Syntax: -
-pair_style peri/pmb --
Examples: -
-pair_style peri/pmb -pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25 --
Description: -
-Style peri/pmb style implements the Peridynamic bond-based prototype -microelastic brittle (PMB) model, which can be used to model materials -at the mesoscopic or macroscopic scale. The canonical paper on -Peridynamics is (Silling). The implementation of -Peridynamics in LAMMPS is described in (Parks). Also see the -PDLAMMPS user -guide for more -details about this particular potential and using it in LAMMPS. -
-The following coefficients must be defined for each pair of atom -types via the pair_coeff command as in the examples -above, or in the data file or restart files read by the -read_data or read_restart -commands, or by mixing as described below: -
-C is the effectively a spring constant for Peridynamic bonds, the -horizon is a cutoff distance for truncating interactions, and s00 and -alpha are used as a bond breaking criteria. The units of c are such -that c/distance = stiffness/volume^2, where stiffness is -energy/distance^2 and volume is distance^3. See the users guide for -more details. -
-Mixing, shift, table, tail correction, restart, rRESPA info: -
-This pair style does not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. -
-This pair style does not support the pair_modify -shift option. -
-The pair_modify table and tail options are not -relevant for this pair style. -
-This pair style writes its information to binary restart -files, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. -
-This pair style can only be used via the pair keyword of the -run_style respa command. It does not support the -inner, middle, outer keywords. -
-Restrictions: -
-The peri/pmb style is part of the "peri" package. It is only -enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info. -
-Related commands: -
- -Default: none -
-(Parks) Parks, Lehoucq, Plimpton, Silling, to appear in Comp Phys -Comm, (2008). -
- - -(Silling) Silling, J Mech Phys Solids, 48, 175-209 (2000). -
- diff --git a/doc/pair_peri_pmb.txt b/doc/pair_peri_pmb.txt deleted file mode 100644 index b38bdcc6ce..0000000000 --- a/doc/pair_peri_pmb.txt +++ /dev/null @@ -1,91 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -pair_style peri/pmb command :h3 - -[Syntax:] - -pair_style peri/pmb :pre - -[Examples:] - -pair_style peri/pmb -pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25 :pre - -[Description:] - -Style {peri/pmb} style implements the Peridynamic bond-based prototype -microelastic brittle (PMB) model, which can be used to model materials -at the mesoscopic or macroscopic scale. The canonical paper on -Peridynamics is "(Silling)"_#Silling. The implementation of -Peridynamics in LAMMPS is described in "(Parks)"_#Parks. Also see the -"PDLAMMPS user -guide"_http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf for more -details about this particular potential and using it in LAMMPS. - -The following coefficients must be defined for each pair of atom -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 or "read_restart"_read_restart.html -commands, or by mixing as described below: - -c (energy/distance/volume^2 units) -horizon (distance units) -s00 (unitless) -alpha (unitless) :ul - -C is the effectively a spring constant for Peridynamic bonds, the -horizon is a cutoff distance for truncating interactions, and s00 and -alpha are used as a bond breaking criteria. The units of c are such -that c/distance = stiffness/volume^2, where stiffness is -energy/distance^2 and volume is distance^3. See the users guide for -more details. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This pair style does not support mixing. Thus, coefficients for all -I,J pairs must be specified explicitly. - -This pair style does not support the "pair_modify"_pair_modify.html -shift option. - -The "pair_modify"_pair_modify.html table and tail options are not -relevant for this pair style. - -This pair style writes its 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. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -The {peri/pmb} style is part of the "peri" package. It is only -enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#2_3 section for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Parks) -[(Parks)] Parks, Lehoucq, Plimpton, Silling, to appear in Comp Phys -Comm, (2008). - -:link(Silling) -[(Silling)] Silling, J Mech Phys Solids, 48, 175-209 (2000). diff --git a/doc/pair_style.txt b/doc/pair_style.txt index 98a04f242a..b81009646f 100644 --- a/doc/pair_style.txt +++ b/doc/pair_style.txt @@ -133,7 +133,8 @@ the pair_style command, and coefficients specified by the associated "pair_style meam"_pair_meam.html - modified embedded atom method (MEAM) "pair_style morse"_pair_morse.html - Morse potential "pair_style morse/opt"_pair_morse.html - optimized version of Morse potential -"pair_style peri/pmb"_pair_peri_pmb.html - peridynamic PMB potential +"pair_style peri/lps"_pair_peri.html - peridynamic LPS potential +"pair_style peri/pmb"_pair_peri.html - peridynamic PMB potential "pair_style reax"_pair_reax.html - ReaxFF potential "pair_style resquared"_pair_resquared.html - Everaers RE-Squared ellipsoidal potential "pair_style soft"_pair_soft.html - Soft (cosine) potential diff --git a/doc/read_dump.txt b/doc/read_dump.txt new file mode 100644 index 0000000000..852c172676 --- /dev/null +++ b/doc/read_dump.txt @@ -0,0 +1,106 @@ +"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 + +read_dump command :h3 + +[Syntax:] + +read_dump filename N col1 col2 ... keyword value ... :pre + +filename = name of dump file to read snapshot from :ulb,l +N = timestamp to read in :l +col1, col2, ... = {x} or {y} or {z} or {xs} or {ys} or {zs} or {xu} or {yu} or {zu} or {ix} or {iy} or {iz} or {vx} or {vy} or {vz} :l +zero or more keyword/value pairs may be appended :l +keyword = {procs} or {box} :l + {procs} value = P + P = number of processors that wrote out dump file + {box} value = {reset} or {ignore} :pre +:ule + +[Examples:] + +read_dump dump.run 1000 x y z +read_dump dump.poly.% 50000 xs ys zs vx vy vz procs 100 :pre + +[Description:] + +Read a snapshot at timestamp N from the specified dump file and use +the specified per-atom column information from the snapshot to +overwrite current per-atom values. The dump file must be in the +native LAMMPS format, as produced by an {atom} or {custom} style +"dump"_dump.html command. + +The specified filename can contain the "%" wild-card character. This +means that individual dump files were written by each of the P +processors the original simulation was running on, where "%" is +replaced by the processor ID from 0 to P-1. If the current simulation +is not running on the same number of processors, then the {procs} +keyword must be used to specify what P was in the original simulation, +so that the current simulation knows which files to read. If the "%" +wild-card character is not used, or the current simulation is running +on the same number of processors, then the {procs} keyword should not +be used. + +{N} is the timestamp of the snapshot that will be read from the dump +file. The file will be scanned until the snapshot with that timestamp +is found. The timestep of the current simulation will not be reset to +{N}. Use the "reset_timestep"_reset_timestep.html command if this is +desired. + +The dump file snapshot defines a simulation box size via its ITEM: BOX +BOUNDS field. If the setting for the optional {box} keyword is +{ignore} then the box size settings are ignored. If the setting for +the {box} keyword is {reset} then the current simulation box size is +reset to the values in the dump snapshot. Note that due to the finite +precision at which numeric values are written into a dump file, box +sizes values which are identical to the current box size may be read +in as slightly different values. Hence you should not reset the box +size if you expect it to be the same. + +The dump file snapshot defines the number of atom in the snapshot via +its ITEM: NUMBER OF ATOMS field. If this number does not match the +number of atoms in the current simulation, then a WARNING is printed. + +The dump file snapshot defines a list of per-atom quantities via its +ITEM: ATOMS field. Any of the quantities listed above may be +specified, in which case that per-atom quantity is read from the dump +file and overwrites the corresponding current quantity. See the +"dump"_dump.html command for an explanation of these quantities. + +Atom IDs must also appear in the dump file. They are used to map +read-in atoms to current atoms one by one. Note that if some current +atoms do not appear in the dump file, their values are not +overwritten. Likewise if atom IDs appear in the dump file which do +not exist in the current simulation, their read-in values are ignored. + +The various flavors of atom coordinates that can appear in the dump +file ({x} or {xs} or {xu}) are all converted into internal LAMMPS +coordinates (equivalent to {x}). Each atom is also remapped to the +current simulation box, if it is outside periodic boundaries. Note +that the current simulation box size may have been reset to the dump +snapshot box size before this takes place. + +IMPORTANT NOTE: Image flags from the dump file ({ix}, {iy}, {iz}) +should only be read-in if the corresponding coordinates are of the {x} +or {xs} form. In this case, the remap of each atom to the (new) +periodic box should update its read-in image flags correctly. If the +read-in coordinates are of the {xu} form, then no corresponding image +flags should be read-in. This is because the image flags are +initialized to 0 when {xu} style coordinates are read. The remap of +atoms to the (new) periodic box should update the re-initialized image +flags correctly. + +[Restrictions:] none + +[Related commands:] + +"read_data"_read_data.html, "read_restart"_read_restart.html + +[Default:] + +The option defaults are box = ignore.