From d1222bd3c051730f0f7a7d9293d35b453b3f1f4c Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Thu, 9 Jan 2020 17:38:50 -0700 Subject: [PATCH 01/14] minor omissions in recent patch release --- doc/src/Commands_pair.rst | 2 +- doc/src/pair_lj.rst | 3 +++ examples/README | 3 +++ 3 files changed, 7 insertions(+), 1 deletion(-) diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index b4371420a7..0844e0a2fe 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -146,7 +146,7 @@ OPT. * :doc:`lj/cut/soft (o) ` * :doc:`lj/cut/thole/long (o) ` * :doc:`lj/cut/tip4p/cut (o) ` - * :doc:`lj/cut/tip4p/long (ot) ` + * :doc:`lj/cut/tip4p/long (got) ` * :doc:`lj/cut/tip4p/long/soft (o) ` * :doc:`lj/expand (gko) ` * :doc:`lj/expand/coul/long (g) ` diff --git a/doc/src/pair_lj.rst b/doc/src/pair_lj.rst index 54140a9faf..2b75c96a89 100644 --- a/doc/src/pair_lj.rst +++ b/doc/src/pair_lj.rst @@ -90,6 +90,9 @@ pair\_style lj/cut/coul/wolf/omp command pair\_style lj/cut/tip4p/cut command ==================================== +pair\_style lj/cut/tip4p/cut/gpu command +==================================== + pair\_style lj/cut/tip4p/cut/omp command ======================================== diff --git a/examples/README b/examples/README index 47463a85d8..fd57d5316d 100644 --- a/examples/README +++ b/examples/README @@ -164,6 +164,9 @@ The MC directory has an example script for using LAMMPS as an energy-evaluation engine in a iterative Monte Carlo energy-relaxation loop. +The TIP4P directory has an example for comparing testing forces +computed on a GPU. + The UNITS directory contains examples of input scripts modeling the same Lennard-Jones liquid model, written in 3 different unit systems: lj, real, and metal. So that you can see how to scale/unscale input From 664227ff11c5dedbadbb64eeae79ed0f5b242295 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Thu, 9 Jan 2020 17:41:02 -0700 Subject: [PATCH 02/14] one more tweak --- examples/README | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/examples/README b/examples/README index fd57d5316d..8412f7b3ee 100644 --- a/examples/README +++ b/examples/README @@ -164,8 +164,8 @@ The MC directory has an example script for using LAMMPS as an energy-evaluation engine in a iterative Monte Carlo energy-relaxation loop. -The TIP4P directory has an example for comparing testing forces -computed on a GPU. +The TIP4P directory has an example for testing forces computed on a +GPU. The UNITS directory contains examples of input scripts modeling the same Lennard-Jones liquid model, written in 3 different unit systems: From 9c207bb751d3de378ae2d40e66b856ea4b26ba02 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 11 Jan 2020 16:20:13 -0500 Subject: [PATCH 03/14] remove outdated .txt file for pair style meam/c --- doc/txt/pair_meamc.txt | 402 ----------------------------------------- 1 file changed, 402 deletions(-) delete mode 100644 doc/txt/pair_meamc.txt diff --git a/doc/txt/pair_meamc.txt b/doc/txt/pair_meamc.txt deleted file mode 100644 index 2831600e08..0000000000 --- a/doc/txt/pair_meamc.txt +++ /dev/null @@ -1,402 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style meam/c command :h3 - -[Syntax:] - -pair_style style :pre - -style = {meam/c} - -[Examples:] - -pair_style meam/c -pair_coeff * * ../potentials/library.meam Si ../potentials/si.meam Si -pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni :pre - -[Description:] - -NOTE: The behavior of the MEAM potential for alloy systems has changed -as of November 2010; see description below of the mixture_ref_t -parameter - -Style {meam/c} computes pairwise interactions for a variety of materials -using modified embedded-atom method (MEAM) potentials -"(Baskes)"_#Baskes. Conceptually, it is an extension to the original -"EAM potentials"_pair_eam.html which adds angular forces. It is -thus suitable for modeling metals and alloys with fcc, bcc, hcp and -diamond cubic structures, as well as covalently bonded materials like -silicon and carbon. Style {meam/c} is a translation of the (now obsolete) -{meam} code from Fortran to C++. It is functionally equivalent to {meam} -but more efficient, and thus {meam} has been removed from LAMMPS after -the 12 December 2018 release. - -In the MEAM formulation, the total energy E of a system of atoms is -given by: - -:c,image(Eqs/pair_meam.jpg) - -where F is the embedding energy which is a function of the atomic -electron density rho, and phi is a pair potential interaction. The -pair interaction is summed over all neighbors J of atom I within the -cutoff distance. As with EAM, the multi-body nature of the MEAM -potential is a result of the embedding energy term. Details of the -computation of the embedding and pair energies, as implemented in -LAMMPS, are given in "(Gullet)"_#Gullet and references therein. - -The various parameters in the MEAM formulas are listed in two files -which are specified by the "pair_coeff"_pair_coeff.html command. -These are ASCII text files in a format consistent with other MD codes -that implement MEAM potentials, such as the serial DYNAMO code and -Warp. Several MEAM potential files with parameters for different -materials are included in the "potentials" directory of the LAMMPS -distribution with a ".meam" suffix. All of these are parameterized in -terms of LAMMPS "metal units"_units.html. - -Note that unlike for other potentials, cutoffs for MEAM potentials are -not set in the pair_style or pair_coeff command; they are specified in -the MEAM potential files themselves. - -Only a single pair_coeff command is used with the {meam} style which -specifies two MEAM files and the element(s) to extract information -for. The MEAM elements are mapped to LAMMPS atom types by specifying -N additional arguments after the 2nd filename in the pair_coeff -command, where N is the number of LAMMPS atom types: - -MEAM library file -Elem1, Elem2, ... -MEAM parameter file -N element names = mapping of MEAM elements to atom types :ul - -See the "pair_coeff"_pair_coeff.html doc page for alternate ways -to specify the path for the potential files. - -As an example, the potentials/library.meam file has generic MEAM -settings for a variety of elements. The potentials/SiC.meam file has -specific parameter settings for a Si and C alloy system. If your -LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si, -and the 4th to be C, you would use the following pair_coeff command: - -pair_coeff * * library.meam Si C sic.meam Si Si Si C :pre - -The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The two filenames are for the library and parameter file respectively. -The Si and C arguments (between the file names) are the two elements -for which info will be extracted from the library file. The first -three trailing Si arguments map LAMMPS atom types 1,2,3 to the MEAM Si -element. The final C argument maps LAMMPS atom type 4 to the MEAM C -element. - -If the 2nd filename is specified as NULL, no parameter file is read, -which simply means the generic parameters in the library file are -used. Use of the NULL specification for the parameter file is -discouraged for systems with more than a single element type -(e.g. alloys), since the parameter file is expected to set element -interaction terms that are not captured by the information in the -library file. - -If a mapping value is specified as NULL, the mapping is not performed. -This can be used when a {meam} potential is used as part of the -{hybrid} pair style. The NULL values are placeholders for atom types -that will be used with other potentials. - -NOTE: If the 2nd filename is NULL, the element names between the two -filenames can appear in any order, e.g. "Si C" or "C Si" in the -example above. However, if the 2nd filename is not NULL (as in the -example above), it contains settings that are Fortran-indexed for the -elements that preceed it. Thus you need to insure you list the -elements between the filenames in an order consistent with how the -values in the 2nd filename are indexed. See details below on the -syntax for settings in the 2nd file. - -The MEAM library file provided with LAMMPS has the name -potentials/library.meam. It is the "meamf" file used by other MD -codes. Aside from blank and comment lines (start with #) which can -appear anywhere, it is formatted as a series of entries, each of which -has 19 parameters and can span multiple lines: - -elt, lat, z, ielement, atwt, alpha, b0, b1, b2, b3, alat, esub, asub, -t0, t1, t2, t3, rozero, ibar - -The "elt" and "lat" parameters are text strings, such as elt = Si or -Cu and lat = dia or fcc. Because the library file is used by Fortran -MD codes, these strings may be enclosed in single quotes, but this is -not required. The other numeric parameters match values in the -formulas above. The value of the "elt" string is what is used in the -pair_coeff command to identify which settings from the library file -you wish to read in. There can be multiple entries in the library -file with the same "elt" value; LAMMPS reads the 1st matching entry it -finds and ignores the rest. - -Other parameters in the MEAM library file correspond to single-element -potential parameters: - -lat = lattice structure of reference configuration -z = number of nearest neighbors in the reference structure - This field is only read for compatibility, the correct - value is inferred from the lattice structure -ielement = atomic number -atwt = atomic weight -alat = lattice constant of reference structure -esub = energy per atom (eV) in the reference structure at equilibrium -asub = "A" parameter for MEAM (see e.g. "(Baskes)"_#Baskes) :pre - -The alpha, b0, b1, b2, b3, t0, t1, t2, t3 parameters correspond to the -standard MEAM parameters in the literature "(Baskes)"_#Baskes (the b -parameters are the standard beta parameters). Note that only parameters -normalized to t0 = 1.0 are supported. The rozero parameter is -an element-dependent density scaling that weights the reference -background density (see e.g. equation 4.5 in "(Gullet)"_#Gullet) and -is typically 1.0 for single-element systems. The ibar parameter -selects the form of the function G(Gamma) used to compute the electron -density; options are - - 0 => G = sqrt(1+Gamma) - 1 => G = exp(Gamma/2) - 2 => not implemented - 3 => G = 2/(1+exp(-Gamma)) - 4 => G = sqrt(1+Gamma) - -5 => G = +-sqrt(abs(1+Gamma)) :pre - -If used, the MEAM parameter file contains settings that override or -complement the library file settings. Examples of such parameter -files are in the potentials directory with a ".meam" suffix. Their -format is the same as is read by other Fortran MD codes. Aside from -blank and comment lines (start with #) which can appear anywhere, each -line has one of the following forms. Each line can also have a -trailing comment (starting with #) which is ignored. - -keyword = value -keyword(I) = value -keyword(I,J) = value -keyword(I,J,K) = value :pre - -The indices I, J, K correspond to the elements selected from the -MEAM library file numbered in the order of how those elements were -selected starting from 1. Thus for the example given below - -pair_coeff * * library.meam Si C sic.meam Si Si Si C :pre - -an index of 1 would refer to Si and an index of 2 to C. - -The recognized keywords for the parameter file are as follows: - -Ec, alpha, rho0, delta, lattce, attrac, repuls, nn2, Cmin, Cmax, rc, delr, -augt1, gsmooth_factor, re - -where - -rc = cutoff radius for cutoff function; default = 4.0 -delr = length of smoothing distance for cutoff function; default = 0.1 -rho0(I) = relative density for element I (overwrites value - read from meamf file) -Ec(I,J) = cohesive energy of reference structure for I-J mixture -delta(I,J) = heat of formation for I-J alloy; if Ec_IJ is input as - zero, then LAMMPS sets Ec_IJ = (Ec_II + Ec_JJ)/2 - delta_IJ -alpha(I,J) = alpha parameter for pair potential between I and J (can - be computed from bulk modulus of reference structure -re(I,J) = equilibrium distance between I and J in the reference - structure -Cmax(I,J,K) = Cmax screening parameter when I-J pair is screened - by K (I<=J); default = 2.8 -Cmin(I,J,K) = Cmin screening parameter when I-J pair is screened - by K (I<=J); default = 2.0 -lattce(I,J) = lattice structure of I-J reference structure: - dia = diamond (interlaced fcc for alloy) - fcc = face centered cubic - bcc = body centered cubic - dim = dimer - b1 = rock salt (NaCl structure) - hcp = hexagonal close-packed - c11 = MoSi2 structure - l12 = Cu3Au structure (lower case L, followed by 12) - b2 = CsCl structure (interpenetrating simple cubic) -nn2(I,J) = turn on second-nearest neighbor MEAM formulation for - I-J pair (see for example "(Lee)"_#Lee). - 0 = second-nearest neighbor formulation off - 1 = second-nearest neighbor formulation on - default = 0 -attrac(I,J) = additional cubic attraction term in Rose energy I-J pair potential - default = 0 -repuls(I,J) = additional cubic repulsive term in Rose energy I-J pair potential - default = 0 -zbl(I,J) = blend the MEAM I-J pair potential with the ZBL potential for small - atom separations "(ZBL)"_#ZBL - default = 1 -gsmooth_factor = factor determining the length of the G-function smoothing - region; only significant for ibar=0 or ibar=4. - 99.0 = short smoothing region, sharp step - 0.5 = long smoothing region, smooth step - default = 99.0 -augt1 = integer flag for whether to augment t1 parameter by - 3/5*t3 to account for old vs. new meam formulations; - 0 = don't augment t1 - 1 = augment t1 - default = 1 -ialloy = integer flag to use alternative averaging rule for t parameters, - for comparison with the DYNAMO MEAM code - 0 = standard averaging (matches ialloy=0 in DYNAMO) - 1 = alternative averaging (matches ialloy=1 in DYNAMO) - 2 = no averaging of t (use single-element values) - default = 0 -mixture_ref_t = integer flag to use mixture average of t to compute the background - reference density for alloys, instead of the single-element values - (see description and warning elsewhere in this doc page) - 0 = do not use mixture averaging for t in the reference density - 1 = use mixture averaging for t in the reference density - default = 0 -erose_form = integer value to select the form of the Rose energy function - (see description below). - default = 0 -emb_lin_neg = integer value to select embedding function for negative densities - 0 = F(rho)=0 - 1 = F(rho) = -asub*esub*rho (linear in rho, matches DYNAMO) - default = 0 -bkgd_dyn = integer value to select background density formula - 0 = rho_bkgd = rho_ref_meam(a) (as in the reference structure) - 1 = rho_bkgd = rho0_meam(a)*Z_meam(a) (matches DYNAMO) - default = 0 :pre - -Rc, delr, re are in distance units (Angstroms in the case of metal -units). Ec and delta are in energy units (eV in the case of metal -units). - -Each keyword represents a quantity which is either a scalar, vector, -2d array, or 3d array and must be specified with the correct -corresponding array syntax. The indices I,J,K each run from 1 to N -where N is the number of MEAM elements being used. - -Thus these lines - -rho0(2) = 2.25 -alpha(1,2) = 4.37 :pre - -set rho0 for the 2nd element to the value 2.25 and set alpha for the -alloy interaction between elements 1 and 2 to 4.37. - -The augt1 parameter is related to modifications in the MEAM -formulation of the partial electron density function. In recent -literature, an extra term is included in the expression for the -third-order density in order to make the densities orthogonal (see for -example "(Wang)"_#Wang2, equation 3d); this term is included in the -MEAM implementation in lammps. However, in earlier published work -this term was not included when deriving parameters, including most of -those provided in the library.meam file included with lammps, and to -account for this difference the parameter t1 must be augmented by -3/5*t3. If augt1=1, the default, this augmentation is done -automatically. When parameter values are fit using the modified -density function, as in more recent literature, augt1 should be set to -0. - -The mixture_ref_t parameter is available to match results with those -of previous versions of lammps (before January 2011). Newer versions -of lammps, by default, use the single-element values of the t -parameters to compute the background reference density. This is the -proper way to compute these parameters. Earlier versions of lammps -used an alloy mixture averaged value of t to compute the background -reference density. Setting mixture_ref_t=1 gives the old behavior. -WARNING: using mixture_ref_t=1 will give results that are demonstrably -incorrect for second-neighbor MEAM, and non-standard for -first-neighbor MEAM; this option is included only for matching with -previous versions of lammps and should be avoided if possible. - -The parameters attrac and repuls, along with the integer selection -parameter erose_form, can be used to modify the Rose energy function -used to compute the pair potential. This function gives the energy of -the reference state as a function of interatomic spacing. The form of -this function is: - -astar = alpha * (r/re - 1.d0) -if erose_form = 0: erose = -Ec*(1+astar+a3*(astar**3)/(r/re))*exp(-astar) -if erose_form = 1: erose = -Ec*(1+astar+(-attrac+repuls/r)*(astar**3))*exp(-astar) -if erose_form = 2: erose = -Ec*(1 +astar + a3*(astar**3))*exp(-astar) -a3 = repuls, astar < 0 -a3 = attrac, astar >= 0 :pre - -Most published MEAM parameter sets use the default values attrac=repulse=0. -Setting repuls=attrac=delta corresponds to the form used in several -recent published MEAM parameter sets, such as "(Valone)"_#Valone - -NOTE: The default form of the erose expression in LAMMPS was corrected -in March 2009. The current version is correct, but may show different -behavior compared with earlier versions of lammps with the attrac -and/or repuls parameters are non-zero. To obtain the previous default -form, use erose_form = 1 (this form does not seem to appear in the -literature). An alternative form (see e.g. "(Lee2)"_#Lee2) is -available using erose_form = 2. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, where types I and J correspond to -two different element types, mixing is performed by LAMMPS with -user-specifiable parameters as described above. You never need to -specify a pair_coeff command with I != J arguments for this style. - -This pair style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -This pair style does not write its information to "binary restart -files"_restart.html, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -The {meam/c} style is provided in the USER-MEAMC package. It is -only enabled if LAMMPS was built with that package. -See the "Build package"_Build_package.html doc page for more info. - -The maximum number of elements, that can be read from the MEAM -library file, is determined at compile time. The default is 5. -If you need support for more elements, you have to change the -define for the constant 'maxelt' at the beginning of the file -src/USER-MEAMC/meam.h and update/recompile LAMMPS. There is no -limit on the number of atoms types. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "pair_style eam"_pair_eam.html, -"pair_style meam/spline"_pair_meam_spline.html - -[Default:] none - -:line - -:link(Baskes) -[(Baskes)] Baskes, Phys Rev B, 46, 2727-2742 (1992). - -:link(Gullet) -[(Gullet)] Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003). -This report may be accessed on-line via "this link"_sandreport. - -:link(sandreport,http://infoserve.sandia.gov/sand_doc/2003/038782.pdf) - -:link(Lee) -[(Lee)] Lee, Baskes, Phys. Rev. B, 62, 8564-8567 (2000). - -:link(Lee2) -[(Lee2)] Lee, Baskes, Kim, Cho. Phys. Rev. B, 64, 184102 (2001). - -:link(Valone) -[(Valone)] Valone, Baskes, Martin, Phys. Rev. B, 73, 214209 (2006). - -:link(Wang2) -[(Wang)] Wang, Van Hove, Ross, Baskes, J. Chem. Phys., 121, 5410 (2004). - -:link(ZBL) -[(ZBL)] J.F. Ziegler, J.P. Biersack, U. Littmark, "Stopping and Ranges -of Ions in Matter", Vol 1, 1985, Pergamon Press. From e1849232b85122eb702f79cc42d6fa6d237b0426 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 11 Jan 2020 16:21:42 -0500 Subject: [PATCH 04/14] remove redundant lj/cut/tip4p/long/gpu entry and correct underline length --- doc/src/Build_extras.rst | 2 +- doc/src/pair_lj.rst | 5 +---- 2 files changed, 2 insertions(+), 5 deletions(-) diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index c02b24641e..2cba59bde0 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -203,7 +203,7 @@ inside the CMake build directory. If the KIM library is already on your system (in a location CMake cannot find it), set the PKG\_CONFIG\_PATH environment variable so that libkim-api can be found. -For using KIM web queries. +For using OpenKIM web queries in LAMMPS. If LMP\_DEBUG\_CURL is set, the libcurl verbose mode will be on, and any libcurl calls within the KIM web query display a lot of information about diff --git a/doc/src/pair_lj.rst b/doc/src/pair_lj.rst index 2b75c96a89..7a46f0a0db 100644 --- a/doc/src/pair_lj.rst +++ b/doc/src/pair_lj.rst @@ -91,7 +91,7 @@ pair\_style lj/cut/tip4p/cut command ==================================== pair\_style lj/cut/tip4p/cut/gpu command -==================================== +======================================== pair\_style lj/cut/tip4p/cut/omp command ======================================== @@ -105,9 +105,6 @@ pair\_style lj/cut/tip4p/long/omp command pair\_style lj/cut/tip4p/long/opt command ========================================= -pair\_style lj/cut/tip4p/long/gpu command -===================================== - Syntax """""" From d7d1d571705e6a4451bdb7b79494b3b0ba653f9f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 11 Jan 2020 16:35:27 -0500 Subject: [PATCH 05/14] remove outdated txt files --- doc/txt/fix_nve_dot.txt | 63 ------------- doc/txt/fix_nve_dotc_langevin.txt | 143 ------------------------------ doc/txt/pair_oxdna.txt | 112 ----------------------- doc/txt/pair_oxdna2.txt | 121 ------------------------- 4 files changed, 439 deletions(-) delete mode 100644 doc/txt/fix_nve_dot.txt delete mode 100644 doc/txt/fix_nve_dotc_langevin.txt delete mode 100644 doc/txt/pair_oxdna.txt delete mode 100644 doc/txt/pair_oxdna2.txt diff --git a/doc/txt/fix_nve_dot.txt b/doc/txt/fix_nve_dot.txt deleted file mode 100644 index fcd8926c13..0000000000 --- a/doc/txt/fix_nve_dot.txt +++ /dev/null @@ -1,63 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nve/dot command :h3 - -[Syntax:] - -fix ID group-ID nve/dot :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -nve/dot = style name of this fix command :l -:ule - -[Examples:] - -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. -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. - -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 -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. -The particles are always considered to have a finite size. - -An example input file can be found in /examples/USER/cgdna/examples/duplex1/. -Further details of the implementation and stability of the integrator are contained in "(Henrich)"_#Henrich3. -The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf. - -:line - -[Restrictions:] - -These pair styles can only be used if LAMMPS was built with the -"USER-CGDNA"_Package_details.html#PKG-USER-CGDNA package and the MOLECULE and ASPHERE package. -See the "Build package"_Build_package.html doc page for more info. - -[Related commands:] - -"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "fix nve"_fix_nve.html - -[Default:] none - -:line - -:link(Davidchack1) -[(Davidchack)] R.L Davidchack, T.E. Ouldridge, and M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015). -:link(Miller1) -[(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002). -:link(Henrich3) -[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). diff --git a/doc/txt/fix_nve_dotc_langevin.txt b/doc/txt/fix_nve_dotc_langevin.txt deleted file mode 100644 index 898ca5132b..0000000000 --- a/doc/txt/fix_nve_dotc_langevin.txt +++ /dev/null @@ -1,143 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix nve/dotc/langevin command :h3 - -[Syntax:] - -fix ID group-ID nve/dotc/langevin Tstart Tstop damp seed keyword value :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -nve/dotc/langevin = style name of this fix command :l -Tstart,Tstop = desired temperature at start/end of run (temperature units) :l -damp = damping parameter (time units) :l -seed = random number seed to use for white noise (positive integer) :l -keyword = {angmom} :l - {angmom} value = factor - factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below :pre -:ule - -[Examples:] - -fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10 -fix 1 all nve/dotc/langevin 0.1 0.1 78.9375 457145 angmom 10 :pre - -[Description:] - -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. -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 -over the standard integrator, permitting slightly larger timestep sizes. - -NOTE: Unlike the "fix langevin"_fix_langevin.html this command performs -also time integration of the translational and quaternion degrees of freedom. - -The total force on each atom will have the form: - -F = Fc + Ff + Fr -Ff = - (m / damp) v -Fr is proportional to sqrt(Kb T m / (dt damp)) :pre - -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 -on a per-particle basis. - -Ff is a frictional drag or viscous damping term proportional to the -particle's velocity. The proportionality constant for each atom is -computed as m/damp, where m is the mass of the particle and damp is -the damping factor specified by the user. - -Fr is a force due to solvent atoms at a temperature T randomly bumping -into the particle. As derived from the fluctuation/dissipation -theorem, its magnitude as shown above is proportional to sqrt(Kb T m / -dt damp), where Kb is the Boltzmann constant, T is the desired -temperature, m is the mass of the particle, dt is the timestep size, -and damp is the damping factor. Random numbers are used to randomize -the direction and magnitude of this force as described in -"(Dunweg)"_#Dunweg3, where a uniform random number is used (instead of -a Gaussian random number) for speed. - -:line - -{Tstart} and {Tstop} have to be constant values, i.e. they cannot -be variables. If used together with the oxDNA force field for -coarse-grained simulation of DNA please note that T = 0.1 in oxDNA units -corresponds to T = 300 K. - -The {damp} parameter is specified in time units and determines how -rapidly the temperature is relaxed. For example, a value of 0.03 -means to relax the temperature in a timespan of (roughly) 0.03 time -units tau (see the "units"_units.html command). -The damp factor can be thought of as inversely related to the -viscosity of the solvent, i.e. a small relaxation time implies a -hi-viscosity solvent and vice versa. See the discussion about gamma -and viscosity in the documentation for the "fix -viscous"_fix_viscous.html command for more details. -Note that the value 78.9375 in the second example above corresponds -to a diffusion constant, which is about an order of magnitude larger -than realistic ones. This has been used to sample configurations faster -in Brownian dynamics simulations. - -The random # {seed} must be a positive integer. A Marsaglia random -number generator is used. Each processor uses the input seed to -generate its own unique seed and its own stream of random numbers. -Thus the dynamics of the system will not be identical on two runs on -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. - -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/. -Further details of the implementation and stability of the integrators are contained in "(Henrich)"_#Henrich4. -The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf. - -:line - -[Restrictions:] - -These pair styles can only be used if LAMMPS was built with the -"USER-CGDNA"_Package_details.html#PKG-USER-CGDNA package and the MOLECULE and ASPHERE package. -See the "Build package"_Build_package.html doc page for more info. - -[Related commands:] - -"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html, "bond_style oxdna/fene"_bond_oxdna.html, "bond_style oxdna2/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html - -[Default:] none - -:line - -:link(Davidchack2) -[(Davidchack)] R.L Davidchack, T.E. Ouldridge, M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015). -:link(Miller2) -[(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002). -:link(Dunweg3) -[(Dunweg)] B. Dunweg, W. Paul, Int. J. Mod. Phys. C, 2, 817-27 (1991). -:link(Henrich4) -[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). diff --git a/doc/txt/pair_oxdna.txt b/doc/txt/pair_oxdna.txt deleted file mode 100644 index 8f3f9933e6..0000000000 --- a/doc/txt/pair_oxdna.txt +++ /dev/null @@ -1,112 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style oxdna/excv command :h3 -pair_style oxdna/stk command :h3 -pair_style oxdna/hbond command :h3 -pair_style oxdna/xstk command :h3 -pair_style oxdna/coaxstk command :h3 - -[Syntax:] - -pair_style style1 :pre - -pair_coeff * * style2 args :pre - -style1 = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk} :ul - -style2 = {oxdna/excv} or {oxdna/stk} or {oxdna/hbond} or {oxdna/xstk} or {oxdna/coaxstk} -args = list of arguments for these particular styles :ul - - {oxdna/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 - seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength) - T = temperature (oxDNA units, 0.1 = 300 K) - xi = temperature-independent coefficient in stacking strength - kappa = coefficient of linear temperature dependence in stacking strength - {oxdna/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 - seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength) - eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs) :pre - -[Examples:] - -pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk -pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna/stk seqdep 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna/hbond seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna/hbond seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 :pre - -[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 -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. Average sequence or sequence-dependent stacking and base-pairing strengths -are supported "(Sulc)"_#Sulc1. Quasi-unique base-pairing between nucleotides can be achieved by using -more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. -This prevents the hybridization of in principle complementary bases within Ntypes/4 bases -up and down along the backbone. - -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 "(Ouldridge-DPhil)"_#Ouldridge-DPhil1 and "(Ouldridge)"_#Ouldridge1 -for a detailed description of the oxDNA force field. - -NOTE: These pair styles have to be used together with the related oxDNA bond style -{oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of -"bond_style oxdna/fene"_bond_oxdna.html). Most of the coefficients -in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model. -Exceptions are the first four coefficients after {oxdna/stk} (seq=seqdep, T=0.1, xi=1.3448 and kappa=2.6568 in the above example) -and the first coefficient after {oxdna/hbond} (seq=seqdep 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. - -Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. -A simple python setup tool which creates single straight or helical DNA strands, -DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. - -Please cite "(Henrich)"_#Henrich1 and the relevant oxDNA articles in any publication that uses this implementation. -The article contains more information on the model, the structure of the input file, the setup tool -and the performance of the LAMMPS-implementation of oxDNA. -The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf. - -:line - -[Restrictions:] - -These pair styles can only be used if LAMMPS was built with the -USER-CGDNA package and the MOLECULE and ASPHERE package. See the -"Build package"_Build_package.html doc page for more info. - -[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 oxdna2/fene"_bond_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html - -[Default:] none - -:line - -:link(Henrich1) -[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). - -:link(Sulc1) -[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012). - -:link(Ouldridge-DPhil1) -[(Ouldrigde-DPhil)] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011). - -:link(Ouldridge1) -[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011). diff --git a/doc/txt/pair_oxdna2.txt b/doc/txt/pair_oxdna2.txt deleted file mode 100644 index 64a686d5d9..0000000000 --- a/doc/txt/pair_oxdna2.txt +++ /dev/null @@ -1,121 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style oxdna2/excv command :h3 -pair_style oxdna2/stk command :h3 -pair_style oxdna2/hbond command :h3 -pair_style oxdna2/xstk command :h3 -pair_style oxdna2/coaxstk command :h3 -pair_style oxdna2/dh command :h3 - -[Syntax:] - -pair_style style1 :pre - -pair_coeff * * style2 args :pre - -style1 = {hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh} :ul - -style2 = {oxdna2/excv} or {oxdna2/stk} or {oxdna2/hbond} or {oxdna2/xstk} or {oxdna2/coaxstk} or {oxdna2/dh} -args = list of arguments for these particular styles :ul - - {oxdna2/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 - seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength) - T = temperature (oxDNA units, 0.1 = 300 K) - xi = temperature-independent coefficient in stacking strength - kappa = coefficient of linear temperature dependence in stacking strength - {oxdna2/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 - seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength) - eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs) - {oxdna2/dh} args = T rhos qeff - T = temperature (oxDNA units, 0.1 = 300 K) - rhos = salt concentration (mole per litre) - qeff = effective charge (elementary charges) :pre - -[Examples:] - -pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh -pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 -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 -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. Average sequence or sequence-dependent stacking and base-pairing strengths -are supported "(Sulc)"_#Sulc2. Quasi-unique base-pairing between nucleotides can be achieved by using -more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. -This prevents the hybridization of in principle complementary bases within Ntypes/4 bases -up and down along the backbone. - -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. - -NOTE: These pair styles have to be used together with the related oxDNA2 bond style -{oxdna2/fene} for the connectivity of the phosphate backbone (see also documentation of -"bond_style oxdna2/fene"_bond_oxdna.html). Most of the coefficients -in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model. -Exceptions are the first four coefficients after {oxdna2/stk} (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 in the above example), -the first coefficient after {oxdna2/hbond} (seq=seqdep in the above example) and the three 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. - -Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. -A simple python setup tool which creates single straight or helical DNA strands, -DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. - -Please cite "(Henrich)"_#Henrich and the relevant oxDNA articles in any publication that uses this implementation. -The article contains more information on the model, the structure of the input file, the setup tool -and the performance of the LAMMPS-implementation of oxDNA. -The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf. - -:line - -[Restrictions:] - -These pair styles can only be used if LAMMPS was built with the -USER-CGDNA package and the MOLECULE and ASPHERE package. See the -"Build package"_Build_package.html doc page for more info. - -[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 - -[Default:] none - -:line - -:link(Henrich) -[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). - -:link(Sulc2) -[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012). - -:link(Snodin) -[(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015). - -:link(Ouldridge-DPhil2) -[(Ouldrigde-DPhil)] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011). - -:link(Ouldridge2) -[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011). From 297d31ab8f44166a0f07723a3ca52fd985b61ba0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 11 Jan 2020 19:02:49 -0500 Subject: [PATCH 06/14] clean up and update general command overview --- doc/src/Commands_all.rst | 96 +++++++++++++++++++++------------------- 1 file changed, 51 insertions(+), 45 deletions(-) diff --git a/doc/src/Commands_all.rst b/doc/src/Commands_all.rst index d47c3299d0..5ad8fff44c 100644 --- a/doc/src/Commands_all.rst +++ b/doc/src/Commands_all.rst @@ -25,26 +25,26 @@ An alphabetic list of all general LAMMPS commands. * :doc:`atom_style ` * :doc:`balance ` * :doc:`bond_coeff ` - * :doc:`bond\_style ` - * :doc:`bond\_write ` + * :doc:`bond_style ` + * :doc:`bond_write ` * :doc:`boundary ` * :doc:`box ` - * :doc:`change\_box ` + * :doc:`change_box ` * :doc:`clear ` - * :doc:`comm\_modify ` - * :doc:`comm\_style ` + * :doc:`comm_modify ` + * :doc:`comm_style ` * :doc:`compute ` - * :doc:`compute\_modify ` - * :doc:`create\_atoms ` - * :doc:`create\_bonds ` - * :doc:`create\_box ` - * :doc:`delete\_atoms ` - * :doc:`delete\_bonds ` + * :doc:`compute_modify ` + * :doc:`create_atoms ` + * :doc:`create_bonds ` + * :doc:`create_box ` + * :doc:`delete_atoms ` + * :doc:`delete_bonds ` * :doc:`dielectric ` - * :doc:`dihedral\_coeff ` - * :doc:`dihedral\_style ` + * :doc:`dihedral_coeff ` + * :doc:`dihedral_style ` * :doc:`dimension ` - * :doc:`displace\_atoms ` + * :doc:`displace_atoms ` * :doc:`dump ` * :doc:`dump adios ` * :doc:`dump image ` @@ -52,75 +52,77 @@ An alphabetic list of all general LAMMPS commands. * :doc:`dump netcdf ` * :doc:`dump netcdf/mpiio ` * :doc:`dump vtk ` - * :doc:`dump\_modify ` - * :doc:`dynamical\_matrix ` + * :doc:`dump_modify ` + * :doc:`dynamical_matrix ` * :doc:`echo ` * :doc:`fix ` - * :doc:`fix\_modify ` + * :doc:`fix_modify ` * :doc:`group ` * :doc:`group2ndx ` * :doc:`hyper ` * :doc:`if ` - * :doc:`improper\_coeff ` - * :doc:`improper\_style ` + * :doc:`improper_coeff ` + * :doc:`improper_style ` * :doc:`include ` + * :doc:`info ` * :doc:`jump ` - * :doc:`kim\_init ` - * :doc:`kim\_interactions ` - * :doc:`kim\_query ` - * :doc:`kspace\_modify ` - * :doc:`kspace\_style ` + * :doc:`kim_init ` + * :doc:`kim_interactions ` + * :doc:`kim_param ` + * :doc:`kim_query ` + * :doc:`kspace_modify ` + * :doc:`kspace_style ` * :doc:`label