Merge branch 'master' into collected-small-changes

# Conflicts:
#	doc/src/Build_development.rst

cmake/Modules/Packages/USER-NETCDF.cmake

@@ -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)

cmake/README.md

@@ -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>

doc/msi2lmp.1

@@ -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

doc/src/2001/README.html

@@ -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-which has been superceded by more current versions.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+which has been superseded by more current versions.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>

doc/src/2001/basics.html

@@ -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>

doc/src/2001/input_commands.html

@@ -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 "temp control", since they conflict and will
+  conjunction with global "temp control", 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
   "temp control" command
 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) 
@@ -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) 

doc/src/99/README.html

@@ -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>

doc/src/99/basics.html

@@ -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>

doc/src/99/input_commands.html

@@ -430,7 +430,7 @@ accuracy criterion effectively determines how many k-space vectors are used
 for PPPM, accuracy criterion determines mesh spacing (see "particle mesh"
   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 -> has effect of applying same force to entire group
   of atoms
 thermostatting constraints (rescale, langevin, nose/hoover) cannot be used in
-  conjuction with global "temp control", since they conflict and will
+  conjunction with global "temp control", 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

doc/src/Build_development.rst

@@ -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

doc/src/Commands_pair.rst

@@ -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>`

doc/src/Errors_messages.rst

@@ -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.
 

doc/src/USER/atc/man_boundary.html

@@ -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">

doc/src/USER/atc/man_hardy_gradients.html

@@ -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>

doc/src/USER/atc/man_hardy_rates.html

@@ -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>

doc/src/molecule.rst

@@ -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

doc/src/pair_coul_slater.rst

@@ -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).
+
+

doc/utils/sphinx-config/false_positives.txt

@@ -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

examples/COUPLE/lammps_nwchem/planewave/nwchem_lammps.out

@@ -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
 
 
 ======================

examples/COUPLE/lammps_quest/lmpqst.cpp

@@ -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;

examples/UNITS/README

@@ -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.

examples/USER/atc/README

@@ -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

examples/USER/atc/fluids/in.bar1d_fluids

@@ -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

examples/USER/atc/fluids/in.conducting_interface

@@ -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

examples/USER/atc/fluids/in.dielectric_interface

@@ -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

examples/USER/atc/fluids/in.shear_flow

@@ -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

examples/USER/atc/fluids/in.shear_no_atoms

@@ -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

examples/USER/atc/thermal/bar1d.screen

@@ -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

examples/USER/atc/thermal/in.bar1d

@@ -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

examples/USER/atc/thermal/in.bar1d_all_atoms

@@ -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

examples/USER/atc/thermal/in.bar1d_combined

@@ -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

examples/USER/atc/thermal/in.bar1d_flux

@@ -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

examples/USER/atc/thermal/in.bar1d_frac_step

@@ -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

examples/USER/cgdna/README

@@ -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 

examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py

@@ -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))
 

examples/USER/cgdna/util/generate.py

@@ -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 = []

examples/USER/diffraction/README

@@ -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 

examples/USER/eff/Li-dendritic/README

@@ -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).

examples/USER/lb/fourspheres/in.fourspheres_default_gamma

@@ -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.                                 #
 #                                                                           #

examples/USER/lb/fourspheres/in.fourspheres_set_gamma

@@ -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.                                 #
 #                                                                           #

examples/USER/manifold/diffusion/plot_msd.gpl

@@ -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]

examples/USER/misc/ees/README

@@ -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
 	

examples/USER/misc/hma/README

@@ -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

examples/USER/misc/slater/in.slater

@@ -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

examples/USER/plumed/reference/p.log

@@ -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

examples/USER/qtb/methane_qbmsst/methane_qtb.mod

@@ -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

examples/USER/qtb/methane_qtb/methane_qtb.in

@@ -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

examples/USER/quip/in.molecular

@@ -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

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

@@ -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

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

@@ -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

examples/USER/smd/aluminum_strip_pull/aluminum_strip_pull.lmp

@@ -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

examples/USER/smd/fluid_structure_interaction/fluid_structure_interaction.lmp

@@ -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
 #
 ####################################################################################################
 

examples/USER/smd/funnel_flow/funnel_flow.lmp

@@ -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
 #
 ####################################################################################################
 

examples/USER/smd/rubber_rings_3d/rubber_rings_3d.lmp

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

examples/USER/smd/rubber_strip_pull/rubber_strip_pull.lmp

@@ -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
 #
 ####################################################################################################
 

examples/USER/tally/in.pe

@@ -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

examples/USER/tally/log.12Jun17.pe.1

@@ -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

examples/USER/tally/log.12Jun17.pe.4

@@ -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

examples/hugoniostat/in.hugoniostat

@@ -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 
 

examples/hugoniostat/log.27Nov18.hugoniostat.g++.1

@@ -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
 

examples/hugoniostat/log.27Nov18.hugoniostat.g++.4

@@ -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
 

examples/reax/HNS/README.txt

@@ -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
 

lib/atc/ATC_Coupling.cpp

@@ -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

lib/atc/ATC_Coupling.h

@@ -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 */

lib/atc/ATC_CouplingEnergy.cpp

@@ -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);
       }

lib/atc/ATC_CouplingMass.cpp

@@ -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);
       }

lib/atc/ATC_CouplingMomentum.cpp

@@ -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);
       }

lib/atc/ATC_CouplingMomentumEnergy.cpp

@@ -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);

lib/atc/ATC_Method.cpp

@@ -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.

lib/atc/ATC_Transfer.cpp

@@ -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()
   {

lib/atc/AtomToMoleculeTransfer.h

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

lib/atc/AtomicRegulator.h

@@ -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 */

lib/atc/CbPotential.h

@@ -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.

lib/atc/ChargeRegulator.cpp

@@ -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;

lib/atc/ConcentrationRegulator.cpp

@@ -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();

lib/atc/DiagonalMatrix.h

@@ -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)

lib/atc/ElasticTimeIntegrator.cpp

@@ -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()");
         }
       }   
     }

lib/atc/ElectronHeatFlux.h

@@ -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

lib/atc/ExtrinsicModelElectrostatic.cpp

@@ -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) {

lib/atc/ExtrinsicModelElectrostatic.h

@@ -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 */

lib/atc/FE_Element.cpp

@@ -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_);

lib/atc/FE_Engine.cpp

@@ -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];

lib/atc/FE_Engine.h

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

lib/atc/FE_Interpolate.cpp

@@ -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.
    *
    *********************************************************/

lib/atc/FieldEulerIntegrator.h

@@ -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);
 

lib/atc/FundamentalAtomicQuantity.h

@@ -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 */

lib/atc/GhostManager.cpp

@@ -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()));
   }
 
   //--------------------------------------------------------

lib/atc/InterscaleOperators.cpp

@@ -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");
       }

lib/atc/InterscaleOperators.h

@@ -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)
     {

lib/atc/KinetoThermostat.h

@@ -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 *\/ */

lib/atc/Kinetostat.cpp

@@ -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)
   {