Use at most one of the -DLAMMPS_SMALLBIG, -DLAMMPS_BIGBIG, -D- -DLAMMPS_SMALLSMALL settings. The default is -DLAMMPS_SMALLBIG. These +
Use at most one of the -DLAMMPS_SMALLBIG, -DLAMMPS_BIGBIG, +-DLAMMPS_SMALLSMALL settings. The default is -DLAMMPS_SMALLBIG. These settings refer to use of 4-byte (small) vs 8-byte (big) integers within LAMMPS, as specified in src/lmptype.h. The only reason to use the BIGBIG setting is to enable simulation of huge molecular systems @@ -1288,7 +1288,7 @@ use this executable to run on a single processor by typing something like: “lmp_win_mpi -in in.lj”.
The screen output from LAMMPS is described in the next section. As it +
The screen output from LAMMPS is described in a section below. As it runs, LAMMPS also writes a log.lammps file with the same information.
Note that this sequence of commands copies the LAMMPS executable (lmp_linux) to the directory with the input files. This may not be diff --git a/doc/atom_style.txt b/doc/atom_style.txt index f25b7ee4b9..a71d27db2f 100644 --- a/doc/atom_style.txt +++ b/doc/atom_style.txt @@ -13,10 +13,10 @@ atom_style command :h3 atom_style style args :pre style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \ - {electron} or {ellipsoid} or {full} or {line} or {meso} or \ + {dpd} or {electron} or {ellipsoid} or {full} or {line} or {meso} or \ {molecular} or {peri} or {smd} or {sphere} or {tri} or \ {template} or {hybrid} :ulb,l - args = none for any style except {body} and {hybrid} + args = none for any style except the following {body} args = bstyle bstyle-args bstyle = style of body particles bstyle-args = additional arguments specific to the bstyle @@ -47,6 +47,10 @@ used before a simulation is setup via a "read_data"_read_data.html, "read_restart"_read_restart.html, or "create_box"_create_box.html command. +NOTE: Many of the atom styles discussed here are only enabled if +LAMMPS was built with a specific package, as listed below in the +Restrictions section. + Once a style is assigned, it cannot be changed, so use a style general enough to encompass all attributes. E.g. with style {bond}, angular terms cannot be used or added later to the model. It is OK to use a @@ -70,6 +74,7 @@ quantities. {bond} | bonds | bead-spring polymers | {charge} | charge | atomic system with charges | {dipole} | charge and dipole moment | system with dipolar particles | +{dpd} | internal temperature and internal energies | DPD particles | {electron} | charge and spin and eradius | electronic force field | {ellipsoid} | shape, quaternion, angular momentum | aspherical particles | {full} | molecular + charge | bio-molecules | @@ -128,6 +133,10 @@ position, which is represented by the eradius = electron size. For the {peri} style, the particles are spherical and each stores a per-particle mass and volume. +The {dpd} style is for dissipative particle dynamics (DPD) particles +which store the particle internal temperature (dpdTheta), internal +conductive energy (uCond) and internal mechanical energy (uMech). + The {meso} style is for smoothed particle hydrodynamics (SPH) particles which store a density (rho), energy (e), and heat capacity (cv). @@ -247,20 +256,34 @@ more instructions on how to use the accelerated styles effectively. This command cannot be used after the simulation box is defined by a "read_data"_read_data.html or "create_box"_create_box.html command. -The {angle}, {bond}, {full}, {molecular}, and {template} styles are -part of the MOLECULE package. The {line} and {tri} styles are part -of the ASPHERE pacakge. The {body} style is part of the BODY package. -The {dipole} style is part of the DIPOLE package. The {peri} style is -part of the PERI package for Peridynamics. The {electron} style is -part of the USER-EFF package for "electronic force -fields"_pair_eff.html. The {meso} style is part of the USER-SPH -package for smoothed particle hydrodyanmics (SPH). See "this PDF -guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. The -{wavepacket} style is part of the USER-AWPMD package for the -"antisymmetrized wave packet MD method"_pair_awpmd.html. They are -only enabled if LAMMPS was built with that package. See the "Making +Many of the styles listed above are only enabled if LAMMPS was built +with a specific package, as listed below. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. +The {angle}, {bond}, {full}, {molecular}, and {template} styles are +part of the MOLECULE package. + +The {line} and {tri} styles are part of the ASPHERE pacakge. + +The {body} style is part of the BODY package. + +The {dipole} style is part of the DIPOLE package. + +The {peri} style is part of the PERI package for Peridynamics. + +The {electron} style is part of the USER-EFF package for "electronic +force fields"_pair_eff.html. + +The {dpd} style is part of the USER-DPD package for dissipative +particle dynamics (DPD). + +The {meso} style is part of the USER-SPH package for smoothed particle +hydrodyanmics (SPH). See "this PDF +guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. + +The {wavepacket} style is part of the USER-AWPMD package for the +"antisymmetrized wave packet MD method"_pair_awpmd.html. + [Related commands:] "read_data"_read_data.html, "pair_style"_pair_style.html diff --git a/doc/compute_dpd.txt b/doc/compute_dpd.txt new file mode 100644 index 0000000000..d1e1d270fb --- /dev/null +++ b/doc/compute_dpd.txt @@ -0,0 +1,67 @@ +"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 + +compute dpd command :h3 + +[Syntax:] + +compute ID group-ID dpd :pre + +ID, group-ID are documented in "compute"_compute.html command +dpd = style name of this compute command :ul + +[Examples:] + +compute 1 all dpd :pre + +[Description:] + +Define a computation that accumulates the total internal conductive +energy (U_cond), the total internal mechanical energy (U_mech), the +total internal energy (U) and the {harmonic} average of the internal +temperature (dpdTheta) for the entire system of particles. See the +"compute dpd/atom"_compute_dpd_atom.html command if you want +per-particle internal energies and internal temperatures. + +The system internal properties are computed according to the following +relations: + +:c,image(Eqs/compute_dpd.jpg) + +where N is the number of particles in the system + +:line + +[Output info:] + +This compute calculates a global vector of length 5 (U_cond, U_mech, +U, dpdTheta, N_particles), which can be accessed by indices 1-5. See +"this section"_Section_howto.html#howto_15 for an overview of LAMMPS +output options. + +The vector values will be in energy and temperature "units"_units.html. + +[Restrictions:] + +The compute {dpd} is only available if LAMMPS is built with the +USER-DPD package and requires the "atom_style dpd"_atom_style.html. + +[Related commands:] + +"compute dpd/atom"_compute_dpd_atom.html, +"thermo_style"_thermo_style.html + +[Default:] none + +:line + +:link(Larentzos) +[(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 +Laboratory, Aberdeen Proving Ground, MD (2014). diff --git a/doc/compute_dpd_atom.txt b/doc/compute_dpd_atom.txt new file mode 100644 index 0000000000..c4be61b45f --- /dev/null +++ b/doc/compute_dpd_atom.txt @@ -0,0 +1,60 @@ +"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 + +compute dpd/atom command :h3 + +[Syntax:] + +compute ID group-ID dpd/atom :pre + +ID, group-ID are documented in "compute"_compute.html command +dpd/atom = style name of this compute command :ul + +[Examples:] + +compute 1 all dpd/atom + +[Description:] + +Define a computation that accesses the per-particle internal +conductive energy (u_cond), internal mechanical energy (u_mech) and +internal temperatures (dpdTheta) for each particle in a group. See +the "compute dpd"_compute_dpd.html command if you want the total +internal conductive energy, the total internal mechanical energy, and +average internal temperature of the entire system or group of dpd +particles. + +[Output info:] + +This compute calculates a per-particle array with 3 columns (u_cond, +u_mech, dpdTheta), which can be accessed by indices 1-3 by any command +that uses per-particle values from a compute as input. See +"Section_howto15"_Section_howto.html#howto_15 for an overview of +LAMMPS output options. + +The per-particle array values will be in energy (u_cond, u_mech) and +temperature (dpdTheta) "units"_units.html. + +[Restrictions:] + +The compute {dpd/atom} is only available if LAMMPS is built with the +USER-DPD package. + +[Related commands:] + +"dump custom"_dump.html, "compute dpd"_compute_dpd.html + +[Default:] none + +:line + +:link(Larentzos) +[(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 +Laboratory, Aberdeen Proving Ground, MD (2014). diff --git a/doc/compute_temp_body.txt b/doc/compute_temp_body.txt new file mode 100755 index 0000000000..04b707bcce --- /dev/null +++ b/doc/compute_temp_body.txt @@ -0,0 +1,131 @@ +"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 + +compute temp/body command :h3 + +[Syntax:] + +compute ID group-ID temp/body keyword value ... :pre + +ID, group-ID are documented in "compute"_compute.html command :ulb,l +temp/body = style name of this compute command :l +zero or more keyword/value pairs may be appended :l +keyword = {bias} or {dof} :l + {bias} value = bias-ID + bias-ID = ID of a temperature compute that removes a velocity bias + {dof} value = {all} or {rotate} + all = compute temperature of translational and rotational degrees of freedom + rotate = compute temperature of just rotational degrees of freedom :pre +:ule + +[Examples:] + +compute 1 all temp/body +compute myTemp mobile temp/body bias tempCOM +compute myTemp mobile temp/body dof rotate :pre + +[Description:] + +Define a computation that calculates the temperature of a group of +body particles, including a contribution from both their +translational and rotational kinetic energy. This differs from the +usual "compute temp"_compute_temp.html command, which assumes point +particles with only translational kinetic energy. + +Only body particles can be included in the group. For 3d particles, +each has 6 degrees of freedom (3 translational, 3 rotational). For 2d +body particles, each has 3 degrees of freedom (2 translational, 1 +rotational). + +NOTE: This choice for degrees of freedom (dof) assumes that all body +particles in your model will freely rotate, sampling all their +rotational dof. It is possible to use a combination of interaction +potentials and fixes that induce no torque or otherwise constrain some +of all of your particles so that this is not the case. Then there are +less dof and you should use the "compute_modify +extra"_compute_modify.html command to adjust the dof accordingly. + +The translational kinetic energy is computed the same as is described +by the "compute temp"_compute_temp.html command. The rotational +kinetic energy is computed as 1/2 I w^2, where I is the inertia tensor +for the aspherical particle and w is its angular velocity, which is +computed from its angular momentum. + +A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute. The formula for the components of the +tensor is the same as the above formula, except that v^2 and w^2 are +replaced by vx*vy and wx*wy for the xy component, and the appropriate +elements of the inertia tensor are used. The 6 components of the +vector are ordered xx, yy, zz, xy, xz, yz. + +The number of atoms contributing to the temperature is assumed to be +constant for the duration of the run; use the {dynamic} option of the +"compute_modify"_compute_modify.html command if this is not the case. + +This compute subtracts out translational degrees-of-freedom due to +fixes that constrain molecular motion, such as "fix +shake"_fix_shake.html and "fix rigid"_fix_rigid.html. This means the +temperature of groups of atoms that include these constraints will be +computed correctly. If needed, the subtracted degrees-of-freedom can +be altered using the {extra} option of the +"compute_modify"_compute_modify.html command. + +See "this howto section"_Section_howto.html#howto_16 of the manual for +a discussion of different ways to compute temperature and perform +thermostatting. + +:line + +The keyword/value option pairs are used in the following ways. + +For the {bias} keyword, {bias-ID} refers to the ID of a temperature +compute that removes a "bias" velocity from each atom. This allows +compute temp/sphere to compute its thermal temperature after the +translational kinetic energy components have been altered in a +prescribed way, e.g. to remove a flow velocity profile. Thermostats +that use this compute will work with this bias term. See the doc +pages for individual computes that calculate a temperature and the doc +pages for fixes that perform thermostatting for more details. + +For the {dof} keyword, a setting of {all} calculates a temperature +that includes both translational and rotational degrees of freedom. A +setting of {rotate} calculates a temperature that includes only +rotational degrees of freedom. + +:line + +[Output info:] + +This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See "this +section"_Section_howto.html#howto_15 for an overview of LAMMPS output +options. + +The scalar value calculated by this compute is "intensive". The +vector values are "extensive". + +The scalar value will be in temperature "units"_units.html. The +vector values will be in energy "units"_units.html. + +[Restrictions:] + +This compute is part of the BODY 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. + +This compute requires that atoms store angular momementum and a +quaternion as defined by the "atom_style body"_atom_style.html +command. + +[Related commands:] + +"compute temp"_compute_temp.html + +[Default:] none diff --git a/doc/package.html b/doc/package.html index 4d8a3b19df..f79f993d3f 100644 --- a/doc/package.html +++ b/doc/package.html @@ -695,7 +695,7 @@ support. These settings are made automatically if the “-sf intel” not used, you must invoke the package intel command in your input script or or via the “-pk intel” command-line switch.
For the KOKKOS package, the option defaults neigh = full, newton = -off, binsize = 0.0, and comm = host. These settings are made +off, binsize = 0.0, and comm = device. These settings are made automatically by the required “-k on” command-line switch. You can change them bu using the package kokkos command in your input script or via the “-pk kokkos” command-line switch.
diff --git a/doc/pair_body_rounded_polygon.txt b/doc/pair_body_rounded_polygon.txt new file mode 100644 index 0000000000..966b14fce4 --- /dev/null +++ b/doc/pair_body_rounded_polygon.txt @@ -0,0 +1,107 @@ +"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 body/rounded/polygon command :h3 + +[Syntax:] + +pair_style body/rounded/polygon cutoff_global cutoff_inner delta_ua c_n :pre + +cutoff_global = global cutoff for COM interactions (distance units) +cutoff_inner = cutoff for vertex-vertex and vertex-edge interactions (distance units) +delta_ua = characteristic contact length (distance units) +c_n = normal friction coefficient (energy time/distance^2) :ul + +[Examples:] + +pair_style body/rounded/polygon 6.0 0.5 0.5 0.1 +pair_coeff 1 1 1.0 100.0 12.0 :pre + +[Description:] + +Style {body/rounded/polygon} implements the pairwise body/body +interactions between 2D convex polygons, as described +in "Fraige"_#Fraige. This pair style is designed for use with +the "rounded/polygon" body style, which is specified as +an argument to the "atom-style body/rounded/polygon" command. +See the "body"_body.html doc page for more details about the body +styles LAMMPS supports. + +The "rounded/polygon" style treats a body particle as a discrete +element model (DEM) polygon composed of N vertices. +The coordinates of a body particle are its center-of-mass (COM). +The initial position of the vertices are specified the data file. +The current implementation follows the multiple contact points model as +described in "Fraige"_#Fraige, but neglects and the contact history +the tangential contact forces for now. + +The parameters {delta_ua} and {c_n} are the characteristic contact length +and the normal friction coefficient, respectively. See Eqs. (1) and (5) +in "Fraige"_#Fraige for more details. + +For style {body/rounded/polygon}, 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: + +sigma = vertex rounded diameter (distance units) +k_n = normal repulsion strength (energy/distance^2) +k_na = normal attraction strength (energy/distance^2) +cutoff = cutoff for COM interactions (distance units) :ul + +The last parameter is optional. If not specified, the global +cutoff specified in the pair_style command is used. + +Note that the current implementation assumes that the edge length +of the polygons (L) should be at least twice greater than +the vertex rounded radius (sigma) so as to distinguish vertex-vertex from +vertex-edge contacts. + +NOTE: Because this pair style requires the body velocities to compute +the friction component of the forces, users should specify +{comm_modify vel yes} in the input script with this pair style. + +:line + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +For atom type pairs I,J and I != J, the epsilon and sigma coefficients +and cutoff distance for all of this pair style can be mixed. The +default mix value is {geometric}. See the "pair_modify" command for +details. + +This pair style does not support the "pair_modify"_pair_modify.html +shift, table, and tail options. + +This pair style does not write its information to "binary restart +files"_restart.html. + +This pair style can only be used via the {pair} keyword of the +"run_style respa"_run_style.html command. It does not support the +{inner}, {middle}, {outer} keywords. + +:line + +[Restrictions:] + +This style is part of the BODY 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. + +Defining particles to be bodies so they participate in body/body or +body/particle interactions requires the use of the "atom_style +body"_atom_style.html command. + +[Related commands:] + +"pair_coeff"_pair_coeff.html + +[Default:] none + +:link(Fraige) +[(Fraige)] F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds, +Particuology, 6, 455 (2008). diff --git a/doc/pair_dpd_conservative.txt b/doc/pair_dpd_conservative.txt new file mode 100644 index 0000000000..41e279a83d --- /dev/null +++ b/doc/pair_dpd_conservative.txt @@ -0,0 +1,72 @@ +"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 dpd/conservative command :h3 + +[Syntax:] + +pair_style dpd/conservative cutoff :pre + +cutoff = global cutoff for DPD interactions (distance units) :ul + +[Examples:] + +pair_style dpd/conservative 2.5 +pair_coeff * * 3.0 2.5 +pair_coeff 1 1 3.0 :pre + +[Description:] + +Style {dpd/conservative} computes the conservative force for +dissipative particle dynamics (DPD). The conservative force on atom I +due to atom J is given by + +:c,image(Eqs/pair_dpd_conservative.jpg) + +where the weighting factor, omega_ij, varies between 0 and 1, and is +chosen to have the following functional form: + +:c,image(Eqs/pair_dpd_omega.jpg) + +where Rij is a unit vector in the direction Ri - Rj, and Rc is the +cutoff. Note that alternative definitions of the weighting function +exist, but would have to be implemented as a separate pair style +command. + +Style {dpd/conservative} differs from the other dpd styles in that the +dissipative and random forces are not computed within the pair style. + +For style {dpd/conservative}, the pairwise energy is due only to the +conservative force term Fc, and is shifted to be zero at the cutoff +distance Rc. The pairwise virial is calculated using only the +conservative term. + +Style {dpd/conservative} requires the following coefficients to 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 +or "read_restart"_read_restart.html commands: + +A (force units) +cutoff (distance units) :ul + +The last coefficient is optional. If not specified, the global DPD +cutoff is used. + +:line + +[Restrictions:] + +The pair style {dpd/conservative} is only available if LAMMPS is built +with the USER-DPD package. + +[Related commands:] + +"pair_coeff"_pair_coeff.html, "pair_dpd"_pair_dpd.html + +[Default:] none diff --git a/doc/pair_dpd_fdt.txt b/doc/pair_dpd_fdt.txt new file mode 100644 index 0000000000..ac31e82e30 --- /dev/null +++ b/doc/pair_dpd_fdt.txt @@ -0,0 +1,136 @@ +"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 dpd/fdt command :h3 +pair_style dpd/fdt/energy command :h3 + +[Syntax:] + +pair_style style args :pre + +style = {dpd/fdt} or {dpd/fdt/energy} +args = list of arguments for a particular style :ul + {dpd/fdt} args = T cutoff seed + T = temperature (temperature units) + cutoff = global cutoff for DPD interactions (distance units) + seed = random # seed (positive integer) + {dpd/fdt/energy} args = cutoff seed + cutoff = global cutoff for DPD interactions (distance units) + seed = random # seed (positive integer) :pre + +[Examples:] + +pair_style dpd/fdt 300.0 2.5 34387 +pair_coeff * * 3.0 1.0 2.5 :pre + +pair_style dpd/fdt/energy 2.5 34387 +pair_coeff * * 3.0 1.0 0.1 2.5 :pre + +[Description:] + +Styles {dpd/fdt} and {dpd/fdt/energy} set the fluctuation-dissipation +theorem parameters and compute the conservative force for dissipative +particle dynamics (DPD). The conservative force on atom I due to atom +J is given by + +:c,image(Eqs/pair_dpd_conservative.jpg) + +where the weighting factor, omega_ij, varies between 0 and 1, and is +chosen to have the following functional form: + +:c,image(Eqs/pair_dpd_omega.jpg) + +where Rij is a unit vector in the direction Ri - Rj, and Rc is the +cutoff. Note that alternative definitions of the weighting function +exist, but would have to be implemented as a separate pair style +command. + +These pair style differ from the other dpd styles in that the +dissipative and random forces are not computed within the pair style. +This style can be combined with the "fix shardlow"_fix_shardlow.html +to perform the stochastic integration of the dissipative and random +forces through the Shardlow splitting algorithm approach. + +The pairwise energy associated with styles {dpd/fdt} and +{dpd/fdt/energy} is only due to the conservative force term Fc, and is +shifted to be zero at the cutoff distance Rc. The pairwise virial is +calculated using only the conservative term. + +For style {dpd/fdt}, the fluctuation-dissipation theorem defines gamma +to be set equal to sigma*sigma/(2 T), where T is the set point +temperature specified as a pair style parameter in the above examples. +This style can be combined with "fix shardlow"_fix_shardlow.html to +perform DPD simulations under isothermal and isobaric conditions (see +"(Lisal)"_#Lisal). 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 or "read_restart"_read_restart.html +commands: + +A (force units) +sigma (force*time^(1/2) units) +cutoff (distance units) :ul + +The last coefficient is optional. If not specified, the global DPD +cutoff is used. + +For style {dpd/fdt/energy}, the fluctuation-dissipation theorem +defines gamma to be set equal to sigma*sigma/(2 dpdTheta), where +dpdTheta is the average internal temperature for the pair. +Furthermore, the fluctuation-dissipation defines alpha*alpha to be set +equal to 2*kB*kappa, where kappa is the mesoparticle thermal +conductivity parameter. This style can be combined with "fix +shardlow"_fix_shardlow.html to perform DPD simulations under +isoenergetic and isoenthalpic conditions (see "(Lisal)"_#Lisal). 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 or "read_restart"_read_restart.html +commands: + +A (force units) +sigma (force*time^(1/2) units) +kappa (1/time units) +cutoff (distance units) :ul + +The last coefficient is optional. If not specified, the global DPD +cutoff is used. + +For style {dpd/fdt/energy}, the particle internal temperature is +related to the particle internal energy through a mesoparticle +equation of state. Thus, an an additional "fix eos"_fix.html must be +specified. + +:line + +[Restrictions:] + +Pair styles {dpd/fdt} and {dpd/fdt/energy} are only available if +LAMMPS is built with the USER-DPD package. + +Pair styles {dpd/fdt} and {dpd/fdt/energy} require use of the +"communicate vel yes"_communicate.html option so that velocites are +stored by ghost atoms. + +Pair style {dpd/fdt/energy} requires "atom_style dpd"_atom_style.html +to be used in order to properly account for the particle internal +energies and temperatures. + +[Related commands:] + +"pair_coeff"_pair_coeff.html, "fix shardlow"_fix_shardlow.html + +[Default:] none + +:line + +:link(Lisal) +[(Lisal)] M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative +particle dynamics as isothermal, isobaric, isoenergetic, and +isoenthalpic conditions using Shardlow-like splitting algorithms.", +J. Chem. Phys., 135, 204105 (2011). diff --git a/doc/read_data.txt b/doc/read_data.txt index d15fa2b835..37c082accf 100644 --- a/doc/read_data.txt +++ b/doc/read_data.txt @@ -527,6 +527,7 @@ body: atom-ID atom-type bodyflag mass x y z bond: atom-ID molecule-ID atom-type x y z charge: atom-ID atom-type q x y z dipole: atom-ID atom-type q x y z mux muy muz +dpd: atom-ID atom-type theta x y z electron: atom-ID atom-type q spin eradius x y z ellipsoid: atom-ID atom-type ellipsoidflag density x y z full: atom-ID molecule-ID atom-type q x y z @@ -534,40 +535,41 @@ line: atom-ID molecule-ID atom-type lineflag density x y z meso: atom-ID atom-type rho e cv x y z molecular: atom-ID molecule-ID atom-type x y z peri: atom-ID atom-type volume density x y z -smd: atom-ID atom-type molecule volume mass kernel_radius contact_radius x y z +smd: atom-ID atom-type molecule volume mass kernel-radius contact-radius x y z sphere: atom-ID atom-type diameter density x y z template: atom-ID molecule-ID template-index template-atom atom-type x y z tri: atom-ID molecule-ID atom-type triangleflag density x y z wavepacket: atom-ID atom-type charge spin eradius etag cs_re cs_im x y z hybrid: atom-ID atom-type x y z sub-style1 sub-style2 ... :tb(s=:) -The keywords have these meanings: +The per-atom values have these meanings and units, listed alphabetically: atom-ID = integer ID of atom -molecule-ID = integer ID of molecule the atom belongs to atom-type = type of atom (1-Ntype) -q = charge on atom (charge units) -diameter = diameter of spherical atom (distance units) -ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles -lineflag = 1 for line segment particles, 0 for point particles -triangleflag = 1 for triangular particles, 0 for point particles bodyflag = 1 for body particles, 0 for point particles -template-index = which molecule within the molecule template the atom is part of -template-atom = which atom within a template molecule the atom is -density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle) -mass = mass of particle (mass units) -volume = volume of particle (distance^3 units) -x,y,z = coordinates of atom -mux,muy,muz = components of dipole moment of atom (dipole units) -rho = density (need units) for SPH particles -e = energy (need units) for SPH particles +contact-radius = ??? (distance units) +cs_re,cs_im = real/imaginary parts of wavepacket coefficients cv = heat capacity (need units) for SPH particles -spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP) +density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle) +diameter = diameter of spherical atom (distance units) +e = energy (need units) for SPH particles +ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles eradius = electron radius (or fixed-core radius) etag = integer ID of electron that each wavepacket belongs to -cs_re,cs_im = real/imaginary parts of wavepacket coefficients -kernel_radius = ??? (distance units) -contact_radius = ??? (distance units) :ul +kernel-radius = ??? (distance units) +lineflag = 1 for line segment particles, 0 for point or spherical particles +mass = mass of particle (mass units) +molecule-ID = integer ID of molecule the atom belongs to +mux,muy,muz = components of dipole moment of atom (dipole units) +q = charge on atom (charge units) +rho = density (need units) for SPH particles +spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP) +template-atom = which atom within a template molecule the atom is +template-index = which molecule within the molecule template the atom is part of +theta = internal temperature of a DPD particle +triangleflag = 1 for triangular particles, 0 for point or sperhical particles +volume = volume of Peridynamic particle (distance^3 units) +x,y,z = coordinates of atom (distance units) :ul The units for these quantities depend on the unit style; see the "units"_units.html command for details. diff --git a/doc/set.txt b/doc/set.txt index d5d0d973c1..184e147d11 100644 --- a/doc/set.txt +++ b/doc/set.txt @@ -23,7 +23,7 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \ {mass} or {density} 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 \ + {smd/contact/radius} or {smd/mass/density} or {dpd/theta} or \ {i_name} or {d_name} :l {type} value = atom type value can be an atom-style variable (see below) @@ -92,6 +92,7 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \ value can be an atom-style variable (see below) {smd/mass/density} = set particle mass based on volume by providing a mass density value can be an atom-style variable (see below) + {dpd/theta} value = internal temperature of DPD particles (temperature units) {i_name} value = value for custom integer vector with name {d_name} value = value for custom floating-point vector with name :pre :ule @@ -389,6 +390,9 @@ other. Note that the SPH smoothing kernel diameter used for computing long range, nonlocal interactions, is set using the {diameter} keyword. +Keyword {dpd/theta} sets the internal temperature of a DPD particle +as defined by the USER-DPD package. + Keywords {i_name} and {d_name} refer to custom integer and floating-point properties that have been added to each atom via the "fix property/atom"_fix_property_atom.html command. When that command