diff --git a/doc/Makefile b/doc/Makefile index 79558674d7..fd087f0344 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -6,6 +6,7 @@ BUILDDIR = /tmp/lammps-docs-$(SHA1) RSTDIR = $(BUILDDIR)/rst VENV = $(BUILDDIR)/docenv TXT2RST = $(VENV)/bin/txt2rst +ANCHORCHECK = $(VENV)/bin/doc_anchor_check PYTHON = $(shell which python3) HAS_PYTHON3 = NO @@ -22,7 +23,7 @@ endif SOURCES=$(wildcard src/*.txt) OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst) -.PHONY: help clean-all clean epub html pdf old venv spelling +.PHONY: help clean-all clean epub html pdf old venv spelling anchor_check # ------------------------------------------ @@ -36,6 +37,7 @@ help: @echo " clean remove all intermediate RST files" @echo " clean-all reset the entire build environment" @echo " txt2html build txt2html tool" + @echo " anchor_check scan for duplicate anchor labels" # ------------------------------------------ @@ -49,11 +51,14 @@ clean: clean-spelling: rm -rf spelling -html: $(OBJECTS) +html: $(OBJECTS) $(ANCHORCHECK) @(\ . $(VENV)/bin/activate ;\ cp -r src/* $(RSTDIR)/ ;\ sphinx-build -j 8 -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\ + echo "############################################" ;\ + doc_anchor_check src/*.txt ;\ + echo "############################################" ;\ deactivate ;\ ) -rm html/searchindex.js @@ -127,6 +132,13 @@ fetch: txt2html: utils/txt2html/txt2html.exe +anchor_check : $(ANCHORCHECK) + @(\ + . $(VENV)/bin/activate ;\ + doc_anchor_check src/*.txt ;\ + deactivate ;\ + ) + # ------------------------------------------ utils/txt2html/txt2html.exe: utils/txt2html/txt2html.cpp @@ -151,7 +163,7 @@ $(VENV): deactivate;\ ) -$(TXT2RST): $(VENV) +$(TXT2RST) $(ANCHORCHECK): $(VENV) @( \ . $(VENV)/bin/activate; \ (cd utils/converters;\ diff --git a/doc/src/Eqs/pair_momb.jpg b/doc/src/Eqs/pair_momb.jpg new file mode 100644 index 0000000000..1e994c6e0f Binary files /dev/null and b/doc/src/Eqs/pair_momb.jpg differ diff --git a/doc/src/Eqs/pair_momb.tex b/doc/src/Eqs/pair_momb.tex new file mode 100644 index 0000000000..4c66e3ce77 --- /dev/null +++ b/doc/src/Eqs/pair_momb.tex @@ -0,0 +1,13 @@ +\documentclass[12pt,fleqn]{article} +\usepackage{amsmath} +\thispagestyle{empty} + +\begin{document} + +\setlength{\jot}{2ex} +\begin{gather*} + E = D_0 [\exp^{-2 \alpha (r-r_0)} - 2\exp^{-\alpha (r-r_0)}] - s_6 \frac{C_6}{r^6} f_{damp}(r,R_r) \\ + f_{damp}(r,R_r) = \frac{1}{1 + \exp^{-d(r/R_r - 1)}} +\end{gather*} + +\end{document} \ No newline at end of file diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index bb7a1452bc..6582d24455 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@

LAMMPS Documentation :c,h3 -10 Mar 2017 version :c,h4 +24 Mar 2017 version :c,h4 Version info: :h4 @@ -39,7 +39,7 @@ directory name created when you unpack a tarball, and at the top of the first page of the manual (this page). If you browse the HTML doc pages on the LAMMPS WWW site, they always -describe the most current version of LAMMPS. :ulb,l +describe the most current [development] version of LAMMPS. :ulb,l If you browse the HTML doc pages included in your tarball, they describe the version you have. :l @@ -67,7 +67,7 @@ Labs and Temple University: "Steve Plimpton"_sjp, sjplimp at sandia.gov :ulb,l Aidan Thompson, athomps at sandia.gov :l -Stan Moore, stamoore at sandia.gov :l +Stan Moore, stamoor at sandia.gov :l "Axel Kohlmeyer"_ako, akohlmey at gmail.com :l :ule diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index 6e526dcb51..63a63b3736 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -687,6 +687,7 @@ package"_Section_start.html#start_3. "eos/cv"_fix_eos_cv.html, "eos/table"_fix_eos_table.html, "eos/table/rx"_fix_eos_table_rx.html, +"filter/corotate"_fix_filter_corotate.html, "flow/gauss"_fix_flow_gauss.html, "gle"_fix_gle.html, "grem"_fix_grem.html, @@ -939,6 +940,8 @@ KOKKOS, o = USER-OMP, t = OPT. "lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html, "lj/charmm/coul/long (giko)"_pair_charmm.html, "lj/charmm/coul/msm"_pair_charmm.html, +"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html, +"lj/charmmfsw/coul/long"_pair_charmm.html, "lj/class2 (gko)"_pair_class2.html, "lj/class2/coul/cut (ko)"_pair_class2.html, "lj/class2/coul/long (gko)"_pair_class2.html, @@ -1034,6 +1037,7 @@ package"_Section_start.html#start_3. "meam/spline (o)"_pair_meam_spline.html, "meam/sw/spline"_pair_meam_sw_spline.html, "mgpt"_pair_mgpt.html, +"momb"_pair_momb.html, "morse/smooth/linear"_pair_morse.html, "morse/soft"_pair_morse.html, "multi/lucy"_pair_multi_lucy.html, @@ -1060,7 +1064,7 @@ package"_Section_start.html#start_3. "table/rx"_pair_table_rx.html, "tersoff/table (o)"_pair_tersoff.html, "thole"_pair_thole.html, -"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c) +"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c) :line @@ -1146,6 +1150,7 @@ USER-OMP, t = OPT. "zero"_dihedral_zero.html, "hybrid"_dihedral_hybrid.html, "charmm (ko)"_dihedral_charmm.html, +"charmmfsh"_dihedral_charmm.html, "class2 (ko)"_dihedral_class2.html, "harmonic (io)"_dihedral_harmonic.html, "helix (o)"_dihedral_helix.html, diff --git a/doc/src/Section_example.txt b/doc/src/Section_example.txt index 60a5ed1285..26dc3b9698 100644 --- a/doc/src/Section_example.txt +++ b/doc/src/Section_example.txt @@ -25,9 +25,7 @@ files and image files. If you uncomment the "dump"_dump.html command in the input script, a text dump file will be produced, which can be animated by various -"visualization programs"_http://lammps.sandia.gov/viz.html. It can -also be animated using the xmovie tool described in the "Additional -Tools"_Section_tools.html section of the LAMMPS documentation. +"visualization programs"_http://lammps.sandia.gov/viz.html. If you uncomment the "dump image"_dump.html command in the input script, and assuming you have built LAMMPS with a JPG library, JPG @@ -53,9 +51,11 @@ Lowercase directories :h4 accelerate: run with various acceleration options (OpenMP, GPU, Phi) balance: dynamic load balancing, 2d system body: body particles, 2d system +cmap: CMAP 5-body contributions to CHARMM force field colloid: big colloid particles in a small particle solvent, 2d system comb: models using the COMB potential coreshell: core/shell model using CORESHELL package +controller: use of fix controller as a thermostat crack: crack propagation in a 2d solid deposit: deposit atoms and molecules on a surface dipole: point dipolar particles, 2d system @@ -64,6 +64,8 @@ eim: NaCl using the EIM potential ellipse: ellipsoidal particles in spherical solvent, 2d system flow: Couette and Poiseuille flow in a 2d channel friction: frictional contact of spherical asperities between 2d surfaces +gcmc: Grand Canonical Monte Carlo (GCMC) via the fix gcmc command +granregion: use of fix wall/region/gran as boundary on granular particles hugoniostat: Hugoniostat shock dynamics indent: spherical indenter into a 2d solid kim: use of potentials in Knowledge Base for Interatomic Models (KIM) @@ -71,6 +73,7 @@ meam: MEAM test for SiC and shear (same as shear examples) melt: rapid melt of 3d LJ system micelle: self-assembly of small lipid-like molecules into 2d bilayers min: energy minimization of 2d LJ melt +mscg: parameterize a multi-scale coarse-graining (MSCG) model msst: MSST shock dynamics nb3b: use of nonbonded 3-body harmonic pair style neb: nudged elastic band (NEB) calculation for barrier finding @@ -89,7 +92,8 @@ snap: NVE dynamics for BCC tantalum crystal using SNAP potential srd: stochastic rotation dynamics (SRD) particles as solvent streitz: use of Streitz/Mintmire potential with charge equilibration tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si -vashishta: use of the Vashishta potential :tb(s=:) +vashishta: use of the Vashishta potential +voronoi: Voronoi tesselation via compute voronoi/atom command :tb(s=:) Here is how you can run and visualize one of the sample problems: diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt index 8cfbe1c46c..a378d8d088 100644 --- a/doc/src/Section_howto.txt +++ b/doc/src/Section_howto.txt @@ -165,9 +165,16 @@ Many of the example input scripts included in the LAMMPS distribution are for 2d models. NOTE: Some models in LAMMPS treat particles as finite-size spheres, as -opposed to point particles. In 2d, the particles will still be -spheres, not disks, meaning their moment of inertia will be the same -as in 3d. +opposed to point particles. See the "atom_style +sphere"_atom_style.html and "fix nve/sphere"_fix_nve_sphere.html +commands for details. By default, for 2d simulations, such particles +will still be modeled as 3d spheres, not 2d discs (circles), meaning +their moment of inertia will be that of a sphere. If you wish to +model them as 2d discs, see the "set density/disc"_set.html command +and the {disc} option for 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. :line @@ -197,7 +204,10 @@ documentation for the formula it computes. "bond_style"_bond_harmonic.html harmonic "angle_style"_angle_charmm.html charmm +"dihedral_style"_dihedral_charmm.html charmmfsh "dihedral_style"_dihedral_charmm.html charmm +"pair_style"_pair_charmm.html lj/charmmfsw/coul/charmmfsh +"pair_style"_pair_charmm.html lj/charmmfsw/coul/long "pair_style"_pair_charmm.html lj/charmm/coul/charmm "pair_style"_pair_charmm.html lj/charmm/coul/charmm/implicit "pair_style"_pair_charmm.html lj/charmm/coul/long :ul @@ -205,6 +215,12 @@ documentation for the formula it computes. "special_bonds"_special_bonds.html charmm "special_bonds"_special_bonds.html amber :ul +NOTE: For CHARMM, the newer {charmmfsw} or {charmmfsh} styles were +released in March 2017. We recommend they be used instead of the +older {charmm} styles. See discussion of the differences on the "pair +charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html +doc pages. + DREIDING is a generic force field developed by the "Goddard group"_http://www.wag.caltech.edu at Caltech and is useful for predicting structures and dynamics of organic, biological and @@ -434,6 +450,12 @@ computations between frozen atoms by using this command: "neigh_modify"_neigh_modify.html exclude :ul +NOTE: By default, for 2d systems, granular particles are still modeled +as 3d spheres, not 2d discs (circles), meaning their moment of inertia +will be the same as in 3d. If you wish to model granular particles in +2d as 2d discs, see the note on this topic in "Section +6.2"_Section_howto.html#howto_2, where 2d simulations are disussed. + :line 6.7 TIP3P water model :link(howto_7),h4 @@ -451,7 +473,7 @@ atoms and the water molecule to run a rigid TIP3P-CHARMM model with a cutoff. The K values can be used if a flexible TIP3P model (without fix shake) is desired. If the LJ epsilon and sigma for HH and OH are set to 0.0, it corresponds to the original 1983 TIP3P model -"(Jorgensen)"_#Jorgensen. +"(Jorgensen)"_#Jorgensen1. O mass = 15.9994 H mass = 1.008 @@ -469,7 +491,7 @@ K of HOH angle = 55 theta of HOH angle = 104.52 :all(b),p These are the parameters to use for TIP3P with a long-range Coulombic -solver (e.g. Ewald or PPPM in LAMMPS), see "(Price)"_#Price for +solver (e.g. Ewald or PPPM in LAMMPS), see "(Price)"_#Price1 for details: O mass = 15.9994 @@ -513,7 +535,7 @@ using the "fix shake"_fix_shake.html command. These are the additional parameters (in real units) to set for O and H atoms and the water molecule to run a rigid TIP4P model with a cutoff -"(Jorgensen)"_#Jorgensen. Note that the OM distance is specified in +"(Jorgensen)"_#Jorgensen1. Note that the OM distance is specified in the "pair_style"_pair_style.html command, not as part of the pair coefficients. @@ -1032,6 +1054,10 @@ profile consistent with the applied shear strain rate. An alternative method for calculating viscosities is provided via the "fix viscosity"_fix_viscosity.html command. +NEMD simulations can also be used to measure transport properties of a fluid +through a pore or channel. Simulations of steady-state flow can be performed +using the "fix flow/gauss"_fix_flow_gauss.html command. + :line 6.14 Finite-size spherical and aspherical particles :link(howto_14),h4 @@ -1834,7 +1860,7 @@ the deformation must be chosen judiciously, and care must be taken to fully equilibrate the deformed cell before sampling the stress tensor. Another approach is to sample the triclinic cell fluctuations that occur in an NPT simulation. This method can also be slow to -converge and requires careful post-processing "(Shinoda)"_#Shinoda +converge and requires careful post-processing "(Shinoda)"_#Shinoda1 :line @@ -1957,9 +1983,12 @@ The extract functions return a pointer to various global or per-atom quantities stored in LAMMPS or to values calculated by a compute, fix, or variable. The pointer returned by the extract_global() function can be used as a permanent reference to a value which may change. For -the other extract functions, the underlying storage may be reallocated -as LAMMPS runs, so you need to re-call the function to assure a -current pointer or returned value(s). +the extract_atom() method, see the extract() method in the +src/atom.cpp file for a list of valid per-atom properties. New names +could easily be added if the property you want is not listed. For the +other extract functions, the underlying storage may be reallocated as +LAMMPS runs, so you need to re-call the function to assure a current +pointer or returned value(s). The lammps_reset_box() function resets the size and shape of the simulation box, e.g. as part of restoring a previously extracted and @@ -1975,11 +2004,15 @@ keyword as a double precision value. The lammps_get_natoms() function returns the total number of atoms in the system and can be used by the caller to allocate space for the lammps_gather_atoms() and lammps_scatter_atoms() functions. The -gather function collects atom info of the requested type (atom coords, -types, forces, etc) from all processors, orders them by atom ID, and -returns a full list to each calling processor. The scatter function -does the inverse. It distributes the same kinds of values, +gather function collects peratom info of the requested type (atom +coords, types, forces, etc) from all processors, orders them by atom +ID, and returns a full list to each calling processor. The scatter +function does the inverse. It distributes the same peratom values, passed by the caller, to each atom owned by individual processors. +Both methods are thus a means to extract or assign (overwrite) any +peratom quantities within LAMMPS. See the extract() method in the +src/atom.cpp file for a list of valid per-atom properties. New names +could easily be added if the property you want is not listed. The lammps_create_atoms() function takes a list of N atoms as input with atom types and coords (required), an optionally atom IDs and @@ -2899,14 +2932,14 @@ Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). [(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 (1990). -:link(Jorgensen) +:link(Jorgensen1) [(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem Phys, 79, 926 (1983). -:link(Price) +:link(Price1) [(Price)] Price and Brooks, J Chem Phys, 121, 10096 (2004). -:link(Shinoda) +:link(Shinoda1) [(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004). :link(MitchellFincham) diff --git a/doc/src/Section_python.txt b/doc/src/Section_python.txt index 50807e2d95..b994a56402 100644 --- a/doc/src/Section_python.txt +++ b/doc/src/Section_python.txt @@ -594,10 +594,10 @@ flag = lmp.set_variable(name,value) # set existing named string-style vari value = lmp.get_thermo(name) # return current value of a thermo keyword natoms = lmp.get_natoms() # total # of atoms as int -data = lmp.gather_atoms(name,type,count) # return atom attribute of all atoms gathered into data, ordered by atom ID +data = lmp.gather_atoms(name,type,count) # return per-atom property of all atoms gathered into data, ordered by atom ID # name = "x", "charge", "type", etc # count = # of per-atom values, 1 or 3, etc -lmp.scatter_atoms(name,type,count,data) # scatter atom attribute of all atoms from data, ordered by atom ID +lmp.scatter_atoms(name,type,count,data) # scatter per-atom property to all atoms from data, ordered by atom ID # name = "x", "charge", "type", etc # count = # of per-atom values, 1 or 3, etc :pre @@ -656,10 +656,10 @@ argument. For extract_atom(), a pointer to internal LAMMPS atom-based data is returned, which you can use via normal Python subscripting. See the extract() method in the src/atom.cpp file for a list of valid names. -Again, new names could easily be added. A pointer to a vector of -doubles or integers, or a pointer to an array of doubles (double **) -or integers (int **) is returned. You need to specify the appropriate -data type via the type argument. +Again, new names could easily be added if the property you want is not +listed. A pointer to a vector of doubles or integers, or a pointer to +an array of doubles (double **) or integers (int **) is returned. You +need to specify the appropriate data type via the type argument. For extract_compute() and extract_fix(), the global, per-atom, or local data calculated by the compute or fix can be accessed. What is @@ -689,12 +689,16 @@ specified group. The get_natoms() method returns the total number of atoms in the simulation, as an int. -The gather_atoms() method returns a ctypes vector of ints or doubles -as specified by type, of length count*natoms, for the property of all -the atoms in the simulation specified by name, ordered by count and -then by atom ID. The vector can be used via normal Python -subscripting. If atom IDs are not consecutively ordered within -LAMMPS, a None is returned as indication of an error. +The gather_atoms() method allows any per-atom property (coordinates, +velocities, etc) to be extracted from LAMMPS. It returns a ctypes +vector of ints or doubles as specified by type, of length +count*natoms, for the named property for all atoms in the simulation. +The data is ordered by count and then by atom ID. See the extract() +method in the src/atom.cpp file for a list of valid names. Again, new +names could easily be added if the property you want is missing. The +vector can be used via normal Python subscripting. If atom IDs are +not consecutively ordered within LAMMPS, a None is returned as +indication of an error. Note that the data structure gather_atoms("x") returns is different from the data structure returned by extract_atom("x") in four ways. @@ -711,14 +715,18 @@ assigning a new values to the extract_atom() array. To do this with the gather_atoms() vector, you need to change values in the vector, then invoke the scatter_atoms() method. -The scatter_atoms() method takes a vector of ints or doubles as -specified by type, of length count*natoms, for the property of all the -atoms in the simulation specified by name, ordered by bount and then -by atom ID. It uses the vector of data to overwrite the corresponding -properties for each atom inside LAMMPS. This requires LAMMPS to have -its "map" option enabled; see the "atom_modify"_atom_modify.html -command for details. If it is not, or if atom IDs are not -consecutively ordered, no coordinates are reset. +The scatter_atoms() method allows any per-atom property (coordinates, +velocities, etc) to be inserted into LAMMPS, overwriting the current +property. It takes a vector of ints or doubles as specified by type, +of length count*natoms, for the named property for all atoms in the +simulation. The data should be ordered by count and then by atom ID. +See the extract() method in the src/atom.cpp file for a list of valid +names. Again, new names could easily be added if the property you +want is missing. It uses the vector of data to overwrite the +corresponding properties for each atom inside LAMMPS. This requires +LAMMPS to have its "map" option enabled; see the +"atom_modify"_atom_modify.html command for details. If it is not, or +if atom IDs are not consecutively ordered, no coordinates are reset. The array of coordinates passed to scatter_atoms() must be a ctypes vector of ints or doubles, allocated and initialized something like @@ -734,7 +742,7 @@ x\[2\] = z coord of atom with ID 1 x\[3\] = x coord of atom with ID 2 ... x\[n3-1\] = z coord of atom with ID natoms -lmp.scatter_coords("x",1,3,x) :pre +lmp.scatter_atoms("x",1,3,x) :pre Alternatively, you can just change values in the vector returned by gather_atoms("x",1,3), since it is a ctypes vector of doubles. diff --git a/doc/src/Section_tools.txt b/doc/src/Section_tools.txt index 83fb7a6bce..03611c7cdb 100644 --- a/doc/src/Section_tools.txt +++ b/doc/src/Section_tools.txt @@ -12,9 +12,12 @@ Section"_Section_modify.html :c LAMMPS is designed to be a computational kernel for performing molecular dynamics computations. Additional pre- and post-processing -steps are often necessary to setup and analyze a simulation. A few -additional tools are provided with the LAMMPS distribution and are -described in this section. +steps are often necessary to setup and analyze a simulation. A +list of such tools can be found on the LAMMPS home page +at "http://lammps.sandia.gov/prepost.html"_http://lammps.sandia.gov/prepost.html + +A few additional tools are provided with the LAMMPS distribution +and are described in this section. Our group has also written and released a separate toolkit called "Pizza.py"_pizza which provides tools for doing setup, analysis, @@ -36,16 +39,16 @@ authors. The source code for each of these codes is in the tools sub-directory of the LAMMPS distribution. There is a Makefile (which you may need to edit for your platform) which will build several of the tools which -reside in that directory. Some of them are larger packages in their -own sub-directories with their own Makefiles. +reside in that directory. Most of them are larger packages in their +own sub-directories with their own Makefiles and/or README files. "amber2lmp"_#amber "binary2txt"_#binary "ch2lmp"_#charmm "chain"_#chain "colvars"_#colvars -"createatoms"_#create -"data2xmovie"_#data +"createatoms"_#createatoms +"drude"_#drude "eam database"_#eamdb "eam generate"_#eamgn "eff"_#eff @@ -56,20 +59,18 @@ own sub-directories with their own Makefiles. "kate"_#kate "lmp2arc"_#arc "lmp2cfg"_#cfg -"lmp2vmd"_#vmd "matlab"_#matlab "micelle2d"_#micelle "moltemplate"_#moltemplate "msi2lmp"_#msi "phonon"_#phonon -"polymer bonding"_#polybond +"polybond"_#polybond "pymol_asphere"_#pymol "python"_#pythontools "reax"_#reax_tool -"restart2data"_#restart +"smd"_#smd "vim"_#vim "xmgrace"_#xmgrace -"xmovie"_#xmovie :ul :line @@ -158,7 +159,7 @@ gmail.com) at ICTP, Italy. :line -createatoms tool :h4,link(create) +createatoms tool :h4,link(createatoms) The tools/createatoms directory contains a Fortran program called createAtoms.f which can generate a variety of interesting crystal @@ -171,16 +172,16 @@ The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov. :line -data2xmovie tool :h4,link(data) +drude tool :h4,link(drude) -The file data2xmovie.c converts a LAMMPS data file into a snapshot -suitable for visualizing with the "xmovie"_#xmovie tool, as if it had -been output with a dump command from LAMMPS itself. The syntax for -running the tool is +The tools/drude directory contains a Python script called +polarizer.py which can add Drude oscillators to a LAMMPS +data file in the required format. -data2xmovie \[options\] < infile > outfile :pre +See the header of the polarizer.py file for details. -See the top of the data2xmovie.c file for a discussion of the options. +The tool is authored by Agilio Padua and Alain Dequidt: agilio.padua +at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr :line @@ -317,18 +318,6 @@ This tool was written by Ara Kooser at Sandia (askoose at sandia.gov). :line -lmp2vmd tool :h4,link(vmd) - -The lmp2vmd sub-directory contains a README.txt file that describes -details of scripts and plugin support within the "VMD -package"_http://www.ks.uiuc.edu/Research/vmd for visualizing LAMMPS -dump files. - -The VMD plugins and other supporting scripts were written by Axel -Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn. - -:line - matlab tool :h4,link(matlab) The matlab sub-directory contains several "MATLAB"_matlabhome scripts for @@ -381,16 +370,14 @@ supports it. It has its own WWW page at msi2lmp tool :h4,link(msi) The msi2lmp sub-directory contains a tool for creating LAMMPS input -data files from Accelrys' Insight MD code (formerly MSI/Biosym and -its Discover MD code). See the README file for more information. +data files from BIOVIA's Materias Studio files (formerly Accelrys' +Insight MD code, formerly MSI/Biosym and its Discover MD code). This tool was written by John Carpenter (Cray), Michael Peachey -(Cray), and Steve Lustig (Dupont). John is now at the Mayo Clinic -(jec at mayo.edu), but still fields questions about the tool. +(Cray), and Steve Lustig (Dupont). Several people contributed changes +to remove bugs and adapt its output to changes in LAMMPS. -This tool may be out-of-date with respect to the current LAMMPS and -Insight versions. Since we don't use it at Sandia, you'll need to -experiment with it yourself. +See the README file for more information. :line @@ -409,7 +396,7 @@ University. :line -polymer bonding tool :h4,link(polybond) +polybond tool :h4,link(polybond) The polybond sub-directory contains a Python-based tool useful for performing "programmable polymer bonding". The Python file @@ -468,48 +455,19 @@ These tools were written by Aidan Thompson at Sandia. :line -restart2data tool :h4,link(restart) +smd tool :h4,link(smd) -NOTE: This tool is now obsolete and is not included in the current -LAMMPS distribution. This is because there is now a -"write_data"_write_data.html command, which can create a data file -from within an input script. Running LAMMPS with the "-r" -"command-line switch"_Section_start.html#start_7 as follows: +The smd sub-directory contains a C++ file dump2vtk_tris.cpp and +Makefile which can be compiled and used to convert triangle output +files created by the Smooth-Mach Dynamics (USER-SMD) package into a +VTK-compatible unstructured grid file. It could then be read in and +visualized by VTK. -lmp_g++ -r restartfile datafile +See the header of dump2vtk.cpp for more details. -is the same as running a 2-line input script: - -read_restart restartfile -write_data datafile - -which will produce the same data file that the restart2data tool used -to create. The following information is included in case you have an -older version of LAMMPS which still includes the restart2data tool. - -The file restart2data.cpp converts a binary LAMMPS restart file into -an ASCII data file. The syntax for running the tool is - -restart2data restart-file data-file (input-file) :pre - -Input-file is optional and if specified will contain LAMMPS input -commands for the masses and force field parameters, instead of putting -those in the data-file. Only a few force field styles currently -support this option. - -This tool must be compiled on a platform that can read the binary file -created by a LAMMPS run, since binary files are not compatible across -all platforms. - -Note that a text data file has less precision than a binary restart -file. Hence, continuing a run from a converted data file will -typically not conform as closely to a previous run as will restarting -from a binary restart file. - -If a "%" appears in the specified restart-file, the tool expects a set -of multiple files to exist. See the "restart"_restart.html and -"write_restart"_write_restart.html commands for info on how such sets -of files are written by LAMMPS, and how the files are named. +This tool was written by the USER-SMD package author, Georg +Ganzenmuller at the Fraunhofer-Institute for High-Speed Dynamics, +Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de). :line @@ -537,32 +495,3 @@ See the README file for details. These files were provided by Vikas Varshney (vv0210 at gmail.com) -:line - -xmovie tool :h4,link(xmovie) - -The xmovie tool is an X-based visualization package that can read -LAMMPS dump files and animate them. It is in its own sub-directory -with the tools directory. You may need to modify its Makefile so that -it can find the appropriate X libraries to link against. - -The syntax for running xmovie is - -xmovie \[options\] dump.file1 dump.file2 ... :pre - -If you just type "xmovie" you will see a list of options. Note that -by default, LAMMPS dump files are in scaled coordinates, so you -typically need to use the -scale option with xmovie. When xmovie runs -it opens a visualization window and a control window. The control -options are straightforward to use. - -Xmovie was mostly written by Mike Uttormark (U Wisconsin) while he -spent a summer at Sandia. It displays 2d projections of a 3d domain. -While simple in design, it is an amazingly fast program that can -render large numbers of atoms very quickly. It's a useful tool for -debugging LAMMPS input and output and making sure your simulation is -doing what you think it should. The animations on the Examples page -of the "LAMMPS WWW site"_lws were created with xmovie. - -I've lost contact with Mike, so I hope he's comfortable with us -distributing his great tool! diff --git a/doc/src/accelerate_intel.txt b/doc/src/accelerate_intel.txt index f7f655a639..581c440bc3 100644 --- a/doc/src/accelerate_intel.txt +++ b/doc/src/accelerate_intel.txt @@ -464,7 +464,7 @@ supported. [References:] -Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakker, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., “Optimizing Classical Molecular Dynamics in LAMMPS,” in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. :ulb,l +Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakker, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. :ulb,l Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. 2016 International Conference for High Performance Computing. In press. :l diff --git a/doc/src/angle_dipole.txt b/doc/src/angle_dipole.txt index 9d105c269d..d91f260d51 100644 --- a/doc/src/angle_dipole.txt +++ b/doc/src/angle_dipole.txt @@ -41,7 +41,7 @@ angle. The torque on the dipole can be obtained by differentiating the potential using the 'chain rule' as in appendix C.3 of -"(Allen)"_#Allen: +"(Allen)"_#Allen1: :c,image(Eqs/angle_dipole_torque.jpg) @@ -121,6 +121,6 @@ This angle style should not be used with SHAKE. [(Orsi)] Orsi & Essex, The ELBA force field for coarse-grain modeling of lipid membranes, PloS ONE 6(12): e28637, 2011. -:link(Allen) +:link(Allen1) [(Allen)] Allen & Tildesley, Computer Simulation of Liquids, Clarendon Press, Oxford, 1987. diff --git a/doc/src/atom_style.txt b/doc/src/atom_style.txt index 3d5c0a4f3d..077636dfd1 100644 --- a/doc/src/atom_style.txt +++ b/doc/src/atom_style.txt @@ -110,7 +110,12 @@ 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. +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 diff --git a/doc/src/compute_chunk_atom.txt b/doc/src/compute_chunk_atom.txt index b3b09ffa71..3a46f79d16 100644 --- a/doc/src/compute_chunk_atom.txt +++ b/doc/src/compute_chunk_atom.txt @@ -148,7 +148,9 @@ described further below where the keywords are discussed. The {binning} styles perform a spatial binning of atoms, and assign an atom the chunk ID corresponding to the bin number it is in. {Nchunk} is set to the number of bins, which can change if the simulation box -size changes. +size changes. This also depends on the setting of the {units} +keyword; e.g. for {reduced} units the number of chunks may not change +even if the box size does. The {bin/1d}, {bin/2d}, and {bin/3d} styles define bins as 1d layers (slabs), 2d pencils, or 3d boxes. The {dim}, {origin}, and {delta} diff --git a/doc/src/compute_coord_atom.txt b/doc/src/compute_coord_atom.txt index 854a5778ec..a88f7ec729 100644 --- a/doc/src/compute_coord_atom.txt +++ b/doc/src/compute_coord_atom.txt @@ -64,7 +64,7 @@ defined by the orientational order parameter calculated by the "compute orientorder/atom"_compute_orientorder_atom.html command. This {cstyle} thus allows one to apply the ten Wolde's criterion to identify crystal-like atoms in a system, as discussed in "ten -Wolde"_#tenWolde. +Wolde"_#tenWolde1. The ID of the previously specified "compute orientorder/atom"_compute_orientorder/atom command is specified as @@ -127,6 +127,6 @@ explained above. :line -:link(tenWolde) +:link(tenWolde1) [(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996). diff --git a/doc/src/compute_dpd.txt b/doc/src/compute_dpd.txt index 11602d3dd8..0e43feb9d2 100644 --- a/doc/src/compute_dpd.txt +++ b/doc/src/compute_dpd.txt @@ -64,7 +64,7 @@ command. :line -:link(Larentzos) +:link(Larentzos1) [(Larentzos)] J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research diff --git a/doc/src/compute_dpd_atom.txt b/doc/src/compute_dpd_atom.txt index 356b2490c7..0532fc60c6 100644 --- a/doc/src/compute_dpd_atom.txt +++ b/doc/src/compute_dpd_atom.txt @@ -59,7 +59,7 @@ command. :line -:link(Larentzos) +:link(Larentzos2) [(Larentzos)] J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research diff --git a/doc/src/compute_modify.txt b/doc/src/compute_modify.txt index acf14526a7..c26b5c2a5f 100644 --- a/doc/src/compute_modify.txt +++ b/doc/src/compute_modify.txt @@ -14,27 +14,29 @@ compute_modify compute-ID keyword value ... :pre compute-ID = ID of the compute to modify :ulb,l one or more keyword/value pairs may be listed :l -keyword = {extra} or {dynamic} :l - {extra} value = N +keyword = {extra/dof} or {extra} or {dynamic/dof} or {dynamic} :l + {extra/dof} value = N N = # of extra degrees of freedom to subtract - {dynamic} value = {yes} or {no} - yes/no = do or do not recompute the number of atoms contributing to the temperature :pre + {extra} syntax is identical to {extra/dof}, will be disabled at some point + {dynamic/dof} value = {yes} or {no} + yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature + {dynamic} syntax is identical to {dynamic/dof}, will be disabled at some point :pre :ule [Examples:] -compute_modify myTemp extra 0 -compute_modify newtemp dynamic yes extra 600 :pre +compute_modify myTemp extra/dof 0 +compute_modify newtemp dynamic/dof yes extra/dof 600 :pre [Description:] Modify one or more parameters of a previously defined compute. Not all compute styles support all parameters. -The {extra} keyword refers to how many degrees-of-freedom are -subtracted (typically from 3N) as a normalizing factor in a -temperature computation. Only computes that compute a temperature use -this option. The default is 2 or 3 for "2d or 3d +The {extra/dof} or {extra} keyword refers to how many +degrees-of-freedom are subtracted (typically from 3N) as a normalizing +factor in a temperature computation. Only computes that compute a +temperature use this option. The default is 2 or 3 for "2d or 3d systems"_dimension.html which is a correction factor for an ensemble of velocities with zero total linear momentum. For compute temp/partial, if one or more velocity components are excluded, the @@ -43,14 +45,21 @@ number for the {extra} parameter if you need to add degrees-of-freedom. See the "compute temp/asphere"_compute_temp_asphere.html command for an example. -The {dynamic} keyword determines whether the number of atoms N in the -compute group is re-computed each time a temperature is computed. -Only compute styles that calculate a temperature use this option. By -default, N is assumed to be constant. If you are adding atoms to the -system (see the "fix pour"_fix_pour.html or "fix -deposit"_fix_deposit.html commands) or expect atoms to be lost -(e.g. due to evaporation), then this option should be used to insure -the temperature is correctly normalized. +The {dynamic/dof} or {dynamic} keyword determines whether the number +of atoms N in the compute group and their associated degrees of +freedom are re-computed each time a temperature is computed. Only +compute styles that calculate a temperature use this option. By +default, N and their DOF are assumed to be constant. If you are +adding atoms or molecules to the system (see the "fix +pour"_fix_pour.html, "fix deposit"_fix_deposit.html, and "fix +gcmc"_fix_gcmc.html commands) or expect atoms or molecules to be lost +(e.g. due to exiting the simulation box or via "fix +evaporation"_fix_evaporation.html), then this option should be used to +insure the temperature is correctly normalized. + +NOTE: The {extra} and {dynamic} keywords should not be used as they +are deprecated (March 2017) and will eventually be disabled. Instead, +use the equivalent {extra/dof} and {dynamic/dof} keywords. [Restrictions:] none @@ -60,5 +69,5 @@ the temperature is correctly normalized. [Default:] -The option defaults are extra = 2 or 3 for 2d or 3d systems and -dynamic = no. +The option defaults are extra/dof = 2 or 3 for 2d or 3d systems and +dynamic/dof = no. diff --git a/doc/src/compute_orientorder_atom.txt b/doc/src/compute_orientorder_atom.txt index 2aa76ab5ac..70c7ef68f7 100644 --- a/doc/src/compute_orientorder_atom.txt +++ b/doc/src/compute_orientorder_atom.txt @@ -78,7 +78,7 @@ normalized complex vector {Ybar_lm} of degree {ldegree}, which must be explicitly included in the keyword {degrees}. This option can be used in conjunction with "compute coord_atom"_compute_coord_atom.html to calculate the ten Wolde's criterion to identify crystal-like -particles, as discussed in "ten Wolde"_#tenWolde. +particles, as discussed in "ten Wolde"_#tenWolde2. The value of {Ql} is set to zero for atoms not in the specified compute group, as well as for atoms that have less than @@ -143,6 +143,6 @@ Phys. Rev. B 28, 784 (1983). [(Mickel)] W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke, J. Chem. Phys. 138, 044501 (2013). -:link(tenWolde) +:link(tenWolde2) [(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996). diff --git a/doc/src/compute_pe_atom.txt b/doc/src/compute_pe_atom.txt index 6de3a79e5b..c312c886a6 100644 --- a/doc/src/compute_pe_atom.txt +++ b/doc/src/compute_pe_atom.txt @@ -49,7 +49,7 @@ pairwise interactions between 1-4 atoms. The energy contribution of these terms is included in the pair energy, not the dihedral energy. The KSpace contribution is calculated using the method in -"(Heyes)"_#Heyes for the Ewald method and a related method for PPPM, +"(Heyes)"_#Heyes1 for the Ewald method and a related method for PPPM, as specified by the "kspace_style pppm"_kspace_style.html command. For PPPM, the calculation requires 1 extra FFT each timestep that per-atom energy is calculated. This "document"_PDF/kspace.pdf @@ -97,5 +97,5 @@ stress/atom"_compute_stress_atom.html :line -:link(Heyes) +:link(Heyes1) [(Heyes)] Heyes, Phys Rev B 49, 755 (1994), diff --git a/doc/src/compute_pressure.txt b/doc/src/compute_pressure.txt index ae62859b17..292e779f72 100644 --- a/doc/src/compute_pressure.txt +++ b/doc/src/compute_pressure.txt @@ -70,7 +70,7 @@ means include all terms except the kinetic energy {ke}. Details of how LAMMPS computes the virial efficiently for the entire system, including for manybody potentials and accounting for the effects of periodic boundary conditions are discussed in -"(Thompson)"_#Thompson. +"(Thompson)"_#Thompson1. The temperature and kinetic energy tensor is not calculated by this compute, but rather by the temperature compute specified with the @@ -150,5 +150,5 @@ stress/atom"_compute_stress_atom.html, :line -:link(Thompson) +:link(Thompson1) [(Thompson)] Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009). diff --git a/doc/src/compute_sna_atom.txt b/doc/src/compute_sna_atom.txt index 82c2ba93aa..e2df706473 100644 --- a/doc/src/compute_sna_atom.txt +++ b/doc/src/compute_sna_atom.txt @@ -24,7 +24,7 @@ twojmax = band limit for bispectrum components (non-negative integer) :l R_1, R_2,... = list of cutoff radii, one for each type (distance units) :l w_1, w_2,... = list of neighbor weights, one for each type :l zero or more keyword/value pairs may be appended :l -keyword = {diagonal} or {rmin0} or {switchflag} :l +keyword = {diagonal} or {rmin0} or {switchflag} or {bzeroflag} :l {diagonal} value = {0} or {1} or {2} or {3} {0} = all j1, j2, j <= twojmax, j2 <= j1 {1} = subset satisfying j1 == j2 @@ -33,7 +33,10 @@ keyword = {diagonal} or {rmin0} or {switchflag} :l {rmin0} value = parameter in distance to angle conversion (distance units) {switchflag} value = {0} or {1} {0} = do not use switching function - {1} = use switching function :pre + {1} = use switching function + {bzeroflag} value = {0} or {1} + {0} = do not subtract B0 + {1} = subtract B0 :pre :ule [Examples:] @@ -50,12 +53,12 @@ for each atom in a group. Bispectrum components of an atom are order parameters characterizing the radial and angular distribution of neighbor atoms. The detailed mathematical definition is given in the paper by Thompson et -al. "(Thompson)"_#Thompson2014 +al. "(Thompson)"_#Thompson20141 The position of a neighbor atom {i'} relative to a central atom {i} is a point within the 3D ball of radius {R_ii' = rcutfac*(R_i + R_i')} -Bartok et al. "(Bartok)"_#Bartok2010, proposed mapping this 3D ball +Bartok et al. "(Bartok)"_#Bartok20101, proposed mapping this 3D ball onto the 3-sphere, the surface of the unit ball in a four-dimensional space. The radial distance {r} within {R_ii'} is mapped on to a third polar angle {theta0} defined by, @@ -92,7 +95,7 @@ The expansion coefficients {u^j_m,m'} are complex-valued and they are not directly useful as descriptors, because they are not invariant under rotation of the polar coordinate frame. However, the following scalar triple products of expansion coefficients can be shown to be -real-valued and invariant under rotation "(Bartok)"_#Bartok2010. +real-valued and invariant under rotation "(Bartok)"_#Bartok20101. :c,image(Eqs/compute_sna_atom3.jpg) @@ -153,6 +156,12 @@ ordered in which they are listed The keyword {switchflag} can be used to turn off the switching function. +The keyword {bzeroflag} determines whether or not {B0}, the bispectrum +components of an atom with no neighbors, are subtracted from +the calculated bispectrum components. This optional keyword is only +available for compute {sna/atom}, as {snad/atom} and {snav/atom} +are unaffected by the removal of constant terms. + NOTE: If you have a bonded system, then the settings of "special_bonds"_special_bonds.html command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This @@ -222,15 +231,15 @@ LAMMPS"_Section_start.html#start_3 section for more info. [Default:] The optional keyword defaults are {diagonal} = 0, {rmin0} = 0, -{switchflag} = 1. +{switchflag} = 1, {bzeroflag} = 0. :line -:link(Thompson2014) +:link(Thompson20141) [(Thompson)] Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint available at "arXiv:1409.3880"_http://arxiv.org/abs/1409.3880 -:link(Bartok2010) +:link(Bartok20101) [(Bartok)] Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010). :link(Meremianin2006) diff --git a/doc/src/compute_stress_atom.txt b/doc/src/compute_stress_atom.txt index d09c8069cc..83b1df68e3 100644 --- a/doc/src/compute_stress_atom.txt +++ b/doc/src/compute_stress_atom.txt @@ -74,7 +74,7 @@ other atoms in the simulation, not just with other atoms in the group. Details of how LAMMPS computes the virial for individual atoms for either pairwise or manybody potentials, and including the effects of -periodic boundary conditions is discussed in "(Thompson)"_#Thompson. +periodic boundary conditions is discussed in "(Thompson)"_#Thompson2. The basic idea for manybody potentials is to treat each component of the force computation between a small cluster of atoms in the same manner as in the formula above for bond, angle, dihedral, etc @@ -89,8 +89,8 @@ pairwise interactions between 1-4 atoms. The virial contribution of these terms is included in the pair virial, not the dihedral virial. The KSpace contribution is calculated using the method in -"(Heyes)"_#Heyes for the Ewald method and by the methodology described -in "(Sirk)"_#Sirk for PPPM. The choice of KSpace solver is specified +"(Heyes)"_#Heyes2 for the Ewald method and by the methodology described +in "(Sirk)"_#Sirk1 for PPPM. The choice of KSpace solver is specified by the "kspace_style pppm"_kspace_style.html command. Note that for PPPM, the calculation requires 6 extra FFTs each timestep that per-atom stress is calculated. Thus it can significantly increase the @@ -159,11 +159,11 @@ The per-atom array values will be in pressure*volume :line -:link(Heyes) +:link(Heyes2) [(Heyes)] Heyes, Phys Rev B 49, 755 (1994), -:link(Sirk) +:link(Sirk1) [(Sirk)] Sirk, Moore, Brown, J Chem Phys, 138, 064505 (2013). -:link(Thompson) +:link(Thompson2) [(Thompson)] Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009). diff --git a/doc/src/compute_temp_cs.txt b/doc/src/compute_temp_cs.txt index 0c22267daa..561b787df6 100644 --- a/doc/src/compute_temp_cs.txt +++ b/doc/src/compute_temp_cs.txt @@ -27,7 +27,7 @@ compute core_shells all temp/cs cores shells :pre Define a computation that calculates the temperature of a system based on the center-of-mass velocity of atom pairs that are bonded to each other. This compute is designed to be used with the adiabatic -core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham. See +core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham1. See "Section 6.25"_Section_howto.html#howto_25 of the manual for an overview of the model as implemented in LAMMPS. Specifically, this compute enables correct temperature calculation and thermostatting of @@ -114,6 +114,6 @@ temp/chunk"_compute_temp_chunk.html :line -:link(MitchellFinchham) +:link(MitchellFinchham1) [(Mitchell and Finchham)] Mitchell, Finchham, J Phys Condensed Matter, 5, 1031-1038 (1993). diff --git a/doc/src/compute_temp_profile.txt b/doc/src/compute_temp_profile.txt index 3b6f774d33..64a6abd283 100644 --- a/doc/src/compute_temp_profile.txt +++ b/doc/src/compute_temp_profile.txt @@ -43,7 +43,7 @@ atoms, after subtracting out a spatially-averaged center-of-mass velocity field, before computing the kinetic energy. This can be useful for thermostatting a collection of atoms undergoing a complex flow, e.g. via a profile-unbiased thermostat (PUT) as described in -"(Evans)"_#Evans. A compute of this style can be used by any command +"(Evans)"_#Evans1. A compute of this style can be used by any command that computes a temperature, e.g. "thermo_modify"_thermo_modify.html, "fix temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_nh.html, etc. @@ -75,7 +75,7 @@ atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the simulation, N = number of atoms in the group, k = Boltzmann constant, and T = temperature. The dim*Nx*Ny*Nz term are degrees of freedom subtracted to adjust for the removal of the center-of-mass velocity in -each of Nx*Ny*Nz bins, as discussed in the "(Evans)"_#Evans paper. +each of Nx*Ny*Nz bins, as discussed in the "(Evans)"_#Evans1 paper. If the {out} keyword is used with a {tensor} value, which is the default, a kinetic energy tensor, stored as a 6-element vector, is @@ -126,7 +126,7 @@ See "this howto section"_Section_howto.html#howto_16 of the manual for a discussion of different ways to compute temperature and perform thermostatting. Using this compute in conjunction with a thermostatting fix, as explained there, will effectively implement a -profile-unbiased thermostat (PUT), as described in "(Evans)"_#Evans. +profile-unbiased thermostat (PUT), as described in "(Evans)"_#Evans1. [Output info:] @@ -178,5 +178,5 @@ The option default is out = tensor. :line -:link(Evans) +:link(Evans1) [(Evans)] Evans and Morriss, Phys Rev Lett, 56, 2172-2175 (1986). diff --git a/doc/src/dihedral_charmm.txt b/doc/src/dihedral_charmm.txt index 87322cb0af..802cf2c4ad 100644 --- a/doc/src/dihedral_charmm.txt +++ b/doc/src/dihedral_charmm.txt @@ -10,21 +10,25 @@ dihedral_style charmm command :h3 dihedral_style charmm/intel command :h3 dihedral_style charmm/kk command :h3 dihedral_style charmm/omp command :h3 +dihedral_style charmmfsh command :h3 [Syntax:] -dihedral_style charmm :pre +dihedral_style style :pre + +style = {charmm} or {charmmfsh} :ul [Examples:] dihedral_style charmm +dihedral_style charmmfsh dihedral_coeff 1 0.2 1 180 1.0 dihedral_coeff 2 1.8 1 0 1.0 dihedral_coeff 1 3.1 2 180 0.5 :pre [Description:] -The {charmm} dihedral style uses the potential +The {charmm} and {charmmfsh} dihedral styles use the potential :c,image(Eqs/dihedral_charmm.jpg) @@ -34,6 +38,11 @@ field (see comment on weighting factors below). See "(Cornell)"_#dihedral-Cornell for a description of the AMBER force field. +NOTE: The newer {charmmfsh} style was released in March 2017. We +recommend it be used instead of the older {charmm} style when running +a simulation with the CHARMM force field. See the discussion below +and more details on the "pair_style charmm"_pair_charmm.html doc page. + The following coefficients must be defined for each dihedral type via the "dihedral_coeff"_dihedral_coeff.html command as in the example above, or in the data file or restart files read by the "read_data"_read_data.html @@ -73,13 +82,23 @@ special_bonds 1-4 scaling factor to 0.0 (which is the default). Otherwise 1-4 non-bonded interactions in dihedrals will be computed twice. -Also note that for AMBER force fields, which use pair styles with -"lj/cut", the special_bonds 1-4 scaling factor should be set to the -AMBER defaults (1/2 and 5/6) and all the dihedral weighting factors -(4th coeff above) must be set to 0.0. In this case, you can use any -pair style you wish, since the dihedral does not need any -Lennard-Jones parameter information and will not compute any 1-4 -non-bonded interactions. +For simulations using the CHARMM force field, the difference between +the {charmm} and {charmmfsh} styles is in the computation of the 1-4 +non-bond interactions, if the distance between the two atoms is within +the switching distance of the pairwise potential defined by the +corresponding CHARMM pair style, i.e. between the inner and outer +cutoffs specified for the pair style. See the discussion on the +"CHARMM pair_style"_pair_charmm.html doc page for details. + +Note that for AMBER force fields, which use pair styles with "lj/cut", +the special_bonds 1-4 scaling factor should be set to the AMBER +defaults (1/2 and 5/6) and all the dihedral weighting factors (4th +coeff above) must be set to 0.0. In this case, you can use any pair +style you wish, since the dihedral does not need any Lennard-Jones +parameter information and will not compute any 1-4 non-bonded +interactions. Likewise the {charmm} or {charmmfsh} styles are +identical in this case since no 1-4 non-bonded interactions are +computed. :line diff --git a/doc/src/dump_molfile.txt b/doc/src/dump_molfile.txt index 3494ba9a91..7e68490a68 100644 --- a/doc/src/dump_molfile.txt +++ b/doc/src/dump_molfile.txt @@ -34,10 +34,7 @@ to one or more files every N timesteps in one of several formats. Only information for atoms in the specified group is dumped. This specific dump style uses molfile plugins that are bundled with the "VMD"_http://www.ks.uiuc.edu/Research/vmd molecular visualization and -analysis program. See "Section 9"_Section_tools.html#vmd of the -manual and the tools/lmp2vmd/README.txt file for more information -about support in VMD for reading and visualizing native LAMMPS dump -files. +analysis program. Unless the filename contains a * character, the output will be written to one single file with the specified format. Otherwise there will be diff --git a/doc/src/fix_ave_chunk.txt b/doc/src/fix_ave_chunk.txt index 8943192176..a8691d3767 100644 --- a/doc/src/fix_ave_chunk.txt +++ b/doc/src/fix_ave_chunk.txt @@ -191,8 +191,15 @@ remain constant for the duration of the simulation. This fix forces the chunk/atom compute specified by chunkID to hold {Nchunk} constant for the appropriate time windows, by not allowing it to re-calculate {Nchunk}, which can also affect how it assigns chunk IDs to atoms. -More details are given on the "compute -chunk/atom"_compute_chunk_atom.html doc page. +This is particularly important to understand if the chunks defined by +the "compute chunk/atom"_compute_chunk_atom.html command are spatial +bins. If its {units} keyword is set to {box} or {lattice}, then the +number of bins {Nchunk} and size of each bin will be fixed over the +{Nfreq} time window, which can affect which atoms are discarded if the +simulation box size changes. If its {units} keyword is set to +{reduced}, then the number of bins {Nchunk} will still be fixed, but +the size of each bin can vary at each timestep if the simulation box +size changes, e.g. for an NPT simulation. :line @@ -290,24 +297,32 @@ It the {norm} setting is {all}, which is the default, a chunk value is summed over all atoms in all {Nrepeat} samples, as is the count of atoms in the chunk. The averaged output value for the chunk on the {Nfreq} timesteps is Total-sum / Total-count. In other words it is an -average over atoms across the entire {Nfreq} timescale. +average over atoms across the entire {Nfreq} timescale. For the +{density/number} and {density/mass} values, the volume (bin volume or +system volume) used in the final normalization will be the volume at +the final {Nfreq} timestep. -If the {norm} setting is {sample}, the chunk value is summed over atoms -for each sample, as is the count, and an "average sample value" is -computed for each sample, i.e. Sample-sum / Sample-count. The output -value for the chunk on the {Nfreq} timesteps is the average of the -{Nrepeat} "average sample values", i.e. the sum of {Nrepeat} "average -sample values" divided by {Nrepeat}. In other words it is an average -of an average. +If the {norm} setting is {sample}, the chunk value is summed over +atoms for each sample, as is the count, and an "average sample value" +is computed for each sample, i.e. Sample-sum / Sample-count. The +output value for the chunk on the {Nfreq} timesteps is the average of +the {Nrepeat} "average sample values", i.e. the sum of {Nrepeat} +"average sample values" divided by {Nrepeat}. In other words it is an +average of an average. For the {density/number} and {density/mass} +values, the volume (bin volume or system volume) used in the +per-sample normalization will be the current volume at each sampling +step. If the {norm} setting is {none}, a similar computation as for the -{sample} setting is done, except the individual "average sample values" -are "summed sample values". A summed sample value is simply the chunk -value summed over atoms in the sample, without dividing by the number -of atoms in the sample. The output value for the chunk on the -{Nfreq} timesteps is the average of the {Nrepeat} "summed sample +{sample} setting is done, except the individual "average sample +values" are "summed sample values". A summed sample value is simply +the chunk value summed over atoms in the sample, without dividing by +the number of atoms in the sample. The output value for the chunk on +the {Nfreq} timesteps is the average of the {Nrepeat} "summed sample values", i.e. the sum of {Nrepeat} "summed sample values" divided by -{Nrepeat}. +{Nrepeat}. For the {density/number} and {density/mass} values, the +volume (bin volume or system volume) used in the per-sample sum +normalization will be the current volume at each sampling step. The {ave} keyword determines how the per-chunk values produced every {Nfreq} steps are averaged with values produced on previous steps that diff --git a/doc/src/fix_deposit.txt b/doc/src/fix_deposit.txt index a1dd5f6434..477c14ea89 100644 --- a/doc/src/fix_deposit.txt +++ b/doc/src/fix_deposit.txt @@ -150,6 +150,12 @@ treated as rigid bodies, use the {rigid} keyword, specifying as its value the ID of a separate "fix rigid/small"_fix_rigid.html command which also appears in your input script. +NOTE: If you wish the new rigid molecules (and other rigid molecules) +to be thermostatted correctly via "fix rigid/small/nvt"_fix_rigid.html +or "fix rigid/small/npt"_fix_rigid.html, then you need to use the +"fix_modify dynamic/dof yes" command for the rigid fix. This is to +inform that fix that the molecule count will vary dynamically. + If you wish to insert molecules via the {mol} keyword, that will have their bonds or angles constrained via SHAKE, use the {shake} keyword, specifying as its value the ID of a separate "fix diff --git a/doc/src/fix_dpd_energy.txt b/doc/src/fix_dpd_energy.txt index db1fb0c703..ed49e5a671 100644 --- a/doc/src/fix_dpd_energy.txt +++ b/doc/src/fix_dpd_energy.txt @@ -70,13 +70,13 @@ mesoparticle equation of state for each particle. :line -:link(Lisal) +:link(Lisal1) [(Lisal)] M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative particle dynamics at isothermal, isobaric, isoenergetic, and isoenthalpic conditions using Shardlow-like splitting algorithms.", J. Chem. Phys., 135, 204105 (2011). -:link(Larentzos) +:link(Larentzos3) [(Larentzos)] J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research diff --git a/doc/src/fix_drude_transform.txt b/doc/src/fix_drude_transform.txt index 6f82c81053..2e094d528c 100644 --- a/doc/src/fix_drude_transform.txt +++ b/doc/src/fix_drude_transform.txt @@ -32,7 +32,7 @@ fix 1 all drude/transform/inverse :pre Transform the coordinates of Drude oscillators from real to reduced and back for thermalizing the Drude oscillators as described in -"(Lamoureux)"_#Lamoureux using a Nose-Hoover thermostat. This fix is +"(Lamoureux)"_#Lamoureux1 using a Nose-Hoover thermostat. This fix is designed to be used with the "thermalized Drude oscillator model"_tutorial_drude.html. Polarizable models in LAMMPS are described in "this Section"_Section_howto.html#howto_25. @@ -160,5 +160,5 @@ files"_restart.html. :line -:link(Lamoureux) +:link(Lamoureux1) [(Lamoureux)] Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003). diff --git a/doc/src/fix_eos_cv.txt b/doc/src/fix_eos_cv.txt index 76b9f79227..4c97304335 100644 --- a/doc/src/fix_eos_cv.txt +++ b/doc/src/fix_eos_cv.txt @@ -53,7 +53,7 @@ command. :line -:link(Larentzos) +:link(Larentzos4) [(Larentzos)] J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research diff --git a/doc/src/fix_filter_corotate.txt b/doc/src/fix_filter_corotate.txt new file mode 100644 index 0000000000..a3339648fa --- /dev/null +++ b/doc/src/fix_filter_corotate.txt @@ -0,0 +1,87 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +fix filter/corotate command :h3 + +[Syntax:] + +fix ID group-ID filter/corotate keyword value ... :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +one or more constraint/value pairs are appended :l +constraint = {b} or {a} or {t} or {m} :l + {b} values = one or more bond types + {a} values = one or more angle types + {t} values = one or more atom types + {m} value = one or more mass values :pre +:ule + +[Examples:] + +timestep 8 +run_style respa 3 2 8 bond 1 pair 2 kspace 3 +fix cor all filter/corotate m 1.0 :pre + +fix cor all filter/corotate b 4 19 a 3 5 2 :pre + +[Description:] + +This fix implements a corotational filter for a mollified impulse +method. In biomolecular simulations, it allows the usage of larger +timesteps for long-range electrostatic interactions. For details, see +"(Fath)"_#Fath2017. + +When using "run_style respa"_run_style.html for a biomolecular +simulation with high-frequency covalent bonds, the outer time-step is +restricted to below ~ 4fs due to resonance problems. This fix filters +the outer stage of the respa and thus a larger (outer) time-step can +be used. Since in large biomolecular simulations the computation of +the long-range electrostatic contributions poses a major bottleneck, +this can significantly accelerate the simulation. + +The filter computes a cluster decomposition of the molecular structure +following the criteria indicated by the options a, b, t and m. This +process is similar to the approach in "fix shake"_fix_shake.html, +however, the clusters are not kept contrained. Instead, the position +is slightly modified only for the computation of long-range forces. A +good cluster decomposition constitutes in building clusters which +contain the fastest covalent bonds inside clusters. + +If the clusters are chosen suitably, the "run_style +respa"_run_style.html is stable for outer time-steps of at least 8fs. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +No information about these fixes is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to these fixes. No global or per-atom quantities are +stored by these fixes for access by various "output +commands"_Section_howto.html#howto_15. No parameter of these fixes +can be used with the {start/stop} keywords of the "run"_run.html +command. These fixes are not invoked during "energy +minimization"_minimize.html. + +[Restrictions:] + +This fix is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +Currently, it does not support "molecule templates"_molecule.html. + +[Related commands:] + + +[Default:] none + +:line + +:link(Fath2017) +[(Fath)] Fath, Hochbruck, Singh, J Comp Phys, 333, 180-198 (2017). diff --git a/doc/src/fix_flow_gauss.txt b/doc/src/fix_flow_gauss.txt index fcdc4e5589..efa58ea65f 100644 --- a/doc/src/fix_flow_gauss.txt +++ b/doc/src/fix_flow_gauss.txt @@ -153,7 +153,7 @@ The option default for the {energy} keyword is energy = no. :link(Strong) [(Strong)] Strong and Eaves, J. Phys. Chem. B 121, 189 (2017). -:link(Evans) +:link(Evans2) [(Evans)] Evans and Morriss, Phys. Rev. Lett. 56, 2172 (1986). :link(Zhu) diff --git a/doc/src/fix_gcmc.txt b/doc/src/fix_gcmc.txt index 6113b4d809..1a419628e9 100644 --- a/doc/src/fix_gcmc.txt +++ b/doc/src/fix_gcmc.txt @@ -23,9 +23,11 @@ T = temperature of the ideal gas reservoir (temperature units) :l mu = chemical potential of the ideal gas reservoir (energy units) :l displace = maximum Monte Carlo translation distance (length units) :l zero or more keyword/value pairs may be appended to args :l -keyword = {mol}, {region}, {maxangle}, {pressure}, {fugacity_coeff}, {full_energy}, {charge}, {group}, {grouptype}, {intra_energy}, or {tfac_insert} +keyword = {mol}, {region}, {maxangle}, {pressure}, {fugacity_coeff}, {full_energy}, {charge}, {group}, {grouptype}, {intra_energy}, {tfac_insert}, or {overlap_cutoff} {mol} value = template-ID template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command + {rigid} value = fix-ID + fix-ID = ID of "fix rigid/small"_fix_rigid.html command {shake} value = fix-ID fix-ID = ID of "fix shake"_fix_shake.html command {region} value = region-ID @@ -41,7 +43,8 @@ keyword = {mol}, {region}, {maxangle}, {pressure}, {fugacity_coeff}, {full_energ type = atom type (int) group-ID = group-ID for inserted atoms (string) {intra_energy} value = intramolecular energy (energy units) - {tfac_insert} value = scale up/down temperature of inserted atoms (unitless) :pre + {tfac_insert} value = scale up/down temperature of inserted atoms (unitless) + {overlap_cutoff} value = maximum pair distance for overlap rejection (distance units) :pre :ule [Examples:] @@ -160,6 +163,17 @@ soon generate an error when it tries to find bonded neighbors. LAMMPS will warn you if any of the atoms eligible for deletion have a non-zero molecule ID, but does not check for this at the time of deletion. +If you wish to insert molecules via the {mol} keyword, that will be +treated as rigid bodies, use the {rigid} keyword, specifying as its +value the ID of a separate "fix rigid/small"_fix_rigid.html +command which also appears in your input script. + +NOTE: If you wish the new rigid molecules (and other rigid molecules) +to be thermostatted correctly via "fix rigid/small/nvt"_fix_rigid.html +or "fix rigid/small/npt"_fix_rigid.html, then you need to use the +"fix_modify dynamic/dof yes" command for the rigid fix. This is to +inform that fix that the molecule count will vary dynamically. + If you wish to insert molecules via the {mol} keyword, that will have their bonds or angles constrained via SHAKE, use the {shake} keyword, specifying as its value the ID of a separate "fix @@ -262,6 +276,17 @@ therefore, you will want to use the current number of atoms is used as a normalizing factor each time temperature is computed. Here is the necessary command: +With some pair_styles, such as "Buckingham"_pair_buck.html, +"Born-Mayer-Huggins"_pair_born.html and "ReaxFF"_pair_reax_c.html, +two atoms placed close to each other may have an arbitrary large, +negative potential energy due to the functional form of the potential. +While these unphysical configurations are inaccessible +to typical dynamical trajectories, +they can be generated by Monte Carlo moves. The {overlap_cutoff} +keyword suppresses these moves by effectively assigning an +infinite positive energy to all new configurations that place any +pair of atoms closer than the specified overlap cutoff distance. + compute_modify thermo_temp dynamic yes :pre If LJ units are used, note that a value of 0.18292026 is used by this @@ -331,10 +356,6 @@ may no longer exist since it might have been deleted by the first fix gcmc command. An existing template molecule will need to be referenced by the user for each subsequent fix gcmc command. -Because molecule insertion does not work in combination with -fix rigid, simulataneous use of fix rigid or fix rigid/small -with this fix is not allowed. - [Related commands:] "fix atom/swap"_fix_atom_swap.html, @@ -344,7 +365,8 @@ with this fix is not allowed. [Default:] -The option defaults are mol = no, maxangle = 10, full_energy = no, +The option defaults are mol = no, maxangle = 10, overlap_cutoff = 0.0, +and full_energy = no, except for the situations where full_energy is required, as listed above. diff --git a/doc/src/fix_halt.txt b/doc/src/fix_halt.txt index 3f7650466f..ced489a54c 100644 --- a/doc/src/fix_halt.txt +++ b/doc/src/fix_halt.txt @@ -121,7 +121,7 @@ halt ID, so that the same condition is not immediately triggered in a subsequent run. The optional {message} keyword determines whether a message is printed -to the screen and logfile when the half condition is triggered. If +to the screen and logfile when the halt condition is triggered. If {message} is set to yes, a one line message with the values that triggered the halt is printed. If {message} is set to no, no message is printed; the run simply exits. The latter may be desirable for diff --git a/doc/src/fix_langevin.txt b/doc/src/fix_langevin.txt index a3d0fb7eaa..534d83f6a9 100644 --- a/doc/src/fix_langevin.txt +++ b/doc/src/fix_langevin.txt @@ -49,7 +49,7 @@ fix 1 all langevin 1.0 1.1 100.0 48279 angmom 3.333 :pre [Description:] -Apply a Langevin thermostat as described in "(Schneider)"_#Schneider +Apply a Langevin thermostat as described in "(Schneider)"_#Schneider1 to a group of atoms which models an interaction with a background implicit solvent. Used with "fix nve"_fix_nve.html, this command performs Brownian dynamics (BD), since the total force on each atom @@ -80,7 +80,7 @@ dt damp), where Kb is the Boltzmann constant, T is the desired temperature, m is the mass of the particle, dt is the timestep size, and damp is the damping factor. Random numbers are used to randomize the direction and magnitude of this force as described in -"(Dunweg)"_#Dunweg, where a uniform random number is used (instead of +"(Dunweg)"_#Dunweg1, where a uniform random number is used (instead of a Gaussian random number) for speed. Note that unless you use the {omega} or {angmom} keywords, the @@ -332,10 +332,10 @@ types, tally = no, zero = no, gjf = no. :line -:link(Dunweg) +:link(Dunweg1) [(Dunweg)] Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991). -:link(Schneider) +:link(Schneider1) [(Schneider)] Schneider and Stoll, Phys Rev B, 17, 1302 (1978). :link(Gronbech-Jensen) diff --git a/doc/src/fix_langevin_drude.txt b/doc/src/fix_langevin_drude.txt index aebf698689..04437e7f36 100644 --- a/doc/src/fix_langevin_drude.txt +++ b/doc/src/fix_langevin_drude.txt @@ -41,7 +41,7 @@ fix 1 all langevin/drude 298.15 100.0 19377 5.0 10.0 83451 zero yes :pre [Description:] -Apply two Langevin thermostats as described in "(Jiang)"_#Jiang for +Apply two Langevin thermostats as described in "(Jiang)"_#Jiang1 for thermalizing the reduced degrees of freedom of Drude oscillators. This link describes how to use the "thermalized Drude oscillator model"_tutorial_drude.html in LAMMPS and polarizable models in LAMMPS @@ -268,6 +268,6 @@ The option defaults are zero = no. :line -:link(Jiang) +:link(Jiang1) [(Jiang)] Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J Phys Chem Lett, 2, 87-92 (2011). diff --git a/doc/src/fix_langevin_eff.txt b/doc/src/fix_langevin_eff.txt index d3112d529d..4a50bfae54 100644 --- a/doc/src/fix_langevin_eff.txt +++ b/doc/src/fix_langevin_eff.txt @@ -37,7 +37,7 @@ fix 1 all langevin/eff 1.0 1.1 10.0 48279 scale 3 1.5 :pre [Description:] -Apply a Langevin thermostat as described in "(Schneider)"_#Schneider +Apply a Langevin thermostat as described in "(Schneider)"_#Schneider2 to a group of nuclei and electrons in the "electron force field"_pair_eff.html model. Used with "fix nve/eff"_fix_nve_eff.html, this command performs Brownian dynamics (BD), since the total force on @@ -106,8 +106,8 @@ The option defaults are scale = 1.0 for all types and tally = no. :line -:link(Dunweg) +:link(Dunweg2) [(Dunweg)] Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991). -:link(Schneider) +:link(Schneider2) [(Schneider)] Schneider and Stoll, Phys Rev B, 17, 1302 (1978). diff --git a/doc/src/fix_lb_pc.txt b/doc/src/fix_lb_pc.txt index 4fd90d7c93..d2b6aafaab 100644 --- a/doc/src/fix_lb_pc.txt +++ b/doc/src/fix_lb_pc.txt @@ -24,7 +24,7 @@ fix 1 all lb/pc :pre Update the positions and velocities of the individual particles described by {group-ID}, experiencing velocity-dependent hydrodynamic forces, using the integration algorithm described in "Mackay et -al."_#Mackay. This integration algorithm should only be used if a +al."_#Mackay1. This integration algorithm should only be used if a user-specified value for the force-coupling constant used in "fix lb/fluid"_fix_lb_fluid.html has been set; do not use this integration algorithm if the force coupling constant has been set by default. @@ -58,5 +58,5 @@ lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html :line -:link(Mackay) +:link(Mackay1) [(Mackay et al.)] Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031. diff --git a/doc/src/fix_lb_viscous.txt b/doc/src/fix_lb_viscous.txt index b88700a136..fcc69d2b43 100644 --- a/doc/src/fix_lb_viscous.txt +++ b/doc/src/fix_lb_viscous.txt @@ -44,7 +44,7 @@ hydrodynamic forces to the particles. :line For further details, as well as descriptions and results of several -test runs, see "Mackay et al."_#Mackay. Please include a citation to +test runs, see "Mackay et al."_#Mackay3. Please include a citation to this paper if this fix is used in work contributing to published research. @@ -90,5 +90,5 @@ lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html :line -:link(Mackay) +:link(Mackay3) [(Mackay et al.)] Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031. diff --git a/doc/src/fix_modify.txt b/doc/src/fix_modify.txt index 9c95cdc452..5e097bb34f 100644 --- a/doc/src/fix_modify.txt +++ b/doc/src/fix_modify.txt @@ -14,11 +14,13 @@ fix_modify fix-ID keyword value ... :pre fix-ID = ID of the fix to modify :ulb,l one or more keyword/value pairs may be appended :l -keyword = {temp} or {press} or {energy} or {respa} :l +keyword = {temp} or {press} or {energy} or {respa} or {dynamic/dof} :l {temp} value = compute ID that calculates a temperature {press} value = compute ID that calculates a pressure {energy} value = {yes} or {no} - {respa} value = {1} to {max respa level} or {0} (for outermost level) :pre + {respa} value = {1} to {max respa level} or {0} (for outermost level) + {dynamic/dof} value = {yes} or {no} + yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature :pre :ule [Examples:] @@ -78,6 +80,27 @@ enabled to support this feature; if not, {fix_modify} will report an error. Active fixes with a custom RESPA level setting are reported with their specified level at the beginning of a r-RESPA run. +The {dynamic/dof} keyword determines whether the number of atoms N in +the fix group and their associated degrees of freedom are re-computed +each time a temperature is computed. Only fix styles that calculate +their own internal temperature use this option. Currently this is +only the "fix rigid/nvt/small"_fix_rigid.html and "fix +rigid/npt/small"_fix_rigid.html commands for the purpose of +thermostatting rigid body translation and rotation. By default, N and +their DOF are assumed to be constant. If you are adding atoms or +molecules to the system (see the "fix pour"_fix_pour.html, "fix +deposit"_fix_deposit.html, and "fix gcmc"_fix_gcmc.html commands) or +expect atoms or molecules to be lost (e.g. due to exiting the +simulation box or via "fix evaporation"_fix_evaporation.html), then +this option should be used to insure the temperature is correctly +normalized. + +NOTE: Other thermostatting fixes, such as "fix nvt"_fix_nh.html, do +not use the {dynamic/dof} keyword because they use a temperature +compute to calculate temperature. See the "compute_modify +dynamic/dof"_compute_modify.html command for a similar way to insure +correct temperature normalization for those thermostats. + [Restrictions:] none [Related commands:] diff --git a/doc/src/fix_nh.txt b/doc/src/fix_nh.txt index 0938509b45..c1cc3e560a 100644 --- a/doc/src/fix_nh.txt +++ b/doc/src/fix_nh.txt @@ -466,16 +466,6 @@ to undergo a slow random walk. This can be mitigated by resetting the momentum at infrequent intervals using the "fix momentum"_fix_momentum.html command. -NOTE: This implementation has been shown to conserve linear momentum -up to machine precision under NVT dynamics. Under NPT dynamics, -for a system with zero initial total linear momentum, the total -momentum fluctuates close to zero. It may occasionally undergo brief -excursions to non-negligible values, before returning close to zero. -Over long simulations, this has the effect of causing the center-of-mass -to undergo a slow random walk. This can be mitigated by resetting -the momentum at infrequent intervals using the -"fix momentum"_fix_momentum.html command. - :line The fix npt and fix nph commands can be used with rigid bodies or diff --git a/doc/src/fix_nh_eff.txt b/doc/src/fix_nh_eff.txt index d90ce52caa..1731f1f331 100644 --- a/doc/src/fix_nh_eff.txt +++ b/doc/src/fix_nh_eff.txt @@ -128,15 +128,15 @@ ploop = 1, nreset = 0, drag = 0.0, dilate = all, and couple = none. :line -:link(Martyna) +:link(Martyna1) [(Martyna)] Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994). :link(Parrinello) [(Parrinello)] Parrinello and Rahman, J Appl Phys, 52, 7182 (1981). -:link(Tuckerman) +:link(Tuckerman1) [(Tuckerman)] Tuckerman, Alejandre, Lopez-Rendon, Jochim, and Martyna, J Phys A: Math Gen, 39, 5629 (2006). -:link(Shinoda) +:link(Shinoda2) [(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004). diff --git a/doc/src/fix_nph_sphere.txt b/doc/src/fix_nph_sphere.txt index e2ce458539..9258f40c76 100644 --- a/doc/src/fix_nph_sphere.txt +++ b/doc/src/fix_nph_sphere.txt @@ -13,14 +13,17 @@ fix nph/sphere/omp command :h3 fix ID group-ID nph/sphere args keyword value ... :pre -ID, group-ID are documented in "fix"_fix.html command -nph/sphere = style name of this fix command -additional barostat related keyword/value pairs from the "fix nph"_fix_nh.html command can be appended :ul +ID, group-ID are documented in "fix"_fix.html command :ulb,l +nph/sphere = style name of this fix command :l +keyword = {disc} :l + {disc} value = none = treat particles as 2d discs, not spheres :pre +additional barostat related keyword/value pairs from the "fix nph"_fix_nh.html command can be appended :l,ule [Examples:] fix 1 all nph/sphere iso 0.0 0.0 1000.0 fix 2 all nph/sphere x 5.0 5.0 1000.0 +fix 2 all nph/sphere x 5.0 5.0 1000.0 disc fix 2 all nph/sphere x 5.0 5.0 1000.0 drag 0.2 fix 2 water nph/sphere aniso 0.0 0.0 1000.0 dilate partial :pre @@ -35,6 +38,12 @@ isenthalpic ensemble. This fix differs from the "fix nph"_fix_nh.html command, which assumes point particles and only updates their position and velocity. +If the {disc} keyword is used, then each particle is treated as a 2d +disc (circle) instead of as a sphere. This is only possible for 2d +simulations, as defined by the "dimension"_dimension.html keyword. +The only difference between discs and spheres in this context is their +moment of inertia, as used in the time integration. + Additional parameters affecting the barostat are specified by keywords and values documented with the "fix nph"_fix_nh.html command. See, for example, discussion of the {aniso}, and {dilate} keywords. @@ -139,6 +148,9 @@ command. All particles in the group must be finite-size spheres. They cannot be point particles. +Use of the {disc} keyword is only allowed for 2d simulations, as +defined by the "dimension"_dimension.html keyword. + [Related commands:] "fix nph"_fix_nh.html, "fix nve_sphere"_fix_nve_sphere.html, "fix diff --git a/doc/src/fix_nphug.txt b/doc/src/fix_nphug.txt index f72bf292ea..ef3ffc4955 100644 --- a/doc/src/fix_nphug.txt +++ b/doc/src/fix_nphug.txt @@ -49,7 +49,7 @@ fix myhug all nphug temp 1.0 1.0 10.0 iso 40.0 40.0 70.0 drag 200.0 tchain 1 pch This command is a variant of the Nose-Hoover "fix npt"_fix_nh.html fix style. It performs time integration of the Hugoniostat equations -of motion developed by Ravelo et al. "(Ravelo)"_#Ravelo. +of motion developed by Ravelo et al. "(Ravelo)"_#Ravelo1. These equations compress the system to a state with average axial stress or pressure equal to the specified target value and that satisfies the Rankine-Hugoniot (RH) @@ -225,5 +225,5 @@ The keyword defaults are the same as those for "fix npt"_fix_nh.html :line -:link(Ravelo) +:link(Ravelo1) [(Ravelo)] Ravelo, Holian, Germann and Lomdahl, Phys Rev B, 70, 014103 (2004). diff --git a/doc/src/fix_npt_sphere.txt b/doc/src/fix_npt_sphere.txt index 767be24bca..24a8fede57 100644 --- a/doc/src/fix_npt_sphere.txt +++ b/doc/src/fix_npt_sphere.txt @@ -15,12 +15,17 @@ fix ID group-ID npt/sphere keyword value ... :pre ID, group-ID are documented in "fix"_fix.html command npt/sphere = style name of this fix command -additional thermostat and barostat related keyword/value pairs from the "fix npt"_fix_nh.html command can be appended :ul +zero or more keyword/value pairs may be appended :l +keyword = {disc} :l + {disc} value = none = treat particles as 2d discs, not spheres :pre +additional thermostat and barostat related keyword/value pairs from the "fix npt"_fix_nh.html command can be appended :l,ule + [Examples:] fix 1 all npt/sphere temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0 fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 +fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 disc fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 drag 0.2 fix 2 water npt/sphere temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partial :pre @@ -42,6 +47,12 @@ degrees of freedom (see below). The translational degrees of freedom can also have a bias velocity removed from them before thermostatting takes place; see the description below. +If the {disc} keyword is used, then each particle is treated as a 2d +disc (circle) instead of as a sphere. This is only possible for 2d +simulations, as defined by the "dimension"_dimension.html keyword. +The only difference between discs and spheres in this context is their +moment of inertia, as used in the time integration. + Additional parameters affecting the thermostat and barostat are specified by keywords and values documented with the "fix npt"_fix_nh.html command. See, for example, discussion of the {temp}, @@ -163,6 +174,9 @@ command. All particles in the group must be finite-size spheres. They cannot be point particles. +Use of the {disc} keyword is only allowed for 2d simulations, as +defined by the "dimension"_dimension.html keyword. + [Related commands:] "fix npt"_fix_nh.html, "fix nve_sphere"_fix_nve_sphere.html, "fix diff --git a/doc/src/fix_nve_dot.txt b/doc/src/fix_nve_dot.txt index 4c80cc2dd4..b1c00cd25c 100644 --- a/doc/src/fix_nve_dot.txt +++ b/doc/src/fix_nve_dot.txt @@ -22,11 +22,11 @@ fix 1 all nve/dot :pre [Description:] -Apply a rigid-body integrator as described in "(Davidchack)"_#Davidchack +Apply a rigid-body integrator as described in "(Davidchack)"_#Davidchack1 to a group of atoms, but without Langevin dynamics. This command performs Molecular dynamics (MD) via a velocity-Verlet algorithm and an evolution operator that rotates -the quaternion degrees of freedom, similar to the scheme outlined in "(Miller)"_#Miller. +the quaternion degrees of freedom, similar to the scheme outlined in "(Miller)"_#Miller1. This command is the equivalent of the "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html without damping and noise and can be used to determine the stability range @@ -55,7 +55,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. :line -:link(Davidchack) +:link(Davidchack1) [(Davidchack)] R.L Davidchack, T.E. Ouldridge, and M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015). -:link(Miller) +:link(Miller1) [(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002). diff --git a/doc/src/fix_nve_dotc_langevin.txt b/doc/src/fix_nve_dotc_langevin.txt index e89151e3b0..19d5b233ce 100644 --- a/doc/src/fix_nve_dotc_langevin.txt +++ b/doc/src/fix_nve_dotc_langevin.txt @@ -29,14 +29,14 @@ fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10 :pre [Description:] Apply a rigid-body Langevin-type integrator of the kind "Langevin C" -as described in "(Davidchack)"_#Davidchack +as described in "(Davidchack)"_#Davidchack2 to a group of atoms, which models an interaction with an implicit background solvent. This command performs Brownian dynamics (BD) via a technique that splits the integration into a deterministic Hamiltonian part and the Ornstein-Uhlenbeck process for noise and damping. The quaternion degrees of freedom are updated though an evolution operator which performs a rotation in quaternion space, preserves -the quaternion norm and is akin to "(Miller)"_#Miller. +the quaternion norm and is akin to "(Miller)"_#Miller2. In terms of syntax this command has been closely modelled on the "fix langevin"_fix_langevin.html and its {angmom} option. But it combines @@ -72,7 +72,7 @@ dt damp), where Kb is the Boltzmann constant, T is the desired temperature, m is the mass of the particle, dt is the timestep size, and damp is the damping factor. Random numbers are used to randomize the direction and magnitude of this force as described in -"(Dunweg)"_#Dunweg, where a uniform random number is used (instead of +"(Dunweg)"_#Dunweg3, where a uniform random number is used (instead of a Gaussian random number) for speed. :line @@ -126,9 +126,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. :line -:link(Davidchack) +:link(Davidchack2) [(Davidchack)] R.L Davidchack, T.E. Ouldridge, M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015). -:link(Miller) +:link(Miller2) [(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002). -:link(Dunweg) +:link(Dunweg3) [(Dunweg)] B. Dunweg, W. Paul, Int. J. Mod. Phys. C, 2, 817-27 (1991). diff --git a/doc/src/fix_nve_manifold_rattle.txt b/doc/src/fix_nve_manifold_rattle.txt index 89a0266f11..e032a7e1cc 100644 --- a/doc/src/fix_nve_manifold_rattle.txt +++ b/doc/src/fix_nve_manifold_rattle.txt @@ -33,7 +33,7 @@ fix step all nve/manifold/rattle 1e-8 100 ellipsoid 2.5 2.5 5.0 every 25 :pre Perform constant NVE integration to update position and velocity for atoms constrained to a curved surface (manifold) in the group each -timestep. The constraint is handled by RATTLE "(Andersen)"_#Andersen +timestep. The constraint is handled by RATTLE "(Andersen)"_#Andersen1 written out for the special case of single-particle constraints as explained in "(Paquay)"_#Paquay2. V is volume; E is energy. This way, the dynamics of particles constrained to curved surfaces can be @@ -92,7 +92,7 @@ manifoldforce"_fix_manifoldforce.html :line -:link(Andersen) +:link(Andersen1) [(Andersen)] Andersen, J. Comp. Phys. 52, 24, (1983). :link(Paquay2) diff --git a/doc/src/fix_nve_sphere.txt b/doc/src/fix_nve_sphere.txt index f5a303ca03..f91a41f515 100644 --- a/doc/src/fix_nve_sphere.txt +++ b/doc/src/fix_nve_sphere.txt @@ -16,16 +16,18 @@ fix ID group-ID nve/sphere :pre ID, group-ID are documented in "fix"_fix.html command :ulb,l nve/sphere = style name of this fix command :l zero or more keyword/value pairs may be appended :l -keyword = {update} +keyword = {update} or {disc} :l {update} value = {dipole} or {dipole/dlm} dipole = update orientation of dipole moment during integration - dipole/dlm = use DLM integrator to update dipole orientation :pre + dipole/dlm = use DLM integrator to update dipole orientation + {disc} value = none = treat particles as 2d discs, not spheres :pre :ule [Examples:] fix 1 all nve/sphere fix 1 all nve/sphere update dipole +fix 1 all nve/sphere disc fix 1 all nve/sphere update dipole/dlm :pre [Description:] @@ -52,6 +54,12 @@ Dullweber-Leimkuhler-McLachlan integration scheme giving better energy conservation and allows slightly longer timesteps at only a small additional computational cost. +If the {disc} keyword is used, then each particle is treated as a 2d +disc (circle) instead of as a sphere. This is only possible for 2d +simulations, as defined by the "dimension"_dimension.html keyword. +The only difference between discs and spheres in this context is their +moment of inertia, as used in the time integration. + :line Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are @@ -98,6 +106,9 @@ command. All particles in the group must be finite-size spheres. They cannot be point particles. +Use of the {disc} keyword is only allowed for 2d simulations, as +defined by the "dimension"_dimension.html keyword. + [Related commands:] "fix nve"_fix_nve.html, "fix nve/asphere"_fix_nve_asphere.html diff --git a/doc/src/fix_nvt_manifold_rattle.txt b/doc/src/fix_nvt_manifold_rattle.txt index a1a2a855de..a620648a46 100644 --- a/doc/src/fix_nvt_manifold_rattle.txt +++ b/doc/src/fix_nvt_manifold_rattle.txt @@ -37,7 +37,7 @@ fix 1 all nvt/manifold/rattle 1e-4 10 cylinder 3.0 temp 1.0 1.0 10.0 [Description:] -This fix combines the RATTLE-based "(Andersen)"_#Andersen time integrator of "fix nve/manifold/rattle"_fix_nve_manifold_rattle.html "(Paquay)"_#Paquay3 with a Nose-Hoover-chain thermostat to sample the +This fix combines the RATTLE-based "(Andersen)"_#Andersen2 time integrator of "fix nve/manifold/rattle"_fix_nve_manifold_rattle.html "(Paquay)"_#Paquay3 with a Nose-Hoover-chain thermostat to sample the canonical ensemble of particles constrained to a curved surface (manifold). This sampling does suffer from discretization bias of O(dt). For a list of currently supported manifolds and their parameters, see "manifolds"_manifolds.html @@ -72,7 +72,7 @@ section for more info. :line -:link(Andersen) +:link(Andersen2) [(Andersen)] Andersen, J. Comp. Phys. 52, 24, (1983). :link(Paquay3) diff --git a/doc/src/fix_nvt_sllod.txt b/doc/src/fix_nvt_sllod.txt index 116e57e53a..82631f22e3 100644 --- a/doc/src/fix_nvt_sllod.txt +++ b/doc/src/fix_nvt_sllod.txt @@ -54,9 +54,9 @@ by fix nvt/sllod. LAMMPS will give an error if this setting is not consistent. The SLLOD equations of motion, originally proposed by Hoover and Ladd -(see "(Evans and Morriss)"_#Evans), were proven to be equivalent to +(see "(Evans and Morriss)"_#Evans3), were proven to be equivalent to Newton's equations of motion for shear flow by "(Evans and -Morriss)"_#Evans. They were later shown to generate the desired +Morriss)"_#Evans3. They were later shown to generate the desired velocity gradient and the correct production of work by stresses for all forms of homogeneous flow by "(Daivis and Todd)"_#Daivis. As implemented in LAMMPS, they are coupled to a Nose/Hoover chain @@ -173,7 +173,7 @@ Same as "fix nvt"_fix_nh.html, except tchain = 1. :line -:link(Evans) +:link(Evans3) [(Evans and Morriss)] Evans and Morriss, Phys Rev A, 30, 1528 (1984). :link(Daivis) diff --git a/doc/src/fix_nvt_sllod_eff.txt b/doc/src/fix_nvt_sllod_eff.txt index e92d1640cd..408eb1da01 100644 --- a/doc/src/fix_nvt_sllod_eff.txt +++ b/doc/src/fix_nvt_sllod_eff.txt @@ -89,6 +89,6 @@ Same as "fix nvt/eff"_fix_nh_eff.html, except tchain = 1. :line -:link(Tuckerman) +:link(Tuckerman2) [(Tuckerman)] Tuckerman, Mundy, Balasubramanian, Klein, J Chem Phys, 106, 5615 (1997). diff --git a/doc/src/fix_nvt_sphere.txt b/doc/src/fix_nvt_sphere.txt index 60943137de..fa1c97bcce 100644 --- a/doc/src/fix_nvt_sphere.txt +++ b/doc/src/fix_nvt_sphere.txt @@ -13,13 +13,17 @@ fix nvt/sphere/omp command :h3 fix ID group-ID nvt/sphere keyword value ... :pre -ID, group-ID are documented in "fix"_fix.html command -nvt/sphere = style name of this fix command -additional thermostat related keyword/value pairs from the "fix nvt"_fix_nh.html command can be appended :ul +ID, group-ID are documented in "fix"_fix.html command :ulb,l +nvt/sphere = style name of this fix command :l +zero or more keyword/value pairs may be appended :l +keyword = {disc} :l + {disc} value = none = treat particles as 2d discs, not spheres :pre +additional thermostat related keyword/value pairs from the "fix nvt"_fix_nh.html command can be appended :l,ule [Examples:] fix 1 all nvt/sphere temp 300.0 300.0 100.0 +fix 1 all nvt/sphere temp 300.0 300.0 100.0 disc fix 1 all nvt/sphere temp 300.0 300.0 100.0 drag 0.2 :pre [Description:] @@ -40,6 +44,12 @@ degrees of freedom (see below). The translational degrees of freedom can also have a bias velocity removed from them before thermostatting takes place; see the description below. +If the {disc} keyword is used, then each particle is treated as a 2d +disc (circle) instead of as a sphere. This is only possible for 2d +simulations, as defined by the "dimension"_dimension.html keyword. +The only difference between discs and spheres in this context is their +moment of inertia, as used in the time integration. + Additional parameters affecting the thermostat are specified by keywords and values documented with the "fix nvt"_fix_nh.html command. See, for example, discussion of the {temp} and {drag} @@ -140,6 +150,9 @@ command. All particles in the group must be finite-size spheres. They cannot be point particles. +Use of the {disc} keyword is only allowed for 2d simulations, as +defined by the "dimension"_dimension.html keyword. + [Related commands:] "fix nvt"_fix_nh.html, "fix nve_sphere"_fix_nve_sphere.html, "fix diff --git a/doc/src/fix_pour.txt b/doc/src/fix_pour.txt index f2c10184dd..54f78287e0 100644 --- a/doc/src/fix_pour.txt +++ b/doc/src/fix_pour.txt @@ -117,6 +117,12 @@ treated as rigid bodies, use the {rigid} keyword, specifying as its value the ID of a separate "fix rigid/small"_fix_rigid.html command which also appears in your input script. +NOTE: If you wish the new rigid molecules (and other rigid molecules) +to be thermostatted correctly via "fix rigid/small/nvt"_fix_rigid.html +or "fix rigid/small/npt"_fix_rigid.html, then you need to use the +"fix_modify dynamic/dof yes" command for the rigid fix. This is to +inform that fix that the molecule count will vary dynamically. + If you wish to insert molecules via the {mol} keyword, that will have their bonds or angles constrained via SHAKE, use the {shake} keyword, specifying as its value the ID of a separate "fix diff --git a/doc/src/fix_press_berendsen.txt b/doc/src/fix_press_berendsen.txt index f0912fe0c8..9c9da8ec7b 100644 --- a/doc/src/fix_press_berendsen.txt +++ b/doc/src/fix_press_berendsen.txt @@ -35,7 +35,7 @@ fix 2 all press/berendsen aniso 0.0 0.0 1000.0 dilate partial :pre [Description:] Reset the pressure of the system by using a Berendsen barostat -"(Berendsen)"_#Berendsen, which rescales the system volume and +"(Berendsen)"_#Berendsen1, which rescales the system volume and (optionally) the atoms coordinates within the simulation box every timestep. @@ -221,7 +221,7 @@ pressure for whatever "units"_units.html are defined. :line -:link(Berendsen) +:link(Berendsen1) [(Berendsen)] Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem Phys, 81, 3684 (1984). diff --git a/doc/src/fix_qeq.txt b/doc/src/fix_qeq.txt index b1a1dd5c42..f9c8ecde63 100644 --- a/doc/src/fix_qeq.txt +++ b/doc/src/fix_qeq.txt @@ -43,8 +43,8 @@ fix 1 all qeq/fire 1 10 1.0e-3 100 my_qeq qdamp 0.2 qstep 0.1 :pre [Description:] Perform the charge equilibration (QEq) method as described in "(Rappe -and Goddard)"_#Rappe and formulated in "(Nakano)"_#Nakano (also known -as the matrix inversion method) and in "(Rick and Stuart)"_#Rick (also +and Goddard)"_#Rappe1 and formulated in "(Nakano)"_#Nakano1 (also known +as the matrix inversion method) and in "(Rick and Stuart)"_#Rick1 (also known as the extended Lagrangian method) based on the electronegativity equilization principle. @@ -97,8 +97,8 @@ below, thus the others can be set to 0.0 if desired. {chi} = electronegativity in energy units {eta} = self-Coulomb potential in energy units {gamma} = shielded Coulomb constant defined by "ReaxFF force field"_#vanDuin in distance units -{zeta} = Slater type orbital exponent defined by the "Streitz-Mintmire"_#Streitz potential in reverse distance units -{qcore} = charge of the nucleus defined by the "Streitz-Mintmire potential"_#Streitz potential in charge units :ul +{zeta} = Slater type orbital exponent defined by the "Streitz-Mintmire"_#Streitz1 potential in reverse distance units +{qcore} = charge of the nucleus defined by the "Streitz-Mintmire potential"_#Streitz1 potential in charge units :ul The {qeq/point} style describes partial charges on atoms as point charges. Interaction between a pair of charged particles is 1/r, @@ -126,7 +126,7 @@ charge densities centered around atoms via the Slater 1{s} orbital, so that the interaction between a pair of charged particles is the product of two Slater 1{s} orbitals. The expression for the Slater 1{s} orbital is given under equation (6) of the -"Streitz-Mintmire"_#Streitz paper. Only the {chi}, {eta}, {zeta}, and +"Streitz-Mintmire"_#Streitz1 paper. Only the {chi}, {eta}, {zeta}, and {qcore} parameters from the {qfile} file are used. This style solves partial charges on atoms via the matrix inversion method. A tolerance of 1.0e-6 is usually a good number. Keyword {alpha} can be used to @@ -194,18 +194,18 @@ LAMMPS"_Section_start.html#start_3 section for more info. :line -:link(Rappe) +:link(Rappe1) [(Rappe and Goddard)] A. K. Rappe and W. A. Goddard III, J Physical Chemistry, 95, 3358-3363 (1991). -:link(Nakano) +:link(Nakano1) [(Nakano)] A. Nakano, Computer Physics Communications, 104, 59-69 (1997). -:link(Rick) +:link(Rick1) [(Rick and Stuart)] S. W. Rick, S. J. Stuart, B. J. Berne, J Chemical Physics 101, 16141 (1994). -:link(Streitz) +:link(Streitz1) [(Streitz-Mintmire)] F. H. Streitz, J. W. Mintmire, Physical Review B, 50, 16, 11996 (1994) diff --git a/doc/src/fix_qeq_reax.txt b/doc/src/fix_qeq_reax.txt index a26934dfb4..76c95e1117 100644 --- a/doc/src/fix_qeq_reax.txt +++ b/doc/src/fix_qeq_reax.txt @@ -28,7 +28,7 @@ fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq :pre [Description:] Perform the charge equilibration (QEq) method as described in "(Rappe -and Goddard)"_#Rappe and formulated in "(Nakano)"_#Nakano. It is +and Goddard)"_#Rappe2 and formulated in "(Nakano)"_#Nakano2. It is typically used in conjunction with the ReaxFF force field model as implemented in the "pair_style reax/c"_pair_reax_c.html command, but it can be used with any potential in LAMMPS, so long as it defines and @@ -36,7 +36,7 @@ uses charges on each atom. The "fix qeq/comb"_fix_qeq_comb.html command should be used to perform charge equilibration with the "COMB potential"_pair_comb.html. For more technical details about the charge equilibration performed by fix qeq/reax, see the -"(Aktulga)"_#Aktulga paper. +"(Aktulga)"_#qeq-Aktulga paper. The QEq method minimizes the electrostatic energy of the system by adjusting the partial charge on individual atoms based on interactions @@ -112,13 +112,13 @@ be used for periodic cell dimensions less than 10 angstroms. :line -:link(Rappe) +:link(Rappe2) [(Rappe)] Rappe and Goddard III, Journal of Physical Chemistry, 95, 3358-3363 (1991). -:link(Nakano) +:link(Nakano2) [(Nakano)] Nakano, Computer Physics Communications, 104, 59-69 (1997). -:link(Aktulga) -(Aktulga) Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, +:link(qeq-Aktulga) +[(Aktulga)] Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, 245-259 (2012). diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt index e086656f5d..03edf61ed8 100644 --- a/doc/src/fix_rigid.txt +++ b/doc/src/fix_rigid.txt @@ -93,7 +93,7 @@ Examples of large rigid bodies are a colloidal particle, or portions of a biomolecule such as a protein. Example of small rigid bodies are patchy nanoparticles, such as those -modeled in "this paper"_#Zhang by Sharon Glotzer's group, clumps of +modeled in "this paper"_#Zhang1 by Sharon Glotzer's group, clumps of granular particles, lipid molecules consiting of one or more point dipoles connected to other spheroids or ellipsoids, irregular particles built from line segments (2d) or triangles (3d), and @@ -299,12 +299,12 @@ perform constant NVE time integration. They are referred to below as the 4 NVE rigid styles. The only difference is that the {rigid} and {rigid/small} styles use an integration technique based on Richardson iterations. The {rigid/nve} and {rigid/small/nve} styles uses the -methods described in the paper by "Miller"_#Miller, which are thought +methods described in the paper by "Miller"_#Miller3, which are thought to provide better energy conservation than an iterative approach. The {rigid/nvt} and {rigid/nvt/small} styles performs constant NVT integration using a Nose/Hoover thermostat with chains as described -originally in "(Hoover)"_#Hoover and "(Martyna)"_#Martyna, which +originally in "(Hoover)"_#Hoover and "(Martyna)"_#Martyna2, which thermostats both the translational and rotational degrees of freedom of the rigid bodies. They are referred to below as the 2 NVT rigid styles. The rigid-body algorithm used by {rigid/nvt} is described in @@ -788,13 +788,13 @@ torque. Also Tchain = Pchain = 10, Titer = 1, Torder = 3. :link(Kamberaj) [(Kamberaj)] Kamberaj, Low, Neal, J Chem Phys, 122, 224114 (2005). -:link(Martyna) +:link(Martyna2) [(Martyna)] Martyna, Klein, Tuckerman, J Chem Phys, 97, 2635 (1992); Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117. -:link(Miller) +:link(Miller3) [(Miller)] Miller, Eleftheriou, Pattnaik, Ndirango, and Newns, J Chem Phys, 116, 8649 (2002). -:link(Zhang) +:link(Zhang1) [(Zhang)] Zhang, Glotzer, Nanoletters, 4, 1407-1413 (2004). diff --git a/doc/src/fix_shake.txt b/doc/src/fix_shake.txt index a860aad128..8b26aaa874 100644 --- a/doc/src/fix_shake.txt +++ b/doc/src/fix_shake.txt @@ -53,7 +53,7 @@ velocities are approximated as finite differences to the trajectories integrated explicitly, as with velocity Verlet which is what LAMMPS uses as an integration method, a second set of constraining forces is required in order to eliminate velocity components along the bonds -("Andersen (1983)"_#Andersen). +("Andersen (1983)"_#Andersen3). In order to formulate individual constraints for SHAKE and RATTLE, focus on a single molecule whose bonds are constrained. Let Ri and Vi @@ -171,7 +171,7 @@ more instructions on how to use the accelerated styles effectively. The velocity constraints lead to a linear system of equations which can be solved analytically. The implementation of the algorithm in -LAMMPS closely follows ("Andersen (1983)"_#Andersen). +LAMMPS closely follows ("Andersen (1983)"_#Andersen3). NOTE: The fix rattle command modifies forces and velocities and thus should be defined after all other integration fixes in your input @@ -223,5 +223,5 @@ SHAKE or RATTLE should not be used to constrain an angle at 180 degrees [(Ryckaert)] J.-P. Ryckaert, G. Ciccotti and H. J. C. Berendsen, J of Comp Phys, 23, 327-341 (1977). -:link(Andersen) +:link(Andersen3) [(Andersen)] H. Andersen, J of Comp Phys, 52, 24-34 (1983). diff --git a/doc/src/fix_shardlow.txt b/doc/src/fix_shardlow.txt index 53bde746a0..8354b4c41c 100644 --- a/doc/src/fix_shardlow.txt +++ b/doc/src/fix_shardlow.txt @@ -30,7 +30,7 @@ nve"_fix_nve.html or "fix nph"_fix_nh.html). The stochastic integration of the dissipative and random forces is performed prior to the deterministic integration of the conservative force. Further details regarding the method are provided in "(Lisal)"_#Lisal and -"(Larentzos1)"_#Larentzos1. +"(Larentzos1)"_#Larentzos1sh. The fix {shardlow} must be used with the "pair_style dpd/fdt"_pair_style.html or "pair_style @@ -83,13 +83,13 @@ particle dynamics as isothermal, isobaric, isoenergetic, and isoenthalpic conditions using Shardlow-like splitting algorithms.", J. Chem. Phys., 135, 204105 (2011). -:link(Larentzos1) +:link(Larentzos1sh) [(Larentzos1)] J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and W.D. Mattson, "Parallel Implementation of Isothermal and Isoenergetic Dissipative Particle Dynamics Using Shardlow-Like Splitting Algorithms", Comput. Phys. Commun., 185, 1987-1998 (2014). -:link(Larentzos2) +:link(Larentzos2sh) [(Larentzos2)] J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research diff --git a/doc/src/fix_srd.txt b/doc/src/fix_srd.txt index 31660fe77a..4e190234fd 100644 --- a/doc/src/fix_srd.txt +++ b/doc/src/fix_srd.txt @@ -72,7 +72,7 @@ viscosity"_fix_viscosity.html, and "fix nvt/sllod"_fix_nvt_sllod.html, can be used in conjunction with the SRD model. For more details on how the SRD model is implemented in LAMMPS, "this -paper"_#Petersen describes the implementation and usage of pure SRD +paper"_#Petersen1 describes the implementation and usage of pure SRD fluids. "This paper"_#Lechman, which is nearly complete, describes the implementation and usage of mixture systems (solute particles in an SRD fluid). See the examples/srd directory for sample input @@ -390,7 +390,7 @@ rescale = yes. :link(Hecht) [(Hecht)] Hecht, Harting, Ihle, Herrmann, Phys Rev E, 72, 011408 (2005). -:link(Petersen) +:link(Petersen1) [(Petersen)] Petersen, Lechman, Plimpton, Grest, in' t Veld, Schunk, J Chem Phys, 132, 174106 (2010). diff --git a/doc/src/fix_temp_berendsen.txt b/doc/src/fix_temp_berendsen.txt index 9c1dd538da..6944860e14 100644 --- a/doc/src/fix_temp_berendsen.txt +++ b/doc/src/fix_temp_berendsen.txt @@ -26,7 +26,7 @@ fix 1 all temp/berendsen 300.0 300.0 100.0 :pre [Description:] Reset the temperature of a group of atoms by using a Berendsen -thermostat "(Berendsen)"_#Berendsen, which rescales their velocities +thermostat "(Berendsen)"_#Berendsen2, which rescales their velocities every timestep. The thermostat is applied to only the translational degrees of freedom @@ -157,7 +157,7 @@ temp/rescale"_fix_temp_rescale.html, "fix langevin"_fix_langevin.html, :line -:link(Berendsen) +:link(Berendsen2) [(Berendsen)] Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem Phys, 81, 3684 (1984). diff --git a/doc/src/fix_thermal_conductivity.txt b/doc/src/fix_thermal_conductivity.txt index a807feaec7..0353c095b2 100644 --- a/doc/src/fix_thermal_conductivity.txt +++ b/doc/src/fix_thermal_conductivity.txt @@ -31,7 +31,7 @@ fix 1 all thermal/conductivity 50 z 20 swap 2 :pre [Description:] Use the Muller-Plathe algorithm described in "this -paper"_#Muller-Plathe to exchange kinetic energy between two particles +paper"_#Muller-Plathe1 to exchange kinetic energy between two particles in different regions of the simulation box every N steps. This induces a temperature gradient in the system. As described below this enables the thermal conductivity of a material to be calculated. This @@ -85,7 +85,7 @@ quantity by time and the cross-sectional area of the simulation box yields a heat flux. The ratio of heat flux to the slope of the temperature profile is proportional to the thermal conductivity of the fluid, in appropriate units. See the "Muller-Plathe -paper"_#Muller-Plathe for details. +paper"_#Muller-Plathe1 for details. NOTE: If your system is periodic in the direction of the heat flux, then the flux is going in 2 directions. This means the effective heat @@ -136,7 +136,7 @@ kinetic energy of atoms that are in constrained molecules, e.g. via "fix shake"_fix_shake.html or "fix rigid"_fix_rigid.html. This is because application of the constraints will alter the amount of transferred momentum. You should, however, be able to use flexible -molecules. See the "Zhang paper"_#Zhang for a discussion and results +molecules. See the "Zhang paper"_#Zhang2 for a discussion and results of this idea. When running a simulation with large, massive particles or molecules @@ -155,9 +155,9 @@ The option defaults are swap = 1. :line -:link(Muller-Plathe) +:link(Muller-Plathe1) [(Muller-Plathe)] Muller-Plathe, J Chem Phys, 106, 6082 (1997). -:link(Zhang) +:link(Zhang2) [(Zhang)] Zhang, Lussetti, de Souza, Muller-Plathe, J Phys Chem B, 109, 15060-15067 (2005). diff --git a/doc/src/fix_viscosity.txt b/doc/src/fix_viscosity.txt index 5fbbc67ca5..f6603be624 100644 --- a/doc/src/fix_viscosity.txt +++ b/doc/src/fix_viscosity.txt @@ -33,7 +33,7 @@ fix 1 all viscosity 50 x z 20 swap 2 vtarget 1.5 :pre [Description:] Use the Muller-Plathe algorithm described in "this -paper"_#Muller-Plathe to exchange momenta between two particles in +paper"_#Muller-Plathe2 to exchange momenta between two particles in different regions of the simulation box every N steps. This induces a shear velocity profile in the system. As described below this enables a viscosity of the fluid to be calculated. This algorithm is @@ -83,7 +83,7 @@ quantity by time and the cross-sectional area of the simulation box yields a momentum flux. The ratio of momentum flux to the slope of the shear velocity profile is proportional to the viscosity of the fluid, in appropriate units. See the "Muller-Plathe -paper"_#Muller-Plathe for details. +paper"_#Muller-Plathe2 for details. NOTE: If your system is periodic in the direction of the momentum flux, then the flux is going in 2 directions. This means the @@ -161,7 +161,7 @@ The option defaults are swap = 1 and vtarget = INF. :line -:link(Muller-Plathe) +:link(Muller-Plathe2) [(Muller-Plathe)] Muller-Plathe, Phys Rev E, 59, 4894-4898 (1999). :link(Maginn) diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt index 7997f6f1d4..e8777d4113 100644 --- a/doc/src/fixes.txt +++ b/doc/src/fixes.txt @@ -42,6 +42,7 @@ Fixes :h1 fix_eos_table_rx fix_evaporate fix_external + fix_filter_corotate fix_flow_gauss fix_freeze fix_gcmc diff --git a/doc/src/info.txt b/doc/src/info.txt index 0b761ccc15..43b430f746 100644 --- a/doc/src/info.txt +++ b/doc/src/info.txt @@ -12,7 +12,7 @@ info command :h3 info args :pre -args = one or more of the following keywords: {out}, {all}, {system}, {communication}, {computes}, {dumps}, {fixes}, {groups}, {regions}, {variables}, {styles}, {time}, or {configuration} +args = one or more of the following keywords: {out}, {all}, {system}, {memory}, {communication}, {computes}, {dumps}, {fixes}, {groups}, {regions}, {variables}, {styles}, {time}, or {configuration} {out} values = {screen}, {log}, {append} filename, {overwrite} filename {styles} values = {all}, {angle}, {atom}, {bond}, {compute}, {command}, {dump}, {dihedral}, {fix}, {improper}, {integrate}, {kspace}, {minimize}, {pair}, {region} :ul @@ -40,6 +40,17 @@ to that file, which is either appended to or overwritten, respectively. The {all} flag activates printing all categories listed below. +The {configuration} category prints some information about the +LAMMPS version as well as architecture and OS it is run on. + +The {memory} category prints some information about the current +memory allocation of MPI rank 0 (this the amount of dynamically +allocated memory reported by LAMMPS classes). Where supported, +also some OS specific information about the size of the reserved +memory pool size (this is where malloc() and the new operator +request memory from) and the maximum resident set size is reported +(this is the maximum amount of physical memory occupied so far). + The {system} category prints a general system overview listing. This includes the unit style, atom style, number of atoms, bonds, angles, dihedrals, and impropers and the number of the respective types, box @@ -93,11 +104,6 @@ region :ul The {time} category prints the accumulated CPU and wall time for the process that writes output (usually MPI rank 0). -The {configuration} command prints some information about the LAMMPS -version and architecture and OS it is run on. Where supported, also -information about the memory consumption provided by the OS is -reported. - [Restrictions:] none [Related commands:] diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt index cb57863ad0..7a6c7191f0 100644 --- a/doc/src/kspace_modify.txt +++ b/doc/src/kspace_modify.txt @@ -206,7 +206,7 @@ beginning of the run to give the desired estimated error. Other cutoffs such as LJ will not be affected. If the grid is not set using the {mesh} command, this command will also attempt to use the optimal grid that minimizes cost using an estimate given by -"(Hardy)"_#Hardy. Note that this cost estimate is not exact, somewhat +"(Hardy)"_#Hardy1. Note that this cost estimate is not exact, somewhat experimental, and still may not yield the optimal parameters. The {pressure/scalar} keyword applies only to MSM. If this option is @@ -235,7 +235,7 @@ collective operations and adequate hardware. The {diff} keyword specifies the differentiation scheme used by the PPPM method to compute forces on particles given electrostatic potentials on the PPPM mesh. The {ik} approach is the default for -PPPM and is the original formulation used in "(Hockney)"_#Hockney. It +PPPM and is the original formulation used in "(Hockney)"_#Hockney1. It performs differentiation in Kspace, and uses 3 FFTs to transfer each component of the computed fields back to real space for total of 4 FFTs per timestep. @@ -271,7 +271,7 @@ speed-up the simulations but introduces some error in the force computations, as shown in "(Wennberg)"_#Wennberg. With {none}, it is assumed that no mixing rule is applicable. Splitting of the dispersion coefficients will be performed as described in -"(Isele-Holder)"_#Isele-Holder. This splitting can be influenced with +"(Isele-Holder)"_#Isele-Holder1. This splitting can be influenced with the {splittol} keywords. Only the eigenvalues that are larger than tol compared to the largest eigenvalues are included. Using this keywords the original matrix of dispersion coefficients is approximated. This @@ -280,7 +280,7 @@ computations of the dispersion part is decreased. The {force/disp/real} and {force/disp/kspace} keywords set the force accuracy for the real and space computations for the dispersion part -of pppm/disp. As shown in "(Isele-Holder)"_#Isele-Holder, optimal +of pppm/disp. As shown in "(Isele-Holder)"_#Isele-Holder1, optimal performance and accuracy in the results is obtained when these values are different. @@ -311,7 +311,7 @@ split = 0, tol = 1.0e-6, and disp/auto = no. :line -:link(Hockney) +:link(Hockney1) [(Hockney)] Hockney and Eastwood, Computer Simulation Using Particles, Adam Hilger, NY (1989). @@ -325,7 +325,7 @@ Adam Hilger, NY (1989). :link(Klapp) [(Klapp)] Klapp, Schoen, J Chem Phys, 117, 8050 (2002). -:link(Hardy) +:link(Hardy1) [(Hardy)] David Hardy thesis: Multilevel Summation for the Fast Evaluation of Forces for the Simulation of Biomolecules, University of Illinois at Urbana-Champaign, (2006). @@ -333,7 +333,7 @@ Illinois at Urbana-Champaign, (2006). :link(Hummer) [(Hummer)] Hummer, Gronbech-Jensen, Neumann, J Chem Phys, 109, 2791 (1998) -:link(Isele-Holder) +:link(Isele-Holder1) [(Isele-Holder)] Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail, J Chem Theory Comput, 9, 5412 (2013). diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt index e5c47e8230..371540bd68 100644 --- a/doc/src/kspace_style.txt +++ b/doc/src/kspace_style.txt @@ -152,7 +152,7 @@ such as when using a barostat. :line The {pppm/disp} and {pppm/disp/tip4p} styles add a mesh-based long-range -dispersion sum option for 1/r^6 potentials "(Isele-Holder)"_#Isele-Holder, +dispersion sum option for 1/r^6 potentials "(Isele-Holder)"_#Isele-Holder2012, similar to the {ewald/disp} style. The 1/r^6 capability means that Lennard-Jones or Buckingham potentials can be used without a cutoff, i.e. they become full long-range potentials. @@ -163,8 +163,8 @@ This can be done by either choosing the Ewald and grid parameters, or by specifying separate accuracies for the real and kspace calculations. When not making any settings, the simulation will stop with an error message. Further information on the influence of the parameters -and how to choose them is described in "(Isele-Holder)"_#Isele-Holder, -"(Isele-Holder2)"_#Isele-Holder2 and the +and how to choose them is described in "(Isele-Holder)"_#Isele-Holder2012, +"(Isele-Holder2)"_#Isele-Holder2013 and the "How-To"_Section_howto.html#howto_24 discussion. :line @@ -182,13 +182,13 @@ currently support the -DFFT_SINGLE compiler switch. :line The {msm} style invokes a multi-level summation method MSM solver, -"(Hardy)"_#Hardy or "(Hardy2)"_#Hardy2, which maps atom charge to a 3d -mesh, and uses a multi-level hierarchy of coarser and coarser meshes -on which direct coulomb solves are done. This method does not use -FFTs and scales as N. It may therefore be faster than the other +"(Hardy)"_#Hardy2006 or "(Hardy2)"_#Hardy2009, which maps atom charge +to a 3d mesh, and uses a multi-level hierarchy of coarser and coarser +meshes on which direct coulomb solves are done. This method does not +use FFTs and scales as N. It may therefore be faster than the other K-space solvers for relatively large problems when running on large -core counts. MSM can also be used for non-periodic boundary conditions and -for mixed periodic and non-periodic boundaries. +core counts. MSM can also be used for non-periodic boundary conditions +and for mixed periodic and non-periodic boundaries. MSM is most competitive versus Ewald and PPPM when only relatively low accuracy forces, about 1e-4 relative error or less accurate, @@ -247,7 +247,7 @@ equation 9 of "(Petersen)"_#Petersen. RMS force errors in K-space for which is similar to equation 32 of "(Kolafa)"_#Kolafa. RMS force errors in K-space for {pppm} are estimated using equation 38 of "(Deserno)"_#Deserno. RMS force errors for {msm} are estimated -using ideas from chapter 3 of "(Hardy)"_#Hardy, with equation 3.197 +using ideas from chapter 3 of "(Hardy)"_#Hardy2006, with equation 3.197 of particular note. When using {msm} with non-periodic boundary conditions, it is expected that the error estimation will be too pessimistic. RMS force errors for dipoles when using {ewald/disp} @@ -366,19 +366,19 @@ and Computation 5, 2322 (2009) [(Toukmaji)] Toukmaji, Sagui, Board, and Darden, J Chem Phys, 113, 10913 (2000). -:link(Isele-Holder) +:link(Isele-Holder2012) [(Isele-Holder)] Isele-Holder, Mitchell, Ismail, J Chem Phys, 137, 174107 (2012). -:link(Isele-Holder2) +:link(Isele-Holder2013) [(Isele-Holder2)] Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail, J Chem Theory Comput 9, 5412 (2013). -:link(Hardy) +:link(Hardy2006) [(Hardy)] David Hardy thesis: Multilevel Summation for the Fast Evaluation of Forces for the Simulation of Biomolecules, University of Illinois at Urbana-Champaign, (2006). -:link(Hardy2) -[(Hardy)] Hardy, Stone, Schulten, Parallel Computing 35 (2009) +:link(Hardy2009) +[(Hardy2)] Hardy, Stone, Schulten, Parallel Computing 35 (2009) 164-177. diff --git a/doc/src/lammps.book b/doc/src/lammps.book index 3186865fb6..85fb9f7e9e 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -168,6 +168,7 @@ fix_eos_table.html fix_eos_table_rx.html fix_evaporate.html fix_external.html +fix_filter_corotate.html fix_flow_gauss.html fix_freeze.html fix_gcmc.html @@ -455,6 +456,7 @@ pair_meam_spline.html pair_meam_sw_spline.html pair_mgpt.html pair_mie.html +pair_momb.html pair_morse.html pair_multi_lucy.html pair_multi_lucy_rx.html diff --git a/doc/src/neb.txt b/doc/src/neb.txt index a5fa03552c..3a62a77a6e 100644 --- a/doc/src/neb.txt +++ b/doc/src/neb.txt @@ -44,7 +44,7 @@ of the energy barrier associated with a transition state, e.g. for an atom to perform a diffusive hop from one energy basin to another in a coordinated fashion with its neighbors. The implementation in LAMMPS follows the discussion in these 3 papers: "(HenkelmanA)"_#HenkelmanA, -"(HenkelmanB)"_#HenkelmanB, and "(Nakano)"_#Nakano. +"(HenkelmanB)"_#HenkelmanB, and "(Nakano)"_#Nakano3. Each replica runs on a partition of one or more processors. Processor partitions are defined at run-time using the -partition command-line @@ -412,5 +412,5 @@ langevin"_fix_langevin.html, "fix viscous"_fix_viscous.html [(HenkelmanB)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113, 9901-9904 (2000). -:link(Nakano) +:link(Nakano3) [(Nakano)] Nakano, Comp Phys Comm, 178, 280-289 (2008). diff --git a/doc/src/package.txt b/doc/src/package.txt index 02afb8d620..a0894b3128 100644 --- a/doc/src/package.txt +++ b/doc/src/package.txt @@ -62,12 +62,13 @@ args = arguments specific to the style :l {no_affinity} values = none {kokkos} args = keyword value ... zero or more keyword/value pairs may be appended - keywords = {neigh} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward} - {neigh} value = {full} or {half} or {n2} or {full/cluster} + keywords = {neigh} or {neigh/qeq} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward} + {neigh} value = {full} or {half} + full = full neighbor list + half = half neighbor list built in thread-safe manner + {neigh/qeq} value = {full} or {half} full = full neighbor list half = half neighbor list built in thread-safe manner - n2 = non-binning neighbor list build, O(N^2) algorithm - full/cluster = full neighbor list with clustered groups of atoms {newton} = {off} or {on} off = set Newton pairwise and bonded flags off (default) on = set Newton pairwise and bonded flags on @@ -392,10 +393,7 @@ default value as listed below. The {neigh} keyword determines how neighbor lists are built. A value of {half} uses a thread-safe variant of half-neighbor lists, -the same as used by most pair styles in LAMMPS. A value of -{n2} uses an O(N^2) algorithm to build the neighbor list without -binning, where N = # of atoms on a processor. It is typically slower -than the other methods, which use binning. +the same as used by most pair styles in LAMMPS. A value of {full} uses a full neighbor lists and is the default. This performs twice as much computation as the {half} option, however that @@ -403,15 +401,9 @@ is often a win because it is thread-safe and doesn't require atomic operations in the calculation of pair forces. For that reason, {full} is the default setting. However, when running in MPI-only mode with 1 thread per MPI task, {half} neighbor lists will typically be faster, -just as it is for non-accelerated pair styles. - -A value of {full/cluster} is an experimental neighbor style, where -particles interact with all particles within a small cluster, if at -least one of the clusters particles is within the neighbor cutoff -range. This potentially allows for better vectorization on -architectures such as the Intel Phi. If also reduces the size of the -neighbor list by roughly a factor of the cluster size, thus reducing -the total memory footprint considerably. +just as it is for non-accelerated pair styles. Similarly, the {neigh/qeq} +keyword determines how neighbor lists are built for "fix qeq/reax/kk"_fix_qeq_reax.html. +If not explicitly set, the value of {neigh/qeq} will match {neigh}. The {newton} keyword sets the Newton flags for pairwise and bonded interactions to {off} or {on}, the same as the "newton"_newton.html @@ -582,9 +574,9 @@ is used. If it is not used, you must invoke the package intel command in your input script or or via the "-pk intel" "command-line switch"_Section_start.html#start_7. -For the KOKKOS package, the option defaults neigh = full, newton = -off, binsize = 0.0, and comm = device. These settings are made -automatically by the required "-k on" "command-line +For the KOKKOS package, the option defaults neigh = full, neigh/qeq + = full, newton = off, binsize = 0.0, and comm = device. These settings + are made automatically by the required "-k on" "command-line switch"_Section_start.html#start_7. You can change them bu using the package kokkos command in your input script or via the "-pk kokkos" "command-line switch"_Section_start.html#start_7. diff --git a/doc/src/pair_bop.txt b/doc/src/pair_bop.txt index 9251fc4e70..2a611e4bd0 100644 --- a/doc/src/pair_bop.txt +++ b/doc/src/pair_bop.txt @@ -137,7 +137,7 @@ and beta_pi,ij)(r_ij). The parameters/coefficients format for the different kinds of BOP files are given below with variables matching the formulation of Ward -("Ward"_#Ward) and Zhou ("Zhou"_#Zhou). Each header line containing a +("Ward"_#Ward) and Zhou ("Zhou"_#Zhou1). Each header line containing a ":" is preceded by a blank line. @@ -258,7 +258,7 @@ Line 2: (A_ij)^(mu*nu) (for e1-e2 and repeats as above) :ul The parameters/coefficients format for the BOP potentials input file containing pre-tabulated functions of g is given below with variables matching the formulation of Ward ("Ward"_#Ward). This format also -assumes the angular functions have the formulation of ("Zhou"_#Zhou). +assumes the angular functions have the formulation of ("Zhou"_#Zhou1). Line 1: # elements N :ul @@ -314,7 +314,7 @@ The rest of the table has the same structure as the previous section The parameters/coefficients format for the BOP potentials input file containing pre-tabulated functions of g is given below with variables matching the formulation of Ward ("Ward"_#Ward). This format also -assumes the angular functions have the formulation of ("Zhou"_#Zhou). +assumes the angular functions have the formulation of ("Zhou"_#Zhou1). Line 1: # elements N :ul @@ -425,5 +425,5 @@ Drautz, and D.G. Pettifor, Phys. Rev. B, 73, 45206 (2006). [(Ward)] D.K. Ward, X.W. Zhou, B.M. Wong, F.P. Doty, and J.A. Zimmerman, Phys. Rev. B, 85,115206 (2012). -:link(Zhou) +:link(Zhou1) [(Zhou)] X.W. Zhou, D.K. Ward, M. Foster (TBP). diff --git a/doc/src/pair_charmm.txt b/doc/src/pair_charmm.txt index 3a1daf6c03..a3c93c7589 100644 --- a/doc/src/pair_charmm.txt +++ b/doc/src/pair_charmm.txt @@ -17,12 +17,14 @@ pair_style lj/charmm/coul/long/opt command :h3 pair_style lj/charmm/coul/long/omp command :h3 pair_style lj/charmm/coul/msm command :h3 pair_style lj/charmm/coul/msm/omp command :h3 +pair_style lj/charmmfsw/coul/charmmfsh command :h3 +pair_style lj/charmmfsw/coul/long command :h3 [Syntax:] pair_style style args :pre -style = {lj/charmm/coul/charmm} or {lj/charmm/coul/charmm/implicit} or {lj/charmm/coul/long} or {lj/charmm/coul/msm} +style = {lj/charmm/coul/charmm} or {lj/charmm/coul/charmm/implicit} or {lj/charmm/coul/long} or {lj/charmm/coul/msm} or {lj/charmmfsw/coul/charmmfsh} or {lj/charmmfsw/coul/long} args = list of arguments for a particular style :ul {lj/charmm/coul/charmm} args = inner outer (inner2) (outer2) inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args) @@ -35,12 +37,20 @@ args = list of arguments for a particular style :ul cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args) {lj/charmm/coul/msm} args = inner outer (cutoff) inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args) + cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args) + {lj/charmmfsw/coul/charmmfsh} args = inner outer (cutoff) + inner, outer = global cutoffs for LJ (and Coulombic if only 2 args) + cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args) + {lj/charmmfsw/coul/long} args = inner outer (cutoff) + inner, outer = global cutoffs for LJ (and Coulombic if only 2 args) cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args) :pre [Examples:] pair_style lj/charmm/coul/charmm 8.0 10.0 pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0 +pair_style lj/charmmfsw/coul/charmmfsh 8.0 10.0 +pair_style lj/charmmfsw/coul/charmmfsh 8.0 10.0 7.0 9.0 pair_coeff * * 100.0 2.0 pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre @@ -51,6 +61,8 @@ pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre pair_style lj/charmm/coul/long 8.0 10.0 pair_style lj/charmm/coul/long 8.0 10.0 9.0 +pair_style lj/charmmfsw/coul/long 8.0 10.0 +pair_style lj/charmmfsw/coul/long 8.0 10.0 9.0 pair_coeff * * 100.0 2.0 pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre @@ -61,21 +73,57 @@ pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre [Description:] -The {lj/charmm} styles compute LJ and Coulombic interactions with an -additional switching function S(r) that ramps the energy and force -smoothly to zero between an inner and outer cutoff. It is a widely -used potential in the "CHARMM"_http://www.scripps.edu/brooks MD code. -See "(MacKerell)"_#pair-MacKerell for a description of the CHARMM force -field. +These pair styles compute Lennard Jones (LJ) and Coulombic +interactions with additional switching or shifting functions that ramp +the energy and/or force smoothly to zero between an inner and outer +cutoff. They are implementations of the widely used CHARMM force +field used in the "CHARMM"_http://www.scripps.edu/brooks MD code (and +others). See "(MacKerell)"_#pair-MacKerell for a description of the +CHARMM force field. + +The styles with {charmm} (not {charmmfsw} or {charmmfsh}) in their +name are the older, original LAMMPS implementations. They compute the +LJ and Coulombic interactions with an energy switching function (esw, +a cubic polynomial, shown in the formula below), which ramps the +energy smoothly to zero between the inner and outer cutoff. This can +cause irregularities in pair-wise forces (due to the discontinuous 2nd +derivative of energy at the boundaries of the switching region), which +in some cases can result in detectable artifacts in an MD simulation. + +The newer styles with {charmmfsw} or {charmmfsh} in their name replace +the energy switching with force switching (fsw) and force shifting +(fsh) functions, for LJ and Coulombic interactions respectively. +These follow the formulas and description given in +"(Steinbach)"_#Steinbach and "(Brooks)"_#Brooks to minimize these +artifacts. + +NOTE: The newer {charmmfsw} or {charmmfsh} styles were released in +March 2017. We recommend they be used instead of the older {charmm} +styles. Eventually code from the new styles will propagate into the +related pair styles (e.g. implicit, accelerator, free energy +variants). + +The general CHARMM formulas are as follows :c,image(Eqs/pair_charmm.jpg) -Both the LJ and Coulombic terms require an inner and outer cutoff. -They can be the same for both formulas or different depending on -whether 2 or 4 arguments are used in the pair_style command. In each -case, the inner cutoff distance must be less than the outer cutoff. -It it typical to make the difference between the 2 cutoffs about 1.0 -Angstrom. +where S(r) is the energy switching function mentioned above for the +{charmm} styles. See the "(Steinbach)"_#Steinbach paper for the +functional forms of the force switching and force shifting functions +used in the {charmmfsw} and {charmmfsh} styles. + +When using the {lj/charmm/coul/charmm styles}, both the LJ and +Coulombic terms require an inner and outer cutoff. They can be the +same for both formulas or different depending on whether 2 or 4 +arguments are used in the pair_style command. For the +{lj/charmmfsw/coul/charmmfsh} style, the LJ term requires both an +inner and outer cutoff, while the Coulombic term requires only one +cutoff. If the Coulomb cutoff is not specified (2 instead of 3 +arguments), the LJ outer cutoff is used for the Coulombic cutoff. In +all cases where an inner and outer cutoff are specified, the inner +cutoff distance must be less than the outer cutoff. It is typical to +make the difference between the inner and outer cutoffs about 2.0 +Angstroms. Style {lj/charmm/coul/charmm/implicit} computes the same formulas as style {lj/charmm/coul/charmm} except that an additional 1/r term is @@ -86,12 +134,18 @@ screening. It is designed for use in a simulation of an unsolvated biomolecule (no explicit water molecules). Styles {lj/charmm/coul/long} and {lj/charmm/coul/msm} compute the same -formulas as style {lj/charmm/coul/charmm} except that an additional -damping factor is applied to the Coulombic term, as described for the -"lj/cut"_pair_lj.html pair styles. Only one Coulombic cutoff is -specified for {lj/charmm/coul/long} and {lj/charmm/coul/msm}; if only -2 arguments are used in the pair_style command, then the outer LJ -cutoff is used as the single Coulombic cutoff. +formulas as style {lj/charmm/coul/charmm} and style +{lj/charmmfsw/coul/long} computes the same formulas as style +{lj/charmmfsw/coul/charmmfsh}, except that an additional damping +factor is applied to the Coulombic term, so it can be used in +conjunction with the "kspace_style"_kspace_style.html command and its +{ewald} or {pppm} or {msm} option. Only one Coulombic cutoff is +specified for these styles; if only 2 arguments are used in the +pair_style command, then the outer LJ cutoff is used as the single +Coulombic cutoff. The Coulombic cutoff specified for these styles +means that pairwise interactions within this distance are computed +directly; interactions outside that distance are computed in +reciprocal space. The following coefficients must be defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in the examples @@ -111,7 +165,7 @@ sigma. The latter 2 coefficients are optional. If they are specified, they are used in the LJ formula between 2 atoms of these types which are also first and fourth atoms in any dihedral. No cutoffs are specified -because this CHARMM force field does not allow varying cutoffs for +because the CHARMM force field does not allow varying cutoffs for individual atom pairs; all pairs use the global cutoff(s) specified in the pair_style command. @@ -148,38 +202,41 @@ mixed. The default mix value is {arithmetic} to coincide with the usual settings for the CHARMM force field. See the "pair_modify" command for details. -None of the lj/charmm pair styles support the +None of the {lj/charmm} or {lj/charmmfsw} pair styles support the "pair_modify"_pair_modify.html shift option, since the Lennard-Jones portion of the pair interaction is smoothed to 0.0 at the cutoff. -The {lj/charmm/coul/long} style supports the -"pair_modify"_pair_modify.html table option since it can tabulate the -short-range portion of the long-range Coulombic interaction. +The {lj/charmm/coul/long} and {lj/charmmfsw/coul/long} styles support +the "pair_modify"_pair_modify.html table option since they can +tabulate the short-range portion of the long-range Coulombic +interaction. -None of the lj/charmm pair styles support the +None of the {lj/charmm} or {lj/charmmfsw} pair styles support the "pair_modify"_pair_modify.html tail option for adding long-range tail corrections to energy and pressure, since the Lennard-Jones portion of the pair interaction is smoothed to 0.0 at the cutoff. -All of the lj/charmm pair styles write their information to "binary -restart files"_restart.html, so pair_style and pair_coeff commands do -not need to be specified in an input script that reads a restart file. +All of the {lj/charmm} and {lj/charmmfsw} pair styles write their +information to "binary restart files"_restart.html, so pair_style and +pair_coeff commands do not need to be specified in an input script +that reads a restart file. -The lj/charmm/coul/long pair style supports the use of the {inner}, -{middle}, and {outer} keywords of the "run_style respa"_run_style.html -command, meaning the pairwise forces can be partitioned by distance at -different levels of the rRESPA hierarchy. The other styles only -support the {pair} keyword of run_style respa. See the -"run_style"_run_style.html command for details. +The {lj/charmm/coul/long} and {lj/charmmfsw/coul/long} pair styles +support the use of the {inner}, {middle}, and {outer} keywords of the +"run_style respa"_run_style.html command, meaning the pairwise forces +can be partitioned by distance at different levels of the rRESPA +hierarchy. The other styles only support the {pair} keyword of +run_style respa. See the "run_style"_run_style.html command for +details. :line [Restrictions:] -The {lj/charmm/coul/charmm} and {lj/charmm/coul/charmm/implicit} -styles are part of the MOLECULE package. The {lj/charmm/coul/long} -style is part of the KSPACE package. They are only enabled if LAMMPS -was built with those packages. See the "Making +All the styles with {coul/charmm} or {coul/charmmfsh} styles are part +of the MOLECULE package. All the styles with {coul/long} style are +part of the KSPACE package. They are only enabled if LAMMPS was built +with those packages. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. Note that the MOLECULE and KSPACE packages are installed by default. @@ -191,6 +248,13 @@ the MOLECULE and KSPACE packages are installed by default. :line +:link(Brooks) +[(Brooks)] Brooks, et al, J Comput Chem, 30, 1545 (2009). + :link(pair-MacKerell) [(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). + +:link(Steinbach) +[(Steinbach)] Steinbach, Brooks, J Comput Chem, 15, 667 (1994). + diff --git a/doc/src/pair_colloid.txt b/doc/src/pair_colloid.txt index 4b78206f12..a0df1d464e 100644 --- a/doc/src/pair_colloid.txt +++ b/doc/src/pair_colloid.txt @@ -39,7 +39,7 @@ where A_cc is the Hamaker constant, a1 and a2 are the radii of the two colloidal particles, and Rc is the cutoff. This equation results from describing each colloidal particle as an integrated collection of Lennard-Jones particles of size sigma and is derived in -"(Everaers)"_#Everaers. +"(Everaers)"_#Everaers1. The colloid-solvent interaction energy is given by @@ -201,5 +201,5 @@ only per-type polydispersity is enabled via the pair_coeff parameters. :line -:link(Everaers) +:link(Everaers1) [(Everaers)] Everaers, Ejtehadi, Phys Rev E, 67, 041710 (2003). diff --git a/doc/src/pair_comb.txt b/doc/src/pair_comb.txt index 92e74bbba3..3a2f380bfa 100644 --- a/doc/src/pair_comb.txt +++ b/doc/src/pair_comb.txt @@ -50,7 +50,7 @@ atoms {i} and {j}, The COMB potentials (styles {comb} and {comb3}) are variable charge potentials. The equilibrium charge on each atom is calculated by the -electronegativity equalization (QEq) method. See "Rick"_#Rick for +electronegativity equalization (QEq) method. See "Rick"_#Rick2 for further details. This is implemented by the "fix qeq/comb"_fix_qeq_comb.html command, which should normally be specified in the input script when running a model with the COMB @@ -187,6 +187,6 @@ S. R. Phillpot, Phys. Rev. B 81, 125328 (2010) Y. Li, Z. Lu, S. R. Phillpot, and S. B. Sinnott, Mat. Sci. & Eng: R 74, 255-279 (2013). -:link(Rick) +:link(Rick2) [(Rick)] S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141 (1994). diff --git a/doc/src/pair_coul.txt b/doc/src/pair_coul.txt index 43bd13127a..4a601e90c0 100644 --- a/doc/src/pair_coul.txt +++ b/doc/src/pair_coul.txt @@ -109,7 +109,7 @@ mimic the screening effect of a polar solvent. :line Style {coul/dsf} computes Coulombic interactions via the damped -shifted force model described in "Fennell"_#Fennell, given by: +shifted force model described in "Fennell"_#Fennell1, given by: :c,image(Eqs/pair_coul_dsf.jpg) @@ -122,7 +122,7 @@ decay to zero. :line Style {coul/wolf} computes Coulombic interactions via the Wolf -summation method, described in "Wolf"_#Wolf, given by: +summation method, described in "Wolf"_#Wolf1, given by: :c,image(Eqs/pair_coul_wolf.jpg) @@ -143,7 +143,7 @@ interactions with a short-range potential. Style {coul/streitz} is the Coulomb pair interaction defined as part of the Streitz-Mintmire potential, as described in "this -paper"_#Streitz, in which charge distribution about an atom is modeled +paper"_#Streitz2, in which charge distribution about an atom is modeled as a Slater 1{s} orbital. More details can be found in the referenced paper. To fully reproduce the published Streitz-Mintmire potential, which is a variable charge potential, style {coul/streitz} must be @@ -205,7 +205,7 @@ added for the "core/shell model"_Section_howto.html#howto_25 to allow charges on core and shell particles to be separated by r = 0.0. Styles {tip4p/cut} and {tip4p/long} implement the coulomb part of -the TIP4P water model of "(Jorgensen)"_#Jorgensen, which introduces +the TIP4P water model of "(Jorgensen)"_#Jorgensen3, which introduces a massless site located a short distance away from the oxygen atom along the bisector of the HOH angle. The atomic types of the oxygen and hydrogen atoms, the bond and angle types for OH and HOH interactions, @@ -325,14 +325,18 @@ hybrid/overlay"_pair_hybrid.html, "kspace_style"_kspace_style.html :line -:link(Wolf) +:link(Wolf1) [(Wolf)] D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem Phys, 110, 8254 (1999). -:link(Fennell) +:link(Fennell1) [(Fennell)] C. J. Fennell, J. D. Gezelter, J Chem Phys, 124, 234104 (2006). -:link(Streitz) +:link(Streitz2) [(Streitz)] F. H. Streitz, J. W. Mintmire, Phys Rev B, 50, 11996-12003 (1994). + +:link(Jorgensen3) +[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem +Phys, 79, 926 (1983). diff --git a/doc/src/pair_coul_diel.txt b/doc/src/pair_coul_diel.txt index fc2042a901..f651cb4b5e 100644 --- a/doc/src/pair_coul_diel.txt +++ b/doc/src/pair_coul_diel.txt @@ -46,10 +46,10 @@ for water at 298K. Examples of the use of this type of Coulomb interaction include implicit solvent simulations of salt ions -"(Lenart)"_#Lenart and of ionic surfactants "(Jusufi)"_#Jusufi. +"(Lenart)"_#Lenart1 and of ionic surfactants "(Jusufi)"_#Jusufi1. Note that this potential is only reasonable for implicit solvent simulations and in combination with coul/cut or coul/long. It is also usually combined -with gauss/cut, see "(Lenart)"_#Lenart or "(Jusufi)"_#Jusufi. +with gauss/cut, see "(Lenart)"_#Lenart1 or "(Jusufi)"_#Jusufi1. The following coefficients must be defined for each pair of atom types via the "pair_coeff"_pair_coeff.html command as in the example @@ -103,10 +103,10 @@ LAMMPS"_Section_start.html#start_2_3 section for more info. [(Stiles)] Stiles , Hubbard, and Kayser, J Chem Phys, 77, 6189 (1982). -:link(Lenart) +:link(Lenart1) [(Lenart)] Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126, 044509 (2007). -:link(Jusufi) +:link(Jusufi1) [(Jusufi)] Jusufi, Hynninen, and Panagiotopoulos, J Phys Chem B, 112, 13783 (2008). diff --git a/doc/src/pair_cs.txt b/doc/src/pair_cs.txt index 3e1390049a..64dfc20d47 100644 --- a/doc/src/pair_cs.txt +++ b/doc/src/pair_cs.txt @@ -44,7 +44,7 @@ pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre [Description:] These pair styles are designed to be used with the adiabatic -core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham. See +core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham2. See "Section 6.25"_Section_howto.html#howto_25 of the manual for an overview of the model as implemented in LAMMPS. @@ -95,6 +95,6 @@ LAMMPS"_Section_start.html#start_3 section for more info. :line -:link(MitchellFinchham) +:link(MitchellFinchham2) [(Mitchell and Finchham)] Mitchell, Finchham, J Phys Condensed Matter, 5, 1031-1038 (1993). diff --git a/doc/src/pair_dipole.txt b/doc/src/pair_dipole.txt index bcf482cda5..a9622b32fd 100644 --- a/doc/src/pair_dipole.txt +++ b/doc/src/pair_dipole.txt @@ -69,7 +69,7 @@ distance, and the vector r = Ri - Rj is the separation vector between the two particles. Note that Eqq and Fqq are simply Coulombic energy and force, Fij = -Fji as symmetric forces, and Tij != -Tji since the torques do not act symmetrically. These formulas are discussed in -"(Allen)"_#Allen and in "(Toukmaji)"_#Toukmaji. +"(Allen)"_#Allen2 and in "(Toukmaji)"_#Toukmaji2. Style {lj/sf/dipole/sf} computes "shifted-force" interactions between pairs of particles that each have a charge and/or a point dipole @@ -77,7 +77,7 @@ moment. In general, a shifted-force potential is a (sligthly) modified potential containing extra terms that make both the energy and its derivative go to zero at the cutoff distance; this removes (cutoff-related) problems in energy conservation and any numerical -instability in the equations of motion "(Allen)"_#Allen. Shifted-force +instability in the equations of motion "(Allen)"_#Allen2. Shifted-force interactions for the Lennard-Jones (E_LJ), charge-charge (Eqq), charge-dipole (Eqp), dipole-charge (Epq) and dipole-dipole (Epp) potentials are computed by these formulas for the energy (E), force @@ -95,11 +95,11 @@ and force, Fij = -Fji as symmetric forces, and Tij != -Tji since the torques do not act symmetrically. The shifted-force formula for the Lennard-Jones potential is reported in "(Stoddard)"_#Stoddard. The original (unshifted) formulas for the electrostatic potentials, forces -and torques can be found in "(Price)"_#Price. The shifted-force +and torques can be found in "(Price)"_#Price2. The shifted-force electrostatic potentials have been obtained by applying equation 5.13 -of "(Allen)"_#Allen. The formulas for the corresponding forces and +of "(Allen)"_#Allen2. The formulas for the corresponding forces and torques have been obtained by applying the 'chain rule' as in appendix -C.3 of "(Allen)"_#Allen. +C.3 of "(Allen)"_#Allen2. If one cutoff is specified in the pair_style command, it is used for both the LJ and Coulombic (q,p) terms. If two cutoffs are specified, @@ -110,7 +110,7 @@ scaled according to this factor. This scale factor is also made available for use with fix adapt. Style {lj/cut/dipole/long} computes long-range point-dipole -interactions as discussed in "(Toukmaji)"_#Toukmaji. Dipole-dipole, +interactions as discussed in "(Toukmaji)"_#Toukmaji2. Dipole-dipole, dipole-charge, and charge-charge interactions are all supported, along with the standard 12/6 Lennard-Jones interactions, which are computed with a cutoff. A "kspace_style"_kspace_style.html must be defined to @@ -119,7 +119,7 @@ ewald/disp"_kspace_style.html support long-range point-dipole interactions. Style {lj/long/dipole/long} also computes point-dipole interactions as -discussed in "(Toukmaji)"_#Toukmaji. Long-range dipole-dipole, +discussed in "(Toukmaji)"_#Toukmaji2. Long-range dipole-dipole, dipole-charge, and charge-charge interactions are all supported, along with the standard 12/6 Lennard-Jones interactions. LJ interactions can be cutoff or long-ranged. @@ -252,16 +252,16 @@ currently supported. :line -:link(Allen) +:link(Allen2) [(Allen)] Allen and Tildesley, Computer Simulation of Liquids, Clarendon Press, Oxford, 1987. -:link(Toukmaji) +:link(Toukmaji2) [(Toukmaji)] Toukmaji, Sagui, Board, and Darden, J Chem Phys, 113, 10913 (2000). :link(Stoddard) [(Stoddard)] Stoddard and Ford, Phys Rev A, 8, 1504 (1973). -:link(Price) +:link(Price2) [(Price)] Price, Stone and Alderton, Mol Phys, 52, 987 (1984). diff --git a/doc/src/pair_dpd_fdt.txt b/doc/src/pair_dpd_fdt.txt index ffd138ddbd..b75e7c323c 100644 --- a/doc/src/pair_dpd_fdt.txt +++ b/doc/src/pair_dpd_fdt.txt @@ -37,7 +37,7 @@ Styles {dpd/fdt} and {dpd/fdt/energy} compute the force for dissipative particle dynamics (DPD) simulations. The {dpd/fdt} style is used to perform DPD simulations under isothermal and isobaric conditions, while the {dpd/fdt/energy} style is used to perform DPD simulations -under isoenergetic and isoenthalpic conditions (see "(Lisal)"_#Lisal). +under isoenergetic and isoenthalpic conditions (see "(Lisal)"_#Lisal3). For DPD simulations in general, the force on atom I due to atom J is given as a sum of 3 terms @@ -111,7 +111,7 @@ calculated using only the conservative term. The forces computed through the {dpd/fdt} and {dpd/fdt/energy} styles can be integrated with the velocity-Verlet integration scheme or the -Shardlow splitting integration scheme described by "(Lisal)"_#Lisal. +Shardlow splitting integration scheme described by "(Lisal)"_#Lisal3. In the cases when these pair styles are combined with the "fix shardlow"_fix_shardlow.html, these pair styles differ from the other dpd styles in that the dissipative and random forces are split @@ -147,7 +147,7 @@ energies and temperatures. :line -:link(Lisal) +:link(Lisal3) [(Lisal)] M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative particle dynamics at isothermal, isobaric, isoenergetic, and isoenthalpic conditions using Shardlow-like splitting algorithms.", diff --git a/doc/src/pair_eim.txt b/doc/src/pair_eim.txt index e74bb364d4..3f068d4040 100644 --- a/doc/src/pair_eim.txt +++ b/doc/src/pair_eim.txt @@ -25,7 +25,7 @@ pair_coeff * * Na Cl ../potentials/ffield.eim Cl NULL Na :pre [Description:] Style {eim} computes pairwise interactions for ionic compounds -using embedded-ion method (EIM) potentials "(Zhou)"_#Zhou. The +using embedded-ion method (EIM) potentials "(Zhou)"_#Zhou2. The energy of the system E is given by :c,image(Eqs/pair_eim1.jpg) @@ -169,6 +169,6 @@ LAMMPS was built with that package. :line -:link(Zhou) +:link(Zhou2) [(Zhou)] Zhou, submitted for publication (2010). Please contact Xiaowang Zhou (Sandia) for details via email at xzhou at sandia.gov. diff --git a/doc/src/pair_gauss.txt b/doc/src/pair_gauss.txt index 8f64122866..92d8b51d8b 100644 --- a/doc/src/pair_gauss.txt +++ b/doc/src/pair_gauss.txt @@ -59,8 +59,8 @@ between pairs of particles: where H determines together with the standard deviation sigma_h the peak height of the Gaussian function, and r_mh the peak position. Examples of the use of the Gaussian potentials include implicit -solvent simulations of salt ions "(Lenart)"_#Lenart and of surfactants -"(Jusufi)"_#Jusufi. In these instances the Gaussian potential mimics +solvent simulations of salt ions "(Lenart)"_#Lenart2 and of surfactants +"(Jusufi)"_#Jusufi2. In these instances the Gaussian potential mimics the hydration barrier between a pair of particles. The hydration barrier is located at r_mh and has a width of sigma_h. The prefactor determines the height of the potential barrier. @@ -178,11 +178,11 @@ LAMMPS"_Section_start.html#start_3 section for more info. [Default:] none -:link(Lenart) +:link(Lenart2) [(Lenart)] Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126, 044509 (2007). -:link(Jusufi) +:link(Jusufi2) [(Jusufi)] Jusufi, Hynninen, and Panagiotopoulos, J Phys Chem B, 112, 13783 (2008). diff --git a/doc/src/pair_gayberne.txt b/doc/src/pair_gayberne.txt index b6171ef93e..8639f220a4 100644 --- a/doc/src/pair_gayberne.txt +++ b/doc/src/pair_gayberne.txt @@ -44,12 +44,12 @@ a particle as "spherical"). For large uniform molecules it has been shown that the energy parameters are approximately representable in terms of local contact -curvatures "(Everaers)"_#Everaers: +curvatures "(Everaers)"_#Everaers2: :c,image(Eqs/pair_gayberne2.jpg) The variable names utilized as potential parameters are for the most -part taken from "(Everaers)"_#Everaers in order to be consistent with +part taken from "(Everaers)"_#Everaers2 in order to be consistent with the "RE-squared pair potential"_pair_resquared.html. Details on the upsilon and mu parameters are given "here"_PDF/pair_resquared_extra.pdf. @@ -203,7 +203,7 @@ spherical particles, or point particles. Spherical particles have all all 3 of their shape parameters equal to 0.0. The Gay-Berne potential does not become isotropic as r increases -"(Everaers)"_#Everaers. The distance-of-closest-approach +"(Everaers)"_#Everaers2. The distance-of-closest-approach approximation used by LAMMPS becomes less accurate when high-aspect ratio ellipsoids are used. @@ -217,7 +217,7 @@ resquared"_pair_resquared.html :line -:link(Everaers) +:link(Everaers2) [(Everaers)] Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003). :link(Berardi) @@ -227,5 +227,5 @@ Berardi, Muccioli, Zannoni, J Chem Phys, 128, 024905 (2008). :link(Perram) [(Perram)] Perram and Rasmussen, Phys Rev E, 54, 6565-6572 (1996). -:link(Allen) +:link(Allen3) [(Allen)] Allen and Germano, Mol Phys 104, 3225-3235 (2006). diff --git a/doc/src/pair_gran.txt b/doc/src/pair_gran.txt index 373a82fa80..62a58b3504 100644 --- a/doc/src/pair_gran.txt +++ b/doc/src/pair_gran.txt @@ -45,7 +45,7 @@ pair_style gran/hooke 200000.0 70000.0 50.0 30.0 0.5 0 :pre The {gran} styles use the following formulas for the frictional force between two granular particles, as described in "(Brilliantov)"_#Brilliantov, "(Silbert)"_#Silbert, and -"(Zhang)"_#Zhang, when the distance r between two particles of radii +"(Zhang)"_#Zhang3, when the distance r between two particles of radii Ri and Rj is less than their contact distance d = Ri + Rj. There is no force between the particles when r > d. @@ -115,7 +115,7 @@ gamma_t is in units of (1/(time*distance)). Note that in the Hookean case, Kn can be thought of as a linear spring constant with units of force/distance. In the Hertzian case, Kn is like a non-linear spring constant with units of force/area or -pressure, and as shown in the "(Zhang)"_#Zhang paper, Kn = 4G / +pressure, and as shown in the "(Zhang)"_#Zhang3 paper, Kn = 4G / (3(1-nu)) where nu = the Poisson ratio, G = shear modulus = E / (2(1+nu)), and E = Young's modulus. Similarly, Kt = 4G / (2-nu). (NOTE: in an earlier version of the manual, we incorrectly stated that @@ -267,5 +267,5 @@ p 5382-5392 (1996). [(Silbert)] Silbert, Ertas, Grest, Halsey, Levine, Plimpton, Phys Rev E, 64, p 051302 (2001). -:link(Zhang) +:link(Zhang3) [(Zhang)] Zhang and Makse, Phys Rev E, 72, p 011301 (2005). diff --git a/doc/src/pair_kolmogorov_crespi_z.txt b/doc/src/pair_kolmogorov_crespi_z.txt index a7bd917caa..0879dc34d0 100644 --- a/doc/src/pair_kolmogorov_crespi_z.txt +++ b/doc/src/pair_kolmogorov_crespi_z.txt @@ -67,6 +67,6 @@ LAMMPS"_Section_start.html#start_3 section for more info. :link(KC05) [(KC05)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005) -:link(vanWijk) -[(vanWijk)] M. M. van Wijk, A. Schuring, M. I. Katsnelson, and A. Fasolino, +:link(vanWijk) +[(vanWijk)] M. M. van Wijk, A. Schuring, M. I. Katsnelson, and A. Fasolino, Physical Review Letters, 113, 135504 (2014) diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt index fdc0b133dd..5c8e31ac42 100644 --- a/doc/src/pair_lj.txt +++ b/doc/src/pair_lj.txt @@ -149,7 +149,7 @@ where kappa is the inverse of the Debye length. This potential is another way to mimic the screening effect of a polar solvent. Style {lj/cut/coul/dsf} computes the Coulombic term via the damped -shifted force model described in "Fennell"_#Fennell, given by: +shifted force model described in "Fennell"_#Fennell2, given by: :c,image(Eqs/pair_coul_dsf.jpg) @@ -180,7 +180,7 @@ model"_Section_howto.html#howto_25 to allow charges on core and shell particles to be separated by r = 0.0. Styles {lj/cut/tip4p/cut} and {lj/cut/tip4p/long} implement the TIP4P -water model of "(Jorgensen)"_#Jorgensen, which introduces a massless +water model of "(Jorgensen)"_#Jorgensen2, which introduces a massless site located a short distance away from the oxygen atom along the bisector of the HOH angle. The atomic types of the oxygen and hydrogen atoms, the bond and angle types for OH and HOH interactions, @@ -311,10 +311,10 @@ installed by default. :line -:link(Jorgensen) +:link(Jorgensen2) [(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem Phys, 79, 926 (1983). -:link(Fennell) +:link(Fennell2) [(Fennell)] C. J. Fennell, J. D. Gezelter, J Chem Phys, 124, 234104 (2006). diff --git a/doc/src/pair_lj_cubic.txt b/doc/src/pair_lj_cubic.txt index e768ac4fba..d33e3ec09b 100644 --- a/doc/src/pair_lj_cubic.txt +++ b/doc/src/pair_lj_cubic.txt @@ -42,7 +42,7 @@ A3*rmin^3/epsilon = 27.93... is given in the paper by Holian and Ravelo "(Holian)"_#Holian. This potential is commonly used to study the shock mechanics of FCC -solids, as in Ravelo et al. "(Ravelo)"_#Ravelo. +solids, as in Ravelo et al. "(Ravelo)"_#Ravelo2. The following coefficients must be defined for each pair of atom types via the "pair_coeff"_pair_coeff.html command as in the example above, @@ -125,5 +125,5 @@ support the {inner}, {middle}, {outer} keywords. :link(Holian) [(Holian)] Holian and Ravelo, Phys Rev B, 51, 11275 (1995). -:link(Ravelo) +:link(Ravelo2) [(Ravelo)] Ravelo, Holian, Germann and Lomdahl, Phys Rev B, 70, 014103 (2004). diff --git a/doc/src/pair_lj_long.txt b/doc/src/pair_lj_long.txt index 517bb3d20b..d559871f9d 100644 --- a/doc/src/pair_lj_long.txt +++ b/doc/src/pair_lj_long.txt @@ -72,12 +72,12 @@ used as cutoffs for the LJ and Coulombic terms respectively. The purpose of this pair style is to capture long-range interactions resulting from both attractive 1/r^6 Lennard-Jones and Coulombic 1/r interactions. This is done by use of the {flag_lj} and {flag_coul} -settings. The "In 't Veld"_#Veld paper has more details on when it is +settings. The "In 't Veld"_#Veld2 paper has more details on when it is appropriate to include long-range 1/r^6 interactions, using this potential. Style {lj/long/tip4p/long} implements the TIP4P water model of -"(Jorgensen)"_#Jorgensen, which introduces a massless site located a +"(Jorgensen)"_#Jorgensen4, which introduces a massless site located a short distance away from the oxygen atom along the bisector of the HOH angle. The atomic types of the oxygen and hydrogen atoms, the bond and angle types for OH and HOH interactions, and the distance to the @@ -221,5 +221,9 @@ the KSPACE package is installed by default. :line -:link(Veld) +:link(Veld2) [(In 't Veld)] In 't Veld, Ismail, Grest, J Chem Phys (accepted) (2007). + +:link(Jorgensen4) +[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem +Phys, 79, 926 (1983). diff --git a/doc/src/pair_lubricate.txt b/doc/src/pair_lubricate.txt index daa2e37b68..501a043801 100644 --- a/doc/src/pair_lubricate.txt +++ b/doc/src/pair_lubricate.txt @@ -41,7 +41,7 @@ Styles {lubricate} and {lubricate/poly} compute hydrodynamic interactions between mono-disperse finite-size spherical particles in a pairwise fashion. The interactions have 2 components. The first is Ball-Melrose lubrication terms via the formulas in "(Ball and -Melrose)"_#Ball +Melrose)"_#Ball1 :c,image(Eqs/pair_lubricate.jpg) @@ -70,7 +70,7 @@ computed. Using a {cutoff} less than 3 radii is recommended if {flaglog} is set to 1. The other component is due to the Fast Lubrication Dynamics (FLD) -approximation, described in "(Kumar)"_#Kumar, which can be +approximation, described in "(Kumar)"_#Kumar1, which can be represented by the following equation :c,image(Eqs/fld.jpg) @@ -217,10 +217,10 @@ The default settings for the optional args are flagHI = 1 and flagVF = :line -:link(Ball) +:link(Ball1) [(Ball)] Ball and Melrose, Physica A, 247, 444-472 (1997). -:link(Kumar) +:link(Kumar1) [(Kumar)] Kumar and Higdon, Phys Rev E, 82, 051401 (2010). See also his thesis for more details: A. Kumar, "Microscale Dynamics in Suspensions of Non-spherical Particles", Thesis, University of diff --git a/doc/src/pair_lubricateU.txt b/doc/src/pair_lubricateU.txt index 52e63ac350..720a8539b8 100644 --- a/doc/src/pair_lubricateU.txt +++ b/doc/src/pair_lubricateU.txt @@ -37,7 +37,7 @@ other types of interactions. The interactions have 2 components. The first is Ball-Melrose lubrication terms via the formulas in "(Ball and -Melrose)"_#Ball +Melrose)"_#Ball2 :c,image(Eqs/pair_lubricate.jpg) @@ -67,7 +67,7 @@ computed. Using a {cutoff} less than 3 radii is recommended if {flaglog} is set to 1. The other component is due to the Fast Lubrication Dynamics (FLD) -approximation, described in "(Kumar)"_#Kumar. The equation being +approximation, described in "(Kumar)"_#Kumar2. The equation being solved to balance the forces and torques is :c,image(Eqs/fld2.jpg) @@ -211,8 +211,8 @@ The default settings for the optional args are flagHI = 1 and flagVF = :line -:link(Ball) +:link(Ball2) [(Ball)] Ball and Melrose, Physica A, 247, 444-472 (1997). -:link(Kumar) +:link(Kumar2) [(Kumar)] Kumar and Higdon, Phys Rev E, 82, 051401 (2010). diff --git a/doc/src/pair_meam.txt b/doc/src/pair_meam.txt index 318f22067f..4fcb7a2e6c 100644 --- a/doc/src/pair_meam.txt +++ b/doc/src/pair_meam.txt @@ -259,7 +259,7 @@ The augt1 parameter is related to modifications in the MEAM formulation of the partial electron density function. In recent literature, an extra term is included in the expression for the third-order density in order to make the densities orthogonal (see for -example "(Wang)"_#Wang, equation 3d); this term is included in the +example "(Wang)"_#Wang2, equation 3d); this term is included in the MEAM implementation in lammps. However, in earlier published work this term was not included when deriving parameters, including most of those provided in the library.meam file included with lammps, and to @@ -363,7 +363,7 @@ This report may be accessed on-line via "this link"_sandreport. :link(Valone) [(Valone)] Valone, Baskes, Martin, Phys. Rev. B, 73, 214209 (2006). -:link(Wang) +:link(Wang2) [(Wang)] Wang, Van Hove, Ross, Baskes, J. Chem. Phys., 121, 5410 (2004). :link(ZBL) diff --git a/doc/src/pair_meam_spline.txt b/doc/src/pair_meam_spline.txt index 08e53cb38c..a02125a6d9 100644 --- a/doc/src/pair_meam_spline.txt +++ b/doc/src/pair_meam_spline.txt @@ -23,7 +23,7 @@ pair_coeff * * Ti.meam.spline Ti Ti Ti :pre The {meam/spline} style computes pairwise interactions for metals using a variant of modified embedded-atom method (MEAM) potentials -"(Lenosky)"_#Lenosky. The total energy E is given by +"(Lenosky)"_#Lenosky1. The total energy E is given by :c,image(Eqs/pair_meam_spline.jpg) @@ -138,7 +138,7 @@ for more info. :line -:link(Lenosky) +:link(Lenosky1) [(Lenosky)] Lenosky, Sadigh, Alonso, Bulatov, de la Rubia, Kim, Voter, Kress, Modelling Simulation Materials Science Engineering, 8, 825 (2000). diff --git a/doc/src/pair_meam_sw_spline.txt b/doc/src/pair_meam_sw_spline.txt index fa80854ed8..fa731799dd 100644 --- a/doc/src/pair_meam_sw_spline.txt +++ b/doc/src/pair_meam_sw_spline.txt @@ -23,8 +23,8 @@ pair_coeff * * Ti.meam.sw.spline Ti Ti Ti :pre The {meam/sw/spline} style computes pairwise interactions for metals using a variant of modified embedded-atom method (MEAM) potentials -"(Lenosky)"_#Lenosky with an additional Stillinger-Weber (SW) term -"(Stillinger)"_#Stillinger in the energy. This form of the potential +"(Lenosky)"_#Lenosky2 with an additional Stillinger-Weber (SW) term +"(Stillinger)"_#Stillinger1 in the energy. This form of the potential was first proposed by Nicklas, Fellinger, and Park "(Nicklas)"_#Nicklas. We refer to it as MEAM+SW. The total energy E is given by @@ -123,11 +123,11 @@ See the "Making LAMMPS"_Section_start.html#start_3 section for more info. :line -:link(Lenosky) +:link(Lenosky2) [(Lenosky)] Lenosky, Sadigh, Alonso, Bulatov, de la Rubia, Kim, Voter, Kress, Modell. Simul. Mater. Sci. Eng. 8, 825 (2000). -:link(Stillinger) +:link(Stillinger1) [(Stillinger)] Stillinger, Weber, Phys. Rev. B 31, 5262 (1985). :link(Nicklas) diff --git a/doc/src/pair_modify.txt b/doc/src/pair_modify.txt index 8a4f291583..03fb80ae5e 100644 --- a/doc/src/pair_modify.txt +++ b/doc/src/pair_modify.txt @@ -112,7 +112,7 @@ see the doc page for individual styles to see which potentials support these options. If N is non-zero, a table of length 2^N is pre-computed for forces and energies, which can shrink their computational cost by up to a factor of 2. The table is indexed via a -bit-mapping technique "(Wolff)"_#Wolff and a linear interpolation is +bit-mapping technique "(Wolff)"_#Wolff1 and a linear interpolation is performed between adjacent table values. In our experiments with different table styles (lookup, linear, spline), this method typically gave the best performance in terms of speed and accuracy. @@ -253,7 +253,7 @@ mixing. See the doc pages for individual pair styles for details. :line -:link(Wolff) +:link(Wolff1) [(Wolff)] Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999). :link(Sun) diff --git a/doc/src/pair_momb.txt b/doc/src/pair_momb.txt new file mode 100644 index 0000000000..77c4f184d9 --- /dev/null +++ b/doc/src/pair_momb.txt @@ -0,0 +1,71 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +pair_style momb command :h3 + +[Syntax:] + +pair_style momb cutoff s6 d :pre + +cutoff = global cutoff (distance units) +s6 = global scaling factor of the exchange-correlation functional used (unitless) +d = damping scaling factor of Grimme's method (unitless) :ul + +[Examples:] + +pair_style momb 12.0 0.75 20.0 +pair_style hybrid/overlay eam/fs lj/charmm/coul/long 10.0 12.0 momb 12.0 0.75 20.0 morse 5.5 :pre + +pair_coeff 1 2 momb 0.0 1.0 1.0 10.2847 2.361 :pre + +[Description:] + +Style {momb} computes pairwise van der Waals (vdW) and short-range +interactions using the Morse potential and "(Grimme)"_#Grimme method +implemented in the Many-Body Metal-Organic (MOMB) force field +described comprehensively in "(Fichthorn)"_#Fichthorn and +"(Zhou)"_#Zhou4. Grimme's method is widely used to correct for +dispersion in density functional theory calculations. + +:c,image(Eqs/pair_momb.jpg) + +For the {momb} pair style, the following coefficients must be defined +for each pair of atoms types via the "pair_coeff"_pair_coeff.html +command as in the examples above, or in the data file or restart files +read by the "read_data"_read_data.html as described below: + +D0 (energy units) +alpha (1/distance units) +r0 (distance units) +C6 (energy*distance^6 units) +Rr (distance units, typically sum of atomic vdW radii) :ul + +:line + +[Restrictions:] + +This style is part of the USER-MISC package. It is only enabled if +LAMMPS is built with that package. See the "Making of +LAMMPS"_Section_start.html#start_3 section for more info. + +[Related commands:] + +"pair_coeff"_pair_coeff.html, "pair_style morse"_pair_morse.html + +[Default:] none + +:line + +:link(Grimme) +[(Grimme)] Grimme, J Comput Chem, 27(15), 1787-1799 (2006). + +:link(Fichthorn) +[(Fichthorn)] Fichthorn, Balankura, Qi, CrystEngComm, 18(29), 5410-5417 (2016). + +:link(Zhou4) +[(Zhou)] Zhou, Saidi, Fichthorn, J Phys Chem C, 118(6), 3366-3374 (2014). diff --git a/doc/src/pair_multi_lucy.txt b/doc/src/pair_multi_lucy.txt index 4978ebfeca..38fd1ede4a 100644 --- a/doc/src/pair_multi_lucy.txt +++ b/doc/src/pair_multi_lucy.txt @@ -23,8 +23,8 @@ pair_coeff * * multibody.table ENTRY1 7.0 :pre [Description:] Style {multi/lucy} computes a density-dependent force following from -the many-body form described in "(Moore)"_#Moore and -"(Warren)"_#Warren as +the many-body form described in "(Moore)"_#Moore1 and +"(Warren)"_#Warren1 as :c,image(Eqs/pair_multi_lucy.jpg) @@ -38,8 +38,8 @@ The density-dependent energy for a given particle is given by: :c,image(Eqs/pair_multi_lucy_energy.jpg) -See the supporting information of "(Brennan)"_#Brennan or the -publication by "(Moore)"_#Moore for more details on the functional +See the supporting information of "(Brennan)"_#Brennan1 or the +publication by "(Moore)"_#Moore1 for more details on the functional form. An interpolation table is used to evaluate the density-dependent @@ -188,12 +188,12 @@ LAMMPS"_Section_start.html#start_3 section for more info. :line -:link(Warren) +:link(Warren1) [(Warren)] Warren, Phys Rev E, 68, 066702 (2003). -:link(Brennan) +:link(Brennan1) [(Brennan)] Brennan, J Chem Phys Lett, 5, 2144-2149 (2014). -:link(Moore) +:link(Moore1) [(Moore)] Moore, J Chem Phys, 144, 104501 (2016). diff --git a/doc/src/pair_multi_lucy_rx.txt b/doc/src/pair_multi_lucy_rx.txt index 75547a71ce..bf5d5636fe 100644 --- a/doc/src/pair_multi_lucy_rx.txt +++ b/doc/src/pair_multi_lucy_rx.txt @@ -33,8 +33,8 @@ equations through the "fix rx"_fix_rx.html command. The species of one CG particle can interact with a species in a neighboring CG particle through a site-site interaction potential model. Style {multi/lucy/rx} computes the site-site density-dependent force -following from the many-body form described in "(Moore)"_#Moore and -"(Warren)"_#Warren as +following from the many-body form described in "(Moore)"_#Moore2 and +"(Warren)"_#Warren2 as :c,image(Eqs/pair_multi_lucy.jpg) @@ -48,8 +48,8 @@ The density-dependent energy for a given particle is given by: :c,image(Eqs/pair_multi_lucy_energy.jpg) -See the supporting information of "(Brennan)"_#Brennan or the -publication by "(Moore)"_#Moore for more details on the functional +See the supporting information of "(Brennan)"_#Brennan2 or the +publication by "(Moore)"_#Moore2 for more details on the functional form. An interpolation table is used to evaluate the density-dependent @@ -214,12 +214,12 @@ LAMMPS"_Section_start.html#start_3 section for more info. :line -:link(Warren) +:link(Warren2) [(Warren)] Warren, Phys Rev E, 68, 066702 (2003). -:link(Brennan) +:link(Brennan2) [(Brennan)] Brennan, J Chem Phys Lett, 5, 2144-2149 (2014). -:link(Moore) +:link(Moore2) [(Moore)] Moore, J Chem Phys, 144, 104501 (2016). diff --git a/doc/src/pair_oxdna.txt b/doc/src/pair_oxdna.txt index 0a07417fd0..61456259c2 100644 --- a/doc/src/pair_oxdna.txt +++ b/doc/src/pair_oxdna.txt @@ -62,8 +62,13 @@ When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html the temperature coefficients have to be matched to the one used in the fix. +<<<<<<< HEAD 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, +======= +Example input and data files can be found in examples/USER/cgdna/examples/duplex1/ and /duplex2/. +A simple python setup tool which creates single straight or helical DNA strands, +>>>>>>> master DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. A technical report with more information on the model, the structure of the input file, the setup tool and the performance of the LAMMPS-implementation of oxDNA diff --git a/doc/src/pair_polymorphic.txt b/doc/src/pair_polymorphic.txt index 1e75518273..c088e8bb22 100644 --- a/doc/src/pair_polymorphic.txt +++ b/doc/src/pair_polymorphic.txt @@ -25,7 +25,7 @@ pair_coeff * * GaN_sw.polymorphic GaN :pre [Description:] The {polymorphic} pair style computes a 3-body free-form potential -("Zhou"_#Zhou) for the energy E of a system of atoms as +("Zhou"_#Zhou3) for the energy E of a system of atoms as :c,image(Eqs/polymorphic1.jpg) :c,image(Eqs/polymorphic2.jpg) @@ -52,18 +52,18 @@ to Stillinger-Weber potential ("SW"_#SW) if we set :c,image(Eqs/polymorphic4.jpg) The potential reduces to Tersoff types of potential -("Tersoff"_#Tersoff or "Albe"_#Albe) if we set +("Tersoff"_#Tersoff or "Albe"_#poly-Albe) if we set :c,image(Eqs/polymorphic5.jpg) :c,image(Eqs/polymorphic6.jpg) -The potential reduces to Rockett-Tersoff ("Wang"_#Wang) type if we set +The potential reduces to Rockett-Tersoff ("Wang"_#Wang3) type if we set :c,image(Eqs/polymorphic7.jpg) :c,image(Eqs/polymorphic6.jpg) :c,image(Eqs/polymorphic8.jpg) -The potential becomes embedded atom method ("Daw"_#Daw) if we set +The potential becomes embedded atom method ("Daw"_#poly-Daw) if we set :c,image(Eqs/polymorphic9.jpg) @@ -208,7 +208,7 @@ files. :line -:link(Zhou) +:link(Zhou3) [(Zhou)] X. W. Zhou, M. E. Foster, R. E. Jones, P. Yang, H. Fan, and F. P. Doty, J. Mater. Sci. Res., 4, 15 (2015). @@ -218,12 +218,12 @@ F. P. Doty, J. Mater. Sci. Res., 4, 15 (2015). :link(Tersoff) [(Tersoff)] J. Tersoff, Phys. Rev. B, 39, 5566 (1989). -:link(Albe) +:link(poly-Albe) [(Albe)] K. Albe, K. Nordlund, J. Nord, and A. Kuronen, Phys. Rev. B, 66, 035205 (2002). -:link(Wang) +:link(Wang3) [(Wang)] J. Wang, and A. Rockett, Phys. Rev. B, 43, 12571 (1991). -:link(Daw) +:link(poly-Daw) [(Daw)] M. S. Daw, and M. I. Baskes, Phys. Rev. B, 29, 6443 (1984). diff --git a/doc/src/pair_reax.txt b/doc/src/pair_reax.txt index d2dc09ac49..7215c12cee 100644 --- a/doc/src/pair_reax.txt +++ b/doc/src/pair_reax.txt @@ -32,7 +32,7 @@ represent the contributions of chemical bonding to the potential energy. There is more than one version of ReaxFF. The version implemented in LAMMPS uses the functional forms documented in the supplemental information of the following paper: -"(Chenoweth)"_#Chenoweth_2008. The version integrated into LAMMPS matches +"(Chenoweth)"_#Chenoweth_20081. The version integrated into LAMMPS matches the most up-to-date version of ReaxFF as of summer 2010. WARNING: pair style reax is now deprecated and will soon be retired. Users @@ -211,6 +211,6 @@ The keyword defaults are {hbcut} = 6, {hbnewflag} = 1, {tripflag} = 1, :line -:link(Chenoweth_2008) +:link(Chenoweth_20081) [(Chenoweth_2008)] Chenoweth, van Duin and Goddard, Journal of Physical Chemistry A, 112, 1040-1053 (2008). diff --git a/doc/src/pair_reax_c.txt b/doc/src/pair_reax_c.txt index bd8d7e44c9..c1d719d22e 100644 --- a/doc/src/pair_reax_c.txt +++ b/doc/src/pair_reax_c.txt @@ -38,7 +38,7 @@ represent the contributions of chemical bonding to the potential energy. There is more than one version of ReaxFF. The version implemented in LAMMPS uses the functional forms documented in the supplemental information of the following paper: "(Chenoweth et al., -2008)"_#Chenoweth_2008. The version integrated into LAMMPS matches +2008)"_#Chenoweth_20082. The version integrated into LAMMPS matches the most up-to-date version of ReaxFF as of summer 2010. For more technical details about the pair reax/c implementation of ReaxFF, see the "(Aktulga)"_#Aktulga paper. The {reax/c} style was initially @@ -336,7 +336,7 @@ mincap = 50. :line -:link(Chenoweth_2008) +:link(Chenoweth_20082) [(Chenoweth_2008)] Chenoweth, van Duin and Goddard, Journal of Physical Chemistry A, 112, 1040-1053 (2008). diff --git a/doc/src/pair_resquared.txt b/doc/src/pair_resquared.txt index 0242bab185..2e0034ed3b 100644 --- a/doc/src/pair_resquared.txt +++ b/doc/src/pair_resquared.txt @@ -24,7 +24,7 @@ pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0 :pre [Description:] Style {resquared} computes the RE-squared anisotropic interaction -"(Everaers)"_#Everaers, "(Babadi)"_#Babadi between pairs of +"(Everaers)"_#Everaers3, "(Babadi)"_#Babadi between pairs of ellipsoidal and/or spherical Lennard-Jones particles. For ellipsoidal interactions, the potential considers the ellipsoid as being comprised of small spheres of size sigma. LJ particles are a single sphere of @@ -69,7 +69,7 @@ two interacting particles. For ellipsoid/ellipsoid interactions, the interaction is computed by the formulas in the supplementary document referenced above. A12 is -the Hamaker constant as described in "(Everaers)"_#Everaers. In LJ +the Hamaker constant as described in "(Everaers)"_#Everaers3. In LJ units: :c,image(Eqs/pair_resquared.jpg) @@ -131,7 +131,7 @@ that type in a "pair_coeff I J" command. For large uniform molecules it has been shown that the epsilon_*_* energy parameters are approximately representable in terms of local -contact curvatures "(Everaers)"_#Everaers: +contact curvatures "(Everaers)"_#Everaers3: :c,image(Eqs/pair_resquared4.jpg) @@ -228,7 +228,7 @@ gayberne"_pair_gayberne.html :line -:link(Everaers) +:link(Everaers3) [(Everaers)] Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003). :link(Babadi) diff --git a/doc/src/pair_sdk.txt b/doc/src/pair_sdk.txt index 7509a52168..212760e03d 100644 --- a/doc/src/pair_sdk.txt +++ b/doc/src/pair_sdk.txt @@ -43,7 +43,7 @@ given by :c,image(Eqs/pair_cmm.jpg) as required for the SDK Coarse-grained MD parametrization discussed in -"(Shinoda)"_#Shinoda and "(DeVane)"_#DeVane. Rc is the cutoff. +"(Shinoda)"_#Shinoda3 and "(DeVane)"_#DeVane. Rc is the cutoff. Style {lj/sdk/coul/long} computes the adds Coulombic interactions with an additional damping factor applied so it can be used in @@ -148,7 +148,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. :line -:link(Shinoda) +:link(Shinoda3) [(Shinoda)] Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007). :link(DeVane) diff --git a/doc/src/pair_smtbq.txt b/doc/src/pair_smtbq.txt index 714188de32..c8d6b21b3f 100644 --- a/doc/src/pair_smtbq.txt +++ b/doc/src/pair_smtbq.txt @@ -51,7 +51,7 @@ pair_coeff * * PathToLammps/potentials/ffield.smtbq.TiO2 O Ti :pre The electrostatic part of the energy consists of two components : self-energy of atom {i} in the form of a second order charge dependent polynomial and a long-range Coulombic electrostatic interaction. The -latter uses the wolf summation method described in "Wolf"_#Wolf, +latter uses the wolf summation method described in "Wolf"_#Wolf2, spherically truncated at a longer cutoff, {Rcoul}. The charge of each ion is modeled by an orbital Slater which depends on the principal quantum number ({n}) of the outer orbital shared by the @@ -117,7 +117,7 @@ neighbors. The SMTB-Q potential is a variable charge potential. The equilibrium charge on each atom is calculated by the electronegativity -equalization (QEq) method. See "Rick"_#Rick for further detail. One +equalization (QEq) method. See "Rick"_#Rick3 for further detail. One can adjust the frequency, the maximum number of iterative loop and the convergence of the equilibrium charge calculation. To obtain the energy conservation in NVE thermodynamic ensemble, we recommend to use @@ -252,10 +252,10 @@ H. Jonsson, J. Phys. Chem. C 2015, 119, 10391-10399 [(SMTB-Q_3)] R. Tetot, N. Salles, S. Landron, E. Amzallag, Surface Science 616, 19-8722 28 (2013) -:link(Wolf) +:link(Wolf2) [(Wolf)] D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem Phys, 110, 8254 (1999). -:link(Rick) +:link(Rick3) [(Rick)] S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141 (1994). diff --git a/doc/src/pair_snap.txt b/doc/src/pair_snap.txt index cb2289259d..ab7313832c 100644 --- a/doc/src/pair_snap.txt +++ b/doc/src/pair_snap.txt @@ -21,8 +21,8 @@ pair_coeff * * InP.snapcoeff In P InP.snapparam In In P P :pre Style {snap} computes interactions using the spectral neighbor analysis potential (SNAP) -"(Thompson)"_#Thompson2014. Like the GAP framework of Bartok et al. -"(Bartok2010)"_#Bartok2010, "(Bartok2013)"_#Bartok2013 +"(Thompson)"_#Thompson20142. Like the GAP framework of Bartok et al. +"(Bartok2010)"_#Bartok20102, "(Bartok2013)"_#Bartok2013 it uses bispectrum components to characterize the local neighborhood of each atom in a very general way. The mathematical definition of the @@ -131,14 +131,15 @@ The SNAP parameter file can contain blank and comment lines (start with #) anywhere. Each non-blank non-comment line must contain one keyword/value pair. The required keywords are {rcutfac} and {twojmax}. Optional keywords are {rfac0}, {rmin0}, {diagonalstyle}, -and {switchflag}. +{switchflag}, and {bzeroflag}. The default values for these keywords are {rfac0} = 0.99363 {rmin0} = 0.0 {diagonalstyle} = 3 -{switchflag} = 0 :ul +{switchflag} = 0 +{bzeroflag} = 1 :ul Detailed definitions of these keywords are given on the "compute sna/atom"_compute_sna_atom.html doc page. @@ -182,10 +183,10 @@ LAMMPS"_Section_start.html#start_3 section for more info. :line -:link(Thompson2014) +:link(Thompson20142) [(Thompson)] Thompson, Swiler, Trott, Foiles, Tucker, J Comp Phys, 285, 316 (2015). -:link(Bartok2010) +:link(Bartok20102) [(Bartok2010)] Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010). :link(Bartok2013) diff --git a/doc/src/pair_srp.txt b/doc/src/pair_srp.txt index c1eff12cbf..3f54445ba8 100644 --- a/doc/src/pair_srp.txt +++ b/doc/src/pair_srp.txt @@ -65,7 +65,7 @@ according to the lever rule, where {L} is the normalized distance from the atom to the point of closest approach of bond {i} and {j}. The {mid} option takes {L} as -0.5 for each interaction as described in "(Sirk)"_#Sirk. +0.5 for each interaction as described in "(Sirk)"_#Sirk2. The following coefficients must be defined via the "pair_coeff"_pair_coeff.html command as in the examples above, or in @@ -161,6 +161,6 @@ The default keyword value is exclude = yes. :line -:link(Sirk) +:link(Sirk2) [(Sirk)] Sirk TW, Sliozberg YR, Brennan JK, Lisal M, Andzelm JW, J Chem Phys, 136 (13) 134903, 2012. diff --git a/doc/src/pair_sw.txt b/doc/src/pair_sw.txt index ccb7c9c96b..6025b9b11b 100644 --- a/doc/src/pair_sw.txt +++ b/doc/src/pair_sw.txt @@ -24,7 +24,7 @@ pair_coeff * * GaN.sw Ga N Ga :pre [Description:] -The {sw} style computes a 3-body "Stillinger-Weber"_#Stillinger +The {sw} style computes a 3-body "Stillinger-Weber"_#Stillinger2 potential for the energy E of a system of atoms as :c,image(Eqs/pair_sw.jpg) @@ -212,5 +212,5 @@ appropriate units if your simulation doesn't use "metal" units. :line -:link(Stillinger) +:link(Stillinger2) [(Stillinger)] Stillinger and Weber, Phys Rev B, 31, 5262 (1985). diff --git a/doc/src/pair_table.txt b/doc/src/pair_table.txt index ba79aee40d..01c577cd98 100644 --- a/doc/src/pair_table.txt +++ b/doc/src/pair_table.txt @@ -64,7 +64,7 @@ computes the energy or force. For the {bitmap} style, the specified {N} is used to create interpolation tables that are 2^N in length. The distance {R} is used to index into the table via a fast bit-mapping technique due to -"(Wolff)"_#Wolff, and a linear interpolation is performed between +"(Wolff)"_#Wolff2, and a linear interpolation is performed between adjacent table values. The following coefficients must be defined for each pair of atoms @@ -268,5 +268,5 @@ This pair style can only be used via the {pair} keyword of the :line -:link(Wolff) +:link(Wolff2) [(Wolff)] Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999). diff --git a/doc/src/pair_tersoff.txt b/doc/src/pair_tersoff.txt index 52e056dfd8..eb4a8993cf 100644 --- a/doc/src/pair_tersoff.txt +++ b/doc/src/pair_tersoff.txt @@ -32,7 +32,7 @@ pair_coeff * * SiCGe.tersoff Si(D) :pre [Description:] The {tersoff} style computes a 3-body Tersoff potential -"(Tersoff_1)"_#Tersoff_1 for the energy E of a system of atoms as +"(Tersoff_1)"_#Tersoff_11 for the energy E of a system of atoms as :c,image(Eqs/pair_tersoff_1.jpg) @@ -136,7 +136,7 @@ be set to 0.0 if desired. Note that the twobody parameters in entries such as SiCC and CSiSi are often the same, due to the common use of symmetric mixing rules, but this is not always the case. For example, the beta and n parameters in -Tersoff_2 "(Tersoff_2)"_#Tersoff_2 are not symmetric. +Tersoff_2 "(Tersoff_2)"_#Tersoff_21 are not symmetric. We chose the above form so as to enable users to define all commonly used variants of the Tersoff potential. In particular, our form @@ -145,7 +145,7 @@ it reduces to the form of "Albe et al."_#Albe when beta = 1 and m = 1. Note that in the current Tersoff implementation in LAMMPS, m must be specified as either 3 or 1. Tersoff used a slightly different but equivalent form for alloys, which we will refer to as Tersoff_2 -potential "(Tersoff_2)"_#Tersoff_2. The {tersoff/table} style implements +potential "(Tersoff_2)"_#Tersoff_21. The {tersoff/table} style implements Tersoff_2 parameterization only. LAMMPS parameter values for Tersoff_2 can be obtained as follows: @@ -242,12 +242,12 @@ appropriate units if your simulation doesn't use "metal" units. :line -:link(Tersoff_1) +:link(Tersoff_11) [(Tersoff_1)] J. Tersoff, Phys Rev B, 37, 6991 (1988). :link(Albe) [(Albe)] J. Nord, K. Albe, P. Erhart, and K. Nordlund, J. Phys.: Condens. Matter, 15, 5649(2003). -:link(Tersoff_2) +:link(Tersoff_21) [(Tersoff_2)] J. Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248) diff --git a/doc/src/pair_tersoff_mod.txt b/doc/src/pair_tersoff_mod.txt index 5e1c4131df..ff703063b3 100644 --- a/doc/src/pair_tersoff_mod.txt +++ b/doc/src/pair_tersoff_mod.txt @@ -31,7 +31,7 @@ pair_coeff * * Si.tersoff.modc Si Si :pre The {tersoff/mod} and {tersoff/mod/c} styles computes a bond-order type interatomic potential "(Kumagai)"_#Kumagai based on a 3-body Tersoff -potential "(Tersoff_1)"_#Tersoff_1, "(Tersoff_2)"_#Tersoff_2 with +potential "(Tersoff_1)"_#Tersoff_12, "(Tersoff_2)"_#Tersoff_22 with modified cutoff function and angular-dependent term, giving the energy E of a system of atoms as @@ -194,10 +194,10 @@ appropriate units if your simulation doesn't use "metal" units. [(Kumagai)] T. Kumagai, S. Izumi, S. Hara, S. Sakai, Comp. Mat. Science, 39, 457 (2007). -:link(Tersoff_1) +:link(Tersoff_12) [(Tersoff_1)] J. Tersoff, Phys Rev B, 37, 6991 (1988). -:link(Tersoff_2) +:link(Tersoff_22) [(Tersoff_2)] J. Tersoff, Phys Rev B, 38, 9902 (1988). :link(Murty) diff --git a/doc/src/pair_tersoff_zbl.txt b/doc/src/pair_tersoff_zbl.txt index f19ac6ad42..18e54749aa 100644 --- a/doc/src/pair_tersoff_zbl.txt +++ b/doc/src/pair_tersoff_zbl.txt @@ -23,9 +23,9 @@ pair_coeff * * SiC.tersoff.zbl Si C Si :pre [Description:] The {tersoff/zbl} style computes a 3-body Tersoff potential -"(Tersoff_1)"_#Tersoff_1 with a close-separation pairwise modification +"(Tersoff_1)"_#zbl-Tersoff_1 with a close-separation pairwise modification based on a Coulomb potential and the Ziegler-Biersack-Littmark -universal screening function "(ZBL)"_#ZBL, giving the energy E of a +universal screening function "(ZBL)"_#zbl-ZBL, giving the energy E of a system of atoms as :c,image(Eqs/pair_tersoff_zbl.jpg) @@ -146,16 +146,16 @@ be set to 0.0 if desired. Note that the twobody parameters in entries such as SiCC and CSiSi are often the same, due to the common use of symmetric mixing rules, but this is not always the case. For example, the beta and n parameters in -Tersoff_2 "(Tersoff_2)"_#Tersoff_2 are not symmetric. +Tersoff_2 "(Tersoff_2)"_#zbl-Tersoff_2 are not symmetric. We chose the above form so as to enable users to define all commonly used variants of the Tersoff portion of the potential. In particular, our form reduces to the original Tersoff form when m = 3 and gamma = -1, while it reduces to the form of "Albe et al."_#Albe when beta = 1 +1, while it reduces to the form of "Albe et al."_#zbl-Albe when beta = 1 and m = 1. Note that in the current Tersoff implementation in LAMMPS, m must be specified as either 3 or 1. Tersoff used a slightly different but equivalent form for alloys, which we will refer to as -Tersoff_2 potential "(Tersoff_2)"_#Tersoff_2. +Tersoff_2 potential "(Tersoff_2)"_#zbl-Tersoff_2. LAMMPS parameter values for Tersoff_2 can be obtained as follows: gamma = omega_ijk, lambda3 = 0 and the value of @@ -253,16 +253,16 @@ units. :line -:link(Tersoff_1) +:link(zbl-Tersoff_1) [(Tersoff_1)] J. Tersoff, Phys Rev B, 37, 6991 (1988). -:link(ZBL) +:link(zbl-ZBL) [(ZBL)] J.F. Ziegler, J.P. Biersack, U. Littmark, 'Stopping and Ranges of Ions in Matter' Vol 1, 1985, Pergamon Press. -:link(Albe) +:link(zbl-Albe) [(Albe)] J. Nord, K. Albe, P. Erhart and K. Nordlund, J. Phys.: Condens. Matter, 15, 5649(2003). -:link(Tersoff_2) +:link(zbl-Tersoff_2) [(Tersoff_2)] J. Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248) diff --git a/doc/src/pair_thole.txt b/doc/src/pair_thole.txt index 923485eaa7..61ca0b5c35 100644 --- a/doc/src/pair_thole.txt +++ b/doc/src/pair_thole.txt @@ -71,8 +71,8 @@ short distances by a function \exp \left( - s_\{ij\} r_\{ij\} \right) \end\{equation\} This function results from an adaptation to point charges -"(Noskov)"_#Noskov of the dipole screening scheme originally proposed -by "Thole"_#Thole. The scaling coefficient \(s_\{ij\} \) is determined +"(Noskov)"_#Noskov1 of the dipole screening scheme originally proposed +by "Thole"_#Thole1. The scaling coefficient \(s_\{ij\} \) is determined by the polarizability of the atoms, \( \alpha_i \), and by a Thole damping parameter \( a \). This Thole damping parameter usually takes a value of 2.6, but in certain force fields the value can depend upon @@ -186,8 +186,8 @@ temp/drude"_compute_temp_drude.html :line -:link(Noskov) +:link(Noskov1) [(Noskov)] Noskov, Lamoureux and Roux, J Phys Chem B, 109, 6705 (2005). -:link(Thole) +:link(Thole1) [(Thole)] Chem Phys, 59, 341 (1981). diff --git a/doc/src/prd.txt b/doc/src/prd.txt index 607c367afd..247d422b1c 100644 --- a/doc/src/prd.txt +++ b/doc/src/prd.txt @@ -48,11 +48,11 @@ replicas of a system. One or more replicas can be used. The total number of steps {N} to run can be interpreted in one of two ways; see discussion of the {time} keyword below. -PRD is described in "this paper"_#Voter by Art Voter. It is a method +PRD is described in "this paper"_#Voter1998 by Art Voter. It is a method for performing accelerated dynamics that is suitable for infrequent-event systems that obey first-order kinetics. A good overview of accelerated dynamics methods for such systems in given in -"this review paper"_#Voter2 from the same group. To quote from the +"this review paper"_#Voter2002prd from the same group. To quote from the paper: "The dynamical evolution is characterized by vibrational excursions within a potential basin, punctuated by occasional transitions between basins." The transition probability is @@ -316,9 +316,9 @@ geom gaussian, and time = steps. :line -:link(Voter) -[(Voter)] Voter, Phys Rev B, 57, 13985 (1998). +:link(Voter1998) +[(Voter1998)] Voter, Phys Rev B, 57, 13985 (1998). -:link(Voter2) -[(Voter2)] Voter, Montalenti, Germann, Annual Review of Materials +:link(Voter2002prd) +[(Voter2002)] Voter, Montalenti, Germann, Annual Review of Materials Research 32, 321 (2002). diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt index 86c123527b..b9924989a6 100644 --- a/doc/src/read_data.txt +++ b/doc/src/read_data.txt @@ -633,6 +633,15 @@ style, in which case the mass of each particle (body or point particle) is specified explicitly. This is because the volume of the body is unknown. +Note that for 2d simulations of spheres, this command will treat them +as spheres when converting density to mass. However, they can also be +modeled as 2d discs (circles) if the "set density/disc"_set.html +command is used to reset their mass after the read_data command is +used. A {disc} keyword can also be used with time integration fixes, +such as "fix nve/sphere"_fix_nve_sphere.html and "fix +nvt/sphere"_fix_nve_sphere.html to time integrate their motion as 2d +discs (not 3d spheres), by changing their moment of inertia. + For atom_style hybrid, following the 5 initial values (ID,type,x,y,z), specific values for each sub-style must be listed. The order of the sub-styles is the same as they were listed in the diff --git a/doc/src/run_style.txt b/doc/src/run_style.txt index b30a17686d..0e3c1a939f 100644 --- a/doc/src/run_style.txt +++ b/doc/src/run_style.txt @@ -130,7 +130,7 @@ options to support this, and strategies are discussed in :line The {respa} style implements the rRESPA multi-timescale integrator -"(Tuckerman)"_#Tuckerman with N hierarchical levels, where level 1 is +"(Tuckerman)"_#Tuckerman3 with N hierarchical levels, where level 1 is the innermost loop (shortest timestep) and level N is the outermost loop (largest timestep). The loop factor arguments specify what the looping factor is between levels. N1 specifies the number of @@ -289,6 +289,6 @@ run_style verlet :pre :line -:link(Tuckerman) +:link(Tuckerman3) [(Tuckerman)] Tuckerman, Berne and Martyna, J Chem Phys, 97, p 1990 (1992). diff --git a/doc/src/set.txt b/doc/src/set.txt index 659eecd30d..6b59bf1332 100644 --- a/doc/src/set.txt +++ b/doc/src/set.txt @@ -20,7 +20,7 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \ {quat/random} or {diameter} or {shape} or \ {length} or {tri} or {theta} or {theta/random} or \ {angmom} or {omega} or \ - {mass} or {density} or {volume} or {image} or \ + {mass} or {density} or {density/disc} or {volume} or {image} or \ {bond} or {angle} or {dihedral} or {improper} or \ {meso/e} or {meso/cv} or {meso/rho} or \ {smd/contact/radius} or {smd/mass/density} or {dpd/theta} or \ @@ -72,7 +72,9 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \ any of wx,wy,wz can be an atom-style variable (see below) {mass} value = per-atom mass (mass units) value can be an atom-style variable (see below) - {density} value = particle density for sphere or ellipsoid (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle) + {density} value = particle density for a sphere or ellipsoid (mass/distance^3 units), or for a triangle (mass/distance^2 units) or line (mass/distance units) particle + value can be an atom-style variable (see below) + {density/disc} value = particle density for a 2d disc or ellipse (mass/distance^2 units) value can be an atom-style variable (see below) {volume} value = particle volume for Peridynamic particle (distance^3 units) value can be an atom-style variable (see below) @@ -318,23 +320,36 @@ must have a per-atom mass attribute, as defined by the "atom_style"_atom_style.html command. See the "mass" command for how to set mass values on a per-type basis. -Keyword {density} also sets the mass of all selected particles, but in -a different way. The particles must have a per-atom mass attribute, -as defined by the "atom_style"_atom_style.html command. If the atom -has a radius attribute (see "atom_style sphere"_atom_style.html) and -its radius is non-zero, its mass is set from the density and particle -volume. If the atom has a shape attribute (see "atom_style +Keyword {density} or {density/disc} also sets the mass of all selected +particles, but in a different way. The particles must have a per-atom +mass attribute, as defined by the "atom_style"_atom_style.html +command. If the atom has a radius attribute (see "atom_style +sphere"_atom_style.html) and its radius is non-zero, its mass is set +from the density and particle volume for 3d systems (the input density +is assumed to be in mass/distance^3 units). For 2d, the default is +for LAMMPS to model particles with a radius attribute as spheres. +However, if the {density/disc} keyword is used, then they can be +modeled as 2d discs (circles). Their mass is set from the density and +particle area (the input density is assumed to be in mass/distance^2 +units). + +If the atom has a shape attribute (see "atom_style ellipsoid"_atom_style.html) and its 3 shape parameters are non-zero, -then its mass is set from the density and particle volume. If the -atom has a length attribute (see "atom_style line"_atom_style.html) -and its length is non-zero, then its mass is set from the density and -line segment length (the input density is assumed to be in -mass/distance units). If the atom has an area attribute (see -"atom_style tri"_atom_style.html) and its area is non-zero, then its -mass is set from the density and triangle area (the input density is -assumed to be in mass/distance^2 units). If none of these cases are -valid, then the mass is set to the density value directly (the input -density is assumed to be in mass units). +then its mass is set from the density and particle volume (the input +density is assumed to be in mass/distance^3 units). The +{density/disc} keyword has no effect; it does not (yet) treat 3d +ellipsoids as 2d ellipses. + +If the atom has a length attribute (see "atom_style +line"_atom_style.html) and its length is non-zero, then its mass is +set from the density and line segment length (the input density is +assumed to be in mass/distance units). If the atom has an area +attribute (see "atom_style tri"_atom_style.html) and its area is +non-zero, then its mass is set from the density and triangle area (the +input density is assumed to be in mass/distance^2 units). + +If none of these cases are valid, then the mass is set to the density +value directly (the input density is assumed to be in mass units). Keyword {volume} sets the volume of all selected particles. Currently, only the "atom_style peri"_atom_style.html command defines diff --git a/doc/src/tad.txt b/doc/src/tad.txt index 04c7d708f6..f5e7c6d653 100644 --- a/doc/src/tad.txt +++ b/doc/src/tad.txt @@ -56,11 +56,11 @@ Run a temperature accelerated dynamics (TAD) simulation. This method requires two or more partitions to perform NEB transition state searches. -TAD is described in "this paper"_#Voter by Art Voter. It is a method +TAD is described in "this paper"_#Voter2000 by Art Voter. It is a method that uses accelerated dynamics at an elevated temperature to generate results at a specified lower temperature. A good overview of accelerated dynamics methods for such systems is given in "this review -paper"_#Voter2 from the same group. In general, these methods assume +paper"_#Voter2002 from the same group. In general, these methods assume that the long-time dynamics is dominated by infrequent events i.e. the system is is confined to low energy basins for long periods, punctuated by brief, randomly-occurring transitions to adjacent @@ -304,9 +304,9 @@ the "timestep"_timestep.html command, and {neb_log} = "none". :line -:link(Voter) -[(Voter)] Sorensen and Voter, J Chem Phys, 112, 9599 (2000) +:link(Voter2000) +[(Voter2000)] Sorensen and Voter, J Chem Phys, 112, 9599 (2000) -:link(Voter2) -[(Voter2)] Voter, Montalenti, Germann, Annual Review of Materials +:link(Voter2002) +[(Voter2002)] Voter, Montalenti, Germann, Annual Review of Materials Research 32, 321 (2002). diff --git a/doc/src/tutorial_drude.txt b/doc/src/tutorial_drude.txt index 518b90854b..b9a167b804 100644 --- a/doc/src/tutorial_drude.txt +++ b/doc/src/tutorial_drude.txt @@ -54,7 +54,7 @@ charge, and force constant can be chosen following different strategies, as in the following examples of polarizable force fields: -"Lamoureux and Roux"_#Lamoureux suggest adopting a global half-stiffness, \ +"Lamoureux and Roux"_#Lamoureux2 suggest adopting a global half-stiffness, \ \(K_D\) = 500 kcal/(mol Ang \(\{\}^2\)) - which corresponds to a force \ constant \(k_D\) = 4184 kJ/(mol Ang \(\{\}^2\)) - for all types of \ core-Drude bond, a global mass \(m_D\) = 0.4 g/mol (or u) for all types \ @@ -83,7 +83,7 @@ from those of the normal atoms. Thermalizing the Drude dipoles at temperatures comparable to the rest of the simulation leads to several problems (kinetic energy transfer, very short timestep, etc.), which can be remediate by the "cold Drude" technique ("Lamoureux and -Roux"_#Lamoureux). +Roux"_#Lamoureux2). Two closely related models are used to represent polarization through "charges on a spring": the core-shell model and the Drude @@ -105,7 +105,7 @@ due to the short distances, so an atom may capture the Drude particle \ (shell) of a neighbor, or the induced dipoles within the same molecule \ may align too much. To avoid this, damping at short of the \ interactions between the point charges composing the induced dipole \ -can be done by "Thole"_#Thole functions. :l +can be done by "Thole"_#Thole2 functions. :l :ole @@ -284,7 +284,7 @@ pair_style hybrid/overlay lj/cut/coul/long 10.0 thole 2.6 10.0 :pre This tells LAMMPS that we are using two pair_styles. The first one is as above ({lj/cut/coul/long 10.0}). The second one is a {thole} -pair_style with default screening factor 2.6 ("Noskov"_#Noskov) and +pair_style with default screening factor 2.6 ("Noskov"_#Noskov2) and cutoff 10.0. Since {hybrid/overlay} does not support mixing rules, the interaction @@ -381,7 +381,7 @@ group DRUDES type 6 7 8 # DPs :pre Note that with the fixes {drude/transform}, it is not required to specify {comm_modify vel yes} because the fixes do it anyway (several times and for the forces also). To avoid the flying ice cube artifact -"(Lamoureux)"_#Lamoureux, where the atoms progressively freeze and the +"(Lamoureux)"_#Lamoureux2, where the atoms progressively freeze and the center of mass of the whole system drifts faster and faster, the {fix momentum} can be used. For instance: @@ -448,21 +448,21 @@ fix INVERSE all drude/transform/inverse :pre :line -:link(Lamoureux) +:link(Lamoureux2) [(Lamoureux)] Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003) :link(Schroeder) [(Schroeder)] Schroeder and Steinhauser, J Chem Phys, 133, 154511 (2010). -:link(Jiang) +:link(Jiang2) [(Jiang)] Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J Phys Chem Lett, 2, 87-92 (2011). -:link(Thole) +:link(Thole2) [(Thole)] Chem Phys, 59, 341 (1981). -:link(Noskov) +:link(Noskov2) [(Noskov)] Noskov, Lamoureux and Roux, J Phys Chem B, 109, 6705 (2005). :link(SWM4-NDP) diff --git a/doc/utils/converters/lammpsdoc/doc_anchor_check.py b/doc/utils/converters/lammpsdoc/doc_anchor_check.py new file mode 100755 index 0000000000..a072ab1a68 --- /dev/null +++ b/doc/utils/converters/lammpsdoc/doc_anchor_check.py @@ -0,0 +1,60 @@ +#! /usr/bin/env python3 +# LAMMPS Documentation Utilities +# +# Scan for duplicate anchor labels in documentation files +# +# Copyright (C) 2017 Richard Berger +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +import re +import sys +import argparse + +def main(): + parser = argparse.ArgumentParser(description='scan for duplicate anchor labels in documentation files') + parser.add_argument('files', metavar='file', nargs='+', help='one or more files to scan') + parsed_args = parser.parse_args() + + anchor_pattern = re.compile(r'^:link\(([^,\)]*)\)') + anchors = {} + + for filename in parsed_args.files: + with open(filename, 'rt') as f: + for line_number, line in enumerate(f): + m = anchor_pattern.match(line) + if m: + label = m.group(1) + if label in anchors: + anchors[label].append((filename, line_number+1)) + else: + anchors[label] = [(filename, line_number+1)] + + count = 0 + + for label in sorted(anchors.keys()): + if len(anchors[label]) > 1: + print(label) + count += 1 + for filename, line_number in anchors[label]: + print(" - %s:%d" % (filename, line_number)) + + + if count > 0: + print("Found %d anchor label errors." % count) + sys.exit(1) + else: + print("No anchor label errors.") + +if __name__ == "__main__": + main() diff --git a/doc/utils/converters/setup.py b/doc/utils/converters/setup.py index b8a6a1a78f..f4656a7f69 100644 --- a/doc/utils/converters/setup.py +++ b/doc/utils/converters/setup.py @@ -12,6 +12,7 @@ setup(name='LAMMPS Documentation Utilities', tests_require=['nose'], entry_points = { "console_scripts": ['txt2html = lammpsdoc.txt2html:main', - 'txt2rst = lammpsdoc.txt2rst:main'] + 'txt2rst = lammpsdoc.txt2rst:main', + 'doc_anchor_check = lammpsdoc.doc_anchor_check:main '] }, ) diff --git a/doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html b/doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html index 22bdc533e9..39ee684a0b 100644 --- a/doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html +++ b/doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html @@ -1,4 +1,5 @@
+
LAMMPS {{ version }}