From 25e2a7a37f32a73efe8b67a2e10dee2edceb5635 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 12 Nov 2019 14:25:45 -0500 Subject: [PATCH 01/64] update bond style table docs about out-of-range errors --- doc/src/bond_table.rst | 5 +- doc/txt/bond_table.txt | 163 ----------------------------------------- 2 files changed, 3 insertions(+), 165 deletions(-) delete mode 100644 doc/txt/bond_table.txt diff --git a/doc/src/bond_table.rst b/doc/src/bond_table.rst index f68288349d..d0ea609aff 100644 --- a/doc/src/bond_table.rst +++ b/doc/src/bond_table.rst @@ -119,8 +119,9 @@ the bond length r (in distance units), the 3rd value is the energy (in energy units), and the 4th is the force (in force units). The bond lengths must range from a LO value to a HI value, and increase from one line to the next. If the actual bond length is ever smaller than -the LO value or larger than the HI value, then the bond energy and -force is evaluated as if the bond were the LO or HI length. +the LO value or larger than the HI value, then the calculation is +aborted with an error, so it is advisable to cover the whole range +of possible bond lengths. Note that one file can contain many sections, each with a tabulated potential. LAMMPS reads the file section by section until it finds diff --git a/doc/txt/bond_table.txt b/doc/txt/bond_table.txt deleted file mode 100644 index 7235214af0..0000000000 --- a/doc/txt/bond_table.txt +++ /dev/null @@ -1,163 +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 - -bond_style table command :h3 -bond_style table/omp command :h3 - -[Syntax:] - -bond_style table style N :pre - -style = {linear} or {spline} = method of interpolation -N = use N values in table :ul - -[Examples:] - -bond_style table linear 1000 -bond_coeff 1 file.table ENTRY1 :pre - -[Description:] - -Style {table} creates interpolation tables of length {N} from bond -potential and force values listed in a file(s) as a function of bond -length. The files are read by the "bond_coeff"_bond_coeff.html -command. - -The interpolation tables are created by fitting cubic splines to the -file values and interpolating energy and force values at each of {N} -distances. During a simulation, these tables are used to interpolate -energy and force values as needed. The interpolation is done in one -of 2 styles: {linear} or {spline}. - -For the {linear} style, the bond length is used to find 2 surrounding -table values from which an energy or force is computed by linear -interpolation. - -For the {spline} style, a cubic spline coefficients are computed and -stored at each of the {N} values in the table. The bond length is -used to find the appropriate set of coefficients which are used to -evaluate a cubic polynomial which computes the energy or force. - -The following coefficients must be defined for each bond type via the -"bond_coeff"_bond_coeff.html command as in the example above. - -filename -keyword :ul - -The filename specifies a file containing tabulated energy and force -values. The keyword specifies a section of the file. The format of -this file is described below. - -:line - -The format of a tabulated file is as follows (without the -parenthesized comments): - -# Bond potential for harmonic (one or more comment or blank lines) :pre - -HAM (keyword is the first text on line) -N 101 FP 0 0 EQ 0.5 (N, FP, EQ parameters) - (blank line) -1 0.00 338.0000 1352.0000 (index, bond-length, energy, force) -2 0.01 324.6152 1324.9600 -... -101 1.00 338.0000 -1352.0000 :pre - -A section begins with a non-blank line whose 1st character is not a -"#"; blank lines or lines starting with "#" can be used as comments -between sections. The first line begins with a keyword which -identifies the section. The line can contain additional text, but the -initial text must match the argument specified in the -"bond_coeff"_bond_coeff.html command. The next line lists (in any -order) one or more parameters for the table. Each parameter is a -keyword followed by one or more numeric values. - -The parameter "N" is required and its value is the number of table -entries that follow. Note that this may be different than the {N} -specified in the "bond_style table"_bond_style.html command. Let -Ntable = {N} in the bond_style command, and Nfile = "N" in the -tabulated file. What LAMMPS does is a preliminary interpolation by -creating splines using the Nfile tabulated values as nodal points. It -uses these to interpolate as needed to generate energy and force -values at Ntable different points. The resulting tables of length -Ntable are then used as described above, when computing energy and -force for individual bond lengths. This means that if you want the -interpolation tables of length Ntable to match exactly what is in the -tabulated file (with effectively no preliminary interpolation), you -should set Ntable = Nfile. - -The "FP" parameter is optional. If used, it is followed by two values -fplo and fphi, which are the derivatives of the force at the innermost -and outermost bond lengths. These values are needed by the spline -construction routines. If not specified by the "FP" parameter, they -are estimated (less accurately) by the first two and last two force -values in the table. - -The "EQ" parameter is also optional. If used, it is followed by a the -equilibrium bond length, which is used, for example, by the "fix -shake"_fix_shake.html command. If not used, the equilibrium bond -length is to the distance in the table with the lowest potential energy. - -Following a blank line, the next N lines list the tabulated values. -On each line, the 1st value is the index from 1 to N, the 2nd value is -the bond length r (in distance units), the 3rd value is the energy (in -energy units), and the 4th is the force (in force units). The bond -lengths must range from a LO value to a HI value, and increase from -one line to the next. If the actual bond length is ever smaller than -the LO value or larger than the HI value, then the bond energy and -force is evaluated as if the bond were the LO or HI length. - -Note that one file can contain many sections, each with a tabulated -potential. LAMMPS reads the file section by section until it finds -one that matches the specified keyword. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restart info:] - -This bond style writes the settings for the "bond_style table" -command to "binary restart files"_restart.html, so a bond_style -command does not need to specified in an input script that reads a -restart file. However, the coefficient information is not stored in -the restart file, since it is tabulated in the potential files. Thus, -bond_coeff commands do need to be specified in the restart input -script. - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the "Build package"_Build_package.html doc page for more -info. - -[Related commands:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html - -[Default:] none From f704079fb7eb7d5673e5f2c79431d4c9f69f179e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 12 Nov 2019 16:13:01 -0500 Subject: [PATCH 02/64] remove trailing whitespace --- src/GRANULAR/fix_pour.cpp | 4 ++-- src/MC/fix_gcmc.cpp | 6 +++--- src/USER-MISC/compute_gyration_shape_chunk.cpp | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp index 2b33b988b8..2255f64eb2 100644 --- a/src/GRANULAR/fix_pour.cpp +++ b/src/GRANULAR/fix_pour.cpp @@ -54,7 +54,7 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) : { if (narg < 6) error->all(FLERR,"Illegal fix pour command"); - if (lmp->kokkos) + if (lmp->kokkos) error->all(FLERR,"Cannot yet use fix pour with the KOKKOS package"); time_depend = 1; @@ -797,7 +797,7 @@ bool FixPour::outside(int dim, double value, double lo, double hi) bool outside_range = (value < lo || value > hi); if (!outside_range || !domain->periodicity[dim]) return outside_range; - // for periodic dimension: + // for periodic dimension: // must perform additional tests if range wraps around the periodic box bool outside_pbc_range = true; diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index 516fe2521d..732e76b77e 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -945,7 +945,7 @@ void FixGCMC::attempt_atomic_insertion() ninsertion_attempts += 1.0; if (ngas >= max_ngas) return; - + // pick coordinates for insertion point double coord[3]; @@ -1300,7 +1300,7 @@ void FixGCMC::attempt_molecule_insertion() ninsertion_attempts += 1.0; if (ngas >= max_ngas) return; - + double com_coord[3]; if (regionflag) { int region_attempt = 0; @@ -1634,7 +1634,7 @@ void FixGCMC::attempt_atomic_insertion_full() ninsertion_attempts += 1.0; if (ngas >= max_ngas) return; - + double energy_before = energy_stored; double coord[3]; diff --git a/src/USER-MISC/compute_gyration_shape_chunk.cpp b/src/USER-MISC/compute_gyration_shape_chunk.cpp index 08484d9301..b493455ebf 100644 --- a/src/USER-MISC/compute_gyration_shape_chunk.cpp +++ b/src/USER-MISC/compute_gyration_shape_chunk.cpp @@ -39,7 +39,7 @@ ComputeGyrationShapeChunk::ComputeGyrationShapeChunk(LAMMPS *lmp, int narg, char int n = strlen(arg[3]) + 1; id_gyration_chunk = new char[n]; strcpy(id_gyration_chunk,arg[3]); - + init(); array_flag = 1; From f1e4f98364bbc4085c1152210fead1732c5f9b0f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 13 Nov 2019 01:04:39 -0500 Subject: [PATCH 03/64] include embedding energy term in PairEAM::single() --- src/MANYBODY/pair_eam.cpp | 19 ++++++++++++++++++- src/MANYBODY/pair_eam.h | 1 + 2 files changed, 19 insertions(+), 1 deletion(-) diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp index 2e118088eb..9d8b0999b5 100644 --- a/src/MANYBODY/pair_eam.cpp +++ b/src/MANYBODY/pair_eam.cpp @@ -43,6 +43,7 @@ PairEAM::PairEAM(LAMMPS *lmp) : Pair(lmp) nmax = 0; rho = NULL; fp = NULL; + need_embed = NULL; map = NULL; type2frho = NULL; @@ -77,6 +78,7 @@ PairEAM::~PairEAM() memory->destroy(rho); memory->destroy(fp); + memory->destroy(need_embed); if (allocated) { memory->destroy(setflag); @@ -151,9 +153,11 @@ void PairEAM::compute(int eflag, int vflag) if (atom->nmax > nmax) { memory->destroy(rho); memory->destroy(fp); + memory->destroy(need_embed); nmax = atom->nmax; memory->create(rho,nmax,"pair:rho"); memory->create(fp,nmax,"pair:fp"); + memory->create(need_embed,nmax,"pair:need_embed"); } double **x = atom->x; @@ -230,6 +234,7 @@ void PairEAM::compute(int eflag, int vflag) p = MIN(p,1.0); coeff = frho_spline[type2frho[type[i]]][m]; fp[i] = (coeff[0]*p + coeff[1])*p + coeff[2]; + need_embed[i] = 1; if (eflag) { phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax); @@ -802,6 +807,18 @@ double PairEAM::single(int i, int j, int itype, int jtype, double r,p,rhoip,rhojp,z2,z2p,recip,phi,phip,psip; double *coeff; + if (need_embed[i]) { + p = rho[i]*rdrho + 1.0; + m = static_cast (p); + m = MAX(1,MIN(m,nrho-1)); + p -= m; + p = MIN(p,1.0); + coeff = frho_spline[type2frho[itype]][m]; + phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; + if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax); + need_embed[i] = 0; + } else phi = 0.0; + r = sqrt(rsq); p = r*rdr + 1.0; m = static_cast (p); @@ -818,7 +835,7 @@ double PairEAM::single(int i, int j, int itype, int jtype, z2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; recip = 1.0/r; - phi = z2*recip; + phi += z2*recip; phip = z2p*recip - phi*recip; psip = fp[i]*rhojp + fp[j]*rhoip + phip; fforce = -psip*recip; diff --git a/src/MANYBODY/pair_eam.h b/src/MANYBODY/pair_eam.h index 8bcb44c347..d55aea0f11 100644 --- a/src/MANYBODY/pair_eam.h +++ b/src/MANYBODY/pair_eam.h @@ -70,6 +70,7 @@ class PairEAM : public Pair { // per-atom arrays double *rho,*fp; + int *need_embed; // potentials as file data From e0646b73e3e6d789ff05f973c1a20713ae8a609d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 13 Nov 2019 01:32:57 -0500 Subject: [PATCH 04/64] revised implementation of inclusion of embedding energy in PairEAM::single() this variant is also ported to USER-OMP and OPT --- src/MANYBODY/pair_eam.cpp | 15 ++++++++------- src/MANYBODY/pair_eam.h | 2 +- src/OPT/pair_eam_opt.cpp | 12 ++++++++---- src/USER-OMP/pair_eam_omp.cpp | 4 ++++ 4 files changed, 21 insertions(+), 12 deletions(-) diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp index 9d8b0999b5..8913b1e9cc 100644 --- a/src/MANYBODY/pair_eam.cpp +++ b/src/MANYBODY/pair_eam.cpp @@ -43,7 +43,7 @@ PairEAM::PairEAM(LAMMPS *lmp) : Pair(lmp) nmax = 0; rho = NULL; fp = NULL; - need_embed = NULL; + count_embed = NULL; map = NULL; type2frho = NULL; @@ -78,7 +78,7 @@ PairEAM::~PairEAM() memory->destroy(rho); memory->destroy(fp); - memory->destroy(need_embed); + memory->destroy(count_embed); if (allocated) { memory->destroy(setflag); @@ -153,11 +153,11 @@ void PairEAM::compute(int eflag, int vflag) if (atom->nmax > nmax) { memory->destroy(rho); memory->destroy(fp); - memory->destroy(need_embed); + memory->destroy(count_embed); nmax = atom->nmax; memory->create(rho,nmax,"pair:rho"); memory->create(fp,nmax,"pair:fp"); - memory->create(need_embed,nmax,"pair:need_embed"); + memory->create(count_embed,nmax,"pair:count_embed"); } double **x = atom->x; @@ -234,7 +234,7 @@ void PairEAM::compute(int eflag, int vflag) p = MIN(p,1.0); coeff = frho_spline[type2frho[type[i]]][m]; fp[i] = (coeff[0]*p + coeff[1])*p + coeff[2]; - need_embed[i] = 1; + count_embed[i] = 0; if (eflag) { phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax); @@ -271,6 +271,7 @@ void PairEAM::compute(int eflag, int vflag) rsq = delx*delx + dely*dely + delz*delz; if (rsq < cutforcesq) { + ++count_embed[i]; jtype = type[j]; r = sqrt(rsq); p = r*rdr + 1.0; @@ -807,7 +808,7 @@ double PairEAM::single(int i, int j, int itype, int jtype, double r,p,rhoip,rhojp,z2,z2p,recip,phi,phip,psip; double *coeff; - if (need_embed[i]) { + if (count_embed[i] > 0) { p = rho[i]*rdrho + 1.0; m = static_cast (p); m = MAX(1,MIN(m,nrho-1)); @@ -816,7 +817,7 @@ double PairEAM::single(int i, int j, int itype, int jtype, coeff = frho_spline[type2frho[itype]][m]; phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax); - need_embed[i] = 0; + phi *= 1.0/static_cast(count_embed[i]); } else phi = 0.0; r = sqrt(rsq); diff --git a/src/MANYBODY/pair_eam.h b/src/MANYBODY/pair_eam.h index d55aea0f11..3f135aaa1f 100644 --- a/src/MANYBODY/pair_eam.h +++ b/src/MANYBODY/pair_eam.h @@ -70,7 +70,7 @@ class PairEAM : public Pair { // per-atom arrays double *rho,*fp; - int *need_embed; + int *count_embed; // potentials as file data diff --git a/src/OPT/pair_eam_opt.cpp b/src/OPT/pair_eam_opt.cpp index ad24aaee63..dbea720488 100644 --- a/src/OPT/pair_eam_opt.cpp +++ b/src/OPT/pair_eam_opt.cpp @@ -80,11 +80,13 @@ void PairEAMOpt::eval() // grow energy array if necessary if (atom->nmax > nmax) { - memory->sfree(rho); - memory->sfree(fp); + memory->destroy(rho); + memory->destroy(fp); + memory->destroy(count_embed); nmax = atom->nmax; - rho = (double *) memory->smalloc(nmax*sizeof(double),"pair:rho"); - fp = (double *) memory->smalloc(nmax*sizeof(double),"pair:fp"); + memory->create(rho,nmax,"pair:rho"); + memory->create(fp,nmax,"pair:fp"); + memory->create(count_embed,nmax,"pair:count_embed"); } double** _noalias x = atom->x; @@ -238,6 +240,7 @@ void PairEAMOpt::eval() ++m; coeff = frho_spline[type2frho[type[i]]][m]; fp[i] = (coeff[0]*p + coeff[1])*p + coeff[2]; + count_embed[i] = 0; if (EFLAG) { double phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax); @@ -280,6 +283,7 @@ void PairEAMOpt::eval() double rsq = delx*delx + dely*dely + delz*delz; if (rsq < tmp_cutforcesq) { + ++count_embed[i]; jtype = type[j] - 1; double r = sqrt(rsq); double rhoip,rhojp,z2,z2p; diff --git a/src/USER-OMP/pair_eam_omp.cpp b/src/USER-OMP/pair_eam_omp.cpp index 99417f27da..1b48214ed4 100644 --- a/src/USER-OMP/pair_eam_omp.cpp +++ b/src/USER-OMP/pair_eam_omp.cpp @@ -51,9 +51,11 @@ void PairEAMOMP::compute(int eflag, int vflag) if (atom->nmax > nmax) { memory->destroy(rho); memory->destroy(fp); + memory->destroy(count_embed); nmax = atom->nmax; memory->create(rho,nthreads*nmax,"pair:rho"); memory->create(fp,nmax,"pair:fp"); + memory->create(count_embed,nmax,"pair:count_embed"); } #if defined(_OPENMP) @@ -198,6 +200,7 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr) p = MIN(p,1.0); coeff = frho_spline[type2frho[type[i]]][m]; fp[i] = (coeff[0]*p + coeff[1])*p + coeff[2]; + count_embed[i] = 0; if (EFLAG) { phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax); @@ -243,6 +246,7 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr) rsq = delx*delx + dely*dely + delz*delz; if (rsq < cutforcesq) { + ++count_embed[i]; jtype = type[j]; r = sqrt(rsq); p = r*rdr + 1.0; From 32753a59e6ae5d8c9b1eadf09e8507033464a957 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 14 Nov 2019 09:42:44 -0500 Subject: [PATCH 05/64] one more whitespace cleanup --- src/fix_print.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/fix_print.cpp b/src/fix_print.cpp index 54132a3ce6..54a706d24b 100644 --- a/src/fix_print.cpp +++ b/src/fix_print.cpp @@ -136,7 +136,7 @@ void FixPrint::init() } else { if (update->ntimestep % nevery) next_print = (update->ntimestep/nevery)*nevery + nevery; - else + else next_print = update->ntimestep; } From 9ea5e402553f807fa615af6fe445a3d118945789 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 14 Nov 2019 12:35:50 -0500 Subject: [PATCH 06/64] move developer's guide tex sources back to src/Developer --- doc/{txt => src}/Developer/.gitignore | 0 doc/{txt => src}/Developer/classes.fig | 0 doc/{txt => src}/Developer/classes.pdf | Bin doc/{txt => src}/Developer/developer.tex | 0 4 files changed, 0 insertions(+), 0 deletions(-) rename doc/{txt => src}/Developer/.gitignore (100%) rename doc/{txt => src}/Developer/classes.fig (100%) rename doc/{txt => src}/Developer/classes.pdf (100%) rename doc/{txt => src}/Developer/developer.tex (100%) diff --git a/doc/txt/Developer/.gitignore b/doc/src/Developer/.gitignore similarity index 100% rename from doc/txt/Developer/.gitignore rename to doc/src/Developer/.gitignore diff --git a/doc/txt/Developer/classes.fig b/doc/src/Developer/classes.fig similarity index 100% rename from doc/txt/Developer/classes.fig rename to doc/src/Developer/classes.fig diff --git a/doc/txt/Developer/classes.pdf b/doc/src/Developer/classes.pdf similarity index 100% rename from doc/txt/Developer/classes.pdf rename to doc/src/Developer/classes.pdf diff --git a/doc/txt/Developer/developer.tex b/doc/src/Developer/developer.tex similarity index 100% rename from doc/txt/Developer/developer.tex rename to doc/src/Developer/developer.tex From 0ef3d0e59adc4744627d5f6f8fdacb734b804893 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 14 Nov 2019 12:36:05 -0500 Subject: [PATCH 07/64] update README --- doc/README | 28 +++++++++++++--------------- 1 file changed, 13 insertions(+), 15 deletions(-) diff --git a/doc/README b/doc/README index 6db4ba3ca7..96b17f9bf5 100644 --- a/doc/README +++ b/doc/README @@ -5,7 +5,7 @@ sub-directories and optionally 2 PDF files and an ePUB file: src content files for LAMMPS documentation html HTML version of the LAMMPS manual (see html/Manual.html) -tools tools and settings for building the documentation +utils utilities and settings for building the documentation Manual.pdf large PDF version of entire manual Developer.pdf small PDF with info about how LAMMPS is structured LAMMPS.epub Manual in ePUB format @@ -25,17 +25,12 @@ the fetched documentation will include those changes (but your source code will not, unless you update your local repository). (b) You can build the HTML and PDF files yourself, by typing "make -html" followed by "make pdf". Note that the PDF make requires the -HTML files already exist. This requires various tools including -Sphinx, which the build process will attempt to download and install -on your system, if not already available. See more details below. - -(c) You can genererate an older, simpler, less-fancy style of HTML -documentation by typing "make old". This will create an "old" -directory. This can be useful if (b) does not work on your box for -some reason, or you want to quickly view the HTML version of a doc -page you have created or edited yourself within the src directory. -E.g. if you are planning to submit a new feature to LAMMPS. +html" or by "make pdf", respectively. This requires various tools +including the Python documentation processing tool Sphinx, which the +build process will attempt to download and install on your system into +a python virtual environment, if not already available. The PDF file +will require a working LaTeX installation with several add-on packages +in addition to the Python/Sphinx setup. See more details below. ---------------- @@ -47,10 +42,9 @@ Options: make html # generate HTML in html dir using Sphinx make pdf # generate 2 PDF files (Manual.pdf,Developer.pdf) # in this dir via htmldoc and pdflatex -make old # generate old-style HTML pages in old dir via txt2html make fetch # fetch HTML doc pages and 2 PDF files from web site # as a tarball and unpack into html dir and 2 PDFs -make epub # generate LAMMPS.epub in ePUB format using Sphinx +make epub # generate LAMMPS.epub in ePUB format using Sphinx make clean # remove intermediate RST files created by HTML build make clean-all # remove entire build folder and any cached data @@ -103,7 +97,11 @@ Installing prerequisites for epub build ## ePUB Same as for HTML. This uses the same tools and configuration -files as the HTML tree. +files as the HTML tree. The ePUB format conversion currently +does not support processing mathematical expressions via MathJAX, +so there will be limitations on some pages. For the time being +until this is resolved, building and using the PDF format file +is recommended instead. For converting the generated ePUB file to a mobi format file (for e-book readers like Kindle, that cannot read ePUB), you From 125b29a686e2688533dd41eb33f2b886451df10e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 14 Nov 2019 13:50:30 -0500 Subject: [PATCH 08/64] replace non-ascii character --- doc/src/Install_conda.rst | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/doc/src/Install_conda.rst b/doc/src/Install_conda.rst index 04b8054353..33188e2540 100644 --- a/doc/src/Install_conda.rst +++ b/doc/src/Install_conda.rst @@ -32,12 +32,10 @@ install the `openkim-models` package If you have problems with the installation you can post issues to `this link `_. - -.. _conda_forge_lammps: https://github.com/conda-forge/lammps-feedstock/issues - -Thanks to Jan Janssen (Max-Planck-Institut für Eisenforschung) for setting +Thanks to Jan Janssen (Max-Planck-Institut fuer Eisenforschung) for setting up the Conda capability. +.. _conda_forge_lammps: https://github.com/conda-forge/lammps-feedstock/issues .. _openkim: https://openkim.org @@ -45,9 +43,6 @@ up the Conda capability. .. _mini_conda_install: https://docs.conda.io/en/latest/miniconda.html - - - .. _lws: http://lammps.sandia.gov .. _ld: Manual.html .. _lc: Commands_all.html From 9c1d5e76cc59597f796c74c22b3ee951f1d9f11a Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 14 Nov 2019 15:15:46 -0500 Subject: [PATCH 09/64] Update docs: angle_charmm --- doc/src/Eqs/angle_charmm.jpg | Bin 3932 -> 0 bytes doc/src/Eqs/angle_charmm.tex | 9 ---- doc/src/angle_charmm.rst | 52 ++++++++++---------- doc/txt/angle_charmm.txt | 89 ----------------------------------- 4 files changed, 25 insertions(+), 125 deletions(-) delete mode 100644 doc/src/Eqs/angle_charmm.jpg delete mode 100644 doc/src/Eqs/angle_charmm.tex delete mode 100644 doc/txt/angle_charmm.txt diff --git a/doc/src/Eqs/angle_charmm.jpg b/doc/src/Eqs/angle_charmm.jpg deleted file mode 100644 index c6e6c297d2020d7c1abc75185316e7d706fe5976..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 3932 zcmbuC_g4}Q_s1bj^rMO9$B9a=%v^~%a956o*?39|a3sz!cZvzla+HE2EKM`BZKWxR z=3d}HP0g*SL6`$^lq=M)pXYnN&mZu8UiX~)%YC2s{pFr}?%f^UodSrTwL4=600M!4 z(|ZBf9Rr*K><0-52!QtQrTzQ&3xY+3zhBLD*SfduwT2!anPOX{DvB=olmJXlIv_2i8>naj=|p_va0U-W<5 z9R&#eV`v4~&QAXS@}Qfsm#K2xu|9IUQwIJ-ZUUue%Sn$B97S6Jqp9Tq z^gO6XvV&{r%8AyCbW(V=8@UpwYL7?-!t6q1w3 z$ik2bhZh6WPxF1O+YkBr-O$zz&u8=6p~#0e=-hxaU5kWg{!0$7fwBx+ha(**@^I6p zaui3KD8{?E@0@*j+Zt?$R-Ws^9uZ?WgK9}78TUJ*{{(QIFSyp+;X5dQ^n<6LH~^*- z7r#z9EDXBvFWf~jX8d=)X5aHUqgC8E3x(`B>EEL}2J84jEl;o1=?{9d@NgRT5&Oyf zDG-m%(H+0~i#b!KzYGO%VHzm2&=iwu^P!CX#$`*l%n1{ObU?oJjeIDi2-#n)q8nYk z9Xw92?(yY2aF@rwl&NT=^Agu$3fLx3#X4sPni`=iBSNEei}DV$=O1LF&=YIX#+3=r zH~=FqDVh`#r9gj;8{hr}V|w9#bHZ+Mv6BKTCuicypRwe^D{g;|YV$+Yr{szfHjlUf zENi%H{%I>r&Mv?}c!|T0ClHf+ShrZF3H@z4KcI#}j4r}(QJDt;WvC5O6-_%7+g^C6 z019H=q>?U2yA`j7Mif+iGcib|HS7YKb$+&RGf}#Jy`tC$@?D$#OdhbAAnY8X&}uFv z^pW}7LR0tZD<*AWD_esovoWML8zQpGX?8!WBa zMuA(((@k~@wQPz%Zijih=F1w+1D5!G@NH*@sDn;6PNcYz9dIT#Vj4@~9zV#Mu}-Xf z5MYQhbe2-M&VPx{-(Ea3f5ouK5**vKp0Ubry{@ADGLQV8elaHEXOG(7L0@e{HPixn zv;BmBY4OI73!2)Kpn}RjJ_eam{u%V^jz#Pb!8KS!*uNa+u9Z(b{4h~rnWOqG9g;+| zN``bIIR!zskB+=fE*G=XA(v~5Pjf|<+7%X4BenulBf@vWGqjQd^E1t1UQcFeM>`{_ zdOsqbtZS~)o;;^j?gFIcztT3o=U(EMosL?wl&2lfr^MCTpnbRjv+x=ixB+{XbAf@_ zZ;tAWF*pSI?UnV*H#Kles^m2tp&lKPQWcfanbCN;$g8RPU9-^rUi~uT_y%F6tk?2u zP$a`}uFAm$Pu9sDe5`)21zSs88QQt)OUf626WQ&mjUKQWp9IsMXt|6s5-^87ghu@E zX-h^H)W!0cTFNe9kSMnc(23cezuH(<`a_xWGcpmDxfS56M^A1@a^Hx+Ot9x?Ts!UR z&3|<&wry4f7T1&<$d(NpyN(FH#((H`KVURi)+5Y4O+TMqS>0}F&9zDigOw*8-kzB~ zd=w=$;;c#3qj_Ns3twpkDYXMZ!l5p^Ipd2}E#?cR*X6%j7R88EzQ2)8 zV2hvY7eie}s9|B|gTY=I`@&qOI*H*)Ra}9MCE=yd#j8H&;0j6LHA2tt>*MjY8s0u_ zA;Q@9w1c&MruIgM!4V|Jpv_mq!cys(=dFB5?6PZ~0-+{JH9_Q$<92v$+Oa!jRXx1W zaq}EERXb`KJ@8b=Pre(1#D08qBoD)!>t6>bF^4`a1Y?G$mpHW_{a{Yy_^C>?k8;9W zJVwuDP(R>D$funqrPtG2--#7?8|QX`@L&M!mSd}W3{ZUed~tR+h`g1+@x}6SF0b~ zQKYRnt}TcN$-E**g?W<)XAL>a5Z2S~JO+O7NbcNrdRqYpG@ zD{!M@$AS6CqM2V#y_u*m{FKjMpf*mDausMNz8MAK zEA+`B1{lSx5*?Hv&PCEwqS7S$*r&#B`K1#uv!&uMb}p9KH^$y0xvp2WJqr?TohbgG zt#AtLTfw_$nF^n~YX?|GhIdStrgc2aZ3aZ+97vtLHYw?T#UUS7~S&>`O#J?0Yte&RzuIKzbZ<~5! zMDgwg4~@VEOQ4c{{=#4Nle+dhS*uoC?=S2ELi*hoN7`5_)IdlS#GteK9U8BjZE;YL z0YBYiI^0i+H!dozqPluA2BXEy9g(dH*>1)}8V2TS4?=Bp=Q3UvkpCpY`xJz@0x|mF zOG?6gAJts;vNvxu?w9NV=-|XUZbBxiKtBSTr!a-jR}_pDj0MqCL(Q{&Uh0RwExmZ@ z56#5W{k8gxSx|NaaXq(6`TIpW!pGg`NewOR{{6Ehz=|A;rw$m~CqPNgKu<_?)T`f+(m7DT>ck7m5+Bk_*G zhbBXxPx>;2dUe7)VFI|N=#y8w3E1HN-$+I5uZVF$tQ-rxaJqtY#(oCy*@hqJ?)YJ8P=4(yZDI+)*{h zkzd5dkC9{`C0Rul_?^viw9jMh!&Js%-j zvg&2pl1p&`c_%K&JZM0*!6y}4P)2VttpQDFb@<7V0;Ww`ayrrsRYsF6GaszGhU1Nb z^&WL0OYEW9tlO%^HyO`O8048J-$+$0VpAiJxdh=Y#j`&Nk;g3bve#T_d6I1S_4C~# z7Drb`bG;D_J8sjJCOqUM*{4rl8XNpT4mD8V#Eek&(NTj0V!!+M96oGs@Uw6^tEB zOe0)D5=sCD7U#KxNf|!Wdt0&Jg(yYbzON;b@+p;6ichke?~>+ti<3gB%FVSDsx^H z(y3r`9z4^h<}dCD%4Fj>fhAJUJ7%<;ifG3&Yb>f%QO??(!<_ZcTy+MqIu5!#m-grF zw#MD_-;~_4X->IxSPmIeNUoYxTT=t>l&j>PuRGgiaj#mvuyy+`b#yY-dI55!%F@(n z&53SU`JC9(6&7PJc}d2@T=wimrJOCLS|FoepyowGU_hQa8s-S0gigTa7( zssqDFlcb&xxRHJp6~>CL8e<6You7^E_Qc2V0*S9*e>z@nH$0{s&JQ>K2Jq$8k7K(c zTnpPre$MROSpJCv?;sz~$)h>8%A({ch+2iQ#i$Y<=URTP$+Pqd?zL>S zSXQn;dj!jN)QFqvtG5bxb@>@V@($|Pvln!r>I`;#gLS}tJYZ>Qi8-+;5;IU7eq$=~ zs0k?JQsxRQP6TOgaVUwd}}?ypq- zmoyT+pI#AuIj$5QnQu1S7e%m-42@k2=pMiQp|Y|-ElXWOLc*?{HOnskYiRF(0au)Y zrf`G(1pM)7v0-@Ju+7O~JOUaw8n9Oi>{LQ}rSeDnQvr&VWi!!~ZR_ qdjxYtKSap6W4YFJdr_j=){W6cu2Mt(fdaz+IsM!2zf3W^BmV<@w}kTm diff --git a/doc/src/Eqs/angle_charmm.tex b/doc/src/Eqs/angle_charmm.tex deleted file mode 100644 index 00b37ba335..0000000000 --- a/doc/src/Eqs/angle_charmm.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K (\theta - \theta_0)^2 + K_{UB} (r - r_{UB})^2 -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/angle_charmm.rst b/doc/src/angle_charmm.rst index 561e6cfab3..92ab8b5ea3 100644 --- a/doc/src/angle_charmm.rst +++ b/doc/src/angle_charmm.rst @@ -1,22 +1,22 @@ -.. index:: angle\_style charmm +.. index:: angle_style charmm -angle\_style charmm command -=========================== +angle_style charmm command +========================== -angle\_style charmm/intel command -================================= +angle_style charmm/intel command +================================ -angle\_style charmm/kk command +angle_style charmm/kk command +============================= + +angle_style charmm/omp command ============================== -angle\_style charmm/omp command -=============================== - Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style charmm @@ -24,7 +24,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style charmm angle_coeff 1 300.0 107.0 50.0 3.0 @@ -34,12 +34,15 @@ Description The *charmm* angle style uses the potential -.. image:: Eqs/angle_charmm.jpg - :align: center +.. math:: -with an additional Urey\_Bradley term based on the distance *r* between -the 1st and 3rd atoms in the angle. K, theta0, Kub, and Rub are -coefficients defined for each angle type. + E = K (\theta - \theta_0)^2 + K_{ub} (r - r_{ub})^2 + + +with an additional Urey\_Bradley term based on the distance :math:`r` between +the 1st and 3rd atoms in the angle. :math:`K`, :math:`\theta_0`, +:math:`K_{ub}`, and :math:`R_{ub}` are coefficients defined for each angle +type. See :ref:`(MacKerell) ` for a description of the CHARMM force field. @@ -49,13 +52,13 @@ The following coefficients must be defined for each angle type via the the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* K (energy/radian\^2) -* theta0 (degrees) -* K\_ub (energy/distance\^2) -* r\_ub (distance) +* :math:`K` (energy/radian\^2) +* :math:`\theta_0` (degrees) +* :math:`K_{ub}` (energy/distance\^2) +* :math:`r_{ub}` (distance) -Theta0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of K are in energy/radian\^2. +:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians +internally; hence the units of :math:`K` are in energy/radian\^2. ---------- @@ -108,8 +111,3 @@ Related commands **(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/angle_charmm.txt b/doc/txt/angle_charmm.txt deleted file mode 100644 index 8b0e298a43..0000000000 --- a/doc/txt/angle_charmm.txt +++ /dev/null @@ -1,89 +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 - -angle_style charmm command :h3 -angle_style charmm/intel command :h3 -angle_style charmm/kk command :h3 -angle_style charmm/omp command :h3 - -[Syntax:] - -angle_style charmm :pre - -[Examples:] - -angle_style charmm -angle_coeff 1 300.0 107.0 50.0 3.0 :pre - -[Description:] - -The {charmm} angle style uses the potential - -:c,image(Eqs/angle_charmm.jpg) - -with an additional Urey_Bradley term based on the distance {r} between -the 1st and 3rd atoms in the angle. K, theta0, Kub, and Rub are -coefficients defined for each angle type. - -See "(MacKerell)"_#angle-MacKerell for a description of the CHARMM force -field. - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy/radian^2) -theta0 (degrees) -K_ub (energy/distance^2) -r_ub (distance) :ul - -Theta0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of K are in energy/radian^2. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the "Build package"_Build_package.html doc page -for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] none - -:line - -:link(angle-MacKerell) -[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, -Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). From 28402ad656fcd4a3ef18b9f508462dc3199811ae Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 14 Nov 2019 15:35:55 -0500 Subject: [PATCH 10/64] Update docs: angle_class2 --- doc/src/Eqs/angle_class2.jpg | Bin 16202 -> 0 bytes doc/src/Eqs/angle_class2.tex | 12 --- doc/src/angle_class2.rst | 102 +++++++++++++------------- doc/txt/angle_class2.txt | 138 ----------------------------------- 4 files changed, 52 insertions(+), 200 deletions(-) delete mode 100644 doc/src/Eqs/angle_class2.jpg delete mode 100644 doc/src/Eqs/angle_class2.tex delete mode 100644 doc/txt/angle_class2.txt diff --git a/doc/src/Eqs/angle_class2.jpg b/doc/src/Eqs/angle_class2.jpg deleted file mode 100644 index f0f2a5152ed00db4ecdfe1c21dab476e69235dc0..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 16202 zcmcJ$XHZk^_xBqRL_k^qQ943|&{V3@tB}w`?;=H7Ksrd3UL-(BKm?>E^j;D=D!obX zP3av0>8OYMex7sYoZpN8`Mr7eo>?<{_MTbmx~@HIeXq}6`|tGM?*MA(3&;xq0RaI( z_2vZpodYNWh;I=Q5#1ubF~r2gw@L2aA-OrI$jM3X(og|`G*mP+wD*`9Xz3W~X=v_q z+-GEAVPj*XWq8Q-kd=#>m5uf9X8`#fKncmDAq3;3N1g`u$E|6_))eaF=K8E#g$ z9|}=(V5iUY27GD{Hrc3;f^Dq9T%Bj1#HDAsn`PAXo2}srg#1)^k$hlTzecGD^-g@;gAHz zQ!hz(#ZSupqrC)!^dFrL=G|#%I0N;o z3VKH+k*t^^k4x*@d)BF8Xt8QP!hmR&wx2TM_VGvk|AYY6jU4m{W zuLNsI7PJ?dZFZUP@UiY~0w!RCMnmyp3G&|jhb`A1$c?CFmI{a2E5M5#$F+}(0zTyG z{wd_%j?#S|+O6P*rwfYYZ?<^ffC55;ve^#ly|8>t6_sP}aXW)JeCiiWksJekM@g(o z(K4EaN=^%FgVh!cR7qke3IoK)nB~t;xa#+kyQq8OfA)H`A5u=$?gfT$deylPy54Jw z$d~RXZW3i(dtPWsH~(QjC!*dH{S4SDFRM*;9@{wjKdd>gEU4*4Cnyo2IiMQZ9;4^agMJPg$$dKTgII>2Xb?eeZl zWJxs^@#xik3byn{Q{L<!mk?xDw4n@4A_sYxwdS%A1&vl|$&5?|#irr`C2+}qgZS)pCcL(wPj2hzwNV7bDl z_xv^M<&LFbxt_c(^^^n>SKd2#Jz-PjnDl1f$HE9DK~0)#;RnoFav*MhH@Qov9dj-6 z#J#KA-TO1N@@Zq*aUb3rR`*Sk_u6|i$2l0X30{lq-e0(!N;1~*t?4oQpyoC?THQAX z(s-6X`K*-K+k{T4X~+6y>{Yxa+z*u5)bddQqv+Ocq894_|D;j>??V&*G7sLhFS}+pLUxm1w>4-!UUZYXDQ0x zDxegaD4|gAKs}PelEFN|jssfV+at*{f{GE{Rv=w-lCND+N zTBEe4?$G0Bs|u?>*xH{a_5LD+`QYiO@>}c1e>PAqRXPXlC5b%96ur|B-RaL?_Odx8 z%Bly4b~`#~_Y(eZh62<39}<{Z{~nubf3?g<^QyZF?YuVqH9WTN9g$47DRE()ko9Ff zJ#9Jw>C}MarCx{s;QGYNR|~JVQsgl0h{#vfyZ!$5%i-Zzkb*)q_zKo z^=ov#ahutK&_;EC#+;QBQ4XqPoTD~}i3J722Avp#b$sUNnEF2Ib??XDdq;XMiTRMe zi0}X6Ce_^HQ+|0Y%5+I(`xmg{?s_2F{TFZmOOfQ46k<^qFV~Dxc;0189?GKSpL_MWT~Q#UdPYnJjwL_Czh^dg zP}E{8Os=gy?7H203ARp65)~ioUmIOPt>GH*j|${!zq!zn7>sIP6{}G^XD>k@v(c^L zaIh-l$jrXWiPrWlm&g2D%Zan7lp}Fe_3f`J3x)(WyJB+JJtYzLmKz%QIrPINyHww# zmPaB!CUB+AGhQzTRn1>i?*12yYv#oGHD5L@##+lKrt>B9X~@^}tIB8s4T-C7MamFf zB-M}alJC}F$rXMA)l(^6RQy#Bds#c30>yl9L)qL^?;J9FeVqZ%jzuP03K z7WlntJlB;v z%?P?!(%k02aWJTZn%6ky$gR?#TLM+^$@WiP>Y3u*6lml7eCa!p zdl9<0X0bYuEVJ>DzmUvfYS9bI3(-pqrXrZ9;zecp_rg<}YYP2rWA3S*@|kYcd=}Ea zij`A|UMauVt2v1g3rP&p4qI9;-uw7l5+f#QA?umAH!EF1j`nR7VT6)DevKy#U%6 z?`^$bMHh8zMc3^?R|e&H5|OzmG)=h@VcDk>Q78-@xKxILM?;NMpaiD z=)mx<*~&B*dQX+4gS8wD0H!%(n9&B$M3frJ03oR{@qW8CpQ_<2rIUak~W|88R< z=2-*zf^OXOsh-A1{lP*V7@~@ProX#RoM^bd*3W<*ifkUZN$KH`+jMBIL`)GmgjHoY#PQ2N^TEgTxbkR0 zQA=z&&5}exk5r+SzSE)`3K{vuxmf*=Of^~xj3gvK5F0l6N;4?uu5+ZilqNHQEID5^ zc4=E>*pVWV(zo%;=aRr|k(-S4tDfEJ54xIaG5TkWSY9@B`USu0@>Lms@9)3)}rKJ`4TZ!`CN89}InqDPr`*ff`!CY?N zSJR#&`->M!C*LIB3;%e5Q*LM;MmBfbxrua0T+n9nBQ(}8IqXj z@2+MISvn99rMLGMP1plYa=eyHAl;SLT@ylTiR%bZ;I?u8r4bTjLjz?L$vNd%sJ?%Z zu^B%bQM0YbaKQuo3&GpT>pS7$xarFxTQJ+6p-{h$M@K1(Y_mBg%7Ywd2#oDVr_a;=goePJ?+4w~27C=4)l0h|hqt7yjptCg!a3bR^4? zgX7n;o#9;(4_B|nT!hKr%jqR5=uXoYK~;I7B)u&@+|kDm>)vve1`fC^|B;p6DNOS8 zyO>g86u1t+V#(dc3lvqE!(LK;7B9b?X&I+uS~-$<=hHRbZxt<8D4e*-jYM`rjP?g+%LZFK67!7%BgYPjxJo0ynqYPcwwI*R zm!em+nr?6K^N(H3;g#$HYVl+T)$>P@XLy??u;3Vp#AXSB zWU+{l;eG$C4ZX!&nG)<@0PC0GGGQOx(S13;;=6AU@IRW*cJ3H9(pBwPzU@T!wEygA za)1{+HUvA*mJXB##HL)s!HY z3x0{4&Iw8pbOmzTjcZ_&)b#g~(x2e7%RgVy@$5qqw~iF;Au#lH$fJ6(*WL|OHRzR+ zRQG(>qdB`Zd$MC(ZNbRTQv9wSn!Un&(jePAli(7VQ)4Q0P`~@Z?GsHww(l^=so4R% zKNof+V?68iT`jW(wetvf#kTR#%l$pP@w7!n@^Rv)t>C@aSAvp5Soi_ zUN9t{;K{_HzM?siLCtv>pIFM?~}`!5tn;y|NH5k2b-&b8a)dRU?Hf{*q{Z>{ZN#A@cn z#PS(D%D1)`r{&ZU&p}KM*i5kHy5wP@R(T`GSzqkJ>Dl}Ew~RZJOSk^z((^fu&NCKW zsW?iMz&HwPq8lGxCS8mCF7xq;Ip-((iT9^KT04jGHwug~vYpFJvEdG+-#CH-_+d7)+l16y zRN%$-Krm$$698O1*4ApfM#x*v| zrDHrZ^1`7_B}h5fUziDTnb-FD%wc>d*@>jlATu7b88#i__yTS4&FU#=v&4s?)uIO) zB6cxY$+#~|ZMx^2m4DqLsqeb~A$YrA_|I&@UqE?@0R??wX`hCt$CmYjE?I*9B($S&o;>`ez|<{U zi`zpl%U|XNo!mcFOPm!R&}{dh$*)3+@|5u)jNg*KuVvxda)PEGd_J3oB^~pyF1m5F zmp|Ax`<=Tt8Aa13OAbSd{#s9!^gmcEnYk^|1v$-2IBRl|B%F%!O@c+G%uuxmKukgt z<#!`LOaBGD&7|zkZOd8@l#d>Z!3}yfX`t$l7Wm?rtfpXCB$U~=v|vn?$XilclGE<` znkbK@!4!UUEvL78PM$LJ0`Xaa)jq7nXKmA;W!JEEZ#(N(|J^^^kiUQ@MHzNthAdit zkc*{w_UtTx>7HQwkB$D+=Tz=Xa3@4|E>Zh^r(d7>JofGQ zcZA&Hyf#6#OmnPfpwv$GXs&D0k;*6M8Nta98bp7pgayiP(qh{a*wtG$4YqHEVugNf zm$tpYj3^f1ZE1VKXU?v4U^W`}Wx}AxFGCq>dJe2BM|d~A#a!RxHe1c$V+N`}2cGf0 z2TIG6c@1W*^X;p7$6Iv^`piV>l#Q^YoCOBNXO~%ir+CAf=9%@YVi#ABPhIdnNmhQl z-;dyn<%9+XNory!zwe4b5ff$cAztQM*?!3lLuzpGv>c5E6Zt4l2WzN{DR)?Qf`aN= zg)Q00fP2Q*-hw37*`frCnF!Y!E?>mAXuNiW^Z=i|w!GU{)#bz)l0_UAA#0!hD&xol z_~HIiqixrr=-zqyQk$z|*bW8y0h@87xno8|gQJ5FWGIIZ_FQ6&0$Y*BMJ?|IJ^npA z(OzXQ&Q=TR=fVqZ)-0c{I3Vy`&whIQV+0iv4e}}|+9+x&7GY5zRaxwQEsV@r56SO z_jadyPvy6)>73S-iRUGm!@Snt#0DF|B(X?rqLhl12sb`A`kE^)sn2yP?$j38v3h^N znixlWc$Yy&5MuSXkSBr=MO1c!4O=o3MGf9R{0m^>Yj>Uzc`-i5V8lP5=qM==MNQw4 z<<`R1S0elRd+l1=y@m@|{ww;X?PXYi&8e zOV^GntDb?poO@tr{nMFnBQuB|Il`KtVT&jP2TU~wbNMjoI&Eaz53lDEem-Q8X(U~2pg1kgFJ71sR6$rrzH9xwT&?vNkXTw- z_8Y3y#UL)w@hLVHXaUc#Q*<&BKPD>urVZhI3*w#nlz=vMI;NzziF3T-s|qlC4y(R8 zPx?8C7hNC!-DSFeyPK|*0#iuueJxO!oUP%B$f^;4km|Ta5vpXg+3i+;^jg!*{UG)@ z&IAbj1R3UqPm~ND0z@|qS<_ZG1UihHB>J79N-@-HVlyDHUsOt8pU+Z^uB~F=uNT`) z81~=CG%54G|@$yr>T+}{AtJOdbA)~G>p4@qoB~J zRgrAIXtH0R)!93{+Z3K+Bl#VRmorvfW>PHN^?n{tNLIT!k;h&={Ya(fWeuZE%u#+1 zjD?aR>#f>10SNm}`yE}#i?8~aOpJHQ;7wR)lffruuZ5sANTt;0s5ju3W?UjeTs%d* zKZk3x3u$LemQsVhVwS2t2eX;StZBLf=YCG=OCKF2wK!sA?|v>Q*TIfT~#sgvF_VBEO+jC97`y~Oft8uo_29?7!O5BlW9fzu09dV8WOcka_mncufI&nJa z_|E=){pqO`SN(FP7t|yLZxAq9SBMrc51HZGBv>VOk1-OIThgqd%&2m8n?CDDO(-{z znB1*lw8nO#L)&Q6gE+(Fxs#y&A(~|u8B}f9*(cL6vbR{({ic*RQ8|(Km>n|z0%#F9 z#L{Ql+0ejW7p_>iFKgj_QI+-G}KOKj}ps-JwCx&!~@M*;DBvN-?FI0heoAttYS{{)TeJ zsG(}X>6sq0dbXyD_r3zc#5vsQf}v)DM~WuXq!;MgKR|thplnl2?uvE)-fsPMI_)># z-5U(wMzI>+8vbs+&<#F(yDv_j9j=h?Vo)Nc!b*hyk{GFf_yp61#GyhlbVrKug?!57 zoK+*Y@d5_t22K9j0*524!knsbR>jvgSuh9}(jN(t9&{c>m-yo4n`W^l`#MRF=x{f{ zrlQwgdxSo8&=xmq$kC(TumS-;Za&`en|c<{1@0z8$sOdhP-Oaj%)?u?t<2o>{aro0 zHz@Z}^;)blS6+Kl)m$ay+!`3PWX*TDTk8fBUzK*i}s0&uvMVwZ_}0maoY4 z@=-`kqUNY(g3CgLX<3vAI37Zub)2{t3~n314oLHydG={|Ds z6UZkjJaZ^;Urk4)-c8OWiKY8NX-``&w=<@1w)2R^zwy@c=CCSSSg;(2fTG%!ZgbDB9$Y&C=Cdl&3L6i$L!E~`;P)_S-XrI z?=rCsh)8?2C+d$cDx#2>NoDw$SdW~A86FjJ@z525AV!=>s2(LsT)?hQuJ(nQzdtL` z%uTZqE1+gtBI9H-4oxZl?2PmT91-Fjpn9MRx=Pd6`JT^+DRa6r?ZF%O=J>pnHNm*? z+?2jpbakRE4Xe^bkU4Ve_4fQg7X?mvl>S@az=ONpZkYP90g2_|ipeqn7UHE?H4SEI z+I?c`e(68*w&` z$I=qtSNxZY9@iI`ue2?Y8AF4MlMHzOSK9tJcmKBrt(q`?{ZkH}64QGC zpXR80lk!EsS%OAT&WMdHY+52`JH)H!&!$xKyYV`ul_}f-Lerax?EKD9u`n#QN!5)A zyU2MC%;`?KD&pPCCc_r}gW$kAVtjKx;8b$|f%|xJ{~RD^k(K2`oT(T0#Lc$!DuU|_ z^1q$_=W4Wx|4J3PH}0idTGAY{k>vATD{EmrP1Su=6dEb}C(6i}x2j+vPz=hVC zfVPVFC3?2f?A14ruiwm!gVW~Su|37)xa3K>onV&+qr!ZhYGm4=)B}t0zQlXFo#M7-i&xKdSd4;iLDq{1hF#S$B9%pJ#InHr|wVQ940gj_98VxRu z{epx(l)y#OsRq?uN6BA(;(r0`y=~R3e*q^joMe-a-Gb>G7oA%+gpZVUL8hl<$3=_= zE#GYXy&5&Xnw+b|_APo@^r&)WU68G?NQVCo+XL3aMt=0ReBagjARBAyKDF}JzpZV< zQf7>*C8(XoE_Mt0I5m3uq`tsXxI(f^Z3$_jHW)TH*gjA9anszOu_4AYmA%14n=y#E zX#5M*pGdMjPVtBgTsB?xvHfQWJa>%#@io)a?@IQ_L~KAArZ7bH)*;VkCNT?RvGLou zBulq73x3~M`xME!-)yZnnP)J)=PgfM+^BP8fNS%_{XQBg z`Q;RaP_>MJ^CNcGe!JFmbiD;})=J**W$UzukE5k5iTDy?x`z@T-oD10dSV?d9_7zD zprtjQ{X~prP>9LAzQaVSHU6o6+bOGVoIl0d&(rh;dt7G!{eUOiMyZ!YF87#xzSheCqVN3bfTc}uM{gu4p!dO?j(g5e_jD(EauAkQO~BBJktXv zVZV$uz^Unm$l+{-cbC+vD0hbwtjm?Aw{>^~J_s z;2@K+gz~&c7j>JYskMuH46oT-=G^1J)2k$N@XrR5*A3i*l9OHC!O$XGs90i!&BELYV2%Xa?56c^~bjyXTmADL5b+tQlXX8}O zy<>V1#cY{DAyAD}K7sf9PLd)!7XXIx)uh-{OqxZE8J1H15PanJ_ABr*f37s8>Fr!V zb;>n~+2OmFZUDN-SqC|mLJvuu>5>Ir!7HasH{BPkDxNiwUsgHr4=f&?lv@aE`ZwJ9YDP!_kVAa+g7v4e8j4#`48NP5nu`W!i*S}sb%Kj%KRYU5p#hck|>8EV$g*_t=XqQ8VL#qrNBx=RLkEz=H?{&7@g`-T-f+n^uoO_Pok z#xqc0J-%0eC67xC0IoPdRlMlE0aViC!OB%rZZarq15z-|whNE5jqtlx=oZJH9MUz8 ze65)BPtdN83z(r{jdO94q`;D@@}y+1lvhXC(_`;8FxVWd!xCQlzOOf5K6_kf%<}R3 z70?JLA6j6L5*h$@^(}EjQ4()cUrK;=kz|Y`2!Qc2mV%QkvOe(UE*}=6rHyq4e&rvx&ax_^oWsnYk zE~_!G=0I*?l87Z(Fu`k14jq?=Y!8n)dQD*O$lZtmPasJe_iQ~zjejm-=HdE)ok3A5 zpXXJFogR`5b+tbLC-RFwR-MWUmNnV+_B$-cMf<2aQNH-_l}o7Vs>ehD8N8~j6Ex)A zgksGq-|`Q8NWAzL;F0E=&Z=ljDS}_rQJ_nnr=E7Uzi`sWPmp&WeQSc2RXoXxZ~FX> zRbq}DNM4b^+)!1CdV(&JQk6nNrWr-9Hy)ZwzqOhm7Iv*R`4G|+n|{a`!Mg?mYmQ2y zi}-6%$Y5e|;S!zZ^OGUi`)rAoB8zP=eq zvG#D6dhx{%H5UYA&2q6*7>!Tv06TC|AiYjR8UDmv8viMKGPKLH^h^I^_v_l}viO^^ z){E6s+yL-)M2g9aUT#%YfHP9dRmd@Eg513C_c&$d>|7YfoRV7lSR$W&T%sxcDJm}m@B6U455dKpUcsOt(bSB#J*^$DtI zNiV%-RCZ>5@#q4LYCI$$ZR2)NG7z{mS$!OVr zL=NRo@Hj2SoQekgN2>bYmnMcyH||~BmptC5(WGEXF@+c`L>oqjCM45CgLuh^sO8v0 z`4oStv0i=B$IQVBN0)$>yl%ErtYlE+mglFShfr!*t6B0F3C`%rJ>(F)M(EgJ`b*+f zU*HM4$VKYMFyB9lw+tW#+5JcHZv88JpkeL12z_Gv=5)BKDg^Jy zh9qz$W(K6|tr>7zFL{&)ZqVT5ueP00jeh~1t=}E2pw2Qd0uFK*6RR8{CNJegGt0V$ zA8x^IZecZ7w!gmi)%Yb^Y;iPl&Vg5(Se`;;)?03dXwy~y_05RGdY-C*E=Y3oxKLdLfc8r&L+gf<@vy2Y zZ$@g2_2{3I$8#{OIi`x&u|1B=ZC%moW-DAv=c|E2?I=sKoI0A^HDGUd@< zg>xZp6teGMq^7f1$8$;a?)m>()c@3||LXYv*5p-3eMmsegP@rY@A@829#`K7Q;LOC zLfH#xR;jS=pCZJQYyvr|*8GCt!FFELsS4UVJPOn+o&4-UB@JMKvlHHuE-I%slWMb= zxD-W?<~cp<@}i&!&mWm#8n^r{Hl6pDdaEA6{tfaFahXs*j}nr>LU8V~Ue@sHl})0pi*E>f zGS(u8R&u~8uNTQ6V4}OjwUfd(=8(*f$hEZ@U*UK@RwjYW&rl2jB4OE{Dj%+Q7Qj%$ zESfet(Pi!q@G4E~<)P6z8hh+KCaN@pybe~N0pHgfq9vT*cA14 zA3EW7b5Fwh+?+HTaCURdZpu(S?$}Xk$iAA3*s^%b;m@=A-RuAVASe0%0yr~-N+?NQ z1_*mK`yy>s0buQH(F&Sjs)Hh^qCFQ)9qkgL#1haf^EM~r$Fg1wb?M+7M&&$e{5bvr z#WMqh6G#c3om1^KaA{BZ4ytci{M_+LvzW%((~gE>(;Gf=Vc(as9s0mN$WeQ#lIT+3 zLhq_eU|ix;<%Xl zyraC_<3{}XIh{Lm$k|k#f3fW%>=2PXYk*WP0eQVylIM;SM$Tq9eA!#(z*FB8qLkl| z#SNINE?kV~u#68Xc;;7T3g6M5hIf;$Zn3s9Ik*kJJ%4*rCbfJ)m7gi07p*fTq-a~8 zGF>jAmTV_gnKFuH-G?;x^(_zx;a+a1y4=dP2!8cLQKU4m-STCNODPd-ku|?swa@|)|Rw4OO z`u&JM#8kGf1BAjq@Y4-4V8@;ukm{=yng$+)HrfCrsX}X!B*`{~+D*!G&#H@<)Nji< zOAl;XZ?H5NOkwi>ox57k1PeZ5;MH6hdn6$EW6!k02mQHwLF<|8kej;1Ea$U1>-M7y z15+bb#e_9uq4|?(gDavPozOXP^@w}J4I!w82fW6CtBIKKKV_+UXjZw9b(3b7k&cv$HZ5#8v4C=*5SgAg)Lok?cFBYGjaUA|Eyds^ikyVx0S~ zw?(XtxzL9IWI4EIZUKq5k4K+7H*}oswYavnIN}d+2V2~_!Id{GZ;N*#OqylgHbA*icStvwZHb; zlor9Qo{zr~G-6J1sbpelsO(uj=DMK)uT#1!XbcuVS={d_#orwr4iggn@qMisEKjCO zks}a}^d}e;EDXk*E=cxT_BoF|>J6D^$Thc{OBr)bh3PXY%b*YwVP(K5ntM`KEV$>C ze}E}}0iFj+=+gtkXm3eMD#qX5be`j1LuItI3T&8`VZz_@b5$~2oa{F(vW4RjSadKQlu8f;_=Zo&CvmLI`gLNjz#NB zG&Na>x%1%iF=h$z9(`Q857N&&9OhAmQR&aoiZiXAy6bZ{8yQeiUrYjRn6c z+GShZgZsB zzZi|jPM6io=l-YHnmbEvbrSM*=8fSiQLZHdzRw^BIrn(Asqj5C75NEe`p#mI=M1yL zg{f)c{^$lVd+#}Q(M~T?8Q{!$s{AV2dwp38?sFUWXHcvl^R>W`O&c$yuY$~*{78?y zLJpC2TWBJiWB^s9sA#5_^{r7*gPRBO;V&T1z+bedu%w%Tyd?45&u!(am~D8 z8E)nQn?a*-`~x9tx$}lIpLr`e0YPOe0;JfTY2C#|(=s*X__=~v!vhk*DL!-sSxs5> z^^|t@{6z>o2MDaX#{%X(VIEoAv8z1+xgX9^nm(MIyT5npq4Tg|g{O7a(xV-*Jq#nE zFU)(%hT>-_X|4X9N5vYsPRV^*c2h>Pg6XB_rW#ghbG9A-0<>w@)}udcvl~4aK7VspDQyrO^Why;C_ZHiSH~+v>E7o<5aWmQ{7NNqwBa9+8eIw^rcTrLUyC3Lzz3 zjMBghzWO236h^bs$9Ym#dFWM}^|Bg;rW$;hQyqL|zW>F6O~??eYbk#u@FX+r`jeT5 zSyPGd+*X3Avoyqnj(_T0)2M>u)}P;`x>XDn`aD>TgJDA@7rhKEhHe4g*rHT0qK>GH z$Jkj_K%krDO%5*@!ehKx*9##E@fLdZz!ZN|JUaKOb?$AwdWt$q^Q`Y5l!*Y>VG{4i zKKueVgJHoN3^@@_`!7CYtZb)v%kM(I}ilG|Tj8Sj->cG%N&7?EZPhq%3Dy`vjD zv+wV!vMJ3gEZqBeGU{hNjS((?BcMqXXiY}$cgJ1`kGVHaM%9-xPKe49$}AWyOXOCl z7qWOKB!xrfhT_b~Rke?qNQSm_W<)Y_C9MC%8}Cj%%&lNH6D(K!vDTe%=fHg_@BmRO zbvDazAXxMlp!jC!z%1+NGOKH;$1-yHNYcD~f#*3!oN#%y1I)7uJ>7F3dzn-PSS;_bZB_tZiQWLK@rjW1coh|eVtX!Iy{4htZTgR&=C$^ zQx}15EN862GAi>=-Gr~A(r$9jUWK)ACb>X2zhSy51t%B$nD~51K)Ha?sZ-Y_#~vCv zOsCK?mW$eT)h#E9&ti0A!)cnnrq~%;|1fKqvvXPZI9MYK>P7CjouENobD89pQ5)*d zphOZHEZnK-eLaLVyqtq4C7n27Ka3@2ndfKw- zH@0KUvtdD?-aJRccZ^w~-t3WmQLURQ%Lgd5MMcE_Y&TgSM7?D8$oMVHRL2&dDUjnd z)kjx}rVI6|2A274Ug)d*eP|69(w{sp)bKOK9- zw2w1!nW2h96ozM06R7cM1-hH44FB>o&bVMG{YV@+!TRbcM(h!Ii@5r@&tCdF9+OlV z!G6R&C};0Ck@}!nzNe}m{%5*QkiL%-wo;_1gj-ffuG;i`(WxghR1o<1ebSYP*?xS@ z-j7E=I0QB?5d;!4xfQ>#V7=0_0v%z=vU0Efhpmg(lCIA1(%SBE%Lr+Vh=>AmP3 z?Thlr1_yoNwiM8s-8i9oa{hW$`#YlEZBm|*GhJsi=Q>{5*1%vdt&5)Bm`gU^dU7U| zPkWhHAuR>i?>6>@9hE>N11$f{+7TZ=ocRcCfc`drUg%QVgV&@Y*ilNXsHC}b05 zU5m*JOowlrS15Bha9i7p+HXoheje_mH5jd$GgaXte&njTP@MMkm0Md5x)h{o|*Dsrij7j>HatJu=ADhov`sE>kQ<2YThb9uWK* zN0Hl93&Hc0Fil)gu`MnoE0}c2EUM59TnO_F1yK2x)UPt`Y|!-E{EsbzmD)OcHMME@|^FeZ%C{E68zW_4p;}|4Do{_ib^Noc@w4 zMziiAyz7uc=Tj#84Gx3SF9_hm#Zd32ZQ@ChN zI#Jv)X7>Y4{@!+??%bngAIaH6;IBw4UHGfHipxizGJi`~%qo1LRaK1a_(~_!uYdIBZV9C8aJ~!kCg9}=^ z{sT}XY6~9OkKpH`?F6%o=am5@lg;pVTiTLN2#MD>qHOui;#?~G%I{5d$2h#l(DQ(x zyZDq^F*M%*q8$QRv*~+ap!{i?f7d~K*InkcfuHru=h=}5$tS$VJ{B)UGXHQiFX-ab zlbvvu0`Ga1+gTgLJ#A4`nX4c^_~}@MC^*WTl(l$SrmoGsc1{R2<2tOpUM?o)S$&6`WFyIP;Dq z+=!BBZ#q4(3kY^#Sh@NYSl#I}t>fzQFpPzhEH w5^}=z@!#OA-6EO&3Nmc#>PJ9zMeIdPj1n^GEG3|u;Qm`A`G5R5zP~g77bvn0c>n+a diff --git a/doc/src/Eqs/angle_class2.tex b/doc/src/Eqs/angle_class2.tex deleted file mode 100644 index e5a542e87a..0000000000 --- a/doc/src/Eqs/angle_class2.tex +++ /dev/null @@ -1,12 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} - E & = & E_a + E_{bb} + E_{ba} \\ - E_a & = & K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4 \\ - E_{bb} & = & M (r_{ij} - r_1) (r_{jk} - r_2) \\ - E_{ba} & = & N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2 (r_{jk} - r_2) (\theta - \theta_0) -\end{eqnarray*} - -\end{document} \ No newline at end of file diff --git a/doc/src/angle_class2.rst b/doc/src/angle_class2.rst index c7e5eb13ef..b045cc6917 100644 --- a/doc/src/angle_class2.rst +++ b/doc/src/angle_class2.rst @@ -1,22 +1,22 @@ -.. index:: angle\_style class2 +.. index:: angle_style class2 -angle\_style class2 command -=========================== +angle_style class2 command +========================== -angle\_style class2/kk command +angle_style class2/kk command +============================= + +angle_style class2/omp command ============================== -angle\_style class2/omp command -=============================== - -angle\_style class2/p6 command -============================== +angle_style class2/p6 command +============================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style class2 @@ -24,44 +24,49 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style class2 - angle_coeff \* 75.0 + angle_coeff * 75.0 angle_coeff 1 bb 10.5872 1.0119 1.5228 - angle_coeff \* ba 3.6551 24.895 1.0119 1.5228 + angle_coeff * ba 3.6551 24.895 1.0119 1.5228 Description """"""""""" The *class2* angle style uses the potential -.. image:: Eqs/angle_class2.jpg - :align: center +.. math:: -where Ea is the angle term, Ebb is a bond-bond term, and Eba is a -bond-angle term. Theta0 is the equilibrium angle and r1 and r2 are + E & = & E_a + E_{bb} + E_{ba} \\ + E_a & = & K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4 \\ + E_{bb} & = & M (r_{ij} - r_1) (r_{jk} - r_2) \\ + E_{ba} & = & N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2 (r_{jk} - r_2) (\theta - \theta_0) + + +where :math:`E_a` is the angle term, :math:`E_{bb}` is a bond-bond term, and :math:`E_{ba}` is a +bond-angle term. :math:`\theta_0` is the equilibrium angle and :math:`r_1` and :math:`r_2` are the equilibrium bond lengths. See :ref:`(Sun) ` for a description of the COMPASS class2 force field. -Coefficients for the Ea, Ebb, and Eba formulas must be defined for +Coefficients for the :math:`E_a`, :math:`E_{bb}`, and :math:`E_{ba}` formulas must be defined for each angle type via the :doc:`angle\_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands. -These are the 4 coefficients for the Ea formula: +These are the 4 coefficients for the :math:`E_a` formula: -* theta0 (degrees) -* K2 (energy/radian\^2) -* K3 (energy/radian\^3) -* K4 (energy/radian\^4) +* :math:`\theta_0` (degrees) +* :math:`K_2` (energy/radian\^2) +* :math:`K_3` (energy/radian\^3) +* :math:`K_4` (energy/radian\^4) -Theta0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of the various K are in per-radian. +:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians +internally; hence the units of the various :math:`K` are in per-radian. -For the Ebb formula, each line in a :doc:`angle\_coeff ` +For the :math:`E_{bb}` formula, each line in a :doc:`angle\_coeff ` command in the input script lists 4 coefficients, the first of which is "bb" to indicate they are BondBond coefficients. In a data file, these coefficients should be listed under a "BondBond Coeffs" heading @@ -69,11 +74,11 @@ and you must leave out the "bb", i.e. only list 3 coefficients after the angle type. * bb -* M (energy/distance\^2) -* r1 (distance) -* r2 (distance) +* :math:`M` (energy/distance\^2) +* :math:`r_1` (distance) +* :math:`r_2` (distance) -For the Eba formula, each line in a :doc:`angle\_coeff ` +For the :math:`E_{ba}` formula, each line in a :doc:`angle\_coeff ` command in the input script lists 5 coefficients, the first of which is "ba" to indicate they are BondAngle coefficients. In a data file, these coefficients should be listed under a "BondAngle Coeffs" heading @@ -81,13 +86,13 @@ and you must leave out the "ba", i.e. only list 4 coefficients after the angle type. * ba -* N1 (energy/distance\^2) -* N2 (energy/distance\^2) -* r1 (distance) -* r2 (distance) +* :math:`N_1` (energy/distance\^2) +* :math:`N_2` (energy/distance\^2) +* :math:`r_1` (distance) +* :math:`r_2` (distance) -The theta0 value in the Eba formula is not specified, since it is the -same value from the Ea formula. +The :math:`\theta_0` value in the :math:`E_{ba}` formula is not specified, +since it is the same value from the :math:`E_a` formula. ---------- @@ -117,17 +122,19 @@ instructions on how to use the accelerated styles effectively. The *class2/p6* angle style uses the *class2* potential expanded to sixth order: -.. image:: Eqs/angle_class2_p6.jpg - :align: center +.. math:: -In this expanded term 6 coefficients for the Ea formula need to be set: + E_{a} = K_2\left(\theta - \theta_0\right)^2 + K_3\left(\theta - \theta_0\right)^3 + K_4\left(\theta - \theta_0\right)^4 + K_5\left(\theta - \theta_0\right)^5 + K_6\left(\theta - \theta_0\right)^6 -* theta0 (degrees) -* K2 (energy/radian\^2) -* K3 (energy/radian\^3) -* K4 (energy/radian\^4) -* K5 (energy/radian\^5) -* K6 (energy/radian\^6) + +In this expanded term 6 coefficients for the :math:`E_a` formula need to be set: + +* :math:`\theta_0` (degrees) +* :math:`K_2` (energy/radian\^2) +* :math:`K_3` (energy/radian\^3) +* :math:`K_4` (energy/radian\^4) +* :math:`K_5` (energy/radian\^5) +* :math:`K_6` (energy/radian\^6) The bond-bond and bond-angle terms remain unchanged. @@ -160,8 +167,3 @@ Related commands **(Sun)** Sun, J Phys Chem B 102, 7338-7364 (1998). - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/angle_class2.txt b/doc/txt/angle_class2.txt deleted file mode 100644 index 5a772f8fa9..0000000000 --- a/doc/txt/angle_class2.txt +++ /dev/null @@ -1,138 +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 - -angle_style class2 command :h3 -angle_style class2/kk command :h3 -angle_style class2/omp command :h3 -angle_style class2/p6 command :h3 - -[Syntax:] - -angle_style class2 :pre - -[Examples:] - -angle_style class2 -angle_coeff * 75.0 -angle_coeff 1 bb 10.5872 1.0119 1.5228 -angle_coeff * ba 3.6551 24.895 1.0119 1.5228 :pre - -[Description:] - -The {class2} angle style uses the potential - -:c,image(Eqs/angle_class2.jpg) - -where Ea is the angle term, Ebb is a bond-bond term, and Eba is a -bond-angle term. Theta0 is the equilibrium angle and r1 and r2 are -the equilibrium bond lengths. - -See "(Sun)"_#angle-Sun for a description of the COMPASS class2 force field. - -Coefficients for the Ea, Ebb, and Eba formulas must be defined for -each angle type via the "angle_coeff"_angle_coeff.html command as in -the example above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands. - -These are the 4 coefficients for the Ea formula: - -theta0 (degrees) -K2 (energy/radian^2) -K3 (energy/radian^3) -K4 (energy/radian^4) :ul - -Theta0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of the various K are in per-radian. - -For the Ebb formula, each line in a "angle_coeff"_angle_coeff.html -command in the input script lists 4 coefficients, the first of which -is "bb" to indicate they are BondBond coefficients. In a data file, -these coefficients should be listed under a "BondBond Coeffs" heading -and you must leave out the "bb", i.e. only list 3 coefficients after -the angle type. - -bb -M (energy/distance^2) -r1 (distance) -r2 (distance) :ul - -For the Eba formula, each line in a "angle_coeff"_angle_coeff.html -command in the input script lists 5 coefficients, the first of which -is "ba" to indicate they are BondAngle coefficients. In a data file, -these coefficients should be listed under a "BondAngle Coeffs" heading -and you must leave out the "ba", i.e. only list 4 coefficients after -the angle type. - -ba -N1 (energy/distance^2) -N2 (energy/distance^2) -r1 (distance) -r2 (distance) :ul - -The theta0 value in the Eba formula is not specified, since it is the -same value from the Ea formula. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -The {class2/p6} angle style uses the {class2} potential expanded to sixth order: - -:c,image(Eqs/angle_class2_p6.jpg) - -In this expanded term 6 coefficients for the Ea formula need to be set: - -theta0 (degrees) -K2 (energy/radian^2) -K3 (energy/radian^3) -K4 (energy/radian^4) -K5 (energy/radian^5) -K6 (energy/radian^6) :ul - -The bond-bond and bond-angle terms remain unchanged. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the CLASS2 -package. For the {class2/p6} style LAMMPS needs to be built with the -USER-MOFFF package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] none - -:line - -:link(angle-Sun) -[(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998). From c25f8b21203f3013fdabe7ffe4aabe3235dcbf86 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 14 Nov 2019 15:43:27 -0500 Subject: [PATCH 11/64] Update docs: angle_cosine --- doc/src/Eqs/angle_cosine.jpg | Bin 2380 -> 0 bytes doc/src/Eqs/angle_cosine.tex | 9 ----- doc/src/angle_cosine.rst | 35 ++++++++--------- doc/txt/angle_cosine.txt | 71 ----------------------------------- 4 files changed, 16 insertions(+), 99 deletions(-) delete mode 100644 doc/src/Eqs/angle_cosine.jpg delete mode 100644 doc/src/Eqs/angle_cosine.tex delete mode 100644 doc/txt/angle_cosine.txt diff --git a/doc/src/Eqs/angle_cosine.jpg b/doc/src/Eqs/angle_cosine.jpg deleted file mode 100644 index 23b9b6431019dfc432e113da50fc9056438cdd9a..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 2380 zcma)8dpOe#8~%-L%$XUo9LB`VawN2~m;XkQNt*Nytje$;nE~%EA?PE5hZK5wfyMC?#bT6*VPY&oV_D5>p8=M zF+lX+)klHtYyy#1g!vzoyu^M#luRC7A-SBU(arDM&X0$T4~#7&kz3-enYMU>J086S zop-|!Hhb>By!bOil}w|!4(OmMvw@ZV4!#g2&iU)w3*lTub$&&{Y-gB7>iee)(Q@Mc zAqXM!YtbXY`!ijPG|^+uhQqcIWZYZzBYgox1%?hP7=>}CQH9y|R9DWwJsnBR4n&pM z?BESOgV_6y7U;6$S{NXTn4}KAg+~Lh{knx6%{*-l%L4m*#v{FU9mcmgROwpF$S7WC zR}(dqYQ`Psz^6~zBIgUcEIf>2fGF(`%rA{B2gAzLk#vm!W-vkbw)Tkcfj!7K5B(={ zRbV<180X=L28s)ZN+Qy#2U8@>mOlH^2cA88{!%aal``z)bGF=KnV3FvGH^jh9h^By z`ZiAK(oUE)2wlwTyHLlPkFuGw%WK#l#2diCD zG&y4P(A+vvhUK#1eRmHh%v2!(5h4l$F&JRXkJ#{{(#q2K)S3K`z^YTW!t<4&$hp0% z&^HnjC1xeXuH25p7uG6X(t(4veV9bfsVe`_i+iP%%3y$RT1ny zDOb7{3U%6)t?&p~g!V4E5MJw>cK>9_s*D;dH9Re@lJmA9Rd%`9aOrxI2=oolJlf`b zv71rg{`ODb_d49)?gwo`c??{JIlX;LRLc*KL~439cd{#M;h|E!j@nFeM2RsD zLhlYFpk6_u3*zIY2KxCMhzO|M!h?%OXbZ+=f7rcKO5E>`G&cQPV*imq-L|P zsq)Ipg0~NK+2F9w`^HX{y6Jw?uLZy^u`L20)-rRPQg@nOR)!JoK|mjF%_&@8Sn3>PFKg~(7;o(v zCz%nOTlqotEVocxV>}%fU`#GB$&K%6~C~+k%)XFou<`r@& z1XaK!TsotI690b51K-_gh)==S^A*+~^@kQg;!Wjf2Hgfr{W8=t&nWw~n`0wn)ng<( z%lmXHI+h-dor*!+{wcJu;}RkOeq^+71h$x9%iS#7p&MfR3a(^^ISs9-B}H@BTRk|K zdY{b_$>@;X9=L(^3dR(N?Wk!LR2gd*E~95`3LLsQP5My!fc@0i<4KE z1pu@rJ9nT~r{}WjEk^B-j2IGn$VW@dA-Uch+I!?%;E>bMG|0C}Oh2KCxSE92<;LCt zB)_zKigdJIdy_BOX8)KIdNSWwHyt+mHB2W{R7+p+{n488kw?xZ z&=LrVv25b>^A+LtF=S1m|A4_lvEIs{@<8bMClJZAFC>pS|%04$o2jGUc9)Ecta+DrPXh=%K#cL8) ztvrHht^Pksi z{;2NpSM0+ze#*k*VCiSRT9{4h8<~q_BG)`@qfQzD(X<#*EZ8 z?{k??7QmmUKbUj}(G7rf)TcY7ToKR9vd@G+5UZRv6ith9YzhA-y<)f%{(IHar@{+t zUR{5DzH)_GP11BJsDpg1`F@dKh&wp2ugVAXxczYI8doK?Ps*#fvyR7SJ2;$uZDXkr z#cu$$?L^>dJoIrk^TEBQY>zN3HZC-kbA|TZRvyt$+bAP5QOBe{>V^Q0MBViTzk0X3 zHlG9H%feImtqxuSVruB1xDGOae#sI9W!p8QF-kfiVRO!cCPGN?CkGv zhW` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* K (energy) +* :math:`K` (energy) ---------- @@ -83,8 +85,3 @@ Related commands :doc:`angle\_coeff ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/angle_cosine.txt b/doc/txt/angle_cosine.txt deleted file mode 100644 index 93fed32c38..0000000000 --- a/doc/txt/angle_cosine.txt +++ /dev/null @@ -1,71 +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 - -angle_style cosine command :h3 -angle_style cosine/omp command :h3 -angle_style cosine/kk command :h3 - -[Syntax:] - -angle_style cosine :pre - -[Examples:] - -angle_style cosine -angle_coeff * 75.0 :pre - -[Description:] - -The {cosine} angle style uses the potential - -:c,image(Eqs/angle_cosine.jpg) - -where K is defined for each angle type. - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the "Build package"_Build_package.html doc page -for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] none From 00fc015e4c338385a400cfffbbd6bb0394224ccd Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 14 Nov 2019 15:47:56 -0500 Subject: [PATCH 12/64] Update docs: angle_cosine_buck6d --- doc/src/Eqs/angle_cosine_buck6d.jpg | Bin 5374 -> 0 bytes doc/src/Eqs/angle_cosine_buck6d.tex | 15 ------- doc/src/angle_cosine_buck6d.rst | 32 ++++++-------- doc/txt/angle_cosine_buck6d.txt | 65 ---------------------------- 4 files changed, 14 insertions(+), 98 deletions(-) delete mode 100644 doc/src/Eqs/angle_cosine_buck6d.jpg delete mode 100644 doc/src/Eqs/angle_cosine_buck6d.tex delete mode 100644 doc/txt/angle_cosine_buck6d.txt diff --git a/doc/src/Eqs/angle_cosine_buck6d.jpg b/doc/src/Eqs/angle_cosine_buck6d.jpg deleted file mode 100644 index 69b668c08603ba4a137317817d16fc2394ec3a41..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 5374 zcmbW4cT`hZ*Z(g~AU1FW$I2t1pbUoe#9_bysgNGhP??05-b0EARxIsi~8z+wOZya1Ox3E=MZoKt{VP6Gh<{9M2j06Z*CpMKZ{ zaC7!9-^LHS{%7Xb!*2iaXMPL9vSLZ3Z#@=^C%~ja5r>*8!ZY#sIJiY;hRRuC3aFSv z7OG;>P$m|MtC#aqNMeyFLW0ns_zAjHZKfV2Co4fHG|IqJYGE)P6r)3np%GA)#Ei`( z5ODF7L=FL!iI<`osSJLENsOUT_#_Hfogk$X@i7q;N}O3l0GVRbsI*L-RHeWvsNi&p zf-P5OX3|ncVPpYML_?Th6e>S0UZvr|Bm$}!lOb0?1!A>WZ<2v6a;5>qMj6yQd zAdv=vTpy!kBlU>}1B#oe(d)rXL>ekBg_};dX!TGG1EwRGjA0mZ92kvfz-bzt0u-TD ztI-h(m@JhJfrxkzi;}B1s~KP&(Lh6_MF_%#U`3or&QYdnp@}*=k||GRr=Sf4DT9w1& zvSSfyfkI7UYb7{S1RRGWTVlfaW+G0L!bpz?(M&0{IHFw6BXCVL0|`xw(<%%o1y@B9 zBJ?y8!lJM+6XJvka=DVnk}|~_t&Bo}We8Y8HeD9RHG!~NE?jL;>r`x{P=`?H_- zi(?7NDJG~EAEOXO5Y=)u5+{=~^kGbSN<2@WDP>6+QUXj#f#DG#ij0bYW}?76og866 zK}b?b3Xz||qndFVnOLqt#FLe5JQuE^lQD9ZEZ#zn#UOcNb)uflB6B!IHV6_=(#Rt; zx&)(A1y3iCO^N9^v5rGDC5o8%OcF6YCLu%5qS1-GL_&s|A~rA(Ds+UAB?Gh7R01yn zr01Zy5GgM)5vq`z%^aagC}M~Sat1`eq_EMLM2d+ag=tjsOc7ox)5kE`ESOr1*CO~j zqgKfWvq4-=x+Q^aRL1KWJU9j=3ey@0F%mUTD~(Z7y1_GW!kn?a(%53U} zEmW`)p(1dFyx3S(hFPEzn^7t;4`l=~G8ig#EG{92m%&o1@Jcva29FI(&q(8C#PC!s z9-PU66IrNO1sDs>#L_d3nVCi`&qy+ZvCMR=fCqweGvRn85~~cu^ANaLss;;zs1&F~ zDOe~5b2AuHA(o8CB@l7AM4?U`LrhC&B&LZqsZ2#WBTd92ff6(c3BnjTMyf?%IT!-Z zK$7s#F`4iLo{`K$i!$L{9y(rxjOBodurORInwTDj6NSa3qX}Sm9N5SMX;>Uugp7}r z;1Zy+44j#fNRlz+EC~)y=L^VioeWQx#l^`JENTMJOjMfVF6Qy|c$;JN^WGy?~j(S2veHz}45q&DX`z2n0B*y@$(peGhXs zF0O9w9uqvhyg?J46RLdxR~I)oS9doLk8iheS?wGL+*Lj2dXZ$#G)`Ep0p^Fy75l9povotmihbIt8WEMM-!{zY>DXD4c z8Dfc4r#EC8O=ipb4I6XwHf`RLU$AFy;lAJY7acuzyyQgb$y28*t1eXkQFHOq<@$!k z>rFRq-n!k|*8ZU5VdtZ+UR&Su7cXDEe)IRx`{55CM?Tp{KY!zLe#!ogQN|GBz>SitqW++1DVJlx#eJSKQJHNk7bH+g})z6_Xh?(XS4eI|NO^!Z=Q@x-|y@NskjliXaKi^K7(&MOM=I*(jH+$!#BJe(2Pr+Osq# zY0~r7j#pG#5M{r=4RbW4|EIUZO$~=8$XK;o!~0@{PxsM3ZzYbPb>Pb^)+jzAZT zFYVyhW?TRG1votQ)a&x~(Y<23=hq!w;O2(tvGvJ%-n>otJY9qRQi;qu88v{xz+E0mBYKv<`GovzxLI{MAH^#TUEquPk=sd}d|`N< zxqNe7>dtKe)3cY@;~VSzzXq8OB<#G_m05G9Q<6K|uPW&vjJB(BU)%lRi!pa+YfplZ zA7Aa1jh~7N&Z$2-elR;QD{e>f!dHYAW!Hn@Z7UNFQOcu+FN4P3423kPwgyyj->C*y z+58S22|hm-c)8V3CTqyt;!)C6{PT?VN!N1UoMR@fkH~CP_upRlVVLLk0e`I)X{xh% z5BYB|>k>y#nTC!$5O!}-apKk8y#2rbObK}O%+U42-A%ViBF6MZQUUe1u2=mi+nKAe ztOt`;&T4_rl*?`H1H!hB_*d}zfQwWZ!chNx}FeLt4Z8r(PbyRotO3t&oe00e2f%dNko=S1d|WVd|v zwuhgwOK;Fxt$blwa(GwI)q5=~e!`tMi$eRhns)`%EehJXXGivl^1Ry6oLi$~Qyf5r z>U#0**4o~~u9uQ0m>Nh!9UHQ+M>lgG_8U8LYUyP!C7+m&ZmYdV6LwXw4sqSrnC2ks z`czw&W>*-}j*KA{g8CWVlRF>u|7&<(z^Xf%OWC=#S>wf7#-ZGYy%k$&_Fo^KcK{0e zc58G00rXd6M>)SuHfd}JIpatZ!JY2;xSf+-pjmA$>00r3Va}sZ1#vqOHNRDkLZRzg z29o#waR@bKDkFJr7PzB2x(j7{*!U!+@jW@qbMUQTUwsj0S0yxQ#ozvm%TD&JJlfa) zidYl2@L9J1(5uGi0Mn}LUl&){OOO0rSTtk1p?g)1_ZYcl-efMV z)1ATZ zj#VjkM9_|02UcU#By%_J@rOj_FR)5xU8satMqt;hcwCr{e(_sAEx3Sl#x}K^Z>6O? z8%L@p$)KI4yhcIo+TN#=M;GkslJ5JwN2M_lf1O*{5jZ301$J>hlRLf6XK&WrFL7i3 zgFDv`{1fy5e7xgh&a{=y>VG~h4d1>V|ME+4SkQ`Q?+rfF7A8Mg92&N4Ud<5LmRsf7 zSO*#d4Y~!I4m7H1r;~e@de0!WgwISVd?g$eNJ`SyJx0wUTTwEfD+?(w6w zh$r@rFZD$^x##o)lN)~W<&)2Mz7gn+`;xZ5sBUV9KAxFPxpXTeGUYD^@N3Rwdv5o$ zrjjAl_56FtvZ3Ua?UB5u7rr6>53dJSO$lNz6LkIfy#Dmbr)xaPz?aM|y^$*0)LE|= zrT0u8JTerUusp%z19ByC#T9D$m+nf7{>Cq|H4b3o#-S@;H^Usjv-fw#Lfv}KG)DbA zCMfQu<-t#Wm>B#ZE6LVR?T-EHr_^-biS{M$;|lhU7WVWY%qN8R8~^2VUDj$1Ic>`0 zwd8-gK5PEq_!roO3n<7F1wETH95_ntz5g?}v2J?g&t+qj@hf9fd%IU;4rBkYo1dL= z06yK#lDXEiV1umr-P0?ENiEZU-GR;DP%c-(UHYS@+1J`u&mP%u**?{_nrGj5d~k2g z=9DX@z#7xb8I}CyP1F1meJ;K4TA;XpQQaDak18y`3(j4+u%NzpdQ^0F`yprtI4kjp zJ^5XfXG=&?nD|_I+WCFs3%zQar~B9_)aOY}-7)`6;$IA2U2`If+TI^E|4sBHtND1+ z>(4ct;CIU6sjK3ftTn$&20$y935em3Qn&W|LdT9TEyS!iPWK3hHC`^?Pzxmub}zq_ zKO8@_;$TPBQ5sB{KeH@&yJ6zA8~N*-x2(!~zEMIK1}=+8X`9{f^uqWCOLpn$UrIMw zVP|`uJbElO)^L)=)mPhswh$E|`=8Y;E+9s0H+iKL)sG+PNdj*!t{OQdqIF02B8r;b z)+x?i2&XlBju-Fd?W9kohn;`m0G_`ZTjT&l#!WdN`i|2*9e<6}E{yMOZMMB|05`n8 zhM3C6R-BZOj$XZUF85|pmUeR^q)}hCDe{_i7nDj`c)8H-hAi#NnQCfo%JI#j*iKqu z>W76E%3H}UNwE}C8Qc~tEbX#3`}Yr-^CJi@Yi^bw2|et(<=-~-P_#JuQ5$jmm=)Or z8p_#nr-ZlkHK5!#o5+XWx z*1%>1GLK(X*fh+HJ3pfhs|Jxv1TAIw528H9#Xp}5Yo#B$Lfx9aPRN>7VW0eLc0lgs zfX#@VKCds6z2pELoE;c<=6R$-T-~hkA zS%hm_13+)HLmpTsmM7bl0Y4`Hapt6;JN#@#j+iuy5PmmWypA>dZV)SUbl3UEe!L1* z#?dvAOZ%Roaus8={ zEMqL27gU-B8hmjmuh#*1K7RW6iHTc3kg;ILj=&2wRZmMRZ%JFrtiG^O=+T>7Kqo#j zZ#Sl2db({SdT^6{_|K>Fra?x)lV7*6i-K6=E!BO%JYfjYe zI{PH!>#|QzKh`IYyZ`0s*0*zG_B?x@t=P>}m2~N1$e%^qE?4ipATLfY`a7N<&Uon& zkJ?jNMX264`PNNag*9mqT)z@xU-Q%#F?;LD@^gAt@7vB4@z{Z@;pd{-JKlTZ4cx4= zxk%<~azXv>wygOMAfNWE{EMrk?lWbsWiDU>Z>q~E_cRqcfa?Kr>(xBm(Det^FYAui z50#xLL0o`z+c@v<-kH-9JB>DrcxLh8$qnS-Phw$i&-9ua+?LQiiv!o3K7Gvjw+BpF zcl_uYP^i=17yFNev{~bAH^&U6(oa2eALj0h+P>iBA>nXv#Ub_q;jnE_*p0w{Hn+Q8 zDL#k)MX&`J4e5J&4gJH2=%QUXxR3C@Z}9PD>Jee-viQh8V!Ps_cc91p)FREqvHRVJ zICmhyMTYU;9e`i7gqB+yIe6C?cG&a-?qSb}&DOChQC61mPLq@rdeCRT-~9bAmcjg| zN44Ib+Odc3d9Ul>Z}z=k;>0Nb(+gXorYH5#BFE`(yN(BX{Yt&we|BZYzAtr>t+me( zA9F@A4gi$XdC(Rxj(+3UmNnM_?B+5YfOCiBtTg?G` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands in the following order: -* K (energy) -* n -* Theta0 (degrees) +* :math:`K` (energy) +* :math:`n` +* :math:`\theta_0` (degrees) -Theta0 is specified in degrees, but LAMMPS converts it to radians +:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians internally. Additional to the cosine term the *cosine/buck6d* angle style computes @@ -73,8 +74,3 @@ Related commands :doc:`angle\_coeff ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/angle_cosine_buck6d.txt b/doc/txt/angle_cosine_buck6d.txt deleted file mode 100644 index 1ce3556ea6..0000000000 --- a/doc/txt/angle_cosine_buck6d.txt +++ /dev/null @@ -1,65 +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 - -angle_style cosine/buck6d command :h3 - -[Syntax:] - -angle_style cosine/buck6d :pre - -[Examples:] - -angle_style cosine/buck6d -angle_coeff 1 cosine/buck6d 1.978350 4 180.000000 :pre - -[Description:] - -The {cosine/buck6d} angle style uses the potential - -:c,image(Eqs/angle_cosine_buck6d.jpg) - -where K is the energy constant, n is the periodic multiplicity and -Theta0 is the equilibrium angle. - -The coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands in the following order: - -K (energy) -n -Theta0 (degrees) :ul - -Theta0 is specified in degrees, but LAMMPS converts it to radians -internally. - -Additional to the cosine term the {cosine/buck6d} angle style computes -the short range (vdW) interaction belonging to the -"pair_buck6d"_pair_buck6d_coul_gauss.html between the end atoms of the -angle. For this reason this angle style only works in combination -with the "pair_buck6d"_pair_buck6d_coul_gauss.html styles and needs -the "special_bonds"_special_bonds.html 1-3 interactions to be weighted -0.0 to prevent double counting. - -:line - -[Restrictions:] - -{cosine/buck6d} can only be used in combination with the -"pair_buck6d"_pair_buck6d_coul_gauss.html style and with a -"special_bonds"_special_bonds.html 0.0 weighting of 1-3 interactions. - -This angle style can only be used if LAMMPS was built with the -USER-MOFFF package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] none From 71304c3b8c121b41781e92c12cbb0cd5f83d9b74 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 14 Nov 2019 15:52:29 -0500 Subject: [PATCH 13/64] Update docs: angle_cosine_delta --- doc/src/Eqs/angle_cosine_delta.jpg | Bin 2576 -> 0 bytes doc/src/Eqs/angle_cosine_delta.tex | 9 ---- doc/src/angle_cosine_delta.rst | 37 +++++++------- doc/txt/angle_cosine_delta.txt | 76 ----------------------------- 4 files changed, 17 insertions(+), 105 deletions(-) delete mode 100644 doc/src/Eqs/angle_cosine_delta.jpg delete mode 100644 doc/src/Eqs/angle_cosine_delta.tex delete mode 100644 doc/txt/angle_cosine_delta.txt diff --git a/doc/src/Eqs/angle_cosine_delta.jpg b/doc/src/Eqs/angle_cosine_delta.jpg deleted file mode 100644 index c6e90bb2c5a7a9f91e93ffadc9f9d31e776f1f7d..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 2576 zcmZuzc{tPy7ye-w2FZTISO*PRZy{s3mMk;bCKOYaP`1I?vX`x>7{=gc9~t|Wm_dw+ z7*xt0B9qWi)>2XP=|120*LUA@p7T8CyyrR3Ie(p(HO+bl97S4KTL5fqY=G6F0jycT z4B+Gdfj}Ibhk=umlMBqp4L*bbFE0j5O;pz{?HjvGKF92?DG>Knh?3IR0_qe>fZqVq@pvK4cL`0XB}q1jNAs z;o|t+a7cgvPA)+qu$-`nmI=4KgSM%ssF=9IDJSQ|yzxJAp<$7&1k!8P48VQ3IA9F? z%txY$WcdGuI&tZ;Md!7l`mvUP0CABGob%=uBBsQs%4v~CdbifzOSxM-B+AJC%)R!Iaq+Vqb>X%fdK+KNU;8+x0ol-p+K#*t~ z)N(Ic^wz90m2?-mu^4jDsNC@v6dzOInD&vFb~~OV*9Y%A>3q6|2M)29u3)c7itiAp zZff{_TqEkmkZ8%|&mqQM^0Aa{*Y;eQOMsA$W4RTZtdKRpZWGVwtYWloPvcVcZj_G| zEGJoft258Qo0VI>cZi%Td4}uYjYA||%4%(|q@4j7NZO-P+p?d%RFPFp)K{j}UM7;w z=2~J!Dc7?LLr`{{I{8Lt;C%U_&zc#J;lTxulw^YeOhw616xlc zXHn<9!;Hh>u2x2cvXRr(2YX7kav3k^Fqg*j$L+lkD(=}QwtXsJIg^jBr7d{GDqr2K z`GL+&oCysu>k;XonM4w{<-H<(DOPpnSKX}9BY(#or0c`=t>^LI6J6uG?K>0iT+mpo zs8k`hMI@0a(eR2Iq|aj!HtTafDnByKohWtqt5L}sYWcyNqwoFU_Diux!!5}%3D*~U z`ZRmCjSuQ1k5KmcX+uwEadN))d!RsxMCKLqyQr#rTxZL(uz4#>6oGkHd!+Ee1nFQ+ zb+uu8AvJuzs#wQ!S6RO6X~c%;*YQeB-2LaY-0FDhIR*>3MVG0u!>&gLz$7tEgMOSJ zN5g&2#-7=u?=F>rJr}G2MZ_z>DYmk-ZKw3R3JYMKscn^1YaH1^fiRw=RO8g=nBh0* zIinc$4!C(v6Sicc5lyU}=+(G;w=Jr;R(KE7t7YC{(^^4l&p4iy#2gQY&<)UR4zKk& zx^W6MdQbWl-S6h+G3GMJxEaR#x&kTwv{io^(4552b00FCI*S9*(U>!oASYV7OZ zGI&;?*!~GwG7`lLcVM&#HN;e8mo;Pw7#z$|eIL1DDLhjsY)vR8n*O;}3Wpo7(9e5C z=HGG^EB(8IkW*%no=Lx=!~({PwEIlE?&DzI+7ikS&bbLYj5amq%h>`6J8+{3$t}g4 z+L7BBt?9AnJkd5U>dqG++iOqw#ErUvnR!V!jGlSyJ3{C8J@O}MIbIi1(mwZ5bweYT z?+3~ogqy1A5R6h$Rx%$OI*HZlWlIl2)}_A?pWEqRLy8Cv-BGD<#p7Tm+0Xc8kHNC| zzE97h#d|)tV}vU6ENDvH#@97#~l5m(JmrNNaTCavSvuzzY>o7%G^B}7xv4EJ? z3u;5{^Ph2QuZ1EQ^l&-YYKcNZt-d}-$HZkB-Z!?Yyg>Ux3t!0~wrgo`keZ(DGbiD< z%$rFhL6Ag9cnU1>(@^V?67R@*!slwe0_G7)kwm4IwzdR%-?W4uMj#Cf~uMP zHu0mb#d8HhVBYt>uofsvn2~y5(58r3hom&~Own%sN}?s8jDIQhU$0vDwOx3Pb2>_dOqB}Uc=DHwuUbntEaq#&pP(V^ z={yYx3%Hs!TW{?L!FYN!q!Lrb@(j_f+mc|5a(%yj_tPwZ(DbXqwc=u!fpt?lU07bP|KeP3 zRWT3btU=zQAgK%(J4+)fH*ZvA6z9wpEdG@6D(!k`yoR9eoeHG(`SWqfX;w{+@snHO zdy_jUY-Ns&LG;K35>^@-p!n>SW(n=;n6_oM&_b>}=+UKq)Ap8@VWc0O8FEnLYJ1z> zcF1;sG}YundKA~j_^yQD9MqW$(@c-Z`#WQM2RGKd^NB2*4?(4TT~Oy$h^KB$t|+Wb zt_K|J3p#P}N=KGy!A^7WkxHp6&KEH+;RtS-tv%0u8Ez*rm4&G!smAge=1zoX5m`=KpeCu-(l|>Ev*wjN+|AyEp!* zpl3KNeyMG3GjOct)pS5TRA(^Ajw&$~cu+mM5aG$ME4RAJzpdOnW4{U7&oZ3mS(H79Dv=J2;xN*Q%jg7Z}_9U@g2#NoV*mrwVM~ za_32t@0a|nU1RY+{29s91@#FTS|jr=rC*9?_X~0cH1}<8##BDZ&+1|psu4%%$~M8~ z$<4DHYO-HtG$o{(R&xpp%u#nCGE>GJr)KAbP!bUb$`zQyQ%a{9&wCiTA(!AX}Z;~M3|v5V1^(;4Qak&dfl z2hJkHXPZ)4S_d2LT@spLebIoC;dwH1z2} zwEv8@PNDEk_sLwpIzoCaI~uV z%LKls9wLQ~Cz|3b@nC1{Ij2#{dBr>LTdF#A29>7x(;Ay+{`dg3q0&1UC$pOofxkqf Q|3wk~n@aj!JI{La9}+FXn*aa+ diff --git a/doc/src/Eqs/angle_cosine_delta.tex b/doc/src/Eqs/angle_cosine_delta.tex deleted file mode 100644 index 918e9e5046..0000000000 --- a/doc/src/Eqs/angle_cosine_delta.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K [1 - \cos(\theta - \theta_0)] -$$ - -\end{document} diff --git a/doc/src/angle_cosine_delta.rst b/doc/src/angle_cosine_delta.rst index be8f209145..9af93cb06a 100644 --- a/doc/src/angle_cosine_delta.rst +++ b/doc/src/angle_cosine_delta.rst @@ -1,16 +1,16 @@ -.. index:: angle\_style cosine/delta +.. index:: angle_style cosine/delta -angle\_style cosine/delta command -================================= +angle_style cosine/delta command +================================ -angle\_style cosine/delta/omp command -===================================== +angle_style cosine/delta/omp command +==================================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style cosine/delta @@ -18,31 +18,33 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style cosine/delta - angle_coeff 2\*4 75.0 100.0 + angle_coeff 2*4 75.0 100.0 Description """"""""""" The *cosine/delta* angle style uses the potential -.. image:: Eqs/angle_cosine_delta.jpg - :align: center +.. math:: -where theta0 is the equilibrium value of the angle, and K is a -prefactor. Note that the usual 1/2 factor is included in K. + E = K [1 - \cos(\theta - \theta_0)] + + +where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a +prefactor. Note that the usual 1/2 factor is included in :math:`K`. The following coefficients must be defined for each angle type via the :doc:`angle\_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* K (energy) -* theta0 (degrees) +* :math:`K` (energy) +* :math:`\theta_0` (degrees) -Theta0 is specified in degrees, but LAMMPS converts it to radians +:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians internally. @@ -85,8 +87,3 @@ Related commands :doc:`angle\_coeff `, :doc:`angle\_style cosine/squared ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/angle_cosine_delta.txt b/doc/txt/angle_cosine_delta.txt deleted file mode 100644 index 1532e39b31..0000000000 --- a/doc/txt/angle_cosine_delta.txt +++ /dev/null @@ -1,76 +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 - -angle_style cosine/delta command :h3 -angle_style cosine/delta/omp command :h3 - -[Syntax:] - -angle_style cosine/delta :pre - -[Examples:] - -angle_style cosine/delta -angle_coeff 2*4 75.0 100.0 :pre - -[Description:] - -The {cosine/delta} angle style uses the potential - -:c,image(Eqs/angle_cosine_delta.jpg) - -where theta0 is the equilibrium value of the angle, and K is a -prefactor. Note that the usual 1/2 factor is included in K. - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy) -theta0 (degrees) :ul - -Theta0 is specified in degrees, but LAMMPS converts it to radians -internally. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the "Build package"_Build_package.html doc page -for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html, "angle_style -cosine/squared"_angle_cosine_squared.html - -[Default:] none From c4511cb2fc2eea7c5ebd9b4eca7fe35136b6b383 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 14 Nov 2019 15:59:40 -0500 Subject: [PATCH 14/64] Update docs: angle_cosine_periodic --- doc/src/Eqs/angle_cosine_periodic.jpg | Bin 3362 -> 0 bytes doc/src/Eqs/angle_cosine_periodic.tex | 9 --- doc/src/angle_cosine_periodic.rst | 45 ++++++------- doc/txt/angle_cosine_periodic.txt | 89 -------------------------- 4 files changed, 21 insertions(+), 122 deletions(-) delete mode 100644 doc/src/Eqs/angle_cosine_periodic.jpg delete mode 100644 doc/src/Eqs/angle_cosine_periodic.tex delete mode 100644 doc/txt/angle_cosine_periodic.txt diff --git a/doc/src/Eqs/angle_cosine_periodic.jpg b/doc/src/Eqs/angle_cosine_periodic.jpg deleted file mode 100644 index a9d7d50cb3ab79f3dafd7c2c76d0338080defedd..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 3362 zcmb7Hc{J1w7ye;1Br#*(4TFXdiO3d}G4{P?Bn-+jG$m^y*&>WFjFhaCEF=5aw=9w6 zwPlTL*@^5bUw!90-~aD(&w0*0=RW5?=iI-Zdop_R6<|l*(7yrD(a{0OKLwmj0J;Dp z0|*3SVEjXjjEtwiXPCf$z{bMDdg+kaM5DsoZ9u7`^E(nAd#>+1xBqAch!6OD2 z6NU>4iwK`I0W3^_I-Ld`9RxUO1q1;)fS%#6$N#~2iU9gT-HSiY-XwFtMGmFBp1dVvaF%Nm6$hpf>*^ULzDuL8Tha6`U2TtwQ?@h(M zMW8HQOade0#++_1(hzv8D0NOKTrEeG9u;k_l0gR_4j3MKB{9$`yiY$u{8-uPpvXt~ zlC0A*F7BX@)Heh9@`KXDZ(6!>^|(d_%Sj7Ob=>KW&% z`RmG-P>x(xdUN#b!lwVqGRi!OgE%!&MuX&B$a}chAg&XggqN$%$}T%FB~ei3<=&(;dhat8((6tUP7y2^@_7nM`W#S)W9qJ*q|({a5w`2nQ&uZ|2-S=`j}hHqV7I9laj2nh0M zWDJv)(+P`bE?ThPyc)QseK-;ji}OKy3~sb(-E46ue!wEPtf#pWmcO7kx2T8P7H0)Y zNrM{^gC8@KKgHN&AUBM(gGysh0PW7k9E}qozXvSsXxpAG`H7%(+Z2iU++iAaly~hO z8@kwrXX)YMyXs1VVVRVz?AABCWPWG8d$D{}upM%n<&mA+j{(0;tKsb!w0z3&K-V(T zbB1*(Us?dT9GY0NCA2!F;U0@E#uOH}XJck7xDu$YtQito2lNHEl}-Sj-e7;5-$YrP zR%CGliMtZk?sD;tqstpsW%jg}{XX6@c>|;(%uYcqvT{df|1?;_R^GWl>BivxYg;nI zb@7o<^3MV<@lWGT7ns&C_}WajX$S;cEfG42?9`z*uRbf~Tp7YZ3{ey5&6KSq2k7nG ztF88`QF&M+1}X?i?R{oq80?06bpU#Z*4`1&bg7AxzZ(-j=QF_x4{N8jd0w<5?rBGo zdccI^n8PK7<8-blH&n||4#gcgZ_0i;+DBuiUU(StWJU1U7_?{#zX_dEA25UAY7PxQ zKu`?r-wy~$c$h;eb+rUxQ)}UCSQu0k9(}7-Wy9QFdX|C=4i$*wX6FPzRhC)ar$U(F z2^-w{T^Yb9%@ruDx$EArLvQp<`6$o@Ur7sDbibACz zUBif)V2=XqS6_>IF0)wokNEyyJ&`c-X|-U5Bs^h2%h3#m5Pr^8(cifJVspx1^SHdG zdLTc|s?n%;#zqgvy-I1>o|kH?NV#zPalRfy)45Ez=mW$?mZsWNeo{Yq&CmCG$xod} zWH_b-mw6E@=<=ZD&3&%A_zk~=9(RGM_}(H7^)&B~PPU3Ml&l#S*M(z=8qoZG|1-+Q zU(j0guWxBIDzK)fq2HFyZ3#K#nOwuSa#Hp}Q4{c>`S5Tl>=0zht$xpC_ei(1aeaOI zXGJQvmQTDw?w4LgW?ZHN%Hf-R*k!Ft*C9lzhz=X|rcC_KOO|CrOfp*#ZPLucb3x21 z^;@folY-clPjaBkZwKD94ncDW4KOt0m9gQiYQ<9hk{9;|9d6ClkS7BS4C3Y~IqR&H z3ZOjW93uk7Jk1W6TV|b4GF;9*Xn1(s)wq-3M$!E7VVR8ub`&FZJ4;hRdVH@QBL1wa2phPA03Z;oYC zJFK%S5U6wG&ow$VA3fVP8R+YO%lGTF%1`Ne0+c`s0r-K(GA|xIv7q(7`+C7BQS3>x zV@FLCX z)#IpLns^6aaElABbQvP^{fjonOL0Yo!Z4_cG{kBZwHHkjAYNoxnp zo5u*-$SE|`G(NrV`kghNl#zE4hBxr*(4iq~)*p=3sUmUpg$yf9KTf?*>Mh!P$^E-dA+oVgBXvhy3V>u30)uQTT$T@H(VnGA%pLQ0dRJLrKO&|_k&6F zhnLk4VurdeDURS$XV0H5Z%z^Ml;=FSJ1#JwGn8Q*8fvi-e(#x$CvjZfNBGq!m5+1e z?QO9(Cc`s3e#~nS^*vRi41O_jzgulM1`W+TJHdBe*=j#o?~&}CLJBl{#mJ`S z@|d>^Pfl8yPnSep=ZLceiN=BbC#Ch-)>H=;qakntoa_BH-*5ud8Wg1cFYo5fa>wkZ zOLlTeYE<~tQaUY0gQ{cXb3IC@8I{n?LK9}A_YdQSJ^seyByi-IV24=ay|~KQ%-qxK zJs~>Tm09{&J6rZAGs5~XwSDEhF7skrjj~a@qq+;u-!<9dOd`0xOOFHvuxXj7^|zhJ zZyhVju3gT3Ehl@Z$PL&=PMTrj3hr>7OMDL-J==0B0oy9|1zFRz?EA%n9x3GzdFR$r?!`^ep;`esS^huWy;sk^;% ks;zDQ#+6Sc-M68H3JFHEK?X;w@2SFn^%neBoOCkwAC}-h1ONa4 diff --git a/doc/src/Eqs/angle_cosine_periodic.tex b/doc/src/Eqs/angle_cosine_periodic.tex deleted file mode 100644 index 69aa1bba6a..0000000000 --- a/doc/src/Eqs/angle_cosine_periodic.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ -E=C\left[ 1-B(-1)^ncos\left( n\theta\right) \right] -$$ - -\end{document} diff --git a/doc/src/angle_cosine_periodic.rst b/doc/src/angle_cosine_periodic.rst index 43e5c0a4bf..caaf15007a 100644 --- a/doc/src/angle_cosine_periodic.rst +++ b/doc/src/angle_cosine_periodic.rst @@ -1,16 +1,16 @@ -.. index:: angle\_style cosine/periodic +.. index:: angle_style cosine/periodic -angle\_style cosine/periodic command -==================================== +angle_style cosine/periodic command +=================================== -angle\_style cosine/periodic/omp command -======================================== +angle_style cosine/periodic/omp command +======================================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style cosine/periodic @@ -18,24 +18,26 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style cosine/periodic - angle_coeff \* 75.0 1 6 + angle_coeff * 75.0 1 6 Description """"""""""" The *cosine/periodic* angle style uses the following potential, which is commonly used in the :doc:`DREIDING ` force field, -particularly for organometallic systems where *n* = 4 might be used -for an octahedral complex and *n* = 3 might be used for a trigonal +particularly for organometallic systems where :math:`n` = 4 might be used +for an octahedral complex and :math:`n` = 3 might be used for a trigonal center: -.. image:: Eqs/angle_cosine_periodic.jpg - :align: center +.. math:: -where C, B and n are coefficients defined for each angle type. + E = C \left[ 1 - B(-1)^n\cos\left( n\theta\right) \right] + + +where :math:`C`, :math:`B` and :math:`n` are coefficients defined for each angle type. See :ref:`(Mayo) ` for a description of the DREIDING force field @@ -44,13 +46,13 @@ The following coefficients must be defined for each angle type via the the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* C (energy) -* B = 1 or -1 -* n = 1, 2, 3, 4, 5 or 6 for periodicity +* :math:`C` (energy) +* :math:`B` = 1 or -1 +* :math:`n` = 1, 2, 3, 4, 5 or 6 for periodicity -Note that the prefactor C is specified and not the overall force -constant K = C / n\^2. When B = 1, it leads to a minimum for the -linear geometry. When B = -1, it leads to a maximum for the linear +Note that the prefactor :math:`C` is specified and not the overall force +constant :math:`K = \frac{C}{n^2}`. When :math:`B = 1`, it leads to a minimum for the +linear geometry. When :math:`B = -1`, it leads to a maximum for the linear geometry. @@ -104,8 +106,3 @@ Related commands **(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 (1990). - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/angle_cosine_periodic.txt b/doc/txt/angle_cosine_periodic.txt deleted file mode 100644 index 039144797f..0000000000 --- a/doc/txt/angle_cosine_periodic.txt +++ /dev/null @@ -1,89 +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 - -angle_style cosine/periodic command :h3 -angle_style cosine/periodic/omp command :h3 - -[Syntax:] - -angle_style cosine/periodic :pre - -[Examples:] - -angle_style cosine/periodic -angle_coeff * 75.0 1 6 :pre - -[Description:] - -The {cosine/periodic} angle style uses the following potential, which -is commonly used in the "DREIDING"_Howto_bioFF.html force field, -particularly for organometallic systems where {n} = 4 might be used -for an octahedral complex and {n} = 3 might be used for a trigonal -center: - -:c,image(Eqs/angle_cosine_periodic.jpg) - -where C, B and n are coefficients defined for each angle type. - -See "(Mayo)"_#cosine-Mayo for a description of the DREIDING force field - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -C (energy) -B = 1 or -1 -n = 1, 2, 3, 4, 5 or 6 for periodicity :ul - -Note that the prefactor C is specified and not the overall force -constant K = C / n^2. When B = 1, it leads to a minimum for the -linear geometry. When B = -1, it leads to a maximum for the linear -geometry. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the "Build package"_Build_package.html doc page -for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] none - -:line - -:link(cosine-Mayo) -[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 -(1990). From de166a3d168e1445f371ec71f203a4289f1d82f2 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 14 Nov 2019 16:19:06 -0500 Subject: [PATCH 15/64] Update docs: angle_cosine_shift --- doc/src/Eqs/angle_cosine_shift.jpg | Bin 3933 -> 0 bytes doc/src/Eqs/angle_cosine_shift.tex | 9 ---- doc/src/angle_cosine_shift.rst | 36 +++++++------- doc/txt/angle_cosine_shift.txt | 73 ----------------------------- 4 files changed, 17 insertions(+), 101 deletions(-) delete mode 100644 doc/src/Eqs/angle_cosine_shift.jpg delete mode 100644 doc/src/Eqs/angle_cosine_shift.tex delete mode 100644 doc/txt/angle_cosine_shift.txt diff --git a/doc/src/Eqs/angle_cosine_shift.jpg b/doc/src/Eqs/angle_cosine_shift.jpg deleted file mode 100644 index d9929939c8a3c9ebedb7ba50d8bf9ee84d5df564..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 3933 zcmb`KcT5wGv%p)56s1_oo-GsC!+WS6C76+u7{1Qe8w2#5lLh$u2- zk0Qge${sRWhENKq%(6F+U*3DkOMZX7a7{Uxb12MuGi#-&ewT# z&c!R4et7Y``aD+FB=U;Z;J9hyhbw|pITQQttUD&&ma(?}d~hS^V}YM}$Hf6QKiiLI zS51?GJ;%T5l^0Hyv%2wH35g9d{lkvY65C$62BM2RNrL?w_$Z4^bOPzup3+YmYtj)|kui)BUaL!4k19H8r{@)h1 zl)t^l*%08bHpo^qm1Ta88K=s)hHlRXhXMQM6}@R)!uYt>OdCff-$bFJrEsnLe~p8+ zX!VXLPH*cdmdzrT^yoK(PLV2(9wg>h+^NdTt#w!uATk_UOGzdLUnSBHm(@M?M_Ht4 z0jue2sl01EW|dtArjhKJiHfaM$5x7*;- z<{s}c;U%_4V;IZ_Ehv|PZCiz{TfY;rL-;FP;FDXwmr|;)p!}5yD%snAp)4?L+8<8R zbmJ&%rzE`gd60hniHQT=BWZYPabN9`lb2CC?0ATeFX=m$j87w@Nt0fk;0tKc<`sj- zv1k|F&7MoTMdRZdX^QpEji6zanQQ9==bd`lnGkN1SdyJ&a@&j(tJk3v|6AA4G@J3G zzxpxd?Ov_L;JA*;o>s?qUWuCS-O@ErTXhW1Wq%6y^uVyy|kdJx|o!Y8A5iPDy3`k}vfgonPLjmZxZK415xX7pl< zkEj#X&d1C=g^sqAFoJkKgwHF>t;-dKWVC|@jXu=s=;+=}pk?@rCM63b^ihkZV%him zt>f0KZ3%8_=Q{a5WM(;CDKqoq-jZvI3)dFE>a5)jvt7%P0Pp2u7=yWkOB z&fu7mz1aa2{qk|YV$p$E$}gO#ZHsfFS9uv-ZMgbzWbp)G!}w5PQ2zvAsy%jm$qFfv zE|{gnk5mzSe%;Y^Q+J_zY=3f1K-6{ZoK=j!$o1D-4%KQ7PilkTsD=So2Q<_+8K3$> ziwP2fgk(qMPe|)3j~!$##4GiFc8*382k+p5#<8i;U_VezRVbwsDZ{n?&XWVxTQ5sZ zm!KE&Y(yTBmKB}`559xMzwGnRg)f8^?T8xQzbHVAzi+4!-fmwrb&D7G!u9RBwFbp5 zQJW)#sUBrJKI+kmDn;L~bXIwOW_L=SZPIrjpUa`-rd(L#ktDb5K#_Qw<6MAU(IyFH z<#+JXPByR9j_TXk=XLz^?Y3|^BHh+)-eqf8AR_Vv5MZaHOATS<*2nw$&>@Kl(gC->ygMP12L(f7ocwf;$?#} zYB5!-ynzeCUmVS|Ky5`wf`4Q2kZwCSCOhSXO2!~J*il+?wL5@&H3MHz3kM|tD`&)a)KRGi9D z_}qfSZ)UHq{f$pN0eJKQjxL% z9Mt7JUm9Cc?}`75h|kDs=bm|8`bK3o?@iyY2$q;MEyeOYRbR>u^DNY#=#V>AzDFtz zFycNGp&mXWA~^K!mh;ZBt2a^J;ghC5*4at7WUYAr@*(geH&A3w&s6iuSbLd=8NU4B zFXGcRXmBz%5d7SFwN-GgLvW%J5+OJ2l0+zpdzs*bk3{HSw{Y^`iJ_=%R{9~B#R<3{ zwg^|TJ;WnxE=eg>ql!Neh>SRWYPcFj#B?anEvXNpVGocaH;DN};T019lU`heHMFKe z#;;>zTSb$kmgKThSwz6Tpb6j$50FGuCrRs2m9iYdQiw!SYp$U-pea!oJB$Ps-RKZj z_dD(Z=k3d#+x+W8`t5&fLXGa0)Z)Ocd!U+MLa86EBVN&-SO1Jv!poKFkn*KKWCjVn zn8=LvfnT^sW%XY@cP6K>e6wp}Mj+w5%nq71$<5w?Q*yyA@d`RoWr&=bJ= zt)p|pbgL>!YPX{ISO(_shia~g&d7um>F6T>fBp*N9)T_W)Ynm>cK5GBY66q z(9G|+uM2F3MQ)4v`9D{mR2pt6B^@n2)a;~&UM<<3l3BTwk!VK?ys;UdTxb-c+8xC7 z^fv?Z2TuaW1joeA$kXiocOA#uD(~m;nmI;a>JwJ6>Br_A`<(v?H&?ku- z_i=G2C1K4p!Fgc~_pFCUm3B8>9G*Q-*PJg>=ZA!jS)j^UW*xdXI*iNu(?i)4K+gauTV9t>O(oA~ITM_3=AF(t%^Z1&! zba~rpB>QD?A(1XzXP~u9Z1nj^=U*Lckf+!Fd70O?W;I&QN1DEmk6SIqMiTrMMZP1lCf|CixKbe;&U}UF|PwSfB<6ZZxjeg(h zmgVcYO(J@ZzQ}lwf;es6skRdw%NrA=$lb*rcs!!6PO`$(N>L-A+%`WPQ8MGk&&`f1i{ zKQGOHKO``z)w~p&SI4BU$I=0xwkcznAGTWE(wdi7TcWhCs~P)m#ak9%BOY39r%V|0 z#IO-v>Qk0<1^YXHkVKPmdV;PEFv444E0%qmflZpU5cw0p%ZL*|XXbNiz1>-lk+pg+ zXzaIn-bv}}azEAwwWVcn+9OS>hYU6UI;?f0X;o#GP#FHuc(ay~*8o3w@0|#yK*CNU zz%9~%f|(T#(z+Z@)%OO1HHh+-8L|nMp^yaPRW55A^?2-5lSGwWynL_=3E8tpI0I! z99VntT2(iY^W%>G+*bt;Xp*C~K#?{{s(Y-MP{ap?Z{``cYKZ91lGNXKb1m3sSl#Xk z0L7g)D}ZIWw`a#7Pd-s{BHHeJ>&G~U=kn4UZP=71uP*HJ1u}s;^5yMGrlnjxAg!-Ewc`%jQI(H(4?P3oL=pHbF8i?@iR)`x$U ztGEdA$Q7{QTTnhG>NRaWd0!`Yt!= zr@qQ%LG7hpz+oAe{uFr&XjJ(%5T|(-qNaGfWq_W;4TyFW)wP;8-oITcLDo$TG>#t) O4JZH4r2jE` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* umin (energy) -* theta (angle) +* :math:`U_{\text{min}}` (energy) +* :math:`\theta` (angle) ---------- @@ -83,8 +86,3 @@ Related commands :doc:`angle\_cosine\_shift\_exp ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/angle_cosine_shift.txt b/doc/txt/angle_cosine_shift.txt deleted file mode 100644 index 65dc0924e5..0000000000 --- a/doc/txt/angle_cosine_shift.txt +++ /dev/null @@ -1,73 +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 - -angle_style cosine/shift command :h3 -angle_style cosine/shift/omp command :h3 - -[Syntax:] - -angle_style cosine/shift :pre - -[Examples:] - -angle_style cosine/shift -angle_coeff * 10.0 45.0 :pre - -[Description:] - -The {cosine/shift} angle style uses the potential - -:c,image(Eqs/angle_cosine_shift.jpg) - -where theta0 is the equilibrium angle. The potential is bounded -between -Umin and zero. In the neighborhood of the minimum E=- Umin + -Umin/4(theta-theta0)^2 hence the spring constant is umin/2. - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -umin (energy) -theta (angle) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -USER-MISC package. - -[Related commands:] - -"angle_coeff"_angle_coeff.html, -"angle_cosine_shift_exp"_angle_cosine_shift_exp.html - -[Default:] none From f2271e294df2e36abba13fb04a6755fb3b2ec06f Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 14 Nov 2019 16:32:17 -0500 Subject: [PATCH 16/64] Update docs: angle_cosine_shift_exp --- doc/src/Eqs/angle_cosine_shift_exp.jpg | Bin 7884 -> 0 bytes doc/src/Eqs/angle_cosine_shift_exp.tex | 13 ---- doc/src/angle_cosine_shift_exp.rst | 48 +++++++------- doc/txt/angle_cosine_shift_exp.txt | 87 ------------------------- 4 files changed, 22 insertions(+), 126 deletions(-) delete mode 100644 doc/src/Eqs/angle_cosine_shift_exp.jpg delete mode 100644 doc/src/Eqs/angle_cosine_shift_exp.tex delete mode 100644 doc/txt/angle_cosine_shift_exp.txt diff --git a/doc/src/Eqs/angle_cosine_shift_exp.jpg b/doc/src/Eqs/angle_cosine_shift_exp.jpg deleted file mode 100644 index 294986de4b66d52f010331b7dd43b72d8d7b64ae..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 7884 zcmd6sRZ!f^x9@*AY%Bx82L=rZ0TOJm0Yb14EQ(8z!3K93dF2q(L4)jj{GTj%N4`E*r3bg!zls=KS#s`b5@zF7utJyq9K2Z)G>fG2+j za5D#}0AwVjq@*Ndes`_`zHduA6TFH6;Ki9ws6J0XOXc7$5?ON&fZme<33$A*CQDqWrU~c?%#S zB_<*!A*CcHrl!+94cNF%?=ZugP=4^~rKk4oq9Sw% z(~WXzcqtu8P%EjAkr*t4Ht`*g2!c_AS#}>ik8|uZ!^q~joaZByhxeaMQ;)0})?W0< zGSyk=fzP1o&F%0~5qDxG&jW8I=Pld%7&rFq-O4wWGP?^7PSzihs7O0y37fY^nzvDt zvjiB0lKoik{%mVatvIx9L4?$Kc6i(6T7AvI zsLUsmMM%46XNUtHtIt`z>o)DCbW52Gp_TlZ&JnCS=%p{L3NJO6oT=Aqp3HfdF8Sn= z6SXzFsQN#{oOFaOi!wP{Np4OZ0Z3b^tw@?bwFc%6Q>&TSF#=wo)$p0=jw#yw^SADT7!oa{Fq6?eL4-(6an zs(iL)KhmzB?qE~go$o!fbPrUSA2!SvHnch7Mn_t=M0o&Y58-8-9TGed*Y5```ntDt z8$Xdo-i?U=Mrmnzg`>a4VXH)Obh6vQFQ}B>)s}#2Q@?v)V0wYp_&#Kqlq6Mq}|JbU=Vh zBBozoaPF>$ut`za_5pO>d(Hj^5W2VSdMIFy0eQBt$g+s6;{2|rd+^UzT|Hp7Q1e;~ z{)5;+8k% zR3FM~{EM;4g(&wdi`%FKQ%qZHEasTvb=KH`!vSgp!;iM6B5f(@SWr7aXzoK@iu5Gn za#OpSBcC?dm2QY#^W$($XnO0}Wo1Mp&~P^zT%43su<_gB<2NI8%3srQ~( znyUXbSbK#mj9F@J_B1+Uol<@y{i#&~47nYO)UrWvmZ5R750m}5%kJ4DCZt<#I>z@ljk zgpe=bMRH}PXb}`fsV}jZoT7_EdCn}a@@P19UB(0!q42g07Q`CojI;UZ?za%Lx|GNY z92As|mkOHAuyUIC>LkB9X1RI-znqC*$<*yo@BU6&d29lDa^|`q`sTy(sKzHcpJuy> zH$VG2l&&+{lx7>0eh1V^2l0IZyyr=(2NV;Q7SSBP1HUT~rt7W#UvELE@LgRW(z*?K zz+V`^j$PT(a*{KIjqq4gfp$JO&F^EHu3l-7|L&G8WsK;D*C~o8U!ho?`pi;MUj=(u z{ol+t$St;DUMh0Tto<17ZR;(0R_F5Zh2!CnZsmKM1WCzq9E-f}zVAG$=qWF+=*t!9 zyM)_F>+e_h(Qx;pj%;`l^VOAq^7wN2!+jtA}{oDKIaq9^N^AB6SUQ6&{JJMw_t zdaQENIMWtYo#M)2%%|N1+Hmid$AxaMkCXA3j@0fpOubTmHhc46R|vVcyu}VvWAukh z#lNC>I-#f|K2^^STPiDG?F1c;wpC1&DuvWHuH}gNTgu$4pTiI?Dy}@(CLFGAyKFDm z&`EUiU4*qYyV(bg=cJ)eNQr$P{-1Ocn>AE>8#ZWc$I~M*zB5`wwmq>`-@wKhZ8ibU z@Y40?nUxb2+1o6hPEQ>D(0k_LbNoUQ>ty7lgPBwOTeVZVrqDK?@O1=qn-o`PctkAZ z)G-WuwMv6Em&mbq9+G(caOhA@{$Qi|22kk!@tS{~(Vf6K7oOzH55#-N2Tm`JTi6BM){Yg!K4~cr9zQCGzmS_8fOF8W#rhL%7_=Kswr+tfG`!D0F|K= zltRU`7*L&-)GeWQuoQ|e(aRM50Cp+RCg8qZ49;K5PYmSlRL#y(y2kg3!zHF-hJAJX z9N@Pk!-yMP`Hqz?<|#cGuvj%!7d&ml49wt!B*WtSY|aYYtf}k;wK*R6#PAe*{Q2Jf z${5o3?d}Ut98Kg{?d=FIy4gR#s+6{^sHlgs|0xb$QNyM%W35Mu7T5(DS!S0kX3H!N z`b6WgdS21s`m3Yyu7;K;=V@bepS|H^Lv;#Vob4Xqc<=nYdJASuulCk< zm;JB7-gWC4Y~9GtSK{))10FJc{f~0CH95GJ73pGTcbCcVAkb|MsWroWf%b~b4B>Mq z8d|xlGYZ`xN1aq5O?5-Bx?ek$Jsfgxz8}9npWO@~{PQ%TKlM!a3}5y`tNN~W z_F|J*_QA`jg|T{K0x~h>B8@_>$4aJ*xZ{}SwK6qrnkR4K_vBrAg-7^noe_wav&Er> zNzhBv4TWeMEnj(uQ&!^@z53Auzfei&qs5xsCQ9?b)VgOY|;FuU{sH^`QDAd)}pDr+FWS<0mZO}qj z>3Qr*U%SCyP2)D*yYgibCv!gBrNwA&yl_4&Iy{^Ge8#B*2ES6fuV|N%QoHRPV1g$= zsq7Rict%KmU7aWjsewRDFT-t0JWQl7#j@2`7GPCJ&nO(?Bc*YQZK1ygF}v;#ikL`* z+R$QEX5?8&&YDa%UEkKkKdl_cGnBJk3YEQbA4*sQO&3lA58Nq~`vK=Uwkxi+Guikk zzxiuCq^kFFr+;&9bgG$Z?d=eWopPu6p3{!wZ1fk?^CY8=wZlvVE!bnDa;z!2vGuEd zIP_EpzPiFnNz}lp8%W;S!+s^0V1^&6bERu=K1b6gIjK3Si&e%;tJ z{Gl{q6@tva*x>GiKd7(Xr|ouoPTALy@#8ttg*$ARl-b5-uxEe4N8ws}NXF)c2c$ql zdQBX^IM9i|eJBOisNWd49=iugoioC2z|Ks;!t21ShWbCE&T*=Pd{>gV))zeQ`QN_Wi-@!JkPWf_*%m{n zy#bQPMo#0ZAseoNTW9|3lU33aW9N}IOE2#>4sgI@j$~@3_Cy3qMdXxt-|gi@Avsul zMS2|99d+bA)oD(x{nM%_>1K56Vq~+BN?QZ7 z<3-ERMZb@e5|cWOS$*<)+9)MNUXUS@g~52#%3+H$Oq6fDG$FcnW8~*O3D`jgSD+;t zVt7mv`^i)RF=B@WFC}=sYsm;Ky1uqJqGvOxTP|f1%=IV~(wZ+q_a%0w&7fkFGnN<2%u z0-B@1A>pz-oQP=QB}o(KImv`ZP)Xs%NSo3`*$rT3;kWS7>>vGVF5{186_OaAGQDJJ z59lIRy_qxS#CSeK4ATy+>pIdN;ucTwjzd!o_UW=Z2FeYz5NC6z5%E% zbGGqH&8FvDCYWAZ#doHI4i^Ly5_wwvOBQ(X7FVky@kWHX1IJit?uX?-uGvY#@051U z6DI;)TvXKSzpHAR&tc~8K3kIxbm=>1m%$#l3O=9N9$vfw(mz=pT?Hn1xainM-K}v{ zH-aOQ@0xjWb;X>7iZQqML(4ex> ztJioK5J0<}&b>(>KansO&Do-kLF=S$yPIGiD-sqT3~Ck{;~#9 z2O(r@&si^NO06LZw7tPa&2lD1{I04Ei`)){%_p=Qp!6Q|`q?u-v@07MX$Et_$IZ@W z_E_HryQ^fqqZ8SgFmRL=NtvvtZeG;AMb3R7J3%eb=3Ak?mB&Pz-^K&EE)dx{T=+Um2%RcJ6w za(ai3jU8|X>$i|2G+zG0#c3>Zq7j}C4bnVjs|XPfOzwmUcYA;#Bj-vhm33qRy8S~5 zYYbC~>;i%LUT7z6x*dpram;&!${W$jWeS$+HYEEhIN*o*T=f=}Nc9ciU)j4Vj8aNP zq9Hv`H)KWaI1_ONdh~UoR?OrlbA^fuc+GOE;q-CWU0w97d_)O~DepgWL`mx9di7&! ziLvasiq5I#s`bbxnjFIJ)|sOkxm)fKUIUJf(LoQT{2^%XXs=p4*po$t)@XE$F^Xzt z@5QFKw1%xhPW14_-5Y@7had-*5X@uyF-1U0c1$C9gDj6A(hsQZUB%Q zxcxZOMlha3gG1-Su7~x<%<#rjwaAo4Nguv^dNW@WWM0gVU`;e@(L4bKMh+40xTo5+ zNk#j}tuQFI{gli2dMfGUZ2rNT7ll{t#K#epAk-rsodC#`d{xy~=SQZc63KASc?&`H znkn5_?YCOhoWd^YP|EfZoI*jVFoJ#AhhF8$mi&At3AF$R)We8lup2Hy{?*|ptaiHd z;CTnvkO~q1W{OPWLYInZpxD!rCoq$>%BjlWuTap_WQVUtwmS&__?*69A2l@L_^6%o zc$G)@9FvB?N7CVzaJ(bpw0ul6vGJT`C=sVZBVwJYyGHAqc0VeQgX0O{V6$RdfDT+C z)!#RV+posP?JZ`WJsyLd@k1tl&{i^fL5=7eX7XMmVJ_{5OVlMM@Yoqxw$6;dt=pZa z6Iyr5@3seXn%g{sf_BFD=sJQU9R%Jd7(Y2tB0B|v>3y0SI2=YO@WAKWYGv53 zcSmq@@9}TciH>*LZ7>U`GkFsRjWELVAE2Dg_W4eE+LU0?Cna@}8VU&=JU*$W!0);D zP(9}?#$1O#?L4&?Lx-lp7VW_b1NnGi=;6e!!Nc;vuW5ps_94OF(XJ-y@r}OQ#HZ~t zYIIV)m+HXvhAw! z4X0cIrkk6qLCT`pvYJ-V66tN-n~(avjXt+&PS+@XVKd{%-%cFl2wr7(1L)uBb#&I+ z`ZBHPx~3Ygd5K6!G5I;av=tdSsc3+MykPx%oV{8xbc+q-R}b#SCdaP$56U70SeW~* z-*noD_65$AJwtXDk7j=k0QVS;cfslw1ZzcovPy`oR;T@rZt0pi2G)o?wXJsakXsK9 z<&3he0swn<0IA78d1X>0EahfeN}0u1JNP<{D!sLaeGvUb_?DuAnD+V3_+JR9gP_8NE;($_>Fawo?aW zSYPSh0Ax+Qeq+aV{dWRT-JjPE4>DEwC;CU4W%IT$XnRjR57xaXx?KqI<6_T6YQZ!1 z4OS{?2>wwBob;>GFQ@fN&i;2br#)*pM+qWr?bJ^ zn7_n3#<(HwotnmjDfS0NHTB+h8*Z5gk}H`3%-$8rBN@#H&%w{C_x^??=E$dN^s5Q> zn2mry8Xj?XZu`r zIoq=er_itgq)t)_bCtK)+iSk1DVNYEFEjH7)G-)ZXiw zE$Rm?u0yLIByCpx`_1N)8nyVMa_MwE9c@iI)6Bs8fTB9?$zZwn#OQTa;sMb|R1010 zTRO(hjHm+GWIop4dA>%maZVrZj>NV+qQwSLya$lC4P?Wnn?pKeqg~I1c{|yEb^QkG z$LXR~E~%DdT2eAv9(l_S;Ej-ze|0`!OfE#7eX9IX!f3?J{FtJV(6BgR7T}G$C(~NS>y)1fKa(tyWpThmUMhIUT z#gvX+_+U!pWC!s89$jSD<*{Ef1pn1t)Xd{f<0|z{f(3(hJT|Cin$=(C)_KvdyN$MG zA(jif45#Er>Ibm)&y~E&kV-3ZdOergo0Mg$uwKxlHy=L@WD(^yU!O=(b=9iv-;1q| zSYhkEn1@vkC^-JGzB+#)-q^JF_8;{siO++c#)Jm7g`bh>c*{n)cPO+xgt1Q(9YOJQ zL76r>DEI3?3=ig5r%*EGRMo6pqwzQhI;QY;b>K6m4=&EkR~INWoma8Be4KZ@>VROK zJeAp5^yja|ng#)Yil0!A`#gIMV;$Z%F6WB?#l%QE5UzZw2)TCyTt}ahS+@DPlfld% z5V>;qA$>tkvjy=?^;B+2J=C@#MhsA1W&16cK33iC1Ei{&Zns+l{g9mpYvUXq??L%K zo_BiZRA+)iJIJkX99F~HXHqeRcn`{}Hb0W5G60a!%DB%=FnW%`_L=D+AGzcuWBWgX zNuKc*E0toFiQst2AS279xx^1TJ#`<$_7*mDSBI6Lw}#|MeLI%C*2niraww*GpKttD z&Bd;u*h;f6Rw`%SaQnHXP|u&z?rvZ~h4MueBTYzRUV@{(q}g?{E`@ub0x%rcogM&X^}P6{k7){V?8pnv}Dz-zO1dl&1n#bU@gA%^(D+Man+x( z(D|>KPufHUH-Mp~^T?9^>DV4fqHOq}Fkr9A>0Uwq)nC7VU1a?ZoVfv#KK)0(`4;5} z2N}X@^Ht}w*te9bOqQf-jG9}hh9xcE&5-nfM z=0=wAvvkrwLxk?`F?ctfoXQ(-%g_8Vvf#H51b49j%gS5s6qlfRVbf{C` z)B)D0h)RtcU$E_Usb z>YvuQIxUH$;8z^b9GZkaKGqp_6>Go1fK*eu*`WO_pP6c__ciA4op+jN;DZm4;SW2* z^%f8sc^dC$1PPimCicthm9ZDb@QKfY;no;D`+KQsbM0)6P<(cp_emWUjLrN|8~@FX8sFayEYa8 diff --git a/doc/src/Eqs/angle_cosine_shift_exp.tex b/doc/src/Eqs/angle_cosine_shift_exp.tex deleted file mode 100644 index 4afa01356c..0000000000 --- a/doc/src/Eqs/angle_cosine_shift_exp.tex +++ /dev/null @@ -1,13 +0,0 @@ -\documentstyle[12pt]{article} - -\begin{document} - -$$ -E=-U_{min} -\frac{e^{-a U(\theta,\theta_0)}-1}{e^a-1} -\quad\mbox{with}\quad -U(\theta,\theta_0) -=-0.5 \left(1+\cos(\theta-\theta_0) \right) -$$ - -\end{document} diff --git a/doc/src/angle_cosine_shift_exp.rst b/doc/src/angle_cosine_shift_exp.rst index b4af85352d..331ccb9da7 100644 --- a/doc/src/angle_cosine_shift_exp.rst +++ b/doc/src/angle_cosine_shift_exp.rst @@ -1,16 +1,16 @@ -.. index:: angle\_style cosine/shift/exp +.. index:: angle_style cosine/shift/exp -angle\_style cosine/shift/exp command -===================================== +angle_style cosine/shift/exp command +==================================== -angle\_style cosine/shift/exp/omp command -========================================= +angle_style cosine/shift/exp/omp command +======================================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style cosine/shift/exp @@ -18,32 +18,33 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style cosine/shift/exp - angle_coeff \* 10.0 45.0 2.0 + angle_coeff * 10.0 45.0 2.0 Description """"""""""" The *cosine/shift/exp* angle style uses the potential -.. image:: Eqs/angle_cosine_shift_exp.jpg - :align: center +.. math:: -where Umin, theta, and a are defined for each angle type. + E = -U_{\text{min}} \frac{e^{-a U(\theta,\theta_0)}-1}{e^a-1} \quad \text{with} \quad U(\theta,\theta_0) = -0.5 \left(1+\cos(\theta-\theta_0) \right) -The potential is bounded between [-Umin:0] and the minimum is -located at the angle theta0. The a parameter can be both positive or +where :math:`U_{\text{min}}`, :math:`\theta`, and :math:`a` are defined for each angle type. + +The potential is bounded between :math:`[-U_{\text{min}}, 0]` and the minimum is +located at the angle :math:`\theta_0`. The a parameter can be both positive or negative and is used to control the spring constant at the equilibrium. -The spring constant is given by k = A exp(A) Umin / [2 (Exp(a)-1)]. -For a > 3, k/Umin = a/2 to better than 5% relative error. For negative -values of the a parameter, the spring constant is essentially zero, +The spring constant is given by :math:`k = A \exp(A) U_{\text{min}} / [2 (\exp(a)-1)]`. +For :math:`a > 3`, :math:`\frac{k}{U_{\text{min}}} = \frac{a}{2}` to better than 5% relative error. For negative +values of the :math:`a` parameter, the spring constant is essentially zero, and anharmonic terms takes over. The potential is furthermore well -behaved in the limit a -> 0, where it has been implemented to linear -order in a for a < 0.001. In this limit the potential reduces to the +behaved in the limit :math:`a \rightarrow 0`, where it has been implemented to linear +order in :math:`a` for :math:`a < 0.001`. In this limit the potential reduces to the cosineshifted potential. The following coefficients must be defined for each angle type via the @@ -51,9 +52,9 @@ The following coefficients must be defined for each angle type via the the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* umin (energy) -* theta (angle) -* A (real number) +* :math:`U_min` (energy) +* :math:`\theta` (angle) +* :math:`A` (real number) ---------- @@ -97,8 +98,3 @@ Related commands :doc:`dihedral\_cosine\_shift\_exp ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/angle_cosine_shift_exp.txt b/doc/txt/angle_cosine_shift_exp.txt deleted file mode 100644 index 3091e83885..0000000000 --- a/doc/txt/angle_cosine_shift_exp.txt +++ /dev/null @@ -1,87 +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 - -angle_style cosine/shift/exp command :h3 -angle_style cosine/shift/exp/omp command :h3 - -[Syntax:] - -angle_style cosine/shift/exp :pre - -[Examples:] - -angle_style cosine/shift/exp -angle_coeff * 10.0 45.0 2.0 :pre - -[Description:] - -The {cosine/shift/exp} angle style uses the potential - -:c,image(Eqs/angle_cosine_shift_exp.jpg) - -where Umin, theta, and a are defined for each angle type. - -The potential is bounded between \[-Umin:0\] and the minimum is -located at the angle theta0. The a parameter can be both positive or -negative and is used to control the spring constant at the -equilibrium. - -The spring constant is given by k = A exp(A) Umin / \[2 (Exp(a)-1)\]. -For a > 3, k/Umin = a/2 to better than 5% relative error. For negative -values of the a parameter, the spring constant is essentially zero, -and anharmonic terms takes over. The potential is furthermore well -behaved in the limit a -> 0, where it has been implemented to linear -order in a for a < 0.001. In this limit the potential reduces to the -cosineshifted potential. - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -umin (energy) -theta (angle) -A (real number) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -USER-MISC package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html, -"angle_cosine_shift"_angle_cosine_shift.html, -"dihedral_cosine_shift_exp"_dihedral_cosine_shift_exp.html - -[Default:] none From 579b1271b04b5d88c90c42c1e136dc4cdb3e3047 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 14 Nov 2019 16:51:06 -0500 Subject: [PATCH 17/64] Update docs: angle_cosine_squared --- doc/src/Eqs/angle_cosine_squared.jpg | Bin 3265 -> 0 bytes doc/src/Eqs/angle_cosine_squared.tex | 9 ---- doc/src/angle_cosine_squared.rst | 37 ++++++------- doc/txt/angle_cosine_squared.txt | 75 --------------------------- 4 files changed, 17 insertions(+), 104 deletions(-) delete mode 100644 doc/src/Eqs/angle_cosine_squared.jpg delete mode 100644 doc/src/Eqs/angle_cosine_squared.tex delete mode 100644 doc/txt/angle_cosine_squared.txt diff --git a/doc/src/Eqs/angle_cosine_squared.jpg b/doc/src/Eqs/angle_cosine_squared.jpg deleted file mode 100644 index b992398b7d0cdd42707f3442eaa2dcf1896e0dc2..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 3265 zcmbuB>pv5W`^PuTAvq@NM&xXSk|@hL*+yYz7*P)0&Z4O4mP6#mEi*F-EwwpsB<8GI zXxCXxl00Myk*lz=l zSO7}^h?kF#j~DbiKp+smz;Qu=-x3oR7CJ5=CMhW)CLwV`S`K_dO6H`5#3{v7GN(@~ zC@7o&E2${StH{YK$RB+G2nzyifoFg~3BXY+Kn?%|@bK^g0sk)$Kc4`QSCHrT)L0w< zp!|e0uYi+I)8Eh16vu25RhBm(xdIGu)Mj8wVop{s<@2vYY|q%bz%N zj=_>E(%<6L;Qw&_9seRGsGA4KB_ludm2?~T+vY;*Z+?F^dJKuC`{X>P zmvHw&<@3@qEJy!4HdLOPk|7XYTr8oeXK56Hd{u7PuItRoy_@SdM(rt;Axk1i1Uxj^ z`h#T*j-*n7+x&5*VP#j(weye9+UGOwHqp)#XKfx<4@MfcY7Zq87vbX&W^m0jJN>Au z-mU}p&Iw|_wCF;SSQ@8mzxgzMkbK3l{k9c_Vr4l8K|k9R>CBeJl8pwE!)nM7VK~#? z#9V;mJoLMrtgm4?(i5Q>ck>nNzAEb%k+5z4+68B_G)S=kwaW8a346_1W#!+z#EFl- zz9|-;4HCcf!0@m#-2otarEYh&V|eu@>UyqaR<6ucs6@K@pD)kU-i2mZkmb$tYoAeeJgILv3c+G z;=zVWC5%o#c+FCadXX;@N?92|xR_0GeW8%y1CPU@9w(5}tkDK;0^f5%W(-FZpDnNJ zo(|M8{!)|nUA3C*S1k2XCFse>*C+V0LIbP0E?il|3ryZ#$G}0=OseAKuYB61>27@p zb(4avcvCNb9W1t_i`G6>W=LPHO|BITbo!uI*DoW+yC6|^IOooophMW$0!L2UpS?954pf!-AAp>bwR-9SvWa?G>(kX?L9 zE5*gORRwqKpPdCy&t5d9pA>M}FJHHaX_1TNu-C7V5x0rmsZnRmCnA8#TdMC(K8^2e zI6hyo(>oZ3&V#d9j-W`ULrCP`aZ|J5IcNskGabpg2OlAjW3P1xQ%M;7XbxlX2w+D0 z!)G3>dah_3>d;4p{B#b(iqOUKgAp+Hv!}gnuGtr$HF?pU8LmyxyF?b);8wfHJK!-y zN}jM|UW&b$tfKq-tE-<4)Co85kJ!9I0>|%3{O~yK3SE3kgdA>Uk-v_T#JZl%(I2s5 zugM$%d^^L6iM>tNvO_eGsf+XO7K4c;nwtp{uSoZr_l7;MzNYEI-r6t4b4&xh+_TbW zqd7@8owqQ9G1NfObl(xwtZRkSoOihTr>1e=FIPXFCo;6xcwYF*AmjRxtfZ)Ql-(Ei zmVYBV!&-Wo|32#WciWgXzPJf75hQG+e|xfd|KUaTKJ|$Qa^Qsa(4W%CR<*eRZX5?+X$a})fXKqS^Of5dtrM`5#8w*MKMfvGhGwBUw;4Hq3Se= z_4a+c;||+8-KTOq_nBw#gXh%xF}FU|T16p`xEWNunb8^Ul4kv&ZI=^Cz3m4}Icy}l zQ{kZ=Cl)p6viv5u7Xmp`97m==Zwyw%@Mo?E(sfOC=B-XHtZ{GVI9qw}!h%k!lv87I zRVW&SxmmQi@z&+s>TX`k^Ebx9=s}b3wQK0|xy(;hZY!#Z#@*43e9!M>S7IxAK@toGESWZO`10^`R{$>pwQtxYb+gQ0X+^+~Z{n0)pqS>TM){na|T)neP zH5_DSbHzqWzYg%tB5&I?UFK;`zG3Uzvz(oec)giLBS4iedw*AzMHJkx!C$Po474$22RypcrWbgyG-)u9ZC%}#@Dl#_7DcbWXgBBz zf=GhM2(2wbO*jD`Q&>fqAX|(2n|Y14h`g}HR6hfE%~ zT)dha6Wm_+y^Y6bHHCXS}e!?rP6_eypQ{(S0P z;jZSIA5oSW?|8gmM zZ6lS(3B#mQh^VCP2lZa@p5q)uon83ZcmtW}#?&5z*QVKcGgFIzgMj)uM@2@upq5n7Y{GqLa3x?&!;OO?whOfD9p zQ(4_mEdnAFG)_!ojQYksjGy}KtW(&ahSOahHkroZ9cNTI1VfO+OUoct8^9%U@rCAZ z5GxOhzmm^}77>ecqUX5*pJm#<*V>rJ8OR!wg+j61#_a|A;^&UfU9h(XNh z@hFtkj~OY{i8f6S`u)J5uE!@!hnKU52Vv)!I+v(nme&iQ>fZng6HX>cW*MQ2z62ZJ zAo%m_5MBNE|BlUFsXqq)6~8FpsYI)$1g;c%fg!tviZ5Nn$5UVGZzfz83gK_9tCF2s zLcW>0l&=aO6;ct0v0Do*gR*m(I?SzMmgaze9n0hC4{R`GOM7tbm|bunOi-@57jK;= zc5z2~e@p@P;$sZ2%?L4AsV|kp#)vx=Ho|cQ-3kwZn_4)B)XX(X~u(P z!-gdf(+g@n-?7@;!nj*Z`xz=u-Z3yNJkRbV>|Q(pCz)0Nkc_M;<_=(L7UVrg(@T*a z$RmIx*lqTiM&=jY*T_Ae$BByCYa{f`Qr3Z4qw$@^=ozk}`f8dR_+vFU1ctm+P`w}S zn1Zk#OriZr4;}5T8ae{V^GO6Ud_FOulL5yvjsVo4uK%Jay7G9`;y)iUg0mu%OeFAo zYftW?y3>AohV@IoUSe#G_bEcQe+>}{6f3vo;@Zig@q!k&JJUs~*Ji7;`*|!&Oc@AC z$pVhNhVoS{0@ccA80A?|8%o%{-h2aOb4&d|mAAv+dYX@m8!3*8P9CTJhkt2u7IGH3 zVGxXzAQELDXv+U4EY<8S#vvd8F_|Psutc<%5MvTwSIh{l1AjbBcv5xjpL{der?;ag zNW^7OrW!)kqyzu$_CiK`YO0SGof0J;iHtUPSw<@)p|6bpqUK%s(9WaTE~R6 z5$L)r_*3XGSZhMr;lQ??mUBn;{%7h>zsS!kI8vhO!c-|-q+tw)07NuvgscDQy@` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* K (energy) -* theta0 (degrees) +* :math:`K` (energy) +* :math:`\theta_0` (degrees) -Theta0 is specified in degrees, but LAMMPS converts it to radians +:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians internally. @@ -85,8 +87,3 @@ Related commands :doc:`angle\_coeff ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/angle_cosine_squared.txt b/doc/txt/angle_cosine_squared.txt deleted file mode 100644 index 07fcb1ceb4..0000000000 --- a/doc/txt/angle_cosine_squared.txt +++ /dev/null @@ -1,75 +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 - -angle_style cosine/squared command :h3 -angle_style cosine/squared/omp command :h3 - -[Syntax:] - -angle_style cosine/squared :pre - -[Examples:] - -angle_style cosine/squared -angle_coeff 2*4 75.0 100.0 :pre - -[Description:] - -The {cosine/squared} angle style uses the potential - -:c,image(Eqs/angle_cosine_squared.jpg) - -where theta0 is the equilibrium value of the angle, and K is a -prefactor. Note that the usual 1/2 factor is included in K. - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy) -theta0 (degrees) :ul - -Theta0 is specified in degrees, but LAMMPS converts it to radians -internally. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the "Build package"_Build_package.html doc page -for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] none From 35f305eac46b24c3b982d7ae993b7013c09ff037 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 14 Nov 2019 17:02:23 -0500 Subject: [PATCH 18/64] Update docs: angle_cross --- doc/src/Eqs/angle_cross.jpg | Bin 7977 -> 0 bytes doc/src/Eqs/angle_cross.tex | 9 ------ doc/src/angle_cross.rst | 46 +++++++++++--------------- doc/txt/angle_cross.txt | 62 ------------------------------------ 4 files changed, 19 insertions(+), 98 deletions(-) delete mode 100644 doc/src/Eqs/angle_cross.jpg delete mode 100644 doc/src/Eqs/angle_cross.tex delete mode 100644 doc/txt/angle_cross.txt diff --git a/doc/src/Eqs/angle_cross.jpg b/doc/src/Eqs/angle_cross.jpg deleted file mode 100644 index b0f3fcf83ac2621807c7ae58772bfbddd1d94824..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 7977 zcmbW5bzD^6xA)I5z|cr{2q-9_bf*F$($b;QT>}g$je;~XAdS-Lz|ai>LkbKzbV!FF zC3*S&e$TzneLa6Y_pbBW=by9pey#UjYkl@U`*!+v3Ap!CNks_&fdBw>_W-xEz%u|3 z7Z-wyg9m{?@bU2oh$xAP2nmVk$SFuEndn)VndliASvmMPS=o5l85y}mAMrfp7ZMU; z;S`q^6OiH)6cYGn5)eK&XZ3oEk0D5p17{mr(k%7QupxYk+ z%blM%pnnT;g;NcSx-gT(C2VjA~U@UAf4h}ZIk_G^77`W_6%&_u_FPd(`Gv|$ zo!7d0`UZwZ7M51lHnw*5P!CTpn75B_Xjpi}hmVm_iAkT6;VG$K(!PGn%P%M_DlVz2 zM%L8U)i*SDcKzt?=|%PRkDm30}z2hcfkXb0kXgeOJrJdPu!B~z03u5G!m-w4QHhef@`a zsewNTqKyOCdOI`h1Ylv9UamW&Bl(!^K6BSE%&GvO%=&U8N2@`5OU(+oIm$KgBBbTr zc^Kwze89I$7csG$A&S+yg`->G)d=nhRo8~vEl@mg)LikY>qdFn@>2FRYw_vErSi}p z!C>^@28+7H2yTt5D(~sH!#7&!m5BrMG31_%c!jwN@J2@Ifs$K%6Rum@fy02*qnyI% z<4PL)6qo>^sqd+G?$PjEH!Z)?kGPg-Mv|=`E9+8*C|>C zS(DRX=ifcgUge7N_h?j%#%^o)6Sc^ijMtRY_v(&SAb0W`5-E7dux_3^cfkf3;JTdR zU=9yT(8QGNa^I{Ge8)5)GD;<{uFB+h{5LAzIDISL?EPJ)(tv8@UXNRkL(2L4f;SOq z!g|csd<%452*b-O z&TF?;EG!?IvSE|x+biO!5X8IV^9^lmhWjBO|3)S3)54Rzm5(NArYQ&~Hg zHULjvIVLKqF9Cku!eT;~VqVDa%{}V|hAXD|atiWbxB09WOU%TI%P}739~6z(Ls7}r z@CAb|XU)SVb|*)oV(xfbuz6H&aiD{_>~1B(CR=dN_!b~?x^j@cd336}az?k{ zJJUi(tQIE(_*cY$7aPeE=O{RfD0Dw8j6D`dx31kBZnBnovcBz(B+du zIIH+VxJp~>R6xz~#xS0{G+>`H#I;^*6|HYJi5utOs7tlaxBnFxY_Q}4jm~~6uow>5 zPs!$)2!HtK(k#nPLEc#hf1Z&*L0-;sh4XU&kwunrz{TD-j9xt%Rx~d%>t|qQhj+6b zqH$DW#vHQ3`{;=<#Z9)?SHFxbb`DD=X(~v+Ojwpm*)8xfFYW_o>dZeb`+B|$ww1Qn zQX9KJwEQLN$MloU*Y{q?{2*d6w*_cUt;OJ{22g$jX6X(3KYB z$N|;!WVmFiwxvGpTRM5*@{b&~ZCQ)*C2S9TDR?Q0n*E7^?a$u=pjD>Fg;%fmP}Imp(^-Cu;X>KTvVnxK5L;@p=D#blt~rwy9Ncm^<>&GtB72rz_EX z@?Gaj=8L7!knbJ%rWt|wb`YjB(Q?3RWUj-#Y($MQ*Vut}T7)#W*B6c`K&Ub7!5Y;w z&}MJc2nNAxfJko>Q9F*}hW)CT^ss%H*`r3S6-qxyQvloZ7_(8@Pa&vsB-fn0>GWGs z-%Cx1mf~BZ9hla6-3{60TKHNbYN1;SD8ewZb3fvQ@H~b7lp=y!yq;K?(nEWszhl81 zTutf6lOuX*angYhbwgYMnNw&F9&Ykbv%c4u@nHV91h4Pdq32{MnbibC8TxUXrrPGJ z=A^+EG@sF!4LhzJUBP?TiVa!Y z%H7EWbY-l~wWjd;Z0*m5Qx5Tv(X~f8{iT-e;3qp5j$fdTwM+_tZ!*n8fHB1!sqNsyhlWSZ(3o)yd+4#D+s#pr`r~#e>8n1 zHNjrDzWrCP2Zzb9;B6{PD8;!R-e3N_!jVmfn{-a4^w zs&M>~W6Fmo7s(*_ihYXb^W4dP+4Zrdeg!Pn#RmAdU0o%hnaPegobJxSh2tA$n z_9MIsH%}*{gKkVkx|7>Gs@QB7!se=3$)|~Gy>>EhX$f*Rzy}1tR#AnE;vvt}d#3Rk z<5^epD!3bC?Y7r^Hw)W~4$e>%W0o>@lvOOEc)QUnv&gQ_*J%wV(7lnzTGd7O>w8DT zTLEz}X9me<5PH-kqxFf$*#1ceqq0g(t4OT)A38lP3KZ!p+`idZg$;HwCMy7X!LwIx ze-Tlzt5#liU}gQ~ulonbs=#IwflKUFh8V~60bL3TDBh9mAM#QRn_c4)<1legBw9-$pm>`=4<-X4unyFfeDa}P6W;p9?%0sd; zVki8xZpMyiE(Le9ybjX$By0D2otihqatJ@`LH@I#YYGc)0lU9Xu8U7KL}3G`rn6p` z`v-E=53?9-uljz)a-bM8L!z@X(&V9_dXW{|!DSe29dWzwY6Um^Jh77$XIqpoC9`~C zY(a2jK!#1{gaLIyVUz|7Kc1JeOT_!K?{RL#Rba=!@f|c1;X3FQtF8t(X&I!6RKtoK zjC!(R4n)L-$j3z5U%)PE^Diqa^KDGLOHPNG1U2icW~>5>c;jZ)V!qXfRe#nOznozu ze<~)9y&6wa6*V|@5er}YWNlNO!|YRyxyKz=(SBH)?OtR!Z)(kOk*k06JiD)8wGq{ZM|H*tYAYZkJ;B;;&N_P`+%) zF@8KTRUzur7*C<_;l|K7%Un~EDUbieS~{p#+OxuRyOrkfN#xgNIHtd!J9+G?@G)&C zEnPZGAhZ~y!SLGc5B*e2gWr>IQ5ro%@@HR#;`eqEaP?W@D+G0Zmyun`{N4!PwQiwF zE0G6-{2nQO1pf3@d(Bx$STz6w|(wU?jy#h zEFDzg@~Wo#X6A4)($i;uS=Db8OzWKg;a(Tk(`8y4$v)qBgp3hLjtadhgEHF(WgJ5T%X_||2Je}hlb?7>ldLEu zno2z9f3XJl^TD;?$jZC7l~ri1@vv~rGooeOQ%zu5({yW$tw}k)iaW>iEvb5*1!wY( z;mF-iMyP&Osj+M9BDk}mQFjYi=a6K^PH>J`m)OyVY-5CD^AM?%`wQZo6p6XxB7*0W z0lilov-wADRZb~FdEfDT2yqA&KSL*F)-u5E+aTwPiVvjjDBdL#b764$8 z1@<(Uk@1aj7sowaT?_O#Ps|U-{rIILZwC2Z#-t45?cxG^k&D)3yJ91mOTQvL+u3V4 z9m_DH;>1+<$}x@ibFGSVE$%)HKA#z%f){#!9Qr|8HX=ykB{#S$ZDO+Av-Fw7GY%1b zELs<*@iG_-D{qj>FN0(;4$A7FAX}qgS(X@ewHJwYL_9 zvc5r*1l$ywlg_)%YI%0qR$;UDq>ukD*e!@Cz1iPuU$ZDKZv-~>IGr52MSmbJspEIB zSf!-9SYZ}BHKxEB?;Md+dZ`;n!j~0trKWjUbjd}+w7%rh*H=cT2W{6iu%?>}hQP!5 zn$I4aPj0vsLAVAUrTBbS9KX>fuLw$g!wuX)Tj9q!Bm#i~Uc*H$E23#xaw#vm zRYgXrF$Q1-kwjE?Vj*Xa`#w!VXMDB=~&}i0i=jXxWLt48$M-|*^B6>8O_-( z>uZji^*OcuD#=-ltis1}4gT2P?%crGUFKbK_7eR>IHIaMJbAhnj&ETJS6sM~ z&*tdyXI$^o#?J+y+jFq}BF3alogC_~sYBHL~e_woNwdMlx+{R#JV=hS56csg$^+gZ8{b6+gd<5d2g%i=5ItAF;igUwu6v zTBBFnmh!`lZQ`BEuMaQAjCTh|P?|s8Ukm;U#(s?TjcGdLnDXF*vMh8n7tAtf>?YS`1k%~WNA8C1%C^-|a0(D~t9dY9XbiY&$AL=@0H*NGS^V&UbmfQpTqBj<~rN< z7KqCh^zyr2;FqIE{x|8ZgJhn1-;7odW2AmQk%U=f*ks&6`m2gk$Q1ASY2_7o=hd(v6bxJ zAqUTz$zc#9{X_s<154Yfp-H+c$>VQmJZtsYn$K_ooF~d$3*RO5?*l=y{P8!fA z8!BWRW4lBC;BZ_-$lP<>nX-f;u>?C+_vgD{b(wpki<&j9U!FK~B9n$f_vpiapyFmi zB$I!(a(hJqTwnj)$^$G&zS&Qrkt-rQYs0_mu8+f5CQEG1n9)+gh2;@RMBj~`%tcmk zB83a_p_qz>wM{J zc=hsfkzL8wsp)7hSNtxWq`_4oN07RNC)34aE^zXg$Gmcv3`K1fdXH%AQ`L^+18jNl zE0Z3&Sd!`C(Vr$BR7{l-cfW?qPirQTdrThHMDCxy=u)$L7yy(d*{NVSk6&=~+G@qu zAcBo6ac2)hJ|w3$TdW-)PdcL%Uw72T1YOkXWfQ6ICRYxDuXT#eH;iz3w3&$-PtsE! zgA^~GA4z?E4-rxpPDN%9lb9mXr56*5jptvE_K}A__pe*@?CZ_Jxv-i;7(Rud1LIpSV16pEH}tis#+(c2N;&RxKt!g5m}GUvR{w z#%q}Q3^|O-;ZSPH;pnuE?Vda;%WwKL=E9ik^8gk4e7071Z?sIGFc9wdIvtx+FHv)y=nC`G2>gp-H=5KN`8J1Dn_p9Ge= zDje5Ae)1ZZlJ{GIXy3Pm4-c^8eAPD0yAWiS)}=hF2#Eqpi?@E;V{{iX-34*RpI`?C zdIm%OPI^UKwvME~ngCr|l3l}hvGfO5na#7BO#ItpzpxjH&3+Byo}Mw@Y7D4}$usA6 zu!VEQGwvzUf{&M-pA)XRdp9=3!S;%jwH6&za=b;UfaF^Stq;ih}eoicEs@kfB-5Zu# zqv1z2@RA z*TTVe-)X;`S`ij4GxCCUx!v}IdTy1VX@CgV7+0d$sJ4)1Ny$@6k{|+LLrT{6;z312 z@%H19fF@1&anF0}=a`S*2s03PB)C3~o~35===GY~=GNx8ftK-oqkT)M)DDmqX=Bev zQpeD!y8t}eo&@WTRwCEqd+NN7^B1+yLB1wmC$m4xMSrA0O7G=tQks z*Ckkm@ve=QNL)`5#NsYz)ejktBUPE+CW^Axhn^bcFv+S~$(1Se0|vs#x}8EB)yEwDgh zh?tXQ@tDkyNUJqKs3eDvE{eyI0K9NI{vV6+>xpJ_g{?WPE6q}O#Mzikq@|I4M z9?^T)AKeRM>!p?s^||g`al$25dP3uH29wYoYN`3tKGJ{mT)FR_PJG3SHD6u)2U91c z6dlr2Vf%yBQ}>-L;oEavSQIsdk2!dTU)PE)F_PqEtwaH9S1LIBZ4Q2gU6y@r1@jm) zV~WQK?qrj%NcWQvDa5h8xuqgrG@|cC)6Ej`dH2xj#$0d{TrU9{XplP48S9&I+98dl z^l`X9s%)J&Td3 zg#>B?jHo86z4Xzhe4&;c<1G-uI~1FAchj@Ca^NH_GaTOYeDa#z+4rhm?+k*VYb)IJ zqPP6?0I9alqk!$hVMoW#bdQ=7TnMhfg&GO{yX@~uAJ-9sn=ZYUA}|ZL<50;{+xykW z22jlihR6~2v2?bEQu?bFn3$Sv`X-k-ac`w8K!4=ndSgUm5E(=}zrr$Ya>#PftLWh92knxR92CtYN87FJwmhKr z><7lW((Y@Z^}?*WbwkT^Lh~m?aP()+_o_rm2|+$XUX+>;-b(qRft8=6^Tu|fqSTWD zul~GDd=8M3X$1}AuU+WtC{lucVvI9sx@p>rFR3ebB%U%p=*&^p*=o?jJ0o7C8?PPP z-4kZmQ=qM#e?uusPR;4njcH~MBGu6OXOS}B>^ZqP(N#qpy!4DWQyTpnmz`n_5@VOF z?vNJScF06q9P))Oe_D3RAA(6?!U{T3YWGCE%HC_Lika}?6EMVdc!Oi_GJQkpKJk1@ zX1~d1wO!CabNZLnG>1siC)`L!Whp?cM*z7&+54|Eb*G#BB0beuInP~)E%Ro-y!(w0rwwOw#PUo6!Ex68tSP(#kQ%1 z$eV*HB>}piwO};op=_p1koZ~94l`d}Bj$Z?9#1f1EJuSIa&?@|8T+Dv>2=iRKl*VC zkQirDtCr)BfBcrF`sraWDIvnV;Y7*2{${^xq0(rR-YK(RgSdf|%qvW=nn$sZ7opO* z!C7b#o1vFX31}()tAWx3a_unD2f~97(hR}`!V^BL(sG2klF+#uhhDEpP^6i0k3Aem zHpwD-TO9~@98k;He20`lRaoBG6-$CWZew+uIVA2~8uj&u<)>{z0>B0TlZoz)(^Zt-xf4~{+nN6Wzc4n8 diff --git a/doc/src/Eqs/angle_cross.tex b/doc/src/Eqs/angle_cross.tex deleted file mode 100644 index 9d1fdcb7f8..0000000000 --- a/doc/src/Eqs/angle_cross.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} -\thispagestyle{empty} -$$ - E = K_{SS} \left(r_{12}-r_{12,0}\right)\left(r_{32}-r_{32,0}\right) + K_{BS0}\left(r_{12}-r_{12,0}\right)\left(\theta-\theta_0\right) + K_{BS1}\left(r_{32}-r_{32,0}\right)\left(\theta-\theta_0\right) -$$ - -\end{document} diff --git a/doc/src/angle_cross.rst b/doc/src/angle_cross.rst index 6c79776493..7dcff0264f 100644 --- a/doc/src/angle_cross.rst +++ b/doc/src/angle_cross.rst @@ -1,13 +1,13 @@ -.. index:: angle\_style cross +.. index:: angle_style cross -angle\_style cross command +angle_style cross command ========================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style cross @@ -15,7 +15,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style cross angle_coeff 1 200.0 100.0 100.0 1.25 1.25 107.0 @@ -26,13 +26,14 @@ Description The *cross* angle style uses a potential that couples the bond stretches of a bend with the angle stretch of that bend: -.. image:: Eqs/angle_cross.jpg - :align: center +.. math:: -where r12,0 is the rest value of the bond length between atom 1 and 2, -r32,0 is the rest value of the bond length between atom 2 and 2, -and theta0 is the rest value of the angle. KSS is the force constant of -the bond stretch-bond stretch term and KBS0 and KBS1 are the force constants + E = K_{SS} \left(r_{12}-r_{12,0}\right)\left(r_{32}-r_{32,0}\right) + K_{BS0}\left(r_{12}-r_{12,0}\right)\left(\theta-\theta_0\right) + K_{BS1}\left(r_{32}-r_{32,0}\right)\left(\theta-\theta_0\right) + +where :math:`r_{12,0}` is the rest value of the bond length between atom 1 and 2, +:math:`r_{32,0}` is the rest value of the bond length between atom 3 and 2, +and :math:`\theta_0` is the rest value of the angle. :math:`K_{SS}` is the force constant of +the bond stretch-bond stretch term and :math:`K_{BS0}` and :math:`K_{BS1}` are the force constants of the bond stretch-angle stretch terms. The following coefficients must be defined for each angle type via the @@ -40,15 +41,15 @@ The following coefficients must be defined for each angle type via the the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* KSS (energy/distance\^2) -* KBS0 (energy/distance/rad) -* KBS1 (energy/distance/rad) -* r12,0 (distance) -* r32,0 (distance) -* theta0 (degrees) +* :math:`K_{SS}` (energy/distance\^2) +* :math:`K_{BS0}` (energy/distance/rad) +* :math:`K_{BS1}` (energy/distance/rad) +* :math:`r_{12,0}` (distance) +* :math:`r_{32,0}` (distance) +* :math:`\theta_0` (degrees) -Theta0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of KBS0 and KBS1 are in energy/distance/radian. +:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians +internally; hence the units of :math:`K_{BS0}` and :math:`K_{BS1}` are in energy/distance/radian. Restrictions """""""""""" @@ -64,12 +65,3 @@ Related commands :doc:`angle\_coeff ` **Default:** none - - ----------- - - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/angle_cross.txt b/doc/txt/angle_cross.txt deleted file mode 100644 index d9d83ed4b6..0000000000 --- a/doc/txt/angle_cross.txt +++ /dev/null @@ -1,62 +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 - -angle_style cross command :h3 - -[Syntax:] - -angle_style cross :pre - -[Examples:] - -angle_style cross -angle_coeff 1 200.0 100.0 100.0 1.25 1.25 107.0 :pre - -[Description:] - -The {cross} angle style uses a potential that couples the bond stretches of -a bend with the angle stretch of that bend: - -:c,image(Eqs/angle_cross.jpg) - -where r12,0 is the rest value of the bond length between atom 1 and 2, -r32,0 is the rest value of the bond length between atom 2 and 2, -and theta0 is the rest value of the angle. KSS is the force constant of -the bond stretch-bond stretch term and KBS0 and KBS1 are the force constants -of the bond stretch-angle stretch terms. - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -KSS (energy/distance^2) -KBS0 (energy/distance/rad) -KBS1 (energy/distance/rad) -r12,0 (distance) -r32,0 (distance) -theta0 (degrees) :ul - -Theta0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of KBS0 and KBS1 are in energy/distance/radian. - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -USER_YAFF package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] none - -:line - - From 954be8483a4d3bb085cec702c956d7a226f80cc2 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 14 Nov 2019 20:44:22 -0500 Subject: [PATCH 19/64] Update docs: angle_dipole --- doc/src/Eqs/angle_dipole_couple.jpg | Bin 2930 -> 0 bytes doc/src/Eqs/angle_dipole_couple.tex | 10 -- doc/src/Eqs/angle_dipole_gamma.jpg | Bin 2709 -> 0 bytes doc/src/Eqs/angle_dipole_gamma.tex | 9 -- doc/src/Eqs/angle_dipole_potential.jpg | Bin 2616 -> 0 bytes doc/src/Eqs/angle_dipole_potential.tex | 9 -- doc/src/Eqs/angle_dipole_torque.jpg | Bin 5110 -> 0 bytes doc/src/Eqs/angle_dipole_torque.tex | 9 -- doc/src/angle_dipole.rst | 87 +++++++++-------- doc/txt/angle_dipole.txt | 126 ------------------------- 10 files changed, 46 insertions(+), 204 deletions(-) delete mode 100644 doc/src/Eqs/angle_dipole_couple.jpg delete mode 100644 doc/src/Eqs/angle_dipole_couple.tex delete mode 100644 doc/src/Eqs/angle_dipole_gamma.jpg delete mode 100644 doc/src/Eqs/angle_dipole_gamma.tex delete mode 100644 doc/src/Eqs/angle_dipole_potential.jpg delete mode 100644 doc/src/Eqs/angle_dipole_potential.tex delete mode 100644 doc/src/Eqs/angle_dipole_torque.jpg delete mode 100644 doc/src/Eqs/angle_dipole_torque.tex delete mode 100644 doc/txt/angle_dipole.txt diff --git a/doc/src/Eqs/angle_dipole_couple.jpg b/doc/src/Eqs/angle_dipole_couple.jpg deleted file mode 100644 index f16849b2f9663e12ec3148d2ecdd8ba8916f00f1..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 2930 zcmaKtc~sI_8^?c$CQhcJqos(HT3Uvdxuv<3B`%Xro92Q`ZWX4fV~PuAWnwC%j^YZ_ zs=4NpONH9xzC>yygoTKKDU>U&=<9Um{p&sF{oH$=f9`Yc^PKO!-}7uTHpc)3M>_{Q z00aU7_FD_sWC6B-6j)MH5-hb9q@<*_Ny|c{w~*hyT}Bovuc!!>heDN9)ORZVs-_Hu z?%K0U4Gu>j5K22WwKX-g)in?rn{B{$2oMYmfk04TvmH{B_tq{V41B95Fi1Tl!9(k+#{`YSo8Q9Kgh2tT81aWlayWEGWVVRa4GB0 zoZOl>!}QHh0A#Ckz#3RXLjNBq{t@LvGhN802*n0e)a4Q)c{pig^hB3}^^w2I+-c{Z zHwn5Bou~}jX_H{h{l>L^p=~^)nu%^O2gIq86;4E9(i#^g*=PQ(VH1E2J&?@2>T=F% zMbkX;uQqhS5wS+Mlb7`&N8(ug61;Ezb($*i$^FzO&%YV;}BLsF?sp6 z`m7zsNuPV)K2|tm2hl>kSpi_5G`C3ZcmI0E>s!j-oNM$cYb*wdj25jCGOBlv@L6lR zat2w8zx*g&aa^f@%Owk7>*Oum*PK0QNG zg|scK2W(S}(?G2~u0_c@=eonxLtv3be*o(a-cD&pwKM&Mrx4uY0cYQ*eSwK*U%W%W$n5hW89(@P4C_if&Faw$Xx2Bi z@K*}@g~VEY{6V*XD()^cx@#x8ZXndjk}v)-QJ$r#E9XGz9j`)3$th82c9U!Qlc!Im z`!V4Va=SD8X1v5Pq6Gt**x*GJ>+lknD_q18wSGuiR_EJ@?`ph#5nhSsUrwSAdT58_ z1!R&@6geyTVt8`Sy!CSSLJ8+0bkU8wD-Ju2T)C2UN$+oY@l*0U@LDDQroFbramG4n zpUT&?Wk%(v&QG0=bHb0cJXO^a1(S<>({5l{=M8L-fyO^8>a&nLqOUhFr32@-w~sVD z;hp*pt+fzG)KA{Wu>-fSdAf)%b0|xgO<<{7D z3kjQDd-mAfpfr)ILnp(M9~3m7?eyFeL{Isc|A`3mu6Fy|14pTHzZi${>v(BxLmwfI z?Hw1=yi&As`wd4s>9OY=HGHRGp2Cyfs9BXCq0uCZfc5OdJ6Hy7b(-twQbEDP=->6z z`$raq!Vrs+1hIv1BryT&y{hDNDI-qlLhj?*_K_ADC#Ugn*un5CNbPvI;<1>$HuIy# zdJNuIc2>~NJ*gPMg+4gwJSJ?(#O4ou@U-7<1rQ_BgEwsEeU|nt-{#A?3r)StHOlyz zPYI}OWW>n>S+cg(|h zYD)+~>mhYmw%>snf;m=FWqAX}3M_lhZAY^trJ4JjCyIY#e4ep@*5bO3H%G)W9gX*N zc+@F3I{f&A@6@WK7jAQYCufP@0k?gTOtJY$8%+T}Lk|2WV z?ZC)0#en`lj$@ zqqxs!k<>Ol+(o!|c8pQp(${WXL1p_Xc`w~^ezlEqf9R?Ltpe*8a$0~ z?S-H&!k%+4AwJceUFUL(UAkfD}DKPGfb3=8E zXf#ka9~Yxj4_jmIzSG`?Xg}24@n}w8&$#l4^f#!H_hJ=2+|ujwBr~BzB<*b-B^d=s zb6@jUilR#&Zs}G&M^N?5obcJ_V(=%<#MOp5dphS~{g?i`c7iB|TsV9I<=c6CL16wK zzs0@ku)D6*9(Pht;2g>K?!2LL&Aj8Vw+u@mqw4ZBt31BRH1<2+Ot3h8`Q%SdA&R;^ zyWXnj9Ky=JA`8vU!;-3eM|zeX`;IJVmxU&h=hWhf8Jwx>vXj|5F|}>QbamAW6;=}u z1{u-Lgg;J_Bp@u*2VUlbtxh#Hbt`zTB6Iuva~XjVoH3GBQBHx@I+1D=ocLbZEv+cH zA~xsV`0Px2$JM&C1)X+r`)b7JLm-GR`@a~CGd+jVse>B3g#V7FOD$xl?xQ|s_~271M9=Oy!QG!dE)%LKuh}wP8|nVO)lHymOR<%yf!idc ziQ)buf0holI8nQ=u%hw`C#KJuoAodTt!)Mw^K;i}wllfd9NHPGZQ9YiE(>c4`GwA4 zPWn>Wg|IrXh-X2YCAM9`#5f8$Ek)c(M&pHH?j%a4Kv;bxn;|>L?~Z=BBp_WbZYox` zNRR5`mRoDd9zy?d&_wgDt#(MZZJozBDDpT%GO0#{*#6+3_g0Rh%wAj}YSbk)=J)!S zdfjqd(t0>q5OQ*s-XBSU;nf(cPA=Kh>M$8@#yCTbVQuK5hvi;easej?{$8-)jGYMkkUM z-X;w#ED_zfjF1-BcbetupXkUnxe!Y-zbVDgd`2F2eBBjw^Fn1XZHVw)=lPr E0Bnnup8x;= diff --git a/doc/src/Eqs/angle_dipole_couple.tex b/doc/src/Eqs/angle_dipole_couple.tex deleted file mode 100644 index a857d83d7a..0000000000 --- a/doc/src/Eqs/angle_dipole_couple.tex +++ /dev/null @@ -1,10 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} --\vec{T_j} & = & \vec{r_{ij}} \times \vec{F_i}\\ -\vec{F_j} & = & -\vec{F_i} \\ -\end{eqnarray*} - -\end{document} diff --git a/doc/src/Eqs/angle_dipole_gamma.jpg b/doc/src/Eqs/angle_dipole_gamma.jpg deleted file mode 100644 index 4bf618e2529f152f2cb27952ccdd0ae7c00417de..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 2709 zcmZWrc{J3E7yr(fiP5u+v1Ke_#8^Z26jPWXWX2LRD&k2on(VUtc$$f& zY-MR7l&HzRlrYKU>DeM;emdvZ@BQ)az32Y(x#ymH?!D)JE`NkS1&G_*;%osB2n1kv z72uBp#{j4R1OgF&?m8$Gx<~LgA;Db{+q)O`8(d660xkxJBc$bJ5R!6IaJa0ptek>^ zl9CcaMg^s!h>}-SQsh4Y_6h-bfDHn{0e%Od0Du62p9TVc31l}f2rK{-+Jz5`10Vqi zNB}GVfdPAeM(iRG0J;Y*A&5{`v6ht5mr-@`5t25*xKR@G22h50S9f1VZYk#-e+&@% zne`~J^NNYK$20!rJiG1%SaYeA-r!)UqOkY(+48b@7+Cr3kA{ST@;LRP0@6|sqR!!* z@u-+nT(`Dh^rLI3o&;RjB|9mU;{J=VnCO^h_cjJIK(U}uFmGR%emz?<3LQB|FDcwW z3DNA9M|XZNUcD3VAKHa-daaW-?q_MXzQ0=G6Hf*0@2K|nsl01eR3d8$#^rInHh&cu zdVTf#upS4ouWQ{xPxp7xNPUAm-pC<+n?7; zoas8fwd5J!?ALhWXsM^MgWp+8N+OhO2R)o5Rc)5Nh-f<=53B0yMX)Aa*#XsG)44ZZ zJzngwi;*n27+!I<9Q+}Oo?SC_9$dIF7=PESzoBvjcREx2ZgG2G)1nf1E}BR6@r&UD zmyI7-HbBg9WK0vT*_5Uj&IeFS98!>^2x`+Bf)f60od2%o#Oa;@=hw>t1%!j|^Jmg; zG!+SF&Es>}rP1bN?SLcE`vCTu$`8v1*X31)LG`mN3k{FK!BBi0dL6clU-17m;HG}Z zsrO&EJ$cgM!7aAeWheF=c_rZ^!zn$6!Q|29t(9UMsV#qOYZ0ldYo?R$XLL+x2kHzK z)}{pWK_AgW_?L__FuOE)g@Zv zcv9mer9ozggY-(pN6sq5#MOIa>P$sZX|5k840FwGcxwlEEB8YZoiF`|x>M#Ogn_rm zTfBMy0A1KZ-F!!@En})-9o`M#!zW;N&rSB#%w*xYI@}!)BR9%ETuUpB^hH-eRGZd@ zCZBlJdr4~`KdtLGwalJ+3$=R2wlLj!KqM>%-`u&b-aPqe9C7bka|W@bqYn9ch=9X| zzws6^Qh-_|Cq*zdz+nIsmE*Rrk5J&lA=c@1b7g)|MT!*jza*~T3?2wxzwIoU79F@nlM-_&{!;;^4P7&2M?c z@2bY@3f%P~S>Bth!YdTq=>0pN5_Y(0d|t44;D9#-VPeXU|C^TOU66_qJ*< zn+zW4PN7ZGt5344QYOxzJrp$+=TT9Uv6K@J#9sW>f1D<09(Nh_Sl2a0Hhj>jJFfFG z@w$oz^2q;ArBukb8yN{Ay?mff_rna~FFpAkWC0)e-Mjro+1P2bA0~!7y^j;po!Kp+ z8{~lPf(Sk!*P>T(ikC%L{_)mAZsa+6TxnylprgvPFm;Mdm**Mr=Kgkka^e+LHJq5@ z11U#c*guNTRMS`}|I(LaHQ(TH`(h{SR+{Z6_N$4edw%LAj}DdO^pw$a%eu|SY+qa( z**`Gmu7rAi;0}|xNy})JGWk9DOTE)|^o3&tl?tDZj6h)>)?TFWG%E=oK9!jfnoL^3 z>c4M#y}K{ty82{y@-xPkOHl?>oJkia?G?tm7K%C5&jxMzM-|SPWc#Jl>x2IYY#@0x zw{+mNvYJDTYRCO5*brk$Oy*Uo^J3UhV{PJc`Hhy8XSW=OhC>-N->w|xU`-2OLmeIA zcNc|)y`)*^FWzWdEoeR3MeJA-lHS7@%aPRH=9n7O>nr>`eSCmj!v|Q-wZ0pJ8JJm5 z{c)R`IrvlZvE*@0d}OOc77QuSN#y)PTP6LC$L`G9sZ}eunsiW&OTZ);9>W&RNXi^O z7jyKaQ0^|rJq*BKzLlQwl{WhD^^1t`os9__=ByMYl{&O~wG?b=E%F&rEu8qa>Pmx~ zS!Ly^>RYiVy&9`y_kUTEb6~!(Y_j>6YD94lD0Q8+juf51nCRAQY?V;Nt*t(f}Jv(A`++Ux>&`$~FHu z%&R5Hhamlj7chDu$Nbt~s{|P{E11~7oxwzVc6Mud$k`ZYoC)^Xk6U_VkBC%?R$B+jREI38`z1NK73ekt(0Fn3P#37kkm$c7z(k3x-s&aX2%%WDsfyQTw>cD9woXiLEA`JVYO&DNCJz{Uo>95#5F}H| zs+s#E@I?OWcw|W5V6ER-gUZS^CGE!6uxtZp3E*#6R-9(WieG4* zrjv2G^p%#fo0RYEkgFA|#etfbo#bUJjoAo7Yv!L-CsdKL6X>U-)UYkaIvG*=ZOf!O&MF0Qbpa`hN_kz zrNkOaMX9A!?ZgO%MpXK z`v9l2fH?pGb8~ZpA>Rc8f$%^Dc%k1B;^*fRfC~u=!-e2*5rmYe$XSVVaJZP9n1r-6 z5{VQMl}E|TprmAwGN)YtKQC|{I0Av-z-cca1%Lo9@Q)k+1;PX7hH`;;zq`6;01!79 z7YGdE0YmtHBz~m1A#fgHIjD%b=~;xlhJ*Jx(PRZP#~b0iKG>YxGV=JR(;0yG$HvRR zabDX0#e*bmyCjE#Ve{nob5Vwgo=^TQe>r-F@N0g-el0ydFO=rJyzdy;V$^9fbe?mJ zN%~V0H${FE_M7sZfMxzg@S=_-eUSoEYzs%l<7Y5>`=@|7p3kQa)$6BxEjRTI8=0vZ zlQJx~LJY2e3MQCxP6~AxSDY`nM&wgyl`RWaM5<@*RIB4GtdQD1%`f)n6lX7VHQJ$r zgtx;^FRkxsK8mP$qKQ4$-$O#~gru3H9zv%vae8A0A%Z{*3MUiUu>F(X-z{xVVdlAg zSJQF=3U#Nd;Qraj!LNf~5qrpTHw$8kvC)!-ON-E@0V{6S)!(~q_7GZx(dOWK{Tl{e zs#!)g;AJYsQn5z<^M77hejun4y{&0Vq$={4LMMx;g4vz!)6@lTW2wa|H2tr%VCjLx zGETTkNVk@YU$rZZfuUWvsWQM%CyRx#_&sGtx2Dd4jCim@PPk&vn$AAt!=|}&BpbQN zrz#pfqrGqAJGIs8;)<=9d(G|}*6X|!p>kIyO>K4I1?PSiL(?bKT%UQ(;&qJ^pX_t7 z^c)y{y`qI??k>9-Wy~{O-yTW`XEKHxN($2(qUPP%YtpxVb*clz{W%GqTFd@!Xr^2Y zW>&Jb$f(Erg%>I@v+#KH#Ytq?$N}aQ*z#Oj$t}{9JYp=3-R+9RU^W*Lp?jx*%JcJ@ zC!fb$`@aQWfK+s=)w&nIB&f#~>F|4PS^i1q6Xd$c2e6~Ny))h$}{gXr5W`YG}k$H5WNHwh_3{)8>iQ23`6IGlpUbR>JH5&O?Vasm$6etp! zf`HeJ24((W#MI)ojDC}bnFa`EKHoCR{w0Iz@D*{f8Qa02P;yL0gFtsy>R4HL#lHu~ zjux;sPAgCE^#v$6wZq8LfrlDO2IM%?^8o?(nC8ZKxZ^V#8qKq7kv#EEAHUR|H<1;! z@w0{T#cfes5)_(q&qSUmijFc2(c#-r63X9hU#@lWYp)bXm55^la|;XxcOM%nvrhBgxpZ~3G*QGhpm7{o1lzq2&i;Ebj0nW|qX zRMuNI!vXvC+T)%N(lS1sK0CF7yGnY?sJl7QpcK-$2Z}xG)(VwMJ<`Qp&am`~wHtSp zKGfD}&lj7)zn$MjHkf4&V?Blq&}!DjC0LJMRlzSI&)9qKl)BJn7zb*%zCj=h)^y2* zxOm>;#A)X;r^fyiz&81=%;BED~U(Kva@;RKuIH5td;?D*c-wHh8@-(cwdR zUpKZ*W^#-+uy5EmX*3-ENIj*jm%T}@EeqvPLk~jD2`mqO(nY-FOS9bo*BqDGI?b#Q z7%Y4)DX*jMXf`BW_R*`k!JMI#!x5X3@J?S(zM9#y2O;7tSCUJ0@s|JaUWHJtPY}jq zbY7Sy(n(9GXJ= zt0B`J)^DdU^Y&X;3vArwd|QX?8tXtqvW@w+r+{p-&JOioH!?Zi-RxnVy7IH23gHs?XEcpC2Mq`NY|syr}GD z`YUv0VhO9xp6x87oU($mS|8Uy42D8fR=>_0sUQY26Jp zY)4F_xx7fBbCjPU06=j7b9d)?!PRn(yFVdyr}z}OgKGxnEsaz{TqYjb_i zqvAlqtKvzB^+C_?M;e{DeoiE^YQZCbuY}05{p_Bxf?1{yyB_*;w1dQ#4sTqayoS6f z=DL=&K+oqgQLu>He@1`u+82UnKlr#-@4{%YK>5PLa;`6FdMrw&Z-ximRxr`If=GT% zkW)PIez+n-9n-p}lo?UT%OgR!+2N6-l-qQr+}cp@-QMJpFi1 z9NA>?i%a7bXMPXW$+f(e66taP5#|L;3LrHYY|`lup=7DY z$rB6;*g_{UD70A)Vb}4Om_n4z^}K?Llv<{QiwfTBm_Q{Tk>JTa= zyKPQzJYh(u;T9uiYW!-65RsJL>-5gi+utorqg@T1;M$kk7{S)R)cA^~+U@+|J(VJK*inR`mKJ_a%6}S^nRtDTQ-BeJ;BJ z6U{~a(}Pyv*@zt5RGh31VhD7@qXp}^}U{-P5)=GomZ zBPfk)+>V{l!$&Pl?!J@f9fkJY8*75Z@-$9OwL6;lBBw^h^L|5@%(OrVx;oQR!FNL& R^l^JB_z(I2!G+W5e*nm(<9h%A diff --git a/doc/src/Eqs/angle_dipole_potential.tex b/doc/src/Eqs/angle_dipole_potential.tex deleted file mode 100644 index 8949835eb7..0000000000 --- a/doc/src/Eqs/angle_dipole_potential.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K (\cos\gamma - \cos\gamma_0)^2 -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/Eqs/angle_dipole_torque.jpg b/doc/src/Eqs/angle_dipole_torque.jpg deleted file mode 100644 index 996a9df3cb3cd51f23678121f6e4765a7aed35e0..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 5110 zcmcIoXHXMdmkuS;r3OSuXbBJ@`hp75OOS*FDM3K`E9IpI3`IZ@LFv*7T~Htq5JPW4 zs&uhXB@{sd(m_E4>Fe&S^ZnUB-_Gv2GtWFT_s(si`USv)(KpZsFfcFx z(7zYpbP9k30GXJXnVEpU0SE-1Vc}$D`EA@B9BiDt+R+%odmG{r>+*@WPl9E;E4Y_NYBViwHHg#Xm%3&XYg^u=G>9IvafzT7Z#4nF@UVV6& z=e&FI1^t&x;d|G7-%IXh7uyti#=!L=m}#4EL`qQ$7i7tyymlge^P78b@0{RrgJH^o z%mjW$MHg}lzO*z%4{w__0pP{=#KrLTt`n6Lmg^H`4_fYI*=8GrZO`Jl$m)qi5)5PM zM3ZU5-+W~d7`;w0Y$eOTCx!%EN1u;LXXwsLnt_Wo7p<1-xw&z8{3|f;XDbxFRIXM` ziE`9@&NCFq2b`;pfwiQpMqe?V9SYH8-yr>oVQgTNjr{j?)o+AopSV;$2jYRX7yq(~ zYz!diTHA{^-k-5=EtGm0)%1>}Se#w*Q7 z)BVODm}wM54rsFTzUM?62$#Sx1`BOYCMlGO0)I|X=(#@UrCiuwpuqG}6~ zpJ|ClkwI&I+L4HmYsE2x8--?T)>;!I;+YS7%KQ6F#&=uC0z#)ASU;qzPL7(8zBPIk zXp^|0cxy5Kg0H;0RY72QvR@BSKMy3I3zEJNOBH`o%?)lDC8at;H4u5-T( zykCKq-?vGYIR*Fy+P#LE=O_fzHtOgFz1ceK>Kw7od5oljZqKGbYt6K;7Pd{tzIjhv zF@5syy4}gTA%swoql}wm7#f>n9kiBzNVYzDsc+}Bde%4~WTM9MuPJBqJMmIeIjK8! z;h)Dja@l-!Sc&gaL0zg<1NO#~A5>(=cYp z&zHFpjmfhatM+DI^~Hk1E=I2+5|WAHAlcn@;v?hd%%4y*_9~}<8}Cj5I|B`;fSear zez}O5#rI9}@_7yUP#A9ONxVf=xTdS!ZCT^uZlo)6G%hdCnRiS5;*T^e-l)p+(Ry9| zGxP5{mb?dfo(G>KyY4;qUkNC>5b5h}Z|vuBWuB{-uS?J-0BxNOkkBJ@r79ViisvK$ zzL~3eUG1;cR?7s`Gs#)^Zd2Y&Jv^*G)d6oLTk6b5l#mc-UQP$`p#kQ=S&e?LJ^6W_ z_}KBX^zah?xfbDwi%ykd)=Xcdl7P*_NHWAuu8$Q8{$xN6gm_Dm6MzFEJFUh%tUYvmv4UmJWFKR)@KmQ>J{DQy?;+&b^RgY_yvC0z}K zVQ6UMf(z%1s?qNhXqOf4f8G*0EPCRuHkOt5|m>L_cq^(xv`#pu!kH)U}p)`W? z5i(^O+b6ZHo(nz!wf=WnJHUO<#e!CFc34Bj$ZKnHs;p=c=t&s+k}$Wq^!zW*r!!k& zv*OlH)nd0&Bo!T4O&QdDx}dV#5VL6?lzz*CFnU?B1Tw{wl2&b@?L# zab-RsS}meTYQqpu)VZ5jwm30cZi%TXS zp_$i^&Swuobfp7*dY1b8K)0#Rsb7DcaH8^)fN=WMZ8$EKKJpbMHDP0_8Mgak`2{$Y z?z^3BC0?s_;S>;bZ*?IH_teV3fhX!3g0#Yl@#mH_ItC)E=YrF7%lFo27`u^os@m5XQBf*VFu^6SpW@kjKA(#jz_vE3L$jl|7_r`l#rp~>ad3+YQV&R_= zr}5GY_4Gn2kB+K4nxXaHkmy(!AA?2=xq~1d4d|Zk+A46*^+^0NP)Ak8QmCK?TU;j= zV^Sd?PO(-`zL_U8P;UOC(*NXZjAKwsCWu-&pHY^ZR&Hd-j-tbQNGv*ZZpLDJOmqnv zy-soaJW1&NaBugvCahJodn&Rm0wpjPpegPkBWRMarVS-*)CH>7UNui$dFy28C($pA zq1u&ygMz^OQXY~)rvM3gxYKXcI{#@nok_A*r;T<|P%hX0ib#a3WS_R`1-v`lWVU@d z|7TjKmvDwg)SJ$C1I}6BrCtblw#C=>edoJYfN=^pjv9nAIIlU;eIsGhbsTt*VgA`ru*cWnWJ66VkZ}yG@t6kTC0c zy;$De@%0rA;u4hn0W%y7I)E}*ZaUR?Pmt4KuXXC)gno$b#Ks*w3z!9oUIUfZx>r?~ ztEyS@Pucyfi>IO-4@VoE5_P6v3AZ_9`b2Z8lLJotU%-#G1NX}^tc88&2J@f&op3E` z8?B7B4NlhWxCf7hu|M!cZxYD}xNTziq<=`~17*tlP?;zxf#0P}Q*$`40{8{=h# zv=^{`W|k6%AyJG1h#H|IgniltB`Es{JuW$VTS5J$|`~DPodKYU78Xt&DM4v5o8^%ay(L+6|f3*s;*h3j?ui z#ySlugdiR!uBNDdG5)$_HFKHy3FYGi&IsYiI zfD{p~HPegLbeVf*m#{bTZ_rU26i!vky&hFRbr2g_C8)@Rm)crh9TdyH$Y;E00L@<{ z->0p(zH7d`R@Hj&|3#nhmx9G&mAq)jdT)j#eTNsKwIGR@wgv zTXK1c4v5UGgeEJS@32Co`z-(wB%TZ+L)XUjLIdL8*KlSG<;;J&?{&?GV{Gh>aFPVO zfxI%vSWPZVGv*d1Xls+o*eeZTG{7 z>uX5rrdPp0gY<_*?Ji|2Z!@->y~FcE5>B1x7iS?Z?P0_%spLVU*B&q0Q>SSPi&vtP zr#4`t(xbdBWnkSCuW@KOT_Iaar@jM{N(`nCh z=0UnqwR5AlmPZnJKN~n^s0v}1XiQLSa3H8ky<;>vbBK2k!?ZP_8)yYLUaRoFha33n zM05G5Z#S2)Ja(6}8bt4?0z!bd#-lS{OxVP@dzZqYN{>|J!1>7y2vhdaeDC7DM=Fe! z-0j45pShMqdUXq5EX#+bV*)67$C0QAg38zS7Mq=i-;suT5ShQ)w^>dlU1%b(z@0v~UHtC+9;2N!qQt znA*ctT$(StDQ+sGeAO=})-vWUNj9D95vj}_;PeljCJB>^)35M$w^RJ|Znf1Em!qU;`VgrW}^S4G=u%J6`76|fRy(1*d!CaJs^4|uewAoo;OM}<4{6dFwG3A_BB?SU) z@Eb+j&(}?|LgiC<7xq|D?FXljwh-LCZ_)&4G7GSD}zdSE43x7 z_d;}+g4=rRKK&Z0msM8sHrd!fvf?a;0rcgF9(?d|F+uU4c9O~)O5?pMlmp?cje3C{-} zli<$$eFcTqMqx9fg$5>Uv_IJd$5>`Q#b;!!m0?75F+?&Lz*2hkO%r#rox_Ux$sxYd zPAGZ7QZ14$V$^9Z9Ml{LwpWaf;+-QGe74zM(_01yA}M>GG6owK=s_WHpJ323`Wd*# zg1U;y6n`bBSClg{eRk=YpT+Uz*VE<0+a$x}Yyy6~u00xBOT4y>&uF%{)i$7S=V=el zq%us1Tx~I_o38k*z4DpTs0gmrqqYS-lR%_SVdMKbB``ZcBXw4m@lNPHi)UJ|FLcM+ zUb;ZcA`~c=@{y9+b6fxv7dG)o`G_sFl#Pk1>JYhp`dfnk%L)IMfdub7$Yi$iQjvs6 zJn1is?|7&{WMl%54#0O~#S*NX8$k6xgisxXZ$BZub`Jbn|MptJSxRlGHg{C4#>#*TZEu&5*54gyg9&0Qt^JxW|k!lWaOFojR#8MX1(FI3cm zDuqRy0=@%76fG5%a$}nBBI}PS+{%r2zATBE4ZsbjH`U1U1im*C4`VY?vmPz<=c8=%5yd6g Y*f9EGOxo`. Specifically, the *dipole* angle -style restrains the orientation of a point dipole mu\_j (embedded in atom -'j') with respect to a reference (bond) vector r\_ij = r\_i - r\_j, where 'i' -is another atom of the same molecule (typically, 'i' and 'j' are also -covalently bonded). +style restrains the orientation of a point dipole :math:`\mu_j` (embedded in atom +:math:`j`) with respect to a reference (bond) vector +:math:`\vec{r_{ij}} = \vec{r_i} - \vec{r_j}`, where :math:`i` is another atom of +the same molecule (typically, :math:`i` and :math:`j` are also covalently bonded). -It is convenient to define an angle gamma between the 'free' vector mu\_j -and the reference (bond) vector r\_ij: +It is convenient to define an angle gamma between the 'free' vector :math:`\vec{\mu_j}` +and the reference (bond) vector :math:`\vec{r_{ij}}`: + +.. math:: + + \cos\gamma = \frac{\vec{\mu_j}\cdot\vec{r_{ij}}}{\mu_j\,r_{ij}} -.. image:: Eqs/angle_dipole_gamma.jpg - :align: center The *dipole* angle style uses the potential: -.. image:: Eqs/angle_dipole_potential.jpg - :align: center +.. math:: -where K is a rigidity constant and gamma0 is an equilibrium (reference) + E = K (\cos\gamma - \cos\gamma_0)^2 + + +where :math:`K` is a rigidity constant and gamma0 is an equilibrium (reference) angle. The torque on the dipole can be obtained by differentiating the potential using the 'chain rule' as in appendix C.3 of :ref:`(Allen) `: -.. image:: Eqs/angle_dipole_torque.jpg - :align: center +.. math:: -Example: if gamma0 is set to 0 degrees, the torque generated by + \vec{T_j} = \frac{2K(\cos\gamma - \cos\gamma_0)}{\mu_j\,r_{ij}}\, \vec{r_{ij}} \times \vec{\mu_j} + + +Example: if :math:`\gamma_0` is set to 0 degrees, the torque generated by the potential will tend to align the dipole along the reference -direction defined by the (bond) vector r\_ij (in other words, mu\_j is -restrained to point towards atom 'i'). +direction defined by the (bond) vector :math:`\vec{r_{ij}}` (in other words, :math:`\vec{\mu_j}` is +restrained to point towards atom :math:`i`). -The dipolar torque T\_j must be counterbalanced in order to conserve +The dipolar torque :math:`\vec{T_j}` must be counterbalanced in order to conserve the local angular momentum. This is achieved via an additional force -couple generating a torque equivalent to the opposite of T\_j: +couple generating a torque equivalent to the opposite of :math:`\vec{T_j}`: -.. image:: Eqs/angle_dipole_couple.jpg - :align: center +.. math:: -where F\_i and F\_j are applied on atoms i and j, respectively. + -\vec{T_j} & = & \vec{r_{ij}} \times \vec{F_i}\\ + \vec{F_j} & = & -\vec{F_i} \\ + + +where :math:`\vec{F_i}` and :math:`\vec{F_j}` are applied on atoms :math:`i` +and :math:`j`, respectively. The following coefficients must be defined for each angle type via the :doc:`angle\_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* K (energy) -* gamma0 (degrees) +* :math:`K` (energy) +* :math:`\gamma_0` (degrees) ---------- @@ -108,17 +118,17 @@ page for more info. .. note:: - In the "Angles" section of the data file, the atom ID 'j' + In the "Angles" section of the data file, the atom ID :math:`j` defining the direction of the dipole vector to restrain must come - before the atom ID of the reference atom 'i'. A third atom ID 'k' must + before the atom ID of the reference atom :math:`i`. A third atom ID :math:`k` must also be provided to comply with the requirement of a valid angle - definition. This atom ID k should be chosen to be that of an atom - bonded to atom 'i' to avoid errors with "lost angle atoms" when running + definition. This atom ID :math:`k` should be chosen to be that of an atom + bonded to atom :math:`i` to avoid errors with "lost angle atoms" when running in parallel. Since the LAMMPS code checks for valid angle definitions, - cannot use the same atom ID of either 'i' or 'j' (this was allowed + cannot use the same atom ID of either :math:`i` or :math:`j` (this was allowed and recommended with older LAMMPS versions). -The "newton" command for intramolecular interactions must be "on" +The :doc:`newton ` command for intramolecular interactions must be "on" (which is the default except when using some accelerator packages). This angle style should not be used with SHAKE. @@ -147,8 +157,3 @@ lipid membranes, PloS ONE 6(12): e28637, 2011. **(Allen)** Allen & Tildesley, Computer Simulation of Liquids, Clarendon Press, Oxford, 1987. - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/angle_dipole.txt b/doc/txt/angle_dipole.txt deleted file mode 100644 index cdb11972ec..0000000000 --- a/doc/txt/angle_dipole.txt +++ /dev/null @@ -1,126 +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 - -angle_style dipole command :h3 -angle_style dipole/omp command :h3 - -[Syntax:] - -angle_style dipole :pre - -[Examples:] - -angle_style dipole -angle_coeff 6 2.1 180.0 :pre - -[Description:] - -The {dipole} angle style is used to control the orientation of a dipolar -atom within a molecule "(Orsi)"_#Orsi. Specifically, the {dipole} angle -style restrains the orientation of a point dipole mu_j (embedded in atom -'j') with respect to a reference (bond) vector r_ij = r_i - r_j, where 'i' -is another atom of the same molecule (typically, 'i' and 'j' are also -covalently bonded). - -It is convenient to define an angle gamma between the 'free' vector mu_j -and the reference (bond) vector r_ij: - -:c,image(Eqs/angle_dipole_gamma.jpg) - -The {dipole} angle style uses the potential: - -:c,image(Eqs/angle_dipole_potential.jpg) - -where K is a rigidity constant and gamma0 is an equilibrium (reference) -angle. - -The torque on the dipole can be obtained by differentiating the -potential using the 'chain rule' as in appendix C.3 of -"(Allen)"_#Allen1: - -:c,image(Eqs/angle_dipole_torque.jpg) - -Example: if gamma0 is set to 0 degrees, the torque generated by -the potential will tend to align the dipole along the reference -direction defined by the (bond) vector r_ij (in other words, mu_j is -restrained to point towards atom 'i'). - -The dipolar torque T_j must be counterbalanced in order to conserve -the local angular momentum. This is achieved via an additional force -couple generating a torque equivalent to the opposite of T_j: - -:c,image(Eqs/angle_dipole_couple.jpg) - -where F_i and F_j are applied on atoms i and j, respectively. - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy) -gamma0 (degrees) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -USER-MISC package. See the "Build package"_Build_package.html doc -page for more info. - -NOTE: In the "Angles" section of the data file, the atom ID 'j' -defining the direction of the dipole vector to restrain must come -before the atom ID of the reference atom 'i'. A third atom ID 'k' must -also be provided to comply with the requirement of a valid angle -definition. This atom ID k should be chosen to be that of an atom -bonded to atom 'i' to avoid errors with "lost angle atoms" when running -in parallel. Since the LAMMPS code checks for valid angle definitions, -cannot use the same atom ID of either 'i' or 'j' (this was allowed -and recommended with older LAMMPS versions). - -The "newton" command for intramolecular interactions must be "on" -(which is the default except when using some accelerator packages). - -This angle style should not be used with SHAKE. - -[Related commands:] - -"angle_coeff"_angle_coeff.html, "angle_hybrid"_angle_hybrid.html - -[Default:] none - -:line - -:link(Orsi) -[(Orsi)] Orsi & Essex, The ELBA force field for coarse-grain modeling of -lipid membranes, PloS ONE 6(12): e28637, 2011. - -:link(Allen1) -[(Allen)] Allen & Tildesley, Computer Simulation of Liquids, -Clarendon Press, Oxford, 1987. From 36a5c73a71ac7d24a013460bb7d867f4f5080282 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 14 Nov 2019 20:49:02 -0500 Subject: [PATCH 20/64] Update docs: angle_fourier --- doc/src/Eqs/angle_fourier.jpg | Bin 4618 -> 0 bytes doc/src/Eqs/angle_fourier.tex | 9 ----- doc/src/angle_fourier.rst | 37 +++++++++--------- doc/txt/angle_fourier.txt | 71 ---------------------------------- 4 files changed, 18 insertions(+), 99 deletions(-) delete mode 100644 doc/src/Eqs/angle_fourier.jpg delete mode 100644 doc/src/Eqs/angle_fourier.tex delete mode 100644 doc/txt/angle_fourier.txt diff --git a/doc/src/Eqs/angle_fourier.jpg b/doc/src/Eqs/angle_fourier.jpg deleted file mode 100644 index e748e67430c11709df92ac52bf1474f6406f6757..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 4618 zcmbtY^;;8;x87($5k@I7LZ*xo`M^Nw5Vj#TdLu+yO1cq2N_zAM6p)Q{fG}E+P6edL z2qmQjk&wE4?{n`zaPK+K^Zs(`m-jj6Iq&84<#zxRQUjp@00Myk_>}`L$pAF~H6;}l z6(#i*P*YRW&|asby|SAO4A-tR-voh}Z!$Bpuyb>;uyV37GvDIB#mU3N%gf8cAs{FK z7UTx=f-lm7Uwz=jN9Jf%y`Zp=z7f*4rHROp`f7+nm9j+>!_Aqwh9{u+ zWopf89|}8FlQ%%A#YU^6&97z%Ufl1$#*&#I?eW9+-d@*89JA|Pk*};C(=Pr}o0ois z7@?YQHlsn8lr_pl5VD}U|L~Zw3jgSxs(~UL%l`zsUYxt>>eMj!`XrX~*T8<&HbPeg z{^`T;ZhkNvP-#zo%L_Ill>Fb94z;<{BxiU4y3jS9Rq)_oTed;{MPHQ*n_V%1N1P;ezvj zZV+V3WgHGSVVNO_%Jd4(@0gzV-}uKXqI)^&s6*X>KEe$Lz9>bp%B>?5y9MW`axPC8^T@xt$iM*;cOvafv>f9SPBC($!aIux0PW;+YQ{aLE)X z#_?L#0>uq3HVQYRkQxlQWjU);Pjri~5z;qyaaY~A*GG0qrAij(Qr?N~1BXqtGQV_( zb`i4gFoR>kYdn&L#KXp8tsRna%QXaID#RV5SnGvEr9bv=mCY?>N%_t%wv-YiX*>$~ms zxSFl21uwtRujK}*ez#R>6K*u<@bvYbeA)g=u;)~oa=kgz=u->W7bxY^A|wjWp4mEY z3wbOURG@qWoxT2UH%?hP6ztkohlj@7d~R z2TO#qc%R@~7kdstvd7lp(z}bHM#aRQSkU~KgzOpYO%BwAPc_!K{b>Hk=qL`qAvjD! z^Wg5{FjKItmfgqC85#M{d8bG+e{aZKSaV$h0vl_PIpVwtiqk8#JL>)-K8!rUhvAR4 zD+jaK?LzAhI!i-LdtKrh;Z0V8v+{nyvDz)^_%xbBB_t7+$#DUn^7;%tza4#!IuD18 z4y~thE|1>5rX`*#}t-Z(Dwgo!{=5eyz zC?-psUc2xo`%aYX|@>5?QiJ} zOY6CvC}0<$d_o_EgS2IV2l9sb-p)5(t(mIbHqqk=deDnekB=2 zi3pUh!l>rQiWG-t^sdAOY}hl}c_a9dl+_%+iBmSuds4>I zVQv{&+)&n+E6!T{QPDWA`aSES;dgJU4^U2kY|49;xt`#I*lZc?51wOPTFt_?U8gLZ zcPj8ojl0*ZM#}Eva!IKx)(T1y%wCL|fsESm>3AA-q1e57=jS6pbr|DtQE!WSt9j*Z zj!_JN_}M;iQWSQYu!=HICVxuad`VB*XQ`B&+T7g!>1^?@$oEGrVY-fc=D%MMTPj;4 zH6=AJ0u3z}#5Gr)y?+xV2Id30q{f_t(UbY0v{%&##qdTy^zRP>4jMI%DgSW$sz>jw zZxhE%V21VVB|Ct$Faj0<0Agrr&X}h_V`g=*+7GYs&?X6F>;b^@4*}xgUTBkOFY~0n z>`3YuTTw6LTGy&}#yQ7ht~VpI-XAnp@o~8r=A@8 z{1y9V{B)PRj|}{QVFxCvlOX`g_c|=<^nCxVlOoPrIcNeqv&8oU=*#zVUHJOTyiQ8Ru6-Ye*<;Sj9 zH8va~c`1Jc&SR$Yo^iW)lw1PLv@n(;iHd&>iBi+kNL4)`DoHFI0Qe@Y7POI@>+`8& z!cX02?m=F7fakx7)q}}6!Zpb_mB&^E>qliWn<-ymk4O;>wJvu$Vn^=8N+i*|KrHY741EG-@ zwLhiENoUIN>Q7w0zuW=+^#aW93MwgdqG-eG2+C2BcJNnRayvcm2e+9E9)P46it@2}6jjL7}kexK3Im0jj3nWWwT`2n3$@fc0z6BMkIO(1d{}bOU>~rvjcC zmda$z($S4;eQ78e5j>B|MfxpFVJ-nasuz@`m&2a!fB#*&1k6{sO!iG?*^8RkH;~LM zSH1?K4qsYKK+)UlEk?9PINQSOjcr|9s0u%)5vyk+39X&lJwEWo$Odz?P95PywY7h~ z?uPQZqP)jN{EUa$;We==_IA*ddubi%5OXECCI@SR*kkl^!RCU|;{!+Hs(%sZ2N~h2 zfmrrA{!2iaUE_o3Ms<;8vd#-LJrDVq1Lz3PIkl7hOL6wkq|(om&n6(%-9c@Ekywju zm}aHvsy07Mo;_DWtc1M>orgI$N-aT@s(j!*u7np#YoqhC$@T}c9oiNx#vP6;Lg(Bc z1Z=@TkwTDK-(^Ezjj=BG1n7T^NziGW$qJ1X<>~aqd5hGaYEwWQ!Syhc{DKy&4yR7aX z8LP3++W&YS(2hqm9rM>IIz+fZb%fljHLyO1-3C74Qy}ul^#LxZINkKu!MKWb9jL}X zpC)yhOVzQ3JBX9Xq0WmtuP(kUTnJQUoLTP1`nU@YY#SemPv+uF2C{iFF=~4d32YcK znl-JoHb3E{k(#kBf;671aq=%(%mhZZXItzJO$w-e9AfhZI~1NB;Is@h75CFQ#^zao zLVa$6n|*G>xTKmza}O?utheIu z3%NMC(rY&LA^SSs<1A(TwCI6&IxSjHMdO&7NzuUx^jiqzLRnPrG&&(>ESD-#0m?iY z6Oddyex0Y?T8B_dK(Dc1t6Vz{wWg=cWU*x_Z05n&Wl{(dQx@-ap-^xGIF$>JXr3!? zFxRaV`qQAnU6q=URxu*sntUpwh;oz-?lh$qs_rX-uARPHu%aDTY+BVP2G$trB7aH% zf8BTffu=o~|7YeBU|g9@n6vr&ot)%t^3bVhd?~J1{F*8VX86QG>gw`W;XS`l3(kg6)Qx&HE6|SH+in^8{4W<_P${ z<7f+d;|`OSW7h=7b&GHW;lk-@Z2B{q;OCwhF;j4zE+5BJxK<2wS&6wNX`p(VCE#rw zMcrcRhj)-sGIMi~A8f&~(;JrjT2aN+J3tx2tvJ~x7*IZR^)T&;m)V|ZS2NT*+v|-R z4OnM#seQAPh?ME0{cl=?2b1Y_pQ>ydoPh?>efx>|9T7au+bgHGrWsSVg8r~WUiTix z2G~1i760US%8Yz$JUcz42n_RhxiQAB^WW}w@n52LZt{ytm6mw$LGb*MLie>sPejyT z0Nfo60)3Opes3Li?WXIRXMgIU{b&HXQ%Ab9R$SO}32^VIX(V)(?l=hh^1_#vVL{FX z#4%>rqe*-9H~Y|p^^KRYb5}G zKR^%f3ECQp(2wRWPmR+@K=;h`uDDI1m(r4M z==Q1Zp7)Hsd}{qZ?KDv`EU3KKN9aY;YVD%v1)cPrl9xR@xuK&9=cyiqxBv4yf3@`3 z#KkX?Q!(Nri)T{ztd+p(Yzm8YO9auhQt`s@&yNYo1q)-fPEJN9!MBCKL`^B#KY1a%4ClaIpD3!uPjk2Yq zNLVy4(ULRZSdyt|!LCtUl1CMb!ijXEkXRKy+@bW{3HJn-@ECoD3kDm+O}NJjaDTa4 z=W_@W57l>P|LGTGSZ>k&`ZLG?X}8)xC0OE^kht`lr#rZ&CzWxg%gihD;c9AIADY7W zJMBk3ohglbJC#*-&6v?%*NARmDjqxnvGWjOOvD>0*{SDZ6;?4TyAiI4*S$Ra=^vQt zUz*t|>IHcq^mrY2TF;X##7VwN-WD@l#$?fnuj(q)kJro%&6p1?_xxXPs2G1zI8j~* QnaueAs2x|eR+psz0w8OqE&u=k diff --git a/doc/src/Eqs/angle_fourier.tex b/doc/src/Eqs/angle_fourier.tex deleted file mode 100644 index f7f76462e3..0000000000 --- a/doc/src/Eqs/angle_fourier.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K [C_0 + C_1 \cos ( \theta) + C_2 \cos( 2 \theta) ] -$$ - -\end{document} diff --git a/doc/src/angle_fourier.rst b/doc/src/angle_fourier.rst index c974081d92..c814b7224e 100644 --- a/doc/src/angle_fourier.rst +++ b/doc/src/angle_fourier.rst @@ -1,42 +1,46 @@ -.. index:: angle\_style fourier +.. index:: angle_style fourier -angle\_style fourier command -============================ +angle_style fourier command +=========================== -angle\_style fourier/omp command -================================ +angle_style fourier/omp command +=============================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style fourier Examples """""""" -angle\_style fourier -angle\_coeff 75.0 1.0 1.0 1.0 +.. code-block:: LAMMPS + + angle_style fourier + angle_coeff 75.0 1.0 1.0 1.0 Description """"""""""" The *fourier* angle style uses the potential -.. image:: Eqs/angle_fourier.jpg - :align: center +.. math:: + + E = K [C_0 + C_1 \cos ( \theta) + C_2 \cos( 2 \theta) ] + The following coefficients must be defined for each angle type via the :doc:`angle\_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* K (energy) -* C0 (real) -* C1 (real) -* C2 (real) +* :math:`K` (energy) +* :math:`C_0` (real) +* :math:`C_1` (real) +* :math:`C_2` (real) ---------- @@ -78,8 +82,3 @@ Related commands :doc:`angle\_coeff ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/angle_fourier.txt b/doc/txt/angle_fourier.txt deleted file mode 100644 index 7dc9975793..0000000000 --- a/doc/txt/angle_fourier.txt +++ /dev/null @@ -1,71 +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 - -angle_style fourier command :h3 -angle_style fourier/omp command :h3 - -[Syntax:] - -angle_style fourier :pre - -[Examples:] - -angle_style fourier -angle_coeff 75.0 1.0 1.0 1.0 - -[Description:] - -The {fourier} angle style uses the potential - -:c,image(Eqs/angle_fourier.jpg) - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy) -C0 (real) -C1 (real) -C2 (real) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] none From 46db670093b327bce7dc61fa9e88add10fce0c84 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 14 Nov 2019 20:52:55 -0500 Subject: [PATCH 21/64] Update docs: angle_fourier_simple --- doc/src/Eqs/angle_fourier_simple.jpg | Bin 2761 -> 0 bytes doc/src/Eqs/angle_fourier_simple.tex | 9 ---- doc/src/angle_fourier_simple.rst | 35 +++++++------- doc/txt/angle_fourier_simple.txt | 70 --------------------------- 4 files changed, 17 insertions(+), 97 deletions(-) delete mode 100644 doc/src/Eqs/angle_fourier_simple.jpg delete mode 100644 doc/src/Eqs/angle_fourier_simple.tex delete mode 100644 doc/txt/angle_fourier_simple.txt diff --git a/doc/src/Eqs/angle_fourier_simple.jpg b/doc/src/Eqs/angle_fourier_simple.jpg deleted file mode 100644 index 6c9297b970e008bf50f77649e564783ec31c8d34..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 2761 zcma);c{J1u8^?bWW2?bTQnq0*Wo$(uAsI_!>}0}B*S$m+gBe>WLY6_-~%7Zqj;k zpqN5fSziC}OK-iJ1(|vq%Q)XQab=(t|0UtU>9JnMQ#r3JK;hM95KH%;SMvQ*pAjBc0slAo34e||MnBJOPHDMX9} zF1s}v5pU}M+T^hOC0nYCO@+p$axctNFb>jhmgaFXu)oqppWjgk(tzj_!hny&umFXbQGdi{6c zgT>H^x>J?xKDVQHSwh3#%UKB?JdtI!Q& zEC-**<(P~_54CsS4v80?(K3w$i`2~ro~}2Hyq@wE1wN{=^7j)FeugS*%e7+E7V`tag?@*Y$FGngxe4y|HAE3k!yi`)C zCj1y!-v#Z`j_)2wdwAW$Juoy{F8}>ZkNHYDULvki)RCB!AO&-fr1ODv{Px%rcZc3L zFK1hu_5KL-H#fAp7}&rBghTtTG}o&FSD zRE=w%{4<_gNOE+jJUSZl5LZ*@Ryo|XmZ|%MQ}INaXmjA(bo<0BDj7OfQKjf5B2;^! z#&Wtk0way@ILCn@-H3gD)KE0XMt(H1782s9jZ$AJ6gO_p!p84o#dN$Qx_x<+yr2Ws z%2p|m==h|Bs5f8+T-y$~yfMZF$?$OC+nf=)YeD*2u4PM1ZGX?ha6ff4Zrll_Dq+@W z@Ktn)Ug0xX9QD*=dFOI^TmD^vlSSr~zz0QBhd+VUe%u#zwg$-Zaq7ZNk^L`tueHdR zp9Pt(%n;r)ltF6dBO`&@sQ!yhWNWMk*@BmlyI|a0xaq!vI;iW86K%F8sSZ%ycOD8t z5TE8%TZ6=`CzMKfYRB;KlEsp3^lY0|=geY}{iP)s)z9BFS@YsWncU1AjGukPLd%7i z`BxL{YvC-VP{kDg*0#_SGEc00&ccf*-27Z)R~812#=6pgidk4BJO6kA{&)n3-FIqD z!0Xg={Uv8&Y9pePUX9YTC^P1|7)I# zFe?_(EK>Kt%Qro)8>1J%Z>0X>QcmBVg1pt}q&>XubB<&UK_a^qNENv>h_C`F!R+kK zYqbjbJ+`GKv?>GwVdLbSky3q({mcK%c0YRM-cH6`Kmu@9tsp4G;kX@nYV~@|ud5v& zik3UQUhsh@4aGlW_`vQ^Zo}gkAMx~=A&#C!rbtg*>ob*(A7JBe$Aj$x<~>8?7N`m> za!DI=;v6YBVnRC+tYNWi&j(C8@pp zQn*<&LBK~P!A!(-J^JGD?lJ3tCX?*2lF4any9DkE(SEBWl|)b{qtKnhF0mxK(dgUy z+QX-JJG)HTG(PYw+ch&?gIROjypd{~ehasFGLUQQmKGNIqR1L<5sQrNW*l+1OZe<{ zH<~f2a_NuWKzrjVaZxdOm%++3{iyks?M;P;I$X|kt}wRYz^Y=B3DJFNgLhk}=vKv` zX5*arjT9~honH c$jusC$%pvuLDidH%rQCh|ZAl8Y@rBX8qao>XgJZ9NXceoFi~ z)E0c+gEd0?ihDKGjmyb#Y|I1BHwa3`mNR`O1A1zq(Rx&Ce_spQ<4gxK;(hWpit2e% z2F9gNUGapO@Mv1AUg89mtbH^HgT*LmsJ5y_{7BfPY|GAa_ZvhVkw*8Q#k3m+Hv^Pp{KJ$&u?1%@*A;6MntGSAWmO}8 z+InBS-&1DLW|^Z~+?v(<;Pc9^_p>PRYWidFecZS<6?&y5tgenh;co5KUN@%J{ z$lqbk=RSI=mrB5!hJAMoPQ{x%g!|mr+VL*6ABYx{rOf%0oWmYONlW}Sk8xDz*?FFE z32q%FCxVZPSszZ+~bn;nu>5RA^AB7aXzj33rA&g#+g!mT}l>`qa)hPpMyE! z@4ktysRcjvWtPRJSz|jb#cs`sxf;Pwika-ImuJNsg4wu+|I$pJJy#IlFi6&5HnOyNla1FFpZlMDRN7lg zzC=`uq$7?EGjk3IAvT)2R8Iom@jEeY39&SH5Ur940cQn0oc~`(ase znNkAWyON2>b63UC_L)ej@i{ErcPz?Kh5Sfc|KOD` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* K (energy) -* c (real) -* n (real) +* :math:`K` (energy) +* :math:`c` (real) +* :math:`n` (real) ---------- @@ -77,8 +81,3 @@ Related commands :doc:`angle\_coeff ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/angle_fourier_simple.txt b/doc/txt/angle_fourier_simple.txt deleted file mode 100644 index ae5d308353..0000000000 --- a/doc/txt/angle_fourier_simple.txt +++ /dev/null @@ -1,70 +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 - -angle_style fourier/simple command :h3 -angle_style fourier/simple/omp command :h3 - -[Syntax:] - -angle_style fourier/simple :pre - -[Examples:] - -angle_style fourier/simple -angle_coeff 100.0 -1.0 1.0 - -[Description:] - -The {fourier/simple} angle style uses the potential - -:c,image(Eqs/angle_fourier_simple.jpg) - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy) -c (real) -n (real) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] none From dcf332f89659adc05673c585ffae3d2db2076db1 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 14 Nov 2019 20:57:34 -0500 Subject: [PATCH 22/64] Update docs: angle_harmonic --- doc/src/Eqs/angle_harmonic.jpg | Bin 2005 -> 0 bytes doc/src/Eqs/angle_harmonic.tex | 9 ---- doc/src/angle_harmonic.rst | 45 +++++++++---------- doc/txt/angle_harmonic.txt | 77 --------------------------------- 4 files changed, 21 insertions(+), 110 deletions(-) delete mode 100644 doc/src/Eqs/angle_harmonic.jpg delete mode 100644 doc/src/Eqs/angle_harmonic.tex delete mode 100644 doc/txt/angle_harmonic.txt diff --git a/doc/src/Eqs/angle_harmonic.jpg b/doc/src/Eqs/angle_harmonic.jpg deleted file mode 100644 index 352be0b5440fac4e5f896212eca6a2dc6ccfd02f..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 2005 zcmZ`)dpOgJAO7xUB4(Qr#)Q?j4jmDiIvXq5Rya$B={PRsPOc?X*1=G6+4z+@40EcJ zJ43Ef$fVqgsg&znBA1ktetypR;o_&apAgOE zuQM{%ch;@2YOnNXMqN?Zj$gsd(!~1UndyU3TG(FlT$@A2s=*pKeaa>mQ|~Zovd8k8 zZ=@(eNSl_I1x!yIIM@tXEk5+2(*xGY?mpd}@g|)tQ?3!@Xhj#12a-c;iinEzVTU7D z@E$fLoLA{Jx}3YvKn#{-ytoNVJ8M`Un!Q2vuIqnE#`qE-i%VX2VuoJcXY_?C&wwRd z_Yk&i4?QX5>RPQ!9LV;(8Mm2*h~uZ_ktcpn`}AqwUb*sNbDIiD8tvj_WFWu1-pCT) zHY<(U0?ef1-?+fmn-?Ep=2#p#tdVQ)4Y*{?GQD z@a|t3E&QZQj(ceDYy|Y26Y*DSb5lD59_L!%=Lw*V1v2(RehQ@l8*|~UeH`kg4j7)(GU59W< zcSuoFadCE~Z$Xk9QmfaNODj3Lc3JGZd^Sim$V>~~3hu=Se&E>~M2 zH0N$y6(+IsyoLf5h$6BYG6U8GM8=fOh8Ah!;r!8C&kvq$o2abS_VK|9+C8F+<$o&PH-p4f4oy7@H5*y5lc)pMSdV zR;t0;At2;^GQNCH>l;^nLKk5mJm_r4ShT+_opSr}dMl3&O?8Vl%h{Fkm}FS$C1G2a zOS2v1zg(CutQaOTCf;SQXlJ!sT=X_?B-Y2xVFa0oMt;f5TFlxGE9m-{=4EyucPL?4 zpL0MlUp!JUAvv``cc#&O)v(^&0`t=2n3p<5%AYISjZlkUSJjh!PgzGh@;(x=4}uc3 zt5p#W1!=7O7{a}1_N@r@8QNLn1vSn9FZ?p5Z@gc{G^!|lpeaVlH!k);)q-M~Y#?b1 zs1|H01uts_4x8w>-LcoG6rPk>24tUc?d^P&?^Pq5Y04A11n@q&LJv2j#@demz`rCh ze8;Kcm{q#&NE~L|v0W&sE3kefTXHQcg?0HTj;95+!LdO|mn)-UwYIB+ba=2Se?#ug z5%@;(pI3@ZnBiO(|8&8=R&o7qD}8TKiA71=U-Xg-MQg{6HsxBL@@AEuAt9yto5nrG z%m-s#=DqX{rz)OBP!|40=n1KkhgbG*^zzX{q|Jnf_d$s1YD6#Xzte}~T&;54wQbTR_*Br^Kiv*#uexcXpl~_HvUF!75SH-`Y z#boc;fV4&Jz0|Ps-o9ZB-@&lH8%YYhUyaHHGcyqmps65TWC79gzkT3SDY)h6mM?z= ze`m0&a{?)-hF-UMv7uKT(-~y{?CL-%0VJ#;8r)SDpf?V;Qd+;hSjeWVI{gZ0LZ~eM zz1N(`=6O(;x~;Jf?ZPkmC|Blu3Gvw@^GmU)@+0| z&?Mu>S2zoJp8gFnXPleT-!z8cUiHW|hM;3+W~Qd6$IdLplsuGG%vfJm6=$wRE8YKt z!#*pd9mUmg{TsMcfufd$U^WL|EFDfvM&uLG1u~HcU4jWyK3(*Anogc#(Z^gris#+J zHAlcds4-F`p(9K`5?QOCswE?TA0qKZR%$WS2CcdptM%li{X=~dv4>l9>YH`$ev2rP zbGiOJC)aBvA-}_Mp2_lj^d!l#ALsFjE9~XpOTY&SX>WDEwHH6u@pLi|^^L~Nh5u3$ z*64<#`ekj7Y!4Yz@o|`f=~cdVX%xxc{QM@~Iw`8a#nU a-AI(ug09UxYtH>s``_E`pW1WZ8u=fX(30Q) diff --git a/doc/src/Eqs/angle_harmonic.tex b/doc/src/Eqs/angle_harmonic.tex deleted file mode 100644 index c566376b5b..0000000000 --- a/doc/src/Eqs/angle_harmonic.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K (\theta - \theta_0)^2 -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/angle_harmonic.rst b/doc/src/angle_harmonic.rst index 87b71ad9ad..1066621729 100644 --- a/doc/src/angle_harmonic.rst +++ b/doc/src/angle_harmonic.rst @@ -1,22 +1,22 @@ -.. index:: angle\_style harmonic +.. index:: angle_style harmonic -angle\_style harmonic command -============================= +angle_style harmonic command +============================ -angle\_style harmonic/intel command -=================================== +angle_style harmonic/intel command +================================== -angle\_style harmonic/kk command +angle_style harmonic/kk command +=============================== + +angle_style harmonic/omp command ================================ -angle\_style harmonic/omp command -================================= - Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style harmonic @@ -24,7 +24,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style harmonic angle_coeff 1 300.0 107.0 @@ -34,22 +34,24 @@ Description The *harmonic* angle style uses the potential -.. image:: Eqs/angle_harmonic.jpg - :align: center +.. math:: -where theta0 is the equilibrium value of the angle, and K is a -prefactor. Note that the usual 1/2 factor is included in K. + E = K (\theta - \theta_0)^2 + + +where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a +prefactor. Note that the usual 1/2 factor is included in :math:`K`. The following coefficients must be defined for each angle type via the :doc:`angle\_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* K (energy/radian\^2) -* theta0 (degrees) +* :math:`K` (energy/radian\^2) +* :math:`\theta_0` (degrees) -Theta0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of K are in energy/radian\^2. +:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians +internally; hence the units of :math:`K` are in energy/radian\^2. ---------- @@ -91,8 +93,3 @@ Related commands :doc:`angle\_coeff ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/angle_harmonic.txt b/doc/txt/angle_harmonic.txt deleted file mode 100644 index b632f68478..0000000000 --- a/doc/txt/angle_harmonic.txt +++ /dev/null @@ -1,77 +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 - -angle_style harmonic command :h3 -angle_style harmonic/intel command :h3 -angle_style harmonic/kk command :h3 -angle_style harmonic/omp command :h3 - -[Syntax:] - -angle_style harmonic :pre - -[Examples:] - -angle_style harmonic -angle_coeff 1 300.0 107.0 :pre - -[Description:] - -The {harmonic} angle style uses the potential - -:c,image(Eqs/angle_harmonic.jpg) - -where theta0 is the equilibrium value of the angle, and K is a -prefactor. Note that the usual 1/2 factor is included in K. - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy/radian^2) -theta0 (degrees) :ul - -Theta0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of K are in energy/radian^2. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] none From aed67fc96e5a190932244c618b7f8ef96d6c2323 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 14 Nov 2019 21:06:14 -0500 Subject: [PATCH 23/64] Update docs: angle_hybrid --- doc/src/angle_hybrid.rst | 35 +++++++--------- doc/txt/angle_hybrid.txt | 91 ---------------------------------------- 2 files changed, 15 insertions(+), 111 deletions(-) delete mode 100644 doc/txt/angle_hybrid.txt diff --git a/doc/src/angle_hybrid.rst b/doc/src/angle_hybrid.rst index e31df56e72..f685beacc8 100644 --- a/doc/src/angle_hybrid.rst +++ b/doc/src/angle_hybrid.rst @@ -1,13 +1,13 @@ -.. index:: angle\_style hybrid +.. index:: angle_style hybrid -angle\_style hybrid command -=========================== +angle_style hybrid command +========================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style hybrid style1 style2 ... @@ -17,11 +17,11 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style hybrid harmonic cosine angle_coeff 1 harmonic 80.0 30.0 - angle_coeff 2\* cosine 50.0 + angle_coeff 2* cosine 50.0 Description """"""""""" @@ -31,19 +31,19 @@ simulation. An angle style is assigned to each angle type. For example, angles in a polymer flow (of angle type 1) could be computed with a *harmonic* potential and angles in the wall boundary (of angle type 2) could be computed with a *cosine* potential. The assignment -of angle type to style is made via the :doc:`angle\_coeff ` +of angle type to style is made via the :doc:`angle_coeff ` command or in the data file. -In the angle\_coeff commands, the name of an angle style must be added +In the :doc:`angle_coeff ` commands, the name of an angle style must be added after the angle type, with the remaining coefficients being those appropriate to that style. In the example above, the 2 angle\_coeff commands set angles of angle type 1 to be computed with a *harmonic* -potential with coefficients 80.0, 30.0 for K, theta0. All other angle -types (2-N) are computed with a *cosine* potential with coefficient -50.0 for K. +potential with coefficients 80.0, 30.0 for :math:`K`, :math:`\theta_0`. All other angle +types :math:`(2 - N)` are computed with a *cosine* potential with coefficient +50.0 for :math:`K`. If angle coefficients are specified in the data file read via the -:doc:`read\_data ` command, then the same rule applies. +:doc:`read_data ` command, then the same rule applies. E.g. "harmonic" or "cosine", must be added after the angle type, for each line in the "Angle Coeffs" section, e.g. @@ -77,7 +77,7 @@ input script, since BondBond (or BondAngle) coefficients need not be specified at all for angle types that are not *class2*\ . An angle style of *none* with no additional coefficients can be used -in place of an angle style, either in a input script angle\_coeff +in place of an angle style, either in a input script :doc:`angle_coeff ` command or in the data file, if you desire to turn off interactions for specific angle types. @@ -95,16 +95,11 @@ for more info. Unlike other angle styles, the hybrid angle style does not store angle coefficient info for individual sub-styles in a :doc:`binary restart files `. Thus when restarting a simulation from a restart -file, you need to re-specify angle\_coeff commands. +file, you need to re-specify :doc:`angle_coeff ` commands. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/angle_hybrid.txt b/doc/txt/angle_hybrid.txt deleted file mode 100644 index 0046c161be..0000000000 --- a/doc/txt/angle_hybrid.txt +++ /dev/null @@ -1,91 +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 - -angle_style hybrid command :h3 - -[Syntax:] - -angle_style hybrid style1 style2 ... :pre - -style1,style2 = list of one or more angle styles :ul - -[Examples:] - -angle_style hybrid harmonic cosine -angle_coeff 1 harmonic 80.0 30.0 -angle_coeff 2* cosine 50.0 :pre - -[Description:] - -The {hybrid} style enables the use of multiple angle styles in one -simulation. An angle style is assigned to each angle type. For -example, angles in a polymer flow (of angle type 1) could be computed -with a {harmonic} potential and angles in the wall boundary (of angle -type 2) could be computed with a {cosine} potential. The assignment -of angle type to style is made via the "angle_coeff"_angle_coeff.html -command or in the data file. - -In the angle_coeff commands, the name of an angle style must be added -after the angle type, with the remaining coefficients being those -appropriate to that style. In the example above, the 2 angle_coeff -commands set angles of angle type 1 to be computed with a {harmonic} -potential with coefficients 80.0, 30.0 for K, theta0. All other angle -types (2-N) are computed with a {cosine} potential with coefficient -50.0 for K. - -If angle coefficients are specified in the data file read via the -"read_data"_read_data.html command, then the same rule applies. -E.g. "harmonic" or "cosine", must be added after the angle type, for each -line in the "Angle Coeffs" section, e.g. - -Angle Coeffs :pre - -1 harmonic 80.0 30.0 -2 cosine 50.0 -... :pre - -If {class2} is one of the angle hybrid styles, the same rule holds for -specifying additional BondBond (and BondAngle) coefficients either via -the input script or in the data file. I.e. {class2} must be added to -each line after the angle type. For lines in the BondBond (or -BondAngle) section of the data file for angle types that are not -{class2}, you must use an angle style of {skip} as a placeholder, e.g. - -BondBond Coeffs :pre - -1 skip -2 class2 3.6512 1.0119 1.0119 -... :pre - -Note that it is not necessary to use the angle style {skip} in the -input script, since BondBond (or BondAngle) coefficients need not be -specified at all for angle types that are not {class2}. - -An angle style of {none} with no additional coefficients can be used -in place of an angle style, either in a input script angle_coeff -command or in the data file, if you desire to turn off interactions -for specific angle types. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the "Build package"_Build_package.html doc page -for more info. - -Unlike other angle styles, the hybrid angle style does not store angle -coefficient info for individual sub-styles in a "binary restart -files"_restart.html. Thus when restarting a simulation from a restart -file, you need to re-specify angle_coeff commands. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] none From c182d3f545d0de9eba2932e8cb960ad83c2457e0 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Thu, 14 Nov 2019 21:15:55 -0500 Subject: [PATCH 24/64] Update docs: fix_restrain --- doc/src/fix_restrain.rst | 58 +++++------ doc/txt/fix_restrain.txt | 209 --------------------------------------- 2 files changed, 29 insertions(+), 238 deletions(-) delete mode 100644 doc/txt/fix_restrain.txt diff --git a/doc/src/fix_restrain.rst b/doc/src/fix_restrain.rst index 0276194bd2..0fc0ccee77 100644 --- a/doc/src/fix_restrain.rst +++ b/doc/src/fix_restrain.rst @@ -7,7 +7,7 @@ Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS fix ID group-ID restrain keyword args ... @@ -39,7 +39,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0 @@ -98,7 +98,7 @@ conventional force field terms. If the restraint is applied during a dynamics run (as opposed to during an energy minimization), a large restraint coefficient can significantly reduce the stable timestep size, especially if the atoms are initially far from the preferred -conformation. You may need to experiment to determine what value of K +conformation. You may need to experiment to determine what value of :math:`K` works best for a given application. For the case of finding a minimum energy structure for a single @@ -107,7 +107,7 @@ parameters or constructing a potential energy surface), commands such as the following may be useful: -.. parsed-literal:: +.. code-block:: LAMMPS # minimize molecule energy with restraints velocity all create 600.0 8675309 mom yes rot yes dist gaussian @@ -134,16 +134,18 @@ The *bond* keyword applies a bond restraint to the specified atoms using the same functional form used by the :doc:`bond\_style harmonic ` command. The potential associated with the restraint is -.. image:: Eqs/bond_harmonic.jpg - :align: center +.. math:: + + E = K (r - r_0)^2 + with the following coefficients: -* K (energy/distance\^2) -* r0 (distance) +* :math:`K` (energy/distance\^2) +* :math:`r_0` (distance) -K and r0 are specified with the fix. Note that the usual 1/2 factor -is included in K. +:math:`K` and :math:`r_0` are specified with the fix. Note that the usual 1/2 factor +is included in :math:`K`. ---------- @@ -153,16 +155,17 @@ The *angle* keyword applies an angle restraint to the specified atoms using the same functional form used by the :doc:`angle\_style harmonic ` command. The potential associated with the restraint is -.. image:: Eqs/angle_harmonic.jpg - :align: center +.. math:: + + E = K (\theta - \theta_0)^2 with the following coefficients: -* K (energy/radian\^2) -* theta0 (degrees) +* :math:`K` (energy/radian\^2) +* :math:`\theta_0` (degrees) -K and theta0 are specified with the fix. Note that the usual 1/2 -factor is included in K. +:math:`K` and :math:`\theta_0` are specified with the fix. Note that the usual 1/2 +factor is included in :math:`K`. ---------- @@ -173,20 +176,22 @@ atoms using a simplified form of the function used by the :doc:`dihedral\_style charmm ` command. The potential associated with the restraint is -.. image:: Eqs/dihedral_charmm.jpg - :align: center +.. math:: + + E = K [ 1 + \cos (n \phi - d) ] + with the following coefficients: -* K (energy) -* n (multiplicity, >= 0) -* d (degrees) = phi0 + 180 +* :math:`K` (energy) +* :math:`n` (multiplicity, >= 0) +* :math:`d` (degrees) = :math:`\phi_0 + 180` -K and phi0 are specified with the fix. Note that the value of the -dihedral multiplicity *n* is set by default to 1. You can use the +:math:`K` and :math:`\phi_0` are specified with the fix. Note that the value of the +dihedral multiplicity :math:`n` is set by default to 1. You can use the optional *mult* keyword to set it to a different positive integer. Also note that the energy will be a minimum when the -current dihedral angle phi is equal to phi0. +current dihedral angle :math:`\phi` is equal to :math:`\phi_0`. ---------- @@ -233,8 +238,3 @@ Restrictions **Related commands:** none **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/fix_restrain.txt b/doc/txt/fix_restrain.txt deleted file mode 100644 index 8e962f4cc9..0000000000 --- a/doc/txt/fix_restrain.txt +++ /dev/null @@ -1,209 +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 restrain command :h3 - -[Syntax:] - -fix ID group-ID restrain keyword args ... :pre - -ID, group-ID are documented in "fix"_fix.html command :ulb,l -restrain = style name of this fix command :l -one or more keyword/arg pairs may be appended :l -keyword = {bond} or {angle} or {dihedral} :l - {bond} args = atom1 atom2 Kstart Kstop r0 - atom1,atom2 = IDs of 2 atoms in bond - Kstart,Kstop = restraint coefficients at start/end of run (energy units) - r0 = equilibrium bond distance (distance units) - {angle} args = atom1 atom2 atom3 Kstart Kstop theta0 - atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom - Kstart,Kstop = restraint coefficients at start/end of run (energy units) - theta0 = equilibrium angle theta (degrees) - {dihedral} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0 keyword/value - atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order - Kstart,Kstop = restraint coefficients at start/end of run (energy units) - phi0 = equilibrium dihedral angle phi (degrees) - keyword/value = optional keyword value pairs. supported keyword/value pairs: - {mult} n = dihedral multiplicity n (integer >= 0, default = 1) :pre -:ule - -[Examples:] - -fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 -fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0 -fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 dihedral 1 2 3 4 2000.0 2000.0 120.0 -fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5 0.0 2000.0 -120.0 dihedral 1 2 3 6 0.0 2000.0 0.0 :pre - -[Description:] - -Restrain the motion of the specified sets of atoms by making them part -of a bond or angle or dihedral interaction whose strength can vary -over time during a simulation. This is functionally similar to -creating a bond or angle or dihedral for the same atoms in a data -file, as specified by the "read_data"_read_data.html command, albeit -with a time-varying pre-factor coefficient, and except for exclusion -rules, as explained below. - -For the purpose of force field parameter-fitting or mapping a molecular -potential energy surface, this fix reduces the hassle and risk -associated with modifying data files. In other words, use this fix to -temporarily force a molecule to adopt a particular conformation. To -create a permanent bond or angle or dihedral, you should modify the -data file. - -NOTE: Adding a bond/angle/dihedral with this command does not apply -the exclusion rules and weighting factors specified by the -"special_bonds"_special_bonds.html command to atoms in the restraint -that are now bonded (1-2,1-3,1-4 neighbors) as a result. If they are -close enough to interact in a "pair_style"_pair_style.html sense -(non-bonded interaction), then the bond/angle/dihedral restraint -interaction will simply be superposed on top of that interaction. - -The group-ID specified by this fix is ignored. - -The second example above applies a restraint to hold the dihedral -angle formed by atoms 1, 2, 3, and 4 near 120 degrees using a constant -restraint coefficient. The fourth example applies similar restraints -to multiple dihedral angles using a restraint coefficient that -increases from 0.0 to 2000.0 over the course of the run. - -NOTE: Adding a force to atoms implies a change in their potential -energy as they move due to the applied force field. For dynamics via -the "run"_run.html command, this energy can be added to the system's -potential energy for thermodynamic output (see below). For energy -minimization via the "minimize"_minimize.html command, this energy -must be added to the system's potential energy to formulate a -self-consistent minimization problem (see below). - -In order for a restraint to be effective, the restraint force must -typically be significantly larger than the forces associated with -conventional force field terms. If the restraint is applied during a -dynamics run (as opposed to during an energy minimization), a large -restraint coefficient can significantly reduce the stable timestep -size, especially if the atoms are initially far from the preferred -conformation. You may need to experiment to determine what value of K -works best for a given application. - -For the case of finding a minimum energy structure for a single -molecule with particular restraints (e.g. for fitting force field -parameters or constructing a potential energy surface), commands such -as the following may be useful: - -# minimize molecule energy with restraints -velocity all create 600.0 8675309 mom yes rot yes dist gaussian -fix NVE all nve -fix TFIX all langevin 600.0 0.0 100 24601 -fix REST all restrain dihedral 2 1 3 8 0.0 5000.0 $\{angle1\} dihedral 3 1 2 9 0.0 5000.0 $\{angle2\} -fix_modify REST energy yes -run 10000 -fix TFIX all langevin 0.0 0.0 100 24601 -fix REST all restrain dihedral 2 1 3 8 5000.0 5000.0 $\{angle1\} dihedral 3 1 2 9 5000.0 5000.0 $\{angle2\} -fix_modify REST energy yes -run 10000 -# sanity check for convergence -minimize 1e-6 1e-9 1000 100000 -# report unrestrained energies -unfix REST -run 0 :pre - -:line - -The {bond} keyword applies a bond restraint to the specified atoms -using the same functional form used by the "bond_style -harmonic"_bond_harmonic.html command. The potential associated with -the restraint is - -:c,image(Eqs/bond_harmonic.jpg) - -with the following coefficients: - -K (energy/distance^2) -r0 (distance) :ul - -K and r0 are specified with the fix. Note that the usual 1/2 factor -is included in K. - -:line - -The {angle} keyword applies an angle restraint to the specified atoms -using the same functional form used by the "angle_style -harmonic"_angle_harmonic.html command. The potential associated with -the restraint is - -:c,image(Eqs/angle_harmonic.jpg) - -with the following coefficients: - -K (energy/radian^2) -theta0 (degrees) :ul - -K and theta0 are specified with the fix. Note that the usual 1/2 -factor is included in K. - -:line - -The {dihedral} keyword applies a dihedral restraint to the specified -atoms using a simplified form of the function used by the -"dihedral_style charmm"_dihedral_charmm.html command. The potential -associated with the restraint is - -:c,image(Eqs/dihedral_charmm.jpg) - -with the following coefficients: - -K (energy) -n (multiplicity, >= 0) -d (degrees) = phi0 + 180 :ul - -K and phi0 are specified with the fix. Note that the value of the -dihedral multiplicity {n} is set by default to 1. You can use the -optional {mult} keyword to set it to a different positive integer. -Also note that the energy will be a minimum when the -current dihedral angle phi is equal to phi0. - -:line - -[Restart, fix_modify, output, run start/stop, minimize info:] - -No information about this fix is written to "binary restart -files"_restart.html. - -The "fix_modify"_fix_modify.html {energy} option is supported by this -fix to add the potential energy associated with this fix to the -system's potential energy as part of "thermodynamic -output"_thermo_style.html. - -The "fix_modify"_fix_modify.html {respa} option is supported by this -fix. This allows to set at which level of the "r-RESPA"_run_style.html -integrator the fix is adding its forces. Default is the outermost level. - -NOTE: If you want the fictitious potential energy associated with the -added forces to be included in the total potential energy of the -system (the quantity being minimized), you MUST enable the -"fix_modify"_fix_modify.html {energy} option for this fix. - -This fix computes a global scalar and a global vector of length 3, -which can be accessed by various "output commands"_Howto_output.html. -The scalar is the total potential energy for {all} the restraints as -discussed above. The vector values are the sum of contributions to the -following individual categories: - -1 = bond energy -2 = angle energy -3 = dihedral energy :ul - -The scalar and vector values calculated by this fix are "extensive". - -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. - -[Restrictions:] none - -[Related commands:] none - -[Default:] none From ec052ea99a33a1129e3432ac4ba9a6c8ce088132 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 15 Nov 2019 10:45:25 -0500 Subject: [PATCH 25/64] Update docs: angle_mm3 --- doc/src/Eqs/angle_mm3.jpg | Bin 9222 -> 0 bytes doc/src/Eqs/angle_mm3.tex | 9 ------- doc/src/angle_mm3.rst | 39 +++++++++++---------------- doc/txt/angle_mm3.txt | 55 -------------------------------------- 4 files changed, 16 insertions(+), 87 deletions(-) delete mode 100644 doc/src/Eqs/angle_mm3.jpg delete mode 100644 doc/src/Eqs/angle_mm3.tex delete mode 100644 doc/txt/angle_mm3.txt diff --git a/doc/src/Eqs/angle_mm3.jpg b/doc/src/Eqs/angle_mm3.jpg deleted file mode 100644 index 5b9f3e34f091f5a2d439294e9c5a1802a2885fb4..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 9222 zcmdscWl&sA)aD%q7~CPa%_NWj3GPm?5Htjbke~w@+y)6A+%1sc?(P~K5(qAXI}8#a zgb;Lj-*0R8tF5itZ};b(u5+uaZ`ZAU?mhRMexAOYyITcFUMMIl03Z+mfbJV`w*bfi zIM~<_Y%ClI1cHl;gGWF?NPv$|Kto1OOu<0Q#K=HPPtOc{%Ervf38klJ7kbRe&BM>n z&%`DoA-Efx#GzMML(>NX#jDPLn$v@EkMfP6<7V!Us?0*3JpSVx}0T^`u@xY{j6!7PgBkZEm0dWmN zZvMP-`N7bhF~HufPtD96IEA6UWZ3zFOiE*KU|F{yVmJBAf<`)`?bbTCLW?QFCrA-Vok` zFF$NcP&`I|Eo6GKy{=b=AYMLQR=}alXqDmm@y8nM2vZh%?}{jU-SA~KI_qk(lvt;; z=J-uuMdfqfU6fC=d5rkrN;lt9YADT-n(e14t)H^B$N3|h9hR*=rC%AQdPH-qq&$w8qTym}wtH*p3MddRIG}wkXDv>BX7;uvsZX_kwpLGW zHJ_4a_fJES2gKmwAD}w%XOv}(v^5`xyS?!B#`1K2<#L8+hhhaf;WF|35dS4ja|@k3 z_^nR5OVxNjZnTi#(EnJ2H=e|Fbyg9R)L>!29@CbBhy8gJHbxOOK-69B`sOd4x71nl z9WaI^)mL!(jL=5N%^+yT$f6>n?lhxhNx&N%6B777t(@hw6HUugw}6ZSAGLxZ#w9q_>yI=-P+Dcu@y z+92IVr+)kFy0!=8`~iAfV)&+CIIy3rJQXF4)PR`DQx5DtAoHj|xS_pDi?SQ19#++> zAW_T_R1}@V3fs?`uIH%%vkGZ3JdRJtA1jgT>JWMU*+*QmBCz@l>v7*1c^26&5=AlR zUB1`XU@tE>@fRtxwM+FC%@S?uJT#;w1O9#hxKdg)4cOnUufX9gi)hf6X%9`cIS z?|arMXcU+6LMpCM=UE8XX3ZG1rPJa;Bgc8^JTX(-+jyxZ&0t1cv8xHNhVTk4djHg13ArN zpBrbdoi53Qu2o!0U79*Id}mc3c^7@YiOp(eIBnh#d4pk6zg5vp`(?qvR!C=Nqb8?H znDJ`_XcwCuTpa&ATrgfyTOKR*(<&gApq6Jrkgtb<^A*zWyiA*3UisSxG{jLb9Q9uP z`f9i}&UY226gZCsxM*wYqmr{9CT%C-u~xOW3LdE+$2?NzmH0)?6qZFu%U*Wlrq6tQ zUdX97#A@(j810}P1S7Eq%Z9ICi{!R9k^&nT=-KPp~)C!n&t8PTEof3G86Tcry)7mNNASIveiBjvz;~ zJ+MX=Hp9jBY{IbcU66edSZ$-V&cAqVYMacEE7zCsBI7iAfokm|^#6 zXriA{5t}ue{};2g@?0AsRHFLB?I`C0Kw7&wS&;_6~g0Wf;uqK_h{sIiV%DA(rYgm%&ATfKwq}6IVZaDx)F2$wr`f#e6CZ>@7bJ z1w%`)O>-Ulm3JlU&^w&wq63ivG@08CiJAoEY`YtNv1(2lnL`%TmM& zn|gW+5hKqZ-vN5xmBPtyhk8U9y1?1Yey)kSY^z?A&TL`Ka<>r{<*N2}xjF1g-`LNI zei&N-6q@n?g|65Jm(7Oacy4r8*3@tO(1Z7lk^Y<^bfHI-?n2ktHS=cU;y!EbPlnQ? z`l9CB+~2o-_0FkL@(pXW+q?si?bhIig1j&m)95md!}s*7mrNhv)1x-O7?^rnR4*N| zbA{%fCc1FGPGh_LsFkrUv&)V#a^7az-d0;v|G-^PXW!BBK^kd;;9<6th*@>Zs>^mI zTr|C*KF`3$?WFLV`dV{%G$9G^}eeEiMj^|~>6 zrI$83&K`jaK2Xd0{vEl91NAG7mI@t%sLMNcP>lbkLs%Z6-;kkO(u1TI`WxSWHj)0| zMyKtNhqydC!$f<`nk4i{5>5+vyf*Oi@O7dq{M7rzYQY%~SkBEFs^IH&`msg`RiB=@ zJ#xmHB7H+sV5Pqi*K6mN5X@ZlwvNDzLAacW?1jC61X~YUDf(tJd7t5M9jLjXNfVGd zsMUbT(1&r_!t5%d!5ohVna`LfOX`>ECcCQ_mQ~<^-+DvUc*g87iNDo5XA=CzZ`WO$ ziSqGveAqX2!l%p`!a3lj0nu0GWo^k74e>tILJIGPuX{^LtVD=Ioh!?KPdyN_cbGBJ zE-S`>)+h*C+4_tPIEV}}aASSL9}>4cKI+j9d@mYw{>>R&v`&}ApxCe~!!Q-=IR?>} zH-~#hTtsxw7$kk^wD9`ov4xrCOv6l;$D}6DcJ5Yt2gv-qPEbF|!l{pP*P8r|*-&+S zxLnksn+l6nr+6nG58P}#bq*XmiScaBvC%?bz7(36`(|!2L^6#2j_o0$B?Bq?x+`yW z(V$XYppRORhjqU1Y;5?FLmp}%vz-v_m-RMdzT8;rmVr&FZOZBncm)TKUfiM|n_c1o zH84321%{X5VBWw%h%n4+^;RKWuYTu zl>P~)%_F;&Hz)TaD<@nNS4{NF0l|u`&m?>BonQGk3rO z?PEf5)XN1#k03#83nY}xhxZlRRcaQ*(4+iO$N1rPbsE<6jGT=T30l)Vj+F$D-fA{O zf^S?GXTrq9BeN$hDJk+~Wtc`lDSrj#HumXsn5GMFq1(*bcy5zK_-Gf%sjWYhRb}fz zCFhfI48d(-!{y`Q#mr20914DTk1M{CehH8bP{US5Zbx|)T|}(q-E!DoeG(8^&p^*9 z^5JC7jcgVCX!#aQvxqAqe%1xanbdk7TcxPOzF-I+o!s^LOF68v-fVYEKX2RcqS&ig z4$}>-Agj)!Z6X$I`D091# z)T3eI^mhG(^Ji{2x!_9DOZGXCG&tT9??bxBE%f9~DA!iT8mCJ!YhAeTBkM*b4e{tc zCAObW{J#*8FZ+o$!<157qKlfroDRHd5Hx)Hn}@mv!ujP4|A|$92srqKz)9Wv(nPa2HC@VJWMq?KVB9NW^)EAmM6Nh&EVf=e`h|LC<1X7A$fDTX%cH9tI@J}#A`Lv~UlGy() zO6rT>i=EG{p(In@Ryu5ykS1t58-iA65v6V_o&R(-9;tVyH@_tIbahTM3eh`JEB0a& zyfhE!pH`Q?qTEVAyO&rs^xvM8%nI38UTmGg>@Sk{boLxSWZeN3X)ph33SF_tIEigJ z_d9`RG>r=VpBbFa8bzrg$^|}`+B(i_>d_OM_W7NGDW}Ik@)Q~%dFKq?89SE|!I>Xw zuBxxJTU0o7ppyD_1~1*`{6C{1S)EPq263zpRB*%+I35H=?Q%AX`I16NNg@{&b&5p~xK64RwKX_n}pOl_n zzjZ2aOW4L!_Q5;*^E*EXEQLlQVDp$m;SHXLn^$9Niu6QYb8P%Ci7ys&8ES?!{8b)r zdd?fGmlt*o%!M3J69(Y4Eho{`1mVC`q;S;pAih<*C)~I{{q;Vu)C3$U5p>XrHfuO6 zVrFAH-qWw3ULPvaO51{)af+v!VDfyXb&ofI58{|f8K<7 zeV{Ct2Uu8SVE5}v`}GXNTE~Rr__n>=MrpEV9e+P1O7FO8vp0|UC*oD$LIbb!?rZ~< zXHs=TM_m9K!|7cHH`*86r&tK5wTvT|FM!V^YgT{bs>7#dTV$sI4SPSEDop69wWba7 zub04Zo7|CDdT?WSgST-i;MCqtF|gISx&tU(nJ#{D+01)5%T3y$j(QX(%k2zV z3Ie7{M?JUvMxM6kKdsMIH`_*P3C?~rvig=pEh;IIs(niV`f;sTBO0BOtFPpL_-LkV zW>0C*`p=nUUqeiP@w1S+g*zb3O=}P3THc-!NZvLfgO?SLmc}Rqr-vm=ex7Niv%g4# z+oVN>D!y&-LSkVo7D1P;BpEKrSH*k*>rE?D%oN4KekSAXBv zJjf68jfFC|kCUp-?a&GF4Z+G^7N(1t8wyab$G4Zale6NKX5OXFRySEc9owY>yaj{wR_= zXj;(>M2GClq73s3=b^#S#`!9RhBKLsao&eQO9IcB3N&0#OCR_+Dm) z@{A`Mb5at4fx1dNNfhn?+`1>eNUq>*34lw;@e?w7U>O=VbJcc2EcHUBW;aM`1z4)<*09AVKUfOfJG|P0j zc}&zd1V%p{1797%Zvi(yZmAk?xjR5k=vGPbR=`)ab_!u2=Ud`a$4v*BpONTj7o7>F z0QGxo*T?Uy9bWb3N7cnHaWgGOzjnJ$B)`!1B}=$cl%3#2492S*8jQa~Ima@6x4gvC z`Vi3i4*XaL2;i3asf}e+r=h@!1Hf6hHbh>ku&; z`n_Rm;FAVD)xs>zhQQFZSkRozx(aSp&BA_)T36<3Y#3=ru%507f-CLBp0MrFo<@Id zB3(Cme0Ix*_EwiWk?h^_4+4HeJx+vmJl40}Z021VI1uo4-X1N>cV^X2b7>)o3zTuqzBD6W! zT*JqqYZ6iC!~0D=zI#%=zM(dj+CVK_Exzqa5NLCE70QSUCu zEJy#Hmo3O4D)T1-;Qozy#+;5XA^A;RK}AdtFt+qS~y@^$_1 zKj*#01kSQG;-8dyd7dij46pju8;D}14+NgY;CraT^nO-;pI90VCz_xbdbB*hIGhz1 z=~gkeH>2?9uwVl0`sHswPpfdh^L{knUZ0h%!Sh*zj+jzZ5b|vA;diwK@4-#gGSGn& zMdV4p@TfFs?LHx1MVa((e$0H?b|n%^fDG4!=|E?RKm!hH*pAwDYn|(sovci8{0r18 zOMe!Hc5$xJGZFbidA{$_x@NAU*)FqAibQX0g0!{iEuyC&gU;EpM) ztLNWhy{iE27-+@RYY07g)1NFty1|M^^&W?IA4Yik=e?`0kY^IMv9tV32-j!Ckl8;} zQ%Z8@{B-K`J3E!)<{tzWUK^I;*t6B9884JS;_C~H`D|7wIp=(-fn|%&rM0}_vt4=K z)DX9IlWMjz%RK3=?DZ&pZDFCP?xcvfKyuieGz`R|#JLCxP-cq+8`MQ+Czb-*ktCk9 zz*+|@q;aB6j4_?I??X#_$-E+U|FYUDaLe?}L!vtE;EiTYj7EgISCh`EIUMTOM1&TN zZC9eistC!SH|82?k9^Eq{M@0Lrx;zD*&<9&fLAw@{KK7L!LWOlr}+7&tfwWOeoNBA z^!MzE^!T(3-m(&PxNT%C+5B(_(#BiT!c@rhm+3`!m0|G*tc!GMv-eVUlHC%BK*2GI zDr(~Qy7|kyEq1xwX-C74E#|jUpvh{j$_%=5Cprc*OJyUe!IIz2P9tR;T6vb4%!TnE=slh77I|=+IAqvCAF!i7sjJ*VG-8U$qozpyTv*}9 zp9Vi_&j3%77teyc`BN~~yv6d$RyUP6a|tsm7RRtzrDr;6VHs-Bj(Cj;4^;N^l4OVGUnK53s zMN8-OPbkk4ny4vsgS$JBG<)EKe#||&$7m?}M^*!;9DmUH*?ZD?**BBVwI4|Fvh!k( za#VjFuG82dI$OUaxP0pIn};6G$pLLCBSk8uGUzn{M0w!{Scxt6;SW0l1ig%vNuSCR zeA7n}^EREwHseh=GHRDtI18Qc(}m-{9WsWdu^dg{L~fh3v%emZrTq zm$M5AkfV=l31;{x8)H!(^7D*k;^ubhVwX5)oL({3H&{_9cDJY4 zEpL7vP6xp>|9}~jEx@pyZja0}f=333!Lw|ginu9h+*XMeX@MOs*ZnK!wXjMH{Z~eR zVUf(5m{IsIT5)!mIG%~HF>jh-+tWpzx4>*14$J57_jP`Q)OWx}$uwnQh%2sPkERU< zR)ic~!~lzZof0e0V=&mdhmSsk2m(!;$QU+$)!R@zLiaE^rA4Wc0NF^8?@oOFn&zWd z${k=8`)@VpbLHStLu=bI7#=7+An3Hz7h*EXNK(0C>yr9#@s%WSIYRS`Caq-Rdtg}+!EOB%8Z_0cordMgWx&bHjW zaZ0>pd>M*U8kn?{C36?PYIQFUKce`D&<Q7L^=56M11ENlqchq{Tu{K;Vl#~iW z3Z7!#_4~6BURt>~X++1MFe0=9pG1xqNdM9()`t#lB(c$KI2fHs(@AiIUnu_Qt|Yz# zX0h)JFRJBpDF>nD5VW)UBYLT7oudd0I4!YGWG&GLCXou*yhJ>j`|GDZJO}T=<$bH%VO{H3P(l{TEGuyH z!24KG%JHsQm#B&_e(qrAQElzBU3phZtfVirK2hySHJFW!Vei5q$0d=Vzjzsbc-tK; zdGX#NCuIG&_6L8XAr2(*Qk=6YFVm=xnB#F{#kC$Qz8d$ZX7v;KNjJoqN#wf6Su=WR z-Y=1^#FLR3?Bv-Qu;AIU8DPqgU+|}PZH}K@uNA=j1M~22eb>J5DB!c7v`enA| zLWap`Wv*+PP1%vehy&{d#RBE+2J0*W%852K3FCnxoEh>7AOmz zk8Z!lj5Mov3sI{P>O=^}(v|Iu@$3S+HiY;qtH3vl2I&(9@XA!*ZO z&5V^XqqzgTIm>(%3~F=XHM>3fQx&o8_f_03gPnIvTK>7rB%2L!Z$^)RSH$BE={VBOoeU?09Zg2ep;DC0APid(>t6Kf+$?A81yYBRII`n-qIDD@FPPqT3j5f=t7d#YW% zo*if^NnC8SXHBK_09!2IP!#CtxUS+O-BJUm)@MJDyDOTzy`0Tg$Q= z4W*LkS#WCH()AV;@~G`6e|%34a4v37QGJ=)kTt^zq^HRz`TSI#F8_B8jnaH`Poe{> z4j|rm#cMZDRXJWhb{PJXLe@SqSt!TxB~~Kj{=h^7yZql{U`=WI&VU;7H&LB4kLq1p zPfWkv0ns(HJpaeAJ!Gv(d3ho*GR0FnkM=h}1WIb}w#sE%N@r#CK`Lq4{ph87b!XHL#%AxYAZptpw*K}I4ukoIWjnAmw@XQv7T<^<< z16}`_-PT7637$tVEUlmlFt^`uK0O31^bQHP9<$Z9EJ&ZO-#@R$fmAo?t5^ z{81ScH^+v35Qr<}ijHtx|G~JRCqo(Bp4~9H@sWo*P1xVc(LYlB3wV)T0;f{GwW_XD zUZvH#@U>W?l7E$hqVGG!v9#g}>#={cd?zHIm1iz9JsUPTsMz)c}5CqQnXH` -.. image:: Eqs/angle_mm3.jpg - :align: center +.. math:: -where theta0 is the equilibrium value of the angle, and K is a -prefactor. The anharmonic prefactors have units deg\^(-n), for example --0.014 deg\^(-1), 5.6(10)\^(-5) deg\^(-2), ... + E = K (\theta - \theta_0)^2 \left[ 1 - 0.014(\theta - \theta_0) + 5.6(10)^{-5} (\theta - \theta_0)^2 - 7.0(10)^{-7} (\theta - \theta_0)^3 + 9(10)^{-10} (\theta - \theta_0)^4 \right] + + +where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a +prefactor. The anharmonic prefactors have units :math:`\deg^{-n}`, for example +:math:`-0.014 \deg^{-1}`, :math:`5.6 \cdot 10^{-5} \deg^{-2}`, ... The following coefficients must be defined for each angle type via the :doc:`angle\_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* K (energy/radian\^2) -* theta0 (degrees) +* :math:`K` (energy/radian\^2) +* :math:`\theta_0` (degrees) -Theta0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of K are in energy/radian\^2. +:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians +internally; hence the units of :math:`K` are in energy/radian\^2. Restrictions """""""""""" @@ -58,12 +60,3 @@ Related commands :doc:`angle\_coeff ` **Default:** none - - ----------- - - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/angle_mm3.txt b/doc/txt/angle_mm3.txt deleted file mode 100644 index 9ae032c4ff..0000000000 --- a/doc/txt/angle_mm3.txt +++ /dev/null @@ -1,55 +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 - -angle_style mm3 command :h3 - -[Syntax:] - -angle_style mm3 :pre - -[Examples:] - -angle_style mm3 -angle_coeff 1 100.0 107.0 :pre - -[Description:] - -The {mm3} angle style uses the potential that is anharmonic in the angle -as defined in "(Allinger)"_#mm3-allinger1989 - -:c,image(Eqs/angle_mm3.jpg) - -where theta0 is the equilibrium value of the angle, and K is a -prefactor. The anharmonic prefactors have units deg^(-n), for example --0.014 deg^(-1), 5.6(10)^(-5) deg^(-2), ... - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy/radian^2) -theta0 (degrees) :ul - -Theta0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of K are in energy/radian^2. - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -USER_YAFF package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] none - -:line - From 5d6137fd691af371761a4a8ee2a811765574915d Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 15 Nov 2019 10:55:06 -0500 Subject: [PATCH 26/64] Update docs: angle_quartic --- doc/src/Eqs/angle_quartic.jpg | Bin 5273 -> 0 bytes doc/src/Eqs/angle_quartic.tex | 9 ---- doc/src/angle_quartic.rst | 41 +++++++++--------- doc/txt/angle_quartic.txt | 77 ---------------------------------- 4 files changed, 19 insertions(+), 108 deletions(-) delete mode 100644 doc/src/Eqs/angle_quartic.jpg delete mode 100644 doc/src/Eqs/angle_quartic.tex delete mode 100644 doc/txt/angle_quartic.txt diff --git a/doc/src/Eqs/angle_quartic.jpg b/doc/src/Eqs/angle_quartic.jpg deleted file mode 100644 index 744ce7a35ff5dcc4aa7079bc5234574762939fa3..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 5273 zcmb`LS5OlSvxb9okQSOs#{>)z{fLN2RX~BzF@T2Rr+`Qa5JY+xq=*ngXd+D#5HNH| zD2h^q&2IU7Cu1>lB1(0c%&qoV`po;%=d z0-yz8q-S7Ypl3V}jEsy-%okah&y9_I}1RYZl8{h2XNK`5C+fz=+7n2MgGsu$1>2=9(({dAN>;`d+_l&*p08 zR)(-JcJj1)7lP8(Z*E1JDSiY7U;t8|y$CX5kPh^ug`||dPn!3q)u~L}FHIG0)n0d) z#)%9zrwEP>os z`%@I0H(lT2d?MPO%`;Z2P%!vrpsZ7ibSt}q?W^gE(Jl)-HhAiWz=^KCp`V_oX6z-0 z{FK!ajG}K%D1r#k>swQKzhB)OqElr>puGDB!ev*E!~jt_f`&ua+oMHK4z&wGa^()ufM+#`K!|A zqfOBAMP{L3p_K%1)Wg;vDGCqT`tXFi@h#VQ5UQ*49a~+BJLxi$0~g1C7e*lQ@+7G; z5R+NWB%H$T!Hq|0q=5={hEw5YdE4wi^TbFpa{*+XFb-+B-yT{sfOqoPo8b)LyxF=P z7;-JTFl}!NOjUkGvb)nQa!@i?zO8Xs;_}=j#s+prX`x<%1g~#3OOzBcW>oGs+UHB0 z^b=DqLj+MbfYUGr=|CNaUZ3XpPQ7^o-A@|o!N!=&u0&|w zf{fX49zGWWNWPZ!T^#7L@P7Hi7W*`mO1~B*KurK9OS~|J_u(;Yh~x`wx(qy1^$<8h zjU-)e?WQ@+`76~PdL2@lc#n%|5IBRfN571XX8UCnvr&{*!gBiswxkkuS81?4kZ;bY z;J#sTptbQKM%QF?4<6Rf&zd^9VR2MayHV45>s>UPpU)knN4jwQ`^_WJ7OQZKNH1pS z)$Yo=PvgHS`a{PWlvioKwtF(!KJJ%HGn zMHvHx?BCa(P0xZPr)oSe-9IUF1y=I+{W6MXCavNczs z9%Np%4U~Pg?sQ6;Jy3GfwPAZu=qbj_#^WzvLc!z_fK@H*lW5{R?{>+Dv2CG`m$fO~ zkT$b+30BoXh0KFKfZtFNuJpHUieuW(dfAl`GuY*d%kii4O%5$ueuF1?fj=g_h^x81f6KYjVSlYns$n+ea*38(dy3lW(`tpCXg@~O8*gTT zj=O)aZ4kGHn_8O&P+?A?lS1~2&mOo3BAw_U44Fw2T}c(j>C(^Zir!M0?@y_n0d9CC z*ZVYdpa^1}0 zsWmRvQ*=fQbNtO;k6CD^XEL|_?$GS3eVYz}JV`@Q5}@U0fR9PYNXTPm+wDu73uz%n zzq{OS)on>o4hV(X^lbmIT`WGb@ycah!Q`$!$q>+CmfR;?EAP}M3#>t%uyfj*`aNB) zxy&@+c*0WAsB=sZ+QO}J4x0{^n>VqaAV{}Ehk579O7ol4=7V%Cw+BU$w4j%iDNEYI z!&$3&UI(j@N0c}bV|#;FU#$moyv?#ZR8~{b#nhrNa@nxCxUNKHeXPj+kpu=i)PkR8O4ESVV(SL*Gr)^547p`tWg ztTvpt2YOE{x(;0WvL_Auss!(M3CiGu9!XqtAWcC|3fr0xL4ka)51n(x zOX74$Ps=A>yP;Y|uNwxb;?;=3psTO7mMQ*!%)x6DUV`oE>&ua;;s)K)GVB@S)($KV zWmTuKn7q?fOM)zPA4?f>Y=x$+IW00Y>>SZ-oC~@}})y4SCqwi$=R1O;?@hP6NS*;*eg!biWpSB&Y@m(8%!L`?DL{ z>EBlO%Bjj8NPi%}{X3?BJq%yi3aP2hZk@^1a}RE~ZBbV=!@HUL=2NDQa(7bsl(l4+=k!;_9x0*eMBk_-7~v_k2QU^V1^JQDnk^wh;5^@?=3 zt+$;6i-t$aV90%oX1F<5=~&X?4LEIt%qYh9NL%HFWg>R_H7dIiSYq!V@xFUUHs!W+ zo4-x?Ea^GzCXS=m5CW)=0`PKb&P^xXiAs0S?(D? zS58vXc+3FW7o_rf`QZ_N?y}ifUAg+o#MTw$;{g7dEPthwpXC_7)?cKsxpVSv0y@5rpHNQ>W{nMQHMtH_lv(?iIzsu+|#i?LB_m1GzK6-^Cvx0~=?6hSC?NHxUL-4?QmiEq(vDZbDHf z1DUh}%!AyMrkRDn%Pbf%w(_nA<57I!ZZ&TsvqdV~(>hLPsw*V}R`s2n)OKg75j%ZT zjmU#l#;KnJ=PxgJL*ZZ;>9%v(TYpaYt9_fyVhc8L9(SjVkZm-L9Cq(_nEr?qbgXN; zU+bAD`3!@|y)J?B*K*Me6Ea0vhxN0HhqE$OQ%P=|3+ah(r4Vs?wWi~hMOsB3z7*FO zTVQInfaW3HB>tKb@2F+LJ)oV};rQg0;0d4FWI zPMmf>{_IU2cCoWqitl-q5*up{bD{oJ0cF;0B0XA;8>Jb}q0mC&s4W9=2eYLw|{7~5^ywSH>4fSk)y<@Kjt}11Ixtb}>D=CLS z{+NC7V3a0XFz#<)0Q2S;^fgi#JYnqpIl|F+h$U_SVmNZ?>tc2IImeA(?h-9#k)36G zA6{NPcwPYV6}%>+9|>U>CTAXD_%e^ejXxD-G3=ZHzQo1eH0~x@nYzY4s_aHPqupNm zw4_9Q!lblcb6-#!3`funA0L|~@q$+P%liv5CN|81`{LxTW!KG}mr(GKTIXubcck+TaAA-pPFT1@u55M}-T=t=dy#Xj+%a@uu$k zfNRS937Y8L8>>M2`AEyK-CvnLFlJ2=r%I=e=Yr9d+HY9T+#D3Gc{4bGLH|Y_c8C}! zaYQN=f~EW0s?4}N-%vvoBf6sSvzD~?w*|bGFYF($AHe=3*KdHD(Z812O{vZAIOnzt zwK|b$tMH4Td^4-R_)@n!pJj*^d<&RLEiI*pIPNkWJC{~{(*G)tsxw5?!rW2h96AH5 z$@cF3zYj9u_fA&7n3kz3_wAbxGL77nq>GEp?=!{p>Rp}j;NRiilu^`KY!4K_~@M zcjD`(51nRlJ{C3n6R$?r@3@gPm*!Ppi}_ExXT%x2dsVgx(RWiCn+^}v;I?w`*WFo1 zs*9zKRs_n&6)_A4wW6D;isj^jP-NflLj)$^^+%b~gx-3}>gOt>LNEE&_TQcmmHx7IZ% zXpW;seLP%u7LD~tkgr6wuVFU&c-dZ#NFnvZzI_seaDNzOctLLJ`>2wQ%M|@t&sG|| zF5kN&*L&*deFk{>P^m{A)rL6E(fgwMgq8g;a>aTbJw-lgE}mKRX|r1YvShAN>fNuX z&a0?NwpxE2$hwnagq?8W1k0H2>b^n&jh`-hF|AUTqGVSh0w)s$MO$*(4T(-BbBZpM zfu5Y>nl}S8k$(J8|37LgHTCOM!3Y1ieXRFL+gn*i*VK9-vmc`t^L63EF3mC!R=CX( zfIbGUI}$XlmW#3XvXdg^*+PHFpt?4O#yG(dT($GF0sce#{|g{w8nef4T;^0Qwt4?o z&W*gH-kchAMt8SV|JD2Z*|2Q&sXm*EU9;Wcrf+g^%?qj~T<@(lxs&N8A*{-(xQBM<)B_<9 z5ZBzf_1ODz2@%&|g)YD-=G&m0&?La#Y!zsA1i4qr{`{7>Lo=kIH$icBkp99y34CP} zP^gnt6dXx0!@W7#xGN4&rJUGRQeMhr<9=Fkbf6QNc!iGw8tgxP!s@uW$-*rf!mY$` zNp=L;lo7W`mpF3Y)qEA%pk+3=&&Ro*!V&)IA$=q+c(JY!9^JW?T_xZi6;mMrgI!TmrrjuT(b1>2680;@v00LI1@bii@x!nYRz?>Y zBo5~@3IG8V_0)G)*ZW*_f=y=~+uRlFmO|gdI-C{U_ZYeUCVt3ELS8Q8z3avZ#HY zzfqj9n%anyK}+95qU-)V8+TRG1XcmAiMtTQ`>S5I*U^(s6_{ bV}-_^gxuO3vCkY`{;$%s|38=uIUD;Qp^F_J diff --git a/doc/src/Eqs/angle_quartic.tex b/doc/src/Eqs/angle_quartic.tex deleted file mode 100644 index ff9ff9a7dc..0000000000 --- a/doc/src/Eqs/angle_quartic.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4 -$$ - -\end{document} diff --git a/doc/src/angle_quartic.rst b/doc/src/angle_quartic.rst index 88773bbca8..104c0be802 100644 --- a/doc/src/angle_quartic.rst +++ b/doc/src/angle_quartic.rst @@ -1,16 +1,16 @@ -.. index:: angle\_style quartic +.. index:: angle_style quartic -angle\_style quartic command -============================ +angle_style quartic command +=========================== -angle\_style quartic/omp command -================================ +angle_style quartic/omp command +=============================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style quartic @@ -18,7 +18,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style quartic angle_coeff 1 129.1948 56.8726 -25.9442 -14.2221 @@ -28,24 +28,26 @@ Description The *quartic* angle style uses the potential -.. image:: Eqs/angle_quartic.jpg - :align: center +.. math:: -where theta0 is the equilibrium value of the angle, and K is a -prefactor. Note that the usual 1/2 factor is included in K. + E = K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4 + + +where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a +prefactor. Note that the usual 1/2 factor is included in :math:`K`. The following coefficients must be defined for each angle type via the :doc:`angle\_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* theta0 (degrees) -* K2 (energy/radian\^2) -* K3 (energy/radian\^3) -* K4 (energy/radian\^4) +* :math:`\theta_0` (degrees) +* :math:`K_2` (energy/radian\^2) +* :math:`K_3` (energy/radian\^3) +* :math:`K_4` (energy/radian\^4) -Theta0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of K are in energy/radian\^2. +:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians +internally; hence the units of :math:`K` are in energy/radian\^2. ---------- @@ -87,8 +89,3 @@ Related commands :doc:`angle\_coeff ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/angle_quartic.txt b/doc/txt/angle_quartic.txt deleted file mode 100644 index b20a06eb8d..0000000000 --- a/doc/txt/angle_quartic.txt +++ /dev/null @@ -1,77 +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 - -angle_style quartic command :h3 -angle_style quartic/omp command :h3 - -[Syntax:] - -angle_style quartic :pre - -[Examples:] - -angle_style quartic -angle_coeff 1 129.1948 56.8726 -25.9442 -14.2221 :pre - -[Description:] - -The {quartic} angle style uses the potential - -:c,image(Eqs/angle_quartic.jpg) - -where theta0 is the equilibrium value of the angle, and K is a -prefactor. Note that the usual 1/2 factor is included in K. - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -theta0 (degrees) -K2 (energy/radian^2) -K3 (energy/radian^3) -K4 (energy/radian^4) :ul - -Theta0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of K are in energy/radian^2. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -USER_MISC package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] none From a20a27880d0f8577638e37237426d536aad8442d Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 15 Nov 2019 11:05:23 -0500 Subject: [PATCH 27/64] Update docs: angle_sdk --- doc/src/angle_sdk.rst | 37 +++++++++---------- doc/txt/angle_sdk.txt | 83 ------------------------------------------- 2 files changed, 17 insertions(+), 103 deletions(-) delete mode 100644 doc/txt/angle_sdk.txt diff --git a/doc/src/angle_sdk.rst b/doc/src/angle_sdk.rst index 01342ad8d4..0af22a5372 100644 --- a/doc/src/angle_sdk.rst +++ b/doc/src/angle_sdk.rst @@ -1,16 +1,16 @@ -.. index:: angle\_style sdk +.. index:: angle_style sdk -angle\_style sdk command -======================== +angle_style sdk command +======================= -angle\_style sdk/omp command -============================ +angle_style sdk/omp command +=========================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style sdk @@ -20,7 +20,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style sdk angle_coeff 1 300.0 107.0 @@ -30,25 +30,27 @@ Description The *sdk* angle style is a combination of the harmonic angle potential, -.. image:: Eqs/angle_harmonic.jpg - :align: center +.. math:: -where theta0 is the equilibrium value of the angle and K a prefactor, + E = K (\theta - \theta_0)^2 + + +where :math:`\theta_0` is the equilibrium value of the angle and :math:`K` a prefactor, with the *repulsive* part of the non-bonded *lj/sdk* pair style between the atoms 1 and 3. This angle potential is intended for coarse grained MD simulations with the CMM parameterization using the :doc:`pair\_style lj/sdk `. Relative to the pair\_style *lj/sdk*\ , however, the energy is shifted by *epsilon*\ , to avoid sudden -jumps. Note that the usual 1/2 factor is included in K. +jumps. Note that the usual 1/2 factor is included in :math:`K`. The following coefficients must be defined for each angle type via the :doc:`angle\_coeff ` command as in the example above: -* K (energy/radian\^2) -* theta0 (degrees) +* :math:`K` (energy/radian\^2) +* :math:`\theta_0` (degrees) -Theta0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of K are in energy/radian\^2. +:math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians +internally; hence the units of :math:`K` are in energy/radian\^2. The also required *lj/sdk* parameters will be extracted automatically from the pair\_style. @@ -93,8 +95,3 @@ Related commands :doc:`pair\_style lj/sdk/coul/long ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/angle_sdk.txt b/doc/txt/angle_sdk.txt deleted file mode 100644 index 9382d560d3..0000000000 --- a/doc/txt/angle_sdk.txt +++ /dev/null @@ -1,83 +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 - -angle_style sdk command :h3 -angle_style sdk/omp command :h3 - -[Syntax:] - -angle_style sdk :pre -angle_style sdk/omp :pre - -[Examples:] - -angle_style sdk -angle_coeff 1 300.0 107.0 :pre - -[Description:] - -The {sdk} angle style is a combination of the harmonic angle potential, - -:c,image(Eqs/angle_harmonic.jpg) - -where theta0 is the equilibrium value of the angle and K a prefactor, -with the {repulsive} part of the non-bonded {lj/sdk} pair style -between the atoms 1 and 3. This angle potential is intended for -coarse grained MD simulations with the CMM parameterization using the -"pair_style lj/sdk"_pair_sdk.html. Relative to the pair_style -{lj/sdk}, however, the energy is shifted by {epsilon}, to avoid sudden -jumps. Note that the usual 1/2 factor is included in K. - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above: - -K (energy/radian^2) -theta0 (degrees) :ul - -Theta0 is specified in degrees, but LAMMPS converts it to radians -internally; hence the units of K are in energy/radian^2. -The also required {lj/sdk} parameters will be extracted automatically -from the pair_style. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -USER-CGSDK package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html, "angle_style -harmonic"_angle_harmonic.html, "pair_style lj/sdk"_pair_sdk.html, -"pair_style lj/sdk/coul/long"_pair_sdk.html - -[Default:] none From e017e7d447a891ae38d6837147f0a8450e31fc63 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 15 Nov 2019 11:13:07 -0500 Subject: [PATCH 28/64] Update docs: angle_zero --- doc/src/angle_zero.rst | 27 ++++++++++------------- doc/txt/angle_zero.txt | 49 ------------------------------------------ 2 files changed, 11 insertions(+), 65 deletions(-) delete mode 100644 doc/txt/angle_zero.txt diff --git a/doc/src/angle_zero.rst b/doc/src/angle_zero.rst index e6b485bc95..e5dab4e3a0 100644 --- a/doc/src/angle_zero.rst +++ b/doc/src/angle_zero.rst @@ -1,13 +1,13 @@ -.. index:: angle\_style zero +.. index:: angle_style zero -angle\_style zero command -========================= +angle_style zero command +======================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style zero *nocoeff* @@ -15,12 +15,12 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style zero angle_style zero nocoeff - angle_coeff \* - angle_coeff \* 120.0 + angle_coeff * + angle_coeff * 120.0 Description """"""""""" @@ -32,14 +32,14 @@ other commands. As an example, the :doc:`compute angle/local ` command can be used to compute the theta values for the list of triplets of angle atoms listed in the data file read by the -:doc:`read\_data ` command. If no angle style is defined, +:doc:`read_data ` command. If no angle style is defined, this command cannot be used. The optional *nocoeff* flag allows to read data files with AngleCoeff -section for any angle style. Similarly, any angle\_coeff commands +section for any angle style. Similarly, any :doc:`angle_coeff ` commands will only be checked for the angle type number and the rest ignored. -Note that the :doc:`angle\_coeff ` command must be used for +Note that the :doc:`angle_coeff ` command must be used for all angle types. If specified, there can be only one value, which is going to be used to assign an equilibrium angle, e.g. for use with :doc:`fix shake `. @@ -51,11 +51,6 @@ Restrictions Related commands """""""""""""""" -:doc:`angle\_style none ` +:doc:`angle_style none ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/angle_zero.txt b/doc/txt/angle_zero.txt deleted file mode 100644 index c6c1958ec8..0000000000 --- a/doc/txt/angle_zero.txt +++ /dev/null @@ -1,49 +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 - -angle_style zero command :h3 - -[Syntax:] - -angle_style zero {nocoeff} :pre - -[Examples:] - -angle_style zero -angle_style zero nocoeff -angle_coeff * -angle_coeff * 120.0 :pre - -[Description:] - -Using an angle style of zero means angle forces and energies are not -computed, but the geometry of angle triplets is still accessible to -other commands. - -As an example, the "compute angle/local"_compute_angle_local.html -command can be used to compute the theta values for the list of -triplets of angle atoms listed in the data file read by the -"read_data"_read_data.html command. If no angle style is defined, -this command cannot be used. - -The optional {nocoeff} flag allows to read data files with AngleCoeff -section for any angle style. Similarly, any angle_coeff commands -will only be checked for the angle type number and the rest ignored. - -Note that the "angle_coeff"_angle_coeff.html command must be used for -all angle types. If specified, there can be only one value, which is -going to be used to assign an equilibrium angle, e.g. for use with -"fix shake"_fix_shake.html. - -[Restrictions:] none - -[Related commands:] - -"angle_style none"_angle_none.html - -[Default:] none From fb64068fbcbfaf5e931d5c7fbb032eacbc08c356 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 15 Nov 2019 11:16:47 -0500 Subject: [PATCH 29/64] Update docs: angle_coeff --- doc/src/angle_coeff.rst | 41 +++++++++---------- doc/txt/angle_coeff.txt | 87 ----------------------------------------- 2 files changed, 18 insertions(+), 110 deletions(-) delete mode 100644 doc/txt/angle_coeff.txt diff --git a/doc/src/angle_coeff.rst b/doc/src/angle_coeff.rst index 1e54f69051..5f9a71371a 100644 --- a/doc/src/angle_coeff.rst +++ b/doc/src/angle_coeff.rst @@ -1,13 +1,13 @@ -.. index:: angle\_coeff +.. index:: angle_coeff -angle\_coeff command -==================== +angle_coeff command +=================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_coeff N args @@ -18,11 +18,11 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_coeff 1 300.0 107.0 - angle_coeff \* 5.0 - angle_coeff 2\*10 5.0 + angle_coeff * 5.0 + angle_coeff 2*10 5.0 Description """"""""""" @@ -30,7 +30,7 @@ Description Specify the angle force field coefficients for one or more angle types. The number and meaning of the coefficients depends on the angle style. Angle coefficients can also be set in the data file read by the -:doc:`read\_data ` command or in a restart file. +:doc:`read_data ` command or in a restart file. N can be specified in one of two ways. An explicit numeric value can be used, as in the 1st example above. Or a wild-card asterisk can be @@ -41,18 +41,18 @@ leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N (inclusive). A middle asterisk means all types from m to n (inclusive). -Note that using an angle\_coeff command can override a previous setting +Note that using an :doc:`angle_coeff ` command can override a previous setting for the same angle type. For example, these commands set the coeffs for all angle types, then overwrite the coeffs for just angle type 2: -.. parsed-literal:: +.. code-block:: LAMMPS - angle_coeff \* 200.0 107.0 1.2 + angle_coeff * 200.0 107.0 1.2 angle_coeff 2 50.0 107.0 A line in a data file that specifies angle coefficients uses the exact -same format as the arguments of the angle\_coeff command in an input +same format as the arguments of the :doc:`angle_coeff ` command in an input script, except that wild-card asterisks should not be used since coefficients for all N types must be listed in the file. For example, under the "Angle Coeffs" section of a data file, the line that @@ -63,7 +63,7 @@ corresponds to the 1st example above would be listed as 1 300.0 107.0 -The :doc:`angle\_style class2 ` is an exception to this +The :doc:`angle_style class2 ` is an exception to this rule, in that an additional argument is used in the input script to allow specification of the cross-term coefficients. See its doc page for details. @@ -73,13 +73,13 @@ doc page for details. The list of all angle styles defined in LAMMPS is given on the -:doc:`angle\_style ` doc page. They are also listed in more +:doc:`angle_style ` doc page. They are also listed in more compact form on the :ref:`Commands angle ` doc page. On either of those pages, click on the style to display the formula it computes and its coefficients as specified by the associated -angle\_coeff command. +:doc:`angle_coeff ` command. ---------- @@ -90,8 +90,8 @@ Restrictions This command must come after the simulation box is defined by a -:doc:`read\_data `, :doc:`read\_restart `, or -:doc:`create\_box ` command. +:doc:`read_data `, :doc:`read_restart `, or +:doc:`create_box ` command. An angle style must be defined before any angle coefficients are set, either in the input script or in a data file. @@ -99,11 +99,6 @@ set, either in the input script or in a data file. Related commands """""""""""""""" -:doc:`angle\_style ` +:doc:`angle_style ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/angle_coeff.txt b/doc/txt/angle_coeff.txt deleted file mode 100644 index 5dc9c13381..0000000000 --- a/doc/txt/angle_coeff.txt +++ /dev/null @@ -1,87 +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 - -angle_coeff command :h3 - -[Syntax:] - -angle_coeff N args :pre - -N = angle type (see asterisk form below) -args = coefficients for one or more angle types :ul - -[Examples:] - -angle_coeff 1 300.0 107.0 -angle_coeff * 5.0 -angle_coeff 2*10 5.0 :pre - -[Description:] - -Specify the angle force field coefficients for one or more angle types. -The number and meaning of the coefficients depends on the angle style. -Angle coefficients can also be set in the data file read by the -"read_data"_read_data.html command or in a restart file. - -N can be specified in one of two ways. An explicit numeric value can -be used, as in the 1st example above. Or a wild-card asterisk can be -used to set the coefficients for multiple angle types. This takes the -form "*" or "*n" or "n*" or "m*n". If N = the number of angle types, -then an asterisk with no numeric values means all types from 1 to N. A -leading asterisk means all types from 1 to n (inclusive). A trailing -asterisk means all types from n to N (inclusive). A middle asterisk -means all types from m to n (inclusive). - -Note that using an angle_coeff command can override a previous setting -for the same angle type. For example, these commands set the coeffs -for all angle types, then overwrite the coeffs for just angle type 2: - -angle_coeff * 200.0 107.0 1.2 -angle_coeff 2 50.0 107.0 :pre - -A line in a data file that specifies angle coefficients uses the exact -same format as the arguments of the angle_coeff command in an input -script, except that wild-card asterisks should not be used since -coefficients for all N types must be listed in the file. For example, -under the "Angle Coeffs" section of a data file, the line that -corresponds to the 1st example above would be listed as - -1 300.0 107.0 :pre - -The "angle_style class2"_angle_class2.html is an exception to this -rule, in that an additional argument is used in the input script to -allow specification of the cross-term coefficients. See its -doc page for details. - -:line - -The list of all angle styles defined in LAMMPS is given on the -"angle_style"_angle_style.html doc page. They are also listed in more -compact form on the "Commands angle"_Commands_bond.html#angle doc -page. - -On either of those pages, click on the style to display the formula it -computes and its coefficients as specified by the associated -angle_coeff command. - -:line - -[Restrictions:] - -This command must come after the simulation box is defined by a -"read_data"_read_data.html, "read_restart"_read_restart.html, or -"create_box"_create_box.html command. - -An angle style must be defined before any angle coefficients are -set, either in the input script or in a data file. - -[Related commands:] - -"angle_style"_angle_style.html - -[Default:] none From cdd56cd08f137de0fdc3bcfa8b60ffd44c51064c Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 15 Nov 2019 11:22:25 -0500 Subject: [PATCH 30/64] Update docs: angle_style --- doc/src/angle_style.rst | 33 +++++------- doc/txt/angle_style.txt | 112 ---------------------------------------- 2 files changed, 14 insertions(+), 131 deletions(-) delete mode 100644 doc/txt/angle_style.txt diff --git a/doc/src/angle_style.rst b/doc/src/angle_style.rst index 6d7c70565b..3e22113d85 100644 --- a/doc/src/angle_style.rst +++ b/doc/src/angle_style.rst @@ -1,13 +1,13 @@ -.. index:: angle\_style +.. index:: angle_style -angle\_style command -==================== +angle_style command +=================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style style @@ -17,7 +17,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style harmonic angle_style charmm @@ -29,19 +29,19 @@ Description Set the formula(s) LAMMPS uses to compute angle interactions between triplets of atoms, which remain in force for the duration of the simulation. The list of angle triplets is read in by a -:doc:`read\_data ` or :doc:`read\_restart ` command +:doc:`read_data ` or :doc:`read_restart ` command from a data or restart file. Hybrid models where angles are computed using different angle potentials can be setup using the *hybrid* angle style. The coefficients associated with a angle style can be specified in a -data or restart file or via the :doc:`angle\_coeff ` command. +data or restart file or via the :doc:`angle_coeff ` command. All angle potentials store their coefficient data in binary restart -files which means angle\_style and :doc:`angle\_coeff ` +files which means angle_style and :doc:`angle_coeff ` commands do not need to be re-specified in an input script that -restarts a simulation. See the :doc:`read\_restart ` +restarts a simulation. See the :doc:`read_restart ` command for details on how to do this. The one exception is that angle\_style *hybrid* only stores the list of sub-styles in the restart file; angle coefficients need to be re-specified. @@ -49,7 +49,7 @@ file; angle coefficients need to be re-specified. .. note:: When both an angle and pair style is defined, the - :doc:`special\_bonds ` command often needs to be used to + :doc:`special_bonds ` command often needs to be used to turn off (or weight) the pairwise interaction that would otherwise exist between 3 bonded atoms. @@ -62,11 +62,11 @@ between the 3 atoms in the angle. Here is an alphabetic list of angle styles defined in LAMMPS. Click on the style to display the formula it computes and coefficients -specified by the associated :doc:`angle\_coeff ` command. +specified by the associated :doc:`angle_coeff ` command. Click on the style to display the formula it computes, any additional arguments specified in the angle\_style command, and coefficients -specified by the associated :doc:`angle\_coeff ` command. +specified by the associated :doc:`angle_coeff ` command. There are also additional accelerated pair styles included in the LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. @@ -115,17 +115,12 @@ individual bond potentials tell if it is part of a package. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` Default """"""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/angle_style.txt b/doc/txt/angle_style.txt deleted file mode 100644 index 2f2da678d8..0000000000 --- a/doc/txt/angle_style.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 - -angle_style command :h3 - -[Syntax:] - -angle_style style :pre - -style = {none} or {hybrid} or {charmm} or {class2} or {cosine} or \ - {cosine/squared} or {harmonic} :ul - -[Examples:] - -angle_style harmonic -angle_style charmm -angle_style hybrid harmonic cosine :pre - -[Description:] - -Set the formula(s) LAMMPS uses to compute angle interactions between -triplets of atoms, which remain in force for the duration of the -simulation. The list of angle triplets is read in by a -"read_data"_read_data.html or "read_restart"_read_restart.html command -from a data or restart file. - -Hybrid models where angles are computed using different angle -potentials can be setup using the {hybrid} angle style. - -The coefficients associated with a angle style can be specified in a -data or restart file or via the "angle_coeff"_angle_coeff.html command. - -All angle potentials store their coefficient data in binary restart -files which means angle_style and "angle_coeff"_angle_coeff.html -commands do not need to be re-specified in an input script that -restarts a simulation. See the "read_restart"_read_restart.html -command for details on how to do this. The one exception is that -angle_style {hybrid} only stores the list of sub-styles in the restart -file; angle coefficients need to be re-specified. - -NOTE: When both an angle and pair style is defined, the -"special_bonds"_special_bonds.html command often needs to be used to -turn off (or weight) the pairwise interaction that would otherwise -exist between 3 bonded atoms. - -In the formulas listed for each angle style, {theta} is the angle -between the 3 atoms in the angle. - -:line - -Here is an alphabetic list of angle styles defined in LAMMPS. Click on -the style to display the formula it computes and coefficients -specified by the associated "angle_coeff"_angle_coeff.html command. - -Click on the style to display the formula it computes, any additional -arguments specified in the angle_style command, and coefficients -specified by the associated "angle_coeff"_angle_coeff.html command. - -There are also additional accelerated pair styles included in the -LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. -The individual style names on the "Commands -angle"_Commands_bond.html#angle doc page are followed by one or more -of (g,i,k,o,t) to indicate which accelerated styles exist. - -"none"_angle_none.html - turn off angle interactions -"zero"_angle_zero.html - topology but no interactions -"hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul - -"charmm"_angle_charmm.html - CHARMM angle -"class2"_angle_class2.html - COMPASS (class 2) angle -"class2/p6"_angle_class2.html - COMPASS (class 2) angle expanded to 6th order -"cosine"_angle_cosine.html - angle with cosine term -"cosine/buck6d"_angle_cosine_buck6d.html - same as cosine with Buckingham term between 1-3 atoms -"cosine/delta"_angle_cosine_delta.html - angle with difference of cosines -"cosine/periodic"_angle_cosine_periodic.html - DREIDING angle -"cosine/shift"_angle_cosine_shift.html - angle cosine with a shift -"cosine/shift/exp"_angle_cosine_shift_exp.html - cosine with shift and exponential term in spring constant -"cosine/squared"_angle_cosine_squared.html - angle with cosine squared term -"cross"_angle_cross.html - cross term coupling angle and bond lengths -"dipole"_angle_dipole.html - angle that controls orientation of a point dipole -"fourier"_angle_fourier.html - angle with multiple cosine terms -"fourier/simple"_angle_fourier_simple.html - angle with a single cosine term -"harmonic"_angle_harmonic.html - harmonic angle -"mm3"_angle_mm3.html - anharmonic angle -"quartic"_angle_quartic.html - angle with cubic and quartic terms -"sdk"_angle_sdk.html - harmonic angle with repulsive SDK pair style between 1-3 atoms -"table"_angle_table.html - tabulated by angle :ul - -:line - -[Restrictions:] - -Angle styles can only be set for atom_styles that allow angles to be -defined. - -Most angle styles are part of the MOLECULE package. They are only -enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. The doc pages for -individual bond potentials tell if it is part of a package. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] - -angle_style none :pre From 10f98e3f109b04e457cad9fe0f96431ccd67f6d5 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 15 Nov 2019 11:42:02 -0500 Subject: [PATCH 31/64] Update docs: angle_none --- doc/src/angle_none.rst | 24 ++++++++++-------------- doc/txt/angle_none.txt | 34 ---------------------------------- 2 files changed, 10 insertions(+), 48 deletions(-) delete mode 100644 doc/txt/angle_none.txt diff --git a/doc/src/angle_none.rst b/doc/src/angle_none.rst index a558096211..e848391932 100644 --- a/doc/src/angle_none.rst +++ b/doc/src/angle_none.rst @@ -1,13 +1,13 @@ -.. index:: angle\_style none +.. index:: angle_style none -angle\_style none command -========================= +angle_style none command +======================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style none @@ -15,7 +15,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style none @@ -24,23 +24,19 @@ Description Using an angle style of none means angle forces and energies are not computed, even if triplets of angle atoms were listed in the data file -read by the :doc:`read\_data ` command. +read by the :doc:`read_data ` command. -See the :doc:`angle\_style zero ` command for a way to +See the :doc:`angle_style zero ` command for a way to calculate angle statistics, but compute no angle interactions. Restrictions """""""""""" - none + +none Related commands """""""""""""""" -:doc:`angle\_style zero ` +:doc:`angle_style zero ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/angle_none.txt b/doc/txt/angle_none.txt deleted file mode 100644 index 1eca5cbbec..0000000000 --- a/doc/txt/angle_none.txt +++ /dev/null @@ -1,34 +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 - -angle_style none command :h3 - -[Syntax:] - -angle_style none :pre - -[Examples:] - -angle_style none :pre - -[Description:] - -Using an angle style of none means angle forces and energies are not -computed, even if triplets of angle atoms were listed in the data file -read by the "read_data"_read_data.html command. - -See the "angle_style zero"_angle_zero.html command for a way to -calculate angle statistics, but compute no angle interactions. - -[Restrictions:] none - -[Related commands:] - -"angle_style zero"_angle_zero.html - -[Default:] none From 71a4755a8e87c25f76700aab1331044410407c8f Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 15 Nov 2019 11:48:00 -0500 Subject: [PATCH 32/64] Update docs: angle_table --- doc/src/angle_table.rst | 29 +++---- doc/txt/angle_table.txt | 166 ---------------------------------------- 2 files changed, 12 insertions(+), 183 deletions(-) delete mode 100644 doc/txt/angle_table.txt diff --git a/doc/src/angle_table.rst b/doc/src/angle_table.rst index 8d50ff7fe1..f63cf167d9 100644 --- a/doc/src/angle_table.rst +++ b/doc/src/angle_table.rst @@ -1,16 +1,16 @@ -.. index:: angle\_style table +.. index:: angle_style table -angle\_style table command -========================== +angle_style table command +========================= -angle\_style table/omp command -============================== +angle_style table/omp command +============================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style table style N @@ -21,7 +21,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS angle_style table linear 1000 angle_coeff 3 file.table ENTRY1 @@ -31,7 +31,7 @@ Description Style *table* creates interpolation tables of length *N* from angle potential and derivative values listed in a file(s) as a function of -angle The files are read by the :doc:`angle\_coeff ` +angle The files are read by the :doc:`angle_coeff ` command. The interpolation tables are created by fitting cubic splines to the @@ -50,7 +50,7 @@ find the appropriate set of coefficients which are used to evaluate a cubic polynomial which computes the energy or derivative. The following coefficients must be defined for each angle type via the -:doc:`angle\_coeff ` command as in the example above. +:doc:`angle_coeff ` command as in the example above. * filename * keyword @@ -85,13 +85,13 @@ A section begins with a non-blank line whose 1st character is not a between sections. The first line begins with a keyword which identifies the section. The line can contain additional text, but the initial text must match the argument specified in the -:doc:`angle\_coeff ` command. The next line lists (in any +:doc:`angle_coeff ` command. The next line lists (in any order) one or more parameters for the table. Each parameter is a keyword followed by one or more numeric values. The parameter "N" is required and its value is the number of table entries that follow. Note that this may be different than the *N* -specified in the :doc:`angle\_style table ` command. Let +specified in the :doc:`angle_style table ` command. Let Ntable = *N* in the angle\_style command, and Nfile = "N" in the tabulated file. What LAMMPS does is a preliminary interpolation by creating splines using the Nfile tabulated values as nodal points. It @@ -176,11 +176,6 @@ for more info. Related commands """""""""""""""" -:doc:`angle\_coeff ` +:doc:`angle_coeff ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/angle_table.txt b/doc/txt/angle_table.txt deleted file mode 100644 index 61c987f587..0000000000 --- a/doc/txt/angle_table.txt +++ /dev/null @@ -1,166 +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 - -angle_style table command :h3 -angle_style table/omp command :h3 - -[Syntax:] - -angle_style table style N :pre - -style = {linear} or {spline} = method of interpolation -N = use N values in table :ul - -[Examples:] - -angle_style table linear 1000 -angle_coeff 3 file.table ENTRY1 :pre - -[Description:] - -Style {table} creates interpolation tables of length {N} from angle -potential and derivative values listed in a file(s) as a function of -angle The files are read by the "angle_coeff"_angle_coeff.html -command. - -The interpolation tables are created by fitting cubic splines to the -file values and interpolating energy and derivative values at each of -{N} angles. During a simulation, these tables are used to interpolate -energy and force values on individual atoms as needed. The -interpolation is done in one of 2 styles: {linear} or {spline}. - -For the {linear} style, the angle is used to find 2 surrounding table -values from which an energy or its derivative is computed by linear -interpolation. - -For the {spline} style, a cubic spline coefficients are computed and -stored at each of the {N} values in the table. The angle is used to -find the appropriate set of coefficients which are used to evaluate a -cubic polynomial which computes the energy or derivative. - -The following coefficients must be defined for each angle type via the -"angle_coeff"_angle_coeff.html command as in the example above. - -filename -keyword :ul - -The filename specifies a file containing tabulated energy and -derivative values. The keyword specifies a section of the file. The -format of this file is described below. - -:line - -The format of a tabulated file is as follows (without the -parenthesized comments): - -# Angle potential for harmonic (one or more comment or blank lines) :pre - -HAM (keyword is the first text on line) -N 181 FP 0 0 EQ 90.0 (N, FP, EQ parameters) - (blank line) -N 181 FP 0 0 (N, FP parameters) -1 0.0 200.5 2.5 (index, angle, energy, derivative) -2 1.0 198.0 2.5 -... -181 180.0 0.0 0.0 :pre - -A section begins with a non-blank line whose 1st character is not a -"#"; blank lines or lines starting with "#" can be used as comments -between sections. The first line begins with a keyword which -identifies the section. The line can contain additional text, but the -initial text must match the argument specified in the -"angle_coeff"_angle_coeff.html command. The next line lists (in any -order) one or more parameters for the table. Each parameter is a -keyword followed by one or more numeric values. - -The parameter "N" is required and its value is the number of table -entries that follow. Note that this may be different than the {N} -specified in the "angle_style table"_angle_style.html command. Let -Ntable = {N} in the angle_style command, and Nfile = "N" in the -tabulated file. What LAMMPS does is a preliminary interpolation by -creating splines using the Nfile tabulated values as nodal points. It -uses these to interpolate as needed to generate energy and derivative -values at Ntable different points. The resulting tables of length -Ntable are then used as described above, when computing energy and -force for individual angles and their atoms. This means that if you -want the interpolation tables of length Ntable to match exactly what -is in the tabulated file (with effectively no preliminary -interpolation), you should set Ntable = Nfile. - -The "FP" parameter is optional. If used, it is followed by two values -fplo and fphi, which are the 2nd derivatives at the innermost and -outermost angle settings. These values are needed by the spline -construction routines. If not specified by the "FP" parameter, they -are estimated (less accurately) by the first two and last two -derivative values in the table. - -The "EQ" parameter is also optional. If used, it is followed by a the -equilibrium angle value, which is used, for example, by the "fix -shake"_fix_shake.html command. If not used, the equilibrium angle is -set to 180.0. - -Following a blank line, the next N lines list the tabulated values. -On each line, the 1st value is the index from 1 to N, the 2nd value is -the angle value (in degrees), the 3rd value is the energy (in energy -units), and the 4th is -dE/d(theta) (also in energy units). The 3rd -term is the energy of the 3-atom configuration for the specified -angle. The last term is the derivative of the energy with respect to -the angle (in degrees, not radians). Thus the units of the last term -are still energy, not force. The angle values must increase from one -line to the next. The angle values must also begin with 0.0 and end -with 180.0, i.e. span the full range of possible angles. - -Note that one file can contain many sections, each with a tabulated -potential. LAMMPS reads the file section by section until it finds -one that matches the specified keyword. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restart info:] - -This angle style writes the settings for the "angle_style table" -command to "binary restart files"_restart.html, so a angle_style -command does not need to specified in an input script that reads a -restart file. However, the coefficient information is not stored in -the restart file, since it is tabulated in the potential files. Thus, -angle_coeff commands do need to be specified in the restart input -script. - -[Restrictions:] - -This angle style can only be used if LAMMPS was built with the -MOLECULE package. See the "Build package"_Build_package.html doc page -for more info. - -[Related commands:] - -"angle_coeff"_angle_coeff.html - -[Default:] none From 7e58920fe37c1224d9912a56687c3437b172009f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 14 Nov 2019 12:35:50 -0500 Subject: [PATCH 33/64] move developer's guide tex sources back to src/Developer --- doc/{txt => src}/Developer/.gitignore | 0 doc/{txt => src}/Developer/classes.fig | 0 doc/{txt => src}/Developer/classes.pdf | Bin doc/{txt => src}/Developer/developer.tex | 0 4 files changed, 0 insertions(+), 0 deletions(-) rename doc/{txt => src}/Developer/.gitignore (100%) rename doc/{txt => src}/Developer/classes.fig (100%) rename doc/{txt => src}/Developer/classes.pdf (100%) rename doc/{txt => src}/Developer/developer.tex (100%) diff --git a/doc/txt/Developer/.gitignore b/doc/src/Developer/.gitignore similarity index 100% rename from doc/txt/Developer/.gitignore rename to doc/src/Developer/.gitignore diff --git a/doc/txt/Developer/classes.fig b/doc/src/Developer/classes.fig similarity index 100% rename from doc/txt/Developer/classes.fig rename to doc/src/Developer/classes.fig diff --git a/doc/txt/Developer/classes.pdf b/doc/src/Developer/classes.pdf similarity index 100% rename from doc/txt/Developer/classes.pdf rename to doc/src/Developer/classes.pdf diff --git a/doc/txt/Developer/developer.tex b/doc/src/Developer/developer.tex similarity index 100% rename from doc/txt/Developer/developer.tex rename to doc/src/Developer/developer.tex From 334a74830d85c7f8b1f6b52fa4733d0e6d7055c6 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 15 Nov 2019 12:48:43 -0500 Subject: [PATCH 34/64] Fix equations --- doc/src/angle_class2.rst | 8 ++++---- doc/src/angle_dipole.rst | 4 ++-- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/doc/src/angle_class2.rst b/doc/src/angle_class2.rst index b045cc6917..9d1ff8e8e7 100644 --- a/doc/src/angle_class2.rst +++ b/doc/src/angle_class2.rst @@ -38,10 +38,10 @@ The *class2* angle style uses the potential .. math:: - E & = & E_a + E_{bb} + E_{ba} \\ - E_a & = & K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4 \\ - E_{bb} & = & M (r_{ij} - r_1) (r_{jk} - r_2) \\ - E_{ba} & = & N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2 (r_{jk} - r_2) (\theta - \theta_0) + E & = E_a + E_{bb} + E_{ba} \\ + E_a & = K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4(\theta - \theta_0)^4 \\ + E_{bb} & = M (r_{ij} - r_1) (r_{jk} - r_2) \\ + E_{ba} & = N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2(r_{jk} - r_2)(\theta - \theta_0) where :math:`E_a` is the angle term, :math:`E_{bb}` is a bond-bond term, and :math:`E_{ba}` is a diff --git a/doc/src/angle_dipole.rst b/doc/src/angle_dipole.rst index 0ad7da5069..351572cc22 100644 --- a/doc/src/angle_dipole.rst +++ b/doc/src/angle_dipole.rst @@ -71,8 +71,8 @@ couple generating a torque equivalent to the opposite of :math:`\vec{T_j}`: .. math:: - -\vec{T_j} & = & \vec{r_{ij}} \times \vec{F_i}\\ - \vec{F_j} & = & -\vec{F_i} \\ + -\vec{T_j} & = \vec{r_{ij}} \times \vec{F_i} \\ + \vec{F_j} & = -\vec{F_i} where :math:`\vec{F_i}` and :math:`\vec{F_j}` are applied on atoms :math:`i` From 3d106c7d47a9ef230e26799f3eca7c35b7f49756 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 14 Nov 2019 13:50:30 -0500 Subject: [PATCH 35/64] replace non-ascii character --- doc/src/Install_conda.rst | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/doc/src/Install_conda.rst b/doc/src/Install_conda.rst index 04b8054353..33188e2540 100644 --- a/doc/src/Install_conda.rst +++ b/doc/src/Install_conda.rst @@ -32,12 +32,10 @@ install the `openkim-models` package If you have problems with the installation you can post issues to `this link `_. - -.. _conda_forge_lammps: https://github.com/conda-forge/lammps-feedstock/issues - -Thanks to Jan Janssen (Max-Planck-Institut für Eisenforschung) for setting +Thanks to Jan Janssen (Max-Planck-Institut fuer Eisenforschung) for setting up the Conda capability. +.. _conda_forge_lammps: https://github.com/conda-forge/lammps-feedstock/issues .. _openkim: https://openkim.org @@ -45,9 +43,6 @@ up the Conda capability. .. _mini_conda_install: https://docs.conda.io/en/latest/miniconda.html - - - .. _lws: http://lammps.sandia.gov .. _ld: Manual.html .. _lc: Commands_all.html From e287cd975bb693f1daaf01ffec5d6d46bc2eed39 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 14 Nov 2019 12:36:05 -0500 Subject: [PATCH 36/64] update README --- doc/README | 28 +++++++++++++--------------- 1 file changed, 13 insertions(+), 15 deletions(-) diff --git a/doc/README b/doc/README index 6db4ba3ca7..96b17f9bf5 100644 --- a/doc/README +++ b/doc/README @@ -5,7 +5,7 @@ sub-directories and optionally 2 PDF files and an ePUB file: src content files for LAMMPS documentation html HTML version of the LAMMPS manual (see html/Manual.html) -tools tools and settings for building the documentation +utils utilities and settings for building the documentation Manual.pdf large PDF version of entire manual Developer.pdf small PDF with info about how LAMMPS is structured LAMMPS.epub Manual in ePUB format @@ -25,17 +25,12 @@ the fetched documentation will include those changes (but your source code will not, unless you update your local repository). (b) You can build the HTML and PDF files yourself, by typing "make -html" followed by "make pdf". Note that the PDF make requires the -HTML files already exist. This requires various tools including -Sphinx, which the build process will attempt to download and install -on your system, if not already available. See more details below. - -(c) You can genererate an older, simpler, less-fancy style of HTML -documentation by typing "make old". This will create an "old" -directory. This can be useful if (b) does not work on your box for -some reason, or you want to quickly view the HTML version of a doc -page you have created or edited yourself within the src directory. -E.g. if you are planning to submit a new feature to LAMMPS. +html" or by "make pdf", respectively. This requires various tools +including the Python documentation processing tool Sphinx, which the +build process will attempt to download and install on your system into +a python virtual environment, if not already available. The PDF file +will require a working LaTeX installation with several add-on packages +in addition to the Python/Sphinx setup. See more details below. ---------------- @@ -47,10 +42,9 @@ Options: make html # generate HTML in html dir using Sphinx make pdf # generate 2 PDF files (Manual.pdf,Developer.pdf) # in this dir via htmldoc and pdflatex -make old # generate old-style HTML pages in old dir via txt2html make fetch # fetch HTML doc pages and 2 PDF files from web site # as a tarball and unpack into html dir and 2 PDFs -make epub # generate LAMMPS.epub in ePUB format using Sphinx +make epub # generate LAMMPS.epub in ePUB format using Sphinx make clean # remove intermediate RST files created by HTML build make clean-all # remove entire build folder and any cached data @@ -103,7 +97,11 @@ Installing prerequisites for epub build ## ePUB Same as for HTML. This uses the same tools and configuration -files as the HTML tree. +files as the HTML tree. The ePUB format conversion currently +does not support processing mathematical expressions via MathJAX, +so there will be limitations on some pages. For the time being +until this is resolved, building and using the PDF format file +is recommended instead. For converting the generated ePUB file to a mobi format file (for e-book readers like Kindle, that cannot read ePUB), you From 08044dcd35c1aa49318fdaf04d6e8b0fffeba109 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 15 Nov 2019 14:21:44 -0500 Subject: [PATCH 37/64] update README for "make pdf" and list dependencies --- doc/README | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/doc/README b/doc/README index 96b17f9bf5..1416584eed 100644 --- a/doc/README +++ b/doc/README @@ -41,7 +41,7 @@ Options: make html # generate HTML in html dir using Sphinx make pdf # generate 2 PDF files (Manual.pdf,Developer.pdf) - # in this dir via htmldoc and pdflatex + # in this dir via Sphinx and PDFLaTeX make fetch # fetch HTML doc pages and 2 PDF files from web site # as a tarball and unpack into html dir and 2 PDFs make epub # generate LAMMPS.epub in ePUB format using Sphinx @@ -88,8 +88,17 @@ This will install virtualenv from the Python Package Index. Installing prerequisites for PDF build -[TBA] - +Same as for HTML plus a compatible LaTeX installation with +support for PDFLaTeX. Also the following LaTeX packages need +to be installed (e.g. from texlive): +- amsmath +- babel +- cmap +- fncychap +- geometry +- hyperref +- hypcap +- times ---------------- Installing prerequisites for epub build From 95de27d8d1760db3c16f18bfa4773ca6615ca4dc Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 15 Nov 2019 14:31:33 -0500 Subject: [PATCH 38/64] correct false positives to not have non-ASCII characters --- doc/utils/sphinx-config/false_positives.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 5b3020c7d1..fee8f2fbe9 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -933,7 +933,7 @@ funcs functionalities functionals funroll -für +fuer fx fy fz From 9a43229c83b39c2777053e1d2c6092d6607ac7ca Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 15 Nov 2019 19:48:58 -0500 Subject: [PATCH 39/64] disable single function for KOKKOS eam styles, since the required data is not available --- src/KOKKOS/pair_eam_kokkos.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp index f6eef5b53c..3358fe709c 100644 --- a/src/KOKKOS/pair_eam_kokkos.cpp +++ b/src/KOKKOS/pair_eam_kokkos.cpp @@ -37,6 +37,7 @@ template PairEAMKokkos::PairEAMKokkos(LAMMPS *lmp) : PairEAM(lmp) { respa_enable = 0; + single_enable = 0; atomKK = (AtomKokkos *) atom; execution_space = ExecutionSpaceFromDevice::space; From 48894884124e319a89003741d967af422484c625 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 15 Nov 2019 19:49:30 -0500 Subject: [PATCH 40/64] rename count_embed to numforce and move the location where numforce is set to 0 --- src/MANYBODY/pair_eam.cpp | 16 ++++++++-------- src/MANYBODY/pair_eam.h | 2 +- src/OPT/pair_eam_opt.cpp | 8 ++++---- src/USER-OMP/pair_eam_omp.cpp | 8 ++++---- 4 files changed, 17 insertions(+), 17 deletions(-) diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp index 8913b1e9cc..5459a92b69 100644 --- a/src/MANYBODY/pair_eam.cpp +++ b/src/MANYBODY/pair_eam.cpp @@ -43,7 +43,7 @@ PairEAM::PairEAM(LAMMPS *lmp) : Pair(lmp) nmax = 0; rho = NULL; fp = NULL; - count_embed = NULL; + numforce = NULL; map = NULL; type2frho = NULL; @@ -78,7 +78,7 @@ PairEAM::~PairEAM() memory->destroy(rho); memory->destroy(fp); - memory->destroy(count_embed); + memory->destroy(numforce); if (allocated) { memory->destroy(setflag); @@ -153,11 +153,11 @@ void PairEAM::compute(int eflag, int vflag) if (atom->nmax > nmax) { memory->destroy(rho); memory->destroy(fp); - memory->destroy(count_embed); + memory->destroy(numforce); nmax = atom->nmax; memory->create(rho,nmax,"pair:rho"); memory->create(fp,nmax,"pair:fp"); - memory->create(count_embed,nmax,"pair:count_embed"); + memory->create(numforce,nmax,"pair:numforce"); } double **x = atom->x; @@ -234,7 +234,6 @@ void PairEAM::compute(int eflag, int vflag) p = MIN(p,1.0); coeff = frho_spline[type2frho[type[i]]][m]; fp[i] = (coeff[0]*p + coeff[1])*p + coeff[2]; - count_embed[i] = 0; if (eflag) { phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax); @@ -260,6 +259,7 @@ void PairEAM::compute(int eflag, int vflag) jlist = firstneigh[i]; jnum = numneigh[i]; + numforce[i] = 0; for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; @@ -271,7 +271,7 @@ void PairEAM::compute(int eflag, int vflag) rsq = delx*delx + dely*dely + delz*delz; if (rsq < cutforcesq) { - ++count_embed[i]; + ++numforce[i]; jtype = type[j]; r = sqrt(rsq); p = r*rdr + 1.0; @@ -808,7 +808,7 @@ double PairEAM::single(int i, int j, int itype, int jtype, double r,p,rhoip,rhojp,z2,z2p,recip,phi,phip,psip; double *coeff; - if (count_embed[i] > 0) { + if (numforce[i] > 0) { p = rho[i]*rdrho + 1.0; m = static_cast (p); m = MAX(1,MIN(m,nrho-1)); @@ -817,7 +817,7 @@ double PairEAM::single(int i, int j, int itype, int jtype, coeff = frho_spline[type2frho[itype]][m]; phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax); - phi *= 1.0/static_cast(count_embed[i]); + phi *= 1.0/static_cast(numforce[i]); } else phi = 0.0; r = sqrt(rsq); diff --git a/src/MANYBODY/pair_eam.h b/src/MANYBODY/pair_eam.h index 3f135aaa1f..add33ab3f0 100644 --- a/src/MANYBODY/pair_eam.h +++ b/src/MANYBODY/pair_eam.h @@ -70,7 +70,7 @@ class PairEAM : public Pair { // per-atom arrays double *rho,*fp; - int *count_embed; + int *numforce; // potentials as file data diff --git a/src/OPT/pair_eam_opt.cpp b/src/OPT/pair_eam_opt.cpp index dbea720488..7dff5cff4b 100644 --- a/src/OPT/pair_eam_opt.cpp +++ b/src/OPT/pair_eam_opt.cpp @@ -82,11 +82,11 @@ void PairEAMOpt::eval() if (atom->nmax > nmax) { memory->destroy(rho); memory->destroy(fp); - memory->destroy(count_embed); + memory->destroy(numforce); nmax = atom->nmax; memory->create(rho,nmax,"pair:rho"); memory->create(fp,nmax,"pair:fp"); - memory->create(count_embed,nmax,"pair:count_embed"); + memory->create(numforce,nmax,"pair:numforce"); } double** _noalias x = atom->x; @@ -240,7 +240,6 @@ void PairEAMOpt::eval() ++m; coeff = frho_spline[type2frho[type[i]]][m]; fp[i] = (coeff[0]*p + coeff[1])*p + coeff[2]; - count_embed[i] = 0; if (EFLAG) { double phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax); @@ -272,6 +271,7 @@ void PairEAMOpt::eval() fast_gamma_t* _noalias tabssi = &tabss[itype1*ntypes*nr]; double* _noalias scale_i = scale[itype1+1]+1; + numforce[i] = 0; for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; @@ -283,7 +283,7 @@ void PairEAMOpt::eval() double rsq = delx*delx + dely*dely + delz*delz; if (rsq < tmp_cutforcesq) { - ++count_embed[i]; + ++numforce[i]; jtype = type[j] - 1; double r = sqrt(rsq); double rhoip,rhojp,z2,z2p; diff --git a/src/USER-OMP/pair_eam_omp.cpp b/src/USER-OMP/pair_eam_omp.cpp index 1b48214ed4..3b0bb54065 100644 --- a/src/USER-OMP/pair_eam_omp.cpp +++ b/src/USER-OMP/pair_eam_omp.cpp @@ -51,11 +51,11 @@ void PairEAMOMP::compute(int eflag, int vflag) if (atom->nmax > nmax) { memory->destroy(rho); memory->destroy(fp); - memory->destroy(count_embed); + memory->destroy(numforce); nmax = atom->nmax; memory->create(rho,nthreads*nmax,"pair:rho"); memory->create(fp,nmax,"pair:fp"); - memory->create(count_embed,nmax,"pair:count_embed"); + memory->create(numforce,nmax,"pair:numforce"); } #if defined(_OPENMP) @@ -200,7 +200,6 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr) p = MIN(p,1.0); coeff = frho_spline[type2frho[type[i]]][m]; fp[i] = (coeff[0]*p + coeff[1])*p + coeff[2]; - count_embed[i] = 0; if (EFLAG) { phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax); @@ -235,6 +234,7 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr) jlist = firstneigh[i]; jnum = numneigh[i]; + numforce[i] = 0; for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; @@ -246,7 +246,7 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr) rsq = delx*delx + dely*dely + delz*delz; if (rsq < cutforcesq) { - ++count_embed[i]; + ++numforce[i]; jtype = type[j]; r = sqrt(rsq); p = r*rdr + 1.0; From 4b6265ae40867f35291c99cde3de1fff946b13ff Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sat, 16 Nov 2019 18:40:26 -0500 Subject: [PATCH 41/64] Update docs: atom_modify --- doc/src/atom_modify.rst | 15 ++-- doc/txt/atom_modify.txt | 175 ---------------------------------------- 2 files changed, 5 insertions(+), 185 deletions(-) delete mode 100644 doc/txt/atom_modify.txt diff --git a/doc/src/atom_modify.rst b/doc/src/atom_modify.rst index ad19f236c1..ac2720d4f2 100644 --- a/doc/src/atom_modify.rst +++ b/doc/src/atom_modify.rst @@ -1,13 +1,13 @@ -.. index:: atom\_modify +.. index:: atom_modify -atom\_modify command -==================== +atom_modify command +=================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS atom_modify keyword values ... @@ -29,7 +29,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS atom_modify map yes atom_modify map hash sort 10000 2.0 @@ -188,8 +188,3 @@ defined, sorting will be turned off. **(Meloni)** Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007). - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/atom_modify.txt b/doc/txt/atom_modify.txt deleted file mode 100644 index d598b4697c..0000000000 --- a/doc/txt/atom_modify.txt +++ /dev/null @@ -1,175 +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 - -atom_modify command :h3 - -[Syntax:] - -atom_modify keyword values ... :pre - -one or more keyword/value pairs may be appended :ulb,l -keyword = {id} or {map} or {first} or {sort} :l - {id} value = {yes} or {no} - {map} value = {yes} or {array} or {hash} - {first} value = group-ID = group whose atoms will appear first in internal atom lists - {sort} values = Nfreq binsize - Nfreq = sort atoms spatially every this many time steps - binsize = bin size for spatial sorting (distance units) :pre -:ule - -[Examples:] - -atom_modify map yes -atom_modify map hash sort 10000 2.0 -atom_modify first colloid :pre - -[Description:] - -Modify certain attributes of atoms defined and stored within LAMMPS, -in addition to what is specified by the "atom_style"_atom_style.html -command. The {id} and {map} keywords must be specified before a -simulation box is defined; other keywords can be specified any time. - -The {id} keyword determines whether non-zero atom IDs can be assigned -to each atom. If the value is {yes}, which is the default, IDs are -assigned, whether you use the "create atoms"_create_atoms.html or -"read_data"_read_data.html or "read_restart"_read_restart.html -commands to initialize atoms. If the value is {no} the IDs for all -atoms are assumed to be 0. - -If atom IDs are used, they must all be positive integers. They should -also be unique, though LAMMPS does not check for this. Typically they -should also be consecutively numbered (from 1 to Natoms), though this -is not required. Molecular "atom styles"_atom_style.html are those -that store bond topology information (styles bond, angle, molecular, -full). These styles require atom IDs since the IDs are used to encode -the topology. Some other LAMMPS commands also require the use of atom -IDs. E.g. some many-body pair styles use them to avoid double -computation of the I-J interaction between two atoms. - -The only reason not to use atom IDs is if you are running an atomic -simulation so large that IDs cannot be uniquely assigned. For a -default LAMMPS build this limit is 2^31 or about 2 billion atoms. -However, even in this case, you can use 64-bit atom IDs, allowing 2^63 -or about 9e18 atoms, if you build LAMMPS with the - DLAMMPS_BIGBIG -switch. This is described on the "Build_settings"_Build_settings.html -doc page. If atom IDs are not used, they must be specified as 0 for -all atoms, e.g. in a data or restart file. - -The {map} keyword determines how atoms with specific IDs are found -when required. An example are the bond (angle, etc) methods which -need to find the local index of an atom with a specific global ID -which is a bond (angle, etc) partner. LAMMPS performs this operation -efficiently by creating a "map", which is either an {array} or {hash} -table, as described below. - -When the {map} keyword is not specified in your input script, LAMMPS -only creates a map for "atom_styles"_atom_style.html for molecular -systems which have permanent bonds (angles, etc). No map is created -for atomic systems, since it is normally not needed. However some -LAMMPS commands require a map, even for atomic systems, and will -generate an error if one does not exist. The {map} keyword thus -allows you to force the creation of a map. The {yes} value will -create either an {array} or {hash} style map, as explained in the next -paragraph. The {array} and {hash} values create an atom-style or -hash-style map respectively. - -For an {array}-style map, each processor stores a lookup table of -length N, where N is the largest atom ID in the system. This is a -fast, simple method for many simulations, but requires too much memory -for large simulations. For a {hash}-style map, a hash table is -created on each processor, which finds an atom ID in constant time -(independent of the global number of atom IDs). It can be slightly -slower than the {array} map, but its memory cost is proportional to -the number of atoms owned by a processor, i.e. N/P when N is the total -number of atoms in the system and P is the number of processors. - -The {first} keyword allows a "group"_group.html to be specified whose -atoms will be maintained as the first atoms in each processor's list -of owned atoms. This in only useful when the specified group is a -small fraction of all the atoms, and there are other operations LAMMPS -is performing that will be sped-up significantly by being able to loop -over the smaller set of atoms. Otherwise the reordering required by -this option will be a net slow-down. The "neigh_modify -include"_neigh_modify.html and "comm_modify group"_comm_modify.html -commands are two examples of commands that require this setting to -work efficiently. Several "fixes"_fix.html, most notably time -integration fixes like "fix nve"_fix_nve.html, also take advantage of -this setting if the group they operate on is the group specified by -this command. Note that specifying "all" as the group-ID effectively -turns off the {first} option. - -It is OK to use the {first} keyword with a group that has not yet been -defined, e.g. to use the atom_modify first command at the beginning of -your input script. LAMMPS does not use the group until a simulation -is run. - -The {sort} keyword turns on a spatial sorting or reordering of atoms -within each processor's sub-domain every {Nfreq} timesteps. If -{Nfreq} is set to 0, then sorting is turned off. Sorting can improve -cache performance and thus speed-up a LAMMPS simulation, as discussed -in a paper by "(Meloni)"_#Meloni. Its efficacy depends on the problem -size (atoms/processor), how quickly the system becomes disordered, and -various other factors. As a general rule, sorting is typically more -effective at speeding up simulations of liquids as opposed to solids. -In tests we have done, the speed-up can range from zero to 3-4x. - -Reordering is performed every {Nfreq} timesteps during a dynamics run -or iterations during a minimization. More precisely, reordering -occurs at the first reneighboring that occurs after the target -timestep. The reordering is performed locally by each processor, -using bins of the specified {binsize}. If {binsize} is set to 0.0, -then a binsize equal to half the "neighbor"_neighbor.html cutoff -distance (force cutoff plus skin distance) is used, which is a -reasonable value. After the atoms have been binned, they are -reordered so that atoms in the same bin are adjacent to each other in -the processor's 1d list of atoms. - -The goal of this procedure is for atoms to put atoms close to each -other in the processor's one-dimensional list of atoms that are also -near to each other spatially. This can improve cache performance when -pairwise interactions and neighbor lists are computed. Note that if -bins are too small, there will be few atoms/bin. Likewise if bins are -too large, there will be many atoms/bin. In both cases, the goal of -cache locality will be undermined. - -NOTE: Running a simulation with sorting on versus off should not -change the simulation results in a statistical sense. However, a -different ordering will induce round-off differences, which will lead -to diverging trajectories over time when comparing two simulations. -Various commands, particularly those which use random numbers -(e.g. "velocity create"_velocity.html, and "fix -langevin"_fix_langevin.html), may generate (statistically identical) -results which depend on the order in which atoms are processed. The -order of atoms in a "dump"_dump.html file will also typically change -if sorting is enabled. - -[Restrictions:] - -The {first} and {sort} options cannot be used together. Since sorting -is on by default, it will be turned off if the {first} keyword is -used with a group-ID that is not "all". - -[Related commands:] none - -[Default:] - -By default, {id} is yes. By default, atomic systems (no bond topology -info) do not use a map. For molecular systems (with bond topology -info), a map is used. The default map style is array if no atom ID is -larger than 1 million, otherwise the default is hash. By default, a -"first" group is not defined. By default, sorting is enabled with a -frequency of 1000 and a binsize of 0.0, which means the neighbor -cutoff will be used to set the bin size. If no neighbor cutoff is -defined, sorting will be turned off. - -:line - -:link(Meloni) -[(Meloni)] Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007). From a1d226f26e695c1be9c997545099b17e53252850 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sat, 16 Nov 2019 18:42:32 -0500 Subject: [PATCH 42/64] Update docs: atom_style --- doc/src/atom_style.rst | 15 +- doc/txt/atom_style.txt | 338 ----------------------------------------- 2 files changed, 5 insertions(+), 348 deletions(-) delete mode 100644 doc/txt/atom_style.txt diff --git a/doc/src/atom_style.rst b/doc/src/atom_style.rst index fac90d428b..d2ebc220d6 100644 --- a/doc/src/atom_style.rst +++ b/doc/src/atom_style.rst @@ -1,13 +1,13 @@ -.. index:: atom\_style +.. index:: atom_style -atom\_style command -=================== +atom_style command +================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS atom_style style args @@ -33,7 +33,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS atom_style atomic atom_style bond @@ -371,8 +371,3 @@ atom\_style atomic **(Grime)** Grime and Voth, to appear in J Chem Theory & Computation (2014). - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/atom_style.txt b/doc/txt/atom_style.txt deleted file mode 100644 index ff96fedab9..0000000000 --- a/doc/txt/atom_style.txt +++ /dev/null @@ -1,338 +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 - -atom_style command :h3 - -[Syntax:] - -atom_style style args :pre - -style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \ - {dpd} or {edpd} or {mdpd} or {tdpd} or {electron} or {ellipsoid} or \ - {full} or {line} or {meso} or {molecular} or {peri} or {smd} or \ - {sphere} or {spin} or {tri} or {template} or {hybrid} :ulb,l - args = none for any style except the following - {body} args = bstyle bstyle-args - bstyle = style of body particles - bstyle-args = additional arguments specific to the bstyle - see the "Howto body"_Howto_body.html doc page for details - {tdpd} arg = Nspecies - Nspecies = # of chemical species - {template} arg = template-ID - template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command - {hybrid} args = list of one or more sub-styles, each with their args :pre - -accelerated styles (with same args) = {angle/kk} or {atomic/kk} or {bond/kk} or {charge/kk} or {full/kk} or {molecular/kk} :l -:ule - -[Examples:] - -atom_style atomic -atom_style bond -atom_style full -atom_style body nparticle 2 10 -atom_style hybrid charge bond -atom_style hybrid charge body nparticle 2 5 -atom_style spin -atom_style template myMols -atom_style tdpd 2 :pre - -[Description:] - -Define what style of atoms to use in a simulation. This determines -what attributes are associated with the atoms. This command must be -used before a simulation is setup via a "read_data"_read_data.html, -"read_restart"_read_restart.html, or "create_box"_create_box.html -command. - -NOTE: Many of the atom styles discussed here are only enabled if -LAMMPS was built with a specific package, as listed below in the -Restrictions section. - -Once a style is assigned, it cannot be changed, so use a style general -enough to encompass all attributes. E.g. with style {bond}, angular -terms cannot be used or added later to the model. It is OK to use a -style more general than needed, though it may be slightly inefficient. - -The choice of style affects what quantities are stored by each atom, -what quantities are communicated between processors to enable forces -to be computed, and what quantities are listed in the data file read -by the "read_data"_read_data.html command. - -These are the additional attributes of each style and the typical -kinds of physical systems they are used to model. All styles store -coordinates, velocities, atom IDs and types. See the -"read_data"_read_data.html, "create_atoms"_create_atoms.html, and -"set"_set.html commands for info on how to set these various -quantities. - -{angle} | bonds and angles | bead-spring polymers with stiffness | -{atomic} | only the default values | coarse-grain liquids, solids, metals | -{body} | mass, inertia moments, quaternion, angular momentum | arbitrary bodies | -{bond} | bonds | bead-spring polymers | -{charge} | charge | atomic system with charges | -{dipole} | charge and dipole moment | system with dipolar particles | -{dpd} | internal temperature and internal energies | DPD particles | -{edpd} | temperature and heat capacity | eDPD particles | -{mdpd} | density | mDPD particles | -{tdpd} | chemical concentration | tDPD particles | -{electron} | charge and spin and eradius | electronic force field | -{ellipsoid} | shape, quaternion, angular momentum | aspherical particles | -{full} | molecular + charge | bio-molecules | -{line} | end points, angular velocity | rigid bodies | -{meso} | rho, e, cv | SPH particles | -{molecular} | bonds, angles, dihedrals, impropers | uncharged molecules | -{peri} | mass, volume | mesoscopic Peridynamic models | -{smd} | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles | -{sphere} | diameter, mass, angular velocity | granular models | -{spin} | magnetic moment | system with magnetic particles | -{template} | template index, template atom | small molecules with fixed topology | -{tri} | corner points, angular momentum | rigid bodies | -{wavepacket} | charge, spin, eradius, etag, cs_re, cs_im | AWPMD :tb(c=3,s=|) - -NOTE: It is possible to add some attributes, such as a molecule ID, to -atom styles that do not have them via the "fix -property/atom"_fix_property_atom.html command. This command also -allows new custom attributes consisting of extra integer or -floating-point values to be added to atoms. See the "fix -property/atom"_fix_property_atom.html doc page for examples of cases -where this is useful and details on how to initialize, access, and -output the custom values. - -All of the above styles define point particles, except the {sphere}, -{ellipsoid}, {electron}, {peri}, {wavepacket}, {line}, {tri}, and -{body} styles, which define finite-size particles. See the "Howto -spherical"_Howto_spherical.html doc page for an overview of using -finite-size particle models with LAMMPS. - -All of the point-particle styles assign mass to particles on a -per-type basis, using the "mass"_mass.html command, The finite-size -particle styles assign mass to individual particles on a per-particle -basis. - -For the {sphere} style, the particles are spheres and each stores a -per-particle diameter and mass. If the diameter > 0.0, the particle -is a finite-size sphere. If the diameter = 0.0, it is a point -particle. Note that by use of the {disc} keyword with the "fix -nve/sphere"_fix_nve_sphere.html, "fix nvt/sphere"_fix_nvt_sphere.html, -"fix nph/sphere"_fix_nph_sphere.html, "fix -npt/sphere"_fix_npt_sphere.html commands, spheres can be effectively -treated as 2d discs for a 2d simulation if desired. See also the "set -density/disc"_set.html command. - -For the {ellipsoid} style, the particles are ellipsoids and each -stores a flag which indicates whether it is a finite-size ellipsoid or -a point particle. If it is an ellipsoid, it also stores a shape -vector with the 3 diameters of the ellipsoid and a quaternion 4-vector -with its orientation. - -For the {dipole} style, a point dipole is defined for each point -particle. Note that if you wish the particles to be finite-size -spheres as in a Stockmayer potential for a dipolar fluid, so that the -particles can rotate due to dipole-dipole interactions, then you need -to use atom_style hybrid sphere dipole, which will assign both a -diameter and dipole moment to each particle. - -For the {electron} style, the particles representing electrons are 3d -Gaussians with a specified position and bandwidth or uncertainty in -position, which is represented by the eradius = electron size. - -For the {peri} style, the particles are spherical and each stores a -per-particle mass and volume. - -The {dpd} style is for dissipative particle dynamics (DPD) particles. -Note that it is part of the USER-DPD package, and is not for use with -the "pair_style dpd or dpd/stat"_pair_dpd.html commands, which can -simply use atom_style atomic. Atom_style dpd extends DPD particle -properties with internal temperature (dpdTheta), internal conductive -energy (uCond), internal mechanical energy (uMech), and internal -chemical energy (uChem). - -The {edpd} style is for energy-conserving dissipative particle -dynamics (eDPD) particles which store a temperature (edpd_temp), and -heat capacity(edpd_cv). - -The {mdpd} style is for many-body dissipative particle dynamics (mDPD) -particles which store a density (rho) for considering -density-dependent many-body interactions. - -The {tdpd} style is for transport dissipative particle dynamics (tDPD) -particles which store a set of chemical concentration. An integer -"cc_species" is required to specify the number of chemical species -involved in a tDPD system. - -The {meso} style is for smoothed particle hydrodynamics (SPH) -particles which store a density (rho), energy (e), and heat capacity -(cv). - -The {smd} style is for a general formulation of Smooth Particle -Hydrodynamics. Both fluids and solids can be modeled. Particles -store the mass and volume of an integration point, a kernel diameter -used for calculating the field variables (e.g. stress and deformation) -and a contact radius for calculating repulsive forces which prevent -individual physical bodies from penetrating each other. - -For the {spin} style, a magnetic spin is associated to each atom. -Those spins have a norm (their magnetic moment) and a direction. - -The {wavepacket} style is similar to {electron}, but the electrons may -consist of several Gaussian wave packets, summed up with coefficients -cs= (cs_re,cs_im). Each of the wave packets is treated as a separate -particle in LAMMPS, wave packets belonging to the same electron must -have identical {etag} values. - -For the {line} style, the particles are idealized line segments and -each stores a per-particle mass and length and orientation (i.e. the -end points of the line segment). - -For the {tri} style, the particles are planar triangles and each -stores a per-particle mass and size and orientation (i.e. the corner -points of the triangle). - -The {template} style allows molecular topology (bonds,angles,etc) to be -defined via a molecule template using the "molecule"_molecule.html -command. The template stores one or more molecules with a single copy -of the topology info (bonds,angles,etc) of each. Individual atoms -only store a template index and template atom to identify which -molecule and which atom-within-the-molecule they represent. Using the -{template} style instead of the {bond}, {angle}, {molecular} styles -can save memory for systems comprised of a large number of small -molecules, all of a single type (or small number of types). See the -paper by Grime and Voth, in "(Grime)"_#Grime, for examples of how this -can be advantageous for large-scale coarse-grained systems. - -NOTE: When using the {template} style with a "molecule -template"_molecule.html that contains multiple molecules, you should -insure the atom types, bond types, angle_types, etc in all the -molecules are consistent. E.g. if one molecule represents H2O and -another CO2, then you probably do not want each molecule file to -define 2 atom types and a single bond type, because they will conflict -with each other when a mixture system of H2O and CO2 molecules is -defined, e.g. by the "read_data"_read_data.html command. Rather the -H2O molecule should define atom types 1 and 2, and bond type 1. And -the CO2 molecule should define atom types 3 and 4 (or atom types 3 and -2 if a single oxygen type is desired), and bond type 2. - -For the {body} style, the particles are arbitrary bodies with internal -attributes defined by the "style" of the bodies, which is specified by -the {bstyle} argument. Body particles can represent complex entities, -such as surface meshes of discrete points, collections of -sub-particles, deformable objects, etc. - -The "Howto body"_Howto_body.html doc page describes the body styles -LAMMPS currently supports, and provides more details as to the kind of -body particles they represent. For all styles, each body particle -stores moments of inertia and a quaternion 4-vector, so that its -orientation and position can be time integrated due to forces and -torques. - -Note that there may be additional arguments required along with the -{bstyle} specification, in the atom_style body command. These -arguments are described on the "Howto body"_Howto_body.html doc page. - -:line - -Typically, simulations require only a single (non-hybrid) atom style. -If some atoms in the simulation do not have all the properties defined -by a particular style, use the simplest style that defines all the -needed properties by any atom. For example, if some atoms in a -simulation are charged, but others are not, use the {charge} style. -If some atoms have bonds, but others do not, use the {bond} style. - -The only scenario where the {hybrid} style is needed is if there is no -single style which defines all needed properties of all atoms. For -example, as mentioned above, if you want dipolar particles which will -rotate due to torque, you need to use "atom_style hybrid sphere -dipole". When a hybrid style is used, atoms store and communicate the -union of all quantities implied by the individual styles. - -When using the {hybrid} style, you cannot combine the {template} style -with another molecular style that stores bond,angle,etc info on a -per-atom basis. - -LAMMPS can be extended with new atom styles as well as new body -styles; see the "Modify"_Modify.html doc page. - -:line - -Styles with a {kk} suffix are 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 on -the "Speed packages"_Speed_packages.html doc page. The accelerated -styles take the same arguments and should produce the same results, -except for round-off and precision issues. - -Note that other acceleration packages in LAMMPS, specifically the GPU, -USER-INTEL, USER-OMP, and OPT packages do not use accelerated atom -styles. - -The accelerated styles are part of the KOKKOS package. They are only -enabled if LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -[Restrictions:] - -This command cannot be used after the simulation box is defined by a -"read_data"_read_data.html or "create_box"_create_box.html command. - -Many of the styles listed above are only enabled if LAMMPS was built -with a specific package, as listed below. See the "Build -package"_Build_package.html doc page for more info. - -The {angle}, {bond}, {full}, {molecular}, and {template} styles are -part of the MOLECULE package. - -The {line} and {tri} styles are part of the ASPHERE package. - -The {body} style is part of the BODY package. - -The {dipole} style is part of the DIPOLE package. - -The {peri} style is part of the PERI package for Peridynamics. - -The {electron} style is part of the USER-EFF package for "electronic -force fields"_pair_eff.html. - -The {dpd} style is part of the USER-DPD package for dissipative -particle dynamics (DPD). - -The {edpd}, {mdpd}, and {tdpd} styles are part of the USER-MESO package -for energy-conserving dissipative particle dynamics (eDPD), many-body -dissipative particle dynamics (mDPD), and transport dissipative particle -dynamics (tDPD), respectively. - -The {meso} style is part of the USER-SPH package for smoothed particle -hydrodynamics (SPH). See "this PDF -guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. - -The {spin} style is part of the SPIN package. - -The {wavepacket} style is part of the USER-AWPMD package for the -"antisymmetrized wave packet MD method"_pair_awpmd.html. - -[Related commands:] - -"read_data"_read_data.html, "pair_style"_pair_style.html - -[Default:] - -atom_style atomic - -:line - -:link(Grime) -[(Grime)] Grime and Voth, to appear in J Chem Theory & Computation -(2014). From 98bd975e9055337ff0bdff29983d1d2db1394833 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sat, 16 Nov 2019 18:53:01 -0500 Subject: [PATCH 43/64] Update docs: bond_class2 --- doc/src/Eqs/bond_class2.jpg | Bin 5142 -> 0 bytes doc/src/Eqs/bond_class2.tex | 9 ---- doc/src/bond_class2.rst | 39 ++++++++--------- doc/txt/bond_class2.txt | 81 ------------------------------------ 4 files changed, 18 insertions(+), 111 deletions(-) delete mode 100644 doc/src/Eqs/bond_class2.jpg delete mode 100644 doc/src/Eqs/bond_class2.tex delete mode 100644 doc/txt/bond_class2.txt diff --git a/doc/src/Eqs/bond_class2.jpg b/doc/src/Eqs/bond_class2.jpg deleted file mode 100644 index 493048100ed395ae9e2186151592ce0ff0f51288..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 5142 zcmeI0X*kq<+sFTtJt4#hV;w15A^Tpoi6~{?VsxRgk7Xv$RPL5<Bjs#dUB8EYQt!`jvufRyjM< zrT22F00K8SQ!$k#uBQ;B@^+XN{!CR`C^nRRjic!0f6loS9;$%uvWN*wOER>|O?&gm z9Z5)|0=0ZL>KPEhP17nXWuj=WYf(ELQ{kzFs;|SY`#XQX>Et?f289j?H@1S-<6Qt6_;`SYu z(BVQ2A?~bC+L>^j{WbDyHNGe4tVvS6(x8UHQRAmKKxk+fQ05lb*lt|0ArG&x#S6J_a2W7g*9^IJFknY=`a@a7Ew$S^& zrh|{xO$>5*l*EQ#*to4%siaEEMBv!dVMaW>j>2>!V`SB1iH6CXsd6~C&L7LCPNydocRP2FzZiWi(bKV9AOcMq@ zO{*7+8*<{f(a+%P>a$0)UHR@PuATq3jok`Brt z{JdktW5;(~tdSH@#>tY+ek1=h3$EXz%Z8j`o;wi0Z+8k2{Z3mf_!R_n@^2D8-02D2 zG?KxTAnp1W1SsH_qR*&+60WK8uwFtj*i~Z9bl^)v&gb(fHsvONedgjF@<^;?3Wc$z z_Kf%n%8XHjILBV;wX6jkrz@d(_xv+Rc%q^g@dDRcS=YEG?9@>0*RGbiOafXCCp`2! z<*SLTK?Y%Y^;ZtRrMC{>+X=6`lC8>}vMHChShhp=wKV3j#@1eN2VOhdF){}xh8uvU?$s|y-A$`j)o0>oLNLel3!E^|ib&}XJ27U?B#evKX|)6rL-4zuqWChO7jO(&kdoLxJ*5 zZ!_^#hyj^}RbwQL0F&wg8TFNHGezzbQM~F`Ix=)Wfr`rmqXC# zJ`42TRb4dFvGq8-*(RW3g`e+9@5873VG7XZC))*H=mfE1n3fXvGbIXeKj&2IEaTfT z|0?3F_z5WnAKmQGLiBODPh4#>kZt}oOYSA*`#iFSoW2{zg*OWa-mY{A0xePj&Eb6- z+Z}vN9SUTmYLzYN?4QV?%z+29Bx@Xk>vXNqSzYY1)!;%?w+Phk;?MH4pl^@w*=<}7 z5{^y@Q|qz*s6Ery52L}mslwaJB6gIYLfU;8Cq4{F`?2P&V!^xx>IaV{yQS{O>I>Q# zf`Ua1Zh~)k?^7B9e?`3qg&2Rxz3+62PDHa8HLH|SsEM>lftE+T0a#_xzFqAAHv2uU zG2eDO0&((nLX+Y9$n2DBZ9lOIoUSQspPRPGc%)e{uSD9fFt762Z^1`oEPP(~yM&Qr zd=s8OE+dWZ0nZR zJvlg)(lR$jnuB_1wBMeqjF2#p4zIt?dP zjP8BMbdghjlm%kd6!EDY%>^D*O>kxC^P^yA%qZLfhiP7l2AYz3FNe2aH$9PR4r76Y zXT+W_RlC2ri0^HK9)`H#@+T9~8+Dw^gIA6DD5i))62-JD{!CnC+PDU(Z>zAK_M6bx zK{%)RCD3Y_gYCB`0uy%t3YxMZsk6~wM&R<*ij%L^pI(zt?A}p+{daEefzig#B+cvy z&iaTqQz_eJH95qh3-UG|UN>+zixo9aD8i#GzHZ{S!WGkPNj2}!)~B@gy)RIKfUi^_ z$u`rrRXaocLU5jZ-?cI5$;87o`I)pl)@FEsa(BySFlr2Xj8Ck*^1)_L#IVw2=7a1| z)~L^%Bfl3L64JgP+~o74K1I{=%4P#ouixTJcrAZ?YpSBF_?7T0^+7kL;k!*kvIYge zM5o~i^pVi~ceS?P9~5*Puv&7LWvZs$Abcl;h8z(Yfgtd`GMi9I}FNgzAy zZNzYI4Z6w-q4}!omVI$LH{|#Pv2K3yI39N(^TH=C_=-fH@zdU0uDyY^j}ebgs7=PPcdk}XJHUR@eI702 z)nt^8zni}XRv(-vP=TKrXzY9_CV?jDagT4}S}(?RR<^aLc_*9p;xOw(Yrd$q>REL4 zz?CeW?4A{OUA~is2LrIjBY|ge{_LCKp<10r*YiU3`Zm5Rc)j;aP(g6XQfjY1NpqdN zqT*6%A5+J18MK6mU}xdw6EKQ>jymI2kscx%zwISpunfG_SJ~(Uzo9*oFSpRI68L@KTnIn_8o(uQ43Irm| zzdBp9eNa+h0g~fG!C;XY6g*QuWk&x zS2uR^k7v%1xA$Y!6?)&~dc-t4oM;XfkTV`qfzB5BvuW4g8eUFbKhN3a$P!SaJSEzx z+jk!%k2+hRRCm#ntE@lXuCHpRZrI4bj`!+!_Ppo$LXwYNRa7dXuH)M~+e1}NwoW@_ zv7G_Ki0|30=9Drb_Q&P9n^$k!6O_M|J19PsyT$hn6a3;7sSO3#2Af!|-Lb4Xv8$*| zFP&cD7)hCG_hJ9>Ox?Cb*H7Kfa$R<-d%Ns==B0^*s|PYF=+RYyjq!np@e4u9ZkcOt z$UsfjxS5BTnDL^QTM8i=Thk5qv3A+c@u;3e*;>&@`r3h=khe`*9i;@x%jllz01pez zB1Zlnq6Ov5&hEivUlzdQ%#z@2T=?*G|8Q&W)4Z1DlZn#WhBb1%3M&avR-+!3u(nYQtPL2fPr)L@~oxtwb!3_JuEH2O02Kv zX@@hwORErPj#GCl|C{!*Iw=^k?)o)XV_dwAx0mw80YPq{@fvy2q;4A*uiu4rVei`- zc2-b5URv)Xq!bLsULk3oWpN7{rC6tcc60G`+654vT6vS=#v#6#EmD6id-m{b zd2+4Tz_xw5IPT~LbknzP@1{5UrT8ZHz?_LBVHo{L`DLb)c9F=>U;N#)SY8B z*+x|**fok~vyYw zK(Fmv6j#%QrKvnI5(}aq?CbC9B5*LW0y`XR`Oh<$&>v#E@AuquEipr*wzWt1`ubw( zBDBF=wK#c&6N8Zu57~yofpx!N9@0TgVGNTnR=&`sB2#I?&FvNW+_H`nFSOw)^9RqW zMbxL0ReucP;xFiR^hD!pA&^WR|PHi&ahU11$zz=JF z9bd|WFNdvW3m0v%Jo^l}JHWE`7l9!52^r3$Eh@lW+2=zh&h(knn#WHU8VfaIJGk}7 z12;H~nlYnIm~RUT1--|4@U;7D*2jB)6?$N=dcZ(Y-C5&!4t$TAkq+6(>rknxR6{pB zLbh+m)DkmSI(lu*o}1<8a-JcarApVV&AIa;{H@sNSA34`sf}A>faztwk?WUp`n0z% zvudOyUArJ9i1|yQ5`&tn3{qu!%pxeWE0{IEj*=3;*JxC2Q4UiSgi4NnH&14>QS2YE z0SQIn0-uGKLs4Xlo4R@o9gS^D&q@3dJUwmQTVI?If==JY`|VaXG}Zv-gdCUf_xSKpzebYIr& zIYQzq_0R7HC0J_Q!1qlYUO)cjCZh?G=$@c39N9j1Rz58`)vfzjqf$Zz7GxTr`QL+) z?OC~cbOZay_1Z8S$^!$w8(%FK(<&JJ6ei0pcfB_joJvN!@8sT}kL80)V{UE}YLuf^ zf0Yz$g%mXjHTcOcv#HI1IwIex?}--Mi3?8rmUc}1MqH{+{K#0!RcV;1C)bz>aR?Qbd zlQroR?imie6~oMBY8cK{1!^xfJ+7Yddhfq;ul=a;s>=nFT4sUEQr_`@weD*@+Klak zqo&ERNdca^y7$7E6IM}<>^M@Q(T-*=H+S`s07UBfhzxR38)(G#qyPuz0=c#n+tdK) zXu^P9g2v6@3-FH*Qk>+``nNU{vY4%wf3=6zxi1rKCmZ;prcG4Eqk3R`GV7$7kB5&c zrcs}e6D%H{TDPb`eoWNrGDn$)R!79+MhnrTriePDJEfvo5ohDuez4yq8EVHLCUyUf z)pjQxYAE0vh8wJMR_5lmhfK)v|C1S{9>63;{(#%mIeO{(C29J?4o4tnZ-LklezKG+ z_3u2UdOGSnDRaASityq6i*t zn-mX}^}n+rcnqU(SYHiSw*M9-hhQ0a# diff --git a/doc/src/Eqs/bond_class2.tex b/doc/src/Eqs/bond_class2.tex deleted file mode 100644 index 0735b61025..0000000000 --- a/doc/src/Eqs/bond_class2.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K_2 (r - r_0)^2 + K_3 (r - r_0)^3 + K_4 (r - r_0)^4 -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/bond_class2.rst b/doc/src/bond_class2.rst index 9a7987fa39..e3098ef6dc 100644 --- a/doc/src/bond_class2.rst +++ b/doc/src/bond_class2.rst @@ -1,19 +1,19 @@ -.. index:: bond\_style class2 +.. index:: bond_style class2 -bond\_style class2 command -========================== +bond_style class2 command +========================= -bond\_style class2/omp command -============================== - -bond\_style class2/kk command +bond_style class2/omp command ============================= +bond_style class2/kk command +============================ + Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style class2 @@ -21,7 +21,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style class2 bond_coeff 1 1.0 100.0 80.0 80.0 @@ -31,10 +31,12 @@ Description The *class2* bond style uses the potential -.. image:: Eqs/bond_class2.jpg - :align: center +.. math:: -where r0 is the equilibrium bond distance. + E = K_2 (r - r_0)^2 + K_3 (r - r_0)^3 + K_4 (r - r_0)^4 + + +where :math:`r_0` is the equilibrium bond distance. See :ref:`(Sun) ` for a description of the COMPASS class2 force field. @@ -43,10 +45,10 @@ The following coefficients must be defined for each bond type via the the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* R0 (distance) -* K2 (energy/distance\^2) -* K3 (energy/distance\^3) -* K4 (energy/distance\^4) +* :math:`r_0` (distance) +* :math:`K_2` (energy/distance\^2) +* :math:`K_3` (energy/distance\^3) +* :math:`K_4` (energy/distance\^4) ---------- @@ -98,8 +100,3 @@ Related commands **(Sun)** Sun, J Phys Chem B 102, 7338-7364 (1998). - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/bond_class2.txt b/doc/txt/bond_class2.txt deleted file mode 100644 index 4390e3613c..0000000000 --- a/doc/txt/bond_class2.txt +++ /dev/null @@ -1,81 +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 - -bond_style class2 command :h3 -bond_style class2/omp command :h3 -bond_style class2/kk command :h3 - -[Syntax:] - -bond_style class2 :pre - -[Examples:] - -bond_style class2 -bond_coeff 1 1.0 100.0 80.0 80.0 :pre - -[Description:] - -The {class2} bond style uses the potential - -:c,image(Eqs/bond_class2.jpg) - -where r0 is the equilibrium bond distance. - -See "(Sun)"_#bond-Sun for a description of the COMPASS class2 force field. - -The following coefficients must be defined for each bond type via the -"bond_coeff"_bond_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -R0 (distance) -K2 (energy/distance^2) -K3 (energy/distance^3) -K4 (energy/distance^4) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the CLASS2 -package. See the "Build package"_Build_package.html doc page for more -info. - -[Related commands:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html - -[Default:] none - -:line - -:link(bond-Sun) -[(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998). From 5f89fde6bce07f13dc7c3561d49eee2e40b5babe Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sat, 16 Nov 2019 18:59:49 -0500 Subject: [PATCH 44/64] Update docs: bond_fene --- doc/src/Eqs/bond_fene.jpg | Bin 8322 -> 0 bytes doc/src/Eqs/bond_fene.tex | 11 ----- doc/src/bond_fene.rst | 45 +++++++++---------- doc/txt/bond_fene.txt | 88 -------------------------------------- 4 files changed, 21 insertions(+), 123 deletions(-) delete mode 100644 doc/src/Eqs/bond_fene.jpg delete mode 100644 doc/src/Eqs/bond_fene.tex delete mode 100644 doc/txt/bond_fene.txt diff --git a/doc/src/Eqs/bond_fene.jpg b/doc/src/Eqs/bond_fene.jpg deleted file mode 100644 index e8b909c08f715e75e1944205135882f64f17985d..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 8322 zcmc(EcTf||*KUyhA|RrGgdzk)C4kfbp@>Lt7K#K!AV>>6kkCO z&_eG;>AiQPUB5f?`{unf@BQoEx%b(bot@d8Ju_#X-E*FEuE(!u0k_nZ)sz7wBqRXU zKLc<*1yBT#lai5a@37uwU|`{5 zVP$9Mj50IL78A`iIge*XU%N;I;2?AL%CwG;Io z?+ka3?D7lg{%?ht*w(S$dJ=841*mX9Dn=c98=7fVaEZe1+Rh z(AGsEQ}rpz`@GJSw^2k&OH69*X1|64G`ivN`3u|kd!rR&&QD-A&8otq_mLVVqYVyY z{!f=}#{K7NXG(zEgJetbdwl#@vE%SgTjiNsEB6xa?w;0Wbec8;ivty?ZA_iK!=dSE z#)E26pp;fZwOO$8k`#!AJD(!Pu3zY;3nLf^4l9XrrX`Al_59NRG^e>lYi z4dk3>YyEMsp&#pRQiM{mJ0h@m!FI8HR1{TjI|`@AXdBztKu{S$R$`oKUq#OA{tI{a@$2dGNz@bNHO`6lHTJH7 zx(O_KuiPxP9L+&QqYiImX%t~Ha7076`i*7CTu<~T2R5o5GNGAjEnaj5^*OcbM1@O` zOQr*%@kOmq(#SnQ&UGUOLrViG4T0o*j9bh26ez1w%x#L#a@1dz;>J@BUJqi-u%s{F z8XK9R)V^KU5Kh9fcqT2wdVIm=ePCm;nYBnX6P}_z(}@+PA08Z>rP~9yUv@C(H)J%< z9hDwpAuzS}LJ-DVb&A0o-OUns_Uik|t69U{3)uH1^QKipzESYvr^^YASofJyz=xip za*|f(dSl2;E_F9oeo6lDt!0rt+ec-3kF79*X^~kL`7EKWX3pt&+8O@3mcxKI>>RV~ z-HqN~B>ldK7)y@+&gaT=W~z)@JC7mw!icV0-fo!_wNU#L$A?oBWiU(1d1+4N$nDSK z4F7=dgM^3Xu9d1C3yxkHvw(B;%a2sk?BAdNgVx2ne8YhOziTiTVz$e{!8z|M?(9hx zd1!vxD%DP-FE=+ps{mPzS2&#j@tSkAMs+gYDc1lfV{*bU*slNC-soq}(NbeC`bR5% zxE<6b>r82w%)(E!_}^6&@8rYk1mvF(x=uN7!P5oC>Y_)@=qORhW)}%y#>=LufHAze zTdX(}gfDtHN=>83WI91M-XC6E9~+0?J}$49Z;0{u7CVG6&)u^E`pOu?2s#RrwzM*w z=2Qelmu5v-#jV@oO_<9;35Ywta%T67KGUz3d&rR0UnSk*i=2-kRZ{uqp?#I(a*t+4 zATD>cBX4~?b$;C^9@PDekIrPEeBb3>@VfRjpuSn~{6unVUD3qHsN;%N$+G1_MR9fD zvj6WtPZ@j-2$8F(eS6`sa`v_@3%mgp9&OOMh(ZLENxMioS|-og4yS&@S$Vzb|2ffG zat-)GnSKAnJ-x6uYVgX>B&#u|#*&q#>;1(SVqMxjM(SOM6*MOWj_}=zO)V%S#rG;Y zZtv9r1rkd4c*)k?Qwt*sc9E2(8+^n;ssZ8J_7M2>b;9n=W7MiSVyHQxGO-e<8nYC< zfKk(4+%{r_ecxOinAy?|z0Jhi_=aWI_pZf-zvS-kf6f*qGB;JvZ~TtEtM@5 zKgc?`J2+Pdb*%aLA=}AVB_|_vG&@#&ZP{M@YlfL!6!4Bpi8d!4BN_qZIrNdf8!BR$%TX!ULz9fszr_w&zFNf$ zXC>PkC7u}}8+Lg5#tM#{$N*^f8k7 z>>dl}peMKAXr!sKHRSv1kYr+A4wePiweK$;kkY0#2K&Gx^Ju+f!_JHz?ET=e0Y6l1U_=HUBEsG%j+^{|8BOmhK%oik6^+ogv~ACBn-_C(SVlGe)VrPaEPLDG zP_sv6D?8OQsGEYvH}tbDdim865)hpZFJUgOyeZdde^ual0{Vx5TLG>~Mb6%A@6MjP z9Wh*?oV=6ACz)$pYLnuL6y&~RbIrsUHm1+^9QIAdH~z=Gkl7bAW*7bK&Re0T^EWjS zaJ2O-^!WY_DjtT4)jbdtscD^7ol`(7)pWB+pf1_cK)3`WA=L}0V(dWyT=(>5L<`)* zQu%x-mN0KKT6TMV@m2EX(DtcA9&{kBZ$j(jOYq*WKaEAGT&vA>{`d79i(+(2a7{aiJqZNbo z>JOA_TEG$1#3a?OvDmg@#zf@BK(+NkuMjA#(z7vX$s7d|AbRw=-o?}56`T9*Ge1>jRk7Yn<$bgib_^_#Tc8Q%ZY-Z_Qd zE3DE#7u8&cx;-vCsV>fa^T{V7spg#jrEc%PvA0lQGvcwn^(fA)Tq`PVtZ=Alzk}O5 zFXvb19n4vZZm!&_+*tz_re?1aoXBh0j~c)m@qq21_9J*rHc!mU?q9^g$uRkO zo#GN^KVaRJf%Chc%jKVUoDeVwPr5&i;J(Fj$L@A}c^aqGh=*6Qhg8rDLKpmV^OI1? z7JXk{8=E6>W1hpj4>h|U!6GB~q_`iw1Ddn~JIJb-RCn1(mZ0pIDNd5S{d>gs;ltnZ zdlpzs`seqK9=Hxv7y`RCZp#v_M9Ku&&jo_~Tvx9H9(y30!2oCA&hyG%k< z(9vB2EKmIM>nF=Z@Kwd|sLzMN$s7&emoJAft#Z|HA^4-a-7cMzdNJRZqgY_Xyd~eI z=3L9!!1U_r2{DdDg7ub=0ZF*)pc1v$Vulq`!`z^@NzKIDcttYyU{eA}K4XZEt-qpc zx5eIV>KT&8%%~U3ZWTRZ;^Kr`3S4y!>xp81=8CV3G(^tj>f6!dUF9M;Xa2Gc^8%^I zr-)l1_cL0Q~tva925xqJRue;Cov}K@K_R*>>p_>d7u^pgpu^b+S;;j&=LlDY|Je)TS zf>wmI{UkQzPelc;0d@r!hB0a~IkkKgy>15GsqtG#Ph@q}BA@R(1l4`gE@c%IDZ?t> zU6<+gkN|+p{GFfIJTbO8gV;g7`EgP!js?bOw~!}T-YYm1qQu&=Ib;__Cz30id{&^5 z=_R^<@Jc3@$0oJY_0dnI!n>=tBpL#%2(3RtYClu)aXbkUVzgL&doKuQ4Rwz$8+VWY zXwwaA4rh!IFM?XXp@&6KIpA8tEP9eeT{h>AYEH19_*0Rk?ek$1`en)m;t z%K$06&sO;HYe?|TMZD!wnlc%gNO4z1q1wKvkuLIOPc%f=GS)m@ z5)GNKR|##KD-)??&)+?(kD85`Wc)T#xRZJ4Of`P2JQ^_5x0bL?&jpMglHqF^8}#(k zG~KW3p@7^lUN3H+fZvSaXw3cG^GCc0qAsNyGA&2nvgdOR>4NnwUq6aVAO@Iw8Q#NJ z$}V9|r~N6u7h419$+d^yZ3*REVVC4j3Ln;bxM^iTZS936N;@p}Pnv?C!W-TJ44_4qW-1)p*?#!Q}v|C9?-V zk;1HcZZ4Ehb7Xy$PivIAm@2*o%=Xk=R#d~c+B`ooo7!!Lx=(?CGW3B@sirBFciCFE z5dI)Md7`t^@rC2;v7FX9^J0a*HesnvX{l*@U%#wKs)@^*jpLP_iKDSi+WS)}FIbI8 znIhPmNXOQL`~a-_2w}(Hr8y}7(YGd~?1ve>2Ecq#l7^SOt9^Tuzcx$`B~x1wCq)A} zcmZD9nPj7zw-l30&Un2rL^zDIK1~fkG8}^q(w z6x?Ucg_;6dk0VFWsm!2=SiIgZLbgNUrxu!na&grC3K(2*D)GzHJ;m5 z`gjyOGuoDLc650LQ;FZKkdfDUX9Jq8-#S$I#LPY|4MA3~*ni+Y2p&G2&Kn)Z8bR1F zWI?bW##m0BUkMMYI8m1de;0LMFh-gNs&6$qD43*L`SIWU#8@A>iOcSj;}QEX>|ZHk z-3FJ*bs8yJG)u=0pr6M!Ste?UmX0FR=B1I6F`S6-}pxaf{isqZBo-VvZUI}$$BD$FNFl=e+$RCAP&l{H@@sag8>pHcL1 zc(|DV)2ZlO`>~SsbbO|vvEUU1c~LT7=KQ!P?i5*2qI8kV681{8WX6al_)iwTa3*hn zDZOzBc6RJ?y?jJ>HP%AlJd3ISovCm0R%rPe5I31f^XVYN5pt@0sCRDiwyw@&TB>^4 z;T-KCTNHLSK4*29m?KX>_+j6O{mgE$g$Xt0izf9DRhOPLc`{9yOEds9Xp&UvCWuh< zrV7saw3Af8Dadd%)~VBpIcXl+BK}iaD2=6(x0l|!DCQdQNG>xQ^m}JyWL)P`uber4 zieWfkw$4a2ClI2#cT+HaQOrT{O^fluP!5b*w&ix=|4QBD&tsCtP1to-O0=KL+d>nHCTKmX5<7kUBvWO-IS?n!@Rg0I#~+AQqDB%buCa-v(hMaCI^O9NKtRLssPm*@Z&hqR*)r;9PgmUl@-H^ zBHL`*z4AKA+9HxzHxA<%t$-k->!7!PW}!D?3V z)h5Hh0U}JHnGd(;A$zh0jzP8d3eVUAbqtKN9c81-iTq!2KdA0o&a;4)N!tFDGI)*z zqgU|!ivCCqV-hkug+0Ae;|~BmF{C>k>dF-9A2uusu=w`4Cal=EVZ>4o6mhZyx1n{{%N{sRIf9Tq3ED& ztbmCE8(bdGoz!(8?myZsh8ZWR1a^!@{FcQ>*WSyVwM^}89`R0Jl!i>r0Sa~T2s&fieOda)4l+& z17eOSA!rCX^qY?Q`^{rLfx(U?LH#2B6aq?_W$sgBLkZGovaa`6PWoIKz)eysp~mVF z_6ZYT3SN?Jtw`%Yrg5HfEYS4FLLHhv*PSf=%tPhlUat-DEh60A=be7_%?05q@Qcl* zW`3*q*d{({txvpIfz4{#>7C{c@>BfU%=_12XIL`O-d9bysihAe%`^b;FU^3KD1hgtW3K>T~5O? zyyl_T0Oi>2c*9wp0$R!=NA^?eF{b6rdD7GRcgC%lA&N$CvD1WMUzpQLwc0{rmC)T_ zo6B2l^&AHyHsQ-)@>xpzVbWU4m3J?hUbY9GW!^beNk@H;S}E=ql${>6>FSq5c3uP4 zN543mBXuIW-Uj9hX{!`=ZHhU%I@RMrl82i^P+4}wmfIGU=14@+PZ0Bg2J)bwxL`58zw9?{eO^?OBpcG|}VbkS6L z|GpXkX$WE)mG`x5j;s1m^YH!=7p&l{v$)mi86OB893sFmtMj@BbxwPJ%-$99k04gH zVeC~g34w&dJ<`#fvZzQKZwJSq-ol?+W2w=z4}!`F;@^|h`yFJ)Z#Tgo-V@^iMnJe2@ZQW2ld{-c$;*KT0L_xUlndW&dRSRjIXJW zjQqQ*DBSR57Ff5ZHpkiUh9-C#Zpr32-?0LEK3VailnHn2oyDr-@Up^ZI-y@Wtn8S} zJszK_3%SpvR|zfCy6-GGE!%*;(oMV36oti#^L$!*3|}vUamwL};fD)w3(4Dy& zlaJj0!Q-F#gV%t+Y-Jwg=D0|E*hywcS|pHyT@*#1#z4fR@*BgQxMpa)6}Y@sx1=~S zgLpy39wVFBlV6RJk(G8aby(9Shn09NoTVSaXL-c4ZQ#c6tj}A;Z*|aTut~Vfx-YLhW zQF?Z=ThG#z$3>7?cslVXK97jDg@I@{@fMA}w4^Soq;58Ia*4R0;gq3JSjyJpO54Qm zk{|hLUGJ=YXRuS+k5uXfudmQf%22OshlKRZSIm@tPyXw;$M|mr;CBJK^+6SPGSc#G zxxbW^m+XAy+RiH_{=$869a7(37S2kPJohL2lM{E2aasy;s(meOF+Ee^Zhqr`T#vHAU0_Z%K0AVmmWD zXn)pU$!rvXpKMyqO)>}>q{`ul`$XGnw8NKm5}(3XN8KkDLG+dY%#GoXz92X>C%U#6ZKrh_H$NTcjb5FCbGsK~9?%4*G&-qbqRwnP_E-&g&H8O@g9T}23mn)9Q-z4jBiuEw4 z?sjVAA~cMuystu_8R^m`fmH>*^n7W53q2dG5%}tQz6LiIb5W;(Q%R%h^T$fW0Bb@4vY!+a9F=LNDZj8*1+#IIb_y~Bz96Q*K0bqt)@h%cg|TWqtPCsco@GR24R zRj%JNp#MnMk*~o-J(B)c9C4srQ7E%>y60`Fxkx9s_kmcUFWprUlCGtecVmSt3PidrPGpuA4 z)ocXrCC+UZv};A;4e~56BgMquoFW2a>%me>B}fU5z)R&>x2YHZ)eL^=a=I?%{Wi@~ zy9!k>5l#>jp`AR=*t-V&`WO~GblRZTSuzreo=TCxpEKEOn7;<930TQskO2xvOv_ds zUqi_k?jHA<#NL@f)*|J3F^aEU#F*BJe3K(bvAdeFPnT<4&L($BoGANup$=7=&vk+r zweJ~q^Ee5YaQt8;`Rmo6zogH-hRK{(G5d%@NXMeG+-$$H&!I`CZHhuo8PCelyz>C RE9+L?f8X-|cyT@PKLAy;0R#X5 diff --git a/doc/src/Eqs/bond_fene.tex b/doc/src/Eqs/bond_fene.tex deleted file mode 100644 index ec4dd8efa2..0000000000 --- a/doc/src/Eqs/bond_fene.tex +++ /dev/null @@ -1,11 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = -0.5 K R_0^2 \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] + - 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - - \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/bond_fene.rst b/doc/src/bond_fene.rst index cd25419544..d952321c20 100644 --- a/doc/src/bond_fene.rst +++ b/doc/src/bond_fene.rst @@ -1,22 +1,22 @@ -.. index:: bond\_style fene +.. index:: bond_style fene -bond\_style fene command -======================== +bond_style fene command +======================= -bond\_style fene/intel command -============================== +bond_style fene/intel command +============================= -bond\_style fene/kk command +bond_style fene/kk command +========================== + +bond_style fene/omp command =========================== -bond\_style fene/omp command -============================ - Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style fene @@ -24,7 +24,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style fene bond_coeff 1 30.0 1.5 1.0 1.0 @@ -34,24 +34,26 @@ Description The *fene* bond style uses the potential -.. image:: Eqs/bond_fene.jpg - :align: center +.. math:: + + E = -0.5 K R_0^2 \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] + 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon + to define a finite extensible nonlinear elastic (FENE) potential :ref:`(Kremer) `, used for bead-spring polymer models. The first term is attractive, the 2nd Lennard-Jones term is repulsive. The -first term extends to R0, the maximum extent of the bond. The 2nd -term is cutoff at 2\^(1/6) sigma, the minimum of the LJ potential. +first term extends to :math:`R_0`, the maximum extent of the bond. The 2nd +term is cutoff at :math:`2^\frac{1}{6} \sigma`, the minimum of the LJ potential. The following coefficients must be defined for each bond type via the :doc:`bond\_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* K (energy/distance\^2) -* R0 (distance) -* epsilon (energy) -* sigma (distance) +* :math:`K` (energy/distance\^2) +* :math:`R_0` (distance) +* :math:`\epsilon` (energy) +* :math:`\sigma` (distance) ---------- @@ -107,8 +109,3 @@ Related commands **(Kremer)** Kremer, Grest, J Chem Phys, 92, 5057 (1990). - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/bond_fene.txt b/doc/txt/bond_fene.txt deleted file mode 100644 index 9ec4017d00..0000000000 --- a/doc/txt/bond_fene.txt +++ /dev/null @@ -1,88 +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 - -bond_style fene command :h3 -bond_style fene/intel command :h3 -bond_style fene/kk command :h3 -bond_style fene/omp command :h3 - -[Syntax:] - -bond_style fene :pre - -[Examples:] - -bond_style fene -bond_coeff 1 30.0 1.5 1.0 1.0 :pre - -[Description:] - -The {fene} bond style uses the potential - -:c,image(Eqs/bond_fene.jpg) - -to define a finite extensible nonlinear elastic (FENE) potential -"(Kremer)"_#fene-Kremer, used for bead-spring polymer models. The first -term is attractive, the 2nd Lennard-Jones term is repulsive. The -first term extends to R0, the maximum extent of the bond. The 2nd -term is cutoff at 2^(1/6) sigma, the minimum of the LJ potential. - -The following coefficients must be defined for each bond type via the -"bond_coeff"_bond_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy/distance^2) -R0 (distance) -epsilon (energy) -sigma (distance) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the "Build package"_Build_package.html doc page for more -info. - -You typically should specify "special_bonds fene"_special_bonds.html -or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond -style. LAMMPS will issue a warning it that's not the case. - -[Related commands:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html - -[Default:] none - -:line - -:link(fene-Kremer) -[(Kremer)] Kremer, Grest, J Chem Phys, 92, 5057 (1990). From a3b3b761efe7c0586c529a5925d0c106a0edeb3e Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sat, 16 Nov 2019 19:07:16 -0500 Subject: [PATCH 45/64] Update docs: bond_fene_expand --- doc/src/Eqs/bond_fene_expand.jpg | Bin 11506 -> 0 bytes doc/src/Eqs/bond_fene_expand.tex | 13 ----- doc/src/bond_fene_expand.rst | 40 ++++++-------- doc/txt/bond_fene_expand.txt | 91 ------------------------------- 4 files changed, 18 insertions(+), 126 deletions(-) delete mode 100644 doc/src/Eqs/bond_fene_expand.jpg delete mode 100644 doc/src/Eqs/bond_fene_expand.tex delete mode 100644 doc/txt/bond_fene_expand.txt diff --git a/doc/src/Eqs/bond_fene_expand.jpg b/doc/src/Eqs/bond_fene_expand.jpg deleted file mode 100644 index 1d04acec326963cf9dd8b1fed6dbce12efa487d8..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 11506 zcmdUVWmH^Ew`Su60)!A;g9e8HjY9|yAq004f;BYmr188!L!g09fY8ASjWz^p+}+*X z9fE6Mc)ywZ-S6I+wdSr_^JC^Y>zwoB)T%mFTWarT*ZtJ}65xrNlByB_0|Nt~@^As} zX94m694u^XY%H9I2M!JnF5Y8&ya$jF5EKCgihp&cD z02o-<04!`Q{KtgYc#i-Ntue8%ad1iTo<7GX6O?<#tVQ`!&%)I+VT_zYNJRAYN3Y#WhI=JW{rf?Y9jaKgGFT3A zRIbN~bjjqHVDg|V+YH!PA`L(h3xz_f`8EB#K25W@e?K4XGTumeBCq+bx zI=dG*2zC;ACVV#9t_9ca*5nDzXp`U&D=$xLm!_DiJ7uOim!Kt00)g5rW9SHiR zW!Xg8>8HPSOHnEuA?@BT6&&T%h2l`a4Rgrq+ z@;+_4Q)S_3?w3*UxrzaC5r$vP{AjO1!#2D4&Oc4g9$P<6O zt8cgM4WAf20tOc!ypZQSe!+r$tx;EdP;-||>>A6+AkXdBQ7&c$110fj163A=Hl%Yb zn$EBp1W%;TX&Fq~?Y#UbvDq?sXM-UVS>W3BF<_DIvZ|lv7KN6qMW2H~iyZ9qQ zFF-4>l^vgc6J|+E>vg*2oIZDFb(y{9OX|wob*qL#f3vrI ziQRl>g}etm=Ebn3lgJgH&@gJF9`v=%PA~}&p}s%@;oZA3qH4c4gs+sEi)$o5N&Lee zx~aOUw${MrotSi!L?I+`MiW@Nx0=AhG>CrjOQa(odpTc1dm zm!9(;Z%*}K;f26b;7Yd`D zXr|$&t6Zw4qw>P|OWsMiu)X+Mh0y$)5^wG1H>TdS#s?><@8nf@0q%`fr+kQgt=k3n z_dm>T`u`z@zt`~};8V};37N*SsnTnI+gTf*d@u|te;ahf@hXLc$zZ&6SpM*$ZfyOn+k+ZOkUy>g{Ron}=D&yS&tiTcEOBM8`1eGP^<4? zgLJC|TskLDmL}Wclu~l=nGhlC*5%_90xj3h>|r(6h; z=&RfV^p;!K0J((<7p5+Qc1a_mvnX;W#zQ);ERK5snj)axv*z8%+FgrBb?m~!GR2;v0P4p9>q5w?l}du-fP7`2s!`blq3e%=^jC*q4aKDM54VqJ z@7!wc0eQM8!H1pJ^?k$9xCN9%jFjH!#&`oPGA`2AgC~;l3^L=0IUP8H7H5w zb+H?*XU^Ua4Q-_L?QPUEIpStx5cx85vhYoY)Yu!#B1q=zY+H{1UDLwvz1o4BTAAnr|)Ds z_wbp)Bd2Hg07ntj+JOnFRcnG=cctuC`EjXvz{vcIylGWs93JPSy)a8Fri)sxhAIMyx7Bt~aCUwPU) z`%dax1E1D1Gb4{6FN!(@5&F|fgolYgqA0$+OD3bWXJ^H$BcUkCI40eoE*434H6ckI z^lq*#+?B{f)vgJe?5;Y=>tNYu`f1lFLzf}6lpIWfzb#M<*z~BLd4<_b>gwRFG2W%*e=FR9N~cLK9@k>zhS%IwLZ3U2<}5yG&Tj zu7j?4jVNqqvaaej8iBPJh`+Zw1;xbG=>_Y66`%q1ol(he!IC#zT#II++>4TgGfmh5 zyrA7Z4mHQbzL^-2(iuLqIyWluxtPB-y$1}A*GcVzE2;#fM>#O0m3iwbD7+I-)l`qx z84~%eZuH*0(3+?L#*DR@)Raaxi~<{PR(Cd|WH?@3X;~fG=n)J0WkxQ#6=eIHJ&H{4 zCwk+W5Fu}B+``au{&Zv!FXYi^wF8*D)2Gb8Q5PNg`L8PwLe+Gtfc?O-vPNM4k%oL) zJ-FyIVSP}1u5MDhFfys6CP02Z;t>(wq(l4gh#Es)3) zeN~nnt8lr&4}!tnrMMUS=bj1G?@O->Ya|1>t;-FJGA+m}xoW1FN#D@PMMOI|9n#^! zpn#A^*mf#M%r{0+7NQO?IE{Eihjy=l5SO((&DN@A@)Dt(ROc(=RQuYfwK~Q659fWE zbe4?##p$q$giX_Rn3;6&a`K;UPyqCZX7ROhQmq-@OqO%X zuQ#irLmvIf?K$+Qvr2EZ2RUv`x>k%$>Wp=A_bm@KuqRai#0`QhGW(HFliK+I2#ghF z98mAP+WxlSnc5mTIm^jbVrJj&KNC5{W!O=Qzo^4)I7ulMvhPlY4ELmwIHG)}pf#=7 zWmHm-J>NtsuPmav7@pg5cn?quo>u#7_C{)XSkn4LizWx|WxD;-?`K+KiruJE_eVc% zVeuF{Fv73-h#;|9U)`xWuSB9ha?a`x^cy3k@)OKQcx{)EoVyYRro6{^Pi?rIk7+gy zbj^$PM2)gN{6g!OG2$*$!UUsiZm+yE>bYMs^UR7gl|j&sKvkIQYd^bEtxlC08^i7V z&xRwL^b%&VrkhVaa8HN4d!7Z(;86w6o;eR2lU(V>VENd(EdQkJ`IL-SKNYoKH85Q@J-|GVK_%+E{TE#T{H#z&%#Xr;=yp+KDBcTRrd-HXb1j&iF8Ng5h$zH#GY11-UN$_ z6X|ru>I`x>6`fRgVxXPp>MfDJJb>rg1J3(dC_J2|{4;v4IQOeU7*y~aYN1dcT2HX=+{wqb27{D-27f@^W{cTRkF3o?nO6a`p>#pE_)AQ@k^82;>+?N~(4F;Bp;jL#R=NKl;op z^C5T@dl7@qcQ&DmEwly2$((J6PbCp*y&|k5jJ+Pbe0P5e)R>uh0xR}XF7RnB7;gj4 zoY6j8vDaZ@F(XvUU20PR0Eh?xg%(Ut@Kb0iJ7E?KbE6FKi}bHQGx|(zMu`#IIJgT} z9NN+1y_I0vilL#?RxQo1RB`MN``(O0Yc&+tX94MsTLPGy`fDM>_U9%% z6cm+L|5Q{u;oFq+ISYEi^7a@eOF5()uMm`h_)bL)E;(d%DhGDlJY!!~0(pnZYj4g` z+(Q2v4e=T8Mw63k5Q*r?e?%;c=VaS0tj8)`sVjGOKZ9M-7-%yy-^T4l!{EvyQ6RPf z*CBv!{OxSBs?arzV#8Fe-N+`P>_v?!-|4%F(Vi>QiR$52s&$tw?0{UB!Mx%3Lljdl z?4&Wrw*RoB!{X|SzdC*WDwn)=MG3l0t&x%7F0C7n6xYCF@;BiBt&!AT$akBGA#sHn zbSQKWxKpRT2ec2~15V7xUfP6}J~va3LI3#fjigCR{=F#k&JaVEQy)jC$`!L!{=M|G zQ)ibK=cB5-&ZnM#XpL{?CIspah`>tS z9ItQ^%&EUF)iLCEIaU+#c9@W3?S?XiriSZiKH+y4FSptd{G1cM`$IX=#I9maNZn8B z#SiGa5XY4+rz7Co(BbcpiOEctD%l~;ioqLrI>>QCy05fOA^=83i8ke(dQTf&D=k(bhbHS$wn}lxM`-NB7HUCBwb`|R7v#@>%O6z`Z{??Xng#T=|;pc^fQPz zp1jl{#LEbaVQC?Jg2iNLp=;jI)(2W6u{A66ai;S%lOL+pX{kZL_p>PuFeUSCWrMjb z*tFAM=HLJF>pVZ*rKr#~wbykiBzrXtcOy`qZ&6>-p1&=J>21NC%xzxxL`XiA-8oVFg z=De;rQ|)ZZJ; zH7TXs>xl+JJC=az)N=|eqkR&o7Nf8B$aw>wqiH|GPC2claqj`o@@;KaNH7H4L@(gq zJ!x)V6_}bz&1YY-VU=&q-R$%l`D*q6^?M3L>sESgYc!k+GP|=84Cc04tD-cy zuo*gW>o7dQdHjWB4=-ZqbJzb<(OO-ocghg;-G!Mo6sG=fwMNIVL*1#Xo@LKpWQS3C zee;IJrXYP0c-Fg3DwMX6a(rkeii*D7+_U=5F86oBzH6=WH+3Z_nW0DA3zsn;^ilum z>PmqYCfmaflKnuarl2Po{)9(ZhqQ?sZ{LA*JK8Ty0JdPen|6eiLmU{5m&4W6On z6Nwn=s&NIcq2*p40dd%t(&=i}FAq7wFaH-Tn*gUW(g{mfOYeu4VaUr)fpZ zaIY$h-m63;-<=*Ne%h{gaNd-)WNm(l|2Iuz!u1c9BVwK)*UL2S_#Dz=#_|PPQIeka zffeHhV65E-(W??FYXGUZ-UG6rTO)qv!)xX1oj%n%Gr52G@+G=iHi*V~=_>fAZ=r}y z@ajZ@bE*w6qO^#yt49io|B~9uCqUYKM0u*_{5rjb5H=?vYHK1f#A@zHEsfqbo>8+0 z&$)>`rPs46M8@Q-_mUZtv^V5)M^XQ3`c=&@FjTYZl8U6EebCT|-29~FxH1i#HV3%8 z9INmaS@uoq)$VQ@n}(NSKygZ(u%@PgC2&W-e%>1&j@$EUokdA`i_yd?1hthvr&YO5 z83o+5Y7Z^tDu|~$MHZovDt~BGLNoTkEZ*X@914}W3|wT`<+fB|k8Ij=1^0~hDuxtQ zx}%R>Sly{GV#~Dy1ZSa(Nju0(h)vgv=T)Z1J3R!oXB}AxgLf4z_)Io!0?K_@UyKQp zRd>u-2EXg8%^2IysDgGmm-CQGq3~92tZ5dNVKCy;6aP?y`auDbyYP;{Wr4t+`rKcB zTw$eLJv_3E*?FPMM;b(E3TYSvP7%?RER{aC;=2_f8=ss(jQM_X4(tpzCk=!SsKE5A zVK77UrAHtLo&N`7sNL`|UfZfD;U+1H+W(y9lS-j*1*r)q^Y@+;kyl`Agfa*NDH?~O z-MV;B}yITB}MnU<>bcAmH*`?)%n(_gyp-+=+EcbZ6}gu0acB`Rz`S){{1dnd*?So zTidz)8X69T31T1Jy~(Jik|j!_oy8xz9^WEBuL11~8i{sGwjF^bBG&b%Z!<-lPi-pt zdDagh4UV{J46nRIM%xu#B$^Xf{AAE8)1DedHDFyLB(g9oRhc@|sa1aFT=ZK-T{JeO zv$?s;)db5AD=D3}QhgoEj^QXxJz-t=oXu0c2E!Y)$_mr-(9gM`jUCOxpJMHyW-oig zsNK+mgkj==VcQ~fBNV`lLhMgP!=tnH(b4pAB`cZ5uc}v`;n-3&W8V~7j8}NL zY?=Db70i0v)Us^-w0uIy0X?Mq&f9IWXL{Z0Fk;~A>!%Y57sf=>3x9sUr%3jG`E%vZ zu0R63X@@Yrh5)x^Hfnwsn>fDD_YO;;syB17{h06MY*|S(-ZIfIAG}7PrQu(v?roX7 zYaRc){-~7-S}`mjX3y+Svi__)H-r!35T%q?SHd z{`?i*Wcgvx${9!D@c7mYxM=s7&tcBqm44TMP7t|@@j%?Xek`qyi8OYcU^^aR0bO~f z(X6;{dtiie9QG3wA4Wf~3pQyc38Lq6yA><(_gy1pyMtl<;|p9|)%WiP*2m_GErTsB zBih@7mi%pYb6}_0JHM{4BLr*rD0=CUXE9@gtim2&tA+>ZhN;%=0zD=LV&#J$OYi_r zF!g$-cC%(KOqa59Br)Pf`?dqLO*bmf-A*SX7BzeSmpLcuDE*Tt!zI55lfA@EHv8N@ zQNIceZhb?sV(E*y)HB5xL;FKf%)6DOpko2YW2x8)rRI$bu?iG}brU~C=-{RC5`3Rr zN~G9Xxa8H!hLY;k2iJ?atXH+jE)Mxm^dM*?hd_fe%+j+mf-}3o?=dEUVZ*kL5Y*va z*>UQHNY<*0R`QE}$2s{XUL!}e&|}YGCu48fq_Gp>glXv*=EOYY>MCmb&z2z*AA|+MWpzJ#8b3z}n30F7=2g#{Z&U4wg5=Bx3=qzlM z`#BK^g;Jwxp*}bTyyy-KSPgIQ+szY+R2%p-Gl#r&5w^3urLsJ@>_vm>hrINH0;~5H zn`S#6-)tNYhWd2QO6P~h4oq>QytyFRgbTodYswScI-lbzcj34( zJO@t#{YkbR)kihjCfkOz!{y`r$<>S8SvEme#24#DrTG6W&}F#sIKfU_(Ps2oI*P6p z4a(Yjqi)_&4$u0DYp)Q(=bbX>Qgs3`N}<9ISz(?PEw z+9A+GHSXcYj8}MIxE=3a%>|0{Gj1aPu6kS|*fj{3EDAhXrFIEl|01;% z;d9SFD#-RsO|R`laD^w_re;l5{8TXF2TO*&k)qH0WpdTfwRSd!<^oolxbHkTu^r_o z$FKcf8%Fdq&6ee>KnUH`2_L(pG|t2-&)X1~fhe4`8*5=xYF7g5*cSv^J>9hz9i6>f_)^tbfcIqi>H(h4i zeh$9}#QH&{<**qFP^1*f)7xoQ#|&&X5I*b07YPX|H&bu|AP`r~Pa*uSsiMs&&4#3@ zzj2eh_&Q!~^zQ;X`OP7H;JKZwN4~8sNfSHC37hDph1_{&)Uc%?+FbmzU~>MVOP-6w z9iP>K72}h!tm3wc_SY*`VFg0VXAz4o`Sq$sV#hAXY=l0^&BFF#ZlO_hN71Y!*{I5l z&yPV~Gn17=S`BR1>VrVOCf4IHSYvcU%}DMCUp&&%C@?|yqGPGH_IxHRb63su4)no~ ztwm+d&veu6$>^aRQzAo_A}Sx5nU#u0XVTak`^@uz%@g1Zwg(? z{$www9nCmjOG3} z;fsNO0FdABuhbhlLdz`EH;=ktn)24Gr0&fGYy;qo&5zF2*2e6LRa#>{)CKDf2GOHV!mPE$A-KEdJNl7Gf#wc6c+NU$@MJ%r>0WR}>7 z($qSZYih9AtvE|ncshTna}*}+*sQ*-1$^zHk+=h1@2X`4uhA*>2o`d4_@ld3)x9Dm zzMweWuQGyvCq80vJ#tU!lGm)q4l(@{O@YowM8ZDJ%s}n(>{dO>G=y5IX=#8D#9=xB zQ&ol_>!74%@H{aru+y$_(=5T9+2!uSJ#5lu!1YVK-x}1;j&DeV2Z5ccFVdC*(3D#u zD9f+cp$!OZW5{|vF80Mf@+!!RA|hzL5IsoT&GPO099A&B9G(K{((Bvh`UR7F z0P#`5=~|MLKEk*XE>fvVXdYOXA8v1a1*#&4>u6t(C#qysj4BaF!F9W)e3iF+Wtkq< z8&zUdNUk<88VeQUd?p2G33~XwWAy_?J!zt=B z+VF6z_R8tcurXh6wyjll&#>PZcvUt;jDN3xo)LXO>=G%FAM{&gigIA*zmqTWh}COcd3oYPp`#f7Ly`9w`1 znU)bJX)_fA1oER1O14%nX7EMm(enCNN{5t_El%U<^?Lv+sjb1_t{etwR4ZfdyAcS$ zb-V|Nn+1;L>p!dtw5oW~XZIdZrh1dDBPkYuArP3v+1N_ZpJG{VP}TH)AeU`xMtx!+y!oHsxIaV^MtEy={Cr$OL(Z4L zHwUpM&Y1)`jJWN3*ya7KSH#yU5=E(^#{AWI1jQ4NodnrBwy{8AYhbL8@%u1a$2Jmu z4wZeM6p%wKDq%+r;@^-O0vDv07S;%3Cuz5Q1qf)WAEu1<_$sd`H8$3f@1?Y`K^ z^}B2OA!E8ttx~1B$ehleDdXi|D^@NaWUynie}P43Hpo7924frVm!CrLAO~4s+0%R_ zm)7sDF;wl(#}aPsTA6D}m!^X}JhYr=Os&3}cQv07zI&(!n(KM|)*I5Y#OYPE5Ss?&JdwD{;ZA9qmBcOIdGo0D}5rm2jF(6 zj1W4W%IU5yP35O2B>hZ#zNm_)H`=kQc)_%+cikM_!CE!X|#IzxBmc*#i+{fQ zZh-dyCMVhC#F&#&UO`gQXSk3k`FKNr?6Gb|6HOtm{qf=G23WpKNzd>mD%NCaqq<-E zk+wc3pW6&)nlCa3S#@lWl<*~7A)$X{!SwWjz!c3C9rwy)=A*4Z40@A(smKpoVqWy( z%A4kAzovJ`LR}SgS;DB2o@t@QriLa2v*gk}03=KeapZ6PKB14&+WqRkx0m+GZrLj} z{y=z_Y3r#-i3ho7S$;YWxnL;9K)3zZPYzH7G?L8o?Pw8r>*rA0L8(FDdd zo0A%3zC`j+HAl)CMxQ7g*Z$@?2|IL|Gd zY*4Sz{^6Bu&oWC?<$jJH>vcw2>sd0phER6Tqg6$A%4?Osk)cxPNm!OLTprs^t(Rtu zSG;aGb4#8u1N(X|4lLp2lRTvCM3%H`6Xl+g>>UpdEHXP`wIZgQw>nIE9(|%PsF)X~ zd|cWPF)*9qdhBkt+p)T||2h4F+_KIj_uxFgz^ny#P*smC1M$+cZ<2_#WXvxs_kF@A zdxWIJvkK3_A_V&}P53X7W56d$jL{#)(=^z7K|>xA!w>49x6;##>RA-AS|9uNGBRu= z?7H;rVs-sypHQ3VwXydXrCL6?zPw{z!s45r{0@axZ2qsc4sh_eomb2Y4igCp2Ic10 zOH`vJz1H#t_M!ee>*9qq6UV!aDNQ80j1XEHnhw!!6lljwBl>?jFYw?b{s|+E#L#NT zFyq{kJDzzIy8D2fd?933`Wea+89!2=aTrw>U3G;r`uE*Xx6IF-w{DIpjbVj8K=5r> zHET`|T6-*lzSOrDX$h5J0?~Vz-}1F3eYSXJ*vqG5T2EsfVWubSXu0k&+AS0T{zPK@ zS^`3z^w6cReiK*jCer`, used for bead-spring polymer models. The first term is attractive, the 2nd Lennard-Jones term is repulsive. The *fene/expand* bond style is similar to *fene* except that an extra -shift factor of delta (positive or negative) is added to *r* to +shift factor of :math:`\Delta` (positive or negative) is added to :math:`r` to effectively change the bead size of the bonded atoms. The first term -now extends to R0 + delta and the 2nd term is cutoff at 2\^(1/6) sigma -+ delta. +now extends to :math:`R_0 + \Delta` and the 2nd term is cutoff at :math:`2^\frac{1}{6} \sigma + \Delta`. The following coefficients must be defined for each bond type via the :doc:`bond\_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* K (energy/distance\^2) -* R0 (distance) -* epsilon (energy) -* sigma (distance) -* delta (distance) +* :math:`K` (energy/distance\^2) +* :math:`R_0` (distance) +* :math:`\epsilon` (energy) +* :math:`\sigma` (distance) +* :math:`\Delta` (distance) ---------- @@ -106,8 +107,3 @@ Related commands **(Kremer)** Kremer, Grest, J Chem Phys, 92, 5057 (1990). - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/bond_fene_expand.txt b/doc/txt/bond_fene_expand.txt deleted file mode 100644 index 4d7d2d5438..0000000000 --- a/doc/txt/bond_fene_expand.txt +++ /dev/null @@ -1,91 +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 - -bond_style fene/expand command :h3 -bond_style fene/expand/omp command :h3 - -[Syntax:] - -bond_style fene/expand :pre - -[Examples:] - -bond_style fene/expand -bond_coeff 1 30.0 1.5 1.0 1.0 0.5 :pre - -[Description:] - -The {fene/expand} bond style uses the potential - -:c,image(Eqs/bond_fene_expand.jpg) - -to define a finite extensible nonlinear elastic (FENE) potential -"(Kremer)"_#feneexpand-Kremer, used for bead-spring polymer models. The first -term is attractive, the 2nd Lennard-Jones term is repulsive. - -The {fene/expand} bond style is similar to {fene} except that an extra -shift factor of delta (positive or negative) is added to {r} to -effectively change the bead size of the bonded atoms. The first term -now extends to R0 + delta and the 2nd term is cutoff at 2^(1/6) sigma -+ delta. - -The following coefficients must be defined for each bond type via the -"bond_coeff"_bond_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy/distance^2) -R0 (distance) -epsilon (energy) -sigma (distance) -delta (distance) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the "Build package"_Build_package.html doc page for more -info. - -You typically should specify "special_bonds fene"_special_bonds.html -or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond -style. LAMMPS will issue a warning it that's not the case. - -[Related commands:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html - -[Default:] none - -:line - -:link(feneexpand-Kremer) -[(Kremer)] Kremer, Grest, J Chem Phys, 92, 5057 (1990). From 5760de058764d4352e8bd51bafd3a77a179290e0 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sat, 16 Nov 2019 19:10:25 -0500 Subject: [PATCH 46/64] Update docs: bond_gromos --- doc/src/Eqs/bond_gromos.jpg | Bin 2161 -> 0 bytes doc/src/Eqs/bond_gromos.tex | 10 ----- doc/src/bond_gromos.rst | 33 ++++++++--------- doc/txt/bond_gromos.txt | 72 ------------------------------------ 4 files changed, 15 insertions(+), 100 deletions(-) delete mode 100644 doc/src/Eqs/bond_gromos.jpg delete mode 100644 doc/src/Eqs/bond_gromos.tex delete mode 100644 doc/txt/bond_gromos.txt diff --git a/doc/src/Eqs/bond_gromos.jpg b/doc/src/Eqs/bond_gromos.jpg deleted file mode 100644 index 479e6b2d3b2ed907e9191564d8b8edbd42ea3f62..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 2161 zcmbW!c{tSj9tZH>_{|u@h_Oy{?51OBX6_hMp=_0&)Alo+4_lz|Wp zKm-K=Q4nDZpt|)=803!t{|-b1gu+DOVhC}Gt%ho8Km-DUB2W+pgF?5uZ*AQJP!vo? zUC&%p_Vi`A233v}k(eu{d9b`m-nRD>R^Qd{4nkZ(5xo<$>qjkZ9bNLCz55IdjSd~Q zu(Yy1a`cSd*>m;|j!te@+&w(Kys!EP1P0N9={FHu`~r`^yz+Tf@MZ1m z`nC%KfPb>K&Oc%Q<3eq@M4(U*3g31?L}*(DqM$H!Jy99+)9}kwSq)NznB2j{-0~)b zroQbbc~`$)aRn@Sau*4@N5VG}oAPO)A1TSbUM%V9^NN%!l zzjDeZQt&e=XC8g6(cu^>U#;VNqzkB~$xj|KK61&im2G9~_3v-vItc+U6wSu4k>>{0 znO@TeKlE6JwiEM{<5{l)IG)j#tf$-&bI(BJxddF&i$V5b$E;|Zi1Ng{p_w;BdSKtR z&Q=VQYxm%d-1Zc_tMZe(!X;T*0!(wB?&8`061S~g6+J6^V0tGuDeTPIYUQBrW3>(x z^#PYr8t7Z->`Wk8;W0!wGyQkKyVt?=Q`$n#%3`Syc*p!A1me$S=M*&+kEJj6ElBU} zBlx;MyT;!j>1O&5qaR5GMk>ZtIaUw%Y9{fk(Vs4;e)x7j@kpa<&?Q1xbY{rVDqSIE zs))?KuNvH5>d_EZ6B|4gekB^;7-wiKe@wxo5E_2N3+xNbkzS~Wk6Pwpd6b#uM-IO3 z582cEshILEh-n1NpQkWX@558v;aX$8G2|^>e72QtOOmS5ACo_S{Mj9^se#Ua(#d?$ zV{w;*h;T8}sFNylamkD~{Qchxojy$@G@>bGPV|V)T@grz>C(HnO*u%9)A26~<-cR4 zK%c7yR#HeugDo9qwgV>%W3UFxfThNnrx>YC?sOIOL)pbvd;g#I8ql0mLOmhyJoqJ&_CTCUwR=n>|dO87~zs_`adl zz-$Ls8s2H9Om!Kj3QW*^EQaO6UCSPFn9Xvpb*O4qO46t~r>B(>RJ0HmpjC$z$N{G< zw##p5f|$B;!N{WF;RRa7v9+A8mvmg`qt`(j@yl`A<5?3e;gT*V`gpwc!T8s)$C-vU zeI?y;Q4KD4Nr{bLmk}S0cmMDbb1!cb^Maj4xPIwadsn9Od&fmE^e3$)8U3nk2jBKN z^0S)yx3L?>g>R6oTzXv+uVcM?5jkB!-0@KPwQ(@KcE8guX1<%Z1}`Inr${>L+>t=n z&Ie$2+z}B|h2Pw_gKe!wu#~KUl@7sj zL%FQ;fpXnzUsdO{E|ZW1y+k(Cpn9?<^{pNML_GLJ!l&D0q~fEUY%8{v8yBITFs)g3 zl@c?VBkj$(>whsgb>gFx-s4*9fN5yj4!a`4rq2zM7`m+kXcP%2E?sBl^RJ)y?dKDN zt!V`dD|G!V-8moU*G&#m<3iv@VClHkMMauU;R1$IDi~W#vp>ok&%OAH>Wif;so~YsA1Hhq^V83~6!3J4 z0jvmtC>pJXBbTi_fLqlbJDy?fOQ4iIj-lWqZ!cDK00ssedZT>V)E;8+Z!hgTO#=v? z)gGG*Niz1PXV9v)yNjO~HKZw&|I+Tcn{tdt!5xh9B5jL@d+$myBrYW z;GV#vB{&`JEjDqsXi8)nNiv#ERtJm3bL{}25v)GsMUgBBySlvDBZ}4Y^wzv%Ne9-0 zz7)>`c?@k({3LAcsw2j#7dJYR>gvX`K?UnK-{?qc%Ns3;Zc4cuddCPeo)<1Yvw`>Y z*J6a)myDa^Oug95KCX3v2l|xco195Pm;Xe4hc=j1H}I6Q;r%@l)|pz~R2bWSCFWG6 zVnSY7rxS6eCsMYw_QgbmhnI=kJ#)+S5OX*E}9;)$dvnl`cr7C2oFZwp6l1DrHU% KJ?()DNB;%3DAbhz diff --git a/doc/src/Eqs/bond_gromos.tex b/doc/src/Eqs/bond_gromos.tex deleted file mode 100644 index 2cd8c39535..0000000000 --- a/doc/src/Eqs/bond_gromos.tex +++ /dev/null @@ -1,10 +0,0 @@ -\documentclass[12pt]{article} -\pagestyle{empty} - -\begin{document} - -$$ - E = K (r^2 - r_0^2)^2 -$$ - -\end{document} diff --git a/doc/src/bond_gromos.rst b/doc/src/bond_gromos.rst index 894fe7b87b..5d0a4ab1c6 100644 --- a/doc/src/bond_gromos.rst +++ b/doc/src/bond_gromos.rst @@ -1,16 +1,16 @@ -.. index:: bond\_style gromos +.. index:: bond_style gromos -bond\_style gromos command -========================== +bond_style gromos command +========================= -bond\_style gromos/omp command -============================== +bond_style gromos/omp command +============================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style gromos @@ -18,7 +18,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style gromos bond_coeff 5 80.0 1.2 @@ -28,19 +28,21 @@ Description The *gromos* bond style uses the potential -.. image:: Eqs/bond_gromos.jpg - :align: center +.. math:: -where r0 is the equilibrium bond distance. Note that the usual 1/4 -factor is included in K. + E = K (r^2 - r_0^2)^2 + + +where :math:`r_0` is the equilibrium bond distance. Note that the usual 1/4 +factor is included in :math:`K`. The following coefficients must be defined for each bond type via the :doc:`bond\_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* K (energy/distance\^4) -* r0 (distance) +* :math:`K` (energy/distance\^4) +* :math:`r_0` (distance) ---------- @@ -82,8 +84,3 @@ Related commands :doc:`bond\_coeff `, :doc:`delete\_bonds ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/bond_gromos.txt b/doc/txt/bond_gromos.txt deleted file mode 100644 index e039e6c411..0000000000 --- a/doc/txt/bond_gromos.txt +++ /dev/null @@ -1,72 +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 - -bond_style gromos command :h3 -bond_style gromos/omp command :h3 - -[Syntax:] - -bond_style gromos :pre - -[Examples:] - -bond_style gromos -bond_coeff 5 80.0 1.2 :pre - -[Description:] - -The {gromos} bond style uses the potential - -:c,image(Eqs/bond_gromos.jpg) - -where r0 is the equilibrium bond distance. Note that the usual 1/4 -factor is included in K. - -The following coefficients must be defined for each bond type via the -"bond_coeff"_bond_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy/distance^4) -r0 (distance) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the "Build package"_Build_package.html doc page for more -info. - -[Related commands:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html - -[Default:] none From 4a1e9d9483005761f68ff0104d38ddbaff259de9 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sat, 16 Nov 2019 19:19:57 -0500 Subject: [PATCH 47/64] Update docs: bond_harmonic --- doc/src/Eqs/bond_harmonic.jpg | Bin 1861 -> 0 bytes doc/src/Eqs/bond_harmonic.tex | 9 ----- doc/src/bond_harmonic.rst | 41 +++++++++---------- doc/txt/bond_harmonic.txt | 74 ---------------------------------- 4 files changed, 19 insertions(+), 105 deletions(-) delete mode 100644 doc/src/Eqs/bond_harmonic.jpg delete mode 100644 doc/src/Eqs/bond_harmonic.tex delete mode 100644 doc/txt/bond_harmonic.txt diff --git a/doc/src/Eqs/bond_harmonic.jpg b/doc/src/Eqs/bond_harmonic.jpg deleted file mode 100644 index fe9ef5619b328950e68963d0e1b731119eb8ec3b..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 1861 zcmaJ?c{JM#8vR8QiAPIF8+#gw+D+-B%7{TNiB~C+ww6*&w1}m)YC}jJOVb9i46i!W zI)sL2iKU8CYpX5gNog=epITaNg<2jNJ!j7RH*@bf_n+@O_dEBW`$^tP{skxy9SM#A z2m}J04+u!!0rmhC41qwv&;x-&q0%rpIP3uOva&LA2zf1@9RBS3D>d8TX^IfX zzis^n95H)Sn{EjsXfB>%Bv5huI$pKz1!hoys)m=E%e}mBJ>EnLUy)R7g!6cYAdC(USat9|M`t%h=&;rp{=K%wFF9ic*^6H5a)@=l8@PDHD~&fqYN#)60`+ zKO(+VTX7y2WO)8!-*13JO-xyJDxUh#C+|DHlYOdKMhr7+qoi;S;}@p9K1{igIn856 zAGadLkF}MSr$DqFXt6r}xRCH$VDjK+?1txzJgsVMlAh}CkskTr|P`;XMSXZBYNo}(}ACi9*48pA6^nVFQ9K1PJ& zN&~I8M&`OPb~xEFW6In3Qy`E%SK!)_(7US~~hp zdc{i+RF1)&M)Vo!MOUGVC4gbkvyCOf2##wgA}-ZB_0#KqO*2&^&sT`+P3ltD{p}fE z%nU+nvPFvdoO_e5LU~n)0y85D4-Sa+9BbcU1ovI?ig-XUJEz4LH~EC>6X#QmXn^7~ ze#qLOQ>NPk>l4(RmN-)fp*+Q|qQU1O^>~~j?rgjsrkpj3IaC6Ds`Sy^tigkHrvGHp z##+|bceRz`**iAOiz4`inwHj>NUj>EDm{CQq+5vN2V3?5@9c?jf81x{_cXxh=%yZA}{$q)ze|1nz#jr`AK8D-zg; zW6=$+p4)}x3}cKD9wOCyXSOwzJ;8;T&`?Rev*{vi`E`-cks*r~XFk1%jd$Z*wNd7^PlNELNd8QOtK}|>PVJz35}Ao`VO8#2bcDsMMhZd3 j)u@WUnXhi;U4!F=>F)A~`ffG_8N~nlSvXV`$>hHQIt*An diff --git a/doc/src/Eqs/bond_harmonic.tex b/doc/src/Eqs/bond_harmonic.tex deleted file mode 100644 index 2461086898..0000000000 --- a/doc/src/Eqs/bond_harmonic.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ - E = K (r - r_0)^2 -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/bond_harmonic.rst b/doc/src/bond_harmonic.rst index 4718656b91..d65f0337f0 100644 --- a/doc/src/bond_harmonic.rst +++ b/doc/src/bond_harmonic.rst @@ -1,22 +1,22 @@ -.. index:: bond\_style harmonic +.. index:: bond_style harmonic -bond\_style harmonic command -============================ +bond_style harmonic command +=========================== -bond\_style harmonic/intel command -================================== +bond_style harmonic/intel command +================================= -bond\_style harmonic/kk command +bond_style harmonic/kk command +============================== + +bond_style harmonic/omp command =============================== -bond\_style harmonic/omp command -================================ - Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style harmonic @@ -24,7 +24,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style harmonic bond_coeff 5 80.0 1.2 @@ -34,19 +34,21 @@ Description The *harmonic* bond style uses the potential -.. image:: Eqs/bond_harmonic.jpg - :align: center +.. math:: -where r0 is the equilibrium bond distance. Note that the usual 1/2 -factor is included in K. + E = K (r - r_0)^2 + + +where :math:`r_0` is the equilibrium bond distance. Note that the usual 1/2 +factor is included in :math:`K`. The following coefficients must be defined for each bond type via the :doc:`bond\_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* K (energy/distance\^2) -* r0 (distance) +* :math:`K` (energy/distance\^2) +* :math:`r_0` (distance) ---------- @@ -88,8 +90,3 @@ Related commands :doc:`bond\_coeff `, :doc:`delete\_bonds ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/bond_harmonic.txt b/doc/txt/bond_harmonic.txt deleted file mode 100644 index 3afdf4ceba..0000000000 --- a/doc/txt/bond_harmonic.txt +++ /dev/null @@ -1,74 +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 - -bond_style harmonic command :h3 -bond_style harmonic/intel command :h3 -bond_style harmonic/kk command :h3 -bond_style harmonic/omp command :h3 - -[Syntax:] - -bond_style harmonic :pre - -[Examples:] - -bond_style harmonic -bond_coeff 5 80.0 1.2 :pre - -[Description:] - -The {harmonic} bond style uses the potential - -:c,image(Eqs/bond_harmonic.jpg) - -where r0 is the equilibrium bond distance. Note that the usual 1/2 -factor is included in K. - -The following coefficients must be defined for each bond type via the -"bond_coeff"_bond_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy/distance^2) -r0 (distance) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the "Build package"_Build_package.html doc page for more -info. - -[Related commands:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html - -[Default:] none From 41c0d690502652bf2700092eed655e6b9fb857fc Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sat, 16 Nov 2019 19:27:59 -0500 Subject: [PATCH 48/64] Update docs: pair_list --- doc/src/pair_list.rst | 54 ++++++++-------- doc/txt/pair_list.txt | 144 ------------------------------------------ 2 files changed, 27 insertions(+), 171 deletions(-) delete mode 100644 doc/txt/pair_list.txt diff --git a/doc/src/pair_list.rst b/doc/src/pair_list.rst index 3a161fb408..b74070c4d3 100644 --- a/doc/src/pair_list.rst +++ b/doc/src/pair_list.rst @@ -1,13 +1,13 @@ -.. index:: pair\_style list +.. index:: pair_style list -pair\_style list command -======================== +pair_style list command +======================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style list listfile cutoff keyword @@ -19,14 +19,14 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style list restraints.txt 200.0 - pair_coeff \* \* + pair_coeff * * pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0 - pair_coeff \* \* lj/cut 1.0 1.0 - pair_coeff 3\* 3\* list + pair_coeff * * lj/cut 1.0 1.0 + pair_coeff 3* 3* list Description """"""""""" @@ -77,36 +77,41 @@ Here is an example file: The style *lj126* computes pairwise interactions with the formula -.. image:: Eqs/pair_lj.jpg - :align: center +.. math:: + + E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_c + and the coefficients: -* epsilon (energy units) -* sigma (distance units) +* :math:`\epsilon` (energy units) +* :math:`\sigma` (distance units) The style *morse* computes pairwise interactions with the formula -.. image:: Eqs/pair_morse.jpg - :align: center +.. math:: + + E = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right] \qquad r < r_c + and the coefficients: -* D0 (energy units) -* alpha (1/distance units) -* r0 (distance units) +* :math:`D_0` (energy units) +* :math:`\alpha` (1/distance units) +* :math:`r_0` (distance units) The style *harmonic* computes pairwise interactions with the formula -.. image:: Eqs/bond_harmonic.jpg - :align: center +.. math:: + + E = K (r - r_0)^2 and the coefficients: -* K (energy units) -* r0 (distance units) +* :math:`K` (energy units) +* :math:`r_0` (distance units) -Note that the usual 1/2 factor is included in K. +Note that the usual 1/2 factor is included in :math:`K`. ---------- @@ -161,8 +166,3 @@ Related commands :doc:`bond\_style harmonic ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/pair_list.txt b/doc/txt/pair_list.txt deleted file mode 100644 index 9500a4c508..0000000000 --- a/doc/txt/pair_list.txt +++ /dev/null @@ -1,144 +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 list command :h3 - -[Syntax:] - -pair_style list listfile cutoff keyword :pre - -listfile = name of file with list of pairwise interactions -cutoff = global cutoff (distance units) -keyword = optional flag {nocheck} or {check} (default is {check}) :ul - -[Examples:] - -pair_style list restraints.txt 200.0 -pair_coeff * * :pre - -pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0 -pair_coeff * * lj/cut 1.0 1.0 -pair_coeff 3* 3* list :pre - -[Description:] - -Style {list} computes interactions between explicitly listed pairs of -atoms with the option to select functional form and parameters for -each individual pair. Because the parameters are set in the list -file, the pair_coeff command has no parameters (but still needs to be -provided). The {check} and {nocheck} keywords enable/disable a test -that checks whether all listed bonds were present and computed. - -This pair style can be thought of as a hybrid between bonded, -non-bonded, and restraint interactions. It will typically be used as -an additional interaction within the {hybrid/overlay} pair style. It -currently supports three interaction styles: a 12-6 Lennard-Jones, a -Morse and a harmonic potential. - -The format of the list file is as follows: - -one line per pair of atoms :ulb,l -empty lines will be ignored :l -comment text starts with a '#' character :l -line syntax: {ID1 ID2 style coeffs cutoff} :l - ID1 = atom ID of first atom - ID2 = atom ID of second atom - style = style of interaction - coeffs = list of coeffs - cutoff = cutoff for interaction (optional) :pre -:ule - -The cutoff parameter is optional. If not specified, the global cutoff -is used. - -Here is an example file: - -# this is a comment :pre - -15 259 lj126 1.0 1.0 50.0 -15 603 morse 10.0 1.2 2.0 10.0 # and another comment -18 470 harmonic 50.0 1.2 5.0 :pre - -The style {lj126} computes pairwise interactions with the formula - -:c,image(Eqs/pair_lj.jpg) - -and the coefficients: - -epsilon (energy units) -sigma (distance units) :ul - -The style {morse} computes pairwise interactions with the formula - -:c,image(Eqs/pair_morse.jpg) - -and the coefficients: - -D0 (energy units) -alpha (1/distance units) -r0 (distance units) :ul - -The style {harmonic} computes pairwise interactions with the formula - -:c,image(Eqs/bond_harmonic.jpg) - -and the coefficients: - -K (energy units) -r0 (distance units) :ul - -Note that the usual 1/2 factor is included in K. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This pair style does not support mixing since all parameters are -explicit for each pair. - -The "pair_modify"_pair_modify.html shift option is supported by this -pair style. - -The "pair_modify"_pair_modify.html table and tail options are not -relevant for this pair style. - -This pair style does not write its information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands need -to be specified in an input script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -This pair style does not use a neighbor list and instead identifies -atoms by their IDs. This has two consequences: 1) The cutoff has to be -chosen sufficiently large, so that the second atom of a pair has to be -a ghost atom on the same node on which the first atom is local; -otherwise the interaction will be skipped. You can use the {check} -option to detect, if interactions are missing. 2) Unlike other pair -styles in LAMMPS, an atom I will not interact with multiple images of -atom J (assuming the images are within the cutoff distance), but only -with the nearest image. - -This style is part of the USER-MISC package. It is only enabled if -LAMMPS is build with that package. See the "Build -package"_Build_package.html doc page on for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, -"pair_style hybrid/overlay"_pair_hybrid.html, -"pair_style lj/cut"_pair_lj.html, -"pair_style morse"_pair_morse.html, -"bond_style harmonic"_bond_harmonic.html - -[Default:] none From fed5d07aa7405f7c9874fce38d4fba0d3b9e267c Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sat, 16 Nov 2019 19:36:17 -0500 Subject: [PATCH 49/64] Update docs: bond_harmonic_shift --- doc/src/Eqs/bond_harmonic_shift.jpg | Bin 5078 -> 0 bytes doc/src/Eqs/bond_harmonic_shift.tex | 9 ---- doc/src/bond_harmonic_shift.rst | 37 +++++++------- doc/txt/bond_harmonic_shift.txt | 76 ---------------------------- 4 files changed, 17 insertions(+), 105 deletions(-) delete mode 100644 doc/src/Eqs/bond_harmonic_shift.jpg delete mode 100644 doc/src/Eqs/bond_harmonic_shift.tex delete mode 100644 doc/txt/bond_harmonic_shift.txt diff --git a/doc/src/Eqs/bond_harmonic_shift.jpg b/doc/src/Eqs/bond_harmonic_shift.jpg deleted file mode 100644 index 3e66d853a5173e56376b35bc8fe6b46c7732274a..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 5078 zcmcIIXEYpIx1*OR(W3`57-L))8BwA~83dyn zm(u`k01Xv2H8mB@6{4Y`p`~M@r@I2yYu6Z<*jU-w*;v`wIJgCPI5_#Z*w}7}+~5-w z6c!fd;1LCi3IPR#goQ3&1Fq2n5ESJU6l{RYet-ag0zh@e;)=-y+v;ryaB@B0aq|f8% zmFsPLXI?hj`0+d>V&!QeXnT0nuqnEfZkNm0)5{U^*lyv(ATP+bLaZtXY)G^RUklWs z)Pj?+RdFG(5N}17jazf)PaWlup$YuHwzGc{M&P+E@?bNomMppANf16j;$_@oq^F(o zO7KQ`?qASkQe*mw6^~uwo{L2~3t~Fjx6IRoJ+pLSk>U98P?LH?8HK6gY5G`5a(9$1 z)^AsS;|0|U=w?t(9=F&0Ks{xkXvy6m4)B`*_Sim0o3_dlPQW6>z z^Tc{EJUuXV0x1CJ(of>&!~&AGdLl#*I_OgB%PTss7y^av|nUl|~e zQU)c4?s|M9Asgkea!@g~r!p`+%e>y~q7i+vm*-PA_@}lP!W5IXVRjQhmv?K0$KL7^ z;Cw2s`_^X{s~(l_lkOJ{g;|xWK>I5UpO0slJl{xC(_r@^*NpKLq2gUlx4!bE>UIx? zt-3T+Cj01k`ZY~u#91IJk)FWE({0)0@3o)nPr13$C*AGljv#d#vc08ZkZ7|7EIhmw zkp?#dwN4?>xA2lj2KBf`jh>a;pcg`?)hmioL!$Bl+EC%Ou^-(|W)D9l?M}hD=IwLp zO(AU-3o{;v{B)ty_b0Pe;48BNY`Nw=(#x>yC0HG^*x9%hXDLU^vDo+*=*9RZ+ppd? zN4*Sc>hbjc{hwC`qfd4o&0`;8U6ogUeRgwN!CeBRCP$-jJM7=(qQYaulHzyb$TP84 z4rfCKX9IWQ@e>?%o08WU|EU(#JCnxOF;2}xFBXbxTiz<&E>?YOz7ew{ziukwsMW}; zc+TniNR)9!%NZ5tmJwer0zBmsr09i?IdA5Ow0PteB&>=Vy8^w;?92q3e(>-;|FjW5!8nzo|1P348qZ1|UB ztK#-VsGTfvq|17S9=Ov9GUczK|^Eck4KX zJ~_{y_9uMq1T)cvm+71sfT@ej%Ps*Klvs!DuyY-dafhLwbVvqz>6y02kfp@> z1^*?$^z9{p6#KI}ETxUV%h(9wJEu_1NS*Nc-Vl`s5x4$dPCYAyoO7(16`S4l^VMK= z2j!k)!7?vD_*%@oU&PUM-P6wNQ3~X7uSNCLXx9c8XB#G)^iI6IH)_Oi&3I9B25@0y97l{ATy;*I352Z5zU1){P<0dr@g64D;R0)gkOWdQ?GRDZFC?}(}b z2i&zxmpnrmYz&hY%QyXX9tn4L60=gWNGd*2uf$ajdya?GNm;q6Wt$j52NN6pJ{8)cKhb>E&ea=n9k*?*= z0)Bf3{oe6C1NGDLqBuDpCDTqfj!hO@nFgn4yw#4<2^yaLw=DqIsMBIrhofGLMIX_o zHROzQxs%nDz-YwCU0UN#L{$8&vziLyiI3QnUOy@}p=y6Tm|S>ozbDO74b-Cvv-~SG zCHD>KNM{ha@)1tw20kn6>3GO@uPOHaAD4h?X{YTk5D&O@LKN<|)};2--pYyt<~*MB znHvv*=UQ4NeS1_m)$g%^d|HtO{y95!6~-jL>}lUkhYB~CEf_D^%UdOvDMG66L&hxm zvKuVmB?u0`AjT-%>V=9>=r@*IFuxTUmBPUIPe8e7*i+7OawEdvu=?12TSn6kiYOh( z)?e7n9gc3C@A;fnTsVE!=MVSf#js_7VD~3#wmwYB450cl^+D(} zhH+mg!ip|-x9FR7Xnf~FE(*uE`l)+WS~fnzA{f#Ef{TFlDesX=^(k($8vrPc;b#hi zYQzth0N&YNd6P1u;4SG-dj-=63jZJTX2>_c)65FCiXY^jyBdR5#t3CqX) z)IR=t_@Hj*iCYC=%dcX?B`C_0#no|(^D_IaOMvIE%*N(rn4+DLa-T=@yCCD2(PQ2m zrl@D`P9S?kc^ur(?bx1y8uF2EWjgZnsI`4>CsWN&{QQdjqhD;N1>6K=%2YvUmunOI zRMeQAkObRtA>YNVCg-8H8_a6y%qK*C!$hDj!~pQ*XKKXYd;GP$_y$J_~}Q#4%bItw1-^uDMubS6=jQz&zL70@;ZFXej{-o)S}OzaRRzYu|^Z{ zpW;IT<1kNC*O(uw)XTmTORgXO4cq}LVw6#IPx45k3_)+kyQ%8U4^F zfuoXDGr`aoJ(F1zu}9vuGKDsxMlMKeCj33QMSG1%Xs2>KB8)PlgGNfQ3#;*DS(B@- zmKBb0xnH2ws;qDj0Y)nx=EndZvX>nDzl?pvY_-HTFuuZrnL&R-@$fh6G!IfJ8-!`f z6^iXFZ7z%rg5T#g+e57q#AHI}wwDr7Tv7{+ND~PGyOwZRoH_nMLG?{aeXielI}N%t zBi6$@xW7+eez>)6SWptY!F&8taCp8|YgQn?;JbH8NoW^XZM1i!^7o6h9-~2e#c;Oe|mJgq-m zD7i|Oto$VgE<%Pj^MJgmeO9rs5OWl<4$UMkI*`y{Amk>fm$xq+Q7`LlsXoP7$ z^SUVvET=9J`y#3Tqh=U^sa>8{NX%Z;F9p8|sXr=TthadhtFWkS;+|8Rh40KJ+ zjltl{SkQS&hdi`(1-4$>-=XAgbY(+>t4Lggx6ZUR)if8yQ%c0jqHE^$ctS94@v1 z$>Vm1IPMQ#8iWM%h$121fht;RXCbh2tDPOOjRk{8W5LYFb8#Agh!^Ls&F_PyiZHWC z=Hb9hS`LBJNY(pQRcJjwKM35aJ02-)@uIBO!&bdXHkOqA+wp^}=6|K5*gt+Z+x!(Y zVjJAFJPno0zXY(WV_~7^n92DaF0-+Fjg9M5hhg4A3Je@aKNTd#KT)7x8_1~YGh@P zx7lT`#={+l0hy4B77H zc?k(B_ot&OPpHBJSE zzNbBqe@P*(lfx8W)?15iP+Yy8j&gJeo@VYbB0;9^>$MrU15bTQK)LnGk3%oM#og#TV0PH97U>{aWe&I8`FU8rk*E(bkGLCtN!va$xt9A zhqik{RE_lTdq0x7eGNp9c;=$9^C~kn27SUBgO2*TxG%)>@j^mKd52JhyWsNudo9IE zUbS(>mZ?2JwAamLcyxGPY4oS2MTp}BmI^^WI6M*0bdr!#HN3d0E z1`a$S6s7wUWqPR2t(3qo{(y0;NmaYQPp6C&H|EYw zJrP{9YJ=`B4MdwfUTjBoE@qdD^={rH5z zX$cl&aOb%`@OtER?=pRDV{AnRMg#x?>wnf4(qKio?9K$=99S@J(S)_#coCYX{++HM z(1cA?Yfg2FfdVdY;@{8Dz` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* Umin (energy) +* :math:`U_{\text{min}}` (energy) -* r0 (distance) +* :math:`r_0` (distance) -* rc (distance) +* :math:`r_c` (distance) ---------- @@ -88,8 +90,3 @@ Related commands :doc:`bond\_harmonic ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/bond_harmonic_shift.txt b/doc/txt/bond_harmonic_shift.txt deleted file mode 100644 index 23d3dcb5d5..0000000000 --- a/doc/txt/bond_harmonic_shift.txt +++ /dev/null @@ -1,76 +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 - -bond_style harmonic/shift command :h3 -bond_style harmonic/shift/omp command :h3 - -[Syntax:] - -bond_style harmonic/shift :pre - -[Examples:] - -bond_style harmonic/shift -bond_coeff 5 10.0 0.5 1.0 :pre - -[Description:] - -The {harmonic/shift} bond style is a shifted harmonic bond that uses -the potential - -:c,image(Eqs/bond_harmonic_shift.jpg) - -where r0 is the equilibrium bond distance, and rc the critical distance. -The potential is -Umin at r0 and zero at rc. The spring constant is -k = Umin / \[ 2 (r0-rc)^2\]. - -The following coefficients must be defined for each bond type via the -"bond_coeff"_bond_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -Umin (energy) :ul -r0 (distance) :ul -rc (distance) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the -USER-MISC package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html, -"bond_harmonic"_bond_harmonic.html - -[Default:] none From 7aa74ac250f38bed0127343a20950dfe06814d96 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sat, 16 Nov 2019 19:53:38 -0500 Subject: [PATCH 50/64] Update docs: bond_harmonic_shift_cut --- doc/src/Eqs/bond_harmonic_shift_cut.jpg | Bin 5184 -> 0 bytes doc/src/Eqs/bond_harmonic_shift_cut.tex | 9 --- doc/src/bond_harmonic_shift_cut.rst | 37 ++++++------ doc/txt/bond_harmonic_shift_cut.txt | 77 ------------------------ 4 files changed, 17 insertions(+), 106 deletions(-) delete mode 100644 doc/src/Eqs/bond_harmonic_shift_cut.jpg delete mode 100644 doc/src/Eqs/bond_harmonic_shift_cut.tex delete mode 100644 doc/txt/bond_harmonic_shift_cut.txt diff --git a/doc/src/Eqs/bond_harmonic_shift_cut.jpg b/doc/src/Eqs/bond_harmonic_shift_cut.jpg deleted file mode 100644 index 06640e4fe0899b858db74b9e9297879ccdb50421..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 5184 zcmbVPcTm$!xBi6^Ksrc=Py(Vfr8fyklp+eR@`_Rfr2B>*q!$IHNkWre6#)?t>AeVn z&_Wl2bO;c-p(7<%?>BSr_s9L`e$URF*_l1F=j`sYXU;>$lji}JyE^(h00;yE^nMS3 zJO#i3YDy|9DoX0#hMJlhOv6A+^Bc_c^mGiY%xr9|%&e^Jocvtumw7o@S-FL|c?ARn z1qIo;L_|d(qWlm+2)PZQrv)rQ1t1VBK*j+400^L<{1fAUKnTJ@wdw#Zz^h5Fq<$9yX>t8&n|OtiO4-l9;4+{)VA@KSMqpORqYuXpELp$ zRe=9(@;LF``*O@E`3FGzCxj+&o*em~;%$oWPVdQMo_b6X$$Xy&8RszHsnndVV?C}} zG-CAiFiSSq`?xsU_>I}atGUeqXv=e_FZTbGZfIXa5 zeCYZtI4iU2XN7*6$@@?helz+!ptON1{T@vN z8QI(A1Nj)=^UUI`vf|yhMkngLK?GT}`;pV>BQk)|Fm0b`KSWk?J^Mf$Jhu~@@#Z`K zDQ6$isX7Udui-NNt~Pm&MY4o_Wg2g4)AgPLq<|S*IH5BI z(0zPQN)0dMMFx22mip5gMy#hI`|cZvCF7RL>uR-+$N(-jeXXQ-g@Wp32hVdvjoK}N zhUlX#`K6o4`P7@zo3CTbA48E!qV=MoW;j#{YD6JBXKi*M0azOi^I}T*`}U(97FFt5 z)z_i3>U>sEPu#CD>(I_hOSzMLXX^$XtT6Dxt9DczZ>=N(AEeeH@}Cpf4J8KS1`t|z$L{T4#uz)nm@RzZvQv#EL7fJv!b`R{b)_y&&20? zuA~v2pGas*WrF*euJB0;`r*mIJCjLE zgGw%)NpAk}y2x`coiS`gTFK!*;RXk>>_$BPXdSa44(GJRcod^_{1@rx!|VIdib@d? zk3IF9Af1i)K(QM8V7~!7 z^SEv$D1&r3JEQ-mxGOQH9$WOo&3Jmzu+b}2dxE4Ht(@r|7{QTnN`wbuCYSAk>@bs0 zPIyXVYsTv{=3GmU##6H0FgDAab)y9hi0|zVBE4$h&hlr&vWrS?wjUL@5$DW!%0Es2$<7&DF&k~cr6lqC!ub#p=n&f+dV3`%WeWG>?A5*tAG2B`TMlm)Ro%u zeF(I3LCvO7TnG2o$lCWcI}wjRRK@tn1n6K5zE%8APUHk?kh)U6{Y>cP%7*Qt^5kP* z2iMNEUEiC0cwV$v3(0H{qi!I0b?gQyp5N}gG`Jt%!Eq$cwo1Tg0 ziUS7R--{9oBNh=E(D4pdGk-L9k9RK@vv6=>boX*Fl<`GK- zVryTe!q+$z|Jwd{8rx(*w?K~WkVaBRu24QK!FCsCj(03u=KlJ+Dv;qUd)C7Q)Aw&(hM7v@ zhh_rQ%)I|LN*g2tn--2_;ISqdNRRv0n9$${3kYN9f2#S{Xu57)WAJPN`o}}AP3&FN z+e9VDJ5+{ATj5+dVMadT5^I@&MsLI|(L*5V;V*-w9Pd5NZ)t9Q;v-i4r?qJp41K|- zu!Q5)nWn*?4(7W(`zcu1)=Eg2++4EJ#}?HiH~BN3zeq&9lUEwDdOY zEAMRAAye^%OmO!%G9b6u+Syfo(<2}Ud!w%7oXH?z@$(?*?XpKR?g9(;$_b0EUCryh zAG<4?!0nj)1iuzud)a=eAL&iI&aggVJ7-Si;<>|AiX3>ca2^cTO{$1YQIszq2-0cA zbzwblZW(J6&<}2U?nA>=p-W@x6a|f#FKQE@ zk>t2@B)BX)5DQgF*41Ty$@^Nq7r(s)UTdpMbip_{EFJe72@>k{ed9j_nELuqhoJ~v@PpWRdxE{O3D~Yw zPH!GH@JtwG%L_iM2{=_Wlfk3&RkwO4v-o8jbR(a6l?mtBDaKF_Xf!J3CK5psdH+Tf z^HfXZn?Aw<_ECP%Qo0TNsauTQKNtnNUn6~#Pv(pe;R6vxmj*sTD7#M~0-92XC&`|w z7Fj)7n-;52Gx8gc6%_O4hl%ffXW?lMH+2Y2RtGOTA9F;1IE~#+UDb`xG=SzswJ~b* zEIa#nhk4Cg=o6dnesPH9!5R}(Rd&;y5Y@@sy0lT1dNe-Z*!x9y%m$EwN_^rnYBMqh zQp4aBwH)4V^Tna;bqe)5 zK1QA$64+jPcfeo|CFw`Igz1vl_NJ*WWmyaJ)EHd%d6rAJPg%9it{mIfGNx!3U-P^h zT5ajn@7caMv~r+uG)!ZS#^Mc=3~hImc;yPW&yh=I=8IKfxK-| znN5PYbO#zOW+qDnzBv9Ot5}p z;TT)ff$?_JO~@W2Y3niHsG2~1FwELdVFOLrd%u5JeMylx`sV9+8M{rm(l1#QFG9Bs zpcuz3xKH->mu6swdfKoD73xW8@@8ACW0bD|Vti|Kn6PGv7!=6Vfgll~b15iaE5E^U>dq5&EUqzLHpG(!@%f z7dfGk?)lE2aL6j3Zs1y+EGx)xU=O9iK9e?#W+ZKLKNQ)4zXQI zQ}eKRsW+SA=Xpb;5zSz8 zRDm(aw3)5g5aGr}d6j+Kyid;w?C0w)tQ?vhu97}z^JP68hWvZM=rzYz2*YT(2i2dY2Sf9YCWAuo^tga1y6VFy%IKKuJ4Pg&j2snqNDL{DD z0M$#{tLEBQ5(qpYQ*C#N5sq3aRXvAU?MaRk6{u~+g9H> z$c+|9Og0B_EU>aZ2oyx&(-gRFpTsgmRS?Ir@lE(et*^&fkMfD( z9gE>V;_0uZ8*v0bpGeiHkdG$^srcG;JmP!AeKOFW;283yy1w=Xp$?6}em(x-wZcT7cho1zGo&ZdZpp<9Z?uV_GG*h=&-qUWPg}1)g((#%-HgF2MetXq;NbrhSn8)GPLGYlPXX$bMDU{}{ zFPaQ+@z$3za9;VsnNjpWPN^(?wUa)prcGeFJbMVY8Gf`j8=lS!{v{$J&0oXEoWdGY zBZ1bs(<){5rN>_xzwt@H?MKt{&;4CrWMn2x?K-1fTsxfi7+a!iRi|qMu2IssG-qqp z1(tnZ>NEs60WBXyr0L2P?FMe8Jx`E~zfI&P&b(L9ZG~g2Xo9SRZp}tAxqJT_>V4)u zY07iOm|c5s={Z8cp;AB3fwfY4TM+j94@&ckp{9A#iyQcr2OlSBf2?Zk z1T^GGP8(z&H6CTIvgscsH56qFlL7N4l?%I!vqF(CPJe3br(l7~m6o7E_lM_??)ZP_Akb=TTIc10CsFx}0JGKQ^O{YZP@D+$QAjOr7$!p(8{O;&R#g428G2mw*@@ zkg1v>10SD^hy6qZ(|-_=a75u_c7%TZ)~rh&QF5w!e0r`rUzM&|;#a(^qJ?xOqfCkBKD+OhXu@=zVFP)ZW4SF_ zMD;I;{x5sS%8h#16=f|j&B&?Gp z1(qk^3h(N4{JmZ3GnuR>8NarSS>=?s4Ex9wk9U$fxKR=tZ#FQQIaw>J-5gY#U!9Bh cu+?oI01f!;JkJ}>rThEekNF?Zt;m!A1 rc. The potential is -Umin -at r0 and zero at rc. The spring constant is k = Umin / [ 2 (r0-rc)\^2]. + E = \frac{U_{\text{min}}}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right] + + +where :math:`r_0` is the equilibrium bond distance, and rc the critical distance. +The bond potential is zero for distances :math:`r > r_c`. The potential is :math:`-U_{\text{min}}` +at :math:`r_0` and zero at :math:`r_c`. The spring constant is :math:`k = U_{\text{min}} / [ 2 (r_0-r_c)\^2]`. The following coefficients must be defined for each bond type via the :doc:`bond\_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* Umin (energy) -* r0 (distance) -* rc (distance) +* :math:`U_{\text{min}}` (energy) +* :math:`r_0` (distance) +* :math:`r_c` (distance) ---------- @@ -87,8 +89,3 @@ Related commands :doc:`bond\_harmonic\_shift ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/bond_harmonic_shift_cut.txt b/doc/txt/bond_harmonic_shift_cut.txt deleted file mode 100644 index 13ccb5843b..0000000000 --- a/doc/txt/bond_harmonic_shift_cut.txt +++ /dev/null @@ -1,77 +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 - -bond_style harmonic/shift/cut command :h3 -bond_style harmonic/shift/cut/omp command :h3 - -[Syntax:] - -bond_style harmonic/shift/cut :pre - -[Examples:] - -bond_style harmonic/shift/cut -bond_coeff 5 10.0 0.5 1.0 :pre - -[Description:] - -The {harmonic/shift/cut} bond style is a shifted harmonic bond that -uses the potential - -:c,image(Eqs/bond_harmonic_shift_cut.jpg) - -where r0 is the equilibrium bond distance, and rc the critical distance. -The bond potential is zero for distances r > rc. The potential is -Umin -at r0 and zero at rc. The spring constant is k = Umin / \[ 2 (r0-rc)^2\]. - -The following coefficients must be defined for each bond type via the -"bond_coeff"_bond_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -Umin (energy) -r0 (distance) -rc (distance) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the -USER-MISC package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html, -"bond_harmonic"_bond_harmonic.html, -"bond_harmonic_shift"_bond_harmonic_shift.html - -[Default:] none From 64c31b377eb681255d0e31aedaf0483e221bb798 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sat, 16 Nov 2019 19:59:59 -0500 Subject: [PATCH 51/64] Update docs: bond_mm3 --- doc/src/Eqs/bond_mm3.jpg | Bin 5814 -> 0 bytes doc/src/Eqs/bond_mm3.tex | 9 ------ doc/src/bond_mm3.rst | 27 ++++++++---------- doc/txt/bond_mm3.txt | 58 --------------------------------------- 4 files changed, 12 insertions(+), 82 deletions(-) delete mode 100644 doc/src/Eqs/bond_mm3.jpg delete mode 100644 doc/src/Eqs/bond_mm3.tex delete mode 100644 doc/txt/bond_mm3.txt diff --git a/doc/src/Eqs/bond_mm3.jpg b/doc/src/Eqs/bond_mm3.jpg deleted file mode 100644 index 2c17739db57e8d147166ab0a4cc768cf80f534af..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 5814 zcmcJTcQD*vyTHF|mDNj@D61|(M3f+UjULf^iO$;JM(;!?RwoET1kp+Kl0=D~=q;>n zB?PM`f?%)T``)?l%$+-T?!7bjIrE(J$9d+=`J88-=Q;D>=kTiljh33G8UO+T0O)!E z_ys@(fDjXt5EDU2NJvOYA!HO#N(ypv3MRT6)KFGtb~aXK7>tAaE-wey9XJfecc1@` zu!xwL7(1_&oTRAi-Fsr9e;)!OB_*XGr(mR{WEACuaf<%01>XhGLI55DLokR7AfN?- zX+ij2fc^TOM4*2N@b3a5022}slR!wx$gd5WXaE8b7)(G2CL$svytWR#-UkS2iRd^* zl!$NW+mUd2LPaCeUPIu@b=~v^69?S)?7bpM$rx@jGBNYq;^pJNEha8;Us6h1<$qPshPQjgQJtPiz~v-+sD_>KOitDDmo@M?pZuKJ>z+1R`!dW+@j)=H>G9e z6_xc3jZMuht!?d}dV2f%2L^{ePfktG%zmAl$E>YmH@p*U9hGv-7{X zKmhokSl9DE!Tu8$?KKwxAt9KM9Y{XgZ^VMz1k3K=I9tOljr@eoBdNXdkso^ZH0PiME(WmbFI{>p>I}$)#!!D{O)>E z%t|KU<74tP3LzI4*Z4&y+rKq(lJAWRYS>(lKy%MadNu}t>Z@L>jl){mlxd&5;Me^p z%!1NW`r72&>Hc%|Md5!;CGU)O0VMhnifs9+-oNG9b%L&z@qn?pgQdqO7PCz!7&b@i zr3f}=OZ4e)MqQ|t#=ye~4nOsoyCFHORAgP~v0K!CRql?V&I&0{H#Cds)V8;RL|;ao zPE}?uoxCcV7g+qlTGNP(=%=Sw(*+lWi|Q&8aa;7~%N^9C_as`KoQ>K0q2UXtVo-VgawLjCAyqq?uaE$JTOfxUJ&WLa_JxbnF%jm@ z;i13`WTB5g23bFvTI=oLzZsO3U$bCIUY5LWZ|JeZqLQAcs}zxzHtKCXn(g=dTql1c zjj>>zFtb>p%UlV5FalT>wT{tSEG;8Xs;JSmK8)+lcOE)PXleU!p7MfI`r9elFfuw! z4=i4ur`kToc|YVvP?y8Mf#(&Wpfc6K{b;eaXH$+Hhu>e9x5eMGBrXt_X^!PYC+(7y zK5eUw>Ye)7H=9}5-=|h46Iz(u>5}BHp|GlM9|{{MQG&&bA-NybCW=;}@7vXoN`_jrA9?MaiPN1kZd!<<~FfRef2kc3mI}@kZf&x@z4VFdyDr;JqqT z52Q*Dn^JctAGsHuL~Nd7r%0!7{`eq$YuQ5c@-;($n2_v6(uY#^l+=Bqr+;}tb}Sl! z6%pALfuOS&OD(e4uWZk^H!o}*8z#7CanJK=_*mX7%wTPtQWizQ1LcO(WJ_qH0%(>5 zB}=)J-6ES(A<2ZQ3nD0LWvINWsJ!Vt(syBz$S`C7SdTafYAUmiSYF@J8h5ZSHq7rB zSAX2l|GtF%0A44b>;^K1R2-Gdf?JQ5f;Lvct);4B zh6CSKxHNL$UczvW)x;EKNHrdy*{1uEOFz@sO1u?8Utf@PFEuR+*Orx!d=na{(loid zR}ya7n|9}O<*0Hv=~)Dmd{wZl8_S0Z`W# z0DXtC*}?dgd4}DpD6vuZ6!Y6_xh4LCRf#tH8>NRui(*CJ9Br#( zNN>L#ReI<^(iB7qKut+&&6lhLO7|Y0>OA==6HuHa8|~UG+0C6I3}XvQaa)>MLn;ug z^dZ8$tnWA;?Nju<8J$$w|1}10DT9JOS~a(=BXL5HW_>kwPRa|cTmw3)_ZXSoo?syqy)Vux zN?EVQu(t$nd+tRZn<~*KdFDC9BnwhxeQ7{yuX$6(T7@DJ#%z?vL)gE)N>@@b3Xz0w zQ`!X-U2Tu4MlLVw-o*oYt?1AEG+|W;DyD%ym8@}piW(ElTrC_u4~eR8(?SUb03X0H zqgx@Tki5~v$Kone_GG*#j3UYVs<7C}@yvf!cs0LM;@(T|$wt@f1bv;PbNA}{M|bI= zbi)GxXmQr^^p&c1AaAHLPcqkoHbTa_NbN)?MT#Gd|sl#u;ZSL-ka@l zku|;_*|mcg-oFpnNS<+gfEgzCvVI=&VZ()&@ppL$C;f%m>GD=KbMWUO_?WM(!H6&a zpz|#W+v|TH%+`aL2nhLcsKq^b1>c^v2uiRt8@A+(+fW_Wcm%9^Xt#Y@LXmBy)^g!AW&I@Sjg<;(UujyIPNhn;3Jpd#u9BY11nwNAOP$ZgKtZ}D(_E8c!An|RgeIx7 z`x)~_uYTCLudRRvYC>2nEk9Wr%m`wBIeTAKB3MS0JC`<}1i!Q`AeMvcP5La^@FW;a z;e;FvGqqosC{n+(MW7mMq(}RzQGW^AHrT3I_K{UP(ngX+B&!1U0VKUT>tQ73k9GUD z!R`TZm5*KtM9MfOUP4ND0w1%T8t3ha+Nde4h*Yo_HT{KXr%EYqXwEK~n`?}sLZK$P zR;&x13lE8N?!HF2ii=R7!R-#UeQlkBBVo$EyWo0;F#`{04ufo>g?B6Rh^{HDDH+r*a zlP2ULqtt3laQJM^IH9S?7s1AO!sQ3mt(tzsm{5pv=b5Y^SHpFy8{TQBSH50{9Kojdd1*?y?H>Uc6>nUh?!zp;&6u?u28|Mf z>oUg327yn8OLoR#jB9>Jre6naeXO~7UWK^1fol(ejq>43cGdZmhsME6e&@Q>0WFWw z>qdF%?fHWC)Xz@3iaE23pK#XeO2QetYL6K0TOuVnk{rhJ#Uz*V-yTo#dhuN=HfHKtJ`>lf!+|(gyLm*Yy`**Lt8DDTh zQv(E)&{k*hWtLT&(`toNA*xPyD{R|gwDk+i)OWY_ge%B;(b z;Y6_gQ8&|ktTL#;k~PK!4}2nB#RKQ`VhR^GRq#OX>~OP5#u=M$wP3K{1h+AnCjSM+lzh>i<+1UN;Br;;V-THORmQkDON~5sof7w^;{6ov zt%bH3{Rt@#Em$;Gmikr2uMz+I?M_**8<#Ar6T@Skr~pCX>XMQh{uL;cU^U92sWFmI z5X-1hq*qxyM+U4thpre0|))T{RN!BX7|PsS_y8I{txg)!*C zd{>4lq$OE3k=QI^v@0lP5azR+I)Dokz+Fhc)MX;QKoD)3{QiyE;i_GyU{fI^RW+Y2hAZm|G(=L-tlO?gLf{`P66%Amo*tcen zP8s^K`t^~PNoo#N4|x*r?>l;Pwa87=1HTw6Z+38gWTQW1kDm-Qu@=1wSc{g29~EZU z8GNL|Rcp#7Ez(A$C?$)~39jASH=L|(sbsO~dJ7d&qfsm-pi&Z`*jeHi6U zoCX>d?q$=!dhYZAh|^LH?7`EfJJEqiI~j>k+2#@LwbPQQ9t$Ib&0%dx z^1dbFSAOo*u-jdhOG+wiozzaB-;BxVCzhM-uKv#79c1>T&Ypo&+@I?aW~Gf$R;qh@ zp2Wv3XWQy5o>OIxZnr&tcE#fSC&?+484q;6pguCWNb;pmS*Mgh4%P_WnP$0^_Vgx5 zC%z*45QuAIiVY%A!YMM}{EDzETU^!<%{mmTmU~VYmT7w-m#+Pa0AbpY|Mg~F-ca7m zH~YU#{8Rd1`KwEP)OAq=Jxa&py{og%n5ZOrA zI?@5G$M?kk zXcc_*unIQYH|?T1p<0_@N2fuOi6qpIMvDf~k&s1IoZC94l9{$@^W> zX4YEmGx?uj(kE-$?_-=}i9Og9I|ItMJct2$wbB~`os3x1uiAtM2U^4T9a0ZCi zo@7lfsrvGK5b}gLp`8`2!Mv^BJ3tr%XQ>sOmgWBbC3)gm3OpleNc^~YXU*L-`L|0q9sU1D&PDNN}LVbI747bAe zS93i)ka*)Z9>DfK^}z#dOSO5cBf9!z7V8jJRJg(sM$ticKq#fZvFVa;NBTil-5^)1 zsV43XoJ*?Mc57h4D=`_%^(KjH=I2~z;~j$h&-?DuvGZKQ@VT{cjub^zz-atJ%C2|| zBbVA3Q8L9r+ryv8pe7LKB&YPmOWkVr1A62}rToBc<>q^h=j-{ZfNhxLY1~z;`$cNX zh1tl{F(jNz;$pCDvxXi-O!))^g^NUGSevAUT~-vCxv}_#RxV4OoIlZ?Uq5wAxGXR$Dep%8}~VB3ey`jLF?zu0qO6lewO2iMijgpOsQPLlrMXZk$*CWF3`p z3@1~dij@VIv>dd{#$WBoh+ajT>g$=CcbCmA%v*A32M1*FrG}A}cd@5dY=JkfouzPO zEZ$kIaDGdg@3aRG@EBU2UoS-tMd9-A{@FA7yKnU0Yqc)aLf6|4#nX7$Bi=OaU93%; zrfGGc=p=XPS`;pXFjyQb?c>3II)1t5>cCf)k;v~1PYJs25&-)D&uVO~rv0q(tfVPm z(w7~s6*CR{4Mc{Cs6s*O9XzMj-s^8^mXM}FyZXA`EnX`2%1M<_2hkf7s!)AJcKrOm E0TN28@Bjb+ diff --git a/doc/src/Eqs/bond_mm3.tex b/doc/src/Eqs/bond_mm3.tex deleted file mode 100644 index 549500ebac..0000000000 --- a/doc/src/Eqs/bond_mm3.tex +++ /dev/null @@ -1,9 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} -\thispagestyle{empty} -$$ - E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + (7/12) 2.55^2(r-r_0)^2 \right] -$$ - -\end{document} diff --git a/doc/src/bond_mm3.rst b/doc/src/bond_mm3.rst index 4096a34d48..5794592ce4 100644 --- a/doc/src/bond_mm3.rst +++ b/doc/src/bond_mm3.rst @@ -1,13 +1,13 @@ -.. index:: bond\_style mm3 +.. index:: bond_style mm3 -bond\_style mm3 command -======================= +bond_style mm3 command +====================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style mm3 @@ -15,7 +15,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style mm3 bond_coeff 1 100.0 107.0 @@ -26,10 +26,12 @@ Description The *mm3* bond style uses the potential that is anharmonic in the bond as defined in :ref:`(Allinger) ` -.. image:: Eqs/bond_mm3.jpg - :align: center +.. math:: -where r0 is the equilibrium value of the bond, and K is a + E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + (7/12) 2.55^2(r-r_0)^2 \right] + + +where :math:`r_0` is the equilibrium value of the bond, and :math:`K` is a prefactor. The anharmonic prefactors have units angstrom\^(-n): -2.55 angstrom\^(-1) and (7/12)2.55\^2 angstrom\^(-2). The code takes care of the necessary unit conversion for these factors internally. @@ -41,8 +43,8 @@ The following coefficients must be defined for each bond type via the the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* K (energy/distance\^2) -* r0 (distance) +* :math:`K` (energy/distance\^2) +* :math:`r_0` (distance) Restrictions """""""""""" @@ -69,8 +71,3 @@ Related commands **(Allinger)** Allinger, Yuh, Lii, JACS, 111(23), 8551-8566 (1989), - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/bond_mm3.txt b/doc/txt/bond_mm3.txt deleted file mode 100644 index c3d0e39f52..0000000000 --- a/doc/txt/bond_mm3.txt +++ /dev/null @@ -1,58 +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 - -bond_style mm3 command :h3 - -[Syntax:] - -bond_style mm3 :pre - -[Examples:] - -bond_style mm3 -bond_coeff 1 100.0 107.0 :pre - -[Description:] - -The {mm3} bond style uses the potential that is anharmonic in the bond -as defined in "(Allinger)"_#mm3-allinger1989 - -:c,image(Eqs/bond_mm3.jpg) - -where r0 is the equilibrium value of the bond, and K is a -prefactor. The anharmonic prefactors have units angstrom^(-n): --2.55 angstrom^(-1) and (7/12)2.55^2 angstrom^(-2). The code takes -care of the necessary unit conversion for these factors internally. -Note that the MM3 papers contains an error in Eq (1): -(7/12)2.55 should be replaced with (7/12)2.55^2 - -The following coefficients must be defined for each bond type via the -"bond_coeff"_bond_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy/distance^2) -r0 (distance) :ul - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the -USER_YAFF package. See the "Build package"_Build_package.html doc -page for more info. - -[Related commands:] - -"bond_coeff"_bond_coeff.html - -[Default:] none - -:line - -:link(mm3-allinger1989) -[(Allinger)] Allinger, Yuh, Lii, JACS, 111(23), 8551-8566 -(1989), From 35181a66d09f6a40806fad810389df0124c8cc91 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sat, 16 Nov 2019 22:08:29 -0500 Subject: [PATCH 52/64] Update docs: bond_morse --- doc/src/Eqs/bond_morse.jpg | Bin 2509 -> 0 bytes doc/src/Eqs/bond_morse.tex | 10 ----- doc/src/bond_morse.rst | 35 ++++++++---------- doc/txt/bond_morse.txt | 73 ------------------------------------- 4 files changed, 16 insertions(+), 102 deletions(-) delete mode 100644 doc/src/Eqs/bond_morse.jpg delete mode 100644 doc/src/Eqs/bond_morse.tex delete mode 100644 doc/txt/bond_morse.txt diff --git a/doc/src/Eqs/bond_morse.jpg b/doc/src/Eqs/bond_morse.jpg deleted file mode 100644 index 6795c9e527d3a06f19f9c379c7b0bdf3e87f7168..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 2509 zcmb7=XHb)g8ihYdC>jJqq?kgevh)pAdeZ>Ljwrn)tY|_BQHtP#va*0Ah%SM^f-D%7 zl28Ps3kC>;qJV((?kc?qf&#gE_s;!!XYTXPoImHxdu9&*J%187dI; z@J9e!KnMf|gF!;yMMy|USVT-zgTw2M%$mXKcl{Fi&MTpVT z1T$8qWatermN5=TJX3pk+)_5en=Jm-Eq7os@MC=G`|N{jUvV%yh!Oi)m40-!>v&~L zG>pjyOrw`bgQY_0dnyrmjLgAHf#Qg7Hf{0uFT2xC)KJKm^Q~K1#%xAT@}~-VMaF=$ zmus`5J_?55#8~$Dx%b7812JKl8*;W3n$O|~Vu+Ebu4FHD%U6&YAl&BmZj7{pPVmrz zLZQ+cp+rZPN@1vCF&JOq;1^DWTRc4HEt4UmHmhFQ4+(Z-uiN^?S#6cd>J678Y6GVy!f3t9C!4hepiMA@Dc5dC0QK9y0avFxR~} zq&7j&S%s9O9PtHw57oIeTUz&P_Z8_Tvv+V(Lq2Hl66u;wJUTXh!eMW6Z0r5;kmG?0 z-6d7uB1p&34`$}5mHC zM=uYf(8_`3Q!!JF>K%0a5j|rI6wkX|cJ8hW0aIM;2y^Mw4kl&|ZI~}o*y(naI3M#W9T8We1l&QL}tB`OD)SJCb&staREx8QYgDRVjeE@8c{6@xU$THj;ZZKEaX4z3 zsl3jSYO~}gcX5F~>x)Ir<($y(ZqAZ~G*k>gp>`o+;~D~1o*knB{vJxcNjK6OTu{qg z1RRpRu}ZX7os_PRVn!{7k;|6|m^5E1EyAFg(mc3%!+wCr)sKC$s3!I2={1)SJ6a zH&RtiG~6lpU!Kwd%!}N>)`_v z2Ho5zu5q3(J-b@%5`B!~)oF2NufcTJ$!ksLephBShb%c*LBBWT?DeSH*N~pLIlQx1 zG7tw+?!5OzIA%r5Un^?gq+AX|W?Rac$gW1HGfro<*+v^(U+{2YMa6FY3IF1ceimJ3 zpfc5Z^X)dyFv!$&!u2OofVn!I>|(m1a-% z=VJ*Jq~*<)#@mF@D}i1*hoG2m!k>@ireRMSWZ+M=(9>In|~V4lZqRfNk^(WX1I=eJo@R;8^4h_E$HgT zhQ+DCYf5pd9hy{{p?>uW`K>>yU3F3hwWD62c3e8F8A2o3rT)F*S2JgBL92Suf^e`n zL&Td*G(OWTn2UY0%b{q^Gv>a@6bMdek!3k{Ke-qT86NF#UuhP}nA@t=M$kF9=Esd{Iw zbnrbjYrNzFKBsH;sMNwyB!l2Pmv93IA1}6pYWm~t=P5OS$ndM=6ZZaR1q6I$Gb z>&15T?M~YZ$WhB4-(G@m;kxhFeyj}~7@a0SrJp*=B=K61#;0$Z_O$W=`&O4bWx};5 zZUU1xZrD!@TyAg^qP62Srk~x8DDzNRj+J5 z58t(%B)1JIO_^Owz9z&DR0pil(8WS!5`jb_R}|r`4iT|2ph=nj)2n@-Um1Vn@qyP) z7a8I(j;@SfZFKyk)-Yr2VwZ)XO#R=Vw6%sTuQQmJS#Yu=(-mIvmp9@3>&8}0UYkK) z3HrQC%0CM=x0R*OhviZCNCD{xd13`C=KDV9qFIEzv&@4cm{=G7s1b*|#S$t5T5=0Q4*!P+xLkEK#O5lIari*htQFy>1VE!R4U z57gBEC#sk*`*P!w{Jm{=3AQpNKIO3)0R{4m3|=m;)8>rLj2~Si37;$q7!8CoO$BK4 X{tu5kbNzR*!;yvXf4csc@`wHfMERky diff --git a/doc/src/Eqs/bond_morse.tex b/doc/src/Eqs/bond_morse.tex deleted file mode 100644 index a0d7a89961..0000000000 --- a/doc/src/Eqs/bond_morse.tex +++ /dev/null @@ -1,10 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -$$ -% E = D \left[ 1 - \exp \left( -\alpha (r - r_0) \right) \right]^2 - E = D \left[ 1 - e^{-\alpha (r - r_0)} \right]^2 -$$ - -\end{document} \ No newline at end of file diff --git a/doc/src/bond_morse.rst b/doc/src/bond_morse.rst index 592bc527c3..26471424c5 100644 --- a/doc/src/bond_morse.rst +++ b/doc/src/bond_morse.rst @@ -1,16 +1,16 @@ -.. index:: bond\_style morse +.. index:: bond_style morse -bond\_style morse command -========================= +bond_style morse command +======================== -bond\_style morse/omp command -============================= +bond_style morse/omp command +============================ Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style morse @@ -18,7 +18,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style morse bond_coeff 5 1.0 2.0 1.2 @@ -28,20 +28,22 @@ Description The *morse* bond style uses the potential -.. image:: Eqs/bond_morse.jpg - :align: center +.. math:: -where r0 is the equilibrium bond distance, alpha is a stiffness -parameter, and D determines the depth of the potential well. + E = D \left[ 1 - e^{-\alpha (r - r_0)} \right]^2 + + +where :math:`r_0` is the equilibrium bond distance, :math:`\alpha` is a stiffness +parameter, and :math:`D` determines the depth of the potential well. The following coefficients must be defined for each bond type via the :doc:`bond\_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* D (energy) -* alpha (inverse distance) -* r0 (distance) +* :math:`D` (energy) +* :math:`\alpha` (inverse distance) +* :math:`r_0` (distance) ---------- @@ -83,8 +85,3 @@ Related commands :doc:`bond\_coeff `, :doc:`delete\_bonds ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/bond_morse.txt b/doc/txt/bond_morse.txt deleted file mode 100644 index 60fd16e17a..0000000000 --- a/doc/txt/bond_morse.txt +++ /dev/null @@ -1,73 +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 - -bond_style morse command :h3 -bond_style morse/omp command :h3 - -[Syntax:] - -bond_style morse :pre - -[Examples:] - -bond_style morse -bond_coeff 5 1.0 2.0 1.2 :pre - -[Description:] - -The {morse} bond style uses the potential - -:c,image(Eqs/bond_morse.jpg) - -where r0 is the equilibrium bond distance, alpha is a stiffness -parameter, and D determines the depth of the potential well. - -The following coefficients must be defined for each bond type via the -"bond_coeff"_bond_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -D (energy) -alpha (inverse distance) -r0 (distance) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the "Build package"_Build_package.html doc page for more -info. - -[Related commands:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html - -[Default:] none From 48485f1e2f909ab0bc7a5be7f7a8fc9c0af3d238 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sat, 16 Nov 2019 22:14:15 -0500 Subject: [PATCH 53/64] Update docs: bond_nonlinear --- doc/src/Eqs/bond_nonlinear.jpg | Bin 3593 -> 0 bytes doc/src/Eqs/bond_nonlinear.tex | 9 ---- doc/src/bond_nonlinear.rst | 33 +++++++------- doc/txt/bond_nonlinear.txt | 78 --------------------------------- 4 files changed, 15 insertions(+), 105 deletions(-) delete mode 100644 doc/src/Eqs/bond_nonlinear.jpg delete mode 100644 doc/src/Eqs/bond_nonlinear.tex delete mode 100644 doc/txt/bond_nonlinear.txt diff --git a/doc/src/Eqs/bond_nonlinear.jpg b/doc/src/Eqs/bond_nonlinear.jpg deleted file mode 100644 index 0f18d8e73fdd11acfd0996f0bf472b6b3757809e..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 3593 zcmd5;X*8Q_*M3M)QA2_nVoD_?rW#sBOH7A|qX^PUs;#Mn3ZXT0I%;-~Iw=tyVyFr+ zR*4vj(yE$@8Y?lhhN_}%T0MHGdiA_(ec$)v`|k1CW5vLPAhrrxQ>CgaBdC&m8|_BBCI$ zn6S{E-BTMGKnMg928n`&Ma9H_MhFRmz<>x;6efl+l9jh1FvjHeyZi1j-ls{8jJ|oq z_JrSc&Zq*?H$;15P0v8-HnN-n4JB31nEKa5z!V zN~v@ufc-kqNvSvfsORq06VK&jlJ#xuk+A6E>>ohX;e<&GR4>TnHI`z3VrU;f%^V_+ zZxQSt4CT7EnJYX01wTL5Q9uoJDKlc)wPq&=Pe1lk=y6n1)DpoQ_96doDW}ygmMD=1 z%~I}!p`3}M!g!jolU5=7DyF=$VS`Ilxs76(`cT~BH~lR#t~WJ|#`EJB{6jJwjc7U& zDN-A2Pu*97}4!OI*L?koO{0o=Fuv4ucJe~X7mQyYh{Kr z!XVu@-74MzlBr9bgeekkH6z)y6hH9Eh$n|+Yn3g|6(`-0DDfmbLM;N1m|{u65Gd9)rNQ5>>c6`Efeo#(T)kZkq2j} zL0x56j!!5<1P9&}EluA(Hwht7BK&KMwqLC4nfVoh=R+6(u`WlY_#!?v?Ef$tCEdwU zIuRyDsXO5OGAstZ-KM|zSA1Ut1CK&4o&Ng5|i1WRpF%q>*YyBfe zP#O^zr+S@nckzps`GBEOW?V&tWKF)};qVwlcdjneafB(uIet}Vd8EYg)$i$Vz$YiH zkOEo!p{IUG^3C-r@Y(|3kf&Piu|2#}p}u~#qO7LRebR34pa&gk)xROYVGg45s+?SrACq0LUM-69YBG>a?w@U!p4w;M%|B~qIOi#(*CpBF|bt}#ruQ2{tnN>+f98L1REbN1O_(D4Z zp(|GMV+aPJNoMX^nY>o2BPqEC#^DMHc5`9>tpD9VD3?t z?{isZpq>Htd~|u(u6{rsX3;#0#H>AC)5|}~tUuknPJk!3c9EJ+QmUr>Qt5bpqb;9W zuPuz1OI7FxCCGM9yf|FSvK?#K_Kks#SS)nLmig(>-+TY5qE}2oJK^c2r?kY?$5aH_ zD-J{!ymgk~qePOeUM#uo+fTV6NvnQVw>?*?O0{cm_86qNl>8%hjnC)89)cgW# zxC4&8s8w*h-u=U^-zFJ#JHQLa9l(bm2^CMPoAn?%YzOLuitv;EDzN?gPdXTTA#t85 zl@~H-X`Cx+tI^U28y!xRYI%8)b5LD}9$%b;RDscov&;i7mghzbTnC6I!&z6Kk$JBDpv(R4f2B|}NBkm3Cw_Qz5(Lu3(_;6VnuJ8_ELE^nz z9lnBRO4r90Jhennqjht!4M%UKZ6Xb)w)%VY?{#XUbzaSvJ9U8A6*tg0FHj1j;>>b% zQ%lTwtIr?5)(P?wE>i~I_~qRdJfg(Sn^m3GJY&#om#%F3PV3l(>Cb+Z6J{S&--Xzv z_n&aj4@Qx-35MA%Fq465FFCo)eNO75CluLVUz#3!{J-Rh`K~jny$47dCHh}DQJ0UVw@Q^K0JRM)u|n* zhDt-GvqcG>0q-7?N@JndraqciNO(m{+-cHUj;dnvdTDOw=>N*wxDR!TP^Pnupo0 z{vVmZbXM#D=zSGesN@eCqT&MjxtIzF^PX!38okf(rQ1i)ALFGLW`ZrnsL=TTH~xt@0~T$_il(H3S*bp{Y`nE zX*_Id85KS!$EOFzSk7%70E_xpa`{I0xoOE=ws8n&{ewDKaJ-P9dIXv>_w1Z5!iMX{ z7?LZxA8%;vYO>`*Fp&L5OaE9j%R0nNOQ+hTo*AuGrUno8dR`Z?L1q@BPj2SdC$=<} zE=()EZ?c*_fm{ln0?ghDy`Xl!nw!Qz^@-!Z-r|z>rca=RIJlb@*i~Mv^gvRPIT}|B z;H+{?Uj;dYkQAgiG(C9l2L&=7g~m(hv&i_rlC`5e{zOU@0@V(cDwxp+vp$dcTCDs} zHPiCpG%g;WntG1UjzDI4&@E^VuKhW&eub66^d-e_e<)9*jC>+rkUhf7+Ft5o-EQSQ zGl$pEIk-q;V3|4YBYW?wSLPy=pZ~~Z04~*pc(ulJSB=c~2yxgrCEfirL=SHEoXZocd7D!8_JYl-v;c(aErDIsv~lDJ9&4O(3bFWyj216MtESoPAcr#R=n?G zagp&fVewuiQf6kACWY-;B3R&alq&QdUOd2PUS4j3R!8Kg2tc=-)3lLSKZRgYkDzlU z^_A|{;0_W#A$;IsM*~a&d}`)chFSJpPVu+#t0Jtm=7U)N`ZHFff)oVe)+7PB_=F{o z4%GlWJ&T-n_iu9?zHs%*)%ekVLd?O{|ghS%=;hGSxD89S{oKg;gRX zc1uUxqw!crY~qMKwLI|tX84%;)9COoM{rHU|BU1uINbG>-%LSkS1sveGgk3hDAg@@ zdO@uJHT+Lxag-Hk8SlAE72#0LlK=ypci2HQ`aKHxMlUWBFaF+os#1DyK~=y{E+6*z zrt6{8^|)W074a%qyw{dZC7sQ;DyW$(?#&LWC4~+4qm57fAuoyEX8m%s*IK88m^SG0 Q{Cx=SpF;ivc)T` of equilibrium -length r0 and maximum extension lamda. +length :math:`r_0` and maximum extension lamda. The following coefficients must be defined for each bond type via the :doc:`bond\_coeff ` command as in the example above, or in the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* epsilon (energy) -* r0 (distance) -* lamda (distance) +* :math:`\epsilon` (energy) +* :math:`r_0` (distance) +* :math:`\lambda` (distance) ---------- @@ -93,8 +95,3 @@ Related commands **(Rector)** Rector, Van Swol, Henderson, Molecular Physics, 82, 1009 (1994). - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/bond_nonlinear.txt b/doc/txt/bond_nonlinear.txt deleted file mode 100644 index af51383213..0000000000 --- a/doc/txt/bond_nonlinear.txt +++ /dev/null @@ -1,78 +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 - -bond_style nonlinear command :h3 -bond_style nonlinear/omp command :h3 - -[Syntax:] - -bond_style nonlinear :pre - -[Examples:] - -bond_style nonlinear -bond_coeff 2 100.0 1.1 1.4 :pre - -[Description:] - -The {nonlinear} bond style uses the potential - -:c,image(Eqs/bond_nonlinear.jpg) - -to define an anharmonic spring "(Rector)"_#Rector of equilibrium -length r0 and maximum extension lamda. - -The following coefficients must be defined for each bond type via the -"bond_coeff"_bond_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -epsilon (energy) -r0 (distance) -lamda (distance) :ul - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the "Build package"_Build_package.html doc page for more -info. - -[Related commands:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html - -[Default:] none - -:line - -:link(Rector) -[(Rector)] Rector, Van Swol, Henderson, Molecular Physics, 82, 1009 (1994). From 2150415888804891c3843536b584758cf680bbcf Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sat, 16 Nov 2019 22:18:22 -0500 Subject: [PATCH 54/64] Update docs: bond_oxdna --- doc/src/Eqs/bond_oxdna_fene.jpg | Bin 3866 -> 0 bytes doc/src/Eqs/bond_oxdna_fene.tex | 10 ---- doc/src/bond_oxdna.rst | 35 ++++++----- doc/txt/bond_oxdna.txt | 99 -------------------------------- 4 files changed, 16 insertions(+), 128 deletions(-) delete mode 100644 doc/src/Eqs/bond_oxdna_fene.jpg delete mode 100644 doc/src/Eqs/bond_oxdna_fene.tex delete mode 100644 doc/txt/bond_oxdna.txt diff --git a/doc/src/Eqs/bond_oxdna_fene.jpg b/doc/src/Eqs/bond_oxdna_fene.jpg deleted file mode 100644 index 3d1157a29a33708fbd54df8ed86b853fb76bc62b..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 3866 zcmbW3c|6o#+sDrs%*f7+7$e(c3uQtm3>r&P4cWKsTlT$CvL;d?{K&p1OhUGhY(Mo& zwrqn?*=1i6=AM4{{XEb8yPx}y`+3gyb)E0)yuR1#e6RO)&UMa*GD4XGY?m~3Gywzx z0EGGg3K?hsI6Xa#o(>L!!5A3e$CwbzOpJ_7JRF>?2tE}52|g4WEr5|06%djXMx({f ziA$c5k(HI@7gbbNz+R9(D~tU#350=xfr*ico0*v#D~J}v{+}D=4Pb`@RfrH2A_QpI zAy9S*r5*572oy>~3#Fr@rKNh`rhW&s>~tK0 zGHUdk1RI!;Hv$`$kP8=9uWUu?_pM>h+WLeu9OF99&4W5AA}S^>AuA_;PC-#g<04*D zOIzoX!F59;V-r&|J9`I5CubK|UqAnVz@Xq;5s^{R_hRnHCMG>ePD%YOEj=&4ps=X8 z5d+@;{>H~pO97n)`&zW-q95G=n3XycYVb`pM)D7k6YeTsRuT-Wics!VTSc_RrDT`{K{oA!4RY^4)KE zwUwyM)KdVbt1E^h9Vi&_n@) zKAj_x?zyC-@y+pGy8TlT{iKkqq|u;A6W4@`L$@M_(nB^c7XKk$EtA9;o?8p4rt$vR z5)c+H=EG>0NDq+()kY^j#>vL%rb*2bD={|>!$*4BgnJ_ej*$EZBI%+BTTK+u>fc2H z>^R;neduHOs)em<`tp&o9-F1)HI=O4RAF1L+CLiYt}FcPQ0rM~3&#V$hE9@u-bmcj zyWg!YMsw$b*Dn>vN^%}!b-v@!Np~e)n~gp)uI=Au^n5u!p}Ap>OuD68%bTh|dxjQm zSLAhtMd35MNI6UHl)0tjB5xYmA}}y2;28uX6MhDZ6V714I|uD(-fOplrC={+lLfI# zE6y3`7I1to(nZp8IRujtX9aBPpcx#>EUaH$wj*ZT7>jBx%`aIj4uRJaEGoU3W?VZr z6t->@*SNSS6;{*~n7Iacm`yGU3UQplDaR~psVn1wZBVqh%{}8mIX-oBBD_3xIl4bs zI04hy%C<^V&eB*G ziEbjg(aD9bVOC6Z;POxVIjqwMLWY;ZmkfWo`XcgGmm)HG!jkuS%oiHdcPpFxjdr3S zV?F8N6UY}8{san`M)fxbP{1PvA_cqx;Ba&R#q(73GDk*;*rI5`ul}?{_PH6m6umvUt3j6jC(c{j`&uP{I>K^XUfR);N%@X zYEF()DIkoRw|L+-#L|?j8(KQw(3Bgul778kNlRQ1qr;Y8fy1EL)LOsVwH#mGZW1N@ z)@D~~YI*6nx3)C<2&)BjAiV{LT(MfjJ2r%i1^+O_NPDloY2D%3A5`io7}HGhzVpgp z63*6$hv3M#ZegO>6mgbh6d0rW)$CK~Qjg~$=%r1UFXpPrGjV;9Uts)deOyT8oJ2!3 z_|hU5@OpfyAvIcsVP0t{L(0NzA;r<8LdZ$FtdjK3Fd9CQ<(oe5uN-L5S0e?t(sCVY zD4ZJ^Q|OC)d|p^7lN@8S!4|~lyMp6W_8BuictYX~9gfbXfLx1Vga3W}JTKpSq_ehN zkc!HjQLpUme*&tK`Lqe$$Xrh)3o`yfu*|!#Vc|+1ZQN-KIo3FrT5P(NU&XTyV~zsavH>Dqd<9Upw+e7Opkc@=rXR4*8IC3&vq= zXK`7ydygE5TB}vzk2N|`meeq}VT0qVp_@*h~2Uj&|fAby%;1Gnr4zIx+W_T?< z4fevOf3{99Ey%_T7AI#q)*fz^HC~ItMuc^Dx6T#1EvA!VoF14h+(9*k6QfPicV>w< zQs%EPPCGc-<|H0Rr!R`-z{|^Ls%oOg=*S2$Vf@y$GZIDlMe;d)$%CHd^3aa5ut29_ zfuSe_B#HvygV|eW+^lyGRrg|Bid{Ywm&Fe6rV@WwtoQ1;^BWC`fMfQf7EkHRtkO1t zLDkV6>&*pE3b@m?XBaC+BUbJ{<=&@;xT%Safs`q`sjtP2%Noxc{DCPlHW_38tW&EN`F_EAL;tlN1z4d%kD`1n_5P(sdm-yI%vyxC=;DHfbi!Kc(PdBmf+DT~Cxm0r2KZLFAe9gY$_Nv11r%uf}anZ|KYWY`!CyY#;M~ zXKAt*r+2@wc|eyz;A)fa&5=#v6XkEI_jPqnU^)5J``ha8c;D+7nTTAQUm6e1`lPId zV0*)@!J)|$_W}=lMQy(ixz-<|Q4nO_zSiZ- zKjLp#*I$5l?&ih({!!xAPbT9^0v;f!W)qZ3Xoww^Z4!%kZXJP!m4w}r{c!XSnjIi< z{?j4NUeKj^&}7IEDNA9Sb- zXsk-wd&SB+(cvlmG}O;tZ@T<-8H;x7` to model the connectivity of the @@ -47,9 +49,9 @@ in the data file or restart files read by the :doc:`read\_data ` or :doc:`read\_restart ` commands: -* epsilon (energy) -* Delta (distance) -* r0 (distance) +* :math:`\epsilon` (energy) +* :math:`\Delta` (distance) +* :math:`r_0` (distance) .. note:: @@ -121,8 +123,3 @@ J. Chem. Phys. 134, 085101 (2011). **(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015). - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/bond_oxdna.txt b/doc/txt/bond_oxdna.txt deleted file mode 100644 index 88afe435e6..0000000000 --- a/doc/txt/bond_oxdna.txt +++ /dev/null @@ -1,99 +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 - -bond_style oxdna/fene command :h3 -bond_style oxdna2/fene command :h3 - -[Syntax:] - -bond_style oxdna/fene :pre -bond_style oxdna2/fene :pre - -[Examples:] - -bond_style oxdna/fene -bond_coeff * 2.0 0.25 0.7525 :pre - -bond_style oxdna2/fene -bond_coeff * 2.0 0.25 0.7564 :pre - -[Description:] - -The {oxdna/fene} and {oxdna2/fene} bond styles use the potential - -:c,image(Eqs/bond_oxdna_fene.jpg) - -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. - -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 the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands: - -epsilon (energy) -Delta (distance) -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 style {oxdna2/dh} have to be defined. -The coefficients in the above example have to be kept fixed and cannot -be changed without reparameterizing the entire model. - -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)"_#Henrich2 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:] - -This bond style 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:] - -"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 - -:line - -:link(Henrich2) -[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, -T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). - -:link(oxdna_fene) -[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, -J. Chem. Phys. 134, 085101 (2011). - -:link(oxdna2) -[(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al., -J. Chem. Phys. 142, 234901 (2015). From d13ec0d09871c794b634970e4d38ca2a44fa985c Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sat, 16 Nov 2019 22:27:08 -0500 Subject: [PATCH 55/64] Update docs: bond_quartic --- doc/src/Eqs/bond_quartic.jpg | Bin 9554 -> 0 bytes doc/src/Eqs/bond_quartic.tex | 11 ---- doc/src/bond_quartic.rst | 64 ++++++++++---------- doc/txt/bond_quartic.txt | 112 ----------------------------------- 4 files changed, 34 insertions(+), 153 deletions(-) delete mode 100644 doc/src/Eqs/bond_quartic.jpg delete mode 100644 doc/src/Eqs/bond_quartic.tex delete mode 100644 doc/txt/bond_quartic.txt diff --git a/doc/src/Eqs/bond_quartic.jpg b/doc/src/Eqs/bond_quartic.jpg deleted file mode 100644 index 9d092883b2ee55c75d9222a41836ed259ec6cc41..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 9554 zcmd6NcTkhT+imD5B}9}O2vw9Oy%!NBAP82P6oJrtks7*mLhsTP6_F;rgeEN@9fZ(3 zgc1UT4goH|`R2~t@4q{D=H9tyXLfdG-`U-F-e=Bxp7ZSWFZk8n>B_^W0nSDkF zAi5cn5R;ISQ<9KV0B)YX8Iys?DeiF6i{4dvMR||QOicQT>&IXQM()>oZmFZ@RW;(O zAz!{$@V?beN*i0co(53+pKCyr^IMB_1hurv1jSWM-{Qg%q?UX^;d&JbQ7WU71pDif{ex z9}b%2e8$_1{IG{zo?$P{Q^o|_MkXpv_P8un<7bM8dtdq12b=$UbvW4 za3x0O6abVLC;+2>E5^~5s%(K%mrXaSysfVRwDKf@-wDLo78SQDv+gdh@|&nQlF zXIAb=ehR(JenA^6yLv~nhee3+COalvZ*{lGT_AN;fBO~M!R=Y((EB2wSHnL2G}u!e z$L%}1cX<0~Ht(5?rz)>o*G!to(Q0m26m`;be4A!A=8lH)>vGD-|2@PgZ|Q6cd|&9s z1&-o`h^%J^`Uq)s~=w1blt79I+Oy4ACH z+5+PB&I$^&uhr;zNz=Wzv*C~Rq2=m`C z)d1F=$*n0O#DBr5gN+TFefHo!9h%0~(GDA%F4a2S8yYp$ zCsonlIuuuP+tD+}?q34=@f5VQ^VoLad4kocaf zjrU#*C@$u<;Ex!C`PR?qg`jE$lD4mc**n&E9@3+;ECP5v=-d4vO!7hM$3

E)%&O8WfF-VnU&^gV0_|b5E>SFM-E9HLEPqtkhpiL_?`web zE0>xD-hQn>f^N0y0Kr>6@ms*Z#1L5Q1y;78GfvN!VcWF8?boGT``ov3r+r^S3-&szv}|L2*WGxkHe%D1XO7XueRNhV=*wG>nGn91e%C7X-(ye=5Cj{wzNS9+DiI37hKMH}ZSfAy&7QMrGkzg{zDe5`6sl?Mtc%>*C7wB z2Jfy`p7y$gl|F(?6(YK&$g%0NWkM_mtx6JKy(#$rx@GXx*hg6INvd5kJNMFJMkc1a z73w7}LKdYI;$506ta*_Ag?}sxqV`tI?eU&q4J;fn`%(fpv-2;G@6ga-@jR&ZBM9V! zf1_WnX7KBc|I{=EjM`7%6tlGqI6r$!OYv`pfR0w}-BVx`wP2NBbKsfzh3eaE?sv8E z2!eE?i7JWE^|~fR{d?InASG4mvn)Hqq}1tJ?n6wGxp-k0H+-`LRlz+J@^&7&qC^~s zY=JCa01LKv$Ar%)?0X;?$LA1BiZ?>msV;uCGMC{iVxubN#Y&tZI>C*D>kK^$)7S)` zGZ~tAQvRY)Zq;JA1!EA>Nq_0Pxyj2hg-SiqjJDuTb&O~KW>X!s{IH)bn zBt%RkLCHH0@S^E-9Xr!TV>`{7FsFAY3oPuBeq7D-5jorS#Aycy8{R>_RRC!@#ho70 zz9sX&^FJO^Sx=N2w?%OW1y5}`U+u+rJ|?L{)(ttkragW7j=kg{($}kF$E~>jvjMfg z2u-qy`t<2V?u4|;s@EM1QGQeApkKnu>BFis94Mm5e zuUZD-ch9+F)n;v9QmnpDbh^NeLC3^VV6DqA^6fW^#)e|kg|MgR{M^kL%mcm#wq*f+(UA9OGGa(S(ziKVe{&|(;WL!Saj zgW7EX?3{U-C^-n|!Hwc3;xl*b<05+K@y3jKypqv}mRaAW=W_BrAERo*t^&$9faR$= zn~X0bUhN64GF>SKgmYO4*iTnUJk{D*6-CyRxXMj>C0~v>@(n+jaJM!8TfnPS=N29)?VU#>Wf_%hSG5py57ru?_wRO7gj}l7Am%M@v!yTLV>nzr#3aY@?;(fcz5rQ$SZ|Gxd*scM=-z|@o#QFm)j@VCE z{yBIpV`&rzX?TK0(Z&;&$4N(`v&609zkuDY3OPnizU;=VFzTGo>>eAi6iE4%y=D|P zO{$kQG-D5pCRq%{>W$toZCyqa9$5W|c12imTtsGDA+F#0&{QD4Ls#y+y2T6FFQj2T z$u9I)rtUC09_-0{RK@JatX}p$P3Lt<8qg!CeZtNJjjg*-bD$e5b(oTYFrr*=kMxLQ zJw~71@>|Wd_R=)ht8dXT32<`H*0?-pVY%(5CZ;AQ%Yv?Gi;(R25Q-NNyO4dstIe0b zG^TEXoeOm8zzn9;Pj}m z$34)eFq=n0FaiESro$3HD@wYgdCh7oJ+@C%klKDoRi1!W#Y+W8zejxvch|CN^ky;< zGn^LFqX&mGktAn7fvpYF*8o-HYrxCWtE1^S>jWLQ2M(@O@67yy;Dbn#Pzv-5SH3d= z;x46so>RUHI`ygrSyt<3Ji0sq?kUTRS+~-ZUSMu!8$9UQHGZV>b zQ^a>YzQ~{V??CMs9h9t32|95vq)iM*iC8%lZMQ;)HxVr$uY~8|P5e}L>Xe7nGFcHf zqBYau)zbw6zx=H}*&pw-t?EnYEcDNrqSLWjr?WJg4AkG=qFsRmYO^B+o0B`El*A{U zc{$0kD|x+3g|xQg)6UQrUBk7;0UYh{O{le8XxncCS=Sqy=&tZurV)GBkQ%~l@SAc5 zyr}kv)ccszJFqk^Eiei$e(70vF7%PG zwXO%8eFG`tkA35Kj(;b%D(2r2%3)gsxlogB;bCmaeU_EtmSX7a!9R*c>W_q+hV0dX zNUYcW{~`sqW2OEnYHq1fv02tY6eQeIS3Lp>II}v%o|sNmv`Vrp&mqnZD)qGK|D5Rp zd0!jl$vbIh-|00s++Q{@KK|k1WDT#RsBb;2D=&VJx1suRTQzaJoG;CEq+`kEO&JiI zxtePbc?}SOkz4~Pa3)TU{j$Q`S^HQesT|pGd;W7e^ly|z2KTSc?=|zlDt4Cn`2`M$ zyo*rPK6f8kNt01#Jz9k=Uo`pMq{r`LiDYi=3!Ok066@|-orYt)l1lK32Ww!W)qcHi zT*A|--DwyoJwe^Zy@!>9zP#tx$x+4V(Eg+Fz_N*JfN$oC0y5eyLVI4acdwyJUt&=7 zWVvF~%ef9&fvWSBTWE>S(wCk(5KXKLU(Zqf-Yu4y?&fe={MOXOuK&*Xr*k@Sx94LO zo5;bMHT_1N(9jh3Tj%3`oHWImf`N11TQwb*g8nvZO5dCw*&A*8>$cXX)m5JWl&tkk z6ejc-KXt!I>0d2cv3X3CHQq2o{R$f-pSuj0;_y*gwi{dlO&kmC#hYR^7hnV`_{eqpGcMCh&R7S zk-EOV>QA%eHmIRc=>V3B+OIFspjxLOjGWY&?h8pPN}jr&cRxkXr0Fl4xl?^+a&Pm9 z10cey)9o#MC%PwGJ7rB@HU!c+d6B#)Ul*5_l+n7}VYKaX9FaqX_}xO3jj0_kH3y$+ zmlTz4wQ3qJqdy9ShtNjK{+(AoDyweH8+%{J@m=#L{P{rf9jOOq5t7Eci8wiX!{N&$ z4FD0Yw3zwgML*&DJW*SIsZbrJ;jX8{L~LE7T?(pP9O_Ck3&nXf&%NteJ2SA>qLHny zl6_`d9Gi-U3jByF#Z^#KM-8!mi9zO9y?5=3?yT@8kfGB1&+;Oj6 z?3R#lAPhz%AMk6u#j|N`w#X3<#n>J%e-uI|j_8n{Wnq)}sy7GRHIGMuA;8L|O9ziC zg62}*c1`Pi*$d7AT3b@kZ|Hy}#GZA+Vq>R-Tp_Q?M{=v4-;u(2sNw;w^FgfoH=p&u zG7X$cRm)#^EoMzi>o<5rP~Z;k)9mAg~ltjq*|QDlWhjDw+Kkhc+Y5^ z{(xBpuJmX~t$8$_@XiPiACutq6s(?vzmD~)NVlIW7QVP&{va`KWMnKNbd|0M&bB}? zUY2jRA{U|(*GCStYVrOSc7E=>M5LU#(7?Zv(PzH*?@C%UsW9#rn04DQr$W5`f)+z3 zRTbbfSpSqzT!`=J_r}JS_gE%bi}T$A{a)U!mhF^p!@0k&I&guAl*_~!cOEdlhk|E`Sx08X?3Xu*mWLx_d??Oodog}2sTL{H;yg8liex57$)5W>e z&a-oH1uLKZczWOrBez74FU#u#imp_OwQ{CuWcO$DsCC4&3}fhaNg4*6h6dW;?M=(F zUiAIOj$kNXJ4{H1k&=HQ+JKTBQ&YyLq5;GGi9-!|_PRtfoY0Nb$q=$e4qW8`K%NAO z#-1}ZrA{`BO%olS?${rye2M-+lw1tdj`7+6C{q8{0oDkEM0uuM17x-wsdeN+L&yG_ ziB3U6Pq))6k4XgnMIvhu)HvHTy#$Z8_09bHybs&0khK0&y9ptf4J=PwQEj^5R@^Q9 zT|svilWPFmHy@n*$=T+c#^m$An_m0KyhCJk?>~Wflnc9RLQKGSBje1^1qHR8%gV>^ zt^rkDYOgn-WZ{aolPvCRG(Ji9o2~)t%jJ>L1rv?2%_D=hug-~$$R@Ce<2;pfIYL}K z-q=^g^^84fkMIe3B=n(3YbPhCk(~Y-&{+L-&2!xDEe7e?DftVH7#)xpqJ}xx%w%IA z0KhGt3;y{3Muf*^zENX@d2O%>YxaI@>RB({cu`u2Eo_+QxT1__gBT9{@Gb{NU?MnA zyBA6ED95lxb&SPZ9K#&&IsW7mzawM#Hr->DZD`9!Y_EEHBWhX5gFI5fs6g>elGXux z%Bq{Ui`b$My#|n$UIPRLe*9mJ0bf}YFV=3E3236#eUX*@@jR=Jwkc|xso}F^EJc69 zFE+{bblL1wXK3zn0!o3rZ|~zbhH@1UN!`EHD)O4PhMbO3&Tq#j5L&}KT)#f*I;qL% zzK*}!ZqRFq8_m649_MWy*HmU^58+JQkt5yRi-15LeSE(O^C_br0|W2I7s5j{Dl$$N zQz{3Q$C8}pdKO>g95<|?W-!G#7926*`;>-T17u+h%#%pUc;7 z?flpf4!T>_*iT`qO1*zZh(6!6X6rLQP(aJ)mQ6Zai{l4qzuET|(lgUICTQ38T-4y? z4?W&(f*3T8Lp$(g#^h9S%QB_glNsXGyOtP+Ulq0dow$={tfmiKUA>$)$>Te4UNyK2 zwf&Z71C8>|w}Of}YV7PP4SsAgO~HaIEAUT&Ue=xwC)FNmgd%o>KKB})E{pxs?(yc_ zzjbVg)7lfJjLAHSW0<{hsbpen&1cdC>3nqtC3#at-FY=|%M;dd(h>^R>C!f~y5zX2wq~|=F0Vf?EP3W2XoOYks zw4*t0@{4tnguf1Zmq{Y%om{arH(1~yG}=sXwerMPhfEKpAPP0n6RC+$=sC_I_BvIK zk56xm+hnKULp6#7V*!+N;vwt9GPJ& zPrE_Hxg-MV#ec?Q(T~5ylOo22malI@`eWKy7Lxp&2~M=m`!b&!J|7yhWsNF7)Dn@< z%?M{&34MWcfyBxV`OF8?9Gp7Z#0(`>NIn;v3<-ANE%n;K(vR^Y&C#8r%Px`MUSF)WX1ok5S(iXK(1W@?Pm~KU`DxZ{wE;4EPtN zYl=7ajWks>tld^?OhQTn;};0vEU2ldZUT= zjLT>ex9Hh5V7Bs^|C-wx5ZLzuW#L%z1=WvrCq>w#1!`qPxN-oDXI683OlVX0TQ?$J z)bBELe%11nW4bRSPn#m)8+YZ5QywsQ1%mP2>l16WX>u0r*&`s}QYC=)!{D;snqy3N*VLM>P_!R^6Uy~RA&_`(4d`viO$8}!Pb6|$IwkX1|Vv|7+ z?&z_ySKTl;gVae}(ma?vE0-ED>US;s(jxM=D31G&`|M3Bcd+;>W=;c>9WFjcQdkrjb+LC1 z2#Xr>fi%7s6S;Em8Wxx?JR+8b^vQXzt6`*+pyIiYCv7f@IivzYVZiw(_598T_21*H z+Z@e`A|bYE0!ASZ=VtB>g;+i3@);R3otoB;L)I0P3gfMOq;$*wtjLTLgc>O9cUEI* zqs#w=qqt+s*mp?wk`(IUTXR0&8CVNGib_0M*xlJ8 z>Z%g)9X8aAKIFN{qrl}Otl^BLzgVEFd(D-#|MQW1%0EFpR|aD!F=^Qfylgg}yaPIC zKvZ?e$`OFS_s6@+JBzu*=Sx!1fKhY#&K=o^hB8`PvTt-Z^_dcjpK$WSxi?Ewf{&;M zOxn%v*Aik8{S`mj(&}IVkx6Zy(-^khs>$sS#bta%eu$4i#onT&l7-@)q7jG0E}kd8 zNfQ>6EC)P6ir>qfVvN*Xyy`iM$7S!QRq<39p%Xi-xb~J8@_D@Hn~y45Gf&=X|1Wk? zf*-UygrQ9#-1#7ZkeOcQoPCV%KdY8DtDjANc2y94lV+Qwu*L6KnT;N3d!*w zWQ7=Bt$Hh1S$%Vh$|O6Ftzb1FB3ddZrLY}jJsDAcXL?n1Zg9ooGIYqlfPG_R5w&mf zXdg0?D;d@f*KzLjpHt(%DtEf@L$b)%%oIT3hrV;|*xk{G?v{>Y9*Wv6ii-4yetVs$|1 zwVD!s>m!}fp}n#2z%RPj0P|hdAI4H&e4Dov6_?*RPNY_;D9G6TCyUrAw-1#<6BCj8 zkP4Xho*RxSn>M!k7r5SXIqV4DGiG~&2^6tJ;|<#duL0Pl^G}P{fIk9(eN>O%Ugbl% z&#ZO8J+temp7om)nFjI^Mm{v`5PZ?2NA_-OfnH&ykhzS%_iKpe9(m`Pp)r%65xS}# z$oqW&aP|ImMr_*am9Lg9^6o5tUIK*`RFh-nR_D&HUU@&Axew&5q@R%<@=La{U{nuPv~;PqmNO3HTf91Cz^fG->w|q?DLEc zwEVgBAX7$_I0rhCuP0uzIG%&|MB^KKQb~lYu5u%f9hE_@*uBO-&0b34kd{${M4z}HEi*j z6tK}eH|Q57>^>W4JLoFRbCIMo;FkzuOn($tklr=b4cms=45^*TZOel5#{iunkO%7p0talR06W8zL9{nU`39?EBd3?ea} z_nNM@OVSY1x6GnY;hsb*@yXn2ho&Vdu=#l#)J&4ui#>vK!3(AvSTx0~?% zzVzGtjpF1xpn8FbMIhp&YGQ4ON^OP#@Q}-!(93Xt&`nZKkWZ;6A0K>K)xD#>l0PNA zFWH(Ym|1Y(wO)M$-7-~7j)3k9bs{-Qbsy@b$*k^V*$QcM!dwuxLpC!#Jl;EynhJs7 zKD@lq*Q-YY-B;wXl3#P1kM-|B1?G*|7^;Eps)ia9tqd)XKU0rFsddr}Siugq?(-}8 z!wN|{J%U5n72{)>fHxUhC{Y4Z+F6p-WKOnbe(~?hiLYq)(v@W)*U;4<NW*Tl zVTAF5U&^uv!bp5e6&Q-2Syhh=k(L1C)MvryYD5IF0v$A`y+zZ4GxDX5TONqAkJ43Xx*f!3zaats1T3^r&Tv7DwfmkIO%*GA0duBq{W+ z-bS!y;$LsHcZ$n5rOA6R@C)9*$|7T^H@Fpxfzl*3#qcfS>4CzaG=h}me~VI^5FGtx{lZ_t+03g=#Frd$_6F7F?V z1-bxo#5_eiZ9Ddf%3Yg7i^AH&>hcdSZXtM22j$h` or :doc:`read\_restart ` commands: -* K (energy/distance\^4) -* B1 (distance) -* B2 (distance) -* Rc (distance) -* U0 (energy) +* :math:`K` (energy/distance\^4) +* :math:`B_1` (distance) +* :math:`B_2` (distance) +* :math:`R_c` (distance) +* :math:`U_0` (energy) This potential was constructed to mimic the FENE bond potential for -coarse-grained polymer chains. When monomers with sigma = epsilon = -1.0 are used, the following choice of parameters gives a quartic -potential that looks nearly like the FENE potential: K = 1200, B1 = --0.55, B2 = 0.25, Rc = 1.3, and U0 = 34.6878. Different parameters -can be specified using the :doc:`bond\_coeff ` command, but -you will need to choose them carefully so they form a suitable bond -potential. +coarse-grained polymer chains. When monomers with :math:`\sigma = \epsilon = 1.0` +are used, the following choice of parameters gives a quartic potential that +looks nearly like the FENE potential: -Rc is the cutoff length at which the bond potential goes smoothly to a -local maximum. If a bond length ever becomes > Rc, LAMMPS "breaks" +.. math:: + + K &= 1200 \\ + B_1 &= -0.55 \\ + B_2 &= 0.25 \\ + R_c &= 1.3 \\ + U_0 &= 34.6878 + +Different parameters can be specified using the :doc:`bond_coeff ` +command, but you will need to choose them carefully so they form a suitable +bond potential. + +:math:`R_c` is the cutoff length at which the bond potential goes smoothly to a +local maximum. If a bond length ever becomes :math:`> R_c`, LAMMPS "breaks" the bond, which means two things. First, the bond potential is turned off by setting its type to 0, and is no longer computed. Second, a pairwise interaction between the two atoms is turned on, since they @@ -75,7 +84,7 @@ Note that when bonds are dumped to a file via the :doc:`dump local ` comma status of broken bonds or permanently delete them, e.g.: -.. parsed-literal:: +.. code-block:: LAMMPS delete_bonds all stats delete_bonds all bond 0 remove @@ -124,8 +133,3 @@ Related commands :doc:`bond\_coeff `, :doc:`delete\_bonds ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/bond_quartic.txt b/doc/txt/bond_quartic.txt deleted file mode 100644 index b7b1ee4ce6..0000000000 --- a/doc/txt/bond_quartic.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 - -bond_style quartic command :h3 -bond_style quartic/omp command :h3 - -[Syntax:] - -bond_style quartic :pre - -[Examples:] - -bond_style quartic -bond_coeff 2 1200 -0.55 0.25 1.3 34.6878 :pre - -[Description:] - -The {quartic} bond style uses the potential - -:c,image(Eqs/bond_quartic.jpg) - -to define a bond that can be broken as the simulation proceeds (e.g. -due to a polymer being stretched). The sigma and epsilon used in the -LJ portion of the formula are both set equal to 1.0 by LAMMPS. - -The following coefficients must be defined for each bond type via the -"bond_coeff"_bond_coeff.html command as in the example above, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: - -K (energy/distance^4) -B1 (distance) -B2 (distance) -Rc (distance) -U0 (energy) :ul - -This potential was constructed to mimic the FENE bond potential for -coarse-grained polymer chains. When monomers with sigma = epsilon = -1.0 are used, the following choice of parameters gives a quartic -potential that looks nearly like the FENE potential: K = 1200, B1 = --0.55, B2 = 0.25, Rc = 1.3, and U0 = 34.6878. Different parameters -can be specified using the "bond_coeff"_bond_coeff.html command, but -you will need to choose them carefully so they form a suitable bond -potential. - -Rc is the cutoff length at which the bond potential goes smoothly to a -local maximum. If a bond length ever becomes > Rc, LAMMPS "breaks" -the bond, which means two things. First, the bond potential is turned -off by setting its type to 0, and is no longer computed. Second, a -pairwise interaction between the two atoms is turned on, since they -are no longer bonded. - -LAMMPS does the second task via a computational sleight-of-hand. It -subtracts the pairwise interaction as part of the bond computation. -When the bond breaks, the subtraction stops. For this to work, the -pairwise interaction must always be computed by the -"pair_style"_pair_style.html command, whether the bond is broken or -not. This means that "special_bonds"_special_bonds.html must be set -to 1,1,1, as indicated as a restriction below. - -Note that when bonds are dumped to a file via the "dump -local"_dump.html command, bonds with type 0 are not included. The -"delete_bonds"_delete_bonds.html command can also be used to query the -status of broken bonds or permanently delete them, e.g.: - -delete_bonds all stats -delete_bonds all bond 0 remove :pre - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the "Build package"_Build_package.html doc page for more -info. - -The {quartic} style requires that "special_bonds"_special_bonds.html -parameters be set to 1,1,1. Three- and four-body interactions (angle, -dihedral, etc) cannot be used with {quartic} bonds. - -[Related commands:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html - -[Default:] none From 9780fd3146b562f4311a77eef1a207865a65dec1 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sat, 16 Nov 2019 22:30:09 -0500 Subject: [PATCH 56/64] Update docs: bond_coeff --- doc/src/bond_coeff.rst | 23 +++++------- doc/txt/bond_coeff.txt | 82 ------------------------------------------ 2 files changed, 9 insertions(+), 96 deletions(-) delete mode 100644 doc/txt/bond_coeff.txt diff --git a/doc/src/bond_coeff.rst b/doc/src/bond_coeff.rst index 45b72cce91..281dfc7095 100644 --- a/doc/src/bond_coeff.rst +++ b/doc/src/bond_coeff.rst @@ -1,13 +1,13 @@ -.. index:: bond\_coeff +.. index:: bond_coeff -bond\_coeff command -=================== +bond_coeff command +================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_coeff N args @@ -18,11 +18,11 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_coeff 5 80.0 1.2 - bond_coeff \* 30.0 1.5 1.0 1.0 - bond_coeff 1\*4 30.0 1.5 1.0 1.0 + bond_coeff * 30.0 1.5 1.0 1.0 + bond_coeff 1*4 30.0 1.5 1.0 1.0 bond_coeff 1 harmonic 200.0 1.0 Description @@ -47,9 +47,9 @@ for the same bond type. For example, these commands set the coeffs for all bond types, then overwrite the coeffs for just bond type 2: -.. parsed-literal:: +.. code-block:: LAMMPS - bond_coeff \* 100.0 1.2 + bond_coeff * 100.0 1.2 bond_coeff 2 200.0 1.2 A line in a data file that specifies bond coefficients uses the exact @@ -97,8 +97,3 @@ Related commands :doc:`bond\_style ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/bond_coeff.txt b/doc/txt/bond_coeff.txt deleted file mode 100644 index 1280ae3fb0..0000000000 --- a/doc/txt/bond_coeff.txt +++ /dev/null @@ -1,82 +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 - -bond_coeff command :h3 - -[Syntax:] - -bond_coeff N args :pre - -N = bond type (see asterisk form below) -args = coefficients for one or more bond types :ul - -[Examples:] - -bond_coeff 5 80.0 1.2 -bond_coeff * 30.0 1.5 1.0 1.0 -bond_coeff 1*4 30.0 1.5 1.0 1.0 -bond_coeff 1 harmonic 200.0 1.0 :pre - -[Description:] - -Specify the bond force field coefficients for one or more bond types. -The number and meaning of the coefficients depends on the bond style. -Bond coefficients can also be set in the data file read by the -"read_data"_read_data.html command or in a restart file. - -N can be specified in one of two ways. An explicit numeric value can -be used, as in the 1st example above. Or a wild-card asterisk can be -used to set the coefficients for multiple bond types. This takes the -form "*" or "*n" or "n*" or "m*n". If N = the number of bond types, -then an asterisk with no numeric values means all types from 1 to N. A -leading asterisk means all types from 1 to n (inclusive). A trailing -asterisk means all types from n to N (inclusive). A middle asterisk -means all types from m to n (inclusive). - -Note that using a bond_coeff command can override a previous setting -for the same bond type. For example, these commands set the coeffs -for all bond types, then overwrite the coeffs for just bond type 2: - -bond_coeff * 100.0 1.2 -bond_coeff 2 200.0 1.2 :pre - -A line in a data file that specifies bond coefficients uses the exact -same format as the arguments of the bond_coeff command in an input -script, except that wild-card asterisks should not be used since -coefficients for all N types must be listed in the file. For example, -under the "Bond Coeffs" section of a data file, the line that -corresponds to the 1st example above would be listed as - -5 80.0 1.2 :pre - -:line - -The list of all bond styles defined in LAMMPS is given on the -"bond_style"_bond_style.html doc page. They are also listed in more -compact form on the "Commands bond"_Commands_bond.html doc page. - -On either of those pages, click on the style to display the formula it -computes and its coefficients as specified by the associated -bond_coeff command. - -:line - -[Restrictions:] - -This command must come after the simulation box is defined by a -"read_data"_read_data.html, "read_restart"_read_restart.html, or -"create_box"_create_box.html command. - -A bond style must be defined before any bond coefficients are set, -either in the input script or in a data file. - -[Related commands:] - -"bond_style"_bond_style.html - -[Default:] none From c5c7e6953c37d5a77fa968fead23b2f63072f44b Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sat, 16 Nov 2019 22:35:06 -0500 Subject: [PATCH 57/64] Update docs: bond_write --- doc/src/bond_write.rst | 24 ++++++---------- doc/txt/bond_write.txt | 64 ------------------------------------------ 2 files changed, 9 insertions(+), 79 deletions(-) delete mode 100644 doc/txt/bond_write.txt diff --git a/doc/src/bond_write.rst b/doc/src/bond_write.rst index 23a6a04815..f7055d42aa 100644 --- a/doc/src/bond_write.rst +++ b/doc/src/bond_write.rst @@ -1,13 +1,13 @@ -.. index:: bond\_write +.. index:: bond_write -bond\_write command -=================== +bond_write command +================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_write btype N inner outer file keyword itype jtype @@ -17,13 +17,12 @@ Syntax * file = name of file to write values to * keyword = section name in file for this set of tabulated values * itype,jtype = 2 atom types (optional) -* Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_write 1 500 0.5 3.5 table.txt Harmonic_1 bond_write 3 1000 0.1 6.0 table.txt Morse @@ -40,14 +39,14 @@ file. The energy and force values are computed at distances from inner to outer for 2 interacting atoms forming a bond of type btype, using the -appropriate :doc:`bond\_coeff ` coefficients. N evenly spaced +appropriate :doc:`bond_coeff ` coefficients. N evenly spaced distances are used. For example, for N = 7, inner = 1.0, and outer = 4.0, values are computed at r = 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0. The file is written in the format used as input for the -:doc:`bond\_style ` *table* option with *keyword* as the +:doc:`bond_style ` *table* option with *keyword* as the section name. Each line written to the file lists an index number (1-N), a distance (in distance units), an energy (in energy units), and a force (in force units). @@ -65,12 +64,7 @@ be specified even if the potential has a finite value at r = 0.0. Related commands """""""""""""""" -:doc:`bond\_style table `, -:doc:`bond\_style `, :doc:`bond\_coeff ` +:doc:`bond_style table `, +:doc:`bond_style `, :doc:`bond_coeff ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/bond_write.txt b/doc/txt/bond_write.txt deleted file mode 100644 index 711bd2c296..0000000000 --- a/doc/txt/bond_write.txt +++ /dev/null @@ -1,64 +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 - -bond_write command :h3 - -[Syntax:] - -bond_write btype N inner outer file keyword itype jtype :pre - -btype = bond types -N = # of values -inner,outer = inner and outer bond length (distance units) -file = name of file to write values to -keyword = section name in file for this set of tabulated values -itype,jtype = 2 atom types (optional) -:ul - -[Examples:] - -bond_write 1 500 0.5 3.5 table.txt Harmonic_1 -bond_write 3 1000 0.1 6.0 table.txt Morse :pre - -[Description:] - -Write energy and force values to a file as a function of distance for -the currently defined bond potential. This is useful for plotting the -potential function or otherwise debugging its values. If the file -already exists, the table of values is appended to the end of the file -to allow multiple tables of energy and force to be included in one -file. - -The energy and force values are computed at distances from inner to -outer for 2 interacting atoms forming a bond of type btype, using the -appropriate "bond_coeff"_bond_coeff.html coefficients. N evenly spaced -distances are used. - -For example, for N = 7, inner = 1.0, and outer = 4.0, -values are computed at r = 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0. - -The file is written in the format used as input for the -"bond_style"_bond_style.html {table} option with {keyword} as the -section name. Each line written to the file lists an index number -(1-N), a distance (in distance units), an energy (in energy units), -and a force (in force units). - -[Restrictions:] - -All force field coefficients for bond and other kinds of interactions -must be set before this command can be invoked. - -Due to how the bond force is computed, an inner value > 0.0 must -be specified even if the potential has a finite value at r = 0.0. - -[Related commands:] - -"bond_style table"_bond_table.html, -"bond_style"_bond_style.html, "bond_coeff"_bond_coeff.html - -[Default:] none From 2a900f85aafc4462a8394ed4562ca68beb9893b3 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sat, 16 Nov 2019 22:40:33 -0500 Subject: [PATCH 58/64] Update docs: bond_style --- doc/src/bond_style.rst | 27 ++++------ doc/txt/bond_style.txt | 115 ----------------------------------------- 2 files changed, 11 insertions(+), 131 deletions(-) delete mode 100644 doc/txt/bond_style.txt diff --git a/doc/src/bond_style.rst b/doc/src/bond_style.rst index f912411972..3c5c97b96b 100644 --- a/doc/src/bond_style.rst +++ b/doc/src/bond_style.rst @@ -1,29 +1,27 @@ -.. index:: bond\_style +.. index:: bond_style -bond\_style command -=================== +bond_style command +================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style style args * style = *none* or *hybrid* or *class2* or *fene* or *fene/expand* or *harmonic* or *morse* or *nonlinear* or *quartic* +* args = none for any style except *hybrid* -.. parsed-literal:: - - args = none for any style except *hybrid* - *hybrid* args = list of one or more styles + * *hybrid* args = list of one or more styles Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style harmonic bond_style fene @@ -74,11 +72,11 @@ between the 2 atoms in the bond. Here is an alphabetic list of bond styles defined in LAMMPS. Click on the style to display the formula it computes and coefficients -specified by the associated :doc:`bond\_coeff ` command. +specified by the associated :doc:`bond_coeff ` command. Click on the style to display the formula it computes, any additional arguments specified in the bond\_style command, and coefficients -specified by the associated :doc:`bond\_coeff ` command. +specified by the associated :doc:`bond_coeff ` command. There are also additional accelerated pair styles included in the LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. @@ -128,9 +126,6 @@ Related commands Default """"""" -bond\_style none +.. code-block:: LAMMPS - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html + bond_style none diff --git a/doc/txt/bond_style.txt b/doc/txt/bond_style.txt deleted file mode 100644 index aba6d3a778..0000000000 --- a/doc/txt/bond_style.txt +++ /dev/null @@ -1,115 +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 - -bond_style command :h3 - -[Syntax:] - -bond_style style args :pre - -style = {none} or {hybrid} or {class2} or {fene} or {fene/expand} or \ - {harmonic} or {morse} or {nonlinear} or {quartic} :ul - args = none for any style except {hybrid} - {hybrid} args = list of one or more styles :pre - -[Examples:] - -bond_style harmonic -bond_style fene -bond_style hybrid harmonic fene :pre - -[Description:] - -Set the formula(s) LAMMPS uses to compute bond interactions between -pairs of atoms. In LAMMPS, a bond differs from a pairwise -interaction, which are set via the "pair_style"_pair_style.html -command. Bonds are defined between specified pairs of atoms and -remain in force for the duration of the simulation (unless the bond -breaks which is possible in some bond potentials). The list of bonded -atoms is read in by a "read_data"_read_data.html or -"read_restart"_read_restart.html command from a data or restart file. -By contrast, pair potentials are typically defined between all pairs -of atoms within a cutoff distance and the set of active interactions -changes over time. - -Hybrid models where bonds are computed using different bond potentials -can be setup using the {hybrid} bond style. - -The coefficients associated with a bond style can be specified in a -data or restart file or via the "bond_coeff"_bond_coeff.html command. - -All bond potentials store their coefficient data in binary restart -files which means bond_style and "bond_coeff"_bond_coeff.html commands -do not need to be re-specified in an input script that restarts a -simulation. See the "read_restart"_read_restart.html command for -details on how to do this. The one exception is that bond_style -{hybrid} only stores the list of sub-styles in the restart file; bond -coefficients need to be re-specified. - -NOTE: When both a bond and pair style is defined, the -"special_bonds"_special_bonds.html command often needs to be used to -turn off (or weight) the pairwise interaction that would otherwise -exist between 2 bonded atoms. - -In the formulas listed for each bond style, {r} is the distance -between the 2 atoms in the bond. - -:line - -Here is an alphabetic list of bond styles defined in LAMMPS. Click on -the style to display the formula it computes and coefficients -specified by the associated "bond_coeff"_bond_coeff.html command. - -Click on the style to display the formula it computes, any additional -arguments specified in the bond_style command, and coefficients -specified by the associated "bond_coeff"_bond_coeff.html command. - -There are also additional accelerated pair styles included in the -LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. -The individual style names on the "Commands bond"_Commands_bond.html -doc page are followed by one or more of (g,i,k,o,t) to indicate which -accelerated styles exist. - -"none"_bond_none.html - turn off bonded interactions -"zero"_bond_zero.html - topology but no interactions -"hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul - -"class2"_bond_class2.html - COMPASS (class 2) bond -"fene"_bond_fene.html - FENE (finite-extensible non-linear elastic) bond -"fene/expand"_bond_fene_expand.html - FENE bonds with variable size particles -"gromos"_bond_gromos.html - GROMOS force field bond -"harmonic"_bond_harmonic.html - harmonic bond -"harmonic/shift"_bond_harmonic_shift.html - shifted harmonic bond -"harmonic/shift/cut"_bond_harmonic_shift_cut.html - shifted harmonic bond with a cutoff -"mm3"_bond_mm3.html - MM3 anharmonic bond -"morse"_bond_morse.html - Morse bond -"nonlinear"_bond_nonlinear.html - nonlinear bond -"oxdna/fene"_bond_oxdna.html - modified FENE bond suitable for DNA modeling -"oxdna2/fene"_bond_oxdna.html - same as oxdna but used with different pair styles -"quartic"_bond_quartic.html - breakable quartic bond -"table"_bond_table.html - tabulated by bond length :ul - -:line - -[Restrictions:] - -Bond styles can only be set for atom styles that allow bonds to be -defined. - -Most bond styles are part of the MOLECULE package. They are only -enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. The doc pages for -individual bond potentials tell if it is part of a package. - -[Related commands:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html - -[Default:] - -bond_style none From 18a86a90efbcc5b8a1b5fb4fc215492230ad003d Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sat, 16 Nov 2019 22:44:28 -0500 Subject: [PATCH 59/64] Update docs: bond_zero --- doc/src/bond_zero.rst | 21 ++++++++----------- doc/txt/bond_zero.txt | 48 ------------------------------------------- 2 files changed, 8 insertions(+), 61 deletions(-) delete mode 100644 doc/txt/bond_zero.txt diff --git a/doc/src/bond_zero.rst b/doc/src/bond_zero.rst index 38e7ecf505..43a0af33e2 100644 --- a/doc/src/bond_zero.rst +++ b/doc/src/bond_zero.rst @@ -1,26 +1,26 @@ -.. index:: bond\_style zero +.. index:: bond_style zero -bond\_style zero command -======================== +bond_style zero command +======================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS - bond_style zero *nocoeff* + bond_style zero [nocoeff] Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style zero bond_style zero nocoeff - bond_coeff \* - bond_coeff \* 2.14 + bond_coeff * + bond_coeff * 2.14 Description """"""""""" @@ -53,8 +53,3 @@ Related commands :doc:`bond\_style none ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/bond_zero.txt b/doc/txt/bond_zero.txt deleted file mode 100644 index 554f26e7f0..0000000000 --- a/doc/txt/bond_zero.txt +++ /dev/null @@ -1,48 +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 - -bond_style zero command :h3 - -[Syntax:] - -bond_style zero {nocoeff} :pre - -[Examples:] - -bond_style zero -bond_style zero nocoeff -bond_coeff * -bond_coeff * 2.14 :pre - -[Description:] - -Using an bond style of zero means bond forces and energies are not -computed, but the geometry of bond pairs is still accessible to other -commands. - -As an example, the "compute bond/local"_compute_bond_local.html -command can be used to compute distances for the list of pairs of bond -atoms listed in the data file read by the "read_data"_read_data.html -command. If no bond style is defined, this command cannot be used. - -The optional {nocoeff} flag allows to read data files with a BondCoeff -section for any bond style. Similarly, any bond_coeff commands -will only be checked for the bond type number and the rest ignored. - -Note that the "bond_coeff"_bond_coeff.html command must be used for -all bond types. If specified, there can be only one value, which is -going to be used to assign an equilibrium distance, e.g. for use with -"fix shake"_fix_shake.html. - -[Restrictions:] none - -[Related commands:] - -"bond_style none"_bond_none.html - -[Default:] none From 1b4e84de94f589109a3adb1fd82b2f540a63d45a Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sat, 16 Nov 2019 22:46:53 -0500 Subject: [PATCH 60/64] Update docs: bond_none --- doc/src/bond_none.rst | 21 ++++++++------------- doc/txt/bond_none.txt | 34 ---------------------------------- 2 files changed, 8 insertions(+), 47 deletions(-) delete mode 100644 doc/txt/bond_none.txt diff --git a/doc/src/bond_none.rst b/doc/src/bond_none.rst index dde5b6d29a..ac838581be 100644 --- a/doc/src/bond_none.rst +++ b/doc/src/bond_none.rst @@ -1,13 +1,13 @@ -.. index:: bond\_style none +.. index:: bond_style none -bond\_style none command -======================== +bond_style none command +======================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style none @@ -15,7 +15,7 @@ Examples """""""" -.. parsed-literal:: +.. code-blocK:: LAMMPS bond_style none @@ -24,9 +24,9 @@ Description Using a bond style of none means bond forces and energies are not computed, even if pairs of bonded atoms were listed in the data file -read by the :doc:`read\_data ` command. +read by the :doc:`read_data ` command. -See the :doc:`bond\_style zero ` command for a way to +See the :doc:`bond_style zero ` command for a way to calculate bond statistics, but compute no bond interactions. Restrictions @@ -35,11 +35,6 @@ Restrictions **Related commands:** none -:doc:`bond\_style zero ` +:doc:`bond_style zero ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/bond_none.txt b/doc/txt/bond_none.txt deleted file mode 100644 index cace1919e1..0000000000 --- a/doc/txt/bond_none.txt +++ /dev/null @@ -1,34 +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 - -bond_style none command :h3 - -[Syntax:] - -bond_style none :pre - -[Examples:] - -bond_style none :pre - -[Description:] - -Using a bond style of none means bond forces and energies are not -computed, even if pairs of bonded atoms were listed in the data file -read by the "read_data"_read_data.html command. - -See the "bond_style zero"_bond_zero.html command for a way to -calculate bond statistics, but compute no bond interactions. - -[Restrictions:] none - -[Related commands:] none - -"bond_style zero"_bond_zero.html - -[Default:] none From ff9f93bbf69d19d4fdbd269a93f6729ceaedb0a1 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sat, 16 Nov 2019 22:51:46 -0500 Subject: [PATCH 61/64] Update docs: bond_table --- doc/src/bond_table.rst | 31 ++++---- doc/txt/bond_table.txt | 163 ----------------------------------------- 2 files changed, 13 insertions(+), 181 deletions(-) delete mode 100644 doc/txt/bond_table.txt diff --git a/doc/src/bond_table.rst b/doc/src/bond_table.rst index f68288349d..c12ea8af44 100644 --- a/doc/src/bond_table.rst +++ b/doc/src/bond_table.rst @@ -1,16 +1,16 @@ -.. index:: bond\_style table +.. index:: bond_style table -bond\_style table command -========================= +bond_style table command +======================== -bond\_style table/omp command -============================= +bond_style table/omp command +============================ Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style table style N @@ -21,7 +21,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style table linear 1000 bond_coeff 1 file.table ENTRY1 @@ -31,14 +31,14 @@ Description Style *table* creates interpolation tables of length *N* from bond potential and force values listed in a file(s) as a function of bond -length. The files are read by the :doc:`bond\_coeff ` +length. The files are read by the :doc:`bond_coeff ` command. The interpolation tables are created by fitting cubic splines to the file values and interpolating energy and force values at each of *N* distances. During a simulation, these tables are used to interpolate energy and force values as needed. The interpolation is done in one -of 2 styles: *linear* or *spline*\ . +of 2 styles: *linear* or *spline*. For the *linear* style, the bond length is used to find 2 surrounding table values from which an energy or force is computed by linear @@ -50,7 +50,7 @@ used to find the appropriate set of coefficients which are used to evaluate a cubic polynomial which computes the energy or force. The following coefficients must be defined for each bond type via the -:doc:`bond\_coeff ` command as in the example above. +:doc:`bond_coeff ` command as in the example above. * filename * keyword @@ -84,14 +84,14 @@ A section begins with a non-blank line whose 1st character is not a between sections. The first line begins with a keyword which identifies the section. The line can contain additional text, but the initial text must match the argument specified in the -:doc:`bond\_coeff ` command. The next line lists (in any +:doc:`bond_coeff ` command. The next line lists (in any order) one or more parameters for the table. Each parameter is a keyword followed by one or more numeric values. The parameter "N" is required and its value is the number of table entries that follow. Note that this may be different than the *N* specified in the :doc:`bond\_style table ` command. Let -Ntable = *N* in the bond\_style command, and Nfile = "N" in the +Ntable = *N* in the bond_style command, and Nfile = "N" in the tabulated file. What LAMMPS does is a preliminary interpolation by creating splines using the Nfile tabulated values as nodal points. It uses these to interpolate as needed to generate energy and force @@ -173,11 +173,6 @@ info. Related commands """""""""""""""" -:doc:`bond\_coeff `, :doc:`delete\_bonds ` +:doc:`bond_coeff `, :doc:`delete_bonds ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/bond_table.txt b/doc/txt/bond_table.txt deleted file mode 100644 index 7235214af0..0000000000 --- a/doc/txt/bond_table.txt +++ /dev/null @@ -1,163 +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 - -bond_style table command :h3 -bond_style table/omp command :h3 - -[Syntax:] - -bond_style table style N :pre - -style = {linear} or {spline} = method of interpolation -N = use N values in table :ul - -[Examples:] - -bond_style table linear 1000 -bond_coeff 1 file.table ENTRY1 :pre - -[Description:] - -Style {table} creates interpolation tables of length {N} from bond -potential and force values listed in a file(s) as a function of bond -length. The files are read by the "bond_coeff"_bond_coeff.html -command. - -The interpolation tables are created by fitting cubic splines to the -file values and interpolating energy and force values at each of {N} -distances. During a simulation, these tables are used to interpolate -energy and force values as needed. The interpolation is done in one -of 2 styles: {linear} or {spline}. - -For the {linear} style, the bond length is used to find 2 surrounding -table values from which an energy or force is computed by linear -interpolation. - -For the {spline} style, a cubic spline coefficients are computed and -stored at each of the {N} values in the table. The bond length is -used to find the appropriate set of coefficients which are used to -evaluate a cubic polynomial which computes the energy or force. - -The following coefficients must be defined for each bond type via the -"bond_coeff"_bond_coeff.html command as in the example above. - -filename -keyword :ul - -The filename specifies a file containing tabulated energy and force -values. The keyword specifies a section of the file. The format of -this file is described below. - -:line - -The format of a tabulated file is as follows (without the -parenthesized comments): - -# Bond potential for harmonic (one or more comment or blank lines) :pre - -HAM (keyword is the first text on line) -N 101 FP 0 0 EQ 0.5 (N, FP, EQ parameters) - (blank line) -1 0.00 338.0000 1352.0000 (index, bond-length, energy, force) -2 0.01 324.6152 1324.9600 -... -101 1.00 338.0000 -1352.0000 :pre - -A section begins with a non-blank line whose 1st character is not a -"#"; blank lines or lines starting with "#" can be used as comments -between sections. The first line begins with a keyword which -identifies the section. The line can contain additional text, but the -initial text must match the argument specified in the -"bond_coeff"_bond_coeff.html command. The next line lists (in any -order) one or more parameters for the table. Each parameter is a -keyword followed by one or more numeric values. - -The parameter "N" is required and its value is the number of table -entries that follow. Note that this may be different than the {N} -specified in the "bond_style table"_bond_style.html command. Let -Ntable = {N} in the bond_style command, and Nfile = "N" in the -tabulated file. What LAMMPS does is a preliminary interpolation by -creating splines using the Nfile tabulated values as nodal points. It -uses these to interpolate as needed to generate energy and force -values at Ntable different points. The resulting tables of length -Ntable are then used as described above, when computing energy and -force for individual bond lengths. This means that if you want the -interpolation tables of length Ntable to match exactly what is in the -tabulated file (with effectively no preliminary interpolation), you -should set Ntable = Nfile. - -The "FP" parameter is optional. If used, it is followed by two values -fplo and fphi, which are the derivatives of the force at the innermost -and outermost bond lengths. These values are needed by the spline -construction routines. If not specified by the "FP" parameter, they -are estimated (less accurately) by the first two and last two force -values in the table. - -The "EQ" parameter is also optional. If used, it is followed by a the -equilibrium bond length, which is used, for example, by the "fix -shake"_fix_shake.html command. If not used, the equilibrium bond -length is to the distance in the table with the lowest potential energy. - -Following a blank line, the next N lines list the tabulated values. -On each line, the 1st value is the index from 1 to N, the 2nd value is -the bond length r (in distance units), the 3rd value is the energy (in -energy units), and the 4th is the force (in force units). The bond -lengths must range from a LO value to a HI value, and increase from -one line to the next. If the actual bond length is ever smaller than -the LO value or larger than the HI value, then the bond energy and -force is evaluated as if the bond were the LO or HI length. - -Note that one file can contain many sections, each with a tabulated -potential. LAMMPS reads the file section by section until it finds -one that matches the specified keyword. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed on the "Speed packages"_Speed_packages.html doc -page. The accelerated styles take the same arguments and should -produce the same results, except for round-off and precision issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Build -package"_Build_package.html doc page for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Run_options.html when you invoke LAMMPS, or you can use the -"suffix"_suffix.html command in your input script. - -See the "Speed packages"_Speed_packages.html doc page for more -instructions on how to use the accelerated styles effectively. - -:line - -[Restart info:] - -This bond style writes the settings for the "bond_style table" -command to "binary restart files"_restart.html, so a bond_style -command does not need to specified in an input script that reads a -restart file. However, the coefficient information is not stored in -the restart file, since it is tabulated in the potential files. Thus, -bond_coeff commands do need to be specified in the restart input -script. - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the "Build package"_Build_package.html doc page for more -info. - -[Related commands:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html - -[Default:] none From d6b1e302f297cddd402afa4a78f68136db66ca89 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sat, 16 Nov 2019 22:59:34 -0500 Subject: [PATCH 62/64] Update docs: bond_hybrid --- doc/src/bond_hybrid.rst | 27 ++++++--------- doc/txt/bond_hybrid.txt | 74 ----------------------------------------- 2 files changed, 11 insertions(+), 90 deletions(-) delete mode 100644 doc/txt/bond_hybrid.txt diff --git a/doc/src/bond_hybrid.rst b/doc/src/bond_hybrid.rst index 34297c2ff9..6b8175858f 100644 --- a/doc/src/bond_hybrid.rst +++ b/doc/src/bond_hybrid.rst @@ -1,13 +1,13 @@ -.. index:: bond\_style hybrid +.. index:: bond_style hybrid -bond\_style hybrid command -========================== +bond_style hybrid command +========================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS bond_style hybrid style1 style2 ... @@ -17,11 +17,11 @@ Examples """""""" -.. parsed-literal:: +.. code-block: LAMMPS bond_style hybrid harmonic fene bond_coeff 1 harmonic 80.0 1.2 - bond_coeff 2\* fene 30.0 1.5 1.0 1.0 + bond_coeff 2* fene 30.0 1.5 1.0 1.0 Description """"""""""" @@ -31,19 +31,19 @@ simulation. A bond style is assigned to each bond type. For example, bonds in a polymer flow (of bond type 1) could be computed with a *fene* potential and bonds in the wall boundary (of bond type 2) could be computed with a *harmonic* potential. The assignment of bond type -to style is made via the :doc:`bond\_coeff ` command or in +to style is made via the :doc:`bond_coeff ` command or in the data file. In the bond\_coeff commands, the name of a bond style must be added after the bond type, with the remaining coefficients being those appropriate to that style. In the example above, the 2 bond\_coeff commands set bonds of bond type 1 to be computed with a *harmonic* -potential with coefficients 80.0, 1.2 for K, r0. All other bond types +potential with coefficients 80.0, 1.2 for :math:`K`, :math:`r_0`. All other bond types (2-N) are computed with a *fene* potential with coefficients 30.0, -1.5, 1.0, 1.0 for K, R0, epsilon, sigma. +1.5, 1.0, 1.0 for :math:`K`, :math:`R_0`, :math:`\epsilon`, :math:`\sigma`. If bond coefficients are specified in the data file read via the -:doc:`read\_data ` command, then the same rule applies. +:doc:`read_data ` command, then the same rule applies. E.g. "harmonic" or "fene" must be added after the bond type, for each line in the "Bond Coeffs" section, e.g. @@ -80,11 +80,6 @@ file, you need to re-specify bond\_coeff commands. Related commands """""""""""""""" -:doc:`bond\_coeff `, :doc:`delete\_bonds ` +:doc:`bond_coeff `, :doc:`delete_bonds ` **Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Commands_all.html diff --git a/doc/txt/bond_hybrid.txt b/doc/txt/bond_hybrid.txt deleted file mode 100644 index 0996f72ce3..0000000000 --- a/doc/txt/bond_hybrid.txt +++ /dev/null @@ -1,74 +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 - -bond_style hybrid command :h3 - -[Syntax:] - -bond_style hybrid style1 style2 ... :pre - -style1,style2 = list of one or more bond styles :ul - -[Examples:] - -bond_style hybrid harmonic fene -bond_coeff 1 harmonic 80.0 1.2 -bond_coeff 2* fene 30.0 1.5 1.0 1.0 :pre - -[Description:] - -The {hybrid} style enables the use of multiple bond styles in one -simulation. A bond style is assigned to each bond type. For example, -bonds in a polymer flow (of bond type 1) could be computed with a -{fene} potential and bonds in the wall boundary (of bond type 2) could -be computed with a {harmonic} potential. The assignment of bond type -to style is made via the "bond_coeff"_bond_coeff.html command or in -the data file. - -In the bond_coeff commands, the name of a bond style must be added -after the bond type, with the remaining coefficients being those -appropriate to that style. In the example above, the 2 bond_coeff -commands set bonds of bond type 1 to be computed with a {harmonic} -potential with coefficients 80.0, 1.2 for K, r0. All other bond types -(2-N) are computed with a {fene} potential with coefficients 30.0, -1.5, 1.0, 1.0 for K, R0, epsilon, sigma. - -If bond coefficients are specified in the data file read via the -"read_data"_read_data.html command, then the same rule applies. -E.g. "harmonic" or "fene" must be added after the bond type, for each -line in the "Bond Coeffs" section, e.g. - -Bond Coeffs :pre - -1 harmonic 80.0 1.2 -2 fene 30.0 1.5 1.0 1.0 -... :pre - -A bond style of {none} with no additional coefficients can be used in -place of a bond style, either in a input script bond_coeff command or -in the data file, if you desire to turn off interactions for specific -bond types. - -:line - -[Restrictions:] - -This bond style can only be used if LAMMPS was built with the MOLECULE -package. See the "Build package"_Build_package.html doc page for more -info. - -Unlike other bond styles, the hybrid bond style does not store bond -coefficient info for individual sub-styles in a "binary restart -files"_restart.html. Thus when restarting a simulation from a restart -file, you need to re-specify bond_coeff commands. - -[Related commands:] - -"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html - -[Default:] none From 3ff3621efac20659b6e55fc09abf90b604bc12ff Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sat, 16 Nov 2019 23:17:08 -0500 Subject: [PATCH 63/64] Fix pdf build --- doc/src/bond_harmonic_shift_cut.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/bond_harmonic_shift_cut.rst b/doc/src/bond_harmonic_shift_cut.rst index 0ea9a3a968..459acfdbfb 100644 --- a/doc/src/bond_harmonic_shift_cut.rst +++ b/doc/src/bond_harmonic_shift_cut.rst @@ -36,7 +36,7 @@ uses the potential where :math:`r_0` is the equilibrium bond distance, and rc the critical distance. The bond potential is zero for distances :math:`r > r_c`. The potential is :math:`-U_{\text{min}}` -at :math:`r_0` and zero at :math:`r_c`. The spring constant is :math:`k = U_{\text{min}} / [ 2 (r_0-r_c)\^2]`. +at :math:`r_0` and zero at :math:`r_c`. The spring constant is :math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`. The following coefficients must be defined for each bond type via the :doc:`bond\_coeff ` command as in the example above, or in From 19b265f845b229ca924220b4732ee9702e49cc59 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sat, 16 Nov 2019 23:57:12 -0500 Subject: [PATCH 64/64] Update CMake-based doc build --- cmake/Modules/Documentation.cmake | 23 +++-------------------- 1 file changed, 3 insertions(+), 20 deletions(-) diff --git a/cmake/Modules/Documentation.cmake b/cmake/Modules/Documentation.cmake index 99f570820a..feff66a9b2 100644 --- a/cmake/Modules/Documentation.cmake +++ b/cmake/Modules/Documentation.cmake @@ -9,9 +9,7 @@ if(BUILD_DOC) set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv) - file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.txt) - file(GLOB PDF_EXTRA_SOURCES ${LAMMPS_DOC_DIR}/src/lammps_commands*.txt ${LAMMPS_DOC_DIR}/src/lammps_support.txt ${LAMMPS_DOC_DIR}/src/lammps_tutorials.txt) - list(REMOVE_ITEM DOC_SOURCES ${PDF_EXTRA_SOURCES}) + file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst) add_custom_command( OUTPUT docenv @@ -28,25 +26,10 @@ if(BUILD_DOC) COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters ) - set(RST_FILES "") - set(RST_DIR ${CMAKE_BINARY_DIR}/rst) - file(MAKE_DIRECTORY ${RST_DIR}) - foreach(TXT_FILE ${DOC_SOURCES}) - get_filename_component(FILENAME ${TXT_FILE} NAME_WE) - set(RST_FILE ${RST_DIR}/${FILENAME}.rst) - list(APPEND RST_FILES ${RST_FILE}) - add_custom_command( - OUTPUT ${RST_FILE} - DEPENDS requirements.txt docenv ${TXT_FILE} - COMMAND ${DOCENV_BINARY_DIR}/txt2rst -o ${RST_DIR} ${TXT_FILE} - ) - endforeach() - add_custom_command( OUTPUT html - DEPENDS ${RST_FILES} - COMMAND ${CMAKE_COMMAND} -E copy_directory ${LAMMPS_DOC_DIR}/src ${RST_DIR} - COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${RST_DIR} html + DEPENDS ${DOC_SOURCES} docenv requirements.txt + COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${LAMMPS_DOC_DIR}/src html ) add_custom_target(