();
qqrd2e_ = lammpsInterface_->qqrd2e();
// note derived method set intialized to true
// note derived method set initialized to true
}
@ -327,7 +327,7 @@ namespace ATC {
//
if (nInfluenceNodes_ < nControlNodes_) throw ATC_Error(" least square not implmented ");
if (nInfluenceNodes_ < nControlNodes_) throw ATC_Error(" least square not implemented ");
if (nInfluenceNodes_ > nControlNodes_) throw ATC_Error(" solve not possible ");
DENS_MAT G(nInfluenceNodes_,nControlNodes_);
DENS_VEC G_I;

2
lib/atc/ConcentrationRegulator.cpp
View File

@ -263,7 +263,7 @@ const double kMinScale_ = 10000.;
volumes_(i) += volumes_(i-1);
}
// record orginal energetic properties
// record original energetic properties
int ntypes = lammpsInterface_->ntypes();
epsilon0_.reset(ntypes);
p_ = lammpsInterface_->potential();

2
lib/atc/DiagonalMatrix.h
View File

@ -472,7 +472,7 @@ inline DiagonalMatrix<double> inv(const DiagonalMatrix<double>& A)
return A.inv();
}
//-----------------------------------------------------------------------------
// general diagonalmatrix assigment
// general diagonalmatrix assignment
//-----------------------------------------------------------------------------
template<typename T>
void DiagonalMatrix<T>::_set_equal(const Matrix<T> &r)

6
lib/atc/ElasticTimeIntegrator.cpp
View File

@ -91,7 +91,7 @@ namespace ATC {
atc_->set_mass_mat_time_filter(MOMENTUM,TimeFilterManager::EXPLICIT_IMPLICIT);
break;
default:
throw ATC_Error("Uknown time integration type in ThermalTimeIntegrator::Initialize()");
throw ATC_Error("Unknown time integration type in ThermalTimeIntegrator::Initialize()");
}
}
@ -102,7 +102,7 @@ namespace ATC {
break;
}
default:
throw ATC_Error("Uknown time integration type in MomentumTimeIntegrator::Initialize()");
throw ATC_Error("Unknown time integration type in MomentumTimeIntegrator::Initialize()");
}
}
else {
@ -120,7 +120,7 @@ namespace ATC {
break;
}
default:
throw ATC_Error("Uknown time integration type in MomentumTimeIntegrator::Initialize()");
throw ATC_Error("Unknown time integration type in MomentumTimeIntegrator::Initialize()");
}
}
}

2
lib/atc/ElectronHeatFlux.h
View File

@ -126,7 +126,7 @@ namespace ATC {
/**
* @class ElectronHeatFluxThermopower
* @brief Class for an electron heat flux proportional to the temperature gradient but with a condu
ctivity proportional to the ratio of the electron and phonon temperatures with the thermopower from teh electric current included
ctivity proportional to the ratio of the electron and phonon temperatures with the thermopower from the electric current included
*/
class ElectronHeatFluxThermopower : public ElectronHeatFlux

2
lib/atc/ExtrinsicModelElectrostatic.cpp
View File

@ -144,7 +144,7 @@ namespace ATC {
}
}
/** switch to account for short range interaces */
/** switch to account for short range interfaces */
else if (strcmp(arg[argIndx],"short_range")==0) {
argIndx++;
if (strcmp(arg[argIndx],"on")==0) {

2
lib/atc/ExtrinsicModelElectrostatic.h
View File

@ -92,7 +92,7 @@ namespace ATC {
/** rhs mask for Poisson solver */
Array2D<bool> rhsMask_;
/** estimate instrinsic charge density */
/** estimate intrinsic charge density */
void add_electrostatic_forces(MATRIX & nodalPotential);
/** correct short range FE electric field */

4
lib/atc/FE_Element.cpp
View File

@ -408,7 +408,7 @@ static const double localCoordinatesTolerance = 1.e-09;
throw ATC_Error("Unrecognized interpolation order specified "
"for element class: \n"
" element only knows how to construct lin "
"and quad elments.");
"and quad elements.");
}
localCoords_.resize(nSD_,numNodes_);
@ -637,7 +637,7 @@ static const double localCoordinatesTolerance = 1.e-09;
throw ATC_Error("Unrecognized interpolation order specified "
"for element class: \n"
" element only knows how to construct lin "
"and quad elments.");
"and quad elements.");
}
localCoords_.resize(nSD_+1, numNodes_);

2
lib/atc/FE_Engine.cpp
View File

@ -349,7 +349,7 @@ namespace ATC{
else throw ATC_Error("not enough element partitions");
}
}
// each segment of the piecewise funcion is length-normalized separately
// each segment of the piecewise function is length-normalized separately
else if (strcmp(arg[argIdx],"position-number-density")==0) {
argIdx++;
double *y = new double[nx];

2
lib/atc/FE_Engine.h
View File

@ -510,7 +510,7 @@ namespace ATC {
/** finite element mesh */
FE_Mesh *feMesh_;
/** auxillary kernel function */
/** auxiliary kernel function */
KernelFunction *kernelFunction_;
/** initialized flag */

4
lib/atc/FE_Interpolate.cpp
View File

@ -564,7 +564,7 @@ namespace ATC {
N = 1.0;
dNdr = 1.0;
// mapping returns the 1d nodes in each dimension that sould be multiplied
// mapping returns the 1d nodes in each dimension that should be multiplied
// to achieve the shape functions in 3d
vector<int> mapping(nSD_);
for (int inode=0; inode<numEltNodes; ++inode) {
@ -890,7 +890,7 @@ namespace ATC {
*
* Note: degenerating quads/hexes can yield simplices
* as well, but this class is for computing these
* shape fucntions _natively_, in their own
* shape functions _natively_, in their own
* triangular/tetrahedral coordinate systems.
*
*********************************************************/

2
lib/atc/FieldEulerIntegrator.h
View File

@ -158,7 +158,7 @@ class FieldImplicitDirectEulerIntegrator : public FieldEulerIntegrator {
/** Destructor */
virtual ~FieldImplicitDirectEulerIntegrator();
/** initalize - init the matrices and inverses */
/** initialize - init the matrices and inverses */
void initialize(const double dt, const double time,
FIELDS & fields);

2
lib/atc/FundamentalAtomicQuantity.h
View File

@ -167,7 +167,7 @@ namespace ATC {
// destructor
virtual ~ComputedAtomQuantity() {};
/** resets compute, must be this way to accomodate atom sorting between runs */
/** resets compute, must be this way to accommodate atom sorting between runs */
virtual void post_exchange() {this->needReset_ = true;};
/** specialized reset to account for forcing lammps to perform the compute */

2
lib/atc/GhostManager.cpp
View File

@ -523,7 +523,7 @@ namespace ATC {
{
compute_distances();
int nlayers = find_layers();
if (nlayers > ((int)gamma_.size())) throw ATC_Error("GhostModifierDampedHarmonicLayers::initialize not enough damping factors specfied " + to_string(gamma_.size()));
if (nlayers > ((int)gamma_.size())) throw ATC_Error("GhostModifierDampedHarmonicLayers::initialize not enough damping factors specified " + to_string(gamma_.size()));
}
//--------------------------------------------------------

2
lib/atc/InterscaleOperators.cpp
View File

@ -157,7 +157,7 @@ namespace ATC{
bool isTemporary = (quantity->memory_type()==TEMPORARY);
for (it = (quantity->dependentQuantities_).begin(); it != (quantity->dependentQuantities_).end(); it++) {
// make sure that if quantity isn't persistent, none of it's depedencies are
// make sure that if quantity isn't persistent, none of it's dependencies are
if ((*it)->memory_type()==PERSISTENT && isTemporary) {
throw ATC_Error("InterscaleManager::dfs_visit - a persistent quantity has a temporary dependency");
}

12
lib/atc/InterscaleOperators.h
View File

@ -245,19 +245,19 @@ namespace ATC {
/** container for molecule sets */
std::map<std::string, SmallMoleculeSet * > smallMoleculeSets_;
/** container for atomic quantities which must be transfered when atoms cross processors */
/** container for atomic quantities which must be transferred when atoms cross processors */
std::set<PerAtomQuantity<double> *> exchangeList_;
/** container for atomic quantities which must be transfered to ghost atoms on other processors */
/** container for atomic quantities which must be transferred to ghost atoms on other processors */
std::vector<PerAtomQuantity<double> *> commList_;
/** container for integer atomic quantities which must be transfered to ghost atoms on other processors */
/** container for integer atomic quantities which must be transferred to ghost atoms on other processors */
std::vector<PerAtomQuantity<int> *> commIntList_;
/** container for atomic diagonal matrices which must be transfered to ghost atoms on other processors */
/** container for atomic diagonal matrices which must be transferred to ghost atoms on other processors */
std::vector<PerAtomDiagonalMatrix<double> *> commDmList_;
/** container for atomic sparse matrices which must be transfered to ghost atoms on other processors */
/** container for atomic sparse matrices which must be transferred to ghost atoms on other processors */
std::vector<PerAtomSparseMatrix<double> *> commSmList_;
/** prefix for labeling associated lammps arrays */
@ -329,7 +329,7 @@ namespace ATC {
(it->second)->set_memory_type(TEMPORARY);
}
/** helper function to perform intialization for dfs of a list */
/** helper function to perform initialization for dfs of a list */
template <typename data>
void dfs_prepare_loop(std::map<std::string,data * > & list)
{

2
lib/atc/KinetoThermostat.h
View File

@ -607,7 +607,7 @@ namespace ATC {
/* /\** change in restricted atomic FE energy over a timestep *\/ */
/* DENS_MAT deltaNodalAtomicEnergy_; */
/* /\** intial restricted atomic FE energy used to compute change *\/ */
/* /\** initial restricted atomic FE energy used to compute change *\/ */
/* DENS_MAT initialNodalAtomicEnergy_; */
/* /\** filtered nodal atomic energy *\/ */

4
lib/atc/Kinetostat.cpp
View File

@ -2233,7 +2233,7 @@ namespace ATC {
// initialize_delta_nodal_atomic_momentum:
// initializes storage for the variable tracking
// the change in the nodal atomic momentum
// that has occured over the past timestep
// that has occurred over the past timestep
//--------------------------------------------------------
void KinetostatFixed::initialize_delta_nodal_atomic_momentum(double dt)
{
@ -2248,7 +2248,7 @@ namespace ATC {
//--------------------------------------------------------
// compute_delta_nodal_atomic_momentum:
// computes the change in the nodal atomic momentum
// that has occured over the past timestep
// that has occurred over the past timestep
//--------------------------------------------------------
void KinetostatFixed::compute_delta_nodal_atomic_momentum(double dt)
{

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