diff --git a/cmake/Modules/Packages/USER-NETCDF.cmake b/cmake/Modules/Packages/USER-NETCDF.cmake index f60c046ab9..921156f1e0 100644 --- a/cmake/Modules/Packages/USER-NETCDF.cmake +++ b/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) diff --git a/cmake/README.md b/cmake/README.md index 9fb5dc3c16..b9dd6d4373 100644 --- a/cmake/README.md +++ b/cmake/README.md @@ -217,7 +217,7 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP CMAKE_VERBOSE_MAKEFILE - Enable verbose output from Makefile builds (useful for debugging), the same can be achived by adding `VERBOSE=1` to the `make` call. + Enable verbose output from Makefile builds (useful for debugging), the same can be achieved by adding `VERBOSE=1` to the `make` call.
off (default)
@@ -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.
diff --git a/doc/msi2lmp.1 b/doc/msi2lmp.1 index 08a442e1de..e1a8c8a2f3 100644 --- a/doc/msi2lmp.1 +++ b/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 \fR, \fB\-class \fR The \-c or \-class option selects the force field class, i.e which pair diff --git a/doc/src/2001/README.html b/doc/src/2001/README.html index d36aa917aa..d57897cd27 100644 --- a/doc/src/2001/README.html +++ b/doc/src/2001/README.html @@ -10,7 +10,7 @@ LAMMPS LAMMPS = Large-scale Atomic/Molecular Massively Parallel Simulator

This is the documentation for the LAMMPS 2001 version, written in F90, -which has been superceded by more current versions. See the LAMMPS WWW Site for more information.

diff --git a/doc/src/2001/basics.html b/doc/src/2001/basics.html index 24ac6de4ca..343fd8d129 100644 --- a/doc/src/2001/basics.html +++ b/doc/src/2001/basics.html @@ -47,7 +47,7 @@ directories:

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

+for a specific machine, you simply type

make machine

diff --git a/doc/src/2001/input_commands.html b/doc/src/2001/input_commands.html index 797d6bec4e..62ef5a5120 100644 --- a/doc/src/2001/input_commands.html +++ b/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) diff --git a/doc/src/99/README.html b/doc/src/99/README.html index 528c1e161d..d85f23970f 100644 --- a/doc/src/99/README.html +++ b/doc/src/99/README.html @@ -10,7 +10,7 @@ LAMMPS LAMMPS = Large-scale Atomic/Molecular Massively Parallel Simulator

This is the documentation for the LAMMPS 99 version, written in F77, -which has been superceded by more current versions. See the LAMMPS WWW Site for more information.

diff --git a/doc/src/99/basics.html b/doc/src/99/basics.html index b6236f4bf9..ef85d35b14 100644 --- a/doc/src/99/basics.html +++ b/doc/src/99/basics.html @@ -45,7 +45,7 @@ directories:

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

+for a specific machine, you simply type

make machine

diff --git a/doc/src/99/input_commands.html b/doc/src/99/input_commands.html index baea02b5c2..5ece32d52b 100644 --- a/doc/src/99/input_commands.html +++ b/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 diff --git a/doc/src/Errors_messages.rst b/doc/src/Errors_messages.rst index da36f18d82..1fafa82a8c 100644 --- a/doc/src/Errors_messages.rst +++ b/doc/src/Errors_messages.rst @@ -7666,7 +7666,7 @@ 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. diff --git a/doc/src/USER/atc/man_boundary.html b/doc/src/USER/atc/man_boundary.html index f3b20fc78b..c4448bc191 100644 --- a/doc/src/USER/atc/man_boundary.html +++ b/doc/src/USER/atc/man_boundary.html @@ -32,7 +32,7 @@ examples

fix_modify AtC boundary type ghost_atoms

description

-

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.

+

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.

restrictions

diff --git a/doc/src/USER/atc/man_hardy_gradients.html b/doc/src/USER/atc/man_hardy_gradients.html index 1874ad152e..1ecfade0ea 100644 --- a/doc/src/USER/atc/man_hardy_gradients.html +++ b/doc/src/USER/atc/man_hardy_gradients.html @@ -38,7 +38,7 @@ examples

description

-

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 fix_modify AtC atom_element_map )

+

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 fix_modify AtC atom_element_map )

restrictions

Must be used with the hardy/field type of AtC fix ( see fix atc command )

diff --git a/doc/src/USER/atc/man_hardy_rates.html b/doc/src/USER/atc/man_hardy_rates.html index 337a92517e..8066543485 100644 --- a/doc/src/USER/atc/man_hardy_rates.html +++ b/doc/src/USER/atc/man_hardy_rates.html @@ -38,7 +38,7 @@ examples

description

-

Requests calculation and ouput of rates (time derivatives) of the fields from the transfer class. For eulerian analysis (see fix_modify AtC atom_element_map ), these rates are the partial time derivatives of the nodal fields, not the full (material) time derivatives.
+

Requests calculation and output of rates (time derivatives) of the fields from the transfer class. For eulerian analysis (see fix_modify AtC atom_element_map ), these rates are the partial time derivatives of the nodal fields, not the full (material) time derivatives.

restrictions

diff --git a/examples/COUPLE/lammps_nwchem/planewave/nwchem_lammps.out b/examples/COUPLE/lammps_nwchem/planewave/nwchem_lammps.out index 27185413eb..92f2ff0037 100644 --- a/examples/COUPLE/lammps_nwchem/planewave/nwchem_lammps.out +++ b/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 ====================== diff --git a/examples/COUPLE/lammps_quest/lmpqst.cpp b/examples/COUPLE/lammps_quest/lmpqst.cpp index 76a89f1d06..6d31a9251b 100644 --- a/examples/COUPLE/lammps_quest/lmpqst.cpp +++ b/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; diff --git a/examples/UNITS/README b/examples/UNITS/README index 3980b38688..7271e5d62b 100644 --- a/examples/UNITS/README +++ b/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. diff --git a/examples/USER/atc/README b/examples/USER/atc/README index aa874f3300..73996edb9a 100644 --- a/examples/USER/atc/README +++ b/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 diff --git a/examples/USER/atc/fluids/in.bar1d_fluids b/examples/USER/atc/fluids/in.bar1d_fluids index af152bfbab..79a6c8a4c2 100644 --- a/examples/USER/atc/fluids/in.bar1d_fluids +++ b/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 diff --git a/examples/USER/atc/fluids/in.conducting_interface b/examples/USER/atc/fluids/in.conducting_interface index 7ee906e45a..c534231fca 100644 --- a/examples/USER/atc/fluids/in.conducting_interface +++ b/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 diff --git a/examples/USER/atc/fluids/in.dielectric_interface b/examples/USER/atc/fluids/in.dielectric_interface index e9cbe7882a..dd6034a0cc 100644 --- a/examples/USER/atc/fluids/in.dielectric_interface +++ b/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 diff --git a/examples/USER/atc/fluids/in.shear_flow b/examples/USER/atc/fluids/in.shear_flow index c5a53b1273..3c06676c64 100644 --- a/examples/USER/atc/fluids/in.shear_flow +++ b/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 diff --git a/examples/USER/atc/fluids/in.shear_no_atoms b/examples/USER/atc/fluids/in.shear_no_atoms index 8bd350f06c..6c778578c9 100644 --- a/examples/USER/atc/fluids/in.shear_no_atoms +++ b/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 diff --git a/examples/USER/atc/thermal/bar1d.screen b/examples/USER/atc/thermal/bar1d.screen index 33f6590e4d..3c7f8db212 100644 --- a/examples/USER/atc/thermal/bar1d.screen +++ b/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 diff --git a/examples/USER/atc/thermal/in.bar1d b/examples/USER/atc/thermal/in.bar1d index 5591f7177d..3f70577ec3 100644 --- a/examples/USER/atc/thermal/in.bar1d +++ b/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 diff --git a/examples/USER/atc/thermal/in.bar1d_all_atoms b/examples/USER/atc/thermal/in.bar1d_all_atoms index 2c8851137f..2219b803ec 100644 --- a/examples/USER/atc/thermal/in.bar1d_all_atoms +++ b/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 diff --git a/examples/USER/atc/thermal/in.bar1d_combined b/examples/USER/atc/thermal/in.bar1d_combined index 767544d2d4..70dafe72be 100644 --- a/examples/USER/atc/thermal/in.bar1d_combined +++ b/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 diff --git a/examples/USER/atc/thermal/in.bar1d_flux b/examples/USER/atc/thermal/in.bar1d_flux index eae32ec5b2..2b79aa6339 100644 --- a/examples/USER/atc/thermal/in.bar1d_flux +++ b/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 diff --git a/examples/USER/atc/thermal/in.bar1d_frac_step b/examples/USER/atc/thermal/in.bar1d_frac_step index eddec44b52..e8540d9151 100644 --- a/examples/USER/atc/thermal/in.bar1d_frac_step +++ b/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 diff --git a/examples/USER/cgdna/README b/examples/USER/cgdna/README index 49b7cd1f84..a403ce0321 100644 --- a/examples/USER/cgdna/README +++ b/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 diff --git a/examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py b/examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py index e5141bc47a..0760d24a0b 100644 --- a/examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py +++ b/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 = [] @@ -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 diff --git a/examples/USER/cgdna/util/generate.py b/examples/USER/cgdna/util/generate.py index eb97f482cc..e175455970 100644 --- a/examples/USER/cgdna/util/generate.py +++ b/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 = [] diff --git a/examples/USER/diffraction/README b/examples/USER/diffraction/README index 265201beb1..e36062923b 100644 --- a/examples/USER/diffraction/README +++ b/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 diff --git a/examples/USER/eff/Li-dendritic/README b/examples/USER/eff/Li-dendritic/README index 24eed28f85..4fdaed1efb 100644 --- a/examples/USER/eff/Li-dendritic/README +++ b/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). diff --git a/examples/USER/lb/fourspheres/in.fourspheres_default_gamma b/examples/USER/lb/fourspheres/in.fourspheres_default_gamma index 2fa161aefa..bce9aec0e9 100755 --- a/examples/USER/lb/fourspheres/in.fourspheres_default_gamma +++ b/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. # # # diff --git a/examples/USER/lb/fourspheres/in.fourspheres_set_gamma b/examples/USER/lb/fourspheres/in.fourspheres_set_gamma index 452d90ba00..8c32051536 100755 --- a/examples/USER/lb/fourspheres/in.fourspheres_set_gamma +++ b/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. # # # diff --git a/examples/USER/misc/ees/README b/examples/USER/misc/ees/README index 9f4cb4f159..bfc55e4375 100644 --- a/examples/USER/misc/ees/README +++ b/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 diff --git a/examples/USER/misc/hma/README b/examples/USER/misc/hma/README index 5af6ec15fa..75c24705d3 100644 --- a/examples/USER/misc/hma/README +++ b/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 diff --git a/examples/USER/plumed/reference/p.log b/examples/USER/plumed/reference/p.log index 29d99077e4..13a63bdbf1 100644 --- a/examples/USER/plumed/reference/p.log +++ b/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 diff --git a/examples/USER/qtb/methane_qbmsst/methane_qtb.mod b/examples/USER/qtb/methane_qbmsst/methane_qtb.mod index 181fb99d00..65bfc5d7f7 100644 --- a/examples/USER/qtb/methane_qbmsst/methane_qtb.mod +++ b/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 diff --git a/examples/USER/qtb/methane_qtb/methane_qtb.in b/examples/USER/qtb/methane_qtb/methane_qtb.in index f0ea94a221..e31f0695b9 100644 --- a/examples/USER/qtb/methane_qtb/methane_qtb.in +++ b/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 diff --git a/examples/USER/quip/in.molecular b/examples/USER/quip/in.molecular index 4253399d7c..08921ef865 100644 --- a/examples/USER/quip/in.molecular +++ b/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 diff --git a/examples/USER/quip/log.24Jul17.molecular.g++.1 b/examples/USER/quip/log.24Jul17.molecular.g++.1 index 28fc63579b..ca1b83c268 100644 --- a/examples/USER/quip/log.24Jul17.molecular.g++.1 +++ b/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 diff --git a/examples/USER/quip/log.24Jul17.molecular.g++.4 b/examples/USER/quip/log.24Jul17.molecular.g++.4 index a8be8e77bb..2226e45bfb 100644 --- a/examples/USER/quip/log.24Jul17.molecular.g++.4 +++ b/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 diff --git a/examples/USER/smd/aluminum_strip_pull/aluminum_strip_pull.lmp b/examples/USER/smd/aluminum_strip_pull/aluminum_strip_pull.lmp index b75bab10e9..50b20a0787 100644 --- a/examples/USER/smd/aluminum_strip_pull/aluminum_strip_pull.lmp +++ b/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 diff --git a/examples/USER/smd/fluid_structure_interaction/fluid_structure_interaction.lmp b/examples/USER/smd/fluid_structure_interaction/fluid_structure_interaction.lmp index 0f7d726e21..e4f3ea603a 100644 --- a/examples/USER/smd/fluid_structure_interaction/fluid_structure_interaction.lmp +++ b/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 # #################################################################################################### diff --git a/examples/USER/smd/funnel_flow/funnel_flow.lmp b/examples/USER/smd/funnel_flow/funnel_flow.lmp index 7cc1e13f4f..b1fde2c2db 100644 --- a/examples/USER/smd/funnel_flow/funnel_flow.lmp +++ b/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 # #################################################################################################### diff --git a/examples/USER/smd/rubber_rings_3d/rubber_rings_3d.lmp b/examples/USER/smd/rubber_rings_3d/rubber_rings_3d.lmp index 956abd6c4a..11b988e818 100644 --- a/examples/USER/smd/rubber_rings_3d/rubber_rings_3d.lmp +++ b/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 # #################################################################################################### diff --git a/examples/USER/smd/rubber_strip_pull/rubber_strip_pull.lmp b/examples/USER/smd/rubber_strip_pull/rubber_strip_pull.lmp index 4e53daf993..0e8be3b9da 100644 --- a/examples/USER/smd/rubber_strip_pull/rubber_strip_pull.lmp +++ b/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 # #################################################################################################### diff --git a/examples/USER/tally/in.pe b/examples/USER/tally/in.pe index c6228cebd0..a7a3360c44 100644 --- a/examples/USER/tally/in.pe +++ b/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 diff --git a/examples/USER/tally/log.12Jun17.pe.1 b/examples/USER/tally/log.12Jun17.pe.1 index 8b0f753414..ecdaee86d5 100644 --- a/examples/USER/tally/log.12Jun17.pe.1 +++ b/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 diff --git a/examples/USER/tally/log.12Jun17.pe.4 b/examples/USER/tally/log.12Jun17.pe.4 index f684fabe01..242cad77f3 100644 --- a/examples/USER/tally/log.12Jun17.pe.4 +++ b/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 diff --git a/examples/hugoniostat/in.hugoniostat b/examples/hugoniostat/in.hugoniostat index 01c2a246fc..571f92b59e 100644 --- a/examples/hugoniostat/in.hugoniostat +++ b/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 diff --git a/examples/hugoniostat/log.27Nov18.hugoniostat.g++.1 b/examples/hugoniostat/log.27Nov18.hugoniostat.g++.1 index 2473641dea..c1381629eb 100644 --- a/examples/hugoniostat/log.27Nov18.hugoniostat.g++.1 +++ b/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 diff --git a/examples/hugoniostat/log.27Nov18.hugoniostat.g++.4 b/examples/hugoniostat/log.27Nov18.hugoniostat.g++.4 index 30f1335ea9..dd0766e81a 100644 --- a/examples/hugoniostat/log.27Nov18.hugoniostat.g++.4 +++ b/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 diff --git a/examples/reax/HNS/README.txt b/examples/reax/HNS/README.txt index 465d64d171..95ffbb0ebb 100644 --- a/examples/reax/HNS/README.txt +++ b/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 diff --git a/lib/atc/ATC_Coupling.cpp b/lib/atc/ATC_Coupling.cpp index 9468064f8d..db72b0cb0c 100644 --- a/lib/atc/ATC_Coupling.cpp +++ b/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 - - = switch to activiate/deactiviate the intial setting of FE intrinsic field to match the projected MD field + - = switch to activiate/deactiviate the initial setting of FE intrinsic field to match the projected MD field \section examples fix_modify atc consistent_fe_initialization on \section description diff --git a/lib/atc/ATC_Coupling.h b/lib/atc/ATC_Coupling.h index 3816a82798..9f406febbe 100644 --- a/lib/atc/ATC_Coupling.h +++ b/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 */ diff --git a/lib/atc/ATC_CouplingEnergy.cpp b/lib/atc/ATC_CouplingEnergy.cpp index 0338054902..c3b07c242d 100644 --- a/lib/atc/ATC_CouplingEnergy.cpp +++ b/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); } diff --git a/lib/atc/ATC_CouplingMass.cpp b/lib/atc/ATC_CouplingMass.cpp index 801752d569..d36643e590 100644 --- a/lib/atc/ATC_CouplingMass.cpp +++ b/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); } diff --git a/lib/atc/ATC_CouplingMomentum.cpp b/lib/atc/ATC_CouplingMomentum.cpp index f59aa525cb..6757245119 100644 --- a/lib/atc/ATC_CouplingMomentum.cpp +++ b/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); } diff --git a/lib/atc/ATC_CouplingMomentumEnergy.cpp b/lib/atc/ATC_CouplingMomentumEnergy.cpp index bf0edc71fb..1fc2931977 100644 --- a/lib/atc/ATC_CouplingMomentumEnergy.cpp +++ b/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); diff --git a/lib/atc/ATC_Method.cpp b/lib/atc/ATC_Method.cpp index 5d61a7bed8..f2173e9575 100644 --- a/lib/atc/ATC_Method.cpp +++ b/lib/atc/ATC_Method.cpp @@ -693,12 +693,12 @@ pecified /*! \page man_boundary fix_modify AtC boundary \section syntax fix_modify AtC boundary type - - = type id for atoms that represent a ficticious + - = type id for atoms that represent a fictitious boundary internal to the FE mesh \section examples fix_modify AtC boundary type ghost_atoms \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. diff --git a/lib/atc/ATC_Transfer.cpp b/lib/atc/ATC_Transfer.cpp index c876f46634..833e1d1f27 100644 --- a/lib/atc/ATC_Transfer.cpp +++ b/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 { fix_modify AtC gradients add temperature velocity stress \n fix_modify AtC gradients delete velocity \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 { fix_modify AtC rates add temperature velocity stress \n fix_modify AtC rates delete stress \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() { diff --git a/lib/atc/AtomToMoleculeTransfer.h b/lib/atc/AtomToMoleculeTransfer.h index c6523137a7..c628ee356f 100644 --- a/lib/atc/AtomToMoleculeTransfer.h +++ b/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_; diff --git a/lib/atc/AtomicRegulator.h b/lib/atc/AtomicRegulator.h index 8fb7de1006..b9fccb902c 100644 --- a/lib/atc/AtomicRegulator.h +++ b/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 */ diff --git a/lib/atc/CbPotential.h b/lib/atc/CbPotential.h index e218ae2254..1d5386fcd5 100644 --- a/lib/atc/CbPotential.h +++ b/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. diff --git a/lib/atc/ChargeRegulator.cpp b/lib/atc/ChargeRegulator.cpp index cbfda69480..bae78a7613 100644 --- a/lib/atc/ChargeRegulator.cpp +++ b/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; diff --git a/lib/atc/ConcentrationRegulator.cpp b/lib/atc/ConcentrationRegulator.cpp index 8055433f5d..4255b919b9 100644 --- a/lib/atc/ConcentrationRegulator.cpp +++ b/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(); diff --git a/lib/atc/DiagonalMatrix.h b/lib/atc/DiagonalMatrix.h index 6c2fe23144..ca3001f225 100644 --- a/lib/atc/DiagonalMatrix.h +++ b/lib/atc/DiagonalMatrix.h @@ -472,7 +472,7 @@ inline DiagonalMatrix inv(const DiagonalMatrix& A) return A.inv(); } //----------------------------------------------------------------------------- -// general diagonalmatrix assigment +// general diagonalmatrix assignment //----------------------------------------------------------------------------- template void DiagonalMatrix::_set_equal(const Matrix &r) diff --git a/lib/atc/ElasticTimeIntegrator.cpp b/lib/atc/ElasticTimeIntegrator.cpp index 9793f6a58e..5e11f1584c 100644 --- a/lib/atc/ElasticTimeIntegrator.cpp +++ b/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()"); } } } diff --git a/lib/atc/ElectronHeatFlux.h b/lib/atc/ElectronHeatFlux.h index 41c89d6c6d..d0bc2a44f2 100644 --- a/lib/atc/ElectronHeatFlux.h +++ b/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 diff --git a/lib/atc/ExtrinsicModelElectrostatic.cpp b/lib/atc/ExtrinsicModelElectrostatic.cpp index b10e77a306..ef3aa52dee 100644 --- a/lib/atc/ExtrinsicModelElectrostatic.cpp +++ b/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) { diff --git a/lib/atc/ExtrinsicModelElectrostatic.h b/lib/atc/ExtrinsicModelElectrostatic.h index c4a0af464d..86cba31471 100644 --- a/lib/atc/ExtrinsicModelElectrostatic.h +++ b/lib/atc/ExtrinsicModelElectrostatic.h @@ -92,7 +92,7 @@ namespace ATC { /** rhs mask for Poisson solver */ Array2D rhsMask_; - /** estimate instrinsic charge density */ + /** estimate intrinsic charge density */ void add_electrostatic_forces(MATRIX & nodalPotential); /** correct short range FE electric field */ diff --git a/lib/atc/FE_Element.cpp b/lib/atc/FE_Element.cpp index 9eec08c483..0d2fc036c7 100644 --- a/lib/atc/FE_Element.cpp +++ b/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_); diff --git a/lib/atc/FE_Engine.cpp b/lib/atc/FE_Engine.cpp index bef135a5f2..5e01709b19 100644 --- a/lib/atc/FE_Engine.cpp +++ b/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]; diff --git a/lib/atc/FE_Engine.h b/lib/atc/FE_Engine.h index 18dae0e6b4..eb59f04eef 100644 --- a/lib/atc/FE_Engine.h +++ b/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 */ diff --git a/lib/atc/FE_Interpolate.cpp b/lib/atc/FE_Interpolate.cpp index 19753a8007..5e5bd5ecf1 100644 --- a/lib/atc/FE_Interpolate.cpp +++ b/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 mapping(nSD_); for (int inode=0; inodeneedReset_ = true;}; /** specialized reset to account for forcing lammps to perform the compute */ diff --git a/lib/atc/GhostManager.cpp b/lib/atc/GhostManager.cpp index 3c9e54b4f5..77594ec406 100644 --- a/lib/atc/GhostManager.cpp +++ b/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())); } //-------------------------------------------------------- diff --git a/lib/atc/InterscaleOperators.cpp b/lib/atc/InterscaleOperators.cpp index 0e218bdef4..f1e5607b6e 100644 --- a/lib/atc/InterscaleOperators.cpp +++ b/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"); } diff --git a/lib/atc/InterscaleOperators.h b/lib/atc/InterscaleOperators.h index 0ddca1dc67..3a4d81212e 100644 --- a/lib/atc/InterscaleOperators.h +++ b/lib/atc/InterscaleOperators.h @@ -245,19 +245,19 @@ namespace ATC { /** container for molecule sets */ std::map 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 *> 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 *> 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 *> 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 *> 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 *> 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 void dfs_prepare_loop(std::map & list) { diff --git a/lib/atc/KinetoThermostat.h b/lib/atc/KinetoThermostat.h index 6f7d113734..bc40f19ed1 100644 --- a/lib/atc/KinetoThermostat.h +++ b/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 *\/ */ diff --git a/lib/atc/Kinetostat.cpp b/lib/atc/Kinetostat.cpp index 8093d5925a..7f95398dcb 100644 --- a/lib/atc/Kinetostat.cpp +++ b/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) { diff --git a/lib/atc/Kinetostat.h b/lib/atc/Kinetostat.h index 691b929e9f..e3e1c17e52 100644 --- a/lib/atc/Kinetostat.h +++ b/lib/atc/Kinetostat.h @@ -806,7 +806,7 @@ namespace ATC { /** change in restricted atomic FE momentum over a timestep */ DENS_MAT deltaNodalAtomicMomentum_; - /** intial restricted atomic FE momentum used to compute change */ + /** initial restricted atomic FE momentum used to compute change */ DENS_MAT initialNodalAtomicMomentum_; /** filtered nodal atomic momentum */ diff --git a/lib/atc/LammpsInterface.cpp b/lib/atc/LammpsInterface.cpp index 9c2223f555..9964a1c4bb 100644 --- a/lib/atc/LammpsInterface.cpp +++ b/lib/atc/LammpsInterface.cpp @@ -631,7 +631,7 @@ LammpsInterface::LatticeType LammpsInterface::lattice_style() const throw ATC_Error("Lattice has not been defined"); } -//* retuns the number of basis vectors +//* returns the number of basis vectors int LammpsInterface::n_basis() const { return lammps_->domain->lattice->nbasis; diff --git a/lib/atc/Material.h b/lib/atc/Material.h index 18cccd8792..5a835d446b 100644 --- a/lib/atc/Material.h +++ b/lib/atc/Material.h @@ -83,7 +83,7 @@ namespace ATC /** each of these is a field function computed at a set of points */ /** if there is only one function it is in the base class - ** otherwise, a subsidary class is setup */ + ** otherwise, a subsidiary class is setup */ /* -----------------------------------------------------------------*/ /** densities */ /* -----------------------------------------------------------------*/ diff --git a/lib/atc/Matrix.cpp b/lib/atc/Matrix.cpp index 0741099872..1b77796b8b 100644 --- a/lib/atc/Matrix.cpp +++ b/lib/atc/Matrix.cpp @@ -81,7 +81,7 @@ DenseMatrix inv(const MATRIX& A) GCK(A,A,info<0,"DenseMatrix::inv() dgetri error: Argument had bad value."); GCHK(info>0,"DenseMatrix::inv() dgetri error: Matrix not invertible."); - // Work size query succeded + // Work size query succeeded lwork = (int)work_dummy[0]; double *work = new double[lwork]; // Allocate vector of appropriate size @@ -287,7 +287,7 @@ double det(const MATRIX& A) double max_eigenvalue(const Matrix& A) { - GCK(A,A,!A.is_size(3,3), "max_eigenvalue only implimented for 3x3"); + GCK(A,A,!A.is_size(3,3), "max_eigenvalue only implemented for 3x3"); const double c0 = det(A); const double c1 = A(1,0)*A(0,1) + A(2,0)*A(0,2) + A(1,2)*A(2,1) - A(0,0)*A(1,1) - A(0,0)*A(2,2) - A(1,1)*A(2,2); diff --git a/lib/atc/Matrix.h b/lib/atc/Matrix.h index 6745ea96db..c93576518c 100644 --- a/lib/atc/Matrix.h +++ b/lib/atc/Matrix.h @@ -150,7 +150,7 @@ protected: //* Matrix operations //@{ -//* Sets C as b*C + a*A[tranpose?]*B[transpose?] +//* Sets C as b*C + a*A[transpose?]*B[transpose?] template void MultAB(const Matrix &A, const Matrix &B, DenseMatrix &C, bool At=0, bool Bt=0, T a=1, T b=0); @@ -622,7 +622,7 @@ Matrix& Matrix::operator+=(const T v) return *this; } //----------------------------------------------------------------------------- -// substracts a constant to this matrix +// subtracts a constant to this matrix //----------------------------------------------------------------------------- template Matrix& Matrix::operator-=(const T v) diff --git a/lib/atc/PhysicsModel.cpp b/lib/atc/PhysicsModel.cpp index 77cc41e972..f5c342c5a0 100644 --- a/lib/atc/PhysicsModel.cpp +++ b/lib/atc/PhysicsModel.cpp @@ -95,7 +95,7 @@ void PhysicsModel::parse_material_file(string fileName) } } else { - throw ATC_Error("units need to be specfied in material file"); + throw ATC_Error("units need to be specified in material file"); } } } diff --git a/lib/atc/SparseMatrix.h b/lib/atc/SparseMatrix.h index 35393187cd..700d2f3af6 100644 --- a/lib/atc/SparseMatrix.h +++ b/lib/atc/SparseMatrix.h @@ -38,9 +38,9 @@ class SparseMatrix : public Matrix friend SparseMatrix operator*(const SparseMatrix &A, const DiagonalMatrix& D); //* SparseMatrix-SparseMatrix multiplication (S * S) friend SparseMatrix operator*(const SparseMatrix &A, const SparseMatrix &B); - //* computes the product of a SparseMatrix tranpose with a SparseVector (M'*v). + //* computes the product of a SparseMatrix transpose with a SparseVector (M'*v). friend SparseVector operator*(const SparseMatrix &M, const SparseVector &v); - //* computes the product of a SparseMatrix tranpose with a SparseVector (M'*v). + //* computes the product of a SparseMatrix transpose with a SparseVector (M'*v). friend SparseVector operator*(const SparseVector &v, const SparseMatrix &M); template diff --git a/lib/atc/SparseVector-inl.h b/lib/atc/SparseVector-inl.h index 760eb66f58..7f2c844bd6 100644 --- a/lib/atc/SparseVector-inl.h +++ b/lib/atc/SparseVector-inl.h @@ -55,7 +55,7 @@ T dot(const SparseVector &a, const SparseVector &b) } return v; } -// Computes the product of a SparseMatrix tranpose with a SparseVector (M'*v). +// Computes the product of a SparseMatrix transpose with a SparseVector (M'*v). template SparseVector operator*(const SparseMatrix &M, const SparseVector &v) { @@ -73,7 +73,7 @@ SparseVector operator*(const SparseMatrix &M, const SparseVector &v) return y; } -// computes the product of a SparseMatrix tranpose with a SparseVector (M'*v). +// computes the product of a SparseMatrix transpose with a SparseVector (M'*v). template SparseVector operator*(const SparseVector &v, const SparseMatrix &M) { diff --git a/lib/atc/SparseVector.h b/lib/atc/SparseVector.h index 4219bb2627..5cb16af527 100644 --- a/lib/atc/SparseVector.h +++ b/lib/atc/SparseVector.h @@ -30,9 +30,9 @@ class SparseVector : public Vector { // for use with gcc friend T dot(const SparseVector &a, const SparseVector &b); #endif - //* computes the product of a SparseMatrix tranpose with a SparseVector (M'*v). + //* computes the product of a SparseMatrix transpose with a SparseVector (M'*v). friend SparseVector operator*(const SparseMatrix &M, const SparseVector &v); - //* computes the product of a SparseMatrix tranpose with a SparseVector (M'*v). + //* computes the product of a SparseMatrix transpose with a SparseVector (M'*v). friend SparseVector operator*(const SparseVector &v, const SparseMatrix &M); public: //* Constructor - sets length of vector (NOT # of nonzeros). @@ -71,9 +71,9 @@ public: void reset (INDEX nRows, INDEX nCols=1, bool zero=0); //* zeros out all elements while preserving sparcity pattern void zero(); - //* TODO impliment copy (or maybe not necessary) + //* TODO implement copy (or maybe not necessary) void copy(const T* ptr, INDEX nRows, INDEX nCols=1); - //* Writes a restart file (TODO impliment this if needed/wanted). + //* Writes a restart file (TODO implement this if needed/wanted). void write_restart(FILE *F) const; //* Adds SparseVector x, scaled by s to this one. Can be different sparcity. void add_scaled(SparseVector& x, const T& s); diff --git a/lib/atc/Stress.cpp b/lib/atc/Stress.cpp index 906b15986e..72656c21ed 100644 --- a/lib/atc/Stress.cpp +++ b/lib/atc/Stress.cpp @@ -328,7 +328,7 @@ StressCauchyBorn::StressCauchyBorn(fstream &fileId, CbData &cb) if (line.size() && line[0]=="pair_coeff") break; } if (line[0] != "pair_coeff" || line.size() != 3) { - throw(ATC_Error("lj/cut needs 2 coefficents")); + throw(ATC_Error("lj/cut needs 2 coefficients")); } delete potential_; potential_ = new CbLjCut(str2dbl(line[1]), str2dbl(line[2]), rc); @@ -341,7 +341,7 @@ StressCauchyBorn::StressCauchyBorn(fstream &fileId, CbData &cb) if (line.size() && line[0]=="pair_coeff") break; } if (line[0] != "pair_coeff" || line.size() != 3) { - throw(ATC_Error("lj/smooth/linear needs 2 coefficents")); + throw(ATC_Error("lj/smooth/linear needs 2 coefficients")); } delete potential_; potential_ = new CbLjSmoothLinear(str2dbl(line[1]), str2dbl(line[2]), rc); diff --git a/lib/atc/ThermalTimeIntegrator.cpp b/lib/atc/ThermalTimeIntegrator.cpp index f68f46b01f..e74d46a20c 100644 --- a/lib/atc/ThermalTimeIntegrator.cpp +++ b/lib/atc/ThermalTimeIntegrator.cpp @@ -87,7 +87,7 @@ namespace ATC { 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 ThermalTimeIntegrator::Initialize()"); + throw ATC_Error("Unknown time integration type in ThermalTimeIntegrator::Initialize()"); } } else { @@ -116,7 +116,7 @@ namespace ATC { break; } default: - throw ATC_Error("Uknown time integration type in ThermalTimeIntegrator::Initialize()"); + throw ATC_Error("Unknown time integration type in ThermalTimeIntegrator::Initialize()"); } } } diff --git a/lib/atc/ThermalTimeIntegrator.h b/lib/atc/ThermalTimeIntegrator.h index f0ce73b9b4..8f5175d8a2 100644 --- a/lib/atc/ThermalTimeIntegrator.h +++ b/lib/atc/ThermalTimeIntegrator.h @@ -273,7 +273,7 @@ namespace ATC { /** change in FE temperature due to atomic motions */ DENS_MAN atomicTemperatureDelta_; - /** fractional step auxilliary storage for restricted atomic energy */ + /** fractional step auxiliary storage for restricted atomic energy */ DENS_MAN * nodalAtomicEnergy_; /** power associated with thermostat for post-processing */ diff --git a/lib/atc/Thermostat.cpp b/lib/atc/Thermostat.cpp index 0ede724371..a602105854 100644 --- a/lib/atc/Thermostat.cpp +++ b/lib/atc/Thermostat.cpp @@ -1460,7 +1460,7 @@ namespace ATC { // initialize_delta_nodal_atomic_energy: // initializes storage for the variable tracking // the change in the nodal atomic energy - // that has occured over the past timestep + // that has occurred over the past timestep //-------------------------------------------------------- void ThermostatIntegratorFixed::initialize_delta_nodal_atomic_energy(double dt) { @@ -1475,7 +1475,7 @@ namespace ATC { //-------------------------------------------------------- // compute_delta_nodal_atomic_energy: // computes the change in the nodal atomic energy - // that has occured over the past timestep + // that has occurred over the past timestep //-------------------------------------------------------- void ThermostatIntegratorFixed::compute_delta_nodal_atomic_energy(double dt) { @@ -1778,7 +1778,7 @@ namespace ATC { // initialize_delta_nodal_atomic_energy: // initializes storage for the variable tracking // the change in the nodal atomic energy - // that has occured over the past timestep + // that has occurred over the past timestep //-------------------------------------------------------- @@ -1795,7 +1795,7 @@ namespace ATC { //-------------------------------------------------------- // compute_delta_nodal_atomic_energy: // computes the change in the nodal atomic energy - // that has occured over the past timestep + // that has occurred over the past timestep //-------------------------------------------------------- void ThermostatIntegratorFixedFiltered::compute_delta_nodal_atomic_energy(double dt) { diff --git a/lib/atc/Thermostat.h b/lib/atc/Thermostat.h index 95d2d1162d..3764d0b835 100644 --- a/lib/atc/Thermostat.h +++ b/lib/atc/Thermostat.h @@ -581,7 +581,7 @@ 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 */ diff --git a/lib/atc/TimeIntegrator.h b/lib/atc/TimeIntegrator.h index ceeb7610fb..ccb9b9f426 100644 --- a/lib/atc/TimeIntegrator.h +++ b/lib/atc/TimeIntegrator.h @@ -362,7 +362,7 @@ namespace ATC { inline void explicit_1(MATRIX & f, const MATRIX & dot_f, double dt) - // 1rst order explict ODE update + // 1rst order explicit ODE update { f = f + dt*dot_f; }; @@ -371,7 +371,7 @@ namespace ATC { const MATRIX & dot_f, const MATRIX & ddot_f, double dt) - // 2nd order explict ODE update + // 2nd order explicit ODE update { f = f + dt*dot_f + .5*dt*dt*ddot_f; }; diff --git a/lib/atc/TransferOperator.h b/lib/atc/TransferOperator.h index 0ab92805be..5f776d04ca 100644 --- a/lib/atc/TransferOperator.h +++ b/lib/atc/TransferOperator.h @@ -466,7 +466,7 @@ namespace ATC { /** reference to shape function matrix */ SPAR_MAN * shapeFunction_; - /** persistant workspace */ + /** persistent workspace */ mutable DENS_MAT _workspace_; @@ -510,7 +510,7 @@ namespace ATC { /** reference to shape function matrix */ SPAR_MAN * shapeFunction_; - /** persistant workspace */ + /** persistent workspace */ mutable DENS_MAT _workspace_; @@ -560,7 +560,7 @@ namespace ATC { DIAG_MAN * weights_; DENS_MAT * reference_; - /** persistant workspace */ + /** persistent workspace */ mutable DENS_MAT _workspace_; @@ -887,7 +887,7 @@ namespace ATC { /** pointer to the mesh being used */ const FE_Mesh * feMesh_; - /** persistant workspace */ + /** persistent workspace */ mutable DENS_MAT _workspace_; diff --git a/lib/awpmd/ivutils/include/logexc.h b/lib/awpmd/ivutils/include/logexc.h index 4c8364671a..80942f60bf 100644 --- a/lib/awpmd/ivutils/include/logexc.h +++ b/lib/awpmd/ivutils/include/logexc.h @@ -42,7 +42,7 @@ enum vbLEVELS{ /// by default all exceptions have vblFATAL level template struct log_exception_traits{ - /// exeption level according to the vbLEVELS + /// exception level according to the vbLEVELS static int level(const exc_t & /* signal */){ return vblFATAL; } /// the string name of exception category static string name(const exc_t & /* signal */){ return typeid(exc_t).name();} @@ -59,7 +59,7 @@ struct log_exception_traits{ /// integer exceptions have the level equal to their value template<> struct log_exception_traits{ - /// exeption level according to the vbLEVELS + /// exception level according to the vbLEVELS static int level(const int &signal){ return signal; } /// the string name of exception category static string name(const int &signal){ @@ -294,7 +294,7 @@ const char *fmt(const char *format,...); /// this may be used to inherit exceptions /// where level and name are defined whithin a class struct log_exception { - /// exeption level according to the vbLEVELS + /// exception level according to the vbLEVELS static int level(const log_exception &signal){ return vblFATAL; } /// the string name of exception category static string name(const log_exception &signal){ return "undefined exception";} diff --git a/lib/awpmd/ivutils/include/wavepacket.h b/lib/awpmd/ivutils/include/wavepacket.h index c4f3837022..337a056e79 100644 --- a/lib/awpmd/ivutils/include/wavepacket.h +++ b/lib/awpmd/ivutils/include/wavepacket.h @@ -168,13 +168,13 @@ public: return imag(b) - real(b)*(imag(a)/real(a)); } - ///\en Transforms derivatives of a function whith respect to WP parameters + ///\en Transforms derivatives of a function with respect to WP parameters /// from internal into physical representation, i. e.:\n /// from df/d{are,aim,b0re,b0im,b1re,b1im,b2re,b2im} (8 values accessed by input iterator d_it in the given order)\n /// to df/d{x0,x1,x2}, df/d{p0,p1,p2}, df/dw, df/dpw /// The supplied inputs (val) are modified by op: val=op(val,phys_der). /// Use operation=eq_second for the supplied inputs to be replaced by new physical derivative values. - /// The inpput and output locations may coinside, an internal buffer is used for transformation. + /// The input and output locations may coinside, an internal buffer is used for transformation. template class operation, class d_it, class dfdx_it, class dfdp_it, class dfdw_it, class dfdpw_it> void int2phys_der(d_it dfdi_,dfdx_it dfdx, dfdp_it dfdp, dfdw_it dfdw, dfdpw_it dfdpw, double h_p=h_plank) const { operation op; diff --git a/lib/awpmd/systems/interact/TCP/wpmd.cpp b/lib/awpmd/systems/interact/TCP/wpmd.cpp index ad5d8e26bc..1e53f3141c 100644 --- a/lib/awpmd/systems/interact/TCP/wpmd.cpp +++ b/lib/awpmd/systems/interact/TCP/wpmd.cpp @@ -217,7 +217,7 @@ int AWPMD::interaction_hartree(int flag, Vector_3P fi, Vector_3P fe_x, // 0. resizing the arrays if needed enum APPROX tmp=HARTREE; - swap(tmp,approx); // do not neeed large matrices + swap(tmp,approx); // do not need large matrices resize(flag); swap(tmp,approx); //1. clearing forces diff --git a/lib/awpmd/systems/interact/TCP/wpmd.h b/lib/awpmd/systems/interact/TCP/wpmd.h index bcb99e2092..e5a7c27697 100644 --- a/lib/awpmd/systems/interact/TCP/wpmd.h +++ b/lib/awpmd/systems/interact/TCP/wpmd.h @@ -201,7 +201,7 @@ inline pair operator*(const pair &right, double le return make_pair(right.first*left,right.second*left); } -// Auxilary class to handle the normalizing term derivatives +// Auxiliary class to handle the normalizing term derivatives class NormDeriv { public: @@ -235,7 +235,7 @@ inline NormDeriv conj(const NormDeriv& src){ return dst; } -///\en Auxilary class to handle derivatives of overlaps +///\en Auxiliary class to handle derivatives of overlaps class OverlapDeriv{ public: WavePacket w1, w2, w12; @@ -496,7 +496,7 @@ public: } protected: - //e translates wp2 to the nearest image postion relative to wp1 + //e translates wp2 to the nearest image position relative to wp1 //e gets the translation vector Vector_3 move_to_image(const WavePacket &wp1, WavePacket &wp2) const { Vector_3 r1=wp1.get_r(); @@ -646,7 +646,7 @@ public: Vector_3P fe_p, double *fe_w, double *fe_pw, Vector_2P fe_c=NULL); - ///\en Creates wave packet acording to the given physical parameters. + ///\en Creates wave packet according to the given physical parameters. /// The function may change its arguments by applying existing constraints! /// Default mass (-1) is the electron mass AWPMD::me. WavePacket create_wp(Vector_3 &x, Vector_3 &v, double &w, double &pw, double mass=-1); diff --git a/lib/awpmd/systems/interact/TCP/wpmd_split.cpp b/lib/awpmd/systems/interact/TCP/wpmd_split.cpp index 691dbac91b..732707d717 100644 --- a/lib/awpmd/systems/interact/TCP/wpmd_split.cpp +++ b/lib/awpmd/systems/interact/TCP/wpmd_split.cpp @@ -351,7 +351,7 @@ int AWPMD_split::interaction_hartree(int flag, Vector_3P fi, Vector_3P fe_x, // resize arrays if needed enum APPROX tmp=HARTREE; - swap(tmp,approx); // do not neeed large matrices + swap(tmp,approx); // do not need large matrices resize(flag); swap(tmp,approx); diff --git a/lib/colvars/colvar.cpp b/lib/colvars/colvar.cpp index fb95bda5ec..1002dc35d8 100644 --- a/lib/colvars/colvar.cpp +++ b/lib/colvars/colvar.cpp @@ -252,7 +252,7 @@ int colvar::init(std::string const &conf) // components may have different types only for scripted functions if (!(is_enabled(f_cv_scripted) || is_enabled(f_cv_custom_function)) && (colvarvalue::check_types(cvcs[i]->value(), cvcs[0]->value())) ) { - cvm::error("ERROR: you are definining this collective variable " + cvm::error("ERROR: you are defining this collective variable " "by using components of different types. " "You must use the same type in order to " "sum them together.\n", INPUT_ERROR); diff --git a/lib/colvars/colvarbias_abf.h b/lib/colvars/colvarbias_abf.h index 5a1a1c8128..1939b61a8b 100644 --- a/lib/colvars/colvarbias_abf.h +++ b/lib/colvars/colvarbias_abf.h @@ -109,7 +109,7 @@ private: colvar_grid_gradient *z_gradients; /// n-dim grid of number of samples on "real" coordinate for eABF z-based estimator colvar_grid_count *z_samples; - /// n-dim grid contining CZAR estimator of "real" free energy gradients + /// n-dim grid containing CZAR estimator of "real" free energy gradients colvar_grid_gradient *czar_gradients; /// n-dim grid of CZAR pmf (dimension 1 to 3) integrate_potential *czar_pmf; diff --git a/lib/colvars/colvarcomp.h b/lib/colvars/colvarcomp.h index b01c7e48e1..1ab7d17031 100644 --- a/lib/colvars/colvarcomp.h +++ b/lib/colvars/colvarcomp.h @@ -1512,7 +1512,7 @@ protected: std::map> string_cv_map; /// Sub-colvar components std::vector cv; - /// Refernce colvar values from path + /// Reference colvar values from path std::vector> ref_cv; /// If all sub-cvs use explicit gradients then we also use it bool use_explicit_gradients; diff --git a/lib/colvars/colvarcomp_protein.cpp b/lib/colvars/colvarcomp_protein.cpp index e0779b602e..3add471c04 100644 --- a/lib/colvars/colvarcomp_protein.cpp +++ b/lib/colvars/colvarcomp_protein.cpp @@ -210,7 +210,7 @@ void colvar::alpha_angles::collect_gradients(std::vector const &atom_ids, s 1.0/(1.0 - (t*t*t*t)) * ( (-2.0 * t) + (-1.0*f)*(-4.0 * (t*t*t)) ); - // Coeficient of this CVC's gradient in the colvar gradient, times coefficient of this + // Coefficient of this CVC's gradient in the colvar gradient, times coefficient of this // angle's gradient in the CVC's gradient cvm::real const coeff = cvc_coeff * theta_norm * dfdt * (1.0/theta_tol); @@ -230,7 +230,7 @@ void colvar::alpha_angles::collect_gradients(std::vector const &atom_ids, s cvm::real const hb_norm = hb_coeff / cvm::real(hb.size()); for (size_t i = 0; i < hb.size(); i++) { - // Coeficient of this CVC's gradient in the colvar gradient, times coefficient of this + // Coefficient of this CVC's gradient in the colvar gradient, times coefficient of this // hbond's gradient in the CVC's gradient cvm::real const coeff = cvc_coeff * 0.5 * hb_norm; @@ -473,7 +473,7 @@ void colvar::dihedPC::collect_gradients(std::vector const &atom_ids, std::v cvm::real const t = (PI / 180.) * theta[i]->value().real_value; cvm::real const dcosdt = - (PI / 180.) * cvm::sin(t); cvm::real const dsindt = (PI / 180.) * cvm::cos(t); - // Coeficient of this dihedPC's gradient in the colvar gradient, times coefficient of this + // Coefficient of this dihedPC's gradient in the colvar gradient, times coefficient of this // dihedral's gradient in the dihedPC's gradient cvm::real const coeff = cvc_coeff * (coeffs[2*i] * dcosdt + coeffs[2*i+1] * dsindt); diff --git a/lib/colvars/colvardeps.h b/lib/colvars/colvardeps.h index 058ac3c78c..63669536fe 100644 --- a/lib/colvars/colvardeps.h +++ b/lib/colvars/colvardeps.h @@ -21,7 +21,7 @@ /// system. They may be enabled or disabled depending on dependencies. /// 2. User features may be enabled based on user input (they may trigger a failure upon dependency resolution, though) /// 3. Static features are static properties of the object, determined -/// programatically at initialization time. +/// programmatically at initialization time. /// /// The following diagram summarizes the dependency tree at the bias, colvar, and colvarcomp levels. /// Isolated and atom group features are not shown to save space. diff --git a/lib/colvars/colvarproxy.h b/lib/colvars/colvarproxy.h index 7a43946c52..ba91afb40e 100644 --- a/lib/colvars/colvarproxy.h +++ b/lib/colvars/colvarproxy.h @@ -334,7 +334,7 @@ class colvarproxy_atom_groups { public: - /// Contructor + /// Constructor colvarproxy_atom_groups(); /// Destructor diff --git a/lib/gpu/README b/lib/gpu/README index 2d98749a40..2ef8ce9556 100644 --- a/lib/gpu/README +++ b/lib/gpu/README @@ -52,7 +52,7 @@ user-gpu_SYSLIB = CUDA libraries needed by this package user-gpu_SYSPATH = path(s) to where those libraries are Because you have the CUDA compilers on your system, you should have -the needed libraries. If the CUDA developement tools were installed +the needed libraries. If the CUDA development tools were installed in the standard manner, the settings in the Makefile.lammps.standard file should work. diff --git a/lib/gpu/cudpp_mini/cudpp.cpp b/lib/gpu/cudpp_mini/cudpp.cpp index da5975406d..e2cd4621a4 100644 --- a/lib/gpu/cudpp_mini/cudpp.cpp +++ b/lib/gpu/cudpp_mini/cudpp.cpp @@ -27,7 +27,7 @@ * defined in cudpp.h. Public interface functions call functions in the * \link cudpp_app Application-Level\endlink interface. The public * interface functions include Plan Interface functions and Algorithm - * Interface functions. Plan Inteface functions are used for creating + * Interface functions. Plan Interface functions are used for creating * CUDPP Plan objects which contain configuration details, intermediate * storage space, and in the case of cudppSparseMatrix(), data. The * Algorithm Interface is the set of functions that do the real work diff --git a/lib/gpu/cudpp_mini/cutil.h b/lib/gpu/cudpp_mini/cutil.h index 3df93fb886..fbf139cda3 100644 --- a/lib/gpu/cudpp_mini/cutil.h +++ b/lib/gpu/cudpp_mini/cutil.h @@ -367,7 +367,7 @@ extern "C" { //! @param w width of the image //! @param h height of the image //! @note If a NULL pointer is passed to this function and it is - //! initialized withing Cutil then cutFree() has to be used to + //! initialized within Cutil then cutFree() has to be used to //! deallocate the memory //////////////////////////////////////////////////////////////////////////// DLL_MAPPING @@ -382,7 +382,7 @@ extern "C" { //! @param w width of the image //! @param h height of the image //! @note If a NULL pointer is passed to this function and it is - //! initialized withing Cutil then cutFree() has to be used to + //! initialized within Cutil then cutFree() has to be used to //! deallocate the memory //////////////////////////////////////////////////////////////////////////// DLL_MAPPING @@ -466,7 +466,7 @@ extern "C" { //////////////////////////////////////////////////////////////////////////// // Command line arguments: General notes // * All command line arguments begin with '--' followed by the token; - // token and value are seperated by '='; example --samples=50 + // token and value are separated by '='; example --samples=50 // * Arrays have the form --model=[one.obj,two.obj,three.obj] // (without whitespaces) //////////////////////////////////////////////////////////////////////////// diff --git a/lib/gpu/cudpp_mini/kernel/scan_kernel.cu b/lib/gpu/cudpp_mini/kernel/scan_kernel.cu index 966634c89b..d8eb477952 100644 --- a/lib/gpu/cudpp_mini/kernel/scan_kernel.cu +++ b/lib/gpu/cudpp_mini/kernel/scan_kernel.cu @@ -46,7 +46,7 @@ * the rows of \a d_blockSums (in elements) in \a blockSumRowPitch, and invoke * with a thread block grid with height greater than 1. * - * This function peforms one level of a recursive, multiblock scan. At the + * This function performs one level of a recursive, multiblock scan. At the * app level, this function is called by cudppScan and cudppMultiScan and used * in combination with vectorAddUniform4() to produce a complete scan. * diff --git a/lib/gpu/lal_base_atomic.h b/lib/gpu/lal_base_atomic.h index e3e9829abc..da17bd928d 100644 --- a/lib/gpu/lal_base_atomic.h +++ b/lib/gpu/lal_base_atomic.h @@ -43,7 +43,7 @@ class BaseAtomic { * \param k_name name for the kernel for force calculation * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_base_charge.h b/lib/gpu/lal_base_charge.h index 64c19554b9..29554ebfd5 100644 --- a/lib/gpu/lal_base_charge.h +++ b/lib/gpu/lal_base_charge.h @@ -44,7 +44,7 @@ class BaseCharge { * \param k_name name for the kernel for force calculation * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_base_dipole.h b/lib/gpu/lal_base_dipole.h index b51c4303cf..eecdcd3aab 100644 --- a/lib/gpu/lal_base_dipole.h +++ b/lib/gpu/lal_base_dipole.h @@ -42,7 +42,7 @@ class BaseDipole { * \param k_name name for the kernel for force calculation * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_base_dpd.h b/lib/gpu/lal_base_dpd.h index 7a75282d0a..b46de2197d 100644 --- a/lib/gpu/lal_base_dpd.h +++ b/lib/gpu/lal_base_dpd.h @@ -42,7 +42,7 @@ class BaseDPD { * \param k_name name for the kernel for force calculation * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_base_ellipsoid.h b/lib/gpu/lal_base_ellipsoid.h index 7deeccbf44..d4bdd9e969 100644 --- a/lib/gpu/lal_base_ellipsoid.h +++ b/lib/gpu/lal_base_ellipsoid.h @@ -44,7 +44,7 @@ class BaseEllipsoid { * \param k_name name for the kernel for force calculation * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_base_three.h b/lib/gpu/lal_base_three.h index f5f36863c4..96ca928edc 100644 --- a/lib/gpu/lal_base_three.h +++ b/lib/gpu/lal_base_three.h @@ -46,7 +46,7 @@ class BaseThree { * \param k_three name for the kernel for 3-body force calculation * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_beck.h b/lib/gpu/lal_beck.h index db26bebeb0..638f1bf626 100644 --- a/lib/gpu/lal_beck.h +++ b/lib/gpu/lal_beck.h @@ -32,7 +32,7 @@ class Beck : public BaseAtomic { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_born.h b/lib/gpu/lal_born.h index 685f4d87a9..2a7f355d69 100644 --- a/lib/gpu/lal_born.h +++ b/lib/gpu/lal_born.h @@ -32,7 +32,7 @@ class Born : public BaseAtomic { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_born_coul_long.h b/lib/gpu/lal_born_coul_long.h index d236b7b57f..e383d18e0c 100644 --- a/lib/gpu/lal_born_coul_long.h +++ b/lib/gpu/lal_born_coul_long.h @@ -32,7 +32,7 @@ class BornCoulLong : public BaseCharge { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_born_coul_long_cs.h b/lib/gpu/lal_born_coul_long_cs.h index df0fa0fcd4..6c4032b3be 100644 --- a/lib/gpu/lal_born_coul_long_cs.h +++ b/lib/gpu/lal_born_coul_long_cs.h @@ -32,7 +32,7 @@ class BornCoulLongCS : public BornCoulLong { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_born_coul_wolf.h b/lib/gpu/lal_born_coul_wolf.h index 4b817ee0ce..fa53f48939 100644 --- a/lib/gpu/lal_born_coul_wolf.h +++ b/lib/gpu/lal_born_coul_wolf.h @@ -32,7 +32,7 @@ class BornCoulWolf : public BaseCharge { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_born_coul_wolf_cs.h b/lib/gpu/lal_born_coul_wolf_cs.h index 1d9de0a457..e5bff1b4cc 100644 --- a/lib/gpu/lal_born_coul_wolf_cs.h +++ b/lib/gpu/lal_born_coul_wolf_cs.h @@ -32,7 +32,7 @@ class BornCoulWolfCS : public BornCoulWolf { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_buck.h b/lib/gpu/lal_buck.h index 3b84066355..7a09fae5dd 100644 --- a/lib/gpu/lal_buck.h +++ b/lib/gpu/lal_buck.h @@ -32,7 +32,7 @@ class Buck : public BaseAtomic { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_buck_coul.h b/lib/gpu/lal_buck_coul.h index 3f8428bfe1..eebba78eb0 100644 --- a/lib/gpu/lal_buck_coul.h +++ b/lib/gpu/lal_buck_coul.h @@ -32,7 +32,7 @@ class BuckCoul : public BaseCharge { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_buck_coul_long.h b/lib/gpu/lal_buck_coul_long.h index 4a70a3a097..e2d69475cf 100644 --- a/lib/gpu/lal_buck_coul_long.h +++ b/lib/gpu/lal_buck_coul_long.h @@ -32,7 +32,7 @@ class BuckCoulLong : public BaseCharge { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_charmm_long.h b/lib/gpu/lal_charmm_long.h index 011083db13..5d9d9ea50b 100644 --- a/lib/gpu/lal_charmm_long.h +++ b/lib/gpu/lal_charmm_long.h @@ -32,7 +32,7 @@ class CHARMMLong : public BaseCharge { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_colloid.h b/lib/gpu/lal_colloid.h index dfbd4dbadd..35426007d8 100644 --- a/lib/gpu/lal_colloid.h +++ b/lib/gpu/lal_colloid.h @@ -32,7 +32,7 @@ class Colloid : public BaseAtomic { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_coul.h b/lib/gpu/lal_coul.h index 6d9b6b1b2b..38472375fb 100644 --- a/lib/gpu/lal_coul.h +++ b/lib/gpu/lal_coul.h @@ -32,7 +32,7 @@ class Coul : public BaseCharge { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_coul_debye.h b/lib/gpu/lal_coul_debye.h index 328c3dd64e..13e4c5b0c6 100644 --- a/lib/gpu/lal_coul_debye.h +++ b/lib/gpu/lal_coul_debye.h @@ -32,7 +32,7 @@ class CoulDebye : public BaseCharge { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_coul_dsf.h b/lib/gpu/lal_coul_dsf.h index e52a51d583..3d57898f81 100644 --- a/lib/gpu/lal_coul_dsf.h +++ b/lib/gpu/lal_coul_dsf.h @@ -32,7 +32,7 @@ class CoulDSF : public BaseCharge { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_coul_long.h b/lib/gpu/lal_coul_long.h index ae25b91dc7..0668e0fd02 100644 --- a/lib/gpu/lal_coul_long.h +++ b/lib/gpu/lal_coul_long.h @@ -32,7 +32,7 @@ class CoulLong : public BaseCharge { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_coul_long_cs.h b/lib/gpu/lal_coul_long_cs.h index 3cfcb80fc8..fc3667d6a0 100644 --- a/lib/gpu/lal_coul_long_cs.h +++ b/lib/gpu/lal_coul_long_cs.h @@ -32,7 +32,7 @@ class CoulLongCS : public CoulLong { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_device.h b/lib/gpu/lal_device.h index 0c4d5f8c43..21bd039c42 100644 --- a/lib/gpu/lal_device.h +++ b/lib/gpu/lal_device.h @@ -41,7 +41,7 @@ class Device { /** Sets up a per-device MPI communicator for load balancing and initializes * the device (>=first_gpu and <=last_gpu) that this proc will be using * Returns: - * - 0 if successfull + * - 0 if successful * - -2 if GPU not found * - -4 if GPU library not compiled for GPU * - -6 if GPU could not be initialized for use @@ -62,7 +62,7 @@ class Device { * \param vel True if velocities need to be stored * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU @@ -76,7 +76,7 @@ class Device { * \param nall Total number of local+ghost particles * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU @@ -100,7 +100,7 @@ class Device { * \param threads_per_atom value to be used by the neighbor list only * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_dipole_lj.h b/lib/gpu/lal_dipole_lj.h index 615784ee8b..bd312324c6 100644 --- a/lib/gpu/lal_dipole_lj.h +++ b/lib/gpu/lal_dipole_lj.h @@ -32,7 +32,7 @@ class DipoleLJ : public BaseDipole { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_dipole_lj_sf.h b/lib/gpu/lal_dipole_lj_sf.h index 20357385a2..ae73508065 100644 --- a/lib/gpu/lal_dipole_lj_sf.h +++ b/lib/gpu/lal_dipole_lj_sf.h @@ -32,7 +32,7 @@ class DipoleLJSF : public BaseDipole { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_dipole_long_lj.h b/lib/gpu/lal_dipole_long_lj.h index 1381e24326..77e22a10a7 100644 --- a/lib/gpu/lal_dipole_long_lj.h +++ b/lib/gpu/lal_dipole_long_lj.h @@ -32,7 +32,7 @@ class DipoleLongLJ : public BaseDipole { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_dpd.h b/lib/gpu/lal_dpd.h index 42ef854522..3c36c39e05 100644 --- a/lib/gpu/lal_dpd.h +++ b/lib/gpu/lal_dpd.h @@ -32,7 +32,7 @@ class DPD : public BaseDPD { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_eam.h b/lib/gpu/lal_eam.h index ce26edc1f4..fa05075883 100644 --- a/lib/gpu/lal_eam.h +++ b/lib/gpu/lal_eam.h @@ -33,7 +33,7 @@ class EAM : public BaseAtomic { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_gauss.h b/lib/gpu/lal_gauss.h index d023310c6d..1399b82d03 100644 --- a/lib/gpu/lal_gauss.h +++ b/lib/gpu/lal_gauss.h @@ -32,7 +32,7 @@ class Gauss : public BaseAtomic { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_gayberne.h b/lib/gpu/lal_gayberne.h index 8792f1f1db..750c739cec 100644 --- a/lib/gpu/lal_gayberne.h +++ b/lib/gpu/lal_gayberne.h @@ -34,7 +34,7 @@ class GayBerne : public BaseEllipsoid { * \return false if there is not sufficient memory or device init prob * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_lj.h b/lib/gpu/lal_lj.h index 01ce85c8ea..c6fec0d159 100644 --- a/lib/gpu/lal_lj.h +++ b/lib/gpu/lal_lj.h @@ -32,7 +32,7 @@ class LJ : public BaseAtomic { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_lj96.h b/lib/gpu/lal_lj96.h index 3fdea5265e..eef6863f37 100644 --- a/lib/gpu/lal_lj96.h +++ b/lib/gpu/lal_lj96.h @@ -32,7 +32,7 @@ class LJ96 : public BaseAtomic { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_lj_class2_long.h b/lib/gpu/lal_lj_class2_long.h index d07b974a90..eac6451b2e 100644 --- a/lib/gpu/lal_lj_class2_long.h +++ b/lib/gpu/lal_lj_class2_long.h @@ -32,7 +32,7 @@ class LJClass2Long : public BaseCharge { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_lj_coul.h b/lib/gpu/lal_lj_coul.h index a262c0837f..0e11162aa5 100644 --- a/lib/gpu/lal_lj_coul.h +++ b/lib/gpu/lal_lj_coul.h @@ -32,7 +32,7 @@ class LJCoul : public BaseCharge { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_lj_coul_debye.h b/lib/gpu/lal_lj_coul_debye.h index 1d3d0ba375..22fcf7234b 100644 --- a/lib/gpu/lal_lj_coul_debye.h +++ b/lib/gpu/lal_lj_coul_debye.h @@ -32,7 +32,7 @@ class LJCoulDebye : public BaseCharge { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_lj_coul_long.h b/lib/gpu/lal_lj_coul_long.h index 7b2d79c2a6..8f77671dc0 100644 --- a/lib/gpu/lal_lj_coul_long.h +++ b/lib/gpu/lal_lj_coul_long.h @@ -32,7 +32,7 @@ class LJCoulLong : public BaseCharge { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_lj_coul_msm.h b/lib/gpu/lal_lj_coul_msm.h index 48d49a8742..6369ce8cb5 100644 --- a/lib/gpu/lal_lj_coul_msm.h +++ b/lib/gpu/lal_lj_coul_msm.h @@ -32,7 +32,7 @@ class LJCoulMSM : public BaseCharge { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_lj_cubic.h b/lib/gpu/lal_lj_cubic.h index 818fb3581b..9578ca27e4 100644 --- a/lib/gpu/lal_lj_cubic.h +++ b/lib/gpu/lal_lj_cubic.h @@ -32,7 +32,7 @@ class LJCubic : public BaseAtomic { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_lj_dsf.h b/lib/gpu/lal_lj_dsf.h index 0195898ca4..b176e087db 100644 --- a/lib/gpu/lal_lj_dsf.h +++ b/lib/gpu/lal_lj_dsf.h @@ -32,7 +32,7 @@ class LJDSF : public BaseCharge { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_lj_expand.h b/lib/gpu/lal_lj_expand.h index a732a3a686..2560d166c7 100644 --- a/lib/gpu/lal_lj_expand.h +++ b/lib/gpu/lal_lj_expand.h @@ -32,7 +32,7 @@ class LJExpand : public BaseAtomic { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_lj_expand_coul_long.h b/lib/gpu/lal_lj_expand_coul_long.h index 64fd9df1ab..404a36e5bc 100644 --- a/lib/gpu/lal_lj_expand_coul_long.h +++ b/lib/gpu/lal_lj_expand_coul_long.h @@ -32,7 +32,7 @@ class LJExpandCoulLong : public BaseCharge { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_lj_gromacs.h b/lib/gpu/lal_lj_gromacs.h index 1e0f72dafc..3dec13c6d7 100644 --- a/lib/gpu/lal_lj_gromacs.h +++ b/lib/gpu/lal_lj_gromacs.h @@ -32,7 +32,7 @@ class LJGROMACS : public BaseAtomic { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_lj_sdk.h b/lib/gpu/lal_lj_sdk.h index ac2b9aafe3..fc50756a3f 100644 --- a/lib/gpu/lal_lj_sdk.h +++ b/lib/gpu/lal_lj_sdk.h @@ -32,7 +32,7 @@ class CGCMM : public BaseAtomic { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_lj_sdk_long.h b/lib/gpu/lal_lj_sdk_long.h index f56687cd7d..608488bd30 100644 --- a/lib/gpu/lal_lj_sdk_long.h +++ b/lib/gpu/lal_lj_sdk_long.h @@ -32,7 +32,7 @@ class CGCMMLong : public BaseCharge { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_lj_tip4p_long.h b/lib/gpu/lal_lj_tip4p_long.h index ab32d1e9f3..90c342e246 100644 --- a/lib/gpu/lal_lj_tip4p_long.h +++ b/lib/gpu/lal_lj_tip4p_long.h @@ -32,7 +32,7 @@ public: * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_mie.h b/lib/gpu/lal_mie.h index 8752fe1748..dfc2ee6e53 100644 --- a/lib/gpu/lal_mie.h +++ b/lib/gpu/lal_mie.h @@ -32,7 +32,7 @@ class Mie : public BaseAtomic { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_morse.h b/lib/gpu/lal_morse.h index ef80fb4235..bf5f1c0f8f 100644 --- a/lib/gpu/lal_morse.h +++ b/lib/gpu/lal_morse.h @@ -32,7 +32,7 @@ class Morse : public BaseAtomic { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_pppm.h b/lib/gpu/lal_pppm.h index 045423e079..65af157513 100644 --- a/lib/gpu/lal_pppm.h +++ b/lib/gpu/lal_pppm.h @@ -39,7 +39,7 @@ class PPPM { /// Clear any previous data and set up for a new LAMMPS run /** Success will be: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -2 if GPU could not be found * - -3 if there is an out of memory error diff --git a/lib/gpu/lal_re_squared.h b/lib/gpu/lal_re_squared.h index 8dc137d829..9e4f4af67a 100644 --- a/lib/gpu/lal_re_squared.h +++ b/lib/gpu/lal_re_squared.h @@ -34,7 +34,7 @@ class RESquared : public BaseEllipsoid { * \return false if there is not sufficient memory or device init prob * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_soft.h b/lib/gpu/lal_soft.h index e72673248c..ff4524b30a 100644 --- a/lib/gpu/lal_soft.h +++ b/lib/gpu/lal_soft.h @@ -32,7 +32,7 @@ class Soft : public BaseAtomic { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_sw.h b/lib/gpu/lal_sw.h index 3546f02eb7..1a2e025ae0 100644 --- a/lib/gpu/lal_sw.h +++ b/lib/gpu/lal_sw.h @@ -32,7 +32,7 @@ class SW : public BaseThree { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_table.h b/lib/gpu/lal_table.h index f667336679..38ae012bee 100644 --- a/lib/gpu/lal_table.h +++ b/lib/gpu/lal_table.h @@ -32,7 +32,7 @@ class Table : public BaseAtomic { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_tersoff.h b/lib/gpu/lal_tersoff.h index fd01af031a..51e64c987b 100644 --- a/lib/gpu/lal_tersoff.h +++ b/lib/gpu/lal_tersoff.h @@ -32,7 +32,7 @@ class Tersoff : public BaseThree { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_tersoff_mod.h b/lib/gpu/lal_tersoff_mod.h index ab1560d951..29a561c71d 100644 --- a/lib/gpu/lal_tersoff_mod.h +++ b/lib/gpu/lal_tersoff_mod.h @@ -32,7 +32,7 @@ class TersoffMod : public BaseThree { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_tersoff_zbl.h b/lib/gpu/lal_tersoff_zbl.h index 0e6cac9587..eb03e9fb02 100644 --- a/lib/gpu/lal_tersoff_zbl.h +++ b/lib/gpu/lal_tersoff_zbl.h @@ -32,7 +32,7 @@ class TersoffZBL : public BaseThree { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_ufm.h b/lib/gpu/lal_ufm.h index aeeaacbe99..65ee15d5b5 100644 --- a/lib/gpu/lal_ufm.h +++ b/lib/gpu/lal_ufm.h @@ -34,7 +34,7 @@ class UFM : public BaseAtomic { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_vashishta.h b/lib/gpu/lal_vashishta.h index c5c96a5b80..2da7a11e1e 100644 --- a/lib/gpu/lal_vashishta.h +++ b/lib/gpu/lal_vashishta.h @@ -32,7 +32,7 @@ class Vashishta : public BaseThree { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_yukawa.h b/lib/gpu/lal_yukawa.h index 4cc23c03e9..7d638d760e 100644 --- a/lib/gpu/lal_yukawa.h +++ b/lib/gpu/lal_yukawa.h @@ -32,7 +32,7 @@ class Yukawa : public BaseAtomic { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_yukawa_colloid.h b/lib/gpu/lal_yukawa_colloid.h index ba69bc4bae..607bc42321 100644 --- a/lib/gpu/lal_yukawa_colloid.h +++ b/lib/gpu/lal_yukawa_colloid.h @@ -32,7 +32,7 @@ class YukawaColloid : public BaseAtomic { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/gpu/lal_zbl.h b/lib/gpu/lal_zbl.h index 9885fcedf2..e205d326c6 100644 --- a/lib/gpu/lal_zbl.h +++ b/lib/gpu/lal_zbl.h @@ -32,7 +32,7 @@ class ZBL : public BaseAtomic { * \param gpu_split fraction of particles handled by device * * Returns: - * - 0 if successfull + * - 0 if successful * - -1 if fix gpu not found * - -3 if there is an out of memory error * - -4 if the GPU library was not compiled for GPU diff --git a/lib/h5md/README b/lib/h5md/README index fb7d82bfcc..4768b50697 100644 --- a/lib/h5md/README +++ b/lib/h5md/README @@ -19,7 +19,7 @@ ch5md is a set of C routines to manipulate H5MD files. H5MD is a file format specification based on [HDF5](http://www.hdfgroup.org/HDF5/) for storing molecular data, whose development is found at . -ch5md is developped by Pierre de Buyl and is released under the 3-clause BSD +ch5md is developed by Pierre de Buyl and is released under the 3-clause BSD license that can be found in the file LICENSE. To use the h5md dump style in lammps, execute diff --git a/lib/kokkos/algorithms/src/Kokkos_Random.hpp b/lib/kokkos/algorithms/src/Kokkos_Random.hpp index e14471a48a..da781de4fe 100644 --- a/lib/kokkos/algorithms/src/Kokkos_Random.hpp +++ b/lib/kokkos/algorithms/src/Kokkos_Random.hpp @@ -102,9 +102,9 @@ namespace Kokkos { //Initializing constructor: calls init(seed,Device_Specific_Number); Pool(unsigned int seed); - //Intialize Pool with seed as a starting seed with a pool_size of num_states + //Initialize Pool with seed as a starting seed with a pool_size of num_states //The Random_XorShift64 generator is used in serial to initialize all states, - //thus the intialization process is platform independent and deterministic. + //thus the initialization process is platform independent and deterministic. void init(unsigned int seed, int num_states); //Get a generator. This will lock one of the states, guaranteeing that each thread diff --git a/lib/kokkos/benchmarks/policy_performance/script_sample_usage.sh b/lib/kokkos/benchmarks/policy_performance/script_sample_usage.sh index f4bfb87f8f..1c2db56648 100755 --- a/lib/kokkos/benchmarks/policy_performance/script_sample_usage.sh +++ b/lib/kokkos/benchmarks/policy_performance/script_sample_usage.sh @@ -2,7 +2,7 @@ # Sample script for benchmarking policy performance -# Suggested enviroment variables to export prior to executing script: +# Suggested environment variables to export prior to executing script: # KNL: # OMP_NUM_THREADS=256 KMP_AFFINITY=compact # Power: diff --git a/lib/kokkos/bin/hpcbind b/lib/kokkos/bin/hpcbind index b185a92821..6af091a7d8 100755 --- a/lib/kokkos/bin/hpcbind +++ b/lib/kokkos/bin/hpcbind @@ -383,7 +383,7 @@ fi # Check unknown arguments ################################################################################ if [[ ${#UNKNOWN_ARGS[*]} > 0 ]]; then - echo "HPCBIND Uknown options: ${UNKNOWN_ARGS[*]}" > >(tee -a ${HPCBIND_LOG}) + echo "HPCBIND Unknown options: ${UNKNOWN_ARGS[*]}" > >(tee -a ${HPCBIND_LOG}) exit 1 fi diff --git a/lib/kokkos/containers/src/Kokkos_UnorderedMap.hpp b/lib/kokkos/containers/src/Kokkos_UnorderedMap.hpp index aed723288f..1406116e26 100644 --- a/lib/kokkos/containers/src/Kokkos_UnorderedMap.hpp +++ b/lib/kokkos/containers/src/Kokkos_UnorderedMap.hpp @@ -102,7 +102,7 @@ public: KOKKOS_FORCEINLINE_FUNCTION bool existing() const { return (m_status & EXISTING); } - /// Did the map fail to insert the key due to insufficent capacity + /// Did the map fail to insert the key due to insufficient capacity KOKKOS_FORCEINLINE_FUNCTION bool failed() const { return m_index == UnorderedMapInvalidIndex; } diff --git a/lib/kokkos/containers/src/Kokkos_Vector.hpp b/lib/kokkos/containers/src/Kokkos_Vector.hpp index 9b151d9505..fb71f476c6 100644 --- a/lib/kokkos/containers/src/Kokkos_Vector.hpp +++ b/lib/kokkos/containers/src/Kokkos_Vector.hpp @@ -110,7 +110,7 @@ public: void assign (size_t n, const Scalar& val) { - /* Resize if necessary (behavour of std:vector) */ + /* Resize if necessary (behaviour of std:vector) */ if(n>span()) DV::resize(size_t (n*_extra_storage)); @@ -177,7 +177,7 @@ public: const_reference back() const {return DV::h_view(_size - 1);} - /* std::algorithms wich work originally with iterators, here they are implemented as member functions */ + /* std::algorithms witch work originally with iterators, here they are implemented as member functions */ size_t lower_bound (const size_t& start, diff --git a/lib/kokkos/containers/unit_tests/TestBitset.hpp b/lib/kokkos/containers/unit_tests/TestBitset.hpp index 371c0288b1..55d0e8b938 100644 --- a/lib/kokkos/containers/unit_tests/TestBitset.hpp +++ b/lib/kokkos/containers/unit_tests/TestBitset.hpp @@ -216,7 +216,7 @@ void test_bitset() bitset_type bitset(test_sizes[i]); - //std::cout << " Check inital count " << std::endl; + //std::cout << " Check initial count " << std::endl; // nothing should be set { Impl::TestBitsetTest< bitset_type > f(bitset); diff --git a/lib/kokkos/containers/unit_tests/TestViewCtorPropEmbeddedDim.hpp b/lib/kokkos/containers/unit_tests/TestViewCtorPropEmbeddedDim.hpp index d4b7cf0bdb..2dd5c56cd9 100644 --- a/lib/kokkos/containers/unit_tests/TestViewCtorPropEmbeddedDim.hpp +++ b/lib/kokkos/containers/unit_tests/TestViewCtorPropEmbeddedDim.hpp @@ -64,7 +64,7 @@ struct TestViewCtorProp_EmbeddedDim { using DynRankViewIntType = typename Kokkos::DynRankView< int, ExecSpace >; using DynRankViewDoubleType = typename Kokkos::DynRankView< double, ExecSpace >; - // Cuda 7.0 has issues with using a lamda in parallel_for to initialize the view - replace with this functor + // Cuda 7.0 has issues with using a lambda in parallel_for to initialize the view - replace with this functor template < class ViewType > struct Functor { diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Locks.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Locks.hpp index 8363a45662..cfc46f0461 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Locks.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Locks.hpp @@ -113,10 +113,10 @@ Kokkos::Impl::CudaLockArrays g_device_cuda_lock_arrays ; #define CUDA_SPACE_ATOMIC_MASK 0x1FFFF -/// \brief Aquire a lock for the address +/// \brief Acquire a lock for the address /// -/// This function tries to aquire the lock for the hash value derived -/// from the provided ptr. If the lock is successfully aquired the +/// This function tries to acquire the lock for the hash value derived +/// from the provided ptr. If the lock is successfully acquired the /// function returns true. Otherwise it returns false. __device__ inline bool lock_address_cuda_space(void* ptr) { @@ -130,7 +130,7 @@ bool lock_address_cuda_space(void* ptr) { /// /// This function releases the lock for the hash value derived /// from the provided ptr. This function should only be called -/// after previously successfully aquiring a lock with +/// after previously successfully acquiring a lock with /// lock_address. __device__ inline void unlock_address_cuda_space(void* ptr) { diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp index c05fbcc6c1..860d94d6c7 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp @@ -309,11 +309,11 @@ public: , m_thread_scratch_size {0,0} , m_chunk_size ( 32 ) { - // Make sure league size is permissable + // Make sure league size is permissible if(league_size_ >= int(Impl::cuda_internal_maximum_grid_count())) Impl::throw_runtime_exception( "Requested too large league_size for TeamPolicy on Cuda execution space."); - // Make sure total block size is permissable + // Make sure total block size is permissible if ( m_team_size * m_vector_length > 1024 ) { Impl::throw_runtime_exception(std::string("Kokkos::TeamPolicy< Cuda > the team size is too large. Team size x vector length must be smaller than 1024.")); } @@ -332,7 +332,7 @@ public: , m_thread_scratch_size {0,0} , m_chunk_size ( 32 ) { - // Make sure league size is permissable + // Make sure league size is permissible if(league_size_ >= int(Impl::cuda_internal_maximum_grid_count())) Impl::throw_runtime_exception( "Requested too large league_size for TeamPolicy on Cuda execution space."); } @@ -348,11 +348,11 @@ public: , m_thread_scratch_size {0,0} , m_chunk_size ( 32 ) { - // Make sure league size is permissable + // Make sure league size is permissible if(league_size_ >= int(Impl::cuda_internal_maximum_grid_count())) Impl::throw_runtime_exception( "Requested too large league_size for TeamPolicy on Cuda execution space."); - // Make sure total block size is permissable + // Make sure total block size is permissible if ( m_team_size * m_vector_length > 1024 ) { Impl::throw_runtime_exception(std::string("Kokkos::TeamPolicy< Cuda > the team size is too large. Team size x vector length must be smaller than 1024.")); } @@ -369,7 +369,7 @@ public: , m_thread_scratch_size {0,0} , m_chunk_size ( 32 ) { - // Make sure league size is permissable + // Make sure league size is permissible if(league_size_ >= int(Impl::cuda_internal_maximum_grid_count())) Impl::throw_runtime_exception( "Requested too large league_size for TeamPolicy on Cuda execution space."); } diff --git a/lib/kokkos/core/src/Kokkos_Concepts.hpp b/lib/kokkos/core/src/Kokkos_Concepts.hpp index 98ae141de4..ca2e8b4eb6 100644 --- a/lib/kokkos/core/src/Kokkos_Concepts.hpp +++ b/lib/kokkos/core/src/Kokkos_Concepts.hpp @@ -284,7 +284,7 @@ public: >::type host_mirror_space ; }; -// For backward compatiblity +// For backward compatibility namespace Impl { diff --git a/lib/kokkos/core/src/Kokkos_CopyViews.hpp b/lib/kokkos/core/src/Kokkos_CopyViews.hpp index f919fdb755..9210f21ab7 100644 --- a/lib/kokkos/core/src/Kokkos_CopyViews.hpp +++ b/lib/kokkos/core/src/Kokkos_CopyViews.hpp @@ -1247,7 +1247,7 @@ void deep_copy typename ViewType::value_type >::value , "deep_copy requires non-const type" ); - // If contigous we can simply do a 1D flat loop + // If contiguous we can simply do a 1D flat loop if(dst.span_is_contiguous()) { typedef Kokkos::View diff --git a/lib/kokkos/core/src/Qthreads/Kokkos_Qthreads_TaskQueue_impl.hpp b/lib/kokkos/core/src/Qthreads/Kokkos_Qthreads_TaskQueue_impl.hpp index 152546fadc..c79332f653 100644 --- a/lib/kokkos/core/src/Qthreads/Kokkos_Qthreads_TaskQueue_impl.hpp +++ b/lib/kokkos/core/src/Qthreads/Kokkos_Qthreads_TaskQueue_impl.hpp @@ -318,7 +318,7 @@ void TaskQueue< ExecSpace >::complete // If 'task' is an aggregate then any of the runnable tasks that // it depends upon may be attempting to complete this 'task'. // Must only transition a task once to complete status. - // This is controled by atomically locking the wait queue. + // This is controlled by atomically locking the wait queue. // Stop other tasks from adding themselves to this task's wait queue // by locking the head of this task's wait queue. diff --git a/lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.cpp b/lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.cpp index 347778f289..1a9a837af7 100644 --- a/lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.cpp +++ b/lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.cpp @@ -638,7 +638,7 @@ void ThreadsExec::initialize // Spawn thread executing the 'driver()' function. // Wait until spawned thread has attempted to initialize. - // If spawning and initialization is successfull then + // If spawning and initialization are successful then // an entry in 's_threads_exec' will be assigned. if ( ThreadsExec::spawn() ) { wait_yield( s_threads_process.m_pool_state , ThreadsExec::Inactive ); @@ -666,7 +666,7 @@ void ThreadsExec::initialize memory_fence(); if ( ! thread_spawn_failed ) { - // Bind process to the core on which it was located before spawning occured + // Bind process to the core on which it was located before spawning occurred if (hwloc_can_bind) { Kokkos::hwloc::bind_this_thread( proc_coord ); } diff --git a/lib/kokkos/core/src/Threads/Kokkos_ThreadsExec_base.cpp b/lib/kokkos/core/src/Threads/Kokkos_ThreadsExec_base.cpp index f6443e146d..4876614245 100644 --- a/lib/kokkos/core/src/Threads/Kokkos_ThreadsExec_base.cpp +++ b/lib/kokkos/core/src/Threads/Kokkos_ThreadsExec_base.cpp @@ -52,7 +52,7 @@ #include #include -/* Standard C++ libaries */ +/* Standard C++ libraries */ #include #include @@ -159,7 +159,7 @@ void ThreadsExec::wait_yield( volatile int & flag , const int value ) #include #include -/* Standard C++ libaries */ +/* Standard C++ libraries */ #include #include diff --git a/lib/kokkos/core/src/impl/Kokkos_Error.cpp b/lib/kokkos/core/src/impl/Kokkos_Error.cpp index 33b0ba918d..dea856606c 100644 --- a/lib/kokkos/core/src/impl/Kokkos_Error.cpp +++ b/lib/kokkos/core/src/impl/Kokkos_Error.cpp @@ -110,7 +110,7 @@ std::string human_memory_size(size_t arg_bytes) */ /* Print call stack into an error stream, - * so one knows in which function the error occured. + * so one knows in which function the error occurred. * * Code copied from: * http://stupefydeveloper.blogspot.com/2008/10/cc-call-stack.html diff --git a/lib/kokkos/core/src/impl/Kokkos_HostBarrier.hpp b/lib/kokkos/core/src/impl/Kokkos_HostBarrier.hpp index 2416edbead..f7f1c4b50f 100644 --- a/lib/kokkos/core/src/impl/Kokkos_HostBarrier.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_HostBarrier.hpp @@ -68,7 +68,7 @@ namespace Kokkos { namespace Impl { // called split_release // // The purporse of the split functions is to allow the last thread to arrive -// an opprotunity to perform some actions before releasing the waiting threads +// an opportunity to perform some actions before releasing the waiting threads // // If all threads have arrived (and split_release has been call if using split_arrive) // before a wait type call, the wait may return quickly diff --git a/lib/kokkos/core/src/impl/Kokkos_HostThreadTeam.cpp b/lib/kokkos/core/src/impl/Kokkos_HostThreadTeam.cpp index ccb8393d08..383b2ec2dc 100644 --- a/lib/kokkos/core/src/impl/Kokkos_HostThreadTeam.cpp +++ b/lib/kokkos/core/src/impl/Kokkos_HostThreadTeam.cpp @@ -253,7 +253,7 @@ int HostThreadTeamData::get_work_stealing() noexcept HostThreadTeamData * const * const pool = (HostThreadTeamData**)( m_pool_scratch + m_pool_members ); - // Attempt from begining failed, try to steal from end of neighbor + // Attempt from beginning failed, try to steal from end of neighbor pair_int_t volatile * steal_range = & ( pool[ m_steal_rank ]->m_work_range ); diff --git a/lib/kokkos/core/src/impl/Kokkos_SharedAlloc.hpp b/lib/kokkos/core/src/impl/Kokkos_SharedAlloc.hpp index b5718573a2..54021a71be 100644 --- a/lib/kokkos/core/src/impl/Kokkos_SharedAlloc.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_SharedAlloc.hpp @@ -267,7 +267,7 @@ public: // Use macros instead of inline functions to reduce // pressure on compiler optimization by reducing - // number of symbols and inline functons. + // number of symbols and inline functions. #if defined( KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST ) diff --git a/lib/kokkos/core/src/impl/Kokkos_TaskNode.hpp b/lib/kokkos/core/src/impl/Kokkos_TaskNode.hpp index 35f8853f1f..49aa4b4b21 100644 --- a/lib/kokkos/core/src/impl/Kokkos_TaskNode.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_TaskNode.hpp @@ -536,7 +536,7 @@ public: void acquire_predecessor_from(runnable_task_type& other) { KOKKOS_EXPECTS(m_predecessor == nullptr || other.m_predecessor == m_predecessor); - // since we're transfering, no need to modify the reference count + // since we're transferring, no need to modify the reference count m_predecessor = other.m_predecessor; other.m_predecessor = nullptr; } @@ -545,7 +545,7 @@ public: void acquire_predecessor_from(runnable_task_type& other) volatile { KOKKOS_EXPECTS(m_predecessor == nullptr || other.m_predecessor == m_predecessor); - // since we're transfering, no need to modify the reference count + // since we're transferring, no need to modify the reference count m_predecessor = other.m_predecessor; other.m_predecessor = nullptr; } diff --git a/lib/kokkos/core/src/impl/Kokkos_TaskQueue_impl.hpp b/lib/kokkos/core/src/impl/Kokkos_TaskQueue_impl.hpp index b5f8db0085..7a0e00a2f2 100644 --- a/lib/kokkos/core/src/impl/Kokkos_TaskQueue_impl.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_TaskQueue_impl.hpp @@ -642,7 +642,7 @@ void TaskQueue< ExecSpace, MemorySpace>::complete // If 'task' is an aggregate then any of the runnable tasks that // it depends upon may be attempting to complete this 'task'. // Must only transition a task once to complete status. - // This is controled by atomically locking the wait queue. + // This is controlled by atomically locking the wait queue. // Stop other tasks from adding themselves to this task's wait queue // by locking the head of this task's wait queue. diff --git a/lib/kokkos/core/src/impl/Kokkos_Traits.hpp b/lib/kokkos/core/src/impl/Kokkos_Traits.hpp index a5af82838f..fc501cb73e 100644 --- a/lib/kokkos/core/src/impl/Kokkos_Traits.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_Traits.hpp @@ -132,7 +132,7 @@ template< typename T , class ... Args > struct are_integral { enum { value = // Accept std::is_integral OR std::is_enum as an integral value - // since a simple enum value is automically convertable to an + // since a simple enum value is automically convertible to an // integral value. ( std::is_integral::value || std::is_enum::value ) && diff --git a/lib/kokkos/core/unit_test/TestTeam.hpp b/lib/kokkos/core/unit_test/TestTeam.hpp index 5f325eb905..ff3977637c 100644 --- a/lib/kokkos/core/unit_test/TestTeam.hpp +++ b/lib/kokkos/core/unit_test/TestTeam.hpp @@ -1068,7 +1068,7 @@ struct TestTeamBroadcast { } ASSERT_EQ( size_t( expected_result ), size_t( total ) ); //printf("team_broadcast with value -- expected_result=%d, total=%d\n",expected_result, total); - //team_broadcast with funtion object + //team_broadcast with function object total = 0; Kokkos::parallel_reduce( policy_type_f( league_size, team_size ), functor, total ); @@ -1078,7 +1078,7 @@ struct TestTeamBroadcast { value_type val = ((i%team_size)*3+1)*2*team_size; expected_result+= val; } - ASSERT_EQ( size_t( expected_result ), size_t( total ) ); //printf("team_broadcast with funtion object -- expected_result=%d, total=%d\n",expected_result, total); + ASSERT_EQ( size_t( expected_result ), size_t( total ) ); //printf("team_broadcast with function object -- expected_result=%d, total=%d\n",expected_result, total); } }; diff --git a/lib/kokkos/core/unit_test/TestTeamVector.hpp b/lib/kokkos/core/unit_test/TestTeamVector.hpp index 45433012f9..46f2c98e37 100644 --- a/lib/kokkos/core/unit_test/TestTeamVector.hpp +++ b/lib/kokkos/core/unit_test/TestTeamVector.hpp @@ -570,7 +570,7 @@ struct functor_vec_single { KOKKOS_INLINE_FUNCTION void operator()( typename policy_type::member_type team ) const { - // Warning: this test case intentionally violates permissable semantics. + // Warning: this test case intentionally violates permissible semantics. // It is not valid to get references to members of the enclosing region // inside a parallel_for and write to it. Scalar value = 0; diff --git a/lib/kokkos/core/unit_test/TestViewCtorPropEmbeddedDim.hpp b/lib/kokkos/core/unit_test/TestViewCtorPropEmbeddedDim.hpp index 0b88052129..7730be2e1d 100644 --- a/lib/kokkos/core/unit_test/TestViewCtorPropEmbeddedDim.hpp +++ b/lib/kokkos/core/unit_test/TestViewCtorPropEmbeddedDim.hpp @@ -60,7 +60,7 @@ struct TestViewCtorProp_EmbeddedDim { using ViewIntType = typename Kokkos::View< int**, ExecSpace >; using ViewDoubleType = typename Kokkos::View< double*, ExecSpace >; - // Cuda 7.0 has issues with using a lamda in parallel_for to initialize the view - replace with this functor + // Cuda 7.0 has issues with using a lambda in parallel_for to initialize the view - replace with this functor template < class ViewType > struct Functor { diff --git a/lib/kokkos/core/unit_test/TestWorkGraph.hpp b/lib/kokkos/core/unit_test/TestWorkGraph.hpp index 248733420b..331d79d72a 100644 --- a/lib/kokkos/core/unit_test/TestWorkGraph.hpp +++ b/lib/kokkos/core/unit_test/TestWorkGraph.hpp @@ -55,7 +55,7 @@ namespace { The algorithm computes the N-th fibonacci number as follows: - Each "task" or "work item" computes the i-th fibonacci number - If a task as (i < 2), it will record the known answer ahead of time. - - If a taks has (i >= 2), it will "spawn" two more tasks to compute + - If a task has (i >= 2), it will "spawn" two more tasks to compute the (i - 1) and (i - 2) fibonacci numbers. We do NOT do any de-duplication of these tasks. De-duplication would result in only (N - 2) tasks which must be run in serial. diff --git a/lib/kokkos/example/fenl/fenl_functors.hpp b/lib/kokkos/example/fenl/fenl_functors.hpp index 96c89de29b..538f009a3f 100644 --- a/lib/kokkos/example/fenl/fenl_functors.hpp +++ b/lib/kokkos/example/fenl/fenl_functors.hpp @@ -250,7 +250,7 @@ public: const typename SetType::insert_result result = node_node_set.insert( key ); - // A successfull insert: the first time this pair was added + // A successful insert: the first time this pair was added if ( result.success() ) { // If row node is owned then increment count diff --git a/lib/kokkos/example/multi_fem/BoxMeshPartition.hpp b/lib/kokkos/example/multi_fem/BoxMeshPartition.hpp index b8f43d2a22..ea5d1de008 100644 --- a/lib/kokkos/example/multi_fem/BoxMeshPartition.hpp +++ b/lib/kokkos/example/multi_fem/BoxMeshPartition.hpp @@ -172,7 +172,7 @@ void box_partition_rcb( const BoxType & root_box , //---------------------------------------------------------------------------- /* Determine local id layout and communication maps for partitioned boxes. * - * Local ids are layed out as follows: + * Local ids are laid out as follows: * { [ owned-interior ids not sent ] , * [ owned-boundary ids to be sent to other processes ] , * [ received ids from processor ( my_part + 1 ) % part_count ] diff --git a/lib/kokkos/example/multi_fem/Implicit.hpp b/lib/kokkos/example/multi_fem/Implicit.hpp index f129c59546..7ca180bd2a 100644 --- a/lib/kokkos/example/multi_fem/Implicit.hpp +++ b/lib/kokkos/example/multi_fem/Implicit.hpp @@ -222,7 +222,7 @@ PerformanceData run( const typename FixtureType::FEMeshType & mesh , } //------------------------------------ - // Solve linear sytem + // Solve linear system cgsolve( mesh.parallel_data_map , linsys_matrix , linsys_rhs , linsys_solution , diff --git a/lib/kokkos/example/multi_fem/Nonlinear.hpp b/lib/kokkos/example/multi_fem/Nonlinear.hpp index b9585c7582..f5e462cc4b 100644 --- a/lib/kokkos/example/multi_fem/Nonlinear.hpp +++ b/lib/kokkos/example/multi_fem/Nonlinear.hpp @@ -389,7 +389,7 @@ PerformanceData run( const typename FixtureType::FEMeshType & mesh , } //------------------------------------ - // Solve linear sytem + // Solve linear system size_t cg_iteration_count = 0 ; double cg_residual_norm = 0 ; diff --git a/lib/kokkos/example/tutorial/03_simple_view/Makefile b/lib/kokkos/example/tutorial/03_simple_view/Makefile index de994a8df9..c9dc3a0fd0 100644 --- a/lib/kokkos/example/tutorial/03_simple_view/Makefile +++ b/lib/kokkos/example/tutorial/03_simple_view/Makefile @@ -43,7 +43,7 @@ include $(KOKKOS_PATH)/Makefile.kokkos build: $(EXE) -#for unit testing only, for best preformance with OpenMP 4.0 or better +#for unit testing only, for best performance with OpenMP 4.0 or better test: $(EXE) ./$(EXE) diff --git a/lib/kokkos/example/tutorial/Algorithms/01_random_numbers/random_numbers.cpp b/lib/kokkos/example/tutorial/Algorithms/01_random_numbers/random_numbers.cpp index 48b0d86cb8..f2095e346f 100644 --- a/lib/kokkos/example/tutorial/Algorithms/01_random_numbers/random_numbers.cpp +++ b/lib/kokkos/example/tutorial/Algorithms/01_random_numbers/random_numbers.cpp @@ -61,10 +61,10 @@ typedef Kokkos::HostSpace::execution_space DefaultHostType; // In Kokkos you are required to create a pool of generator states, so that threads can // grep their own. On CPU architectures the pool size is equal to the thread number, // on CUDA about 128k states are generated (enough to give every potentially simultaneously -// running thread its own state). With a kernel a thread is required to aquire a state from the +// running thread its own state). With a kernel a thread is required to acquire a state from the // pool and later return it. // On CPUs the Random number generator is deterministic if using the same number of threads. -// On GPUs (i.e. using the CUDA backend it is not deterministic because threads aquire states via +// On GPUs (i.e. using the CUDA backend it is not deterministic because threads acquire states via // atomics. // A Functor for generating uint64_t random numbers templated on the GeneratorPool type @@ -97,7 +97,7 @@ struct generate_random { for(int k = 0;k *> \verbatim *> -*> DLALSA is an itermediate step in solving the least squares problem +*> DLALSA is an intermediate step in solving the least squares problem *> by computing the SVD of the coefficient matrix in compact form (The *> singular vectors are computed as products of simple orthorgonal *> matrices.). diff --git a/lib/linalg/dlasd7.f b/lib/linalg/dlasd7.f index e0ddedeb57..66f665cf88 100644 --- a/lib/linalg/dlasd7.f +++ b/lib/linalg/dlasd7.f @@ -400,7 +400,7 @@ VL( I ) = VLW( IDXI ) 50 CONTINUE * -* Calculate the allowable deflation tolerence +* Calculate the allowable deflation tolerance * EPS = DLAMCH( 'Epsilon' ) TOL = MAX( ABS( ALPHA ), ABS( BETA ) ) diff --git a/lib/linalg/iparam2stage.F b/lib/linalg/iparam2stage.F index 7062b45aac..ecf30dbea8 100644 --- a/lib/linalg/iparam2stage.F +++ b/lib/linalg/iparam2stage.F @@ -87,14 +87,14 @@ *> *> \param[in] NBI *> \verbatim -*> NBI is INTEGER which is the used in the reduciton, +*> NBI is INTEGER which is the used in the reduction, * (e.g., the size of the band), needed to compute workspace * and LHOUS2. *> \endverbatim *> *> \param[in] IBI *> \verbatim -*> IBI is INTEGER which represent the IB of the reduciton, +*> IBI is INTEGER which represent the IB of the reduction, * needed to compute workspace and LHOUS2. *> \endverbatim *> diff --git a/lib/message/README b/lib/message/README index dafb94e9ef..e6e7d2103d 100644 --- a/lib/message/README +++ b/lib/message/README @@ -2,7 +2,7 @@ This directory contains the CSlib library which is required to use the MESSAGE package and its client/server commands in a LAMMPS input script. -The CSlib libary is included in the LAMMPS distribution. A fuller +The CSlib library is included in the LAMMPS distribution. A fuller version including documentation and test programs is available at http://cslib.sandia.gov. It was developed by Steve Plimpton at Sandia National Laboratories. diff --git a/lib/molfile/molfile_plugin.h b/lib/molfile/molfile_plugin.h index c79e7a5abf..057c403369 100644 --- a/lib/molfile/molfile_plugin.h +++ b/lib/molfile/molfile_plugin.h @@ -662,7 +662,7 @@ typedef struct { int **bondtype, int *nbondtypes, char ***bondtypename); /** - * XXX this function will be augmented and possibly superceded by a + * XXX this function will be augmented and possibly superseded by a * new QM-capable version named read_timestep(), when finished. * * Read the next timestep from the file. Return MOLFILE_SUCCESS, or diff --git a/lib/plumed/README b/lib/plumed/README index 0d5f52f6b2..6b9b22bbce 100644 --- a/lib/plumed/README +++ b/lib/plumed/README @@ -3,7 +3,7 @@ to use the PLUMED package and its fix plumed command in a LAMMPS input script. PLUMED should only be downloaded into this directory if you wish to statically link the library. If you wish to link PLUMED as a dynamic library (as we recommend) then you can compile and build PLUMED -separately to LAMMPS. To use PLUMED in conjuction with LAMMPS you then simply +separately to LAMMPS. To use PLUMED in conjunction with LAMMPS you then simply need to ensure that the PLUMED library is in your path at runtime. More info about the PLUMED library can be found at http://www.plumed.org. diff --git a/lib/poems/SystemProcessor.h b/lib/poems/SystemProcessor.h index 3be168c34d..f376890e99 100644 --- a/lib/poems/SystemProcessor.h +++ b/lib/poems/SystemProcessor.h @@ -124,7 +124,7 @@ POEMSChain * SystemProcessor::AddNewChain(POEMSNode * currentNode){ return NULL; } int * tmp; - POEMSNode * nextNode = NULL; //nextNode stores the proposed next node to add to the chain. this will be checked to make sure no backtracking is occuring before being assigned as the current node. + POEMSNode * nextNode = NULL; //nextNode stores the proposed next node to add to the chain. this will be checked to make sure no backtracking is occurring before being assigned as the current node. POEMSChain * newChain = new POEMSChain; //make a new POEMSChain object. This will be the object returned if(currentNode->links.GetNumElements() == 0) //if we have no links from this node, then the whole chain is only one node. Add this node to the chain and return it; mark node as visited for future reference @@ -226,7 +226,7 @@ bool SystemProcessor::setLinkVisited(POEMSNode * firstNode, POEMSNode * secondNo //cout << "Checking link between nodes " << firstNode->idNumber << " and " << secondNode->idNumber << "... "; ListElement * tmp = firstNode->links.GetHeadElement(); //get the head element of the list of pointers for node 1 ListElement * tmp2 = firstNode->taken.GetHeadElement(); //get the head element of the list of bool isVisited flags for node 1 - while(tmp->value != NULL || tmp2->value != NULL) //go through untill we reach the end of the lists + while(tmp->value != NULL || tmp2->value != NULL) //go through until we reach the end of the lists { if(tmp->value == secondNode) //if we find the link to the other node { diff --git a/lib/poems/fastmatrixops.h b/lib/poems/fastmatrixops.h index e7ccdbd0ca..c7e29f8903 100644 --- a/lib/poems/fastmatrixops.h +++ b/lib/poems/fastmatrixops.h @@ -38,7 +38,7 @@ void FastLUSubs(Mat3x3& LU, Matrix& B, Matrix& C, int *indx); // Appropriate For void FastLUSubs(Mat4x4& LU, Matrix& B, Matrix& C, int *indx); // Appropriate Forward and Back Substitution void FastLUSubs(Mat6x6& LU, Matrix& B, Matrix& C, int *indx); // Appropriate Forward and Back Substitution // The following LUSubsLH routine is incomplete at the moment. -void FastLUSubsLH(Matrix& B, Matrix& LU, Matrix& C, int *indx); // Appropriate Forward and Back Subsitution +void FastLUSubsLH(Matrix& B, Matrix& LU, Matrix& C, int *indx); // Appropriate Forward and Back Substitution void FastTripleSum(Vect3& a, Vect3& b, Vect3& c, Vect3& d); // d = a+b+c void FastTripleSumPPM(Vect3& a, Vect3& b, Vect3& c, Vect3& d); // d = a+b-c diff --git a/lib/poems/joint.cpp b/lib/poems/joint.cpp index 3bdd7b5fcd..3477c7e336 100644 --- a/lib/poems/joint.cpp +++ b/lib/poems/joint.cpp @@ -186,12 +186,12 @@ Mat3x3* Joint::Get_kCpk(){ } Matrix Joint::GetForward_sP(){ - cerr << "ERROR: Forward Spatial Partial Velocity is not suported for joint type " << GetType() << endl; + cerr << "ERROR: Forward Spatial Partial Velocity is not supported for joint type " << GetType() << endl; exit(0); } Matrix Joint::GetBackward_sP(){ - cerr << "ERROR: Backward Spatial Partial Velocity is not suported for joint type " << GetType() << endl; + cerr << "ERROR: Backward Spatial Partial Velocity is not supported for joint type " << GetType() << endl; exit(0); } diff --git a/lib/poems/matrixfun.cpp b/lib/poems/matrixfun.cpp index d193114679..9aa2818555 100644 --- a/lib/poems/matrixfun.cpp +++ b/lib/poems/matrixfun.cpp @@ -209,7 +209,7 @@ Matrix operator+ (const VirtualMatrix &A, const VirtualMatrix &B){ // addit Bcols = B.GetNumCols(); if( !((Arows == Brows) && (Acols == Bcols)) ){ - cerr << "Dimesion mismatch in matrix addition" << endl; + cerr << "Dimension mismatch in matrix addition" << endl; exit(1); } @@ -234,7 +234,7 @@ Matrix operator- (const VirtualMatrix &A, const VirtualMatrix &B){ // subtr Bcols = B.GetNumCols(); if( !((Arows == Brows) && (Acols == Bcols)) ){ - cerr << "Dimesion mismatch in matrix addition" << endl; + cerr << "Dimension mismatch in matrix addition" << endl; exit(1); } @@ -259,7 +259,7 @@ Matrix operator* (const VirtualMatrix &A, const VirtualMatrix &B){ // multi Bcols = B.GetNumCols(); if(Acols != Brows){ - cerr << "Dimesion mismatch in matrix multiplication" << endl; + cerr << "Dimension mismatch in matrix multiplication" << endl; exit(1); } diff --git a/lib/poems/poemstree.h b/lib/poems/poemstree.h index 8f8e80ab66..d330fdad26 100644 --- a/lib/poems/poemstree.h +++ b/lib/poems/poemstree.h @@ -455,7 +455,7 @@ void Tree::Delete(const int& item) TreeNode *DNodePtr, *PNodePtr, *RNodePtr; // search for a node containing data value item. obtain its - // node adress and that of its parent + // node address and that of its parent if ((DNodePtr = FindNode (item, PNodePtr)) == NULL) return; @@ -576,7 +576,7 @@ TreeNode *Tree::CopyTree(TreeNode *t) // us the postorder scanning algorithm to traverse the nodes in -// the tree and delete each node as the vist operation +// the tree and delete each node as the visit operation void Tree::DeleteTree(TreeNode *t) { if (t != NULL) { diff --git a/lib/qmmm/README b/lib/qmmm/README index 13d17c055e..196aa4d7e0 100644 --- a/lib/qmmm/README +++ b/lib/qmmm/README @@ -31,7 +31,7 @@ will need to perform the remaining steps manually, as outlined below. ------------------------------------------------- WARNING: This is code depending on two software packages that are -independently maitained and are under continuous active developement. +independently maitained and are under continuous active development. It is thus much easier to break the QM/MM interface without noticing. Thus please test *very* carefully before using this software for production calculations. diff --git a/lib/scafacos/README b/lib/scafacos/README index e5f1ecd92c..86335d9f98 100644 --- a/lib/scafacos/README +++ b/lib/scafacos/README @@ -3,7 +3,7 @@ is required to use the KSPACE scafacos and its kspace_style scafacos command in a LAMMPS input script. The ScaFaCoS library is available at http://scafacos.de or -on github at https://github.com/scafacos, the libary was +on github at https://github.com/scafacos, the library was developed by a consortium of different universities in Germany (Bonn, Chemnitz, Stuttgart, Wuppertal) and the Research Centre Juelich (Juelich Supercomputing Centre). @@ -47,17 +47,17 @@ Instructions: are: direct, ewald, fmm, p2nfft The other solvers might work, but support is purely experimental at the moment. To - give a list of solvers, use a comma seperated + give a list of solvers, use a comma separated list. --fcs-disable-doc: disables the compilation of the documentation, e.g. if no Latex is available on the system. 4.) To build the library after configuration, run 'make' from the base folder. -5.) To install the libray in the designated installation folder, run 'make install'. +5.) To install the library in the designated installation folder, run 'make install'. Installation is required, as ScaFaCoS does not support an in-source build! -6.) Create two soft links to this directory (lib/scafacos) to where the libary +6.) Create two soft links to this directory (lib/scafacos) to where the library is installed. E.g. if you built ScaFaCoS in the default install directory: % ln -s /usr/local/include includelink % ln -s /usr/local/lib liblink diff --git a/potentials/BNCH-old.ILP b/potentials/BNCH-old.ILP index 30219e2a1e..2830172a86 100644 --- a/potentials/BNCH-old.ILP +++ b/potentials/BNCH-old.ILP @@ -1,5 +1,5 @@ # Interlayer Potential (ILP) for bilayer graphene/graphene, graphene/hBN and hBN/hBN junctions -# The parameters below are fitted against the HSE + MBD DFT referece data from 3.1 A to 15 A. +# The parameters below are fitted against the HSE + MBD DFT reference data from 3.1 A to 15 A. # Cite J. Chem.Theory Comput. 2016, 12, 2896-905 and J. Phys. Chem. C 2017, 121, 22826-22835. # beta alpha delta epsilon C d sR reff C6 S rcut diff --git a/potentials/BNCH.ILP b/potentials/BNCH.ILP index ed58adf946..eb15c35e0b 100644 --- a/potentials/BNCH.ILP +++ b/potentials/BNCH.ILP @@ -1,5 +1,5 @@ # Interlayer Potential (ILP) for bilayer graphene/graphene, graphene/hBN and hBN/hBN junctions -# The parameters below are fitted against the HSE + MBD DFT referece data from 2.5 A to 15 A. +# The parameters below are fitted against the HSE + MBD DFT reference data from 2.5 A to 15 A. # Cite as W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Letters 18, 6009-6016 (2018). # # ----------------- Repulsion Potential ------------------++++++++++++++ Vdw Potential ++++++++++++++++************ diff --git a/potentials/BNC_MBD_bulk.ILP b/potentials/BNC_MBD_bulk.ILP index 9502e0a89a..9093f01447 100644 --- a/potentials/BNC_MBD_bulk.ILP +++ b/potentials/BNC_MBD_bulk.ILP @@ -1,5 +1,5 @@ # Interlayer Potential (ILP) for graphite, bulk-hBN and their heterojunctions -# The parameters below are fitted against the HSE + MBD DFT referece data from 2 A to 10 A. +# The parameters below are fitted against the HSE + MBD DFT reference data from 2 A to 10 A. # Cite as W. Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020). # # ------------------------------ Repulsion Potential --------------------++++++++++++++ Vdw Potential ++++++++++++++++************ diff --git a/potentials/BNC_TS_bulk.ILP b/potentials/BNC_TS_bulk.ILP index 1baca2ace0..13de8b25fc 100644 --- a/potentials/BNC_TS_bulk.ILP +++ b/potentials/BNC_TS_bulk.ILP @@ -1,5 +1,5 @@ # Interlayer Potential (ILP) for graphite, bulk-hBN and their heterojunctions -# The parameters below are fitted against the HSE + TS DFT referece data from 2 A to 10 A. +# The parameters below are fitted against the HSE + TS DFT reference data from 2 A to 10 A. # Cite as W. Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020). # # ------------------------------ Repulsion Potential ------------------++++++++++++++ Vdw Potential ++++++++++++++++************ diff --git a/python/examples/pylammps/montecarlo/mc.ipynb b/python/examples/pylammps/montecarlo/mc.ipynb index 86a2a8bc95..8509845a3d 100644 --- a/python/examples/pylammps/montecarlo/mc.ipynb +++ b/python/examples/pylammps/montecarlo/mc.ipynb @@ -887,7 +887,7 @@ " // Register the callback with on_msg.\n", " comm.on_msg(function(msg) {\n", " //console.log('receiving', msg['content']['data'], msg);\n", - " // Pass the mpl event to the overriden (by mpl) onmessage function.\n", + " // Pass the mpl event to the overridden (by mpl) onmessage function.\n", " ws.onmessage(msg['content']['data'])\n", " });\n", " return ws;\n", diff --git a/python/lammps.py b/python/lammps.py index 484c30d9ac..bbe9c07a30 100644 --- a/python/lammps.py +++ b/python/lammps.py @@ -1037,7 +1037,7 @@ def get_thermo_data(output): items = line.split() # Convert thermo output and store it. # It must have the same number of columns and - # all of them must be convertable to floats. + # all of them must be convertible to floats. # Otherwise we ignore the line if len(items) == len(columns): try: diff --git a/src/COLLOID/pair_lubricateU.cpp b/src/COLLOID/pair_lubricateU.cpp index e8715cec36..b0e21256ac 100644 --- a/src/COLLOID/pair_lubricateU.cpp +++ b/src/COLLOID/pair_lubricateU.cpp @@ -988,7 +988,7 @@ void PairLubricateU::compute_RU() fy = vxmu2f*fy; fz = vxmu2f*fz; - // Add to the total forc + // Add to the total force f[i][0] -= fx; f[i][1] -= fy; @@ -1449,7 +1449,7 @@ void PairLubricateU::compute_RE() fy = vxmu2f*fy; fz = vxmu2f*fz; - // Add to the total forc + // Add to the total force f[i][0] -= fx; f[i][1] -= fy; @@ -1614,7 +1614,7 @@ void PairLubricateU::compute_RE(double **x) fy = vxmu2f*fy; fz = vxmu2f*fz; - // Add to the total forc + // Add to the total force f[i][0] -= fx; f[i][1] -= fy; diff --git a/src/COLLOID/pair_lubricateU_poly.cpp b/src/COLLOID/pair_lubricateU_poly.cpp index 0f16d94300..6b6727172d 100644 --- a/src/COLLOID/pair_lubricateU_poly.cpp +++ b/src/COLLOID/pair_lubricateU_poly.cpp @@ -849,7 +849,7 @@ void PairLubricateUPoly::compute_RU(double **x) fy = vxmu2f*fy; fz = vxmu2f*fz; - // Add to the total forc + // Add to the total force f[i][0] -= fx; f[i][1] -= fy; @@ -1044,7 +1044,7 @@ void PairLubricateUPoly::compute_RE(double **x) fy = vxmu2f*fy; fz = vxmu2f*fz; - // Add to the total forc + // Add to the total force f[i][0] -= fx; f[i][1] -= fy; diff --git a/src/CORESHELL/pair_born_coul_wolf_cs.cpp b/src/CORESHELL/pair_born_coul_wolf_cs.cpp index 398c2ba1ee..870a776a22 100644 --- a/src/CORESHELL/pair_born_coul_wolf_cs.cpp +++ b/src/CORESHELL/pair_born_coul_wolf_cs.cpp @@ -98,7 +98,7 @@ void PairBornCoulWolfCS::compute(int eflag, int vflag) if (rsq < cutsq[itype][jtype]) { rsq += EPSILON; - // Add EPISLON for case: r = 0; Interaction must be removed + // Add EPSILON for case: r = 0; Interaction must be removed // by special bond r2inv = 1.0/rsq; diff --git a/src/CORESHELL/pair_coul_wolf_cs.cpp b/src/CORESHELL/pair_coul_wolf_cs.cpp index 20b7339480..997a202e00 100644 --- a/src/CORESHELL/pair_coul_wolf_cs.cpp +++ b/src/CORESHELL/pair_coul_wolf_cs.cpp @@ -93,7 +93,7 @@ void PairCoulWolfCS::compute(int eflag, int vflag) if (rsq < cut_coulsq) { rsq += EPSILON; - // Add EPISLON for case: r = 0; Interaction must be removed + // Add EPSILON for case: r = 0; Interaction must be removed // by special bond r = sqrt(rsq); prefactor = qqrd2e*qtmp*q[j]/r; diff --git a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp index b00b5a0b56..4e488abc15 100644 --- a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp +++ b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp @@ -249,7 +249,7 @@ void PairBornCoulWolfCSGPU::cpu_compute(int start, int inum, int eflag, jtype = type[j]; if (rsq < cutsq[itype][jtype]) { - rsq += EPSILON; // Add EPISLON for case: r = 0; Interaction must be removed by special bond + rsq += EPSILON; // Add EPSILON for case: r = 0; Interaction must be removed by special bond r2inv = 1.0/rsq; if (rsq < cut_coulsq) { diff --git a/src/KIM/README b/src/KIM/README index e61f47426f..d01ea42a7c 100644 --- a/src/KIM/README +++ b/src/KIM/README @@ -11,7 +11,7 @@ maintains the code that implements these commands. Using this package requires the KIM-API library and its models (interatomic potentials) to be downloaded and installed on your system. The library can be downloaded and built in lib/kim or -elsewhere on your system, which must be done before bulding LAMMPS +elsewhere on your system, which must be done before building LAMMPS with this package. Details of the download, build, and install process for the KIM-API are given in the lib/kim/README file, and scripts are provided to help automate the process. Also see the diff --git a/src/KIM/kim_units.cpp b/src/KIM/kim_units.cpp index 45f9b81a35..b059ec0d73 100644 --- a/src/KIM/kim_units.cpp +++ b/src/KIM/kim_units.cpp @@ -140,7 +140,7 @@ double const kcal_si = 4184.0; // [J] kilocalorie (heat energy // involved in warming up one // kilogram of water by one // degree Kelvin) -double const ev_si = 1.6021766208e-19; // [J] electon volt (amount of +double const ev_si = 1.6021766208e-19; // [J] electron volt (amount of // energy gained or lost by the // charge of a single electron // moving across an electric diff --git a/src/KOKKOS/atom_vec_bond_kokkos.cpp b/src/KOKKOS/atom_vec_bond_kokkos.cpp index 74c05a506c..4475131d77 100644 --- a/src/KOKKOS/atom_vec_bond_kokkos.cpp +++ b/src/KOKKOS/atom_vec_bond_kokkos.cpp @@ -625,7 +625,7 @@ struct AtomVecBondKokkos_PackExchangeFunctor { _lo(lo),_hi(hi){ // 3 comp of x, 3 comp of v, 1 tag, 1 type, 1 mask, 1 image, 1 molecule, 3 nspecial, // maxspecial special, 1 num_bond, bond_per_atom bond_type, bond_per_atom bond_atom, - // 1 to store buffer lenght + // 1 to store buffer length elements = 16+atom->maxspecial+atom->bond_per_atom+atom->bond_per_atom; const int maxsendlist = (buf.template view().extent(0)* buf.template view().extent(1))/elements; diff --git a/src/KOKKOS/comm_kokkos.cpp b/src/KOKKOS/comm_kokkos.cpp index 774d7040cc..a1ece37efd 100644 --- a/src/KOKKOS/comm_kokkos.cpp +++ b/src/KOKKOS/comm_kokkos.cpp @@ -478,7 +478,7 @@ void CommKokkos::reverse_comm_dump(Dump *dump) atoms exchanged with all 6 stencil neighbors send out atoms that have left my box, receive ones entering my box atoms will be lost if not inside some proc's box - can happen if atom moves outside of non-periodic bounary + can happen if atom moves outside of non-periodic boundary or if atom moves more than one proc away this routine called before every reneighboring for triclinic, atoms must be in lamda coords (0-1) before exchange is called diff --git a/src/KOKKOS/comm_tiled_kokkos.cpp b/src/KOKKOS/comm_tiled_kokkos.cpp index fc6de0a0d7..a29d9f63b3 100644 --- a/src/KOKKOS/comm_tiled_kokkos.cpp +++ b/src/KOKKOS/comm_tiled_kokkos.cpp @@ -113,7 +113,7 @@ void CommTiledKokkos::reverse_comm() atoms exchanged with procs that touch sub-box in each of 3 dims send out atoms that have left my box, receive ones entering my box atoms will be lost if not inside a touching proc's box - can happen if atom moves outside of non-periodic bounary + can happen if atom moves outside of non-periodic boundary or if atom moves more than one proc away this routine called before every reneighboring for triclinic, atoms must be in lamda coords (0-1) before exchange is called diff --git a/src/KOKKOS/fix_eos_table_rx_kokkos.h b/src/KOKKOS/fix_eos_table_rx_kokkos.h index 91d73f1036..21ec3d203b 100644 --- a/src/KOKKOS/fix_eos_table_rx_kokkos.h +++ b/src/KOKKOS/fix_eos_table_rx_kokkos.h @@ -207,6 +207,6 @@ Self-explanatory. E: Maxit exceeded in secant solver -The maximum number of interations was exceeded in the secant solver +The maximum number of iterations was exceeded in the secant solver */ diff --git a/src/KOKKOS/npair_ssa_kokkos.cpp b/src/KOKKOS/npair_ssa_kokkos.cpp index 5234c4e6d2..f9708e5fe8 100644 --- a/src/KOKKOS/npair_ssa_kokkos.cpp +++ b/src/KOKKOS/npair_ssa_kokkos.cpp @@ -234,7 +234,7 @@ int NPairSSAKokkosExecute::exclusion(const int &i,const int &j, /* ---------------------------------------------------------------------- binned neighbor list construction with full Newton's 3rd law - for use by Shardlow Spliting Algorithm + for use by Shardlow Splitting Algorithm each owned atom i checks its own bin and other bins in Newton stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ diff --git a/src/KOKKOS/pair_exp6_rx_kokkos.cpp b/src/KOKKOS/pair_exp6_rx_kokkos.cpp index 8698687377..f3f63c98b2 100644 --- a/src/KOKKOS/pair_exp6_rx_kokkos.cpp +++ b/src/KOKKOS/pair_exp6_rx_kokkos.cpp @@ -1944,7 +1944,7 @@ void PairExp6rxKokkos::getMixingWeights(int id,double &epsilon1,doub fraction2 = nMolecules2/nTotal; } - // If Site1 or Site2 matches is a fluid, then compute the paramters + // If Site1 or Site2 matches is a fluid, then compute the parameters if (isOneFluidApprox(isite1) || isOneFluidApprox(isite2)) { if (isite1 == d_params[iparam].ispecies || isite2 == d_params[iparam].ispecies) continue; rmi = d_params[iparam].rm; @@ -2271,7 +2271,7 @@ void PairExp6rxKokkos::getMixingWeightsVect(const int np_total, int } } - // If Site1 or Site2 matches is a fluid, then compute the paramters + // If Site1 or Site2 matches is a fluid, then compute the parameters if (isOneFluidApprox(isite1) || isOneFluidApprox(isite2)) { if (isite1 == d_params[iparam].ispecies || isite2 == d_params[iparam].ispecies) continue; diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp index 7085f06101..08a0c18f9c 100644 --- a/src/KOKKOS/pppm_kokkos.cpp +++ b/src/KOKKOS/pppm_kokkos.cpp @@ -836,7 +836,7 @@ void PPPMKokkos::allocate() h_rho_coeff = k_rho_coeff.h_view; // create 2 FFTs and a Remap - // 1st FFT keeps data in FFT decompostion + // 1st FFT keeps data in FFT decomposition // 2nd FFT returns data in 3d brick decomposition // remap takes data from 3d brick to FFT decomposition diff --git a/src/KOKKOS/sna_kokkos.h b/src/KOKKOS/sna_kokkos.h index 133db2139f..48d9114fbf 100644 --- a/src/KOKKOS/sna_kokkos.h +++ b/src/KOKKOS/sna_kokkos.h @@ -228,7 +228,7 @@ private: // data for bispectrum coefficients - // Same accross all SNAKokkos + // Same across all SNAKokkos t_sna_1d cglist; t_sna_2d rootpqarray; diff --git a/src/KOKKOS/sna_kokkos_impl.h b/src/KOKKOS/sna_kokkos_impl.h index c8c9a07e3e..ef3312bd16 100644 --- a/src/KOKKOS/sna_kokkos_impl.h +++ b/src/KOKKOS/sna_kokkos_impl.h @@ -877,7 +877,7 @@ void SNAKokkos::compute_uarray(const typename Kokkos::TeamPolicyall(FLERR,"Matrix factorization to split dispersion coefficients failed"); @@ -1454,7 +1454,7 @@ int PPPMDisp::qr_alg(double **A, double **Q, int n) // allocate an auxiliary matrix Qi memory->create(Qi,n,n,"pppm/disp:Qi"); - // alllocate an auxillary matrices for the matrix multiplication + // alllocate an auxiliary matrices for the matrix multiplication memory->create(C,n,n,"pppm/disp:C"); memory->create(D,n,n,"pppm/disp:D"); memory->create(E,n,n,"pppm/disp:E"); @@ -3657,7 +3657,7 @@ void PPPMDisp::set_n_pppm_6() // initial value for the grid spacing h = h_x = h_y = h_z = 4.0/g_ewald_6; - // decrease grid spacing untill required precision is obtained + // decrease grid spacing until required precision is obtained int count = 0; while(1) { @@ -5760,7 +5760,7 @@ void PPPMDisp::fieldforce_c_ad() ekx *= hx_inv; eky *= hy_inv; ekz *= hz_inv; - // convert E-field to force and substract self forces + // convert E-field to force and subtract self forces const double qfactor = force->qqrd2e * scale; s1 = x[i][0]*hx_inv; diff --git a/src/KSPACE/pppm_disp_tip4p.cpp b/src/KSPACE/pppm_disp_tip4p.cpp index bc46152e2b..45217eb7a5 100644 --- a/src/KSPACE/pppm_disp_tip4p.cpp +++ b/src/KSPACE/pppm_disp_tip4p.cpp @@ -335,7 +335,7 @@ void PPPMDispTIP4P::fieldforce_c_ad() eky *= hy_inv; ekz *= hz_inv; - // convert E-field to force and substract self forces + // convert E-field to force and subtract self forces const double qfactor = force->qqrd2e * scale; s1 = x[i][0]*hx_inv; diff --git a/src/KSPACE/pppm_stagger.cpp b/src/KSPACE/pppm_stagger.cpp index 7b708d0355..d7466ee0d4 100644 --- a/src/KSPACE/pppm_stagger.cpp +++ b/src/KSPACE/pppm_stagger.cpp @@ -876,7 +876,7 @@ void PPPMStagger::fieldforce_ad() eky *= hy_inv; ekz *= hz_inv; - // convert E-field to force and substract self forces + // convert E-field to force and subtract self forces const double qfactor = qqrd2e * scale / float(nstagger); diff --git a/src/KSPACE/pppm_tip4p.cpp b/src/KSPACE/pppm_tip4p.cpp index 5a0ced3674..e2019d3f83 100644 --- a/src/KSPACE/pppm_tip4p.cpp +++ b/src/KSPACE/pppm_tip4p.cpp @@ -327,7 +327,7 @@ void PPPMTIP4P::fieldforce_ad() eky *= hy_inv; ekz *= hz_inv; - // convert E-field to force and substract self forces + // convert E-field to force and subtract self forces const double qfactor = qqrd2e * scale; diff --git a/src/MAKE/MACHINES/Makefile.redsky b/src/MAKE/MACHINES/Makefile.redsky index 551952181e..8e943bbb78 100644 --- a/src/MAKE/MACHINES/Makefile.redsky +++ b/src/MAKE/MACHINES/Makefile.redsky @@ -16,7 +16,7 @@ SHELL = /bin/sh # IMPORTANT NOTE: # to run efficiently on RedSky, use the "numa_wrapper" mpiexec option, -# to insure proceses and their memory are locked to specific cores +# to insure processes and their memory are locked to specific cores # e.g. in your batch script: # nodes=$SLURM_JOB_NUM_NODES # cores=8 diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp index 1d9dd18887..84565a2e50 100644 --- a/src/MANYBODY/pair_airebo.cpp +++ b/src/MANYBODY/pair_airebo.cpp @@ -2081,9 +2081,9 @@ double PairAIREBO::bondorder(int i, int j, double rij[3], This function calculates S(t_b(b_ij*)) as specified in the AIREBO paper. To do so, it needs to compute b_ij*, i.e. the bondorder given that the -atoms i and j are placed a ficticious distance rijmag_mod apart. +atoms i and j are placed a fictitious distance rijmag_mod apart. Now there are two approaches to calculate the resulting forces: -1. Carry through the ficticious distance and corresponding vector +1. Carry through the fictitious distance and corresponding vector rij_mod, correcting afterwards using the derivative of r/|r|. 2. Perform all the calculations using the real distance, and do not use a correction, only using rijmag_mod where necessary. diff --git a/src/MANYBODY/pair_bop.h b/src/MANYBODY/pair_bop.h index eca0ec52b8..ea8da2844e 100644 --- a/src/MANYBODY/pair_bop.h +++ b/src/MANYBODY/pair_bop.h @@ -48,12 +48,12 @@ class PairBOP : public Pair { int maxbopn; // maximum size of bop neighbor list for allocation int maxnall; // maximum size of bop neighbor list for allocation int *map; // mapping from atom types to elements - int nelements; // # of unique elments + int nelements; // # of unique elements int nr; // increments for the BOP pair potential int ntheta; // increments for the angle function int npower; // power of the angular function int nBOt; // second BO increments - int bop_types; // number of elments in potential + int bop_types; // number of elements in potential int npairs; // number of element pairs char **elements; // names of unique elements int ***elem2param; diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp index cc97fd9e9b..7c29f44afc 100644 --- a/src/MANYBODY/pair_lcbop.cpp +++ b/src/MANYBODY/pair_lcbop.cpp @@ -256,7 +256,7 @@ void PairLCBOP::SR_neigh() double **x = atom->x; - if (atom->nmax > maxlocal) { // ensure ther is enough space + if (atom->nmax > maxlocal) { // ensure there is enough space maxlocal = atom->nmax; // for atoms and ghosts allocated memory->destroy(SR_numneigh); memory->sfree(SR_firstneigh); diff --git a/src/MISC/dump_xtc.cpp b/src/MISC/dump_xtc.cpp index 1a2b71ab6d..a28d6acdfa 100644 --- a/src/MISC/dump_xtc.cpp +++ b/src/MISC/dump_xtc.cpp @@ -439,7 +439,7 @@ int xdropen(XDR *xdrs, const char *filename, const char *type) } xdrmodes[xdrid] = *type; - /* next test isn't usefull in the case of C language + /* next test isn't useful in the case of C language * but is used for the Fortran interface * (C users are expected to pass the address of an already allocated * XDR staructure) @@ -610,7 +610,7 @@ static int sizeofints( const int num_of_ints, unsigned int sizes[]) | this routine is used internally by xdr3dfcoord, to send a set of | small integers to the buffer. | Multiplication with fixed (specified maximum ) sizes is used to get - | to one big, multibyte integer. Allthough the routine could be + | to one big, multibyte integer. Although the routine could be | modified to handle sizes bigger than 16777216, or more than just | a few integers, this is not done, because the gain in compression | isn't worth the effort. Note that overflowing the multiplication @@ -758,7 +758,7 @@ static void receiveints(int buf[], const int num_of_ints, int num_of_bits, | using multiplication by *precision and rounding to the nearest integer. | Then the minimum and maximum value are calculated to determine the range. | The limited range of integers so found, is used to compress the coordinates. - | In addition the differences between succesive coordinates is calculated. + | In addition the differences between successive coordinates is calculated. | If the difference happens to be 'small' then only the difference is saved, | compressing the data even more. The notion of 'small' is changed dynamically | and is enlarged or reduced whenever needed or possible. diff --git a/src/MISC/fix_deposit.cpp b/src/MISC/fix_deposit.cpp index 5279b2df36..90b1063924 100644 --- a/src/MISC/fix_deposit.cpp +++ b/src/MISC/fix_deposit.cpp @@ -569,7 +569,7 @@ void FixDeposit::pre_exchange() // old code: unsuccessful if no proc performed insertion of an atom // don't think that check is necessary - // if get this far, should always be succesful + // if get this far, should always be successful // would be hard to undo partial insertion for a molecule // better to check how many atoms could be inserted (w/out inserting) // then sum to insure all are inserted, before doing actual insertion diff --git a/src/MPIIO/restart_mpiio.cpp b/src/MPIIO/restart_mpiio.cpp index e8ef5c6c4e..db511c7bc0 100644 --- a/src/MPIIO/restart_mpiio.cpp +++ b/src/MPIIO/restart_mpiio.cpp @@ -120,7 +120,7 @@ void RestartMPIIO::write(MPI_Offset headerOffset, int send_size, double *buf) if the consolidated chunksize is greater than INT_MAX can only happen in extreme situation of reading restart file on much fewer ranks than written and with relatively large data sizes - follow the collective IO call with rank independant IO to read remaining data + follow the collective IO call with rank independent IO to read remaining data ------------------------------------------------------------------------- */ void RestartMPIIO::read(MPI_Offset chunkOffset, bigint chunkSize, double *buf) diff --git a/src/MSCG/README b/src/MSCG/README index ed0ef37452..ab64c26792 100644 --- a/src/MSCG/README +++ b/src/MSCG/README @@ -8,7 +8,7 @@ developed by Jacob Wagner in Greg Voth's group at the University of Chicago. The library can be downloaded and built in lib/mscg or elsewhere on -your system, which must be done before bulding LAMMPS with this +your system, which must be done before building LAMMPS with this package. Details of the download, build, and install process for MSCG are given in the lib/mscg/README file. Also see the LAMMPS manual for general information on building LAMMPS with external libraries. The diff --git a/src/PERI/fix_peri_neigh.h b/src/PERI/fix_peri_neigh.h index 79006ab541..247ceaaa43 100644 --- a/src/PERI/fix_peri_neigh.h +++ b/src/PERI/fix_peri_neigh.h @@ -63,8 +63,8 @@ class FixPeriNeigh : public Fix { int maxpartner; // max # of peridynamic neighs for any atom int *npartner; // # of neighbors for each atom tagint **partner; // neighs for each atom, stored as global IDs - double **deviatorextention; // Deviatoric extention - double **deviatorBackextention; // Deviatoric back extention + double **deviatorextention; // Deviatoric extension + double **deviatorBackextention; // Deviatoric back extension double **deviatorPlasticextension; // Deviatoric plastic extension double *lambdaValue; double **r0; // initial distance to partners diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp index 1cef9635a9..1d9f3819ff 100644 --- a/src/PERI/pair_peri_ves.cpp +++ b/src/PERI/pair_peri_ves.cpp @@ -317,7 +317,7 @@ void PairPeriVES::compute(int eflag, int vflag) dr - (theta[i]* r0[i][jj] / 3.0); deltaed = deviatoric_extension-deviatorextention[i][jj]; - // back extention at current step + // back extension at current step edbNp1 = deviatorextention[i][jj]*(1-decay) + deviatorBackextention[i][jj]*decay+betai*deltaed; @@ -357,7 +357,7 @@ void PairPeriVES::compute(int eflag, int vflag) // find stretch in bond I-J and break if necessary // use s0 from previous timestep - // store current deviatoric extention + // store current deviatoric extension deviatorextention[i][jj]=deviatoric_extension; deviatorBackextention[i][jj]=edbNp1; diff --git a/src/PYTHON/fix_python_move.h b/src/PYTHON/fix_python_move.h index 7b830a3d20..2220709970 100644 --- a/src/PYTHON/fix_python_move.h +++ b/src/PYTHON/fix_python_move.h @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. Pair zero is a dummy pair interaction useful for requiring a - force cutoff distance in the absense of pair-interactions or + force cutoff distance in the absence of pair-interactions or with hybrid/overlay if a larger force cutoff distance is required. This can be used in conjunction with bond/create to create bonds diff --git a/src/PYTHON/pair_python.h b/src/PYTHON/pair_python.h index 69671f7322..4c3c00a70d 100644 --- a/src/PYTHON/pair_python.h +++ b/src/PYTHON/pair_python.h @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. Pair zero is a dummy pair interaction useful for requiring a - force cutoff distance in the absense of pair-interactions or + force cutoff distance in the absence of pair-interactions or with hybrid/overlay if a larger force cutoff distance is required. This can be used in conjunction with bond/create to create bonds diff --git a/src/REPLICA/fix_event_hyper.h b/src/REPLICA/fix_event_hyper.h index 4c5d4a93ee..af685ee539 100644 --- a/src/REPLICA/fix_event_hyper.h +++ b/src/REPLICA/fix_event_hyper.h @@ -29,7 +29,7 @@ class FixEventHyper : public FixEvent { int event_number; // event counter bigint event_timestep; // timestep of last event on any replica bigint clock; // total elapsed timesteps across all replicas - int replica_number; // replica where last event occured + int replica_number; // replica where last event occurred int correlated_event; // 1 if last event was correlated, 0 otherwise int ncoincident; // # of simultaneous events on different replicas diff --git a/src/REPLICA/fix_event_prd.h b/src/REPLICA/fix_event_prd.h index 0924fb2bdc..363de31e9d 100644 --- a/src/REPLICA/fix_event_prd.h +++ b/src/REPLICA/fix_event_prd.h @@ -29,7 +29,7 @@ class FixEventPRD : public FixEvent { int event_number; // event counter bigint event_timestep; // timestep of last event on any replica bigint clock; // total elapsed timesteps across all replicas - int replica_number; // replica where last event occured + int replica_number; // replica where last event occurred int correlated_event; // 1 if last event was correlated, 0 otherwise int ncoincident; // # of simultaneous events on different replicas diff --git a/src/REPLICA/fix_hyper_global.cpp b/src/REPLICA/fix_hyper_global.cpp index 62ba35abfc..bc5df921c6 100644 --- a/src/REPLICA/fix_hyper_global.cpp +++ b/src/REPLICA/fix_hyper_global.cpp @@ -189,7 +189,7 @@ void FixHyperGlobal::pre_neighbor() // closest current I or J atoms to old I may now be ghost atoms // closest_image() returns the ghost atom index in that case // also compute max drift of any atom in a bond - // drift = displacement from quenched coord while event has not yet occured + // drift = displacement from quenched coord while event has not yet occurred // NOTE: drift calc is now done in bond_build(), between 2 quenched states for (i = 0; i < nall_old; i++) old2now[i] = -1; diff --git a/src/REPLICA/fix_hyper_local.cpp b/src/REPLICA/fix_hyper_local.cpp index dc02432751..eebcd08bdd 100644 --- a/src/REPLICA/fix_hyper_local.cpp +++ b/src/REPLICA/fix_hyper_local.cpp @@ -379,7 +379,7 @@ void FixHyperLocal::pre_neighbor() // closest current I or J atoms to old I may now be ghost atoms // closest_image() returns the ghost atom index in that case // also compute max drift of any atom in a bond - // drift = displacement from quenched coord while event has not yet occured + // drift = displacement from quenched coord while event has not yet occurred // NOTE: drift calc is now done in bond_build(), between 2 quenched states for (i = 0; i < nall_old; i++) old2now[i] = -1; @@ -796,7 +796,7 @@ void FixHyperLocal::pre_reverse(int /* eflag */, int /* vflag */) rmaxeverbig = rmax2all[1]; } - // if requsted, check for any biased bonds that are too close to each other + // if requested, check for any biased bonds that are too close to each other // keep a running count for output // requires 2 additional local comm operations @@ -887,7 +887,7 @@ void FixHyperLocal::build_bond_list(int natom) // reset Vmax to current bias coeff average // only if requested and elapsed time >= resetfreq - // ave = curent ave of all bias coeffs + // ave = current ave of all bias coeffs // if reset, adjust all Cij to keep Cij*Vmax unchanged if (resetfreq >= 0) { diff --git a/src/REPLICA/prd.cpp b/src/REPLICA/prd.cpp index f631cc6a0a..63e569d0c2 100644 --- a/src/REPLICA/prd.cpp +++ b/src/REPLICA/prd.cpp @@ -608,7 +608,7 @@ void PRD::quench() if replica_num is non-negative only check for event on replica_num if multiple events, choose one at random return -1 if no event - else return ireplica = world in which event occured + else return ireplica = world in which event occurred ------------------------------------------------------------------------- */ int PRD::check_event(int replica_num) diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index 9f6a1e5d46..d77bf988a6 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -2185,7 +2185,7 @@ void FixRigid::setup_bodies_static() /* ---------------------------------------------------------------------- one-time initialization of dynamic rigid body attributes set vcm and angmom, computed explicitly from constituent particles - not done if body properites read from file, e.g. for overlapping particles + not done if body properties read from file, e.g. for overlapping particles ------------------------------------------------------------------------- */ void FixRigid::setup_bodies_dynamic() @@ -2279,7 +2279,7 @@ void FixRigid::setup_bodies_dynamic() /* ---------------------------------------------------------------------- read per rigid body info from user-provided file - which = 0 to read everthing except 6 moments of inertia + which = 0 to read everything except 6 moments of inertia which = 1 to read 6 moments of inertia flag inbody = 0 for bodies whose info is read from file nlines = # of lines of rigid body info diff --git a/src/RIGID/fix_rigid_nh.h b/src/RIGID/fix_rigid_nh.h index 08208e5aac..1126e7bb50 100644 --- a/src/RIGID/fix_rigid_nh.h +++ b/src/RIGID/fix_rigid_nh.h @@ -54,7 +54,7 @@ class FixRigidNH : public FixRigid { int kspace_flag; // 1 if KSpace invoked, 0 if not int nrigidfix; // number of rigid fixes - int *rfix; // indicies of rigid fixes + int *rfix; // indices of rigid fixes double vol0; // reference volume double t0; // reference temperature diff --git a/src/RIGID/fix_rigid_nh_small.h b/src/RIGID/fix_rigid_nh_small.h index 207c2d0a11..e04290aee8 100644 --- a/src/RIGID/fix_rigid_nh_small.h +++ b/src/RIGID/fix_rigid_nh_small.h @@ -53,7 +53,7 @@ class FixRigidNHSmall : public FixRigidSmall { int kspace_flag; // 1 if KSpace invoked, 0 if not int nrigidfix; // number of rigid fixes - int *rfix; // indicies of rigid fixes + int *rfix; // indices of rigid fixes double vol0; // reference volume double t0; // reference temperature diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index 0b2c2d967f..9974a7f888 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -1091,7 +1091,7 @@ void FixRigidSmall::final_integrate_respa(int ilevel, int /*iloop*/) when unwrapped by true image flags then set_xv() will compute huge displacements every step to reset coords of all the body atoms to be back inside the box, ditto for triclinic box flip - note: so just want to avoid that numeric probem? + note: so just want to avoid that numeric problem? ------------------------------------------------------------------------- */ void FixRigidSmall::pre_neighbor() @@ -2320,7 +2320,7 @@ void FixRigidSmall::setup_bodies_static() /* ---------------------------------------------------------------------- one-time initialization of dynamic rigid body attributes vcm and angmom, computed explicitly from constituent particles - not done if body properites read from file, e.g. for overlapping particles + not done if body properties read from file, e.g. for overlapping particles ------------------------------------------------------------------------- */ void FixRigidSmall::setup_bodies_dynamic() @@ -2426,7 +2426,7 @@ void FixRigidSmall::setup_bodies_dynamic() /* ---------------------------------------------------------------------- read per rigid body info from user-provided file - which = 0 to read everthing except 6 moments of inertia + which = 0 to read everything except 6 moments of inertia which = 1 to read just 6 moments of inertia flag inbody = 0 for local bodies this proc initializes from file nlines = # of lines of rigid body info, 0 is OK diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp index 054985ba72..3342f02194 100644 --- a/src/RIGID/fix_shake.cpp +++ b/src/RIGID/fix_shake.cpp @@ -3082,7 +3082,7 @@ void FixShake::correct_coordinates(int vflag) { dtfsq = 0.5 * update->dt * update->dt * force->ftm2v; FixShake::post_force(vflag); - // integrate coordiantes: x' = xnp1 + dt^2/2m_i * f, where f is the constraining force + // integrate coordinates: x' = xnp1 + dt^2/2m_i * f, where f is the constraining force // NOTE: After this command, the coordinates geometry of the molecules will be correct! double dtfmsq; diff --git a/src/SPIN/README b/src/SPIN/README index ad296c69b7..6dbad91d8d 100644 --- a/src/SPIN/README +++ b/src/SPIN/README @@ -9,7 +9,7 @@ atom in the system * implementing magnetic pair interactions and magnetic forces * thermostating and applying a transverse damping to the magnetic spins * performing geodesic NEB calculations -* computing and outputing magnetic quantities +* 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 diff --git a/src/SPIN/min_spin.cpp b/src/SPIN/min_spin.cpp index e39eb18744..f6a6b90891 100644 --- a/src/SPIN/min_spin.cpp +++ b/src/SPIN/min_spin.cpp @@ -127,7 +127,7 @@ int MinSpin::iterate(int maxiter) ntimestep = ++update->ntimestep; niter++; - // optimize timestep accross processes / replicas + // optimize timestep across processes / replicas // need a force calculation for timestep optimization if (iter == 0) energy_force(0); diff --git a/src/SPIN/min_spin_cg.cpp b/src/SPIN/min_spin_cg.cpp index 8815ad89db..de1ef39f66 100644 --- a/src/SPIN/min_spin_cg.cpp +++ b/src/SPIN/min_spin_cg.cpp @@ -205,7 +205,7 @@ int MinSpinCG::iterate(int maxiter) ntimestep = ++update->ntimestep; niter++; - // optimize timestep accross processes / replicas + // optimize timestep across processes / replicas // need a force calculation for timestep optimization if (use_line_search) { diff --git a/src/SPIN/min_spin_lbfgs.cpp b/src/SPIN/min_spin_lbfgs.cpp index 7f6d7692cd..df12782528 100644 --- a/src/SPIN/min_spin_lbfgs.cpp +++ b/src/SPIN/min_spin_lbfgs.cpp @@ -217,7 +217,7 @@ int MinSpinLBFGS::iterate(int maxiter) ntimestep = ++update->ntimestep; niter++; - // optimize timestep accross processes / replicas + // optimize timestep across processes / replicas // need a force calculation for timestep optimization if (use_line_search) { diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp index d5eec91f50..cb193356d8 100644 --- a/src/SRD/fix_srd.cpp +++ b/src/SRD/fix_srd.cpp @@ -454,7 +454,7 @@ void FixSRD::setup(int /*vflag*/) setup_search_stencil(); } else nbins2 = 0; - // perform first bining of SRD and big particles and walls + // perform first binding of SRD and big particles and walls // set reneighflag to turn off SRD rotation // don't do SRD rotation in setup, only during timestepping @@ -1067,7 +1067,7 @@ void FixSRD::vbin_comm(int ishift) // send/recv bins in both directions in each dimension // don't send if nsend = 0 - // due to static bins aliging with proc boundary + // due to static bins aligning with proc boundary // due to dynamic bins across non-periodic global boundary // copy to self if sendproc = me // MPI send to another proc if sendproc != me @@ -1169,7 +1169,7 @@ void FixSRD::xbin_comm(int ishift, int nval) // send/recv bins in both directions in each dimension // don't send if nsend = 0 - // due to static bins aliging with proc boundary + // due to static bins aligning with proc boundary // due to dynamic bins across non-periodic global boundary // copy to self if sendproc = me // MPI send to another proc if sendproc != me diff --git a/src/USER-ATC/fix_atc.cpp b/src/USER-ATC/fix_atc.cpp index 0e9cd02ad6..2165132856 100644 --- a/src/USER-ATC/fix_atc.cpp +++ b/src/USER-ATC/fix_atc.cpp @@ -123,7 +123,7 @@ FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), # be used as a localization function \n fix AtC kernel quartic_sphere 10.0 \n \n # create a uniform 1 x 1 x 1 mesh that covers region contain the group \n - # with periodicity this effectively creats a system average \n + # with periodicity this effectively creates a system average \n fix_modify AtC mesh create 1 1 1 box p p p \n\n # change from default lagrangian map to eulerian \n # refreshed every 100 steps \n diff --git a/src/USER-DIFFRACTION/README b/src/USER-DIFFRACTION/README index 5488cd3416..00203aeae2 100644 --- a/src/USER-DIFFRACTION/README +++ b/src/USER-DIFFRACTION/README @@ -1,4 +1,4 @@ -This package contains the commands neeed to calculate x-ray and +This package contains the commands needed to calculate x-ray and electron diffraction intensities based on kinematic diffraction theory. Detailed discription of the computation can be found in the following works: diff --git a/src/USER-DIFFRACTION/compute_saed.cpp b/src/USER-DIFFRACTION/compute_saed.cpp index 3ae25f223c..7b5b2f4f5b 100644 --- a/src/USER-DIFFRACTION/compute_saed.cpp +++ b/src/USER-DIFFRACTION/compute_saed.cpp @@ -75,7 +75,7 @@ ComputeSAED::ComputeSAED(LAMMPS *lmp, int narg, char **arg) : if (lambda < 0) error->all(FLERR,"Compute SAED: Wavelength must be greater than zero"); - // Define atom types for atomic scattering factor coefficents + // Define atom types for atomic scattering factor coefficients int iarg = 4; ztype = new int[ntypes]; for (int i = 0; i < ntypes; i++){ @@ -394,7 +394,7 @@ void ComputeSAED::compute_vector() */ - // determining paramater set to use based on maximum S = sin(theta)/lambda + // determining parameter set to use based on maximum S = sin(theta)/lambda double Smax = Kmax / 2; int offset = 0; // offset the ASFSAED matrix for appropriate value @@ -449,8 +449,8 @@ void ComputeSAED::compute_vector() Fatom1 = 0.0; Fatom2 = 0.0; - // Calculate the atomic structre factor by type - // determining paramater set to use based on S = sin(theta)/lambda <> 2 + // Calculate the atomic structure factor by type + // determining parameter set to use based on S = sin(theta)/lambda <> 2 for (int ii = 0; ii < ntypes; ii++){ f[ii] = 0; for (int C = 0; C < 5; C++){ diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.cpp b/src/USER-DIFFRACTION/fix_saed_vtk.cpp index c3a72e494b..b6c00c2374 100644 --- a/src/USER-DIFFRACTION/fix_saed_vtk.cpp +++ b/src/USER-DIFFRACTION/fix_saed_vtk.cpp @@ -98,7 +98,7 @@ FixSAEDVTK::FixSAEDVTK(LAMMPS *lmp, int narg, char **arg) : if (strcmp(compute_saed->style,"saed") != 0) error->all(FLERR,"Fix saed/vtk has invalid compute assigned"); - // Gather varialbes from specified compute_saed + // Gather variables from specified compute_saed double *saed_var = compute_saed->saed_var; lambda = saed_var[0]; Kmax = saed_var[1]; diff --git a/src/USER-DPD/fix_rx.h b/src/USER-DPD/fix_rx.h index ca87fc51fd..e2f9f5b88b 100644 --- a/src/USER-DPD/fix_rx.h +++ b/src/USER-DPD/fix_rx.h @@ -124,7 +124,7 @@ class FixRX : public Fix { // ODE Diagnostics //int nSteps; //!< # of accepted steps taken over all atoms. - //int nIters; //!< # of attemped steps for all atoms. + //int nIters; //!< # of attempted steps for all atoms. //int nFuncs; //!< # of RHS evaluations for all atoms. //int nFails; //!< # of ODE systems that failed (for some reason). diff --git a/src/USER-DPD/npair_half_bin_newton_ssa.cpp b/src/USER-DPD/npair_half_bin_newton_ssa.cpp index 2139173d47..4fb5714d11 100644 --- a/src/USER-DPD/npair_half_bin_newton_ssa.cpp +++ b/src/USER-DPD/npair_half_bin_newton_ssa.cpp @@ -64,7 +64,7 @@ NPairHalfBinNewtonSSA::~NPairHalfBinNewtonSSA() /* ---------------------------------------------------------------------- binned neighbor list construction with full Newton's 3rd law - for use by Shardlow Spliting Algorithm + for use by Shardlow Splitting Algorithm each owned atom i checks its own bin and other bins in Newton stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ diff --git a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp index f5d5467a9c..fa4f761663 100644 --- a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp +++ b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp @@ -587,7 +587,7 @@ void PairLJCutTholeLong::write_data_all(FILE *fp) /* ---------------------------------------------------------------------- */ // No point in having single() since it has no information about topology or Drude particles. -// Charges qi and qj are defined by the user (or 1.0 by defaut) +// Charges qi and qj are defined by the user (or 1.0 by default) /* ---------------------------------------------------------------------- */ diff --git a/src/USER-DRUDE/pair_thole.cpp b/src/USER-DRUDE/pair_thole.cpp index 129ed57900..4dd6cb12c0 100644 --- a/src/USER-DRUDE/pair_thole.cpp +++ b/src/USER-DRUDE/pair_thole.cpp @@ -369,7 +369,7 @@ double PairThole::single(int i, int j, int itype, int jtype, double qi,qj,factor_f,factor_e,dcoul,asr,exp_asr; // single() has no information about topology or Drude particles. - // Charges qi and qj are defined by the user (or 1.0 by defaut) + // Charges qi and qj are defined by the user (or 1.0 by default) qi = atom->q[i]; qj = atom->q[j]; diff --git a/src/USER-INTEL/README b/src/USER-INTEL/README index 786033ca85..650e2c3a2d 100644 --- a/src/USER-INTEL/README +++ b/src/USER-INTEL/README @@ -36,7 +36,7 @@ be added or changed in the Makefile depending on the version: 2017 update 2 - No changes needed 2017 updates 3 or 4 - Use -xCOMMON-AVX512 and not -xHost or -xCORE-AVX512 -2018 inital release - Use -xCOMMON-AVX512 and not -xHost or -xCORE-AVX512 +2018 initial release - Use -xCOMMON-AVX512 and not -xHost or -xCORE-AVX512 2018u1 or newer - Use -xHost or -xCORE-AVX512 and -qopt-zmm-usage=high ----------------------------------------------------------------------------- diff --git a/src/USER-INTEL/pair_airebo_intel.cpp b/src/USER-INTEL/pair_airebo_intel.cpp index eedf45d75e..e6e8503bb0 100644 --- a/src/USER-INTEL/pair_airebo_intel.cpp +++ b/src/USER-INTEL/pair_airebo_intel.cpp @@ -4480,7 +4480,7 @@ exceed_limits: * Calculate the lennard-jones interaction. * Uses the above hash-map, and outlines the calculation if the bondorder is * needed. - * Agressively compresses to get the most values calculated. + * Aggressively compresses to get the most values calculated. */ template static void aut_lennard_jones(KernelArgsAIREBOT * ka) { diff --git a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp index f3f81651fc..ff8a9869b7 100644 --- a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp +++ b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp @@ -487,7 +487,7 @@ void PairLJCharmmCoulCharmmIntel::pack_force_const(ForceConst &fc, // Repeat cutsq calculation because done after call to init_style if (cut_lj > cut_coul) error->all(FLERR, - "Intel varient of lj/charmm/coul/long expects lj cutoff<=coulombic"); + "Intel variant of lj/charmm/coul/long expects lj cutoff<=coulombic"); for (int i = 1; i <= atom->ntypes; i++) { for (int j = i; j <= atom->ntypes; j++) { double cut; diff --git a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.h b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.h index 64d6077477..a48a84b5ce 100644 --- a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.h +++ b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.h @@ -92,7 +92,7 @@ E: The 'package intel' command is required for /intel styles Self-explanatory. -E: Intel varient of lj/charmm/coul/charmm expects lj cutoff<=coulombic +E: Intel variant of lj/charmm/coul/charmm expects lj cutoff<=coulombic The intel accelerated version of the CHARMM style requires that the Lennard-Jones cutoff is not greater than the coulombic cutoff. diff --git a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp b/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp index b4697ad122..5a4069e199 100644 --- a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp @@ -557,7 +557,7 @@ void PairLJCharmmCoulLongIntel::pack_force_const(ForceConst &fc, // Repeat cutsq calculation because done after call to init_style if (cut_lj > cut_coul) error->all(FLERR, - "Intel varient of lj/charmm/coul/long expects lj cutoff<=coulombic"); + "Intel variant of lj/charmm/coul/long expects lj cutoff<=coulombic"); for (int i = 1; i <= atom->ntypes; i++) { for (int j = i; j <= atom->ntypes; j++) { double cut; diff --git a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.h b/src/USER-INTEL/pair_lj_charmm_coul_long_intel.h index 0066745078..31b2182cb5 100644 --- a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.h +++ b/src/USER-INTEL/pair_lj_charmm_coul_long_intel.h @@ -96,7 +96,7 @@ E: The 'package intel' command is required for /intel styles Self-explanatory. -E: Intel varient of lj/charmm/coul/long expects lj cutoff<=coulombic +E: Intel variant of lj/charmm/coul/long expects lj cutoff<=coulombic The intel accelerated version of the CHARMM style requires that the Lennard-Jones cutoff is not greater than the coulombic cutoff. diff --git a/src/USER-INTEL/pppm_disp_intel.cpp b/src/USER-INTEL/pppm_disp_intel.cpp index 9d075c78a1..c3711ef404 100644 --- a/src/USER-INTEL/pppm_disp_intel.cpp +++ b/src/USER-INTEL/pppm_disp_intel.cpp @@ -348,7 +348,7 @@ void PPPMDispIntel::compute(int eflag, int vflag) } if (function[1]) { - //perfrom calculations for geometric mixing + //perform calculations for geometric mixing if (fix->precision() == FixIntel::PREC_MODE_MIXED) { particle_map(delxinv_6, delyinv_6, delzinv_6, shift_6, diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp index 7f8d9d5675..d62a5bba2a 100644 --- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp +++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp @@ -149,7 +149,7 @@ FixNVEManifoldRattle::FixNVEManifoldRattle( LAMMPS *lmp, int &narg, char **arg, nevery = force->inumeric(FLERR,arg[argi+1]); next_output = update->ntimestep + nevery; if (comm->me == 0) { - fprintf(screen,"Outputing every %d steps, next is %d\n", + fprintf(screen,"Outputting every %d steps, next is %d\n", nevery, next_output); } argi += 2; diff --git a/src/USER-MANIFOLD/manifold_thylakoid.cpp b/src/USER-MANIFOLD/manifold_thylakoid.cpp index e4ef039832..e473f00a03 100644 --- a/src/USER-MANIFOLD/manifold_thylakoid.cpp +++ b/src/USER-MANIFOLD/manifold_thylakoid.cpp @@ -142,7 +142,7 @@ void manifold_thylakoid::init_domains() { if (wB + 2*lB > LT) { char msg[2048]; - sprintf(msg,"LT = %f not large enough to accomodate bridge with " + sprintf(msg,"LT = %f not large enough to accommodate bridge with " "wB = %f and lB = %f! %f > %f\n", LT, wB, lB, wB + 2*lB, LT); error->one(FLERR,msg); } diff --git a/src/USER-MEAMC/README b/src/USER-MEAMC/README index c1faf7c0c4..dcb70d670c 100644 --- a/src/USER-MEAMC/README +++ b/src/USER-MEAMC/README @@ -19,7 +19,7 @@ The original Fortran implementation was created by Use "make yes-user-meamc" to enable this package when building LAMMPS. -In your LAMMPS input script, specifiy +In your LAMMPS input script, specify pair_style meam/c to enable the use of this implementation. All parameters, input files and outputs are exactly identical to these used with pair_style meam. diff --git a/src/USER-MEAMC/meam_funcs.cpp b/src/USER-MEAMC/meam_funcs.cpp index a67cbf2833..706075ffd0 100644 --- a/src/USER-MEAMC/meam_funcs.cpp +++ b/src/USER-MEAMC/meam_funcs.cpp @@ -271,7 +271,7 @@ MEAM::get_Zij(const lattice_t latt) return 12; case B2: return 8; - case CH4: // DYNAMO currenly implemented this way while it needs two Z values, 4 and 1 + case CH4: // DYNAMO currently implemented this way while it needs two Z values, 4 and 1 return 4; case LIN: case ZIG: diff --git a/src/USER-MEAMC/meam_setup_done.cpp b/src/USER-MEAMC/meam_setup_done.cpp index 8dfebe8ed5..b37f56dda2 100644 --- a/src/USER-MEAMC/meam_setup_done.cpp +++ b/src/USER-MEAMC/meam_setup_done.cpp @@ -95,7 +95,7 @@ MEAM::alloyparams(void) for (i = 0; i < this->neltypes; i++) { for (j = 0; j < this->neltypes; j++) { // Treat off-diagonal pairs - // If i>j, set all equal to ij, set all equal to i j) { this->re_meam[i][j] = this->re_meam[j][i]; diff --git a/src/USER-MGPT/pair_mgpt.cpp b/src/USER-MGPT/pair_mgpt.cpp index 0634872c70..213f73f05a 100644 --- a/src/USER-MGPT/pair_mgpt.cpp +++ b/src/USER-MGPT/pair_mgpt.cpp @@ -118,7 +118,7 @@ void PairMGPT::make_bond(const double xx[][3],int i,int j,bond_data *bptr) { double t0,t1; - /* Check that alignment requirements for SIMD code are fullfilled */ + /* Check that alignment requirements for SIMD code are fulfilled */ assert( (((unsigned long long int) (bptr->H.m )) & 31) == 0 ); assert( (((unsigned long long int) (bptr->Hx.m)) & 31) == 0 ); assert( (((unsigned long long int) (bptr->Hy.m)) & 31) == 0 ); diff --git a/src/USER-MISC/compute_cnp_atom.cpp b/src/USER-MISC/compute_cnp_atom.cpp index 3a1d5271c6..34882b0272 100644 --- a/src/USER-MISC/compute_cnp_atom.cpp +++ b/src/USER-MISC/compute_cnp_atom.cpp @@ -161,7 +161,7 @@ void ComputeCNPAtom::compute_peratom() numneigh = list->numneigh; firstneigh = list->firstneigh; - // find the neigbors of each atom within cutoff using full neighbor list + // find the neighbors of each atom within cutoff using full neighbor list // nearest[] = atom indices of nearest neighbors, up to MAXNEAR // do this for all atoms, not just compute group // since CNP calculation requires neighbors of neighbors diff --git a/src/USER-MISC/compute_stress_mop.cpp b/src/USER-MISC/compute_stress_mop.cpp index 2f932321e1..c403ed3247 100644 --- a/src/USER-MISC/compute_stress_mop.cpp +++ b/src/USER-MISC/compute_stress_mop.cpp @@ -318,7 +318,7 @@ void ComputeStressMop::compute_pairs() if (newton_pair || j < nlocal) { - //check if ij pair is accross plane, add contribution to pressure + //check if ij pair is across plane, add contribution to pressure if ( ((xi[dir]>pos) && (xj[dir]pos1) && (xj[dir]single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair); diff --git a/src/USER-MISC/compute_stress_mop_profile.cpp b/src/USER-MISC/compute_stress_mop_profile.cpp index 5f6d0a36b2..9649a61090 100644 --- a/src/USER-MISC/compute_stress_mop_profile.cpp +++ b/src/USER-MISC/compute_stress_mop_profile.cpp @@ -333,7 +333,7 @@ void ComputeStressMopProfile::compute_pairs() pos = coord[ibin][0]; pos1 = coordp[ibin][0]; - //check if ij pair is accross plane, add contribution to pressure + //check if ij pair is across plane, add contribution to pressure if ( ((xi[dir]>pos) && (xj[dir]pos1) && (xj[dir]pos) && (xj[dir]pos1) && (xj[dir]f_unspecified) && (i==0)) err_msg << "\n (This sometimes occurs if users forget to specify the \"NOF\" option.)\n"; error->one(FLERR, err_msg.str().c_str()); diff --git a/src/USER-MISC/dihedral_table_cut.cpp b/src/USER-MISC/dihedral_table_cut.cpp index 8d530253c2..194c25f536 100644 --- a/src/USER-MISC/dihedral_table_cut.cpp +++ b/src/USER-MISC/dihedral_table_cut.cpp @@ -1140,7 +1140,7 @@ void DihedralTableCut::read_table(Table *tb, char *file, char *keyword) if (! line_ss) { stringstream err_msg; err_msg << "Read error in table "<< keyword<<", near line "<f_unspecified) && (i==0)) err_msg << "\n (This sometimes occurs if users forget to specify the \"NOF\" option.)\n"; error->one(FLERR, err_msg.str().c_str()); diff --git a/src/USER-MISC/fix_flow_gauss.cpp b/src/USER-MISC/fix_flow_gauss.cpp index 218ba3cfa6..c7b7f86d37 100644 --- a/src/USER-MISC/fix_flow_gauss.cpp +++ b/src/USER-MISC/fix_flow_gauss.cpp @@ -188,7 +188,7 @@ void FixFlowGauss::post_force(int /*vflag*/) for (ii=0; ii<3; ii++) a_app[ii] = -f_tot[ii] / mTot; - //apply added accelleration to each atom + //apply added acceleration to each atom double f_app[3]; double peAdded=0.0; for( ii = 0; iiuniverse_all(FLERR,"Unkown method parameter for fix pimd"); + else error->universe_all(FLERR,"Unknown method parameter for fix pimd"); } else if(strcmp(arg[i],"fmass")==0) { @@ -79,7 +79,7 @@ FixPIMD::FixPIMD(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) nhc_nchain = atoi(arg[i+1]); if(nhc_nchain<2) error->universe_all(FLERR,"Invalid nhc value for fix pimd"); } - else error->universe_all(arg[i],i+1,"Unkown keyword for fix pimd"); + else error->universe_all(arg[i],i+1,"Unknown keyword for fix pimd"); } /* Initiation */ diff --git a/src/USER-MISC/fix_pimd.h b/src/USER-MISC/fix_pimd.h index c298af0b69..bed5b0a256 100644 --- a/src/USER-MISC/fix_pimd.h +++ b/src/USER-MISC/fix_pimd.h @@ -61,7 +61,7 @@ class FixPIMD : public Fix { void spring_force(); - /* fictious mass */ + /* fictitious mass */ double fmass, *mass; diff --git a/src/USER-MISC/fix_wall_reflect_stochastic.cpp b/src/USER-MISC/fix_wall_reflect_stochastic.cpp index bb6ffd7698..18bb7ec011 100644 --- a/src/USER-MISC/fix_wall_reflect_stochastic.cpp +++ b/src/USER-MISC/fix_wall_reflect_stochastic.cpp @@ -71,7 +71,7 @@ FixWallReflectStochastic(LAMMPS *lmp, int narg, char **arg) : seedfix = force->inumeric(FLERR,arg[4]); - if (seedfix <= 0) error->all(FLERR,"Random seed must be a postive number"); + if (seedfix <= 0) error->all(FLERR,"Random seed must be a positive number"); int iarg = 5; while (iarg < narg) { @@ -114,7 +114,7 @@ FixWallReflectStochastic(LAMMPS *lmp, int narg, char **arg) : if ((wallvel[nwall][dir] !=0) & (dir == dim)) error->all(FLERR,"The wall velocity must be tangential"); - // DIFFUSIVE = no accomodation coeffs + // DIFFUSIVE = no accommodation coeffs // MAXWELL = one for all dimensions // CCL = one for each dimension diff --git a/src/USER-MISC/pair_cosine_squared.cpp b/src/USER-MISC/pair_cosine_squared.cpp index 7c0cb3372d..7f3f6259d4 100644 --- a/src/USER-MISC/pair_cosine_squared.cpp +++ b/src/USER-MISC/pair_cosine_squared.cpp @@ -180,7 +180,7 @@ void PairCosineSquared::coeff(int narg, char **arg) } /* ---------------------------------------------------------------------- - init specific to this pair style (unneccesary) + init specific to this pair style (unnecessary) ------------------------------------------------------------------------- */ /* diff --git a/src/USER-MISC/pair_coul_shield.cpp b/src/USER-MISC/pair_coul_shield.cpp index 980b4a71d5..e6916f0d22 100644 --- a/src/USER-MISC/pair_coul_shield.cpp +++ b/src/USER-MISC/pair_coul_shield.cpp @@ -102,7 +102,7 @@ void PairCoulShield::compute(int eflag, int vflag) rsq = delx*delx + dely*dely + delz*delz; jtype = type[j]; - // only include the interation between different layers + // only include the interaction between different layers if (rsq < cutsq[itype][jtype] && atom->molecule[i] != atom->molecule[j]) { r = sqrt(rsq); r3 = rsq*r; diff --git a/src/USER-MISC/pair_drip.cpp b/src/USER-MISC/pair_drip.cpp index 20ec3abcf9..020216f503 100644 --- a/src/USER-MISC/pair_drip.cpp +++ b/src/USER-MISC/pair_drip.cpp @@ -405,7 +405,7 @@ void PairDRIP::compute(int eflag, int vflag) Param& p = params[iparam_ij]; double rcutsq = p.rcutsq; - // only include the interation between different layers + // only include the interaction between different layers if (rsq < rcutsq && atom->molecule[i] != atom->molecule[j]) { double fj[DIM] = {0., 0., 0.}; diff --git a/src/USER-MISC/pair_e3b.cpp b/src/USER-MISC/pair_e3b.cpp index ae324e0a4a..46f22e714d 100644 --- a/src/USER-MISC/pair_e3b.cpp +++ b/src/USER-MISC/pair_e3b.cpp @@ -31,7 +31,7 @@ #include "domain.h" #include "citeme.h" -//these are defined here to avoid confusing hardcoded indicies, but +//these are defined here to avoid confusing hardcoded indices, but //they do not allow flexibility. If they are changed the code will break #define DIM 3 #define NUMH 2 //number of hydrogen atoms per water molecule diff --git a/src/USER-MISC/pair_extep.cpp b/src/USER-MISC/pair_extep.cpp index df232e029c..62ef24da85 100644 --- a/src/USER-MISC/pair_extep.cpp +++ b/src/USER-MISC/pair_extep.cpp @@ -718,7 +718,7 @@ void PairExTeP::read_file(char *file) // reallocate with new size words = new char*[params_per_line+1]; - // intialize F_corr_data to all zeros + // initialize F_corr_data to all zeros for (int iel=0;ielmolecule[i] != atom->molecule[j]) { int iparam_ij = elem2param[map[itype]][map[jtype]]; @@ -593,7 +593,7 @@ void PairILPGrapheneHBN::calc_FRep(int eflag, int /* vflag */) delz = ztmp - x[j][2]; rsq = delx*delx + dely*dely + delz*delz; - // only include the interation between different layers + // only include the interaction between different layers if (rsq < cutsq[itype][jtype] && atom->molecule[i] != atom->molecule[j]) { int iparam_ij = elem2param[map[itype]][map[jtype]]; @@ -675,7 +675,7 @@ void PairILPGrapheneHBN::calc_FRep(int eflag, int /* vflag */) } /* ---------------------------------------------------------------------- - create ILP neighbor list from main neighbor list to calcualte normals + create ILP neighbor list from main neighbor list to calculate normals ------------------------------------------------------------------------- */ void PairILPGrapheneHBN::ILP_neigh() diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp index 92fbc4e9c0..3f624fc785 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp @@ -502,7 +502,7 @@ void PairKolmogorovCrespiFull::calc_FvdW(int eflag, int /* vflag */) delz = ztmp - x[j][2]; rsq = delx*delx + dely*dely + delz*delz; - // only include the interation between different layers + // only include the interaction between different layers if (rsq < cutsq[itype][jtype] && atom->molecule[i] != atom->molecule[j]) { int iparam_ij = elem2param[map[itype]][map[jtype]]; @@ -593,7 +593,7 @@ void PairKolmogorovCrespiFull::calc_FRep(int eflag, int /* vflag */) delz = ztmp - x[j][2]; rsq = delx*delx + dely*dely + delz*delz; - // only include the interation between different layers + // only include the interaction between different layers if (rsq < cutsq[itype][jtype] && atom->molecule[i] != atom->molecule[j]) { int iparam_ij = elem2param[map[itype]][map[jtype]]; diff --git a/src/USER-MISC/pair_mesocnt.cpp b/src/USER-MISC/pair_mesocnt.cpp index b073705dda..4864dab950 100644 --- a/src/USER-MISC/pair_mesocnt.cpp +++ b/src/USER-MISC/pair_mesocnt.cpp @@ -866,7 +866,7 @@ void PairMesoCNT::read_data(FILE *fp, double *data, } } - // warn if data was read incompletely, e.g. colums were missing + // warn if data was read incompletely, e.g. columns were missing if (cerror) { char str[128]; @@ -934,7 +934,7 @@ void PairMesoCNT::read_data(FILE *fp, double **data, } } - // warn if data was read incompletely, e.g. colums were missing + // warn if data was read incompletely, e.g. columns were missing if (cerror) { char str[128]; diff --git a/src/USER-OMP/msm_cg_omp.cpp b/src/USER-OMP/msm_cg_omp.cpp index 3c5439db5d..7ca01dbd6a 100644 --- a/src/USER-OMP/msm_cg_omp.cpp +++ b/src/USER-OMP/msm_cg_omp.cpp @@ -199,7 +199,7 @@ void MSMCGOMP::compute(int eflag, int vflag) } - // compute direct interation for top grid level for non-periodic + // compute direct interaction for top grid level for non-periodic // and for second from top grid level for periodic if (active_flag[levels-1]) { diff --git a/src/USER-OMP/pair_airebo_omp.cpp b/src/USER-OMP/pair_airebo_omp.cpp index 7890c8aed3..aedf5056a6 100644 --- a/src/USER-OMP/pair_airebo_omp.cpp +++ b/src/USER-OMP/pair_airebo_omp.cpp @@ -1848,9 +1848,9 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag, This function calculates S(t_b(b_ij*)) as specified in the AIREBO paper. To do so, it needs to compute b_ij*, i.e. the bondorder given that the -atoms i and j are placed a ficticious distance rijmag_mod apart. +atoms i and j are placed a fictitious distance rijmag_mod apart. Now there are two approaches to calculate the resulting forces: -1. Carry through the ficticious distance and corresponding vector +1. Carry through the fictitious distance and corresponding vector rij_mod, correcting afterwards using the derivative of r/|r|. 2. Perform all the calculations using the real distance, and do not use a correction, only using rijmag_mod where necessary. diff --git a/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp b/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp index 7735d6fde4..d8eedc6c0b 100644 --- a/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp +++ b/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp @@ -66,7 +66,7 @@ void PairLJLongTIP4PLongOMP::compute(int eflag, int vflag) ev_init(eflag,vflag); // reallocate hneigh_thr & newsite_thr if necessary - // initialize hneigh_thr[0] to -1 on steps when reneighboring occured + // initialize hneigh_thr[0] to -1 on steps when reneighboring occurred // initialize hneigh_thr[2] to 0 every step const int nlocal = atom->nlocal; const int nall = nlocal + atom->nghost; @@ -354,7 +354,7 @@ void PairLJLongTIP4PLongOMP::compute(int eflag, int vflag) void PairLJLongTIP4PLongOMP::compute_inner() { // reallocate hneigh_thr & newsite_thr if necessary - // initialize hneigh_thr[0] to -1 on steps when reneighboring occured + // initialize hneigh_thr[0] to -1 on steps when reneighboring occurred // initialize hneigh_thr[2] to 0 every step const int nall = atom->nlocal + atom->nghost; @@ -432,7 +432,7 @@ void PairLJLongTIP4PLongOMP::compute_outer(int eflag, int vflag) const int nall = atom->nlocal + atom->nghost; // reallocate hneigh_thr & newsite_thr if necessary - // initialize hneigh_thr[0] to -1 on steps when reneighboring occured + // initialize hneigh_thr[0] to -1 on steps when reneighboring occurred // initialize hneigh_thr[2] to 0 every step if (atom->nmax > nmax) { diff --git a/src/USER-OMP/pppm_cg_omp.cpp b/src/USER-OMP/pppm_cg_omp.cpp index 1117979f1f..f9967bf52a 100644 --- a/src/USER-OMP/pppm_cg_omp.cpp +++ b/src/USER-OMP/pppm_cg_omp.cpp @@ -281,7 +281,7 @@ void PPPMCGOMP::compute_gf_ad() } } thr->timer(Timer::KSPACE); - } // end of paralle region + } // end of parallel region // compute the coefficients for the self-force correction @@ -570,7 +570,7 @@ void PPPMCGOMP::fieldforce_ad() eky *= hy_inv; ekz *= hz_inv; - // convert E-field to force and substract self forces + // convert E-field to force and subtract self forces const double qi = q[i]; const double qfactor = qqrd2e * scale * qi; diff --git a/src/USER-OMP/pppm_disp_tip4p_omp.cpp b/src/USER-OMP/pppm_disp_tip4p_omp.cpp index bdd8f23ee4..ec294cd56d 100644 --- a/src/USER-OMP/pppm_disp_tip4p_omp.cpp +++ b/src/USER-OMP/pppm_disp_tip4p_omp.cpp @@ -951,7 +951,7 @@ void PPPMDispTIP4POMP::fieldforce_c_ad() eky *= hy_inv; ekz *= hz_inv; - // convert E-field to force and substract self forces + // convert E-field to force and subtract self forces const double qi = q[i]; const double qfactor = qqrd2e * scale * qi; diff --git a/src/USER-OMP/pppm_omp.cpp b/src/USER-OMP/pppm_omp.cpp index c6aaafaa31..b9b39826ff 100644 --- a/src/USER-OMP/pppm_omp.cpp +++ b/src/USER-OMP/pppm_omp.cpp @@ -281,7 +281,7 @@ void PPPMOMP::compute_gf_ad() } } thr->timer(Timer::KSPACE); - } // end of paralle region + } // end of parallel region // compute the coefficients for the self-force correction @@ -578,7 +578,7 @@ void PPPMOMP::fieldforce_ad() eky *= hy_inv; ekz *= hz_inv; - // convert E-field to force and substract self forces + // convert E-field to force and subtract self forces const double qi = q[i]; const double qfactor = qqrd2e * scale * qi; diff --git a/src/USER-OMP/pppm_tip4p_omp.cpp b/src/USER-OMP/pppm_tip4p_omp.cpp index 322730b573..359b5dcc8d 100644 --- a/src/USER-OMP/pppm_tip4p_omp.cpp +++ b/src/USER-OMP/pppm_tip4p_omp.cpp @@ -283,7 +283,7 @@ void PPPMTIP4POMP::compute_gf_ad() } } thr->timer(Timer::KSPACE); - } // end of paralle region + } // end of parallel region // compute the coefficients for the self-force correction @@ -681,7 +681,7 @@ void PPPMTIP4POMP::fieldforce_ad() eky *= hy_inv; ekz *= hz_inv; - // convert E-field to force and substract self forces + // convert E-field to force and subtract self forces const double qi = q[i]; const double qfactor = qqrd2e * scale * qi; diff --git a/src/USER-OMP/thr_data.h b/src/USER-OMP/thr_data.h index 2c1e42a3a3..4853d6dbbf 100644 --- a/src/USER-OMP/thr_data.h +++ b/src/USER-OMP/thr_data.h @@ -146,7 +146,7 @@ class ThrData { //////////////////////////////////////////////////////////////////////// // helper functions operating on data replicated for thread support // //////////////////////////////////////////////////////////////////////// -// generic per thread data reduction for continous arrays of nthreads*nmax size +// generic per thread data reduction for continuous arrays of nthreads*nmax size void data_reduce_thr(double *, int, int, int, int); } #endif diff --git a/src/USER-PHONON/fix_phonon.h b/src/USER-PHONON/fix_phonon.h index 91a380247a..f75139ce42 100644 --- a/src/USER-PHONON/fix_phonon.h +++ b/src/USER-PHONON/fix_phonon.h @@ -73,7 +73,7 @@ class FixPhonon : public Fix { double *M_inv_sqrt; - class FFT3d *fft; // to do fft via the fft3d wraper + class FFT3d *fft; // to do fft via the fft3d wrapper int nxlo,nxhi,mysize; // size info for local MPI_FFTW int mynpt,mynq,fft_nsend; int *fft_cnts, *fft_disp; diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index b2bb66b288..44e2bd172e 100644 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -617,7 +617,7 @@ void FixBondReact::post_constructor() delete [] exclude_PARENT_group; // on to statted_tags (system-wide thermostat) - // intialize per-atom statted_flags to 1 + // initialize per-atom statted_flags to 1 // (only if not already initialized by restart) if (fix3->restart_reset != 1) { int flag; @@ -650,7 +650,7 @@ void FixBondReact::post_constructor() statted_id = new char[len]; strcpy(statted_id,idprop); - // intialize per-atom statted_tags to 1 + // initialize per-atom statted_tags to 1 // need to correct for smooth restarts //int flag; //int index = atom->find_custom(statted_id,flag); @@ -1325,7 +1325,7 @@ void FixBondReact::make_a_guess() // if so, this constitutes a fail // because still undergoing a previous reaction! // could technically fail unnecessarily during a wrong guess if near edge atoms - // we accept this temporary and infrequent decrease in reaction occurences + // we accept this temporary and infrequent decrease in reaction occurrences for (int i = 0; i < nxspecial[atom->map(glove[pion][1])][0]; i++) { if (atom->map(xspecial[atom->map(glove[pion][1])][i]) < 0) { @@ -1922,7 +1922,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn) { // landlocked_atoms are atoms for which all topology is contained in reacted template // if dihedrals/impropers exist: this means that edge atoms are not in their 1-3 neighbor list - // note: due to various usage/defintions of impropers, treated same as dihedrals + // note: due to various usage/definitions of impropers, treated same as dihedrals // if angles exist: this means edge atoms not in their 1-2 neighbors list // if just bonds: this just means that edge atoms are not landlocked // Note: landlocked defined in terms of reacted template diff --git a/src/USER-SMD/atom_vec_smd.cpp b/src/USER-SMD/atom_vec_smd.cpp index 604504c5a7..ef14eacdc2 100644 --- a/src/USER-SMD/atom_vec_smd.cpp +++ b/src/USER-SMD/atom_vec_smd.cpp @@ -219,7 +219,7 @@ int AtomVecSMD::pack_comm_vel(int n, int *list, double *buf, int pbc_flag, int * // no need to communicate x0 here, as it is not changed by time integration // if x0 is changed when the ref config is updated, this communication is performed in the fix_integrate/tlsph - // similarily, rmass could be removed here. + // similarly, rmass could be removed here. // radius should be communicated here for future time-integration of the radius with ulsph (not implemented yet) int i, j, m; double dx, dy, dz, dvx, dvy, dvz; diff --git a/src/USER-SMD/pair_smd_tlsph.cpp b/src/USER-SMD/pair_smd_tlsph.cpp index 82b7c8ff9d..cad9923054 100644 --- a/src/USER-SMD/pair_smd_tlsph.cpp +++ b/src/USER-SMD/pair_smd_tlsph.cpp @@ -913,7 +913,7 @@ void PairTlsph::settings(int narg, char **arg) { /* * default value for update_threshold for updates of reference configuration: * The maximum relative displacement which is tracked by the construction of LAMMPS' neighborlists - * is the folowing. + * is the following. */ cut_comm = MAX(neighbor->cutneighmax, comm->cutghostuser); // cutoff radius within which ghost atoms are communicated. diff --git a/src/USER-SMD/pair_smd_tlsph.h b/src/USER-SMD/pair_smd_tlsph.h index 62e7ce2295..31a238d564 100644 --- a/src/USER-SMD/pair_smd_tlsph.h +++ b/src/USER-SMD/pair_smd_tlsph.h @@ -195,7 +195,7 @@ protected: private: double **Lookup; // holds per-type material parameters for the quantities defined in enum statement above. - bool first; // if first is true, do not perform any computations, beacuse reference configuration is not ready yet. + bool first; // if first is true, do not perform any computations, because reference configuration is not ready yet. }; } diff --git a/src/USER-SMD/pair_smd_triangulated_surface.cpp b/src/USER-SMD/pair_smd_triangulated_surface.cpp index f9052be087..53a93df7f7 100644 --- a/src/USER-SMD/pair_smd_triangulated_surface.cpp +++ b/src/USER-SMD/pair_smd_triangulated_surface.cpp @@ -481,7 +481,7 @@ double PairTriSurf::memory_usage() { % Release: 1.2 Fixed Bug because of typo in region 5 20101013 % Release: 1.3 Fixed Bug because of typo in region 2 20101014 - % Possible extention could be a version tailored not to return the distance + % Possible extension could be a version tailored not to return the distance % and additionally the closest point, but instead return only the closest % point. Could lead to a small speed gain. diff --git a/src/USER-SMD/smd_material_models.cpp b/src/USER-SMD/smd_material_models.cpp index 5ee67fbb4e..096600df52 100644 --- a/src/USER-SMD/smd_material_models.cpp +++ b/src/USER-SMD/smd_material_models.cpp @@ -263,7 +263,7 @@ void LinearPlasticStrength(const double G, const double yieldStress, const Matri if (J2 < yieldStress) { /* - * no yielding has occured. + * no yielding has occurred. * final deviatoric stress is trial deviatoric stress */ sigma_dev_rate__ = dev_rate; @@ -274,7 +274,7 @@ void LinearPlasticStrength(const double G, const double yieldStress, const Matri } else { //printf("yiedl\n"); /* - * yielding has occured + * yielding has occurred */ plastic_strain_increment = (J2 - yieldStress) / (3.0 * G); @@ -288,7 +288,7 @@ void LinearPlasticStrength(const double G, const double yieldStress, const Matri * new deviatoric stress rate */ sigma_dev_rate__ = sigmaFinal_dev__ - sigmaInitial_dev; - //printf("yielding has occured.\n"); + //printf("yielding has occurred.\n"); } } @@ -344,7 +344,7 @@ void JohnsonCookStrength(const double G, const double cp, const double espec, co if (J2 < yieldStress) { /* - * no yielding has occured. + * no yielding has occurred. * final deviatoric stress is trial deviatoric stress */ sigma_dev_rate__ = dev_rate; @@ -355,7 +355,7 @@ void JohnsonCookStrength(const double G, const double cp, const double espec, co } else { //printf("yiedl\n"); /* - * yielding has occured + * yielding has occurred */ plastic_strain_increment = (J2 - yieldStress) / (3.0 * G); @@ -369,7 +369,7 @@ void JohnsonCookStrength(const double G, const double cp, const double espec, co * new deviatoric stress rate */ sigma_dev_rate__ = sigmaFinal_dev__ - sigmaInitial_dev; - //printf("yielding has occured.\n"); + //printf("yielding has occurred.\n"); } } @@ -452,7 +452,7 @@ double JohnsonCookFailureStrain(const double p, const Matrix3d Sdev, const doubl } // determine stress triaxiality - double triax = p / (vm + 0.01 * fabs(p)); // have softening in denominator to avoid divison by zero + double triax = p / (vm + 0.01 * fabs(p)); // have softening in denominator to avoid division by zero if (triax < 0.0) { triax = 0.0; } else if (triax > 3.0) { diff --git a/src/USER-SMTBQ/pair_smtbq.h b/src/USER-SMTBQ/pair_smtbq.h index 05e4b67242..c83e1b5cf1 100644 --- a/src/USER-SMTBQ/pair_smtbq.h +++ b/src/USER-SMTBQ/pair_smtbq.h @@ -56,8 +56,8 @@ protected: double rmin,dr,ds; // table parameter int kmax; bigint Qstep; // Frequency of charge resolution - double precision; // acuracy of convergence - int loopmax; // max of interation + double precision; // accuracy of convergence + int loopmax; // max of iteration double cutmax; // max cutoff for all elements int nelements; // # of unique elements diff --git a/src/USER-UEF/fix_nh_uef.cpp b/src/USER-UEF/fix_nh_uef.cpp index 8873688eb7..a3a2dc476c 100644 --- a/src/USER-UEF/fix_nh_uef.cpp +++ b/src/USER-UEF/fix_nh_uef.cpp @@ -53,7 +53,7 @@ static const char cite_user_uef_package[] = "}\n\n"; /* ---------------------------------------------------------------------- - * Parse fix specific keywords, do some error checking, and initalize + * Parse fix specific keywords, do some error checking, and initialize * temp/pressure fixes ---------------------------------------------------------------------- */ FixNHUef::FixNHUef(LAMMPS *lmp, int narg, char **arg) : diff --git a/src/USER-VTK/dump_vtk.h b/src/USER-VTK/dump_vtk.h index 8df14c7f34..e8de87f11c 100644 --- a/src/USER-VTK/dump_vtk.h +++ b/src/USER-VTK/dump_vtk.h @@ -185,7 +185,7 @@ E: Compute used in dump between runs is not current The compute was not invoked on the current timestep, therefore it cannot be used in a dump between runs. -E: Threshhold for an atom property that isn't allocated +E: 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. diff --git a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp index 022b93a0d2..37fc143e8b 100644 --- a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp @@ -166,7 +166,7 @@ void PairLJSwitch3CoulGaussLong::compute(int eflag, int vflag) forcelj = r6inv*(12.0*lj3[itype][jtype]*r6inv - 6.0*lj4[itype][jtype]); // Correction for Gaussian radii if (lj2[itype][jtype]==0.0) { - // This means a point charge is considerd, so the correction is zero + // This means a point charge is considered, so the correction is zero expn2 = 0.0; erfc2 = 0.0; forcecoul2 = 0.0; diff --git a/src/VORONOI/README b/src/VORONOI/README index 9a83c95a8d..ede104a678 100644 --- a/src/VORONOI/README +++ b/src/VORONOI/README @@ -7,7 +7,7 @@ developed by Chris H. Rycroft while at UC Berkeley / Lawrence Berkeley Laboratory. That library can be downloaded and built in lib/voronoi or elsewhere -on your system, which must be done before bulding LAMMPS with this +on your system, which must be done before building LAMMPS with this package. Details of the download, build, and install process for Voro++ are given in the lib/voronoi/README file, and scripts are provided to help automate the process. Also see the LAMMPS manual for diff --git a/src/comm.cpp b/src/comm.cpp index f5b1c0246b..6a762036d1 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -845,7 +845,7 @@ void Comm::ring(int n, int nper, void *inbuf, int messtag, rendezvous communication operation three stages: first comm sends inbuf from caller decomp to rvous decomp - callback operates on data in rendevous decomp + callback operates on data in rendezvous decomp second comm sends outbuf from rvous decomp back to caller decomp inputs: which = perform (0) irregular or (1) MPI_All2allv communication @@ -977,7 +977,7 @@ rendezvous_all2all(int n, char *inbuf, int insize, int inorder, int *procs, bigint *offsets; char *inbuf_a2a,*outbuf_a2a; - // create procs and inbuf for All2all if necesary + // create procs and inbuf for All2all if necessary if (!inorder) { memory->create(procs_a2a,nprocs,"rendezvous:procs"); @@ -1080,7 +1080,7 @@ rendezvous_all2all(int n, char *inbuf, int insize, int inorder, int *procs, return 0; // all nout_rvous are 0, no 2nd irregular } - // create procs and outbuf for All2all if necesary + // create procs and outbuf for All2all if necessary if (!outorder) { memory->create(procs_a2a,nprocs,"rendezvous_a2a:procs"); diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index ecf382ab03..c5ec8b35f4 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -567,7 +567,7 @@ void CommBrick::reverse_comm() atoms exchanged with all 6 stencil neighbors send out atoms that have left my box, receive ones entering my box atoms will be lost if not inside a stencil proc's box - can happen if atom moves outside of non-periodic bounary + can happen if atom moves outside of non-periodic boundary or if atom moves more than one proc away this routine called before every reneighboring for triclinic, atoms must be in lamda coords (0-1) before exchange is called diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 57b7f7e91e..a7eb6dfe80 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -618,7 +618,7 @@ void CommTiled::reverse_comm() atoms exchanged with procs that touch sub-box in each of 3 dims send out atoms that have left my box, receive ones entering my box atoms will be lost if not inside a touching proc's box - can happen if atom moves outside of non-periodic bounary + can happen if atom moves outside of non-periodic boundary or if atom moves more than one proc away this routine called before every reneighboring for triclinic, atoms must be in lamda coords (0-1) before exchange is called diff --git a/src/compute_cna_atom.cpp b/src/compute_cna_atom.cpp index 054798f637..c11f4016b5 100644 --- a/src/compute_cna_atom.cpp +++ b/src/compute_cna_atom.cpp @@ -142,7 +142,7 @@ void ComputeCNAAtom::compute_peratom() numneigh = list->numneigh; firstneigh = list->firstneigh; - // find the neigbours of each atom within cutoff using full neighbor list + // find the neighbours of each atom within cutoff using full neighbor list // nearest[] = atom indices of nearest neighbors, up to MAXNEAR // do this for all atoms, not just compute group // since CNA calculation requires neighbors of neighbors diff --git a/src/compute_orientorder_atom.cpp b/src/compute_orientorder_atom.cpp index dcb104fc3a..3dafd08a0f 100644 --- a/src/compute_orientorder_atom.cpp +++ b/src/compute_orientorder_atom.cpp @@ -508,7 +508,7 @@ void ComputeOrientOrderAtom::calc_boop(double **rlist, // TODO: // 1. [done]Need to allocate extra memory in qnarray[] for this option // 2. [done]Need to add keyword option - // 3. [done]Need to caclulate Clebsch-Gordan/Wigner 3j coefficients + // 3. [done]Need to calculate Clebsch-Gordan/Wigner 3j coefficients // (Can try getting them from boop.py first) // 5. [done]Compare to bcc values in /Users/athomps/netapp/codes/MatMiner/matminer/matminer/featurizers/boop.py // 6. [done]I get the right answer for W_l, but need to make sure that factor of 1/sqrt(l+1) is right for cglist diff --git a/src/dump_image.cpp b/src/dump_image.cpp index 7e6bc0c44c..a78c214e08 100644 --- a/src/dump_image.cpp +++ b/src/dump_image.cpp @@ -403,7 +403,7 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) : image->buffers(); - // communication neede for bonds colored by atoms + // communication needed for bonds colored by atoms if (bondflag) { if (bcolor == ATOM || bdiam == ATOM) comm_forward = 3; diff --git a/src/fix_balance.cpp b/src/fix_balance.cpp index 5ca1ec124a..83973efab7 100644 --- a/src/fix_balance.cpp +++ b/src/fix_balance.cpp @@ -239,7 +239,7 @@ void FixBalance::pre_exchange() /* ---------------------------------------------------------------------- compute final imbalance factor based on nlocal after comm->exchange() - only do this if rebalancing just occured + only do this if rebalancing just occurred ------------------------------------------------------------------------- */ void FixBalance::pre_neighbor() diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp index 9d84c4bb62..727065dafb 100644 --- a/src/fix_deform.cpp +++ b/src/fix_deform.cpp @@ -971,7 +971,7 @@ void FixDeform::restart(char *buf) set[i].hi_initial = set_restart[i].hi_initial; set[i].vol_initial = set_restart[i].vol_initial; set[i].tilt_initial = set_restart[i].tilt_initial; - // check if style settings are consitent (should do the whole set?) + // check if style settings are consistent (should do the whole set?) if (set[i].style != set_restart[i].style) samestyle = 0; if (set[i].substyle != set_restart[i].substyle) diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp index cfe9a9572e..604660e7c4 100644 --- a/src/fix_tmd.cpp +++ b/src/fix_tmd.cpp @@ -13,7 +13,7 @@ /* ---------------------------------------------------------------------- Contributing authors: Paul Crozier (SNL) - Christian Burisch (Bochum Univeristy, Germany) + Christian Burisch (Bochum University, Germany) ------------------------------------------------------------------------- */ #include "fix_tmd.h" diff --git a/src/hashlittle.cpp b/src/hashlittle.cpp index c3824b71fe..5c336c2082 100644 --- a/src/hashlittle.cpp +++ b/src/hashlittle.cpp @@ -173,7 +173,7 @@ uint32_t LAMMPS_NS::hashlittle(const void *key, size_t length, uint32_t initval) * rest of the string. Every machine with memory protection I've seen * does it on word boundaries, so is OK with this. But VALGRIND will * still catch it and complain. The masking trick does make the hash - * noticably faster for short strings (like English words). + * noticeably faster for short strings (like English words). */ #ifndef VALGRIND diff --git a/src/input.cpp b/src/input.cpp index 6adf37e847..7024814896 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -1177,7 +1177,7 @@ void Input::print() if (narg < 1) error->all(FLERR,"Illegal print command"); // copy 1st arg back into line (copy is being used) - // check maxline since arg[0] could have been exanded by variables + // check maxline since arg[0] could have been expanded by variables // substitute for $ variables (no printing) and print arg int n = strlen(arg[0]) + 1; diff --git a/src/kspace.h b/src/kspace.h index 4bae983364..5a0790b63d 100644 --- a/src/kspace.h +++ b/src/kspace.h @@ -64,7 +64,7 @@ class KSpace : protected Pointers { double accuracy; // accuracy of KSpace solver (force units) double accuracy_absolute; // user-specified accuracy in force units double accuracy_relative; // user-specified dimensionless accuracy - // accurary = acc_rel * two_charge_force + // accuracy = acc_rel * two_charge_force double accuracy_real_6; // real space accuracy for // dispersion solver (force units) double accuracy_kspace_6; // reciprocal space accuracy for diff --git a/src/lammps.cpp b/src/lammps.cpp index 4b09429b52..0e3ec7d062 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -785,7 +785,7 @@ void LAMMPS::create() /* ---------------------------------------------------------------------- check suffix consistency with installed packages - invoke package-specific deafult package commands + invoke package-specific default package commands only invoke if suffix is set and enabled also check if suffix2 is set called from LAMMPS constructor and after clear() command diff --git a/src/my_pool_chunk.h b/src/my_pool_chunk.h index a313e45f05..da196f5ec9 100644 --- a/src/my_pool_chunk.h +++ b/src/my_pool_chunk.h @@ -18,7 +18,7 @@ MyPoolChunk = templated class for storing chunks of datums in pages replaces many small mallocs with a few large mallocs pages are never freed, so can reuse w/out reallocs usage: - continously get() and put() chunks as needed + continuously get() and put() chunks as needed NOTE: could add a clear() if retain info on mapping of pages to bins inputs: template T = one datum, e.g. int, double, struct diff --git a/src/neigh_request.cpp b/src/neigh_request.cpp index 1ad111d9c5..006ff5e87b 100644 --- a/src/neigh_request.cpp +++ b/src/neigh_request.cpp @@ -37,7 +37,7 @@ NeighRequest::NeighRequest(LAMMPS *lmp) : Pointers(lmp) half = 1; full = 0; - // attribute flags, mutiple can be set to 1 + // attribute flags, multiple can be set to 1 // default is every reneighboring, not occasional // default is use newton_pair setting in force // default is no neighbors of ghosts diff --git a/src/pair_zero.h b/src/pair_zero.h index 058edbd053..3af37aedb4 100644 --- a/src/pair_zero.h +++ b/src/pair_zero.h @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. Pair zero is a dummy pair interaction useful for requiring a - force cutoff distance in the absense of pair-interactions or + force cutoff distance in the absence of pair-interactions or with hybrid/overlay if a larger force cutoff distance is required. This can be used in conjunction with bond/create to create bonds diff --git a/src/reset_ids.cpp b/src/reset_ids.cpp index 857738e841..4f81abd3fd 100644 --- a/src/reset_ids.cpp +++ b/src/reset_ids.cpp @@ -86,7 +86,7 @@ void ResetIDs::command(int narg, char ** /* arg */) tag[i] = 0; } - // assign new contigous IDs to owned atoms via tag_extend() + // assign new contiguous IDs to owned atoms via tag_extend() atom->tag_extend(); diff --git a/src/write_restart.cpp b/src/write_restart.cpp index 4b84e790b8..924584892b 100644 --- a/src/write_restart.cpp +++ b/src/write_restart.cpp @@ -299,7 +299,7 @@ void WriteRestart::write(char *file) // max_size = largest buffer needed by any proc // NOTE: are assuming size_restart() returns 32-bit int // for a huge one-proc problem, nlocal could be 32-bit - // but nlocal * doubles-peratom could oveflow + // but nlocal * doubles-peratom could overflow int max_size; int send_size = atom->avec->size_restart(); diff --git a/tools/amber2lmp/amber2lammps.py b/tools/amber2lmp/amber2lammps.py index 16b8ded46a..cb0820f96c 100644 --- a/tools/amber2lmp/amber2lammps.py +++ b/tools/amber2lmp/amber2lammps.py @@ -7,7 +7,7 @@ # # Modified by Vikas Varshney, U Akron, 5 July 2005, as described in README # Bug Fixed :Third argument in Dihedral Coeffs section is an integer - Ketan S Khare September 26, 2011 -# Modified by Vikas Varshney, Oct 8, 2013 to include additional flags (Atomic_Number, Coulombic and van der Waals 1-4 factors which are included in newer vesions of .top and .crd files in amber12. +# Modified by Vikas Varshney, Oct 8, 2013 to include additional flags (Atomic_Number, Coulombic and van der Waals 1-4 factors which are included in newer versions of .top and .crd files in amber12. #============================================================ diff --git a/tools/ch2lmp/charmm2lammps.pl b/tools/ch2lmp/charmm2lammps.pl index b53bd00541..c1ec8ad895 100755 --- a/tools/ch2lmp/charmm2lammps.pl +++ b/tools/ch2lmp/charmm2lammps.pl @@ -12,7 +12,7 @@ # - $project.psf ; CHARMM configs # - top_$forcefield.rtf ; # - par_$forcefield.prm ; -# Ouput: +# Output: # - $project.data ; LAMMPS data file # - $project.in ; LAMMPS input file # - $project_ctrl.pdb ; PDB control file @@ -329,7 +329,7 @@ } - sub PSFDihedrals # hack to accomodate + sub PSFDihedrals # hack to accommodate { # LAMMPS' way of calc $idihedral = 0; # LJ 1-4 interactions return $ndihedral if (($dihedral_flag = $ndihedral ? 1 : 0)); @@ -1785,7 +1785,7 @@ $C_flag = 0; } - # Quit if one of the atom types dosen't exist + # Quit if one of the atom types doesn't exist if ( $C_counter == 0 or ($CA_counter == 0 and $CA_GLY_counter == 0 and $CA_PRO_counter == 0) or ($N_counter == 0 and $N_PRO_counter == 0) ) { diff --git a/tools/ch2lmp/example/par_all27_na.prm b/tools/ch2lmp/example/par_all27_na.prm index b721c37393..542d30e917 100644 --- a/tools/ch2lmp/example/par_all27_na.prm +++ b/tools/ch2lmp/example/par_all27_na.prm @@ -124,7 +124,7 @@ ON2 P3 300.0 1.68 !PPI2, from nad/ppi, adm jr. 7/01 ON3 P3 480.0 1.53 !PPI2, from nad/ppi, adm jr. 7/01 ON4 P3 237.0 1.58 !PPI2, from MP_1, ADM Jr. NN5 HN1 460.0 1.01 !sugar model, adm jr. -!@@@@@@@@@ Begining of endocyclic bonds for deoxy-ribose @@@@@@@@@ +!@@@@@@@@@ Beginning of endocyclic bonds for deoxy-ribose @@@@@@@@@ CN7B ON6 260.0 1.420 ! From exp CN7B CN8 200.0 1.518 ! From exp CN7 ON6 240.0 1.446 ! Fom exp. @@ -135,21 +135,21 @@ CN7 HN7 309.0 1.111 !Alkanes, sacred CN8 HN8 309.0 1.111 !Alkanes, sacred CN7B HN7 309.0 1.111 ! From CN8 HN7 (NF) !@@@@@@@@@ End of endocyclic bonds for deoxy-ribose @@@@@@@@@ -!@@@@@@@@@ Begining of endocyclic bonds for ribose @@@@@@@@@ +!@@@@@@@@@ Beginning of endocyclic bonds for ribose @@@@@@@@@ CN7B ON6B 260.0 1.420 ! From CN7B ON6 CN7 ON6B 240.0 1.480 ! From CN7 ON6 CN7B CN7B 200.0 1.450 ! CN7 CN7B 222.5 1.460 ! Specific to RNA !@@@@@@@@@ End of endocyclic bonds for ribose @@@@@@@@@ -!@@@@@@@@@ Begining of endocyclic bonds for arabinose @@@@@@@@@ -! Transfered from DNA +!@@@@@@@@@ Beginning of endocyclic bonds for arabinose @@@@@@@@@ +! Transferred from DNA CN7B CN7C 200.0 1.518 ! For arabinose, from CN7B CN8 CN7 CN7C 222.5 1.516 ! For arabinose, from CN7 CN8 CN7C HN7 309.0 1.111 ! From CN8 HN7 !@@@@@@@@@ End of endocyclic bonds for arabinose @@@@@@@@@ -!@@@@@@@@@ Begining of exocyclic bonds for deoxy-ribose @@@@@@@@@ +!@@@@@@@@@ Beginning of exocyclic bonds for deoxy-ribose @@@@@@@@@ CN7 CN8B 222.5 1.512 ! From exp. CN8B ON2 320.0 1.44 ! From exp !CN8B ON5 250.0 1.44 ! From CN8B ON2 @@ -169,19 +169,19 @@ CN8B HN8 309.0 1.111 !Alkanes, sacred ON5 HN5 545.0 0.960 !RIBOSE, MeOH !@@@@@@@@@ End of exocyclic bonds for deoxy-ribose @@@@@@@@@ -!@@@@@@@@@ Begining of exocyclic bonds for ribose @@@@@@@@@ +!@@@@@@@@@ Beginning of exocyclic bonds for ribose @@@@@@@@@ !CN7B ON5 250.0 1.400 ! From CN7 ON5 CN7B ON5 428.0 1.400 ! check adm jr., !FC should be 428.000 based on Meoh !@@@@@@@@@ End of exocyclic bonds for ribose @@@@@@@@@ -!@@@@@@@@@ Begining of exocyclic bonds for arabinose @@@@@@@@@ +!@@@@@@@@@ Beginning of exocyclic bonds for arabinose @@@@@@@@@ !CN7C ON5 250.0 1.400 ! From CN7 ON5 CN7C ON5 428.0 1.400 ! check adm jr., !FC should be 428.000 based on Meoh !@@@@@@@@@ End of exocyclic bonds for arabinose @@@@@@@@@ -!@@@@@@@@@ Begining of bonds for nucleotide analogue @@@@@@@@@ +!@@@@@@@@@ Beginning of bonds for nucleotide analogue @@@@@@@@@ CN8 ON2 340.0 1.44 ! !@@@@@@@@@ End of bonds for nucleotide analogue @@@@@@@@@ @@ -1075,9 +1075,9 @@ CN7 ON6 CN7B NR1 0.0 3 0.0 CN7 ON6B CN7B NR1 0.0 3 0.0 ! RNUS NR1 CN7B CN8 CN7 0.0 3 0.0 !%%%%%%% new terms for dna and the deoxyribose-based model compounds %%%%%% -! The following is for: THF3P (model for espilon), THFM3P (model for puckering), +! The following is for: THF3P (model for epsilon), THFM3P (model for puckering), ! THF5P (model for gamma and beta), THFCH3IM (model for chi), nucleotide analogue -!@@@@@@ Begining of chi +!@@@@@@ Beginning of chi !============= added for torsion about chi in adenine ============ !For link from sugar to base: CN7B NN2 CN4 HN3 0.3 2 180.0 ! NF @@ -1214,7 +1214,7 @@ HN7 CN7B CN7B NN2B 0.0 3 0.0 HN7 CN7C CN7B NN2 0.0 3 0.0 HN7 CN7C CN7B NN2B 0.0 3 0.0 -!@@@@@@ Begining of torsions involving exocyclic sugar atoms: +!@@@@@@ Beginning of torsions involving exocyclic sugar atoms: !======= CN7 CN8B ON2 P = C4'-C5'-O5'-P CN7 CN8B ON2 P 0.2 1 120.0 !bet C4'-C5'-O5'-P, adm jr. ! the following differ significantly from the alcohols @@ -1354,7 +1354,7 @@ HN7 CN7 CN7 ON5 0.195 3 0.0 !======== CN7 CN7 ON2 P = C4'-C3'-O3'-P CN7 CN7 ON2 P 0.6 5 0.0 !eps CN7 CN7 ON2 P 0.2 4 0.0 !eps, locat of 200 mimima -CN7 CN7 ON2 P 0.0 3 180.0 !eps, barE beteen minima +CN7 CN7 ON2 P 0.0 3 180.0 !eps, barE between minima CN7 CN7 ON2 P 0.4 2 0.0 !eps, relE of 200 vs 275 min CN7 CN7 ON2 P 1.9 1 180.0 !eps !======== CN8 CN7 ON2 P = C2'-C3'-O3'-P @@ -1378,20 +1378,20 @@ CN7B CN7 ON5 HN5 0.8 3 0.0 ! RNA CN7B CN7 ON5 HN5 0.5 1 0.0 ! RNA CN7C CN7 ON5 HN5 0.8 3 0.0 ! Arabinose (from DNA) CN7C CN7 ON5 HN5 0.5 1 0.0 ! Arabinose (from DNA) -! Was simply transfered from HN7 CN7 ON2 P +! Was simply transferred from HN7 CN7 ON2 P ! adm jr. should convert to alcohol term (see ribose etc) HN7 CN7 ON5 HN5 0.0 3 0.0 HN7 CN7 CN8B HN8 0.195 3 0.0 !gam H-C4'-C5'-H HN7 CN7 CN7 CN8B 0.195 3 0.0 !gam H-C3'-C4'-C5' !@@@@@@ End of torsions involving exocyclic atoms: -!@@@@@@ Begining of torsions for endocyclic atoms only: +!@@@@@@ Beginning of torsions for endocyclic atoms only: CN8 CN7B ON6 CN7 0.6 6 180.0 !C2'-C1'-O4'-C4' CN8 CN7 CN7 ON6 0.0 3 0.0 !C2'-C3'-C4'-O4' CN7B CN7B ON6B CN7 0.0 6 0.0 ! RNA, Lowers barrier CN7B CN7 CN7 ON6B 0.0 3 0.0 ! RNA CN7C CN7B ON6 CN7 0.6 6 180.0 ! Arabinose (from DNA) CN7C CN7 CN7 ON6 0.0 3 0.0 ! Arabinose (from DNA) -!======== CN7 CN8 CN7B ON6 for nucleosides, transfered from ========= +!======== CN7 CN8 CN7B ON6 for nucleosides, transferred from ========= !======== CN7 CN8 CN8 ON6 from thfoh ============================== CN7 CN8 CN7B ON6 0.6 6 0.0 ! C3'-C2'-C1'-O4', adjust barrier CN7 CN7B CN7B ON6B 0.4 6 0.0 ! RNA @@ -1402,7 +1402,7 @@ CN7B CN8 CN7 CN7 0.4 6 0.0 ! good for amplitudes CN7B CN7B CN7 CN7 0.0 6 0.0 ! RNA CN7B CN7B CN8 CN7 0.0 6 0.0 ! RNA, 25P1 CN7B CN7C CN7 CN7 0.4 6 0.0 ! Arabinose (from DNA) -!======== CN7 CN7 ON6 CN7B for nucleosides, transfered from ======== +!======== CN7 CN7 ON6 CN7B for nucleosides, transferred from ======== !======== CN7 CN7 ON6 CN8 from thfohch3 ============================ CN7 CN7 ON6 CN7B 0.6 6 180.0 ! C3'-C4'-O4'-C1' CN7 CN7 ON6B CN7B 0.0 6 180.0 ! RNA @@ -1438,7 +1438,7 @@ HN7 CN7 CN7C HN7 0.195 3 0.0 !Arabinose (from DNA), H-C3'-C2'-H HN7 CN7C CN7 CN7 0.195 3 0.0 !Arabinose (from DNA), useful *cccc* !@@@@@@ End of torsions for endocyclic atoms only -!@@@@@@ Begining of torsions specifically defined for RNA @@@@@@ +!@@@@@@ Beginning of torsions specifically defined for RNA @@@@@@ ! N9-C1'-C2'-O2': NN2 CN7B CN7B ON5 0.000 3 0.0 ! Adenine and cytosine NN2B CN7B CN7B ON5 0.000 3 0.0 ! Guanine and uracil @@ -1461,7 +1461,7 @@ HN5 ON5 CN7B CN7 0.300 3 0.0 ! 030298 HN5 ON5 CN7B CN7 0.000 1 0.0 ! 030298 !@@@@@@ End of torsions specifically defined for RNA @@@@@@ -!@@@@@@ Begining of torsions specifically defined for arabinose @@@@@@ +!@@@@@@ Beginning of torsions specifically defined for arabinose @@@@@@ ON6 CN7B CN7C ON5 0.000 3 0.0 ! the following differ significantly from the protein based ! alcohol parameters (based on ethanol, see above) diff --git a/tools/colvars/abf_data.cpp b/tools/colvars/abf_data.cpp index 8b1ebd0a96..2ce2b927eb 100644 --- a/tools/colvars/abf_data.cpp +++ b/tools/colvars/abf_data.cpp @@ -82,7 +82,7 @@ ABFdata::ABFdata(const char *gradFileName) pos[i] = 0; for (unsigned int i = 0; i < scalar_dim; i++) { - // Here we do the Euclidian division iteratively + // Here we do the Euclidean division iteratively for (int k = Nvars - 1; k > 0; k--) { if (pos[k] == sizes[k]) { pos[k] = 0; @@ -213,7 +213,7 @@ void ABFdata::write_histogram(const char *fileName) pos[i] = 0; for (index = 0; index < scalar_dim; index++) { - // Here we do the Euclidian division iteratively + // Here we do the Euclidean division iteratively for (i = Nvars - 1; i > 0; i--) { if (pos[i] == sizes[i]) { pos[i] = 0; @@ -271,7 +271,7 @@ void ABFdata::write_bias(const char *fileName) } for (index = 0; index < scalar_dim; index++) { - // Here we do the Euclidian division iteratively + // Here we do the Euclidean division iteratively for (i = Nvars - 1; i > 0; i--) { if (pos[i] == sizes[i]) { pos[i] = 0; @@ -316,7 +316,7 @@ void ABFdata::write_field(double *field, const char *fileName) f = field; for (index = 0; index < scalar_dim; index++) { - // Here we do the Euclidian division iteratively + // Here we do the Euclidean division iteratively for (i = Nvars - 1; i > 0; i--) { if (pos[i] == sizes[i]) { pos[i] = 0; diff --git a/tools/doxygen/README b/tools/doxygen/README index c6a6229995..847acf2bb9 100644 --- a/tools/doxygen/README +++ b/tools/doxygen/README @@ -73,7 +73,7 @@ Results The doxygen documentation for LAMMPS is created in the following directories: - "tools/doxygen/doc" = LAMMPS documetation in "doxygen" html format. + "tools/doxygen/doc" = LAMMPS documentation in "doxygen" html format. In order to read the html documentation, start with loading the "index.html" file into an internet browser of choice from this directory. The generation of other formats (pdf, docbook, rtf or man) is disabled by default but can be diff --git a/tools/eff/lmp2radii.c b/tools/eff/lmp2radii.c index b62da070ba..f7ec790b1b 100644 --- a/tools/eff/lmp2radii.c +++ b/tools/eff/lmp2radii.c @@ -1759,7 +1759,7 @@ PyMODINIT_FUNC PyInit_lmp2radii(void) Py_ssize_t __pyx_5 = 0; PyObject *__pyx_6 = 0; __pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /*--- Libary function declarations ---*/ + /*--- Library function declarations ---*/ __pyx_init_filenames(); /*--- Initialize various global constants etc. ---*/ if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} diff --git a/tools/i-pi/drivers/LJ.f90 b/tools/i-pi/drivers/LJ.f90 index 342425f29e..8341c64be7 100644 --- a/tools/i-pi/drivers/LJ.f90 +++ b/tools/i-pi/drivers/LJ.f90 @@ -182,7 +182,7 @@ start = 1 DO i = 1, natoms - 1 - ! Only loops over the neigbour list, not all the atoms. + ! Only loops over the neighbour list, not all the atoms. DO j = start, index_list(i) CALL vector_separation(cell_h, cell_ih, atoms(i,:), atoms(n_list(j),:), rij, r2) IF (r2 < rc*rc) THEN ! Only calculates contributions between neighbouring particles. diff --git a/tools/i-pi/drivers/SG.f90 b/tools/i-pi/drivers/SG.f90 index 42d3e4945d..bb243b3469 100644 --- a/tools/i-pi/drivers/SG.f90 +++ b/tools/i-pi/drivers/SG.f90 @@ -250,7 +250,7 @@ start = 1 DO i = 1, natoms - 1 - ! Only loops over the neigbour list, not all the atoms. + ! Only loops over the neighbour list, not all the atoms. DO j = start, index_list(i) CALL vector_separation(cell_h, cell_ih, atoms(i,:), atoms(n_list(j),:), rij, r2) IF (r2 < rc*rc) THEN ! Only calculates contributions between neighbouring particles. diff --git a/tools/i-pi/ipi/engine/ensembles.py b/tools/i-pi/ipi/engine/ensembles.py index 9660ca983c..ef592405b0 100644 --- a/tools/i-pi/ipi/engine/ensembles.py +++ b/tools/i-pi/ipi/engine/ensembles.py @@ -104,7 +104,7 @@ class Ensemble(dobject): conserved quantity the dependencies are defined in bind. Args: - beads: The beads object from whcih the bead positions are taken. + beads: The beads object from which the bead positions are taken. nm: A normal modes object used to do the normal modes transformation. cell: The cell object from which the system box is taken. bforce: The forcefield object from which the force and virial are @@ -303,7 +303,7 @@ class NVTEnsemble(NVEEnsemble): higher simulation temperature, as is appropriate. Args: - beads: The beads object from whcih the bead positions are taken. + beads: The beads object from which the bead positions are taken. nm: A normal modes object used to do the normal modes transformation. cell: The cell object from which the system box is taken. bforce: The forcefield object from which the force and virial are @@ -422,7 +422,7 @@ class NPTEnsemble(NVTEnsemble): higher simulation temperature, as is appropriate. Args: - beads: The beads object from whcih the bead positions are taken. + beads: The beads object from which the bead positions are taken. nm: A normal modes object used to do the normal modes transformation. cell: The cell object from which the system box is taken. bforce: The forcefield object from which the force and virial are diff --git a/tools/i-pi/ipi/engine/outputs.py b/tools/i-pi/ipi/engine/outputs.py index fb5ebda96e..605d6a3b2d 100644 --- a/tools/i-pi/ipi/engine/outputs.py +++ b/tools/i-pi/ipi/engine/outputs.py @@ -85,7 +85,7 @@ class PropertyOutput(dobject): self.simul = simul # Checks as soon as possible if some asked-for properties are - # missing or mispelled + # missing or misspelled for what in self.outlist: key = getkey(what) if not key in self.simul.properties.property_dict.keys(): @@ -218,7 +218,7 @@ class TrajectoryOutput(dobject): self.simul = simul - # Checks as soon as possible if some asked-for trajs are missing or mispelled + # Checks as soon as possible if some asked-for trajs are missing or misspelled key = getkey(self.what) if not key in self.simul.trajs.traj_dict.keys(): print "Computable trajectories list: ", self.simul.trajs.traj_dict.keys() diff --git a/tools/i-pi/ipi/engine/properties.py b/tools/i-pi/ipi/engine/properties.py index a76aca1faf..e9c9646708 100644 --- a/tools/i-pi/ipi/engine/properties.py +++ b/tools/i-pi/ipi/engine/properties.py @@ -141,7 +141,7 @@ def help_latex(idict, standalone=True): } """ rstr += "\n\\begin{document}\n" - rstr += "The following are the different allowable ouputs:\n\\par" + rstr += "The following are the different allowable outputs:\n\\par" for out in sorted(idict): rstr += "\\ipiitem{" + out + "}" diff --git a/tools/i-pi/ipi/engine/simulation.py b/tools/i-pi/ipi/engine/simulation.py index 3c16a99621..eba03cc036 100644 --- a/tools/i-pi/ipi/engine/simulation.py +++ b/tools/i-pi/ipi/engine/simulation.py @@ -172,7 +172,7 @@ class Simulation(dobject): self.forces.run() - # prints inital configuration -- only if we are not restarting + # prints initial configuration -- only if we are not restarting if (self.step == 0): self.step = -1 for o in self.outputs: diff --git a/tools/i-pi/ipi/engine/thermostats.py b/tools/i-pi/ipi/engine/thermostats.py index 1fb048ec27..943deb47fd 100644 --- a/tools/i-pi/ipi/engine/thermostats.py +++ b/tools/i-pi/ipi/engine/thermostats.py @@ -532,9 +532,9 @@ class ThermoGLE(Thermostat): J. Chem. Phys. 134, 084104 (2011)). Attributes: - ns: The number of auxilliary degrees of freedom. + ns: The number of auxiliary degrees of freedom. s: An array holding all the momenta, including the ones for the - auxilliary degrees of freedom. + auxiliary degrees of freedom. Depend objects: A: Drift matrix giving the damping time scales for all the different @@ -560,7 +560,7 @@ class ThermoGLE(Thermostat): SST = Constants.kb*(self.C - np.dot(self.T,np.dot(self.C,self.T.T))) - # Uses a symetric decomposition rather than Cholesky, since it is more stable + # Uses a symmetric decomposition rather than Cholesky, since it is more stable return root_herm(SST) def get_C(self): @@ -675,10 +675,10 @@ class ThermoNMGLE(Thermostat): GLE for each normal mode Attributes: - ns: The number of auxilliary degrees of freedom. + ns: The number of auxiliary degrees of freedom. nb: The number of beads. s: An array holding all the momenta, including the ones for the - auxilliary degrees of freedom. + auxiliary degrees of freedom. Depend objects: A: Drift matrix giving the damping time scales for all the different diff --git a/tools/i-pi/ipi/tests/README b/tools/i-pi/ipi/tests/README index 17df9d7a7c..029c87a726 100644 --- a/tools/i-pi/ipi/tests/README +++ b/tools/i-pi/ipi/tests/README @@ -3,7 +3,7 @@ * This is the directory containing the tests that can be run with nosetests. * Files: - - common.py: Common helper funtions for use in the tests. + - common.py: Common helper functions for use in the tests. - datest.py: Tests the dependency utility and some of the numpy facilities. - test_*.py: The actual tests for at least some of the code basis. diff --git a/tools/i-pi/ipi/utils/depend.py b/tools/i-pi/ipi/utils/depend.py index 4b87323533..6c7f4ce24d 100644 --- a/tools/i-pi/ipi/utils/depend.py +++ b/tools/i-pi/ipi/utils/depend.py @@ -209,7 +209,7 @@ class depend_base(object): further down the dependency tree until either all objects have been tainted, or it reaches only objects that have already been tainted. Note that in the case of a dependency loop the initial setting of _tainted to - True prevents an infinite loop occuring. + True prevents an infinite loop occurring. Also, in the case of a synchro object, the manually set quantity is not tainted, as it is assumed that synchro objects only depend on each other. diff --git a/tools/i-pi/ipi/utils/inputvalue.py b/tools/i-pi/ipi/utils/inputvalue.py index d1bbc631fd..aae989a3c9 100644 --- a/tools/i-pi/ipi/utils/inputvalue.py +++ b/tools/i-pi/ipi/utils/inputvalue.py @@ -252,7 +252,7 @@ class Input(object): called, so that their tags are written between the start and end tags of this object, as is required for the xml format. - This also adds an indent to the lower levels of the xml heirarchy, + This also adds an indent to the lower levels of the xml hierarchy, so that it is easy to see which tags contain other tags. Args: diff --git a/tools/i-pi/ipi/utils/io/io_xml.py b/tools/i-pi/ipi/utils/io/io_xml.py index 5e43854408..fbf8867aaf 100644 --- a/tools/i-pi/ipi/utils/io/io_xml.py +++ b/tools/i-pi/ipi/utils/io/io_xml.py @@ -119,7 +119,7 @@ class xml_handler(ContentHandler): Adds the opening tag to the list of open tags, adds a new space in the buffer, reads the appropriate attributes and adds a new level to the - heirarchy. + hierarchy. Args: name: The tag_name. @@ -139,7 +139,7 @@ class xml_handler(ContentHandler): def characters(self, data): """Reads data. - Adds the data to the buffer of the current level of the heirarchy. + Adds the data to the buffer of the current level of the hierarchy. Data is read as a string, and needs to be converted to the required type later. diff --git a/tools/ipp/ipp b/tools/ipp/ipp index a7eac67247..081d19e243 100644 --- a/tools/ipp/ipp +++ b/tools/ipp/ipp @@ -2,7 +2,7 @@ # ipp: a preprocessor script # author : Reese Jones rjones@sandia.gov (based on dprepro [Sandia]) # to do : -# priority (overide file defaults e.g. a=1 pfile a=2 -> a=2) +# priority (override file defaults e.g. a=1 pfile a=2 -> a=2) # also order precedence: a=10 -p p.file b=12 # nested if/else/endif blocks diff --git a/tools/lmp2cfg/lmp2cfg.f b/tools/lmp2cfg/lmp2cfg.f index 80071f53db..14a5d5c56d 100644 --- a/tools/lmp2cfg/lmp2cfg.f +++ b/tools/lmp2cfg/lmp2cfg.f @@ -96,7 +96,7 @@ C clear data array. c-------------------------------------------------------------------- -c-------This section writes each ts to a seperate .cfg file---------- +c-------This section writes each ts to a separate .cfg file---------- ciframe='.cfg' write(snapshot,'(i5.5,a4)')iframe,ciframe open(unit=iframe+20,file=snapshot,status='new', diff --git a/tools/matlab/readdump_one.m b/tools/matlab/readdump_one.m index 762ca9bb20..7be751c888 100644 --- a/tools/matlab/readdump_one.m +++ b/tools/matlab/readdump_one.m @@ -124,7 +124,7 @@ varargout{1}.x_bound = x_bound; varargout{1}.y_bound = y_bound; varargout{1}.z_bound = z_bound; varargout{1}.atom_data = atom_data; -varargout{1}.position = p; %gives postion of ITEM: TIMESTEP line +varargout{1}.position = p; %gives position of ITEM: TIMESTEP line %------------------------------ fclose(dump); diff --git a/tools/matlab/readlog.m b/tools/matlab/readlog.m index 1fc88243ff..073b6c22ee 100644 --- a/tools/matlab/readlog.m +++ b/tools/matlab/readlog.m @@ -34,7 +34,7 @@ while feof(fid) == 0 end %------------------------------------------------------- - %---------Seperate column headings---------------------- + %---------Separate column headings---------------------- j=1; k=1; Ch=''; diff --git a/tools/matlab/readrdf.m b/tools/matlab/readrdf.m index 540bea7daf..4ec253942f 100644 --- a/tools/matlab/readrdf.m +++ b/tools/matlab/readrdf.m @@ -1,5 +1,5 @@ function varargout = readrdf(varargin) -% Function to read Radial Distribution Funtion output from LAMMPS +% Function to read Radial Distribution Function output from LAMMPS % Input % 'bin' --> number of bins in rdf histogram % 'runtime' --> Run length of each of the run commands diff --git a/tools/moltemplate/README.txt b/tools/moltemplate/README.txt index ca6a013244..97f68a85de 100644 --- a/tools/moltemplate/README.txt +++ b/tools/moltemplate/README.txt @@ -51,7 +51,7 @@ e.g. via: Updates to this distribution method are less frequent, than others, so if you need a more recent version, you can download it as a .tar.gz or .zip -archive from the moltemplate home page or GitHub (see linke above). After +archive from the moltemplate home page or GitHub (see link above). After downloading an archive and unpacking it, you should have 3 folders. moltemplate/ <-- source code and force fields @@ -65,7 +65,7 @@ the unpacked source archive: pip install . --user If you want to install into a system folder, then you need to run pip with -superuser priviledges. e.g. with: +superuser privileges. e.g. with: sudo pip install . diff --git a/tools/msi2lmp/frc_files/cvff.frc b/tools/msi2lmp/frc_files/cvff.frc index e3791aa86d..ba27e305e4 100644 --- a/tools/msi2lmp/frc_files/cvff.frc +++ b/tools/msi2lmp/frc_files/cvff.frc @@ -15,7 +15,7 @@ #version cvff.frc 2.4 01-Mar-02 ! Currently Insight does not handle version numbers on lines correctly. -! It uses the first occurence of a line, so when making changes you +! It uses the first occurrence of a line, so when making changes you ! can either comment the original out temporarily or put the correct ! line first. @@ -4624,7 +4624,7 @@ for silicate, copied directly from previous si and o parameters. @Date 07-Nov-91 #reference 15 -Adding a torsion parametr, cp cp o c = 1.8 so that the rotation barrier +Adding a torsion parameter, cp cp o c = 1.8 so that the rotation barrier around bond cp-o in anisole matches the experimental value ~3.0kcal/mole and the equilibrium geometry of anisole has torsion angle cp-cp-o-c =0 @Author Shenghua Shi diff --git a/tools/msi2lmp/frc_files/cvff_aug.frc b/tools/msi2lmp/frc_files/cvff_aug.frc index 75af9ace24..c9e19624fd 100644 --- a/tools/msi2lmp/frc_files/cvff_aug.frc +++ b/tools/msi2lmp/frc_files/cvff_aug.frc @@ -123,7 +123,7 @@ ! Currently Insight does not handle version numbers on lines correctly. -! It uses the first occurence of a line, so when making changes you +! It uses the first occurrence of a line, so when making changes you ! can either comment the original out temporarily or put the correct ! line first. @@ -5080,7 +5080,7 @@ for silicate, copied directly from previous si and o parameters. @Date 07-Nov-91 #reference 15 -Adding a torsion parametr, cp cp o c = 1.8 so that the rotation barrier +Adding a torsion parameter, cp cp o c = 1.8 so that the rotation barrier around bond cp-o in anisole matches the experimental value ~3.0kcal/mole and the equilibrium geometry of anisole has torsion angle cp-cp-o-c =0 @Author Shenghua Shi diff --git a/tools/msi2lmp/frc_files/oplsaa.frc b/tools/msi2lmp/frc_files/oplsaa.frc index fff69c819c..02a7dce867 100644 --- a/tools/msi2lmp/frc_files/oplsaa.frc +++ b/tools/msi2lmp/frc_files/oplsaa.frc @@ -1,6 +1,6 @@ !BIOSYM forcefield 1 -! This is a modified version of msi2lmp for use specifically wtih the +! This is a modified version of msi2lmp for use specifically with the ! OPLS force field. No out-of-plane or cross-terms are included. ! Atom types from SPC water and CLAYFF are also included. diff --git a/tools/msi2lmp/src/ReadCarFile.c b/tools/msi2lmp/src/ReadCarFile.c index 7932f7d6e2..7cde0914c4 100644 --- a/tools/msi2lmp/src/ReadCarFile.c +++ b/tools/msi2lmp/src/ReadCarFile.c @@ -227,7 +227,7 @@ void ReadCarFile(void) /* Search coordinates to find lowest and highest for x, y, and z */ if (periodic == 0) { - /* Added if/else statment STLM Oct 5 2010 */ + /* Added if/else statement STLM Oct 5 2010 */ if (TriclinicFlag == 0) { /* no need to re-center the box, if we use min/max values */ center[0] = center[1] = center[2] = 0.0; diff --git a/tools/phonon/dynmat.cpp b/tools/phonon/dynmat.cpp index 3b7bfe8268..36dcc97aba 100644 --- a/tools/phonon/dynmat.cpp +++ b/tools/phonon/dynmat.cpp @@ -408,7 +408,7 @@ void DynMat::EnforceASR() for (int i = 0; i < fftdim; ++i){ printf("%lg ", egvs[i]); if (i%10 == 9) printf("\n"); - if (i == 99){ printf("...... (%d more skiped)", fftdim-100); break;} + if (i == 99){ printf("...... (%d more skipped)", fftdim-100); break;} } printf("\n"); for (int i = 0; i < 80; ++i) printf("="); diff --git a/tools/phonon/green.cpp b/tools/phonon/green.cpp index 35514c03fb..16b2588a41 100644 --- a/tools/phonon/green.cpp +++ b/tools/phonon/green.cpp @@ -140,7 +140,7 @@ return; } /*------------------------------------------------------------------------------ - * Private method to compute the LDOS via the recusive method for system with + * Private method to compute the LDOS via the recursive method for system with * many atoms *----------------------------------------------------------------------------*/ void Green::Recursion() @@ -217,7 +217,7 @@ return; } /*------------------------------------------------------------------------------ - * Private method to compute the LDOS via the recusive method for system with + * Private method to compute the LDOS via the recursive method for system with * a few atoms (less than NMAX) *----------------------------------------------------------------------------*/ void Green::recursion() diff --git a/tools/polybond/lmpsdata.py b/tools/polybond/lmpsdata.py index 36cd6a0aa3..338090ed34 100644 --- a/tools/polybond/lmpsdata.py +++ b/tools/polybond/lmpsdata.py @@ -3,7 +3,7 @@ # lmpsdata.py # # For reading, writing and manipulating lammps data files -# For calculation of certain properities using lammps data files +# For calculation of certain proprieties using lammps data files # For creating VMD input text files using lammps data files # All x,y,z calculations assume the information includes image flags @@ -328,7 +328,7 @@ class Lmpsdata: if no modifications to any of the lammpsdata structures (modflag=0) Use Keywords to write lammpsdata structures directly if modifications to any of the lammpsdata structures (modflag=1) - Key Lammpsdata structures like atom numbers, coeficient numbers + Key Lammpsdata structures like atom numbers, coefficient numbers need to be modified to match the other modified lammpsdata structures This section will still use the keywords to write lammpsdata structures. For all modflags, the code will write data to the file until all of the @@ -403,7 +403,7 @@ class Lmpsdata: for line in self.atoms: f.write('\n') #creates a new line for adding body data for item in line: - f.write(' {0}'.format(item)) #adds in each peice of body data with space imbetween + f.write(' {0}'.format(item)) #adds in each piece of body data with space imbetween f.write('\n') #allows space to be added between the end of body data and a new keyword elif row=='Velocities': f.write('\n{0}'.format(row)) #new line between header and body portion or two body keywords @@ -411,7 +411,7 @@ class Lmpsdata: for line in self.velocities: f.write('\n') #creates a new line for adding body data for item in line: - f.write(' {0}'.format(item)) #adds in each peice of body data with space imbetween + f.write(' {0}'.format(item)) #adds in each piece of body data with space imbetween f.write('\n') #allows space to be added between the end of body data and a new keyword elif row=='Masses': f.write('\n{0}'.format(row)) #new line between header and body portion or two body keywords @@ -419,7 +419,7 @@ class Lmpsdata: for line in self.masses: f.write('\n') #creates a new line for adding body data for item in line: - f.write(' {0}'.format(item)) #adds in each peice of body data with space imbetween + f.write(' {0}'.format(item)) #adds in each piece of body data with space imbetween f.write('\n') #allows space to be added between the end of body data and a new keyword elif row=='Shapes': f.write('\n{0}'.format(row)) #new line between header and body portion or two body keywords @@ -427,7 +427,7 @@ class Lmpsdata: for line in self.shapes: f.write('\n') #creates a new line for adding body data for item in line: - f.write(' {0}'.format(item)) #adds in each peice of body data with space imbetween + f.write(' {0}'.format(item)) #adds in each piece of body data with space imbetween f.write('\n') #allows space to be added between the end of body data and a new keyword elif row=='Dipoles': f.write('\n{0}'.format(row)) #new line between header and body portion or two body keywords @@ -435,7 +435,7 @@ class Lmpsdata: for line in self.dipoles: f.write('\n') #creates a new line for adding body data for item in line: - f.write(' {0}'.format(item)) #adds in each peice of body data with space imbetween + f.write(' {0}'.format(item)) #adds in each piece of body data with space imbetween f.write('\n') #allows space to be added between the end of body data and a new keyword elif row=='Bonds': f.write('\n{0}'.format(row)) #new line between header and body portion or two body keywords @@ -443,7 +443,7 @@ class Lmpsdata: for line in self.bonds: f.write('\n') #creates a new line for adding body data for item in line: - f.write(' {0}'.format(item)) #adds in each peice of body data with space imbetween + f.write(' {0}'.format(item)) #adds in each piece of body data with space imbetween f.write('\n') #allows space to be added between the end of body data and a new keyword elif row=='Angles': f.write('\n{0}'.format(row)) #new line between header and body portion or two body keywords @@ -451,7 +451,7 @@ class Lmpsdata: for line in self.angles: f.write('\n') #creates a new line for adding body data for item in line: - f.write(' {0}'.format(item)) #adds in each peice of body data with space imbetween + f.write(' {0}'.format(item)) #adds in each piece of body data with space imbetween f.write('\n') #allows space to be added between the end of body data and a new keyword elif row=='Dihedrals': f.write('\n{0}'.format(row)) #new line between header and body portion or two body keywords @@ -459,14 +459,14 @@ class Lmpsdata: for line in self.dihedrals: f.write('\n') #creates a new line for adding body data for item in line: - f.write(' {0}'.format(item)) #adds in each peice of body data with space imbetween + f.write(' {0}'.format(item)) #adds in each piece of body data with space imbetween elif row=='Impropers': f.write('\n{0}'.format(row)) #new line between header and body portion or two body keywords f.write('\n') #new line between body keyword and body data for line in self.impropers: f.write('\n') #creates a new line for adding body data for item in line: - f.write(' {0}'.format(item)) #adds in each peice of body data with space imbetween + f.write(' {0}'.format(item)) #adds in each piece of body data with space imbetween f.write('\n') #allows space to be added between the end of body data and a new keyword elif row=='Pair Coeffs': f.write('\n{0}'.format(row)) #new line between header and body portion or two body keywords @@ -474,7 +474,7 @@ class Lmpsdata: for line in self.paircoef: f.write('\n') #creates a new line for adding body data for item in line: - f.write(' {0}'.format(item)) #adds in each peice of body data with space imbetween + f.write(' {0}'.format(item)) #adds in each piece of body data with space imbetween f.write('\n') #allows space to be added between the end of body data and a new keyword elif row=='Bond Coeffs': f.write('\n{0}'.format(row)) #new line between header and body portion or two body keywords @@ -482,7 +482,7 @@ class Lmpsdata: for line in self.bondcoef: f.write('\n') #creates a new line for adding body data for item in line: - f.write(' {0}'.format(item)) #adds in each peice of body data with space imbetween + f.write(' {0}'.format(item)) #adds in each piece of body data with space imbetween f.write('\n') #allows space to be added between the end of body data and a new keyword elif row=='Angle Coeffs': f.write('\n{0}'.format(row)) #new line between header and body portion or two body keywords @@ -490,7 +490,7 @@ class Lmpsdata: for line in self.anglecoef: f.write('\n') #creates a new line for adding body data for item in line: - f.write(' {0}'.format(item)) #adds in each peice of body data with space imbetween + f.write(' {0}'.format(item)) #adds in each piece of body data with space imbetween f.write('\n') #allows space to be added between the end of body data and a new keyword elif row=='Dihedral Coeffs': f.write('\n{0}'.format(row)) #new line between header and body portion or two body keywords @@ -498,7 +498,7 @@ class Lmpsdata: for line in self.dihedralcoef: f.write('\n') #creates a new line for adding body data for item in line: - f.write(' {0}'.format(item)) #adds in each peice of body data with space imbetween + f.write(' {0}'.format(item)) #adds in each piece of body data with space imbetween f.write('\n') #allows space to be added between the end of body data and a new keyword elif row=='Improper Coeffs': f.write('\n{0}'.format(row)) #new line between header and body portion or two body keywords @@ -506,7 +506,7 @@ class Lmpsdata: for line in self.impropercoef: f.write('\n') #creates a new line for adding body data for item in line: - f.write(' {0}'.format(item)) #adds in each peice of body data with space imbetween + f.write(' {0}'.format(item)) #adds in each piece of body data with space imbetween f.write('\n') #allows space to be added between the end of body data and a new keyword else: pass @@ -514,7 +514,7 @@ class Lmpsdata: def atomorder(self): """Takes self.atoms and organizes the atom id from least to greatest. - If the atom ids are allready ordered this algorithm will do nothing.""" + If the atom ids are already ordered this algorithm will do nothing.""" current=range(len(self.atoms[0])) # initialize current [assumes self.atoms coloumn #'s does not change] for i in range(1,len(self.atoms)): #when i=0, self.atoms will not change; therefore its skipped for k in range(len(self.atoms[i])): @@ -715,7 +715,7 @@ class Lmpsdata: extracts the individual molecules' data back into lmpsdata. This extraction takes place through a 4 step process. Step 1: Use a molecule's keywords to alter the lmpsdata data structures to empty. - To acomplish this procedure use the lmpsdata method deletebodydata. + To accomplish this procedure use the lmpsdata method deletebodydata. Step 2: Add the molecules' atoms to lmpsdata's atoms using the method addatoms. Return a list of atom id changes for each molecule. Step 3: Utilize each molecules list of atom id changes to change their data's atom id numbers. @@ -966,7 +966,7 @@ def distance(a,coord,atomtype): class particlesurface: def __init__(self,particle,cutoff,atomid,atomtype,shape='sphere'): """Builds a particle surface with a specific shape from a particle - The atoms choosen from the surface will have the specific atomid + The atoms chosen from the surface will have the specific atomid atomid will be given in terms of an integer and not a string.""" self.particle=particle.atoms self.atomtype=atomtype @@ -1026,7 +1026,7 @@ class particlesurface: def deleteatoms(self,structure,rows): """delete atoms from particle and shifts the structure down""" new=[] - #mulitple copying of b to the rows being replaced. + #multiple copying of b to the rows being replaced. if rows==[]: for line in structure: new.append(line) #if no rows need replacing copy structure @@ -1081,7 +1081,7 @@ class particlesurface: self.particle.append([]) self.surface.append([]) - pposition=len(self.particle)-1 #particle postion + pposition=len(self.particle)-1 #particle position sposition=len(self.surface)-1 #surface position # Adds the atom id number to the new row @@ -1122,7 +1122,7 @@ class particlesurface: def createxyz(self,file,data,routine='mass', values=None): - """This shows the particle surface. To show the particle surface after bonding has occured, + """This shows the particle surface. To show the particle surface after bonding has occurred, you will need to extract the particle than reinsert the particle into the class and use createxyz. Two possible routines one to use the masses from data and the other to use the atom type and values supplied by the user. The mass version is assessed by setting the routine to 'mass' which is the default method. @@ -1199,7 +1199,7 @@ def molecules(data,init,final,processors, method='all'): p.join() return molecule -class Lmpsmolecule: #Technically should be a meta class but written as a seperate class for easier coding. +class Lmpsmolecule: #Technically should be a meta class but written as a separate class for easier coding. def __init__(self,moleculenum,data,method): """initiates lammps molecule structures and than extract the appropriate molecular structures from the base class data""" @@ -1510,7 +1510,7 @@ class Lmpsmolecule: #Technically should be a meta class but written as a seperat """delete rows in a structure and shifts the structure up rows must be in increasing order for this algorithm to work correctly""" new=[] - #mulitple copying of b to the rows being replaced. + #multiple copying of b to the rows being replaced. if rows==[]: for line in structure: new.append(line) #if no rows need replacing copy structure @@ -1598,7 +1598,7 @@ class Lmpsmolecule: #Technically should be a meta class but written as a seperat if nextatoms[i]==atom: #checking if atom is in next atom del nextatoms[i] #delete the atom at i break - if nextatoms==[]: break #all bonds from find bonds have allready been added to bondedatoms + if nextatoms==[]: break #all bonds from find bonds have already been added to bondedatoms #append next atoms into bondedatoms #copy next atoms into prevatoms @@ -1607,7 +1607,7 @@ class Lmpsmolecule: #Technically should be a meta class but written as a seperat bondedatoms.append(atom) prevatoms.append(atom) - #iterative proccess for finding the rest of the atoms bonded to atomnumbers in the direction of atomid. + #iterative process for finding the rest of the atoms bonded to atomnumbers in the direction of atomid. while prevatoms!=[]: nextatoms=self.findbonds(prevatoms) #need to remove atoms from nextatoms which are in the prevatoms @@ -1616,7 +1616,7 @@ class Lmpsmolecule: #Technically should be a meta class but written as a seperat if nextatoms[i]==atom: #checking if atom is in next atom del nextatoms[i] #delete the atom at i break - if nextatoms==[]: break #all bonds from find bonds have allready been added to bondedatoms + if nextatoms==[]: break #all bonds from find bonds have already been added to bondedatoms #append next atoms into bondedatoms #copy next atoms into prevatoms @@ -1694,8 +1694,8 @@ class Lmpsmolecule: #Technically should be a meta class but written as a seperat def listorder(self,struct): """Takes struct and organizes the list from least to greatest. - If the list is allready ordered this algorithm will do nothing.""" - if len(struct)==1: return struct #with the length at 1; thier is only one element and theirfore nothing to order + If the list is already ordered this algorithm will do nothing.""" + if len(struct)==1: return struct #with the length at 1; there is only one element and therefore nothing to order for i in range(1,len(struct)): #when i=0, struct will not change; therefore its skipped copy=struct[i] for j in range(i-1,-1,-1): @@ -1756,8 +1756,8 @@ class Lmpsmolecule: #Technically should be a meta class but written as a seperat The second index correspons with the molecule/particle combination The third index corresponds with whether the value is the molecule or the particle Always bonds the two ends of the molecule that meet cutoff requirement. - All other possible bonds are randomly choosen until the required bondnumbers are met. - After every bond is choosen, the particle object's boolean list is updated, and possiblebonds is updated. + All other possible bonds are randomly chosen until the required bondnumbers are met. + After every bond is chosen, the particle object's boolean list is updated, and possiblebonds is updated. The update to possiblebonds involves removing the row from which the bonded molecule's atom is located and also removing the particle atom and it's corresponding bonded atom from other rows of possiblebonds. The final bonds are all stored in self.bonding as a 2 dimensional list""" @@ -1896,7 +1896,7 @@ class Lmpsmolecule: #Technically should be a meta class but written as a seperat # Alters the charge of the molecule's atoms bonded to the particle to newcharge self.modifyatom(self.bondinginformation[i][0]+1,3,newcharge) - #This is a seperate loop so atom id's and row indexes for previous steps wont get out of sync + #This is a separate loop so atom id's and row indexes for previous steps wont get out of sync #create atomnumbers to begin deletion process. atomnumbers=[] for i in range(len(self.bondinginformation)): @@ -1906,7 +1906,7 @@ class Lmpsmolecule: #Technically should be a meta class but written as a seperat #Than delete those atoms and all molecule structures which contain those atoms. self.deleteatoms(atomnumbers,atomid) - print 'begining deletion process of the surface atoms for which the molecule atoms have replaced' + print 'beginning deletion process of the surface atoms for which the molecule atoms have replaced' #Goes through the bondinginformation and superficially removes the surfaceatom for i in range(len(self.bondinginformation)): particle.removesurfatom(self.bondinginformation[i][1]) #uses the row number diff --git a/tools/pymol_asphere/src/cartesian.cpp b/tools/pymol_asphere/src/cartesian.cpp index a244d07dac..e137c51e7a 100644 --- a/tools/pymol_asphere/src/cartesian.cpp +++ b/tools/pymol_asphere/src/cartesian.cpp @@ -879,7 +879,7 @@ double c::closest_approach(const cPt &l1_1, const cPt &l1_2, const cPt &l2_1, double tc, tN, tD = D; // compute the closest points between the two lines - if (D < 0.00000000001) { // parrallel lines + if (D < 0.00000000001) { // parallel lines sN = 0.0; sD = 1.0; tN = e; tD = c; } else { // get the closest points on the infinite lines sN = (b*e - c*d); @@ -936,7 +936,7 @@ void c::closest_approach_points(const cPt &l1_1, const cPt &l1_2, double tc, tN, tD = D; // compute the closest points between the two lines - if (D < 0.00000000001) { // parrallel lines + if (D < 0.00000000001) { // parallel lines sN = 0.0; sD = 1.0; tN = e; tD = c; } else { // get the closest points on the infinite lines sN = (b*e - c*d); diff --git a/tools/pymol_asphere/src/error.h b/tools/pymol_asphere/src/error.h index f14af6f253..c0775d6506 100644 --- a/tools/pymol_asphere/src/error.h +++ b/tools/pymol_asphere/src/error.h @@ -112,7 +112,7 @@ class Notice { * to format it for the string. Forced newlines can be specified with \n * * Programs can check whether or not errors have been generated using the [] - * operator and can 'handle' them by outputing the message or dismissing + * operator and can 'handle' them by outputting the message or dismissing * them without any output * * Notices are generated using the public Notice class (see Notice()) diff --git a/tools/reax/reaxc_bond.pl b/tools/reax/reaxc_bond.pl index 9b0fa50672..cc0fd8f238 100755 --- a/tools/reax/reaxc_bond.pl +++ b/tools/reax/reaxc_bond.pl @@ -126,7 +126,7 @@ sub bonds { } close (OUTPUT2); #close the temp file as output - open INPUT3, ") { next if(/Frame/); split; diff --git a/tools/replica/reorder_remd_traj.py b/tools/replica/reorder_remd_traj.py index 5f4f316b14..01a179351d 100644 --- a/tools/replica/reorder_remd_traj.py +++ b/tools/replica/reorder_remd_traj.py @@ -160,7 +160,7 @@ def get_byte_index(rep_inds, byteindfns, intrajfns): :param intrajfns: list of (unordered) input traj filenames """ for n in rep_inds: - # check if the byte indices for this traj has aleady been computed + # check if the byte indices for this traj has already been computed if os.path.isfile(byteindfns[n]): continue # extract bytes diff --git a/tools/spin/interpolate_gneb/README b/tools/spin/interpolate_gneb/README index ab30373249..cf52ccb274 100644 --- a/tools/spin/interpolate_gneb/README +++ b/tools/spin/interpolate_gneb/README @@ -20,7 +20,7 @@ geodesic dist to next replica All those information can be provided by the verbose output of a neb/spin calculation -The progam outputs the interpolation result, and the +The program outputs the interpolation result, and the interpolated MEP in "interpolation_result.dat". This code is a courtesy of Aleksei Ivanov, University of diff --git a/tools/xmgrace/lammpsplot.cpp b/tools/xmgrace/lammpsplot.cpp index 7badb5652b..848c53a091 100644 --- a/tools/xmgrace/lammpsplot.cpp +++ b/tools/xmgrace/lammpsplot.cpp @@ -29,7 +29,7 @@ public: }; -/* This function splits the sentence into array of strings seperated by " "*/ +/* This function splits the sentence into array of strings separated by " "*/ sentence split(const string& s) { sentence a; s_type i=0;