Fix whitespace

doc/github-development-workflow.md

@@ -25,10 +25,10 @@ In the interest of consistency, ONLY ONE of the core LAMMPS developers
 should doing the merging itself.  This is currently
 [@akohlmey](https://github.com/akohlmey) (Axel Kohlmeyer).
 If this assignment needs to be changed, it shall be done right after a
-stable release.  If the currently assigned developer cannot merge outstanding pull 
+stable release.  If the currently assigned developer cannot merge outstanding pull
-requests in a timely manner, or in other extenuating circumstances, 
+requests in a timely manner, or in other extenuating circumstances,
 other core LAMMPS developers with merge rights can merge pull requests,
-when necessary. 
+when necessary.
 
 ## Pull Requests
 

doc/include-file-conventions.md

@@ -65,7 +65,7 @@ Header files will typically contain the definition of a (single) class.
 These header files should have as few include statements as possible.
 This is particularly important for classes that implement a "style" and
 thus use a macro of the kind `SomeStyle(some/name,SomeName)`. These will
-all be included in the auto-generated `"some_style.h"` files which 
+all be included in the auto-generated `"some_style.h"` files which
 results in a high potential for direct or indirect symbol name clashes.
 
 In the ideal case, the header would only include one file defining the

doc/src/compute_mesont.rst

@@ -26,23 +26,23 @@ Examples
 Description
 """""""""""
 
-These computes define computations for the stretching (estretch), bending 
+These computes define computations for the stretching (estretch), bending
-(ebend), and intertube (etube) per-node (atom) and total energies. The 
+(ebend), and intertube (etube) per-node (atom) and total energies. The
-evaluated value is selected by a parameter passed to the compute: estretch, 
+evaluated value is selected by a parameter passed to the compute: estretch,
 ebend, etube.
 
 **Output info:**
 
-These computes calculate per-node (per-atom) vectors, which can be accessed by 
+These computes calculate per-node (per-atom) vectors, which can be accessed by
-any command that uses per-atom values from a compute as input, and global 
+any command that uses per-atom values from a compute as input, and global
-scalars. See the :doc:`Howto output <Howto_output>` doc page for an overview of 
+scalars. See the :doc:`Howto output <Howto_output>` doc page for an overview of
 LAMMPS output options.
 
 The computed values are provided in energy :doc:`units <units>`.
 
 Restrictions
 """"""""""""
-These computes are part of the USER-MESONT package. They are only enabled if 
+These computes are part of the USER-MESONT package. They are only enabled if
 LAMMPS is built with that package. See the :doc:`Build package <Build_package>`
 doc page for more info. In addition, :doc:`mesont pair_style <pair_style>`
 must be used.

doc/src/compute_orientorder_atom.rst

@@ -26,7 +26,7 @@ Syntax
        *wl* value = yes or no
        *wl/hat* value = yes or no
        *components* value = ldegree
-       *chunksize* value = number of atoms in each pass 
+       *chunksize* value = number of atoms in each pass
 
 Examples
 """"""""

doc/src/compute_property_atom.rst

@@ -64,7 +64,7 @@ Syntax
            end12x, end12y, end12z = end points of line segment
            corner123x, corner123y, corner123z = corner points of triangle
            nbonds = number of bonds assigned to an atom
-           buckling = buckling flag used in mesoscopic simulation of nanotubes 
+           buckling = buckling flag used in mesoscopic simulation of nanotubes
 
   .. parsed-literal::
 

doc/src/pair_mesont_tpm.rst

@@ -9,7 +9,7 @@ Syntax
 
 .. parsed-literal::
 
-   pair_style mesont/tpm cut table_path BendingMode TPMType 
+   pair_style mesont/tpm cut table_path BendingMode TPMType
 
 * cut = the cutoff distance
 * table_path = the path to the potential table
@@ -114,7 +114,7 @@ study the thermal transport properties of carbon nanotube films
 The methods for modeling of
 the mechanical energy dissipation into heat (energy exchange between the
 dynamic degrees of freedom of the mesoscopic model and the energy of atomic
-vibrations that are not explicitly represented in the model) 
+vibrations that are not explicitly represented in the model)
 :ref:`(Zhigilei10) <Zhigilei10>` and mesoscopic description of covalent cross-links
 between nanotubes :ref:`(Banna) <Banna>` have also been developed but are not
 included in this first release of the LAMMPS implementation of the force field.
@@ -144,7 +144,7 @@ pair interactions.
 The cutoff distance should be set to be at least :math:`max\left[2L,\sqrt{L^2/2+(2R+T_{cut})^2}\right]` ,
 where L is the maximum segment length, R is the maximum tube radius, and
 :math:`T_{cut}` = 10.2 A is the maximum distance between the surfaces of interacting
-segments. Because of the use of extended chain concept at CNT ends, the recommended 
+segments. Because of the use of extended chain concept at CNT ends, the recommended
 cutoff is 3L.
 
 The MESONT-TABTP_10_10.xrs potential file provided with LAMMPS (see the

src/GPU/Install.sh

@@ -32,7 +32,7 @@ action fix_gpu.cpp
 action fix_gpu.h
 action gpu_extra.h
 action pair_beck_gpu.cpp
-action pair_beck_gpu.h 
+action pair_beck_gpu.h
 action pair_born_coul_long_gpu.cpp pair_born_coul_long.cpp
 action pair_born_coul_long_gpu.h pair_born_coul_long.cpp
 action pair_born_coul_long_cs_gpu.cpp pair_born_coul_long_cs.cpp
@@ -71,9 +71,9 @@ action pair_lj_sf_dipole_sf_gpu.cpp pair_lj_sf_dipole_sf.cpp
 action pair_lj_sf_dipole_sf_gpu.h pair_lj_sf_dipole_sf.cpp
 action pair_eam_alloy_gpu.cpp pair_eam.cpp
 action pair_eam_alloy_gpu.h pair_eam.cpp
-action pair_eam_fs_gpu.cpp pair_eam.cpp 
+action pair_eam_fs_gpu.cpp pair_eam.cpp
 action pair_eam_fs_gpu.h pair_eam.cpp
-action pair_eam_gpu.cpp pair_eam.cpp 
+action pair_eam_gpu.cpp pair_eam.cpp
 action pair_eam_gpu.h pair_eam.cpp
 action pair_gauss_gpu.cpp
 action pair_gauss_gpu.h
@@ -112,7 +112,7 @@ action pair_lj_sdk_coul_long_gpu.h pair_lj_sdk_coul_long.cpp
 action pair_lj_sdk_gpu.cpp pair_lj_sdk.cpp
 action pair_lj_sdk_gpu.h pair_lj_sdk.cpp
 action pair_mie_cut_gpu.cpp
-action pair_mie_cut_gpu.h 
+action pair_mie_cut_gpu.h
 action pair_morse_gpu.cpp
 action pair_morse_gpu.h
 action pair_resquared_gpu.cpp pair_resquared.cpp

src/KOKKOS/Install.sh

@@ -31,7 +31,7 @@ action () {
 KOKKOS_INSTALLED=0
 if (test -e ../Makefile.package) then
   KOKKOS_INSTALLED=`grep DLMP_KOKKOS ../Makefile.package | wc -l`
-fi 
+fi
 
 if (test $mode = 1) then
   if (test $KOKKOS_INSTALLED = 0) then
@@ -45,14 +45,14 @@ fi
 
 # list of files with optional dependcies
 
-action angle_charmm_kokkos.cpp angle_charmm.cpp 
+action angle_charmm_kokkos.cpp angle_charmm.cpp
 action angle_charmm_kokkos.h angle_charmm.h
-action angle_class2_kokkos.cpp angle_class2.cpp 
+action angle_class2_kokkos.cpp angle_class2.cpp
 action angle_class2_kokkos.h angle_class2.h
-action angle_cosine_kokkos.cpp angle_cosine.cpp 
+action angle_cosine_kokkos.cpp angle_cosine.cpp
 action angle_cosine_kokkos.h angle_cosine.h
-action angle_harmonic_kokkos.cpp angle_harmonic.cpp 
+action angle_harmonic_kokkos.cpp angle_harmonic.cpp
-action angle_harmonic_kokkos.h angle_harmonic.h 
+action angle_harmonic_kokkos.h angle_harmonic.h
 action atom_kokkos.cpp
 action atom_kokkos.h
 action atom_vec_angle_kokkos.cpp atom_vec_angle.cpp
@@ -75,7 +75,7 @@ action atom_vec_molecular_kokkos.cpp atom_vec_molecular.cpp
 action atom_vec_molecular_kokkos.h atom_vec_molecular.h
 action atom_vec_sphere_kokkos.cpp atom_vec_sphere.cpp
 action atom_vec_sphere_kokkos.h atom_vec_sphere.h
-action bond_class2_kokkos.cpp bond_class2.cpp 
+action bond_class2_kokkos.cpp bond_class2.cpp
 action bond_class2_kokkos.h bond_class2.h
 action bond_fene_kokkos.cpp bond_fene.cpp
 action bond_fene_kokkos.h bond_fene.h
@@ -93,9 +93,9 @@ action compute_temp_kokkos.cpp
 action compute_temp_kokkos.h
 action dihedral_charmm_kokkos.cpp dihedral_charmm.cpp
 action dihedral_charmm_kokkos.h dihedral_charmm.h
-action dihedral_class2_kokkos.cpp dihedral_class2.cpp 
+action dihedral_class2_kokkos.cpp dihedral_class2.cpp
 action dihedral_class2_kokkos.h dihedral_class2.h
-action dihedral_harmonic_kokkos.cpp dihedral_harmonic.cpp 
+action dihedral_harmonic_kokkos.cpp dihedral_harmonic.cpp
 action dihedral_harmonic_kokkos.h dihedral_harmonic.h
 action dihedral_opls_kokkos.cpp dihedral_opls.cpp
 action dihedral_opls_kokkos.h dihedral_opls.h
@@ -109,7 +109,7 @@ action fix_deform_kokkos.h
 action fix_enforce2d_kokkos.cpp
 action fix_enforce2d_kokkos.h
 action fix_eos_table_rx_kokkos.cpp fix_eos_table_rx.cpp
-action fix_eos_table_rx_kokkos.h fix_eos_table_rx.h  
+action fix_eos_table_rx_kokkos.h fix_eos_table_rx.h
 action fix_freeze_kokkos.cpp fix_freeze.cpp
 action fix_freeze_kokkos.h fix_freeze.h
 action fix_gravity_kokkos.cpp
@@ -156,7 +156,7 @@ action fix_rx_kokkos.cpp fix_rx.cpp
 action fix_rx_kokkos.h fix_rx.h
 action gridcomm_kokkos.cpp gridcomm.cpp
 action gridcomm_kokkos.h gridcomm.h
-action improper_class2_kokkos.cpp improper_class2.cpp 
+action improper_class2_kokkos.cpp improper_class2.cpp
 action improper_class2_kokkos.h improper_class2.h
 action improper_harmonic_kokkos.cpp improper_harmonic.cpp
 action improper_harmonic_kokkos.h improper_harmonic.h

src/Make.sh

@@ -1,4 +1,4 @@
-# Make.sh = update Makefile.lib, Makefile.shlib, Makefile.list 
+# Make.sh = update Makefile.lib, Makefile.shlib, Makefile.list
 #           or style_*.h files
 # Syntax: sh Make.sh style
 #         sh Make.sh Makefile.lib
@@ -31,7 +31,7 @@ style () {
       rm -f style_$3.h
       touch style_$3.h
       rm -f Obj_*/$4.d
-      if (test $5) then 
+      if (test $5) then
         rm -f Obj_*/$5.d
       fi
       rm -f Obj_*/lammps.d
@@ -39,14 +39,14 @@ style () {
   elif (test ! -e style_$3.h) then
     mv style_$3.tmp style_$3.h
     rm -f Obj_*/$4.d
-    if (test $5) then 
+    if (test $5) then
       rm -f Obj_*/$5.d
     fi
     rm -f Obj_*/lammps.d
   elif (test "`diff --brief style_$3.h style_$3.tmp`" != "") then
     mv style_$3.tmp style_$3.h
     rm -f Obj_*/$4.d
-    if (test $5) then 
+    if (test $5) then
       rm -f Obj_*/$5.d
     fi
     rm -f Obj_*/lammps.d

src/OPT/Install.sh

@@ -41,7 +41,7 @@ action pair_lj_cut_coul_long_opt.h pair_lj_cut_coul_long.cpp
 action pair_lj_cut_opt.cpp
 action pair_lj_cut_opt.h
 action pair_lj_cut_tip4p_long_opt.cpp pair_lj_cut_tip4p_long.cpp
-action pair_lj_cut_tip4p_long_opt.h pair_lj_cut_tip4p_long.cpp 
+action pair_lj_cut_tip4p_long_opt.h pair_lj_cut_tip4p_long.cpp
 action pair_lj_long_coul_long_opt.cpp pair_lj_long_coul_long.cpp
 action pair_lj_long_coul_long_opt.h pair_lj_long_coul_long.cpp
 action pair_morse_opt.cpp

src/SPIN/README

@@ -1,5 +1,5 @@
-The SPIN package enables coupled spin dynamics and molecular 
+The SPIN package enables coupled spin dynamics and molecular
-dynamics simulations. 
+dynamics simulations.
 
 The package provides the following features:
 
@@ -12,11 +12,11 @@ atom in the system
 * computing and outputting magnetic quantities
 * minimizing the energy or total torque of a magnetic system
 
-The different options provided by this package are explained in the 
+The different options provided by this package are explained in the
 LAMMPS documentation.
 
-Once you have successfully built LAMMPS with this package, you can test 
+Once you have successfully built LAMMPS with this package, you can test
-it using one of the input files provided from the examples/SPIN dir. 
+it using one of the input files provided from the examples/SPIN dir.
 For example:
 
 ./lmp_serial < lammps/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp

src/USER-ADIOS/Install.sh

@@ -52,7 +52,7 @@ if (test $1 = 1) then
          "installation directory or adios2-config should be in PATH"
   fi
 
-  if [ "$CONFIGSCRIPT" != "none" ]; then 
+  if [ "$CONFIGSCRIPT" != "none" ]; then
     ADIOS2_INC=`$CONFIGSCRIPT --cxx-flags`
     ADIOS2_LIB=`$CONFIGSCRIPT --cxx-libs`
 

src/USER-ADIOS/README

@@ -1,16 +1,16 @@
 This package provides the adios dump and read_dump styles.
 
-See the doc page for the "dump adios" and "read_dump ... format adios" commands. 
+See the doc page for the "dump adios" and "read_dump ... format adios" commands.
 These styles require having ADIOS 2.x itself installed on your system.
 
-Configure LAMMPS with CMake 
+Configure LAMMPS with CMake
- a. set the environment variable 
+ a. set the environment variable
-        ADIOS2_DIR 
+        ADIOS2_DIR
     to the ADIOS 2.x installation path
- b. use the cmake option 
+ b. use the cmake option
-       -D PKG_USER-ADIOS=yes 
+       -D PKG_USER-ADIOS=yes
 
-The person who created this package is Norbert Podhorszki (Oak Ridge National Laboratory); 
+The person who created this package is Norbert Podhorszki (Oak Ridge National Laboratory);
 If you need help, please submit a ticket at the OLCF ticket user support mentioning his name in the ticket.
 https://www.olcf.ornl.gov/support/submit-ticket
 

src/USER-BOCS/README

@@ -1,7 +1,7 @@
-This user package implements the pressure correction to the barostat as 
+This user package implements the pressure correction to the barostat as
 outlined in:
 
-N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that 
+N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
 accurately describe the structure, pressure, and compressibility of
 molecular liquids," J. Chem. Phys. 143, 243148 (2015).
 

src/USER-CGDNA/README.md

@@ -2,49 +2,49 @@ This package contains a LAMMPS implementation of coarse-grained
 models of DNA, which can be used to model sequence-specific
 DNA strands.
 
-Please cite 
+Please cite
 
 [![DOI](https://zenodo.org/badge/132764768.svg)](https://zenodo.org/badge/latestdoi/132764768)
 
-as well as [1] and the relevant oxDNA, oxDNA2 and oxRNA2 articles 
+as well as [1] and the relevant oxDNA, oxDNA2 and oxRNA2 articles
 in any publication that uses this package.
 
-See the doc pages and [2,3,4,5,6] for the individual bond and pair styles. 
+See the doc pages and [2,3,4,5,6] for the individual bond and pair styles.
 The packages contains also a new Langevin-type rigid-body integrator,
 which has also its own doc page and is explained in [7].
 
 [1] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge,
-"Coarse-grained simulation of DNA using LAMMPS", 
+"Coarse-grained simulation of DNA using LAMMPS",
 Eur. Phys. J. E 41, 57 (2018).
 
-[2] T. Ouldridge, A. Louis, J. Doye, "Structural, mechanical, 
+[2] T. Ouldridge, A. Louis, J. Doye, "Structural, mechanical,
 and thermodynamic properties of a coarse-grained DNA model",
 J. Chem. Phys. 134, 085101 (2011).
 
-[3] T.E. Ouldridge, "Coarse-grained modelling of DNA and DNA 
+[3] T.E. Ouldridge, "Coarse-grained modelling of DNA and DNA
 self-assembly", DPhil. University of Oxford (2011).
 
 [4] B.E. Snodin, F. Randisi, M. Mosayebi, et al., "Introducing
 Improved structural properties and salt dependence into a coarse-grained
 model of DNA", J. Chem. Phys. 142, 234901 (2015).
 
-[5] P. Sulc, F. Romano, T.E. Ouldridge, et al., "A nucleotide-level 
+[5] P. Sulc, F. Romano, T.E. Ouldridge, et al., "A nucleotide-level
 coarse-grained model of RNA", J. Chem. Phys. 140, 235102 (2014).
 
-[6] P. Sulc, F. Romano, T.E. Ouldridge, et al., "Sequence-dependent 
+[6] P. Sulc, F. Romano, T.E. Ouldridge, et al., "Sequence-dependent
 thermodynamics of a coarse-grained DNA model",
-J. Chem. Phys. 137, 135101 (2012). 
+J. Chem. Phys. 137, 135101 (2012).
 
-[7] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and 
+[7] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and
-gradient thermostats for rigid body dynamics", J. Chem. Phys. 142, 
+gradient thermostats for rigid body dynamics", J. Chem. Phys. 142,
 144114 (2015).
 
 Example input and data files can be found in
-/examples/USER/cgdna/examples/oxDNA/, /oxDNA2/ and /oxRNA2/. 
+/examples/USER/cgdna/examples/oxDNA/, /oxDNA2/ and /oxRNA2/.
-Python setup tools which create single straight or helical DNA or RNA 
+Python setup tools which create single straight or helical DNA or RNA
-strands as well as DNA or RNA duplexes or arrays of duplexes can be 
+strands as well as DNA or RNA duplexes or arrays of duplexes can be
-found in /examples/USER/cgdna/util/. A technical report with more 
+found in /examples/USER/cgdna/util/. A technical report with more
-general information on the model, its implementation and performance 
+general information on the model, its implementation and performance
 as well as the structure of the data and input file can be found
 in /doc/src/PDF/USER-CGDNA.pdf.
 
@@ -65,7 +65,7 @@ oliver d o t henrich a t strath d o t ac d o t uk
 
 ** Bond styles provided by this package:
 
-bond_oxdna_fene.cpp:    backbone connectivity, 
+bond_oxdna_fene.cpp:    backbone connectivity,
                         a modified FENE potential (see [2,3])
 
 bond_oxdna2_fene.cpp:   corresponding bond style in oxDNA2 (see [4])
@@ -86,20 +86,20 @@ pair_oxdna_xstk.cpp:    cross-stacking interaction between nucleotides
 
 pair_oxdna_coaxstk.cpp: coaxial stacking interaction between nucleotides
 
-pair_oxdna2_excv.cpp, pair_oxdna2_coaxstk.cpp: 
+pair_oxdna2_excv.cpp, pair_oxdna2_coaxstk.cpp:
                         corresponding pair styles in oxDNA2 (see [4])
 
-pair_oxrna2_excv.cpp, pair_oxrna2_stk.cpp, pair_oxrna2_hbond.cpp, 
+pair_oxrna2_excv.cpp, pair_oxrna2_stk.cpp, pair_oxrna2_hbond.cpp,
-pair_oxrna2_xstk.cpp: 
+pair_oxrna2_xstk.cpp:
                         corresponding pair styles in oxDNA2 (see [5])
 
-pair_oxdna2_dh.cpp, pair_oxrna2_dh.cpp:  
+pair_oxdna2_dh.cpp, pair_oxrna2_dh.cpp:
                Debye-Hueckel electrostatic interaction between backbone sites
 
 
 ** Fixes provided by this package:
 
 fix_nve_dotc_langevin.cpp:  fix for Langevin-type rigid body integrator "C"
-                            in above Ref. [7] 
+                            in above Ref. [7]
 
 fix_nve_dot.cpp:  NVE-type rigid body integrator without noise

src/USER-DIFFRACTION/README

@@ -1,41 +1,41 @@
 This package contains the commands needed to calculate x-ray and
-electron diffraction intensities based on kinematic diffraction 
+electron diffraction intensities based on kinematic diffraction
 theory. Detailed discription of the computation can be found in the
 following works:
 
-Coleman, S.P., Spearot, D.E., Capolungo, L.  (2013) Virtual 
+Coleman, S.P., Spearot, D.E., Capolungo, L.  (2013) Virtual
-diffraction analysis of Ni [010] symmetric tilt grain boundaries, 
+diffraction analysis of Ni [010] symmetric tilt grain boundaries,
-Modelling and Simulation in Materials Science and Engineering, 21 
+Modelling and Simulation in Materials Science and Engineering, 21
 055020. doi:10.1088/0965-0393/21/5/055020
 
-Coleman, S.P., Sichani, M.M., Spearot, D.E.  (2014) A computational 
+Coleman, S.P., Sichani, M.M., Spearot, D.E.  (2014) A computational
-algorithm to produce virtual x-ray and electron diffraction patterns 
+algorithm to produce virtual x-ray and electron diffraction patterns
-from atomistic simulations, JOM, 66 (3), 408-416. 
+from atomistic simulations, JOM, 66 (3), 408-416.
-doi:10.1007/s11837-013-0829-3 
+doi:10.1007/s11837-013-0829-3
 
-Coleman, S.P., Pamidighantam, S. Van Moer, M., Wang, Y., Koesterke, L. 
+Coleman, S.P., Pamidighantam, S. Van Moer, M., Wang, Y., Koesterke, L.
-Spearot D.E (2014) Performance improvement and workflow development 
+Spearot D.E (2014) Performance improvement and workflow development
-of virtual diffraction calculations, XSEDE14, 
+of virtual diffraction calculations, XSEDE14,
 doi:10.1145/2616498.2616552
 
 ---------------------------------
 
 User-diffraction includes:
 
-1) compute_xrd :  calculate x-ray diffraction intensities as a 
+1) compute_xrd :  calculate x-ray diffraction intensities as a
                   scattering angle (2theta)
 
 2) compute_xrd_consts.h :  coefficients used for x-ray atomic
                            scattering factors listed by element
 
-3) compute saed : calculate 3D diffraction intensities for the 
+3) compute saed : calculate 3D diffraction intensities for the
-                  purpose of creating selected area electron 
+                  purpose of creating selected area electron
                   diffraction patterns
 
 4) compute_xrd_consts.h :  coefficients used for electron atomic
                            scattering factors listed by element
 
-3) fix saed/vtk :  writes 3D diffraction intensity data calculated 
+3) fix saed/vtk :  writes 3D diffraction intensity data calculated
                    with "compute saed" in vtk format
 
 
@@ -48,8 +48,8 @@ examples/USER/diffraction.
 
 AUTHOR INFORMATION:
 
-The person who created this package is Shawn P. Coleman 
+The person who created this package is Shawn P. Coleman
-(shawn.p.coleman8.ctr at mail.mil) while at the University of 
+(shawn.p.coleman8.ctr at mail.mil) while at the University of
 Arkansas.  Contact him directly if you have questions.
 
 Co-Author:  Douglas Spearot (University of Arkansas)

src/USER-EFF/README

@@ -46,7 +46,7 @@ Chemistry and Chemical Engineering, 139-74
 Phone: (626) 395-3591
 e-mail: ajaramil@wag.caltech.edu
 
-Co-Authors: 
+Co-Authors:
 Julius Su (jsu@wag.caltech.edu)
 William A. Goddard III (wag@wag.caltech.edu)
 
@@ -57,11 +57,11 @@ LAMMPS architecture and for their help in customizing some of the
 required LAMMPS core modules.
 
 Version 01/2010: Special thanks to:
-- Hai Xiao (Caltech) for reviewing the fixed-core implementation and 
+- Hai Xiao (Caltech) for reviewing the fixed-core implementation and
   providing useful insights to improve it, and for his work on the effective core pseudopotential.
-- Vaclav Cvicek (Caltech) for thoroughly revising the units, for finding a bug in the 
+- Vaclav Cvicek (Caltech) for thoroughly revising the units, for finding a bug in the
   fix_langevin_eff radial scaling factors, and for suggesting changes to clean-up the code.
-- Patrick Theofanis (Caltech) for providing an optimized set of parameters for the Si ECP 
+- Patrick Theofanis (Caltech) for providing an optimized set of parameters for the Si ECP
   (default) and for providing basic cases.
 - Qi An (Caltech) for providing feedback on usage, application cases, and testing.
 
@@ -76,16 +76,16 @@ different eFF energy components (eke, epauli, ecoul and errestrain),
 fixed radial scaling factors in the eff langevin thermostat.
 
 12/2011: Added support for "zero" option in fix langevin/eff (see doc), and
-adjusted fix_langevin_eff.cpp to correctly thermostat between nuclear and electronic dof 
+adjusted fix_langevin_eff.cpp to correctly thermostat between nuclear and electronic dof
 (required additional scaling of friction term in the Langevin equations of motion).
 Radial electron mass now scales as a function of system dimension.
 
 Bug fixes:
 (10-2011): Thanks to Christian Chenard-Lemire (U Montreal) for reporting a bug in the
 fixed pair_eff_cut.cpp fixedcore-pseudocore interactions (an incorrect index and a missing
-elec-core call to account for the 2 electrons from the fixed core.)     
+elec-core call to account for the 2 electrons from the fixed core.)
-(12-2011): Corrected undefined natom variable in fix_langevin_eff (recent changes in 
+(12-2011): Corrected undefined natom variable in fix_langevin_eff (recent changes in
-main fix_langevin class caused compilation error in user-eff).  
+main fix_langevin class caused compilation error in user-eff).
 Corrected thermostat in fix langevin/eff as described in version 12/2011.
 
 

src/USER-FEP/README

@@ -17,6 +17,6 @@ Applied Physics/Theory of Polymers and Soft Matter,
 Eindhoven University of Technology (TU/e), The Netherlands
 Contact him in case of problems with this pair style.
 
-Pair styles lj/class2/soft were contributed by Evangelos Voyiatzis at 
+Pair styles lj/class2/soft were contributed by Evangelos Voyiatzis at
 Technical University of Darmstadt (e.voyiatzis at theo.chemie.tu-darmstadt.de)
 Contact him in case of problems with these pair styles.

src/USER-INTEL/TEST/run_benchmarks.sh

@@ -6,7 +6,7 @@
 
 # --------------------- MPI Launch Command
 
-export MPI="mpirun"           
+export MPI="mpirun"
 #export MPI="numactl -p 1 mpirun"    # -- Systems w/ MCDRAM in flat mode
 
 # ------------- Name and location of the LAMMPS binary

src/USER-LB/README

@@ -39,15 +39,15 @@ cdennist@uwo.ca
 
 Fixes provided by this package:
 
-fix_lb_fluid.cpp:  fix used to create the lattice-Boltzmann fluid on a 
+fix_lb_fluid.cpp:  fix used to create the lattice-Boltzmann fluid on a
 		   grid covering the LAMMPS simulation domain.
 
-fix_momentum_lb.cpp:  fix used to subtract off the total (atom plus fluid) 
+fix_momentum_lb.cpp:  fix used to subtract off the total (atom plus fluid)
 		      linear momentum from the system.
 
 fix_pc.cpp:  integration algorithm for individual atoms.
 
-fix_rigid_pc_sphere.cpp:  integration algorithm for rigid spherical 
+fix_rigid_pc_sphere.cpp:  integration algorithm for rigid spherical
 			  collections of atoms.
 
 fix_viscous_lb.cpp:  fix to add the fluid force to the atoms when using a

src/USER-MESONT/README

@@ -1,19 +1,19 @@
-USER-MESONT is a LAMMPS package for simulation of nanomechanics of carbon 
+USER-MESONT is a LAMMPS package for simulation of nanomechanics of carbon
-nanotubes (CNTs). The model is based on a coarse-grained representation 
+nanotubes (CNTs). The model is based on a coarse-grained representation
-of CNTs as "flexible cylinders" consisting of a variable number of 
+of CNTs as "flexible cylinders" consisting of a variable number of
-segments. Internal interactions within a CNT and the van der Waals 
+segments. Internal interactions within a CNT and the van der Waals
-interaction between the tubes are described by a mesoscopic force 
+interaction between the tubes are described by a mesoscopic force
-field designed and parameterized based on the results of atomic-level 
+field designed and parameterized based on the results of atomic-level
-molecular dynamics simulations. The description of the force field 
+molecular dynamics simulations. The description of the force field
 is provided in the papers listed below.
 
 --
 
-This package was created by Maxim Shugaev (mvs9t@virginia.edu) 
+This package was created by Maxim Shugaev (mvs9t@virginia.edu)
 at the University of Virginia.
-The Fortran library implementing basic level functions describing stretching, 
+The Fortran library implementing basic level functions describing stretching,
 bending, and intertube components of the mesoscopic CNT force field, used
-by this package is developed by Alexey N. Volkov (avolkov1@ua.edu) 
+by this package is developed by Alexey N. Volkov (avolkov1@ua.edu)
 at the University of Alabama.
 
 --
@@ -21,69 +21,69 @@ at the University of Alabama.
 The following commands are contained in this package:
 
 atom_style mesont
-  This command enables mesont atom_style containing variables used for 
+  This command enables mesont atom_style containing variables used for
   further commands in USER-MESONT.
 
-pair_style mesont/tpm cut table_path BendingMode TPMType 
+pair_style mesont/tpm cut table_path BendingMode TPMType
-  This command activates a pair_style describing CNT mesoscopic tubular 
+  This command activates a pair_style describing CNT mesoscopic tubular
-  potential model (TPM) force field. "cut" is cutoff distance that should 
+  potential model (TPM) force field. "cut" is cutoff distance that should
-  be set to be at least max(2.0*L, sqrt(L^2/2 + (2.0*R + Tcut)^2)), 
+  be set to be at least max(2.0*L, sqrt(L^2/2 + (2.0*R + Tcut)^2)),
-  where L is the maximum segment length, R is the maximum tube radius, 
+  where L is the maximum segment length, R is the maximum tube radius,
-  and Tcut = 10.2 A is the maximum distance between surfaces of interacting 
+  and Tcut = 10.2 A is the maximum distance between surfaces of interacting
   segments. However, the recommended cutoff is 3L.
 
 compute mesont
-  This command allows evaluation of per atom and total values of stretching, 
+  This command allows evaluation of per atom and total values of stretching,
-  bending, and intertube interaction components of energies. Use the following 
+  bending, and intertube interaction components of energies. Use the following
   flags: 'estretch', 'ebend', 'etube'.
 
 --
 
 References:
 
-L. V. Zhigilei, C. Wei, and D. Srivastava, Mesoscopic model for dynamic 
+L. V. Zhigilei, C. Wei, and D. Srivastava, Mesoscopic model for dynamic
 simulations of carbon nanotubes, Phys. Rev. B 71, 165417, 2005.
 
-A. N. Volkov and L. V. Zhigilei, Structural stability of carbon nanotube 
+A. N. Volkov and L. V. Zhigilei, Structural stability of carbon nanotube
 films: The role of bending buckling, ACS Nano 4, 6187-6195, 2010.
 
-A. N. Volkov, K. R. Simov, and L. V. Zhigilei, Mesoscopic model for simulation 
+A. N. Volkov, K. R. Simov, and L. V. Zhigilei, Mesoscopic model for simulation
-of CNT-based materials, Proceedings of the ASME International Mechanical 
+of CNT-based materials, Proceedings of the ASME International Mechanical
-Engineering Congress and Exposition (IMECE2008), ASME paper IMECE2008-68021, 
+Engineering Congress and Exposition (IMECE2008), ASME paper IMECE2008-68021,
 2008.
 
-A. N. Volkov and L. V. Zhigilei, Mesoscopic interaction potential for carbon 
+A. N. Volkov and L. V. Zhigilei, Mesoscopic interaction potential for carbon
-nanotubes of arbitrary length and orientation, J. Phys. Chem. C 114, 5513-5531, 
+nanotubes of arbitrary length and orientation, J. Phys. Chem. C 114, 5513-5531,
 2010.
 
-B. K. Wittmaack, A. H. Banna, A. N. Volkov, L. V. Zhigilei, Mesoscopic 
+B. K. Wittmaack, A. H. Banna, A. N. Volkov, L. V. Zhigilei, Mesoscopic
-modeling of structural self-organization of carbon nanotubes into vertically 
+modeling of structural self-organization of carbon nanotubes into vertically
 aligned networks of nanotube bundles, Carbon 130, 69-86, 2018.
 
-B. K. Wittmaack, A. N. Volkov, L. V. Zhigilei, Mesoscopic modeling of the 
+B. K. Wittmaack, A. N. Volkov, L. V. Zhigilei, Mesoscopic modeling of the
-uniaxial compression and recovery of vertically aligned carbon nanotube 
+uniaxial compression and recovery of vertically aligned carbon nanotube
 forests, Compos. Sci. Technol. 166, 66-85, 2018.
 
-B. K. Wittmaack, A. N. Volkov, L. V. Zhigilei, Phase transformation as the 
+B. K. Wittmaack, A. N. Volkov, L. V. Zhigilei, Phase transformation as the
-mechanism of mechanical deformation of vertically aligned carbon nanotube 
+mechanism of mechanical deformation of vertically aligned carbon nanotube
 arrays: Insights from mesoscopic modeling, Carbon 143, 587-597, 2019.
 
-A. N. Volkov and L. V. Zhigilei, Scaling laws and mesoscopic modeling of 
+A. N. Volkov and L. V. Zhigilei, Scaling laws and mesoscopic modeling of
-thermal conductivity in carbon nanotube materials, Phys. Rev. Lett. 104, 
+thermal conductivity in carbon nanotube materials, Phys. Rev. Lett. 104,
 215902, 2010.
 
-A. N. Volkov, T. Shiga, D. Nicholson, J. Shiomi, and L. V. Zhigilei, Effect 
+A. N. Volkov, T. Shiga, D. Nicholson, J. Shiomi, and L. V. Zhigilei, Effect
-of bending buckling of carbon nanotubes on thermal conductivity of carbon 
+of bending buckling of carbon nanotubes on thermal conductivity of carbon
 nanotube materials, J. Appl. Phys. 111, 053501, 2012.
 
-A. N. Volkov and L. V. Zhigilei, Heat conduction in carbon nanotube materials: 
+A. N. Volkov and L. V. Zhigilei, Heat conduction in carbon nanotube materials:
-Strong effect of intrinsic thermal conductivity of carbon nanotubes, Appl. 
+Strong effect of intrinsic thermal conductivity of carbon nanotubes, Appl.
 Phys. Lett. 101, 043113, 2012.
 
-W. M. Jacobs, D. A. Nicholson, H. Zemer, A. N. Volkov, and L. V. Zhigilei, 
+W. M. Jacobs, D. A. Nicholson, H. Zemer, A. N. Volkov, and L. V. Zhigilei,
-Acoustic energy dissipation and thermalization in carbon nanotubes: Atomistic 
+Acoustic energy dissipation and thermalization in carbon nanotubes: Atomistic
 modeling and mesoscopic description, Phys. Rev. B 86, 165414, 2012.
 
-A. N. Volkov and A. H. Banna, Mesoscopic computational model of covalent 
+A. N. Volkov and A. H. Banna, Mesoscopic computational model of covalent
-cross-links and mechanisms of load transfer in cross-linked carbon nanotube 
+cross-links and mechanisms of load transfer in cross-linked carbon nanotube
 films with continuous networks of bundles, Comp. Mater. Sci. 176, 109410, 2020.

src/USER-MGPT/README

@@ -1,17 +1,17 @@
-This package contains a fast implementation for LAMMPS of quantum-based 
+This package contains a fast implementation for LAMMPS of quantum-based
-MGPT multi-ion potentials.  The MGPT or model GPT method derives from 
+MGPT multi-ion potentials.  The MGPT or model GPT method derives from
-first-principles DFT-based generalized pseudopotential theory (GPT) 
+first-principles DFT-based generalized pseudopotential theory (GPT)
-through a series of systematic approximations valid for mid-period 
+through a series of systematic approximations valid for mid-period
 transition metals with nearly half-filled d bands.  The MGPT method
-was originally developed by John Moriarty at Lawrence Livermore 
+was originally developed by John Moriarty at Lawrence Livermore
 National Lab (LLNL).
 
-In the general matrix representation of MGPT, which can also be applied 
+In the general matrix representation of MGPT, which can also be applied
-to f-band actinide metals, the multi-ion potentials are evaluated on the 
+to f-band actinide metals, the multi-ion potentials are evaluated on the
-fly during a simulation through d- or f-state matrix multiplication, and 
+fly during a simulation through d- or f-state matrix multiplication, and
-the forces that move the ions are determined analytically.  The mgpt 
+the forces that move the ions are determined analytically.  The mgpt
 pair style in this package calculates forces and energies using an
-optimized matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL.  
+optimized matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL.
 
 See the doc page for the pair_style mgpt command for full details on
 using this package in LAMMPS. In particular, the user should note that
@@ -22,10 +22,10 @@ steps to perform constant-volume calculations and simulations.  It is
 strongly recommended that the user work through and understand these
 examples before proceeding to more complex simulations.
 
-Specific MGPT potential data for the transition metals tantalum 
+Specific MGPT potential data for the transition metals tantalum
 (Ta4 and Ta6.8x potentials), molybdenum (Mo5.2 potentials), and
-vanadium (V6.1 potentials) are contained in the LAMMPS "potentials" 
+vanadium (V6.1 potentials) are contained in the LAMMPS "potentials"
-directory.  It is expected that MGPT potentials for additional 
+directory.  It is expected that MGPT potentials for additional
 materials will be added over time.
 
 The persons who created the USER-MGPT package are Tomas Oppelstrup

src/USER-MOFFF/README

@@ -1,32 +1,32 @@
-This Package implements pair, angle and improper styles needed to employ 
+This Package implements pair, angle and improper styles needed to employ
-the MOF-FF force field by Schmid and coworkers with LAMMPS. 
+the MOF-FF force field by Schmid and coworkers with LAMMPS.
 MOF-FF is a first principles derived force field with the primary aim
-to simulate MOFs and related porous framework materials, using spherical 
+to simulate MOFs and related porous framework materials, using spherical
 Gaussian charges. It is described in S. Bureekaew et al., Phys. Stat. Sol. B
 2013, 250, 1128-1141.
-For the usage of MOF-FF see the example in the example directory as 
+For the usage of MOF-FF see the example in the example directory as
 well as the "MOF+" website (https://www.mofplus.org/content/show/MOF-FF).
-The package provides the following features: 
+The package provides the following features:
 
-* a dispersion damped Buckhingham potential with spherical Gaussian type 
+* a dispersion damped Buckhingham potential with spherical Gaussian type
 charges (dsf and long-range treatment of charges)
 
 * a modified angle/class2 including 6th order polynomial
 
-* a modified angle/cosine style which adds a dispersion damped Buckhingham 
+* a modified angle/cosine style which adds a dispersion damped Buckhingham
 1-3 interaction analog to the dihedral/charmm style
 
-* an improper style following the Wilson-Decius definition of the 
+* an improper style following the Wilson-Decius definition of the
 out-of-plane angle
 
 See the file doc/drude_tutorial.html for getting started.
-See the doc pages for "pair_style buck6d/coul/gauss", "anlge_style class2", 
+See the doc pages for "pair_style buck6d/coul/gauss", "anlge_style class2",
 "angle_style cosine/buck6d", and "improper_style inversion/harmonic"
-commands to get started. Also see the above mentioned website and 
+commands to get started. Also see the above mentioned website and
 literature for further documentation about the force field.
 
 There are example scripts for using this force field in examples/USER/mofff.
 
 The creators of this package are Hendrik Heenen (hendrik.heenen at mytum.de)
-and Rochus Schmid (rochus.schmid at rub.de). Contact them directly if you 
+and Rochus Schmid (rochus.schmid at rub.de). Contact them directly if you
 have questions.

src/USER-PLUMED/README

@@ -1,43 +1,43 @@
 This package implements the "fix plumed" command, which can be used
 in a LAMMPS input script.
 
-The fix allows enhanced sampling methods such as umbrella sampling and 
+The fix allows enhanced sampling methods such as umbrella sampling and
-metadynamics to be used.  Furthermore, PLUMED can be used to perform a 
+metadynamics to be used.  Furthermore, PLUMED can be used to perform a
 wide range of analyses on trajectories on the fly as they are generated.
 
 The package uses the "PLUMED" library, whose source code is not included
-in the LAMMPS source code distribution. The files in the USER-PLUMED package 
+in the LAMMPS source code distribution. The files in the USER-PLUMED package
-folder implement an interface between LAMMPS and PLUMED, that are written 
+folder implement an interface between LAMMPS and PLUMED, that are written
 and maintained by Gareth Tribello (gareth.tribello@gmail.com).
 
-PLUMED must instead be downloaded and compiled separately to LAMMPS.  This building 
+PLUMED must instead be downloaded and compiled separately to LAMMPS.  This building
-and compiling of PLUMED can be done before or after the building of LAMMPS as LAMMPS 
+and compiling of PLUMED can be done before or after the building of LAMMPS as LAMMPS
-can call PLUMED as a dynamic library.  There is also the possibility to link PLUEMD 
+can call PLUMED as a dynamic library.  There is also the possibility to link PLUEMD
-statically.  In this case a copy of PLUMED must be downloaded into the lib/plumed 
+statically.  In this case a copy of PLUMED must be downloaded into the lib/plumed
-directory.  This copy of PLUMED will then always be linked into the code at compile 
+directory.  This copy of PLUMED will then always be linked into the code at compile
-time. 
+time.
 
 However you decide to link PLUMED (statically or dynamically) you must run the command:
 
 make yes-user-plumed
 
-before compiling LAMMPS in order to enable the module.   In addition, if you have chosen to 
+before compiling LAMMPS in order to enable the module.   In addition, if you have chosen to
-link PLUMED dynamically you must ensure that PLUMED is in your 
+link PLUMED dynamically you must ensure that PLUMED is in your
-PATH when running a LAMMPS calculation that takes advantage of PLUMED.  If 
+PATH when running a LAMMPS calculation that takes advantage of PLUMED.  If
-PLUMED is linked as a runtime library and if PLUMED is not in the PATH an error will be returned whenever LAMMPS encounters 
+PLUMED is linked as a runtime library and if PLUMED is not in the PATH an error will be returned whenever LAMMPS encounters
-the fix plumed command in its input.  To be clear, however, a LAMMPS executable that was dynamically linked with PLUMED will run 
+the fix plumed command in its input.  To be clear, however, a LAMMPS executable that was dynamically linked with PLUMED will run
-even if PLUMED is not in the path if as long as the input does not contain a fix 
+even if PLUMED is not in the path if as long as the input does not contain a fix
 plumed command.
 
-If you wish to statically link PLUMED you must download PLUMED to the /lib/plumed directory before compiling LAMMPS.  You can 
+If you wish to statically link PLUMED you must download PLUMED to the /lib/plumed directory before compiling LAMMPS.  You can
-download a tar ball into that directory or you can clone the plumed2 repository from github there.  Once you have created a 
+download a tar ball into that directory or you can clone the plumed2 repository from github there.  Once you have created a
-directory containing a distribution of PLUMED within /lib/plumed you then must build PLUMED within that directory by issuing 
+directory containing a distribution of PLUMED within /lib/plumed you then must build PLUMED within that directory by issuing
-the usual commands.  It is worth noting that we have provided a script that will download and build PLUMED for you with 
+the usual commands.  It is worth noting that we have provided a script that will download and build PLUMED for you with
 a minimal set of options.  To run this script you need to issue the following command:
 
 make lib-plumed args="-b"
 
-in the src directory. 
+in the src directory.
 
 More info about the PLUMED library can be found at:
 
@@ -55,8 +55,8 @@ M. Bonomi, D. Branduardi, G. Bussi, C. Camilloni, D. Provasi, P. Raiteri, D. Don
 Comp. Phys. Comm. 180, 1961 (2009)
 https://doi.org/10.1016/j.cpc.2009.05.011
 
-Instructions explaining how to use PLUMED and LAMMPS in tandem can be found on the PLUMED website, which also gives 
+Instructions explaining how to use PLUMED and LAMMPS in tandem can be found on the PLUMED website, which also gives
-numerous example scripts for PLUMED as well as citations to articles that dcoment the various methods that are 
+numerous example scripts for PLUMED as well as citations to articles that dcoment the various methods that are
 implemented within PLUMED.
 
 There are also example scripts for using this package in the folder

src/USER-QUIP/README

@@ -1,6 +1,6 @@
 This package provides the pair_style quip command. This pair style
 provides an interface to the QUIP/libAtoms library, which includes a
-variety of interatomic potentials, including Gaussian Approximation  
+variety of interatomic potentials, including Gaussian Approximation
 Potential (GAP) models.
 
 See lib/quip/README for more information on how to build LAMMPS

src/USER-SCAFACOS/Install.sh

@@ -46,7 +46,7 @@ if (test $1 = 1) then
 
 elif (test $1 = 0) then
 
-  if (test -e ../Makefile.package) then 
+  if (test -e ../Makefile.package) then
     sed -i -e 's/`.*scafacos.*` //' ../Makefile.package
     sed -i -e 's/[^ \t]*scafacos[^ \t]* //' ../Makefile.package
   fi

src/USER-SPH/README

@@ -1,13 +1,13 @@
 This package implements smoothed particle hydrodynamics (SPH) in
 LAMMPS.  Currently, the package has the following features:
 
-* Tait, ideal gas, Lennard-Jones equation of states, full support for 
+* Tait, ideal gas, Lennard-Jones equation of states, full support for
   complete (i.e. internal-energy dependent) equations of state
 * plain or Monaghans XSPH integration of the equations of motion
 * density continuity or density summation to propagate the density field
-* commands to set internal energy and density of particles from the 
+* commands to set internal energy and density of particles from the
   input script
-* output commands to access internal energy and density for dumping and 
+* output commands to access internal energy and density for dumping and
   thermo output
 
 See the file doc/USER/sph/SPH_LAMMPS_userguide.pdf to get started.

src/USER-TALLY/README

@@ -7,7 +7,7 @@ users have asked for such a facility over time.
 The currently provided compute styles are mostly meant as a
 demonstration for how to use this facility and provide an
 alternative approach to using features like compute group/group
-or compute heat/flux. Its application is limited to pairwise 
+or compute heat/flux. Its application is limited to pairwise
 additive potentials that use the standard Pair::ev_tally()
 method to accumulate energy (and virial).
 

src/VORONOI/README

@@ -20,8 +20,8 @@ you can test it using an input file from the examples dir:
 
 ./lmp_serial < lammps/examples/voronoi/in.voronoi | grep '^TEST_'
 
-The output should conclude with 'TEST_DONE' and every line should 
+The output should conclude with 'TEST_DONE' and every line should
-report an error of 0%. 
+report an error of 0%.
 
 == Credits and license ==