From 1a77135ed65b932eadbc646df4e0114ed3c62cfe Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 21 Jun 2017 09:38:10 -0400 Subject: [PATCH] whitespace cleanup in docs --- doc/src/Section_commands.txt | 2 +- doc/src/Section_howto.txt | 44 +++---- doc/src/Section_packages.txt | 174 +++++++++++++-------------- doc/src/Section_python.txt | 2 +- doc/src/accelerate_intel.txt | 36 +++--- doc/src/bond_oxdna.txt | 8 +- doc/src/compute_cnp_atom.txt | 2 +- doc/src/dump_vtk.txt | 4 +- doc/src/fix_box_relax.txt | 2 +- doc/src/fix_eos_table_rx.txt | 28 ++--- doc/src/fix_filter_corotate.txt | 4 +- doc/src/fix_gcmc.txt | 2 +- doc/src/fix_grem.txt | 6 +- doc/src/fix_ipi.txt | 12 +- doc/src/fix_mscg.txt | 4 +- doc/src/fix_nve_dot.txt | 8 +- doc/src/fix_nve_dotc_langevin.txt | 32 ++--- doc/src/fix_nvk.txt | 2 +- doc/src/fix_spring.txt | 2 +- doc/src/neb.txt | 2 +- doc/src/pair_agni.txt | 12 +- doc/src/pair_buck.txt | 2 +- doc/src/pair_exp6_rx.txt | 26 ++-- doc/src/pair_kolmogorov_crespi_z.txt | 24 ++-- doc/src/pair_multi_lucy_rx.txt | 6 +- doc/src/pair_oxdna.txt | 18 +-- doc/src/pair_oxdna2.txt | 16 +-- doc/src/pair_table_rx.txt | 6 +- doc/src/python.txt | 2 +- doc/src/tutorial_github.txt | 2 +- doc/src/tutorial_pylammps.txt | 18 +-- 31 files changed, 254 insertions(+), 254 deletions(-) diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index bcffc30549..0fbab732c8 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -1073,7 +1073,7 @@ package"_Section_start.html#start_3. "table/rx"_pair_table_rx.html, "tersoff/table (o)"_pair_tersoff.html, "thole"_pair_thole.html, -"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c) +"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c) :line diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt index 579cb68474..f2f2561af8 100644 --- a/doc/src/Section_howto.txt +++ b/doc/src/Section_howto.txt @@ -1938,7 +1938,7 @@ documentation in the src/library.cpp file for details, including which quantities can be queried by name: void *lammps_extract_global(void *, char *) -void lammps_extract_box(void *, double *, double *, +void lammps_extract_box(void *, double *, double *, double *, double *, double *, int *, int *) void *lammps_extract_atom(void *, char *) void *lammps_extract_compute(void *, char *, int, int) @@ -2682,14 +2682,14 @@ bond_coeff 2 25.724 0.0 :pre When running dynamics with the adiabatic core/shell model, the following issues should be considered. The relative motion of -the core and shell particles corresponds to the polarization, -hereby an instantaneous relaxation of the shells is approximated +the core and shell particles corresponds to the polarization, +hereby an instantaneous relaxation of the shells is approximated and a fast core/shell spring frequency ensures a nearly constant -internal kinetic energy during the simulation. +internal kinetic energy during the simulation. Thermostats can alter this polarization behaviour, by scaling the -internal kinetic energy, meaning the shell will not react freely to -its electrostatic environment. -Therefore it is typically desirable to decouple the relative motion of +internal kinetic energy, meaning the shell will not react freely to +its electrostatic environment. +Therefore it is typically desirable to decouple the relative motion of the core/shell pair, which is an imaginary degree of freedom, from the real physical system. To do that, the "compute temp/cs"_compute_temp_cs.html command can be used, in conjunction with @@ -2721,13 +2721,13 @@ fix thermostatequ all nve # integrator as needed f fix_modify thermoberendsen temp CSequ thermo_modify temp CSequ # output of center-of-mass derived temperature :pre -The pressure for the core/shell system is computed via the regular -LAMMPS convention by "treating the cores and shells as individual -particles"_#MitchellFincham2. For the thermo output of the pressure -as well as for the application of a barostat, it is necessary to -use an additional "pressure"_compute_pressure compute based on the -default "temperature"_compute_temp and specifying it as a second -argument in "fix modify"_fix_modify.html and +The pressure for the core/shell system is computed via the regular +LAMMPS convention by "treating the cores and shells as individual +particles"_#MitchellFincham2. For the thermo output of the pressure +as well as for the application of a barostat, it is necessary to +use an additional "pressure"_compute_pressure compute based on the +default "temperature"_compute_temp and specifying it as a second +argument in "fix modify"_fix_modify.html and "thermo_modify"_thermo_modify.html resulting in: (...) @@ -2757,18 +2757,18 @@ temp/cs"_compute_temp_cs.html command to the {temp} keyword of the velocity all create 1427 134 bias yes temp CSequ velocity all scale 1427 temp CSequ :pre -To maintain the correct polarizability of the core/shell pairs, the -kinetic energy of the internal motion shall remain nearly constant. -Therefore the choice of spring force and mass ratio need to ensure -much faster relative motion of the 2 atoms within the core/shell pair -than their center-of-mass velocity. This allows the shells to -effectively react instantaneously to the electrostatic environment and +To maintain the correct polarizability of the core/shell pairs, the +kinetic energy of the internal motion shall remain nearly constant. +Therefore the choice of spring force and mass ratio need to ensure +much faster relative motion of the 2 atoms within the core/shell pair +than their center-of-mass velocity. This allows the shells to +effectively react instantaneously to the electrostatic environment and limits energy transfer to or from the core/shell oscillators. This fast movement also dictates the timestep that can be used. The primary literature of the adiabatic core/shell model suggests that the fast relative motion of the core/shell pairs only allows negligible -energy transfer to the environment. +energy transfer to the environment. The mentioned energy transfer will typically lead to a small drift in total energy over time. This internal energy can be monitored using the "compute chunk/atom"_compute_chunk_atom.html and "compute @@ -2790,7 +2790,7 @@ pairs as chunks. For example if core/shell pairs are the only molecules: -read_data NaCl_CS_x0.1_prop.data +read_data NaCl_CS_x0.1_prop.data compute prop all property/atom molecule compute cs_chunk all chunk/atom c_prop compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt index 14b2c0baa3..24506379c3 100644 --- a/doc/src/Section_packages.txt +++ b/doc/src/Section_packages.txt @@ -585,7 +585,7 @@ do not recommend building with other acceleration packages installed make yes-kokkos make machine :pre - + make no-kokkos make machine :pre @@ -839,13 +839,13 @@ written and read in parallel. Note that MPIIO is part of the standard message-passing interface (MPI) library, so you should not need any additional compiler or link settings, beyond what LAMMPS normally uses for MPI on your system. - + make yes-mpiio make machine :pre - + make no-mpiio make machine :pre - + [Supporting info:] src/MPIIO: filenames -> commands @@ -855,7 +855,7 @@ src/MPIIO: filenames -> commands "read_restart"_read_restart.html :ul :line - + MSCG package :link(mscg),h4 [Contents:] @@ -914,7 +914,7 @@ lib/mscg/README examples/mscg :ul :line - + OPT package :link(OPT),h4 [Contents:] @@ -1387,7 +1387,7 @@ atomic information to continuum fields. [Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia). [Install or un-install:] - + Before building LAMMPS with this package, you must first build the ATC library in lib/atc. You can do this manually if you prefer; follow the instructions in lib/atc/README. You can also do it in one step @@ -1420,10 +1420,10 @@ usual manner: make yes-user-atc make machine :pre - + make no-user-atc make machine :pre - + [Supporting info:] src/USER-ATC: filenames -> commands @@ -1446,7 +1446,7 @@ model. [Author:] Ilya Valuev (JIHT, Russia). [Install or un-install:] - + Before building LAMMPS with this package, you must first build the AWPMD library in lib/awpmd. You can do this manually if you prefer; follow the instructions in lib/awpmd/README. You can also do it in @@ -1479,10 +1479,10 @@ usual manner: make yes-user-awpmd make machine :pre - + make no-user-awpmd make machine :pre - + [Supporting info:] src/USER-AWPMD: filenames -> commands @@ -1505,13 +1505,13 @@ stability. [Author:] Oliver Henrich (University of Strathclyde, Glasgow). [Install or un-install:] - + make yes-user-cgdna make machine :pre - + make no-user-cgdna make machine :pre - + [Supporting info:] src/USER-CGDNA: filenames -> commands @@ -1536,13 +1536,13 @@ acids. [Author:] Axel Kohlmeyer (Temple U). [Install or un-install:] - + make yes-user-cgsdk make machine :pre - + make no-user-cgsdk make machine :pre - + [Supporting info:] src/USER-CGSDK: filenames -> commands @@ -1570,7 +1570,7 @@ by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and Jerome Henin (LISM, CNRS, Marseille, France). [Install or un-install:] - + Before building LAMMPS with this package, you must first build the COLVARS library in lib/colvars. You can do this manually if you prefer; follow the instructions in lib/colvars/README. You can also @@ -1594,10 +1594,10 @@ usual manner: make yes-user-colvars make machine :pre - + make no-user-colvars make machine :pre - + [Supporting info:] src/USER-COLVARS: filenames -> commands @@ -1619,13 +1619,13 @@ intensities based on kinematic diffraction theory. [Author:] Shawn Coleman while at the U Arkansas. [Install or un-install:] - + make yes-user-diffraction make machine :pre - + make no-user-diffraction make machine :pre - + [Supporting info:] src/USER-DIFFRACTION: filenames -> commands @@ -1654,13 +1654,13 @@ algorithm. Brennan (ARL). [Install or un-install:] - + make yes-user-dpd make machine :pre - + make no-user-dpd make machine :pre - + [Supporting info:] src/USER-DPD: filenames -> commands @@ -1696,13 +1696,13 @@ tools/drude. Devemy (CNRS), and Agilio Padua (U Blaise Pascal). [Install or un-install:] - + make yes-user-drude make machine :pre - + make no-user-drude make machine :pre - + [Supporting info:] src/USER-DRUDE: filenames -> commands @@ -1734,13 +1734,13 @@ tools/eff; see its README file. [Author:] Andres Jaramillo-Botero (CalTech). [Install or un-install:] - + make yes-user-eff make machine :pre - + make no-user-eff make machine :pre - + [Supporting info:] src/USER-EFF: filenames -> commands @@ -1773,13 +1773,13 @@ for using this package in tools/fep; see its README file. [Author:] Agilio Padua (Universite Blaise Pascal Clermont-Ferrand) [Install or un-install:] - + make yes-user-fep make machine :pre - + make no-user-fep make machine :pre - + [Supporting info:] src/USER-FEP: filenames -> commands @@ -1836,13 +1836,13 @@ file. You can then install/un-install the package and build LAMMPS in the usual manner: - + make yes-user-h5md make machine :pre - + make no-user-h5md make machine :pre - + [Supporting info:] src/USER-H5MD: filenames -> commands @@ -1908,7 +1908,7 @@ explained in "Section 5.3.2"_accelerate_intel.html. make yes-user-intel yes-user-omp make machine :pre - + make no-user-intel no-user-omp make machine :pre @@ -1938,13 +1938,13 @@ can be used to model MD particles influenced by hydrodynamic forces. Ontario). [Install or un-install:] - + make yes-user-lb make machine :pre - + make no-user-lb make machine :pre - + [Supporting info:] src/USER-LB: filenames -> commands @@ -1972,13 +1972,13 @@ matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL. [Authors:] Tomas Oppelstrup and John Moriarty (LLNL). [Install or un-install:] - + make yes-user-mgpt make machine :pre - + make no-user-mgpt make machine :pre - + [Supporting info:] src/USER-MGPT: filenames -> commands @@ -2000,13 +2000,13 @@ dihedral, improper, or command style. src/USER-MISC/README file. [Install or un-install:] - + make yes-user-misc make machine :pre - + make no-user-misc make machine :pre - + [Supporting info:] src/USER-MISC: filenames -> commands @@ -2031,13 +2031,13 @@ n = grad(g). Netherlands; since 2017: Brandeis University, Waltham, MA, USA) [Install or un-install:] - + make yes-user-manifold make machine :pre - + make no-user-manifold make machine :pre - + [Supporting info:] src/USER-MANIFOLD: filenames -> commands @@ -2080,7 +2080,7 @@ at [Author:] Axel Kohlmeyer (Temple U). [Install or un-install:] - + Note that the lib/molfile/Makefile.lammps file has a setting for a dynamic loading library libdl.a that should is typically present on all systems, which is required for LAMMPS to link with this package. @@ -2090,10 +2090,10 @@ lib/molfile/Makefile.lammps for details. make yes-user-molfile make machine :pre - + make no-user-molfile make machine :pre - + [Supporting info:] src/USER-MOLFILE: filenames -> commands @@ -2128,7 +2128,7 @@ tools: [Author:] Lars Pastewka (Karlsruhe Institute of Technology). [Install or un-install:] - + Note that to follow these steps, you need the standard NetCDF software package installed on your system. The lib/netcdf/Makefile.lammps file has settings for NetCDF include and library files that LAMMPS needs to @@ -2138,7 +2138,7 @@ lib/netcdf/README for details. make yes-user-netcdf make machine :pre - + make no-user-netcdf make machine :pre @@ -2178,10 +2178,10 @@ Once you have an appropriate Makefile.machine, you can install/un-install the package and build LAMMPS in the usual manner: [Install or un-install:] - + make yes-user-omp make machine :pre - + make no-user-omp make machine :pre @@ -2213,13 +2213,13 @@ relations, directly from molecular dynamics simulations. [Author:] Ling-Ti Kong (Shanghai Jiao Tong University). [Install or un-install:] - + make yes-user-phonon make machine :pre - + make no-user-phonon make machine :pre - + [Supporting info:] src/USER-PHONON: filenames -> commands @@ -2235,7 +2235,7 @@ USER-QMMM package :link(USER-QMMM),h4 A "fix qmmm"_fix_qmmm.html command which allows LAMMPS to be used in a QM/MM simulation, currently only in combination with the "Quantum -ESPRESSO"_espresso package. +ESPRESSO"_espresso package. :link(espresso,http://www.quantum-espresso.org) @@ -2275,7 +2275,7 @@ usual manner: make yes-user-qmmm make machine :pre - + make no-user-qmmm make machine :pre @@ -2284,7 +2284,7 @@ for a QM/MM simulation. You must also build Quantum ESPRESSO and create a new executable which links LAMMPS and Quanutm ESPRESSO together. These are steps 3 and 4 described in the lib/qmmm/README file. - + [Supporting info:] src/USER-QMMM: filenames -> commands @@ -2312,13 +2312,13 @@ simulation. [Author:] Yuan Shen (Stanford U). [Install or un-install:] - + make yes-user-qtb make machine :pre - + make no-user-qtb make machine :pre - + [Supporting info:] src/USER-QTB: filenames -> commands @@ -2362,10 +2362,10 @@ usual manner: make yes-user-quip make machine :pre - + make no-user-quip make machine :pre - + [Supporting info:] src/USER-QUIP: filenames -> commands @@ -2388,13 +2388,13 @@ for monitoring molecules as bonds are created and destroyed. [Author:] Hasan Metin Aktulga (MSU) while at Purdue University. [Install or un-install:] - + make yes-user-reaxc make machine :pre - + make no-user-reaxc make machine :pre - + [Supporting info:] src/USER-REAXC: filenames -> commands @@ -2451,10 +2451,10 @@ usual manner: make yes-user-smd make machine :pre - + make no-user-smd make machine :pre - + [Supporting info:] src/USER-SMD: filenames -> commands @@ -2477,13 +2477,13 @@ ionocovalent bonds in oxides. Tetot (LAAS-CNRS, France). [Install or un-install:] - + make yes-user-smtbq make machine :pre - + make no-user-smtbq make machine :pre - + [Supporting info:] src/USER-SMTBQ: filenames -> commands @@ -2516,13 +2516,13 @@ property/atom"_compute_property_atom.html command. Dynamics, Ernst Mach Institute, Germany). [Install or un-install:] - + make yes-user-sph make machine :pre - + make no-user-sph make machine :pre - + [Supporting info:] src/USER-SPH: filenames -> commands @@ -2544,13 +2544,13 @@ stress, etc) about individual interactions. [Author:] Axel Kohlmeyer (Temple U). [Install or un-install:] - + make yes-user-tally make machine :pre - + make no-user-tally make machine :pre - + [Supporting info:] src/USER-TALLY: filenames -> commands @@ -2577,7 +2577,7 @@ system. [Authors:] Richard Berger (JKU) and Daniel Queteschiner (DCS Computing). [Install or un-install:] - + The lib/vtk/Makefile.lammps file has settings for accessing VTK files and its library, which are required for LAMMPS to build and link with this package. If the settings are not valid for your system, check if @@ -2590,10 +2590,10 @@ usual manner: make yes-user-vtk make machine :pre - + make no-user-vtk make machine :pre - + [Supporting info:] src/USER-VTK: filenames -> commands diff --git a/doc/src/Section_python.txt b/doc/src/Section_python.txt index 718e9e229c..1e67fca321 100644 --- a/doc/src/Section_python.txt +++ b/doc/src/Section_python.txt @@ -714,7 +714,7 @@ stored in the "image" property. All three image flags are stored in a packed format in a single integer, so count would be 1 to retrieve that integer, however also a count value of 3 can be used and then the image flags will be unpacked into 3 individual integers, ordered -in a similar fashion as coordinates. +in a similar fashion as coordinates. Note that the data structure gather_atoms("x") returns is different from the data structure returned by extract_atom("x") in four ways. diff --git a/doc/src/accelerate_intel.txt b/doc/src/accelerate_intel.txt index ed9e4ae833..f5bd66aeba 100644 --- a/doc/src/accelerate_intel.txt +++ b/doc/src/accelerate_intel.txt @@ -42,11 +42,11 @@ precision mode. Performance improvements are shown compared to LAMMPS {without using other acceleration packages} as these are under active development (and subject to performance changes). The measurements were performed using the input files available in -the src/USER-INTEL/TEST directory with the provided run script. -These are scalable in size; the results given are with 512K -particles (524K for Liquid Crystal). Most of the simulations are +the src/USER-INTEL/TEST directory with the provided run script. +These are scalable in size; the results given are with 512K +particles (524K for Liquid Crystal). Most of the simulations are standard LAMMPS benchmarks (indicated by the filename extension in -parenthesis) with modifications to the run length and to add a +parenthesis) with modifications to the run length and to add a warmup run (for use with offload benchmarks). :c,image(JPG/user_intel.png) @@ -64,30 +64,30 @@ simulation rates and instructions to reproduce. In most molecular dynamics software, parallelization parameters (# of MPI, OpenMP, and vectorization) can change the results due -to changing the order of operations with finite-precision +to changing the order of operations with finite-precision calculations. The USER-INTEL package is deterministic. This means that the results should be reproducible from run to run with the -{same} parallel configurations and when using determinstic +{same} parallel configurations and when using determinstic libraries or library settings (MPI, OpenMP, FFT). However, there are differences in the USER-INTEL package that can change the order of operations compared to LAMMPS without acceleration: Neighbor lists can be created in a different order :ulb,l Bins used for sorting atoms can be oriented differently :l -The default stencil order for PPPM is 7. By default, LAMMPS will -calculate other PPPM parameters to fit the desired acuracy with +The default stencil order for PPPM is 7. By default, LAMMPS will +calculate other PPPM parameters to fit the desired acuracy with this order :l The {newton} setting applies to all atoms, not just atoms shared between MPI tasks :l Vectorization can change the order for adding pairwise forces :l :ule -The precision mode (described below) used with the USER-INTEL -package can change the {accuracy} of the calculations. For the -default {mixed} precision option, calculations between pairs or -triplets of atoms are performed in single precision, intended to +The precision mode (described below) used with the USER-INTEL +package can change the {accuracy} of the calculations. For the +default {mixed} precision option, calculations between pairs or +triplets of atoms are performed in single precision, intended to be within the inherent error of MD simulations. All accumulation -is performed in double precision to prevent the error from growing +is performed in double precision to prevent the error from growing with the number of atoms in the simulation. {Single} precision mode should not be used without appropriate validation. @@ -106,7 +106,7 @@ $t should be 2 for Intel Xeon CPUs and 2 or 4 for Intel Xeon Phi :l For some of the simple 2-body potentials without long-range electrostatics, performance and scalability can be better with the "newton off" setting added to the input script :l -If using {kspace_style pppm} in the input script, add +If using {kspace_style pppm} in the input script, add "kspace_modify diff ad" for better performance :l :ule @@ -115,12 +115,12 @@ For Intel Xeon Phi CPUs: Runs should be performed using MCDRAM. :ulb,l :ule -For simulations using {kspace_style pppm} on Intel CPUs +For simulations using {kspace_style pppm} on Intel CPUs supporting AVX-512: Add "kspace_modify diff ad" to the input script :ulb,l -The command-line option should be changed to -"-pk intel 0 omp $r lrt yes -sf intel" where $r is the number of +The command-line option should be changed to +"-pk intel 0 omp $r lrt yes -sf intel" where $r is the number of threads minus 1. :l Do not use thread affinity (set KMP_AFFINITY=none) :l The "newton off" setting may provide better scalability :l @@ -352,7 +352,7 @@ follow in the input script. NOTE: The USER-INTEL package will perform better with modifications to the input script when "PPPM"_kspace_style.html is used: -"kspace_modify diff ad"_kspace_modify.html should be added to the +"kspace_modify diff ad"_kspace_modify.html should be added to the input script. Long-Range Thread (LRT) mode is an option to the "package diff --git a/doc/src/bond_oxdna.txt b/doc/src/bond_oxdna.txt index f9b35a167c..2add6f4c2f 100644 --- a/doc/src/bond_oxdna.txt +++ b/doc/src/bond_oxdna.txt @@ -30,7 +30,7 @@ The {oxdna/fene} and {oxdna2/fene} bond styles use the potential to define a modified finite extensible nonlinear elastic (FENE) potential "(Ouldridge)"_#oxdna_fene to model the connectivity of the phosphate backbone -in the oxDNA force field for coarse-grained modelling of DNA. +in the oxDNA force field for coarse-grained modelling of DNA. The following coefficients must be defined for the bond type via the "bond_coeff"_bond_coeff.html command as given in the above example, or in @@ -43,8 +43,8 @@ r0 (distance) :ul NOTE: The oxDNA bond style has to be used together with the corresponding oxDNA pair styles for excluded volume interaction {oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk} -and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of -"pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2 "(Snodin)"_#oxdna2 bond style the analogous pair styles and an additional Debye-Hueckel pair +and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of +"pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2 "(Snodin)"_#oxdna2 bond style the analogous pair styles and an additional Debye-Hueckel pair style {oxdna2/dh} have to be defined. The coefficients in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model. @@ -66,7 +66,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. [Related commands:] -"pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html +"pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html [Default:] none diff --git a/doc/src/compute_cnp_atom.txt b/doc/src/compute_cnp_atom.txt index 9aa63c84de..16a51f5241 100644 --- a/doc/src/compute_cnp_atom.txt +++ b/doc/src/compute_cnp_atom.txt @@ -42,7 +42,7 @@ where the index {j} goes over the {n}i nearest neighbors of atom {i}, and the index {k} goes over the {n}ij common nearest neighbors between atom {i} and atom {j}. Rik and Rjk are the vectors connecting atom {k} to atoms {i} and {j}. The quantity in the double sum is computed -for each atom. +for each atom. The CNP calculation is sensitive to the specified cutoff value. You should ensure that the appropriate nearest neighbors of an atom are diff --git a/doc/src/dump_vtk.txt b/doc/src/dump_vtk.txt index 21502e7f49..d4d28c81fc 100644 --- a/doc/src/dump_vtk.txt +++ b/doc/src/dump_vtk.txt @@ -16,7 +16,7 @@ ID = user-assigned name for the dump group-ID = ID of the group of atoms to be dumped vtk = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) N = dump every this many timesteps -file = name of file to write dump info to +file = name of file to write dump info to args = same as arguments for "dump_style custom"_dump.html :ul [Examples:] @@ -83,7 +83,7 @@ Triclinic simulation boxes (non-orthogonal) are saved as hexahedrons in either legacy .vtk or .vtu XML format. Style {vtk} allows you to specify a list of atom attributes to be -written to the dump file for each atom. The list of possible attributes +written to the dump file for each atom. The list of possible attributes is the same as for the "dump_style custom"_dump.html command; see its doc page for a listing and an explanation of each attribute. diff --git a/doc/src/fix_box_relax.txt b/doc/src/fix_box_relax.txt index 54decd6282..e3d75ee858 100644 --- a/doc/src/fix_box_relax.txt +++ b/doc/src/fix_box_relax.txt @@ -245,7 +245,7 @@ appear the system is converging to your specified pressure. The solution for this is to either (a) zero the velocities of all atoms before performing the minimization, or (b) make sure you are monitoring the pressure without its kinetic component. The latter can -be done by outputting the pressure from the pressure compute this +be done by outputting the pressure from the pressure compute this command creates (see below) or a pressure compute you define yourself. NOTE: Because pressure is often a very sensitive function of volume, diff --git a/doc/src/fix_eos_table_rx.txt b/doc/src/fix_eos_table_rx.txt index e8d515e1f3..e5e4f772f6 100644 --- a/doc/src/fix_eos_table_rx.txt +++ b/doc/src/fix_eos_table_rx.txt @@ -45,14 +45,14 @@ species {j} in particle {i}, {u_j} is the internal energy of species j, {DeltaH_f,j} is the heat of formation of species {j}, N is the number of molecules represented by the coarse-grained particle, kb is the Boltzmann constant, and T is the temperature of the system. Additionally, -it is possible to modify the concentration-dependent particle internal -energy relation by adding an energy correction, temperature-dependent +it is possible to modify the concentration-dependent particle internal +energy relation by adding an energy correction, temperature-dependent correction, and/or a molecule-dependent correction. An energy correction can -be specified as a constant (in energy units). A temperature correction can be -specified by multiplying a temperature correction coefficient by the -internal temperature. A molecular correction can be specified by -by multiplying a molecule correction coefficient by the average number of -product gas particles in the coarse-grain particle. +be specified as a constant (in energy units). A temperature correction can be +specified by multiplying a temperature correction coefficient by the +internal temperature. A molecular correction can be specified by +by multiplying a molecule correction coefficient by the average number of +product gas particles in the coarse-grain particle. Fix {eos/table/rx} creates interpolation tables of length {N} from {m} internal energy values of each species {u_j} listed in a file as a @@ -72,12 +72,12 @@ The second filename specifies a file containing heat of formation {DeltaH_f,j} for each species. In cases where the coarse-grain particle represents a single molecular -species (i.e., no reactions occur and fix {rx} is not present in the input file), -fix {eos/table/rx} can be applied in a similar manner to fix {eos/table} -within a non-reactive DPD simulation. In this case, the heat of formation +species (i.e., no reactions occur and fix {rx} is not present in the input file), +fix {eos/table/rx} can be applied in a similar manner to fix {eos/table} +within a non-reactive DPD simulation. In this case, the heat of formation filename is replaced with the heat of formation value for the single species. -Additionally, the energy correction and temperature correction coefficients may -also be specified as fix arguments. +Additionally, the energy correction and temperature correction coefficients may +also be specified as fix arguments. :line @@ -138,8 +138,8 @@ used as the species name must correspond with the tags used to define the reactions with the "fix rx"_fix_rx.html command. Alternatively, corrections to the EOS can be included by specifying -three additional columns that correspond to the energy correction, -the temperature correction coefficient and molecule correction +three additional columns that correspond to the energy correction, +the temperature correction coefficient and molecule correction coefficient. In this case, the format of the file is as follows: # HEAT OF FORMATION TABLE (one or more comment or blank lines) :pre diff --git a/doc/src/fix_filter_corotate.txt b/doc/src/fix_filter_corotate.txt index a3339648fa..b782d285c7 100644 --- a/doc/src/fix_filter_corotate.txt +++ b/doc/src/fix_filter_corotate.txt @@ -70,8 +70,8 @@ minimization"_minimize.html. [Restrictions:] -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Making +This fix is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. Currently, it does not support "molecule templates"_molecule.html. diff --git a/doc/src/fix_gcmc.txt b/doc/src/fix_gcmc.txt index 7ac607a2f1..41ec38cffb 100644 --- a/doc/src/fix_gcmc.txt +++ b/doc/src/fix_gcmc.txt @@ -406,7 +406,7 @@ the user for each subsequent fix gcmc command. [Default:] The option defaults are mol = no, maxangle = 10, overlap_cutoff = 0.0, -fugacity_coeff = 1, and full_energy = no, +fugacity_coeff = 1, and full_energy = no, except for the situations where full_energy is required, as listed above. diff --git a/doc/src/fix_grem.txt b/doc/src/fix_grem.txt index 3fc5c1a10e..661f68ed99 100644 --- a/doc/src/fix_grem.txt +++ b/doc/src/fix_grem.txt @@ -85,13 +85,13 @@ No information about this fix is written to "binary restart files"_restart.html. The "thermo_modify"_thermo_modify.html {press} option is supported -by this fix to add the rescaled kinetic pressure as part of +by this fix to add the rescaled kinetic pressure as part of "thermodynamic output"_thermo_style.html. [Restrictions:] -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Making +This fix is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. [Related commands:] diff --git a/doc/src/fix_ipi.txt b/doc/src/fix_ipi.txt index b1533830bc..07e8025d77 100644 --- a/doc/src/fix_ipi.txt +++ b/doc/src/fix_ipi.txt @@ -58,14 +58,14 @@ input are listed in the same order as in the data file of LAMMPS. The initial configuration is ignored, as it will be substituted with the coordinates received from i-PI before forces are ever evaluated. -A note of caution when using potentials that contain long-range +A note of caution when using potentials that contain long-range electrostatics, or that contain parameters that depend on box size: all of these options will be initialized based on the cell size in the -LAMMPS-side initial configuration and kept constant during the run. -This is required to e.g. obtain reproducible and conserved forces. -If the cell varies too wildly, it may be advisable to reinitialize -these interactions at each call. This behavior can be requested by -setting the {reset} switch. +LAMMPS-side initial configuration and kept constant during the run. +This is required to e.g. obtain reproducible and conserved forces. +If the cell varies too wildly, it may be advisable to reinitialize +these interactions at each call. This behavior can be requested by +setting the {reset} switch. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_mscg.txt b/doc/src/fix_mscg.txt index 0e09f8a9c5..7d16967955 100644 --- a/doc/src/fix_mscg.txt +++ b/doc/src/fix_mscg.txt @@ -57,7 +57,7 @@ simulations is as follows: Perform all-atom simulations on the system to be coarse grained. Generate a trajectory mapped to the coarse-grained model. Create input files for the MS-CG library. -Run the range finder functionality of the MS-CG library. +Run the range finder functionality of the MS-CG library. Run the force matching functionality of the MS-CG library. Check the results of the force matching. Run coarse-grained simulations using the new coarse-grained potentials. :ol @@ -70,7 +70,7 @@ Step 2 can be performed using a Python script (what is the name?) provided with the MS-CG library which defines the coarse-grained model and converts a standard LAMMPS dump file for an all-atom simulation (step 1) into a LAMMPS dump file which has the positions of and forces -on the coarse-grained beads. +on the coarse-grained beads. In step 3, an input file named "control.in" is needed by the MS-CG library which sets parameters for the range finding and force matching diff --git a/doc/src/fix_nve_dot.txt b/doc/src/fix_nve_dot.txt index b1c00cd25c..7ad51f3768 100644 --- a/doc/src/fix_nve_dot.txt +++ b/doc/src/fix_nve_dot.txt @@ -23,13 +23,13 @@ fix 1 all nve/dot :pre [Description:] Apply a rigid-body integrator as described in "(Davidchack)"_#Davidchack1 -to a group of atoms, but without Langevin dynamics. +to a group of atoms, but without Langevin dynamics. This command performs Molecular dynamics (MD) -via a velocity-Verlet algorithm and an evolution operator that rotates -the quaternion degrees of freedom, similar to the scheme outlined in "(Miller)"_#Miller1. +via a velocity-Verlet algorithm and an evolution operator that rotates +the quaternion degrees of freedom, similar to the scheme outlined in "(Miller)"_#Miller1. This command is the equivalent of the "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html -without damping and noise and can be used to determine the stability range +without damping and noise and can be used to determine the stability range in a NVE ensemble prior to using the Langevin-type DOTC-integrator (see also "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html). The command is equivalent to the "fix nve"_fix_nve.html. diff --git a/doc/src/fix_nve_dotc_langevin.txt b/doc/src/fix_nve_dotc_langevin.txt index 19d5b233ce..5de8e663c4 100644 --- a/doc/src/fix_nve_dotc_langevin.txt +++ b/doc/src/fix_nve_dotc_langevin.txt @@ -28,20 +28,20 @@ fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10 :pre [Description:] -Apply a rigid-body Langevin-type integrator of the kind "Langevin C" +Apply a rigid-body Langevin-type integrator of the kind "Langevin C" as described in "(Davidchack)"_#Davidchack2 to a group of atoms, which models an interaction with an implicit background solvent. This command performs Brownian dynamics (BD) -via a technique that splits the integration into a deterministic Hamiltonian -part and the Ornstein-Uhlenbeck process for noise and damping. +via a technique that splits the integration into a deterministic Hamiltonian +part and the Ornstein-Uhlenbeck process for noise and damping. The quaternion degrees of freedom are updated though an evolution operator which performs a rotation in quaternion space, preserves the quaternion norm and is akin to "(Miller)"_#Miller2. -In terms of syntax this command has been closely modelled on the -"fix langevin"_fix_langevin.html and its {angmom} option. But it combines -the "fix nve"_fix_nve.html and the "fix langevin"_fix_langevin.html in -one single command. The main feature is improved stability +In terms of syntax this command has been closely modelled on the +"fix langevin"_fix_langevin.html and its {angmom} option. But it combines +the "fix nve"_fix_nve.html and the "fix langevin"_fix_langevin.html in +one single command. The main feature is improved stability over the standard integrator, permitting slightly larger timestep sizes. NOTE: Unlike the "fix langevin"_fix_langevin.html this command performs @@ -57,7 +57,7 @@ Fc is the conservative force computed via the usual inter-particle interactions ("pair_style"_pair_style.html, "bond_style"_bond_style.html, etc). -The Ff and Fr terms are implicitly taken into account by this fix +The Ff and Fr terms are implicitly taken into account by this fix on a per-particle basis. Ff is a frictional drag or viscous damping term proportional to the @@ -77,7 +77,7 @@ a Gaussian random number) for speed. :line -{Tstart} and {Tstop} have to be constant values, i.e. they cannot +{Tstart} and {Tstop} have to be constant values, i.e. they cannot be variables. The {damp} parameter is specified in time units and determines how @@ -98,16 +98,16 @@ different numbers of processors. The keyword/value option has to be used in the following way: -This fix has to be used together with the {angmom} keyword. The -particles are always considered to have a finite size. -The keyword {angmom} enables thermostatting of the rotational degrees of -freedom in addition to the usual translational degrees of freedom. +This fix has to be used together with the {angmom} keyword. The +particles are always considered to have a finite size. +The keyword {angmom} enables thermostatting of the rotational degrees of +freedom in addition to the usual translational degrees of freedom. -The scale factor after the {angmom} keyword gives the ratio of the rotational to +The scale factor after the {angmom} keyword gives the ratio of the rotational to the translational friction coefficient. An example input file can be found in /examples/USER/cgdna/examples/duplex2/. -A technical report with more information on this integrator can be found +A technical report with more information on this integrator can be found "here"_PDF/USER-CGDNA-overview.pdf. :line @@ -120,7 +120,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. [Related commands:] -"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html, +"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html, [Default:] none diff --git a/doc/src/fix_nvk.txt b/doc/src/fix_nvk.txt index 271483b441..49fd8217ab 100644 --- a/doc/src/fix_nvk.txt +++ b/doc/src/fix_nvk.txt @@ -27,7 +27,7 @@ timestep. V is volume; K is kinetic energy. This creates a system trajectory consistent with the isokinetic ensemble. The equations of motion used are those of Minary et al in -"(Minary)"_#nvk-Minary, a variant of those initially given by Zhang in +"(Minary)"_#nvk-Minary, a variant of those initially given by Zhang in "(Zhang)"_#nvk-Zhang. The kinetic energy will be held constant at its value given when fix diff --git a/doc/src/fix_spring.txt b/doc/src/fix_spring.txt index 5f94f4cdae..014a43aacc 100644 --- a/doc/src/fix_spring.txt +++ b/doc/src/fix_spring.txt @@ -89,7 +89,7 @@ NOTE: The center of mass of a group of atoms is calculated in group can straddle a periodic boundary. See the "dump"_dump.html doc page for a discussion of unwrapped coordinates. It also means that a spring connecting two groups or a group and the tether point can cross -a periodic boundary and its length be calculated correctly. +a periodic boundary and its length be calculated correctly. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/neb.txt b/doc/src/neb.txt index a4afc2fe6d..d2e8be3f03 100644 --- a/doc/src/neb.txt +++ b/doc/src/neb.txt @@ -344,7 +344,7 @@ informations can help understanding what is going wrong. For instance when the path angle becomes accute the definition of tangent used in the NEB calculation is questionable and the NEB cannot may diverge "(Maras)"_#Maras2. - + When running on multiple partitions, LAMMPS produces additional log files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For a diff --git a/doc/src/pair_agni.txt b/doc/src/pair_agni.txt index 27fb6c10fe..06dcccb9d9 100644 --- a/doc/src/pair_agni.txt +++ b/doc/src/pair_agni.txt @@ -40,8 +40,8 @@ vectorial atomic forces. Only a single pair_coeff command is used with the {agni} style which specifies an AGNI potential file containing the parameters of the -force field for the needed elements. These are mapped to LAMMPS atom -types by specifying N additional arguments after the filename in the +force field for the needed elements. These are mapped to LAMMPS atom +types by specifying N additional arguments after the filename in the pair_coeff command, where N is the number of LAMMPS atom types: filename @@ -52,13 +52,13 @@ to specify the path for the force field file. An AGNI force field is fully specified by the filename which contains the parameters of the force field, i.e., the reference training environments -used to construct the machine learning force field. Example force field -and input files are provided in the examples/USER/misc/agni directory. +used to construct the machine learning force field. Example force field +and input files are provided in the examples/USER/misc/agni directory. :line -Styles with {omp} suffix is functionally the same as the corresponding -style without the suffix. They have been optimized to run faster, depending +Styles with {omp} suffix is functionally the same as the corresponding +style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated style takes the same arguments and should produce the same results, except for round-off and precision diff --git a/doc/src/pair_buck.txt b/doc/src/pair_buck.txt index 49161404c3..e705e735fb 100644 --- a/doc/src/pair_buck.txt +++ b/doc/src/pair_buck.txt @@ -75,7 +75,7 @@ Lennard-Jones 12/6) given by :c,image(Eqs/pair_buck.jpg) where rho is an ionic-pair dependent length parameter, and Rc is the -cutoff on both terms. +cutoff on both terms. The styles with {coul/cut} or {coul/long} or {coul/msm} add a Coulombic term as described for the "lj/cut"_pair_lj.html pair styles. diff --git a/doc/src/pair_exp6_rx.txt b/doc/src/pair_exp6_rx.txt index 47045a5933..cbc17d357d 100644 --- a/doc/src/pair_exp6_rx.txt +++ b/doc/src/pair_exp6_rx.txt @@ -55,33 +55,33 @@ defined in the reaction kinetics files specified with the "fix rx"_fix_rx.html command or they must correspond to the tag "1fluid", signifying interaction with a product species mixture determined through a one-fluid approximation. The interaction potential is -weighted by the geometric average of either the mole fraction concentrations -or the number of molecules associated with the interacting coarse-grained -particles (see the {fractional} or {molecular} weighting pair style options). +weighted by the geometric average of either the mole fraction concentrations +or the number of molecules associated with the interacting coarse-grained +particles (see the {fractional} or {molecular} weighting pair style options). The coarse-grained potential is stored before and after the reaction kinetics solver is applied, where the difference is defined to be the internal chemical energy (uChem). -The fourth argument specifies the type of scaling that will be used +The fourth argument specifies the type of scaling that will be used to scale the EXP-6 parameters as reactions occur. Currently, there are three scaling options: {exponent}, {polynomial} and {none}. -Exponent scaling requires two additional arguments for scaling +Exponent scaling requires two additional arguments for scaling the {Rm} and {epsilon} parameters, respectively. The scaling factor -is computed by phi^exponent, where phi is the number of molecules -represented by the coarse-grain particle and exponent is specified +is computed by phi^exponent, where phi is the number of molecules +represented by the coarse-grain particle and exponent is specified as a pair coefficient argument for {Rm} and {epsilon}, respectively. -The {Rm} and {epsilon} parameters are multiplied by the scaling +The {Rm} and {epsilon} parameters are multiplied by the scaling factor to give the scaled interaction parameters for the CG particle. -Polynomial scaling requires a filename to be specified as a pair +Polynomial scaling requires a filename to be specified as a pair coeff argument. The file contains the coefficients to a fifth order -polynomial for the {alpha}, {epsilon} and {Rm} parameters that depend -upon phi (the number of molecules represented by the CG particle). +polynomial for the {alpha}, {epsilon} and {Rm} parameters that depend +upon phi (the number of molecules represented by the CG particle). The format of a polynomial file is provided below. The {none} option to the scaling does not have any additional pair coeff -arguments. This is equivalent to specifying the {exponent} option with +arguments. This is equivalent to specifying the {exponent} option with {Rm} and {epsilon} exponents of 0.0 and 0.0, respectively. The final argument specifies the interaction cutoff (optional). @@ -102,7 +102,7 @@ parenthesized comments): # POLYNOMIAL FILE (one or more comment or blank lines) :pre # General Functional Form: -# A*phi^5 + B*phi^4 + C*phi^3 + D*phi^2 + E*phi + F +# A*phi^5 + B*phi^4 + C*phi^3 + D*phi^2 + E*phi + F # # Parameter A B C D E F (blank) diff --git a/doc/src/pair_kolmogorov_crespi_z.txt b/doc/src/pair_kolmogorov_crespi_z.txt index 0879dc34d0..c7a6d4194f 100644 --- a/doc/src/pair_kolmogorov_crespi_z.txt +++ b/doc/src/pair_kolmogorov_crespi_z.txt @@ -24,25 +24,25 @@ pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C :pre [Description:] -The {kolmogorov/crespi/z} style computes the Kolmogorov-Crespi interaction -potential as described in "(KC05)"_#KC05. An important simplification is made, -which is to take all normals along the z-axis. +The {kolmogorov/crespi/z} style computes the Kolmogorov-Crespi interaction +potential as described in "(KC05)"_#KC05. An important simplification is made, +which is to take all normals along the z-axis. :c,image(Eqs/pair_kolmogorov_crespi_z.jpg) -It is important to have a suffiently large cutoff to ensure smooth forces. -Energies are shifted so that they go continously to zero at the cutoff assuming +It is important to have a suffiently large cutoff to ensure smooth forces. +Energies are shifted so that they go continously to zero at the cutoff assuming that the exponential part of {Vij} (first term) decays sufficiently fast. This shift is achieved by the last term in the equation for {Vij} above. -This potential is intended for interactions between two layers of graphene. -Therefore, to avoid interaction between layers in multi-layered materials, -each layer should have a separate atom type and interactions should only +This potential is intended for interactions between two layers of graphene. +Therefore, to avoid interaction between layers in multi-layered materials, +each layer should have a separate atom type and interactions should only be computed between atom types of neighbouring layers. -The parameter file (e.g. CC.KC), is intended for use with metal -"units"_units.html, with energies in meV. An additional parameter, {S}, -is available to facilitate scaling of energies in accordance with +The parameter file (e.g. CC.KC), is intended for use with metal +"units"_units.html, with energies in meV. An additional parameter, {S}, +is available to facilitate scaling of energies in accordance with "(vanWijk)"_#vanWijk. This potential must be used in combination with hybrid/overlay. @@ -64,7 +64,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. :line -:link(KC05) +:link(KC05) [(KC05)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005) :link(vanWijk) diff --git a/doc/src/pair_multi_lucy_rx.txt b/doc/src/pair_multi_lucy_rx.txt index bf5d5636fe..77ed223e2a 100644 --- a/doc/src/pair_multi_lucy_rx.txt +++ b/doc/src/pair_multi_lucy_rx.txt @@ -97,9 +97,9 @@ tags must either correspond to the species defined in the reaction kinetics files specified with the "fix rx"_fix_rx.html command or they must correspond to the tag "1fluid", signifying interaction with a product species mixture determined through a one-fluid approximation. -The interaction potential is weighted by the geometric average of -either the mole fraction concentrations or the number of molecules -associated with the interacting coarse-grained particles (see the +The interaction potential is weighted by the geometric average of +either the mole fraction concentrations or the number of molecules +associated with the interacting coarse-grained particles (see the {fractional} or {molecular} weighting pair style options). The coarse-grained potential is stored before and after the reaction kinetics solver is applied, where the difference is defined to be the internal chemical energy (uChem). diff --git a/doc/src/pair_oxdna.txt b/doc/src/pair_oxdna.txt index 0a07417fd0..d9734f122d 100644 --- a/doc/src/pair_oxdna.txt +++ b/doc/src/pair_oxdna.txt @@ -39,17 +39,17 @@ pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1 [Description:] -The {oxdna} pair styles compute the pairwise-additive parts of the oxDNA force field -for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the +The {oxdna} pair styles compute the pairwise-additive parts of the oxDNA force field +for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the excluded volume interaction {oxdna/excv}, the stacking {oxdna/stk}, cross-stacking {oxdna/xstk} and coaxial stacking interaction {oxdna/coaxstk} as well as the hydrogen-bonding interaction {oxdna/hbond} between complementary pairs of nucleotides on opposite strands. -The exact functional form of the pair styles is rather complex, which manifests itself in the 144 coefficients -in the above example. The individual potentials consist of products of modulation factors, -which themselves are constructed from a number of more basic potentials -(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms. +The exact functional form of the pair styles is rather complex, which manifests itself in the 144 coefficients +in the above example. The individual potentials consist of products of modulation factors, +which themselves are constructed from a number of more basic potentials +(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms. We refer to "(Ouldridge-DPhil)"_#Ouldridge-DPhil1 and "(Ouldridge)"_#Ouldridge1 for a detailed description of the oxDNA force field. @@ -57,8 +57,8 @@ NOTE: These pair styles have to be used together with the related oxDNA bond sty {oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of "bond_style oxdna/fene"_bond_oxdna.html). With one exception the coefficients in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model. -The exception is the first coefficient after {oxdna/stk} (T=0.1 in the above example). -When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html +The exception is the first coefficient after {oxdna/stk} (T=0.1 in the above example). +When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html the temperature coefficients have to be matched to the one used in the fix. @@ -79,7 +79,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. [Related commands:] -"bond_style oxdna/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html, +"bond_style oxdna/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html, "bond_style oxdna2/fene"_bond_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html [Default:] none diff --git a/doc/src/pair_oxdna2.txt b/doc/src/pair_oxdna2.txt index 1cc562d5f1..1728a0bc7b 100644 --- a/doc/src/pair_oxdna2.txt +++ b/doc/src/pair_oxdna2.txt @@ -45,17 +45,17 @@ pair_coeff * * oxdna2/dh 0.1 1.0 0.815 :pre [Description:] -The {oxdna2} pair styles compute the pairwise-additive parts of the oxDNA force field -for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the +The {oxdna2} pair styles compute the pairwise-additive parts of the oxDNA force field +for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the excluded volume interaction {oxdna2/excv}, the stacking {oxdna2/stk}, cross-stacking {oxdna2/xstk} and coaxial stacking interaction {oxdna2/coaxstk}, electrostatic Debye-Hueckel interaction {oxdna2/dh} as well as the hydrogen-bonding interaction {oxdna2/hbond} between complementary pairs of nucleotides on opposite strands. -The exact functional form of the pair styles is rather complex. -The individual potentials consist of products of modulation factors, -which themselves are constructed from a number of more basic potentials -(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms. +The exact functional form of the pair styles is rather complex. +The individual potentials consist of products of modulation factors, +which themselves are constructed from a number of more basic potentials +(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms. We refer to "(Snodin)"_#Snodin and the original oxDNA publications "(Ouldridge-DPhil)"_#Ouldridge-DPhil2 and "(Ouldridge)"_#Ouldridge2 for a detailed description of the oxDNA2 force field. @@ -63,7 +63,7 @@ NOTE: These pair styles have to be used together with the related oxDNA2 bond st {oxdna2/fene} for the connectivity of the phosphate backbone (see also documentation of "bond_style oxdna2/fene"_bond_oxdna.html). Almost all coefficients in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model. -Exceptions are the first coefficient after {oxdna2/stk} (T=0.1 in the above example) and the coefficients +Exceptions are the first coefficient after {oxdna2/stk} (T=0.1 in the above example) and the coefficients after {oxdna2/dh} (T=0.1, rhos=1.0, qeff=0.815 in the above example). When using a Langevin thermostat e.g. through "fix langevin"_fix_langevin.html or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html the temperature coefficients have to be matched to the one used in the fix. @@ -86,7 +86,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. [Related commands:] "bond_style oxdna2/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html, -"bond_style oxdna/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html +"bond_style oxdna/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html [Default:] none diff --git a/doc/src/pair_table_rx.txt b/doc/src/pair_table_rx.txt index d089a4f9da..f93af21da4 100644 --- a/doc/src/pair_table_rx.txt +++ b/doc/src/pair_table_rx.txt @@ -85,9 +85,9 @@ tags must either correspond to the species defined in the reaction kinetics files specified with the "fix rx"_fix_rx.html command or they must correspond to the tag "1fluid", signifying interaction with a product species mixture determined through a one-fluid approximation. -The interaction potential is weighted by the geometric average of -either the mole fraction concentrations or the number of molecules -associated with the interacting coarse-grained particles (see the +The interaction potential is weighted by the geometric average of +either the mole fraction concentrations or the number of molecules +associated with the interacting coarse-grained particles (see the {fractional} or {molecular} weighting pair style options). The coarse-grained potential is stored before and after the reaction kinetics solver is applied, where the difference is defined to be the internal chemical energy (uChem). diff --git a/doc/src/python.txt b/doc/src/python.txt index e00b90234c..c6538ded45 100644 --- a/doc/src/python.txt +++ b/doc/src/python.txt @@ -489,7 +489,7 @@ python"_Section_python.html. Note that it is important that the stand-alone LAMMPS executable and the LAMMPS shared library be consistent (built from the same source code files) in order for this to work. If the two have been built at different times using -different source files, problems may occur. +different source files, problems may occur. [Related commands:] diff --git a/doc/src/tutorial_github.txt b/doc/src/tutorial_github.txt index d6ec22589b..3e10b821ae 100644 --- a/doc/src/tutorial_github.txt +++ b/doc/src/tutorial_github.txt @@ -86,7 +86,7 @@ machine via HTTPS: or, if you have set up your GitHub account for using SSH keys, via SSH: $ git clone git@github.com:/lammps.git :pre - + You can find the proper URL by clicking the "Clone or download"-button: :c,image(JPG/tutorial_https_block.png) diff --git a/doc/src/tutorial_pylammps.txt b/doc/src/tutorial_pylammps.txt index 0b4fb32ed2..78cdd241fb 100644 --- a/doc/src/tutorial_pylammps.txt +++ b/doc/src/tutorial_pylammps.txt @@ -36,7 +36,7 @@ lammps.PyLammps :h4 higher-level abstraction built on top of original C-Types interface manipulation of Python objects -communication with LAMMPS is hidden from API user +communication with LAMMPS is hidden from API user shorter, more concise Python better IPython integration, designed for quick prototyping :ul @@ -328,7 +328,7 @@ IPyLammps Examples :h2 Examples of IPython notebooks can be found in the python/examples/pylammps subdirectory. To open these notebooks launch {jupyter notebook} inside this -directory and navigate to one of them. If you compiled and installed +directory and navigate to one of them. If you compiled and installed a LAMMPS shared library with exceptions, PNG, JPEG and FFMPEG support you should be able to rerun all of these notebooks. @@ -399,19 +399,19 @@ natoms = L.system.natoms :pre for i in range(niterations): iatom = random.randrange(0, natoms) current_atom = L.atoms\[iatom\] :pre - + x0, y0 = current_atom.position :pre - + dx = deltamove * random.uniform(-1, 1) dy = deltamove * random.uniform(-1, 1) :pre - + current_atom.position = (x0+dx, y0+dy) :pre - + L.run(1, "pre no post no") :pre - + e = L.eval("pe") energies.append(e) :pre - + if e <= elast: naccept += 1 elast = e @@ -460,4 +460,4 @@ Feedback and Contributing :h2 If you find this Python interface useful, please feel free to provide feedback and ideas on how to improve it to Richard Berger (richard.berger@temple.edu). We also want to encourage people to write tutorial style IPython notebooks showcasing LAMMPS usage -and maybe their latest research results. +and maybe their latest research results.