+Syntax: +
+compute ID group-ID style args ++
Examples: +
+compute 1 all temp +compute newtemp flow temp/partial 1 1 0 +compute 3 all ke/atom ++
Description: +
+Create a computation that will be performed on a group of atoms. +
+In LAMMPS, a "compute" is used in several ways. Computes that +calculate one or more values for the entire group of atoms can output +those values via the thermo_style custom command. +Or the values can be referenced in a variable equal +command. Computes that calculate a temperature or pressure are used +by fixes that do thermostatting or barostatting and when atom +velocities are created. Computes that calculate one or more values +for each atom in the group can output those values via the dump +custom command. +
+LAMMPS creates its own computes for thermodynamic output and dumping +atom snapshots. Likewise fixes that compute temperature or pressure +create their own computes. These are discussed in the documentation +for thermo_style, dump custom, and +specific fix commands. +
+In all these cases, the default computes can be replaced by computes +defined in the input script, as described by the +thermo_modify and fix modify +commands. Code for new computes can also be added to LAMMPS (see +this section of the manaul) and their +calculations accessed in the various ways described above. +
+Properties of a compute can be modified via the +compute_modify command. +
+Compute can be deleted with the uncompute command. +
+Each compute style has its own doc page which describes its arguments +and what it does. Here is an alphabetic list of compute styles +defined in LAMMPS: +
+Restrictions: none +
+Related commands: +
+ +Default: none +
+ diff --git a/doc/compute.txt b/doc/compute.txt new file mode 100644 index 0000000000..1af41aa58e --- /dev/null +++ b/doc/compute.txt @@ -0,0 +1,81 @@ +"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 command :h3 + +[Syntax:] + +compute ID group-ID style args :pre + +ID = user-assigned name for the computation +group-ID = ID of the group of atoms to perform the computation on +style = one of a list of possible style names (see below) +args = arguments used by a particular style :ul + +[Examples:] + +compute 1 all temp +compute newtemp flow temp/partial 1 1 0 +compute 3 all ke/atom :pre + +[Description:] + +Create a computation that will be performed on a group of atoms. + +In LAMMPS, a "compute" is used in several ways. Computes that +calculate one or more values for the entire group of atoms can output +those values via the "thermo_style custom"_thermo_style.html command. +Or the values can be referenced in a "variable equal"_variable.html +command. Computes that calculate a temperature or pressure are used +by fixes that do thermostatting or barostatting and when atom +velocities are created. Computes that calculate one or more values +for each atom in the group can output those values via the "dump +custom"_dump.html command. + +LAMMPS creates its own computes for thermodynamic output and dumping +atom snapshots. Likewise fixes that compute temperature or pressure +create their own computes. These are discussed in the documentation +for "thermo_style"_thermo_style.html, "dump custom"_dump.html, and +specific "fix"_fix.html commands. + +In all these cases, the default computes can be replaced by computes +defined in the input script, as described by the +"thermo_modify"_thermo_modify.html and "fix modify"_fix_modify.html +commands. Code for new computes can also be added to LAMMPS (see +"this section"_Section_modify.html of the manaul) and their +calculations accessed in the various ways described above. + +Properties of a compute can be modified via the +"compute_modify"_compute_modify.html command. + +Compute can be deleted with the "uncompute"_uncompute.html command. + +Each compute style has its own doc page which describes its arguments +and what it does. Here is an alphabetic list of compute styles +defined in LAMMPS: + +"centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom +"epair/atom"_compute_epair_atom.html - pairwise energy for each atom +"etotal/atom"_compute_etotal_atom.html - total energy (ke + epair) for each atom +"ke/atom"_compute_ke_atom.html - kinetic energy for each atom +"pressure"_compute_pressure.html - total pressure and pressure tensor +"rotate/dipole"_compute_rotate_dipole.html - rotational energy of dipolar atoms +"rotate/gran"_compute_rotate_gran.html - rotational energy of granular atoms +"stress/atom"_compute_stress_atom.html - stress tensor for each atom +"temp"_compute_temp.html - temperature of group of atoms +"temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity +"temp/ramp"_compute_temp_ramp.html - temperature after subtracting a ramped velocity component +"temp/region"_compute_temp_region.html - temperature of a region of atoms :ul + +[Restrictions:] none + +[Related commands:] + +"uncompute"_uncompute.html, "compute_modify"_compute_modify.html + +[Default:] none diff --git a/doc/compute_centro_atom.html b/doc/compute_centro_atom.html new file mode 100644 index 0000000000..95444f9184 --- /dev/null +++ b/doc/compute_centro_atom.html @@ -0,0 +1,61 @@ + +Syntax: +
+compute ID group-ID ke/atom ++
Examples: +
+compute 1 all ke/atom ++
Description: +
+Define a computation that calculates the centro-symmetry parameter for +each atom in a group. This can be output via the dump +custom command. +
+This parameter is computed using the following formula from +(Kelchner) +
+
+where the 12 nearest neighbors are found and Ri and Ri+6 are the +vectors from the central atom to the opposite pair of nearest +neighbors. In solid state systems this is a useful measure of the +local lattice disorder around an atom and can be used to characterize +whether the atom is part of a perfect lattice, a local defect (e.g. a +dislocation or stacking fault), or at a surface. +
+The neighbor list needed to compute this quantity is constructed each +time the calculation is performed (i.e. each time a snapshot of atoms +is dumped). Thus it can be inefficient to compute/dump this quantity +too frequently or to have multiple compute/dump commands, each of a +centro/atom style. +
+Restrictions: none +
+Related commands: none +
+Default: none +
+(Kelchner) Kelchner, Plimpton, Hamilton, Phys Rev B, 58, 11085 (1998). +
+ diff --git a/doc/compute_centro_atom.txt b/doc/compute_centro_atom.txt new file mode 100644 index 0000000000..39bab91c4d --- /dev/null +++ b/doc/compute_centro_atom.txt @@ -0,0 +1,55 @@ +"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 ke/atom command :h3 + +[Syntax:] + +compute ID group-ID ke/atom :pre + +ID, group-ID are documented in "compute"_compute.html command +ke/atom = style name of this compute command :ul + +[Examples:] + +compute 1 all ke/atom :pre + +[Description:] + +Define a computation that calculates the centro-symmetry parameter for +each atom in a group. This can be output via the "dump +custom"_dump.html command. + +This parameter is computed using the following formula from +"(Kelchner)"_#Kelchner + +:c,image(Eqs/centro_symmetry.jpg) + +where the 12 nearest neighbors are found and Ri and Ri+6 are the +vectors from the central atom to the opposite pair of nearest +neighbors. In solid state systems this is a useful measure of the +local lattice disorder around an atom and can be used to characterize +whether the atom is part of a perfect lattice, a local defect (e.g. a +dislocation or stacking fault), or at a surface. + +The neighbor list needed to compute this quantity is constructed each +time the calculation is performed (i.e. each time a snapshot of atoms +is dumped). Thus it can be inefficient to compute/dump this quantity +too frequently or to have multiple compute/dump commands, each of a +{centro/atom} style. + +[Restrictions:] none + +[Related commands:] none + +[Default:] none + +:line + +:link(Kelchner) +[(Kelchner)] Kelchner, Plimpton, Hamilton, Phys Rev B, 58, 11085 (1998). diff --git a/doc/compute_epair_atom.html b/doc/compute_epair_atom.html new file mode 100644 index 0000000000..7197554ef3 --- /dev/null +++ b/doc/compute_epair_atom.html @@ -0,0 +1,52 @@ + +Syntax: +
+compute ID group-ID epair/atom ++
Examples: +
+compute 1 all epair/atom ++
Description: +
+Define a computation that computes the per-atom pairwise energy for +each atom in a group. This can be output via the dump +custom command. +
+The pairwise energy for each atom is computed by looping over its +neighbors and computing the energy associated with the defined +pair_style command for each IJ pair (divided by 2). +Thus the sum of per-atom energy for all atoms should give the total +pairwise energy of the system. +
+For force fields that include a contribution to the pairwise energy +that is computed as part of dihedral terms (i.e. 1-4 interactions), +this contribution is not included in the per-atom pairwise energy. +
+Computation of per-atom pairwise energy requires a loop thru the +neighbor list and inter-processor communication, so it can be +inefficient to compute/dump this quantity too frequently or to have +multiple compute/dump commands, each of a epair/atom style. +
+Restrictions: none +
+Related commands: none +
+Default: none +
+ diff --git a/doc/compute_epair_atom.txt b/doc/compute_epair_atom.txt new file mode 100644 index 0000000000..f970e2c703 --- /dev/null +++ b/doc/compute_epair_atom.txt @@ -0,0 +1,47 @@ +"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 epair/atom command :h3 + +[Syntax:] + +compute ID group-ID epair/atom :pre + +ID, group-ID are documented in "compute"_compute.html command +epair/atom = style name of this compute command :ul + +[Examples:] + +compute 1 all epair/atom :pre + +[Description:] + +Define a computation that computes the per-atom pairwise energy for +each atom in a group. This can be output via the "dump +custom"_dump.html command. + +The pairwise energy for each atom is computed by looping over its +neighbors and computing the energy associated with the defined +"pair_style"_pair_style.html command for each IJ pair (divided by 2). +Thus the sum of per-atom energy for all atoms should give the total +pairwise energy of the system. + +For force fields that include a contribution to the pairwise energy +that is computed as part of dihedral terms (i.e. 1-4 interactions), +this contribution is not included in the per-atom pairwise energy. + +Computation of per-atom pairwise energy requires a loop thru the +neighbor list and inter-processor communication, so it can be +inefficient to compute/dump this quantity too frequently or to have +multiple compute/dump commands, each of a {epair/atom} style. + +[Restrictions:] none + +[Related commands:] none + +[Default:] none diff --git a/doc/compute_etotal_atom.html b/doc/compute_etotal_atom.html new file mode 100644 index 0000000000..d150d212a5 --- /dev/null +++ b/doc/compute_etotal_atom.html @@ -0,0 +1,50 @@ + +Syntax: +
+compute ID group-ID etotal/atom compute-ID ++
Examples: +
+compute 1 all etotal/atom atomEng ++
Description: +
+Define a computation that computes the total energy (kinetic + +pairwise) for each atom in a group. This can be output via the dump +custom command. +
+The kinetic energy for each atom is computed the same way as in the +compute ke/atom command, namely as 1/2 m v^2. +
+The pairwise energy is not calculated by this compute, but rather by +the epair/atom compute specified as the last +argument of the command. +
+Note that the total energy per atom as defined here does not include +contributions due to bonds, angles, etc that the atom is part of. +
+Restrictions: none +
+Related commands: +
+ +Default: none +
+ diff --git a/doc/compute_etotal_atom.txt b/doc/compute_etotal_atom.txt new file mode 100644 index 0000000000..9fdcd6c678 --- /dev/null +++ b/doc/compute_etotal_atom.txt @@ -0,0 +1,45 @@ +"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 etotal/atom command :h3 + +[Syntax:] + +compute ID group-ID etotal/atom compute-ID :pre + +ID, group-ID are documented in "compute"_compute.html command +etotal/atom = style name of this compute command +compute-ID = ID of compute that calculates per-atom pairwise energy :ul + +[Examples:] + +compute 1 all etotal/atom atomEng :pre + +[Description:] + +Define a computation that computes the total energy (kinetic + +pairwise) for each atom in a group. This can be output via the "dump +custom"_dump.html command. + +The kinetic energy for each atom is computed the same way as in the +"compute ke/atom"_compute_ke_atom.html command, namely as 1/2 m v^2. + +The pairwise energy is not calculated by this compute, but rather by +the "epair/atom compute"_compute_epair_atom.html specified as the last +argument of the command. + +Note that the total energy per atom as defined here does not include +contributions due to bonds, angles, etc that the atom is part of. + +[Restrictions:] none + +[Related commands:] + +"compute epair/atom"_compute_epair_atom.html + +[Default:] none diff --git a/doc/compute_ke_atom.html b/doc/compute_ke_atom.html new file mode 100644 index 0000000000..79cca562d5 --- /dev/null +++ b/doc/compute_ke_atom.html @@ -0,0 +1,42 @@ + +Syntax: +
+compute ID group-ID ke/atom ++
Examples: +
+compute 1 all ke/atom ++
Description: +
+Define a computation that calculates the per-atom kinetic energy for +each atom in a group. This can be output via the dump +custom command. +
+The kinetic energy is simply 1/2 m v^2, where m is the mass and v is +the velocity of each atom. +
+Restrictions: none +
+Related commands: +
+ +Default: none +
+ diff --git a/doc/compute_ke_atom.txt b/doc/compute_ke_atom.txt new file mode 100644 index 0000000000..04dc1fc493 --- /dev/null +++ b/doc/compute_ke_atom.txt @@ -0,0 +1,37 @@ +"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 ke/atom command :h3 + +[Syntax:] + +compute ID group-ID ke/atom :pre + +ID, group-ID are documented in "compute"_compute.html command +ke/atom = style name of this compute command :ul + +[Examples:] + +compute 1 all ke/atom :pre + +[Description:] + +Define a computation that calculates the per-atom kinetic energy for +each atom in a group. This can be output via the "dump +custom"_dump.html command. + +The kinetic energy is simply 1/2 m v^2, where m is the mass and v is +the velocity of each atom. + +[Restrictions:] none + +[Related commands:] + +"dump custom"_dump.html + +[Default:] none diff --git a/doc/temp_modify.html b/doc/compute_modify.html similarity index 54% rename from doc/temp_modify.html rename to doc/compute_modify.html index 02f1a75ce2..176b74e1fb 100644 --- a/doc/temp_modify.html +++ b/doc/compute_modify.html @@ -9,13 +9,13 @@Syntax:
-temp_modify temp-ID keyword value ... +compute_modify compute-ID keyword value ...-
Examples:
-temp_modify mine extra 0 -temp_modify mine dynamic yes +compute_modify myTemp extra 0 +compute_modify newtemp dynamic yes extra 600Description:
-Modify the parameters of a previously defined temperature method. -This can either be the default temperature defined by LAMMPS (ID = -default) or a user-defined temperature created by using the -temperature command. +
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 the -temperature computation. The default is 3 which is a correction -factor for an ensemble of velocities with zero total linear momentum. +subtracted (typically from 3N) as a normalizing factor in a +temperature computation. Only computes that compute a temperature use +this option. The default is 3 which is a correction factor for an +ensemble of velocities with zero total linear momentum.
The dynamic keyword determines whether the number of atoms N in the -temperature group is re-computed each time the temperature is -computed. By default, N is assumed to be constant. If you are adding -atoms to the system (see the fix pour or fix +compute group is re-computed each time a temperature is computed. +Only compute styles that compute 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 or fix deposit commands) or expect atoms to be lost (e.g. due to evaporation), then this option can be used to insure the temperature is correctly normalized. @@ -57,7 +57,7 @@ temperature is correctly normalized.
Related commands:
-Default:
diff --git a/doc/temp_modify.txt b/doc/compute_modify.txt similarity index 52% rename from doc/temp_modify.txt rename to doc/compute_modify.txt index ec13f9403d..795c28cda2 100644 --- a/doc/temp_modify.txt +++ b/doc/compute_modify.txt @@ -6,13 +6,13 @@ :line -temp_modify command :h3 +compute_modify command :h3 [Syntax:] -temp_modify temp-ID keyword value ... :pre +compute_modify compute-ID keyword value ... :pre -temp-ID = ID of temperature to modify :ulb,l +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 @@ -23,25 +23,25 @@ keyword = {extra} or {dynamic} :l [Examples:] -temp_modify mine extra 0 -temp_modify mine dynamic yes :pre +compute_modify myTemp extra 0 +compute_modify newtemp dynamic yes extra 600 :pre [Description:] -Modify the parameters of a previously defined temperature method. -This can either be the default temperature defined by LAMMPS (ID = -{default}) or a user-defined temperature created by using the -"temperature"_temperature.html command. +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 the -temperature computation. The default is 3 which is a correction -factor for an ensemble of velocities with zero total linear momentum. +subtracted (typically from 3N) as a normalizing factor in a +temperature computation. Only computes that compute a temperature use +this option. The default is 3 which is a correction factor for an +ensemble of velocities with zero total linear momentum. The {dynamic} keyword determines whether the number of atoms N in the -temperature group is re-computed each time the temperature is -computed. 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 +compute group is re-computed each time a temperature is computed. +Only compute styles that compute 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 can be used to insure the temperature is correctly normalized. @@ -50,7 +50,7 @@ temperature is correctly normalized. [Related commands:] -"temperature"_temperature.html +"compute"_compute.html [Default:] diff --git a/doc/compute_pressure.html b/doc/compute_pressure.html new file mode 100644 index 0000000000..6cb0ae6179 --- /dev/null +++ b/doc/compute_pressure.html @@ -0,0 +1,70 @@ + +LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands + + + + + + + +
+ +compute pressure command +
+Syntax: +
+compute ID group-ID pressure compute-ID ++
Examples: +
+compute 1 all pressure myTemp ++
Description: +
+Define a computation that calculates the pressure of atoms averaged +over the entire system. The specified group must be "all". See the +dump custom command for how to dump the per-atom stress +tensor if you want more localized information about pressure (stress) +in your system. +
+The pressure is computed by the standard formula +
+
+where N is the number of atoms in the system (see discussion of DOF +below), Kb is the Boltzmann constant, T is the temperature, V is the +system volume, and the second term is the virial, computed within +LAMMPS for all pairwise as well as 2-body, 3-body, 4-body bonded +interactions. +
+A 6-component pressure tensor is also calculated by this compute which +can be output by the thermo_style custom command. +The formula for the components of the tensor is the same as in above +formula, except that the first term uses the components of the kinetic +energy tensor (vx * vy instead of v^2 for temperature) and the second +term uses Rx * Fy for the Wxy component of the virial tensor, etc. +
+The temperature and kinetic energy tensor is not calculated by this +compute, but rather by the temperature compute specified as the last +argument of the command. Normally this compute should calculate the +temperature of all atoms for consistency with the virial term, but any +compute style that calculates temperature can be used, e.g. one that +excludes frozen atoms or other degrees of freedom. +
+Note that the N is the above formula is really degrees-of-freedom/3 +where the DOF is specified by the temperature compute. See the +various compute temperature styles for details. +
+Restrictions: none +
+Related commands: +
+ +Default: none +
+ diff --git a/doc/compute_pressure.txt b/doc/compute_pressure.txt new file mode 100644 index 0000000000..c36ad297e9 --- /dev/null +++ b/doc/compute_pressure.txt @@ -0,0 +1,65 @@ +"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 pressure command :h3 + +[Syntax:] + +compute ID group-ID pressure compute-ID :pre + +ID, group-ID are documented in "compute"_compute.html command +pressure = style name of this compute command +compute-ID = ID of compute that calculates temperature :ul + +[Examples:] + +compute 1 all pressure myTemp :pre + +[Description:] + +Define a computation that calculates the pressure of atoms averaged +over the entire system. The specified group must be "all". See the +"dump custom"_dump.html command for how to dump the per-atom stress +tensor if you want more localized information about pressure (stress) +in your system. + +The pressure is computed by the standard formula + +:c,image(Eqs/pressure.jpg) + +where N is the number of atoms in the system (see discussion of DOF +below), Kb is the Boltzmann constant, T is the temperature, V is the +system volume, and the second term is the virial, computed within +LAMMPS for all pairwise as well as 2-body, 3-body, 4-body bonded +interactions. + +A 6-component pressure tensor is also calculated by this compute which +can be output by the "thermo_style custom"_thermo_style.html command. +The formula for the components of the tensor is the same as in above +formula, except that the first term uses the components of the kinetic +energy tensor (vx * vy instead of v^2 for temperature) and the second +term uses Rx * Fy for the Wxy component of the virial tensor, etc. + +The temperature and kinetic energy tensor is not calculated by this +compute, but rather by the temperature compute specified as the last +argument of the command. Normally this compute should calculate the +temperature of all atoms for consistency with the virial term, but any +compute style that calculates temperature can be used, e.g. one that +excludes frozen atoms or other degrees of freedom. + +Note that the N is the above formula is really degrees-of-freedom/3 +where the DOF is specified by the temperature compute. See the +various "compute temperature"_compute.html styles for details. + +[Restrictions:] none + +[Related commands:] + +"compute temp"_compute_temp.html, "thermo_style"_themo_style.html + +[Default:] none diff --git a/doc/compute_rotate_dipole.html b/doc/compute_rotate_dipole.html new file mode 100644 index 0000000000..645303ef8a --- /dev/null +++ b/doc/compute_rotate_dipole.html @@ -0,0 +1,40 @@ + +Syntax: +
+compute ID group-ID rotate/dipole ++
Examples: +
+compute 1 all rotate/dipole ++
Description: +
+Define a computation that calculates the total rotational energy of a +group of dipolar atoms. +
+The rotational energy is calculated as the sum of 1/2 I w^2 over all +the atoms in the group, where I is the moment of inertia of a +disk/spherical (2d/3d) particle, and w is its angular velocity. +
+Restrictions: none +
+Related commands: none +
+Default: none +
+ diff --git a/doc/compute_rotate_dipole.txt b/doc/compute_rotate_dipole.txt new file mode 100644 index 0000000000..ba7d2e32d8 --- /dev/null +++ b/doc/compute_rotate_dipole.txt @@ -0,0 +1,35 @@ +"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 rotate/dipole command :h3 + +[Syntax:] + +compute ID group-ID rotate/dipole :pre + +ID, group-ID are documented in "compute"_compute.html command +rotate/dipole = style name of this compute command :ul + +[Examples:] + +compute 1 all rotate/dipole :pre + +[Description:] + +Define a computation that calculates the total rotational energy of a +group of dipolar atoms. + +The rotational energy is calculated as the sum of 1/2 I w^2 over all +the atoms in the group, where I is the moment of inertia of a +disk/spherical (2d/3d) particle, and w is its angular velocity. + +[Restrictions:] none + +[Related commands:] none + +[Default:] none diff --git a/doc/compute_rotate_gran.html b/doc/compute_rotate_gran.html new file mode 100644 index 0000000000..15c0c3e2cf --- /dev/null +++ b/doc/compute_rotate_gran.html @@ -0,0 +1,40 @@ + +Syntax: +
+compute ID group-ID rotate/gran ++
Examples: +
+compute 1 all rotate/gran ++
Description: +
+Define a computation that calculates the total rotational energy of a +group of granular atoms. +
+The rotational energy is calculated as the sum of 1/2 I w^2 over all +the atoms in the group, where I is the moment of inertia of a +disk/spherical (2d/3d) particle, and w is its angular velocity. +
+Restrictions: none +
+Related commands: none +
+Default: none +
+ diff --git a/doc/compute_rotate_gran.txt b/doc/compute_rotate_gran.txt new file mode 100644 index 0000000000..7c20ecda89 --- /dev/null +++ b/doc/compute_rotate_gran.txt @@ -0,0 +1,35 @@ +"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 rotate/gran command :h3 + +[Syntax:] + +compute ID group-ID rotate/gran :pre + +ID, group-ID are documented in "compute"_compute.html command +rotate/gran = style name of this compute command :ul + +[Examples:] + +compute 1 all rotate/gran :pre + +[Description:] + +Define a computation that calculates the total rotational energy of a +group of granular atoms. + +The rotational energy is calculated as the sum of 1/2 I w^2 over all +the atoms in the group, where I is the moment of inertia of a +disk/spherical (2d/3d) particle, and w is its angular velocity. + +[Restrictions:] none + +[Related commands:] none + +[Default:] none diff --git a/doc/compute_stress_atom.html b/doc/compute_stress_atom.html new file mode 100644 index 0000000000..1234549657 --- /dev/null +++ b/doc/compute_stress_atom.html @@ -0,0 +1,64 @@ + +Syntax: +
+compute ID group-ID stress/atom ++
Examples: +
+compute 1 mobile stress/atom ++
Description: +
+Define a computation that computes the per-atom stress tensor for each +atom in a group. The 6 components can be output via the dump +custom command. +
+The stress tensor is computed for only pairwise forces where the ab +component of stress on atom i is given by +
+
+where the first term is a kinetic energy component for atom i, j +loops over the N neighbors of atom i, and Fb is one of 3 +components of force on atom i due to atom j. Both a and b +take on values x,y,z to generate the 6 components of the symmetric +tensor. +
+Note that this formula for stress does not include virial +contributions from intra-molecular interactions (e.g. bonds, angles, +torsions, etc). Also note that this quantity is the negative of the +per-atom pressure tensor. It is also really a stress-volume +formulation. It would need to be divided by a per-atom volume to have +units of stress, but an individual atom's volume is not easy to +compute in a deformed solid. Thus, if you sum the diagonal components +of the per-atom stress tensor for all atoms in the system and divide +the sum by 3V, where V is the volume of the system, you should get -P, +where P is the total pressure of the system. +
+Computation of per-atom stress tensor components requires a loop thru +the neighbor list and inter-processor communication, so it can be +inefficient to compute/dump this quantity too frequently or to have +multiple compute/dump commands, each of a stress/atom style. +
+Restrictions: none +
+Related commands: none +
+Default: none +
+ diff --git a/doc/compute_stress_atom.txt b/doc/compute_stress_atom.txt new file mode 100644 index 0000000000..d8b4b950c2 --- /dev/null +++ b/doc/compute_stress_atom.txt @@ -0,0 +1,59 @@ +"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 stress/atom command :h3 + +[Syntax:] + +compute ID group-ID stress/atom :pre + +ID, group-ID are documented in "compute"_compute.html command +stress/atom = style name of this compute command :ul + +[Examples:] + +compute 1 mobile stress/atom :pre + +[Description:] + +Define a computation that computes the per-atom stress tensor for each +atom in a group. The 6 components can be output via the "dump +custom"_dump.html command. + +The stress tensor is computed for only pairwise forces where the {ab} +component of stress on atom {i} is given by + +:c,image(Eqs/stress_tensor.jpg) + +where the first term is a kinetic energy component for atom {i}, {j} +loops over the {N} neighbors of atom {i}, and {Fb} is one of 3 +components of force on atom {i} due to atom {j}. Both {a} and {b} +take on values x,y,z to generate the 6 components of the symmetric +tensor. + +Note that this formula for stress does not include virial +contributions from intra-molecular interactions (e.g. bonds, angles, +torsions, etc). Also note that this quantity is the negative of the +per-atom pressure tensor. It is also really a stress-volume +formulation. It would need to be divided by a per-atom volume to have +units of stress, but an individual atom's volume is not easy to +compute in a deformed solid. Thus, if you sum the diagonal components +of the per-atom stress tensor for all atoms in the system and divide +the sum by 3V, where V is the volume of the system, you should get -P, +where P is the total pressure of the system. + +Computation of per-atom stress tensor components requires a loop thru +the neighbor list and inter-processor communication, so it can be +inefficient to compute/dump this quantity too frequently or to have +multiple compute/dump commands, each of a {stress/atom} style. + +[Restrictions:] none + +[Related commands:] none + +[Default:] none diff --git a/doc/compute_temp.html b/doc/compute_temp.html new file mode 100644 index 0000000000..cdad72776e --- /dev/null +++ b/doc/compute_temp.html @@ -0,0 +1,64 @@ + +Syntax: +
+compute ID group-ID temp ++
Examples: +
+compute 1 all temp +compute myTemp mobile temp ++
Description: +
+Define a computation that calculates the temperature of a group of +atoms. A compute of this style can be used by any command that +computes a temperature, e.g. thermo_modify, fix +temp/rescale, fix npt, etc. +
+The temperature is calculated by the formula KE = dim/2 N k T, where +KE = total kinetic energy of the group of 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. +
+A 6-component kinetic energy tensor is also calculated by this compute +for use in the computation of a pressure tensor. The formula for the +components of the tensor is the same as the above formula, except that +v^2 is replaced by vx * vy for the xy component, etc. +
+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 command if this is not the case. +
+This compute subtracts out degrees-of-freedom due to fixes that +constrain molecular motion, such as fix shake and +fix rigid. 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 command. +
+Restrictions: none +
+Related commands: +
+compute temp/partial, compute +temp/region, compute +pressure +
+Default: none +
+ diff --git a/doc/compute_temp.txt b/doc/compute_temp.txt new file mode 100644 index 0000000000..2bbe0bd249 --- /dev/null +++ b/doc/compute_temp.txt @@ -0,0 +1,59 @@ +"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 command :h3 + +[Syntax:] + +compute ID group-ID temp :pre + +ID, group-ID are documented in "compute"_compute.html command +temp = style name of this compute command :ul + +[Examples:] + +compute 1 all temp +compute myTemp mobile temp :pre + +[Description:] + +Define a computation that calculates the temperature of a group of +atoms. 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_npt.html, etc. + +The temperature is calculated by the formula KE = dim/2 N k T, where +KE = total kinetic energy of the group of 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. + +A 6-component kinetic energy tensor is also calculated by this compute +for use in the computation of a pressure tensor. The formula for the +components of the tensor is the same as the above formula, except that +v^2 is replaced by vx * vy for the xy component, etc. + +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 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. + +[Restrictions:] none + +[Related commands:] + +"compute temp/partial"_compute_temp_partial.html, "compute +temp/region"_compute_temp_region.html, "compute +pressure"_compute_pressure.html + +[Default:] none diff --git a/doc/compute_temp_partial.html b/doc/compute_temp_partial.html new file mode 100644 index 0000000000..12b5c0aaaf --- /dev/null +++ b/doc/compute_temp_partial.html @@ -0,0 +1,68 @@ + +Syntax: +
+compute ID group-ID temp/partial xflag yflag zflag ++
Examples: +
+compute newT flow temp/partial 1 1 0 ++
Description: +
+Define a compute to calculate the temperature of a group of atoms, +after excluding one or more velocity components. A compute of this +style can be used by any command that computes a temperature, +e.g. thermo_modify, fix +temp/rescale, fix npt, etc. +
+The temperature is calculated by the formula KE = dim/2 N k T, where +KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), +dim = dimensionality of the simulation, N = number of atoms in the +group, k = Boltzmann constant, and T = temperature. The calculation +of KE excludes the x, y, or z dimensions if xflag, yflag, or zflag = +0. The dim parameter is adjusted to give the correct number of +degrees of freedom. +
+A 6-component kinetic energy tensor is also calculated by this compute +for use in the calculation of a pressure tensor. The formula for the +components of the tensor is the same as the above formula, except that +v^2 is replaced by vx * vy for the xy component, etc. +
+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 command if this is not the case. +
+This compute subtracts out degrees-of-freedom due to fixes that +constrain molecular motion, such as fix shake and +fix rigid. 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 command. +
+Restrictions: none +
+Related commands: +
+compute temp, compute +temp/region, compute +pressure +
+Default: none +
+ diff --git a/doc/compute_temp_partial.txt b/doc/compute_temp_partial.txt new file mode 100644 index 0000000000..273acad20e --- /dev/null +++ b/doc/compute_temp_partial.txt @@ -0,0 +1,63 @@ +"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/partial command :h3 + +[Syntax:] + +compute ID group-ID temp/partial xflag yflag zflag :pre + +ID, group-ID are documented in "compute"_compute.html command +temp/partial = style name of this compute command +xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension :ul + +[Examples:] + +compute newT flow temp/partial 1 1 0 :pre + +[Description:] + +Define a compute to calculate the temperature of a group of atoms, +after excluding one or more velocity components. 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_npt.html, etc. + +The temperature is calculated by the formula KE = dim/2 N k T, where +KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), +dim = dimensionality of the simulation, N = number of atoms in the +group, k = Boltzmann constant, and T = temperature. The calculation +of KE excludes the x, y, or z dimensions if xflag, yflag, or zflag = +0. The dim parameter is adjusted to give the correct number of +degrees of freedom. + +A 6-component kinetic energy tensor is also calculated by this compute +for use in the calculation of a pressure tensor. The formula for the +components of the tensor is the same as the above formula, except that +v^2 is replaced by vx * vy for the xy component, etc. + +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 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. + +[Restrictions:] none + +[Related commands:] + +"compute temp"_compute_temp.html, "compute +temp/region"_compute_temp_region.html, "compute +pressure"_compute_pressure.html + +[Default:] none diff --git a/doc/compute_temp_ramp.html b/doc/compute_temp_ramp.html new file mode 100644 index 0000000000..01fdf2de29 --- /dev/null +++ b/doc/compute_temp_ramp.html @@ -0,0 +1,82 @@ + +Syntax: +
+compute ID group-ID temp/ramp vdim vlo vhi dim clo chi keyword value ... ++
units value = lattice or box ++
Examples: +
+temperature 2nd middle ramp vx 0 8 y 2 12 units lattice ++
Description: +
+Define a computation that calculates the temperature of a group of +atoms, while subtracting out an imposed velocity on the system before +computing the kinetic energy. A compute of this style can be used by +any command that computes a temperature, +e.g. thermo_modify, fix +temp/rescale, fix npt, etc. +
+The meaning of the arguments for this command is the same as for the +velocity command which was presumably used to impose +the velocity. +
+The units keyword determines the meaning of the distance units used +for coordinates (c1,c2) and velocities (vlo,vhi). A box value +selects standard distance units as defined by the units +command, e.g. Angstroms for units = real or metal. A lattice value +means the distance units are in lattice spacings; e.g. velocity = +lattice spacings / tau. The lattice command must have +been previously used to define the lattice spacing. +
+A 6-component kinetic energy tensor is also calculated by this compute +for use in the calculation of a pressure tensor. The formula for the +components of the tensor is the same as the above formula, except that +v^2 is replaced by vx * vy for the xy component, etc. +
+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 command if this is not the case. +
+This compute subtracts out degrees-of-freedom due to fixes that +constrain molecular motion, such as fix shake and +fix rigid. 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 command. +
+Restrictions: none +
+Related commands: +
+compute temp, compute +temp/region, compute +pressure +
+Default: +
+The option default is units = lattice. +
+ diff --git a/doc/compute_temp_ramp.txt b/doc/compute_temp_ramp.txt new file mode 100644 index 0000000000..a84df80e19 --- /dev/null +++ b/doc/compute_temp_ramp.txt @@ -0,0 +1,77 @@ +"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/ramp command :h3 + +[Syntax:] + +compute ID group-ID temp/ramp vdim vlo vhi dim clo chi keyword value ... :pre + +ID, group-ID are documented in "compute"_compute.html command +temp/ramp = style name of this compute command +vdim = {vx} or {vy} or {vz} +vlo,vhi = subtract velocities between vlo and vhi (velocity units) +dim = {x} or {y} or {z} +clo,chi = lower and upper bound of domain to subtract from (distance units) +zero or more keyword/value pairs may be appended to the args +keyword = {units} :ul + {units} value = {lattice} or {box} :pre + +[Examples:] + +temperature 2nd middle ramp vx 0 8 y 2 12 units lattice :pre + +[Description:] + +Define a computation that calculates the temperature of a group of +atoms, while subtracting out an imposed velocity on the system before +computing the kinetic energy. 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_npt.html, etc. + +The meaning of the arguments for this command is the same as for the +"velocity"_velocity.html command which was presumably used to impose +the velocity. + +The {units} keyword determines the meaning of the distance units used +for coordinates (c1,c2) and velocities (vlo,vhi). A {box} value +selects standard distance units as defined by the "units"_units.html +command, e.g. Angstroms for units = real or metal. A {lattice} value +means the distance units are in lattice spacings; e.g. velocity = +lattice spacings / tau. The "lattice"_lattice.html command must have +been previously used to define the lattice spacing. + +A 6-component kinetic energy tensor is also calculated by this compute +for use in the calculation of a pressure tensor. The formula for the +components of the tensor is the same as the above formula, except that +v^2 is replaced by vx * vy for the xy component, etc. + +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 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. + +[Restrictions:] none + +[Related commands:] + +"compute temp"_compute_temp.html, "compute +temp/region"_compute_temp_region.html, "compute +pressure"_compute_pressure.html + +[Default:] + +The option default is units = lattice. + diff --git a/doc/compute_temp_region.html b/doc/compute_temp_region.html new file mode 100644 index 0000000000..7a311bc188 --- /dev/null +++ b/doc/compute_temp_region.html @@ -0,0 +1,76 @@ + +Syntax: +
+compute ID group-ID temp/region region-ID ++
Examples: +
+temperature mine flow region boundary ++
Description: +
+Define a computation that calculates the temperature of a group of +atoms in a geometric region. This can be useful for thermostatting +one portion of the simulation box. E.g. a McDLT simulation where one +side is cooled, and the other side is heated. A compute of this style +can be used by any command that computes a temperature, +e.g. thermo_modify, fix +temp/rescale, etc. +
+Note that a region-style temperature can be used to thermostat with +fix temp/rescale or fix +langevin, but should probably not be used with +Nose/Hoover style fixes (>fix nvt, fix +npt, or fix nph), if the +degrees-of-freedom included in the computed T varies with time. +
+The temperature is calculated by the formula KE = dim/2 N k T, where +KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), +dim = 2 or 3 = dimensionality of the simulation, N = number of atoms +in both the group and region, k = Boltzmann constant, and T = +temperature. +
+A 6-component kinetic energy tensor is also calculated by this compute +for use in the computation of a pressure tensor. The formula for the +components of the tensor is the same as the above formula, except that +v^2 is replaced by vx * vy for the xy component, etc. +
+The number of atoms contributing to the temperature is compute each +time the temperature is evaluated since it is assumed atoms can +enter/leave the region. Thus there is no need to use the dynamic +option of the compute_modify command for this +compute style. +
+Unlike other compute styles that calculate temperature, this compute +does NOT currently subtract out degrees-of-freedom due to fixes that +constrain molecular motion, such as fix shake and +fix rigid. If needed the subtracted +degrees-of-freedom can be altered using the extra option of the +compute_modify command. +
+Restrictions: none +
+Related commands: +
+compute temp, compute +pressure +
+Default: none +
+ diff --git a/doc/compute_temp_region.txt b/doc/compute_temp_region.txt new file mode 100644 index 0000000000..a3d1bbfbe3 --- /dev/null +++ b/doc/compute_temp_region.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 + +compute temp/region command :h3 + +[Syntax:] + +compute ID group-ID temp/region region-ID :pre + +ID, group-ID are documented in "compute"_compute.html command +temp/region = style name of this compute command +region-ID = ID of region to use for choosing atoms :ul + +[Examples:] + +temperature mine flow region boundary :pre + +[Description:] + +Define a computation that calculates the temperature of a group of +atoms in a geometric region. This can be useful for thermostatting +one portion of the simulation box. E.g. a McDLT simulation where one +side is cooled, and the other side is heated. 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, etc. + +Note that a {region}-style temperature can be used to thermostat with +"fix temp/rescale"_fix_temp_rescale.html or "fix +langevin"_fix_langevin.html, but should probably not be used with +Nose/Hoover style fixes ("fix nvt"_fix_nvt.html, fix +npt"_fix_npt.html, or "fix nph"_fix_nph.html), if the +degrees-of-freedom included in the computed T varies with time. + +The temperature is calculated by the formula KE = dim/2 N k T, where +KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), +dim = 2 or 3 = dimensionality of the simulation, N = number of atoms +in both the group and region, k = Boltzmann constant, and T = +temperature. + +A 6-component kinetic energy tensor is also calculated by this compute +for use in the computation of a pressure tensor. The formula for the +components of the tensor is the same as the above formula, except that +v^2 is replaced by vx * vy for the xy component, etc. + +The number of atoms contributing to the temperature is compute each +time the temperature is evaluated since it is assumed atoms can +enter/leave the region. Thus there is no need to use the {dynamic} +option of the "compute_modify"_compute_modify.html command for this +compute style. + +Unlike other compute styles that calculate temperature, this compute +does NOT currently subtract out degrees-of-freedom due to fixes that +constrain molecular motion, such as "fix shake"_fix_shake.html and +"fix rigid"_fix_rigid.html. If needed the subtracted +degrees-of-freedom can be altered using the {extra} option of the +"compute_modify"_compute_modify.html command. + +[Restrictions:] none + +[Related commands:] + +"compute temp"_compute_temp.html, "compute +pressure"_compute_pressure.html + +[Default:] none diff --git a/doc/dihedral_style_charmm.html b/doc/dihedral_charmm.html similarity index 100% rename from doc/dihedral_style_charmm.html rename to doc/dihedral_charmm.html diff --git a/doc/dihedral_style_charmm.txt b/doc/dihedral_charmm.txt similarity index 100% rename from doc/dihedral_style_charmm.txt rename to doc/dihedral_charmm.txt diff --git a/doc/dihedral_style_class2.html b/doc/dihedral_class2.html similarity index 100% rename from doc/dihedral_style_class2.html rename to doc/dihedral_class2.html diff --git a/doc/dihedral_style_class2.txt b/doc/dihedral_class2.txt similarity index 100% rename from doc/dihedral_style_class2.txt rename to doc/dihedral_class2.txt diff --git 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doc/dihedral_hybrid.txt diff --git a/doc/dihedral_style_multi_harmonic.html b/doc/dihedral_multi_harmonic.html similarity index 100% rename from doc/dihedral_style_multi_harmonic.html rename to doc/dihedral_multi_harmonic.html diff --git a/doc/dihedral_style_multi_harmonic.txt b/doc/dihedral_multi_harmonic.txt similarity index 100% rename from doc/dihedral_style_multi_harmonic.txt rename to doc/dihedral_multi_harmonic.txt diff --git a/doc/dihedral_style_none.html b/doc/dihedral_none.html similarity index 100% rename from doc/dihedral_style_none.html rename to doc/dihedral_none.html diff --git a/doc/dihedral_style_none.txt b/doc/dihedral_none.txt similarity index 100% rename from doc/dihedral_style_none.txt rename to doc/dihedral_none.txt diff --git a/doc/dihedral_style_opls.html b/doc/dihedral_opls.html similarity index 100% rename from doc/dihedral_style_opls.html rename to doc/dihedral_opls.html diff --git a/doc/dihedral_style_opls.txt b/doc/dihedral_opls.txt similarity index 100% rename from doc/dihedral_style_opls.txt rename to doc/dihedral_opls.txt diff --git a/doc/improper_style_class2.html b/doc/improper_class2.html similarity index 100% rename from doc/improper_style_class2.html rename to doc/improper_class2.html diff --git a/doc/improper_style_class2.txt b/doc/improper_class2.txt similarity index 100% rename from doc/improper_style_class2.txt rename to doc/improper_class2.txt diff --git a/doc/improper_style_cvff.html b/doc/improper_cvff.html similarity index 100% rename from doc/improper_style_cvff.html rename to doc/improper_cvff.html diff --git a/doc/improper_style_cvff.txt b/doc/improper_cvff.txt similarity index 100% rename from doc/improper_style_cvff.txt rename to doc/improper_cvff.txt diff --git a/doc/improper_style_harmonic.html b/doc/improper_harmonic.html similarity index 100% rename from doc/improper_style_harmonic.html rename to doc/improper_harmonic.html diff --git a/doc/improper_style_harmonic.txt b/doc/improper_harmonic.txt similarity index 100% rename from doc/improper_style_harmonic.txt rename to doc/improper_harmonic.txt diff --git a/doc/improper_style_hybrid.html b/doc/improper_hybrid.html similarity index 100% rename from doc/improper_style_hybrid.html rename to doc/improper_hybrid.html diff --git a/doc/improper_style_hybrid.txt b/doc/improper_hybrid.txt similarity index 100% rename from doc/improper_style_hybrid.txt rename to doc/improper_hybrid.txt diff --git a/doc/improper_style_none.html b/doc/improper_none.html similarity index 100% rename from doc/improper_style_none.html rename to doc/improper_none.html diff --git a/doc/improper_style_none.txt b/doc/improper_none.txt similarity index 100% rename from doc/improper_style_none.txt rename to doc/improper_none.txt diff --git a/doc/pair_style_buck.html b/doc/pair_buck.html similarity index 97% rename from doc/pair_style_buck.html rename to doc/pair_buck.html index c6ad4e203a..bfd0522bfd 100644 --- a/doc/pair_style_buck.html +++ b/doc/pair_buck.html @@ -58,7 +58,7 @@ Lennard-Jones 12/6) given byRc is the cutoff.
The buck/coul/cut and buck/coul/long styles add a Coulombic term -as described for the lj/cut pair styles. +as described for the lj/cut pair styles.
The following coefficients must be defined for each pair of atoms types via the pair_coeff command as in the examples diff --git a/doc/pair_style_buck.txt b/doc/pair_buck.txt similarity index 98% rename from doc/pair_style_buck.txt rename to doc/pair_buck.txt index 33ff85369c..49aaa35044 100644 --- a/doc/pair_style_buck.txt +++ b/doc/pair_buck.txt @@ -52,7 +52,7 @@ Lennard-Jones 12/6) given by Rc is the cutoff. The {buck/coul/cut} and {buck/coul/long} styles add a Coulombic term -as described for the "lj/cut"_pair_style_lj.html pair styles. +as described for the "lj/cut"_pair_lj.html pair styles. The following coefficients must be defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in the examples diff --git a/doc/pair_style_charmm.html b/doc/pair_charmm.html similarity index 87% rename from doc/pair_style_charmm.html rename to doc/pair_charmm.html index 347d429f77..6890064dc2 100644 --- a/doc/pair_style_charmm.html +++ b/doc/pair_charmm.html @@ -15,11 +15,13 @@
Syntax:
pair_style style args-
lj/charmm/coul/charmm args = inner outer (inner2) (outer2) @@ -45,6 +47,7 @@ pair_coeff * * 100.0 2.0 pair_coeff 1 1 100.0 2.0 150.0 3.5
pair_style lj/charmm/coul/long 8.0 10.0 +pair_style lj/charmm/coul/long/opt 8.0 10.0 pair_style lj/charmm/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 @@ -83,6 +86,11 @@ applied to the Coulombic term, as in the discussion for pair style command, then the outer LJ cutoff is used as the single Coulombic cutoff. +Style lj/charmm/coul/long/opt is an optimized version of style +lj/charmm/coul/long that should give identical answers. Depending +on system size and the processor you are running on, it may be 5-25% +faster (for the pairwise portion of the run time). +
The following coefficients must be defined for each pair of atoms types via the pair_coeff command as in the examples above, or in the data file or restart files read by the @@ -109,9 +117,11 @@ the pair_style command.
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 package(s). See the Making -LAMMPS section for more info. +style is part of the "kspace" package. The lj/charmm/coul/long/opt +style is part of the "opt" package and also requires the "kspace" +package. They are only enabled if LAMMPS was built with those +package(s). See the Making LAMMPS section +for more info.
On some 64-bit machines, compiling with -O3 appears to break the Coulombic tabling option used by the lj/charmm/coul/long style. See diff --git a/doc/pair_style_charmm.txt b/doc/pair_charmm.txt similarity index 87% rename from doc/pair_style_charmm.txt rename to doc/pair_charmm.txt index 26ce8d1ede..3ed6b22804 100644 --- a/doc/pair_style_charmm.txt +++ b/doc/pair_charmm.txt @@ -9,12 +9,13 @@ pair_style lj/charmm/coul/charmm command :h3 pair_style lj/charmm/coul/charmm/implicit command :h3 pair_style lj/charmm/coul/long command :h3 +pair_style lj/charmm/coul/long/opt command :h3 [Syntax:] pair_style style args :pre -style = {lj/charmm/coul/charmm} or {lj/charmm/coul/charmm/implicit} or {lj/charmm/coul/long} +style = {lj/charmm/coul/charmm} or {lj/charmm/coul/charmm/implicit} or {lj/charmm/coul/long} or {lj/charmm/coul/long/opt} 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) @@ -39,6 +40,7 @@ pair_coeff * * 100.0 2.0 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/opt 8.0 10.0 pair_style lj/charmm/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 @@ -77,6 +79,11 @@ applied to the Coulombic term, as in the discussion for pair style command, then the outer LJ cutoff is used as the single Coulombic cutoff. +Style {lj/charmm/coul/long/opt} is an optimized version of style +{lj/charmm/coul/long} that should give identical answers. Depending +on system size and the processor you are running on, it may be 5-25% +faster (for the pairwise portion of the run time). + 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 @@ -103,9 +110,11 @@ the pair_style command. 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 package(s). See the "Making -LAMMPS"_Section_start.html#2_2 section for more info. +style is part of the "kspace" package. The {lj/charmm/coul/long/opt} +style is part of the "opt" package and also requires the "kspace" +package. They are only enabled if LAMMPS was built with those +package(s). See the "Making LAMMPS"_Section_start.html#2_3 section +for more info. On some 64-bit machines, compiling with -O3 appears to break the Coulombic tabling option used by the {lj/charmm/coul/long} style. See diff --git a/doc/pair_style_class2.html b/doc/pair_class2.html similarity index 97% rename from doc/pair_style_class2.html rename to doc/pair_class2.html index 5cbf5eb1b1..f744574b98 100644 --- a/doc/pair_style_class2.html +++ b/doc/pair_class2.html @@ -57,7 +57,7 @@ pair_coeff 1 1 100.0 3.5 9.0
Rc is the cutoff.
The lj/class2/coul/cut and lj/class2/coul/long styles add a -Coulombic term as described for the lj/cut pair +Coulombic term as described for the lj/cut pair styles.
See (Sun) for a description of the COMPASS class2 force field. diff --git a/doc/pair_style_class2.txt b/doc/pair_class2.txt similarity index 97% rename from doc/pair_style_class2.txt rename to doc/pair_class2.txt index aac3710f52..d2da005415 100644 --- a/doc/pair_style_class2.txt +++ b/doc/pair_class2.txt @@ -51,7 +51,7 @@ The {lj/class2} styles compute a 6/9 Lennard-Jones potential given by Rc is the cutoff. The {lj/class2/coul/cut} and {lj/class2/coul/long} styles add a -Coulombic term as described for the "lj/cut"_pair_style_lj.html pair +Coulombic term as described for the "lj/cut"_pair_lj.html pair styles. See "(Sun)"_#Sun for a description of the COMPASS class2 force field. diff --git a/doc/pair_style_dpd.html b/doc/pair_dpd.html similarity index 100% rename from doc/pair_style_dpd.html rename to doc/pair_dpd.html diff --git a/doc/pair_style_dpd.txt b/doc/pair_dpd.txt similarity index 100% rename from doc/pair_style_dpd.txt rename to doc/pair_dpd.txt diff --git a/doc/pair_style_eam.html b/doc/pair_eam.html similarity index 92% rename from doc/pair_style_eam.html rename to doc/pair_eam.html index ca2c94d78d..2a0f090ce7 100644 --- a/doc/pair_style_eam.html +++ b/doc/pair_eam.html @@ -19,18 +19,21 @@
pair_style style-
Examples:
pair_style eam +pair_style eam/opt pair_coeff * * cuu3 pair_coeff 1*3 1*3 niu3.eam
pair_style eam/alloy +pair_style eam/alloy/opt pair_coeff * * ../potentials/nialhjea.eam.alloy Ni Al Ni Ni
pair_style eam/fs +pair_style eam/fs/opt pair_coeff * * nialhjea.eam.fs Ni Al Ni Ni
Description: @@ -48,6 +51,11 @@ nature of the EAM potential is a result of the embedding energy term. Both summations in the formula are over all neighbors J of atom I within the cutoff distance.
+Style eam/opt is an optimized version of style eam that should +give identical answers. Depending on system size and the processor +you are running on, it may be 5-25% faster (for the pairwise portion +of the run time). +
The cutoff distance and the tabulated values of the functionals F, rho, and phi are listed in one or more files which are specified by the pair_coeff command. These are ASCII text files @@ -145,6 +153,11 @@ above, setfl files contain explicit tabulated values for alloy interactions. Thus they allow more generality than funcfl files for modeling alloys.
+Style eam/alloy/opt is an optimized version of style eam/alloy +that should give identical answers. Depending on system size and the +processor you are running on, it may be 5-25% faster (for the pairwise +portion of the run time). +
For style eam/alloy, potential values are read from a file that is in the DYNAMO multi-element setfl format, except that element names (Ni, Cu, etc) are added to one of the lines in the file. If the @@ -236,6 +249,11 @@ so that different elements can contribute differently to the total electron density at an atomic site depending on the identity of the element at that atomic site.
+Style eam/fs/opt is an optimized version of style eam/fs that +should give identical answers. Depending on system size and the +processor you are running on, it may be 5-25% faster (for the pairwise +portion of the run time). +
The associated pair_coeff command for style eam/fs reads a DYNAMO setfl file that has been extended to include additional rho_alpha_beta arrays of tabulated values. A discussion of @@ -298,7 +316,11 @@ are listed.
Restrictions: none +
Restrictions: +
+The opt styles are part of the "opt" package. They are only enabled +if LAMMPS was built with that package. See the Making +LAMMPS section for more info.
Related commands:
diff --git a/doc/pair_style_eam.txt b/doc/pair_eam.txt similarity index 92% rename from doc/pair_style_eam.txt rename to doc/pair_eam.txt index 10a742d2e2..6949244b7a 100644 --- a/doc/pair_style_eam.txt +++ b/doc/pair_eam.txt @@ -14,18 +14,21 @@ pair_style eam/fs command :h3 pair_style style :pre -style = {eam} or {eam/alloy} or {eam/fs} :ul +style = {eam} or {eam/alloy} or {eam/fs} or {eam/opt} or {eam/alloy/opt} or {eam/fs/opt} :ul [Examples:] pair_style eam +pair_style eam/opt pair_coeff * * cuu3 pair_coeff 1*3 1*3 niu3.eam :pre pair_style eam/alloy +pair_style eam/alloy/opt pair_coeff * * ../potentials/nialhjea.eam.alloy Ni Al Ni Ni :pre pair_style eam/fs +pair_style eam/fs/opt pair_coeff * * nialhjea.eam.fs Ni Al Ni Ni :pre [Description:] @@ -43,6 +46,11 @@ nature of the EAM potential is a result of the embedding energy term. Both summations in the formula are over all neighbors J of atom I within the cutoff distance. +Style {eam/opt} is an optimized version of style {eam} that should +give identical answers. Depending on system size and the processor +you are running on, it may be 5-25% faster (for the pairwise portion +of the run time). + The cutoff distance and the tabulated values of the functionals F, rho, and phi are listed in one or more files which are specified by the "pair_coeff"_pair_coeff.html command. These are ASCII text files @@ -140,6 +148,11 @@ above, {setfl} files contain explicit tabulated values for alloy interactions. Thus they allow more generality than {funcfl} files for modeling alloys. +Style {eam/alloy/opt} is an optimized version of style {eam/alloy} +that should give identical answers. Depending on system size and the +processor you are running on, it may be 5-25% faster (for the pairwise +portion of the run time). + For style {eam/alloy}, potential values are read from a file that is in the DYNAMO multi-element {setfl} format, except that element names (Ni, Cu, etc) are added to one of the lines in the file. If the @@ -231,6 +244,11 @@ so that different elements can contribute differently to the total electron density at an atomic site depending on the identity of the element at that atomic site. +Style {eam/fs/opt} is an optimized version of style {eam/fs} that +should give identical answers. Depending on system size and the +processor you are running on, it may be 5-25% faster (for the pairwise +portion of the run time). + The associated "pair_coeff"_pair_coeff.html command for style {eam/fs} reads a DYNAMO {setfl} file that has been extended to include additional rho_alpha_beta arrays of tabulated values. A discussion of @@ -293,7 +311,11 @@ are listed. :line -[Restrictions:] none +[Restrictions:] + +The {opt} styles are part of the "opt" package. They are only enabled +if LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#2_3 section for more info. [Related commands:] diff --git a/doc/pair_style_gran.html b/doc/pair_gran.html similarity index 100% rename from doc/pair_style_gran.html rename to doc/pair_gran.html diff --git a/doc/pair_style_gran.txt b/doc/pair_gran.txt similarity index 100% rename from doc/pair_style_gran.txt rename to doc/pair_gran.txt diff --git a/doc/pair_style_hybrid.html b/doc/pair_hybrid.html similarity index 100% rename from doc/pair_style_hybrid.html rename to doc/pair_hybrid.html diff --git a/doc/pair_style_hybrid.txt b/doc/pair_hybrid.txt similarity index 100% rename from doc/pair_style_hybrid.txt rename to doc/pair_hybrid.txt diff --git a/doc/pair_style_lj.html b/doc/pair_lj.html similarity index 81% rename from doc/pair_style_lj.html rename to doc/pair_lj.html index c26d5505cf..bc5479fcd9 100644 --- a/doc/pair_style_lj.html +++ b/doc/pair_lj.html @@ -11,6 +11,8 @@pair_style style args-
lj/cut args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
+ lj/cut/opt args = cutoff
+ cutoff = global cutoff for Lennard Jones interactions (distance units)
lj/cut/coul/cut args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
@@ -48,6 +52,7 @@
Examples:
pair_style lj/cut 2.5
+pair_style lj/cut/opt 2.5
pair_coeff * * 1 1
pair_coeff 1 1 1 1.1 2.8
@@ -82,6 +87,11 @@ given by
Rc is the cutoff.
+Style lj/cut/opt is an optimized version of style lj/cut that
+should give identical answers. Depending on system size and the
+processor you are running on, it may be 5-25% faster (for the pairwise
+portion of the run time).
+
Style lj/cut/coul/cut adds a Coulombic pairwise interaction given by
@@ -114,9 +124,16 @@ interactions outside that distance are computed in K-space.
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
-massless charge site are specified as pair_style arguments. See the
-howto section for more information on how to
-use this pair style.
+massless charge site are specified as pair_style arguments.
+
+IMPORTANT NOTE: For each TIP4P water molecule in your system, the atom
+IDs for the O and 2 H atoms must be consecutive, with the O atom
+first. This is to enable LAMMPS to "find" the 2 H atoms associated
+with each O atom. For example, if the atom ID of an O atom in a TIP4P
+water molecule is 500, then its 2 H atoms must have IDs 501 and 502.
+
+See the howto section for more information on
+how to use the TIP4P pair style.
The following coefficients must be defined for each pair of atoms
types via the pair_coeff command as in the examples
@@ -148,8 +165,10 @@ Coulombic cutoff specified in the pair_style command.
Restrictions:
-The lj/cut/coul/long styles is part of the "kspace" package. It is
-only enabled if LAMMPS was built with that package. See the Making
+The lj/cut/coul/long style is part of the "kspace" package. It is
+only enabled if LAMMPS was built with that package. The lj/cut/opt
+style is part of the "opt" package. It is only enabled if LAMMPS was
+built with that package. See the Making
LAMMPS section for more info.
On some 64-bit machines, compiling with -O3 appears to break the
diff --git a/doc/pair_style_lj.txt b/doc/pair_lj.txt
similarity index 80%
rename from doc/pair_style_lj.txt
rename to doc/pair_lj.txt
index 25ac0ff6c7..5730d0a91c 100644
--- a/doc/pair_style_lj.txt
+++ b/doc/pair_lj.txt
@@ -7,6 +7,7 @@
:line
pair_style lj/cut command :h3
+pair_style lj/cut/opt command :h3
pair_style lj/cut/coul/cut command :h3
pair_style lj/cut/coul/debye command :h3
pair_style lj/cut/coul/long command :h3
@@ -16,11 +17,13 @@ pair_style lj/cut/coul/long/tip4p command :h3
pair_style style args :pre
-style = {lj/cut} or {lj/cut/coul/cut} or {lj/cut/coul/debye} or \
-{lj/cut/coul/long} or {lj/cut/coul/long/tip4p}
+style = {lj/cut} or {lj/cut/opt} or {lj/cut/coul/cut} or {lj/cut/coul/debye} \
+ or {lj/cut/coul/long} or {lj/cut/coul/long/tip4p}
args = list of arguments for a particular style :ul
{lj/cut} args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
+ {lj/cut/opt} args = cutoff
+ cutoff = global cutoff for Lennard Jones interactions (distance units)
{lj/cut/coul/cut} args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
@@ -41,6 +44,7 @@ args = list of arguments for a particular style :ul
[Examples:]
pair_style lj/cut 2.5
+pair_style lj/cut/opt 2.5
pair_coeff * * 1 1
pair_coeff 1 1 1 1.1 2.8 :pre
@@ -75,6 +79,11 @@ given by
Rc is the cutoff.
+Style {lj/cut/opt} is an optimized version of style {lj/cut} that
+should give identical answers. Depending on system size and the
+processor you are running on, it may be 5-25% faster (for the pairwise
+portion of the run time).
+
Style {lj/cut/coul/cut} adds a Coulombic pairwise interaction given by
:c,image(Eqs/pair_coulomb.jpg)
@@ -107,9 +116,16 @@ Style {lj/cut/coul/long/tip4p} implements the TIP4P water model of
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
-massless charge site are specified as pair_style arguments. See the
-"howto section"_Section_howto.html#4_8 for more information on how to
-use this pair style.
+massless charge site are specified as pair_style arguments.
+
+IMPORTANT NOTE: For each TIP4P water molecule in your system, the atom
+IDs for the O and 2 H atoms must be consecutive, with the O atom
+first. This is to enable LAMMPS to "find" the 2 H atoms associated
+with each O atom. For example, if the atom ID of an O atom in a TIP4P
+water molecule is 500, then its 2 H atoms must have IDs 501 and 502.
+
+See the "howto section"_Section_howto.html#4_8 for more information on
+how to use the TIP4P 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
@@ -141,9 +157,11 @@ Coulombic cutoff specified in the pair_style command.
[Restrictions:]
-The {lj/cut/coul/long} styles is part of the "kspace" package. It is
-only enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#2_2 section for more info.
+The {lj/cut/coul/long} style is part of the "kspace" package. It is
+only enabled if LAMMPS was built with that package. The {lj/cut/opt}
+style is part of the "opt" 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.
On some 64-bit machines, compiling with -O3 appears to break the
Coulombic tabling option used by the {lj/cut/coul/long} style. See
diff --git a/doc/pair_style_lj_expand.html b/doc/pair_lj_expand.html
similarity index 100%
rename from doc/pair_style_lj_expand.html
rename to doc/pair_lj_expand.html
diff --git a/doc/pair_style_lj_expand.txt b/doc/pair_lj_expand.txt
similarity index 100%
rename from doc/pair_style_lj_expand.txt
rename to doc/pair_lj_expand.txt
diff --git a/doc/pair_style_lj_smooth.html b/doc/pair_lj_smooth.html
similarity index 100%
rename from doc/pair_style_lj_smooth.html
rename to doc/pair_lj_smooth.html
diff --git a/doc/pair_style_lj_smooth.txt b/doc/pair_lj_smooth.txt
similarity index 100%
rename from doc/pair_style_lj_smooth.txt
rename to doc/pair_lj_smooth.txt
diff --git a/doc/pair_style_meam.html b/doc/pair_meam.html
similarity index 95%
rename from doc/pair_style_meam.html
rename to doc/pair_meam.html
index 95eec0a590..3fdfd3a095 100644
--- a/doc/pair_style_meam.html
+++ b/doc/pair_meam.html
@@ -26,7 +26,7 @@ pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni
Style meam computes pairwise interactions for a variety of materials
using modified embedded-atom method (MEAM) potentials
(Baskes). Conceptually, it is an extension to the original
-EAM potentials which adds angular forces. It is
+EAM potentials which adds angular forces. It is
thus suitable for modeling metals and alloys with fcc, bcc, hcp and
diamond cubic structures, as well as covalently bonded materials like
silicon and carbon.
@@ -50,7 +50,7 @@ These are ASCII text files in a format consistent with other MD codes
that implement MEAM potentials, such as the serial DYNAMO code and
Warp. Several MEAM potential files with parameters for different
materials are included in the "potentials" directory of the LAMMPS
-distribution with a ",meam" suffix. All of these are parameterized in
+distribution with a ".meam" suffix. All of these are parameterized in
terms of LAMMPS metal units.
Note that unlike for other potentials, cutoffs for MEAM potentials are
@@ -178,8 +178,8 @@ where N is the number of MEAM elements being used.
rho0(2) = 2.25
alpha(1,2) = 4.37
-mean set rho0 for the 2nd element to the value 2.25 and set alpha for
-the alloy interaction between elements 1 and 2 to 4.37.
+
set rho0 for the 2nd element to the value 2.25 and set alpha for the
+alloy interaction between elements 1 and 2 to 4.37.
@@ -187,7 +187,7 @@ the alloy interaction between elements 1 and 2 to 4.37.
Related commands:
-
Default: none
diff --git a/doc/pair_style_meam.txt b/doc/pair_meam.txt
similarity index 95%
rename from doc/pair_style_meam.txt
rename to doc/pair_meam.txt
index 2da4baa798..9244e92f77 100644
--- a/doc/pair_style_meam.txt
+++ b/doc/pair_meam.txt
@@ -23,7 +23,7 @@ pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni :pre
Style {meam} computes pairwise interactions for a variety of materials
using modified embedded-atom method (MEAM) potentials
"(Baskes)"_#Baskes. Conceptually, it is an extension to the original
-"EAM potentials"_pair_style_eam.html which adds angular forces. It is
+"EAM potentials"_pair_eam.html which adds angular forces. It is
thus suitable for modeling metals and alloys with fcc, bcc, hcp and
diamond cubic structures, as well as covalently bonded materials like
silicon and carbon.
@@ -47,7 +47,7 @@ These are ASCII text files in a format consistent with other MD codes
that implement MEAM potentials, such as the serial DYNAMO code and
Warp. Several MEAM potential files with parameters for different
materials are included in the "potentials" directory of the LAMMPS
-distribution with a ",meam" suffix. All of these are parameterized in
+distribution with a ".meam" suffix. All of these are parameterized in
terms of LAMMPS "metal units"_units.html.
Note that unlike for other potentials, cutoffs for MEAM potentials are
@@ -175,8 +175,8 @@ Thus these lines
rho0(2) = 2.25
alpha(1,2) = 4.37 :pre
-mean set rho0 for the 2nd element to the value 2.25 and set alpha for
-the alloy interaction between elements 1 and 2 to 4.37.
+set rho0 for the 2nd element to the value 2.25 and set alpha for the
+alloy interaction between elements 1 and 2 to 4.37.
:line
@@ -184,7 +184,7 @@ the alloy interaction between elements 1 and 2 to 4.37.
[Related commands:]
-"pair_coeff"_pair_coeff.html, "pair_style eam"_pair_style_eam.html
+"pair_coeff"_pair_coeff.html, "pair_style eam"_pair_eam.html
[Default:] none
@@ -197,4 +197,4 @@ the alloy interaction between elements 1 and 2 to 4.37.
[(Gullet)] Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003).
This report may be accessed on-line via "this link"_sandreport.
-:link(sandreport,http://www.prod.sandia.gov/cgi-bin/techlib/access-control.pl/2003/038782.pdf)
\ No newline at end of file
+:link(sandreport,http://www.prod.sandia.gov/cgi-bin/techlib/access-control.pl/2003/038782.pdf)
diff --git a/doc/pair_style_morse.html b/doc/pair_morse.html
similarity index 74%
rename from doc/pair_style_morse.html
rename to doc/pair_morse.html
index c91435e9c8..a489fae1e8 100644
--- a/doc/pair_style_morse.html
+++ b/doc/pair_morse.html
@@ -11,6 +11,8 @@
pair_style morse command
+pair_style morse/opt command
+
Syntax:
pair_style morse cutoff
@@ -20,6 +22,7 @@
Examples:
pair_style morse 2.5
+pair_style morse/opt 2.5
pair_coeff * * 100.0 2.0 1.5
pair_coeff 1 1 100.0 2.0 1.5 3.0
@@ -45,12 +48,21 @@ commands:
The last coefficient is optional. If not specified, the global morse
cutoff is used.
+Style morse/opt is an optimized version of style morse that should
+give identical answers. Depending on system size and the processor
+you are running on, it may be 5-25% faster (for the pairwise portion
+of the run time).
+
Restrictions:
The morse potential does not support the
pair_modify mix option. Coefficients for all i,j
pairs must be specified explicitly.
+The morse/opt style is part of the "opt" package. It is only
+enabled if LAMMPS was built with that package. See the Making
+LAMMPS section for more info.
+
Related commands:
pair_coeff
diff --git a/doc/pair_style_morse.txt b/doc/pair_morse.txt
similarity index 72%
rename from doc/pair_style_morse.txt
rename to doc/pair_morse.txt
index 433e0a9503..f673db8a9f 100644
--- a/doc/pair_style_morse.txt
+++ b/doc/pair_morse.txt
@@ -7,6 +7,7 @@
:line
pair_style morse command :h3
+pair_style morse/opt command :h3
[Syntax:]
@@ -17,6 +18,7 @@ cutoff = global cutoff for Morse interactions (distance units) :ul
[Examples:]
pair_style morse 2.5
+pair_style morse/opt 2.5
pair_coeff * * 100.0 2.0 1.5
pair_coeff 1 1 100.0 2.0 1.5 3.0 :pre
@@ -42,12 +44,21 @@ cutoff (distance units) :ul
The last coefficient is optional. If not specified, the global morse
cutoff is used.
+Style {morse/opt} is an optimized version of style {morse} that should
+give identical answers. Depending on system size and the processor
+you are running on, it may be 5-25% faster (for the pairwise portion
+of the run time).
+
[Restrictions:]
The {morse} potential does not support the
"pair_modify"_pair_modify.hmtl {mix} option. Coefficients for all i,j
pairs must be specified explicitly.
+The {morse/opt} style is part of the "opt" 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
diff --git a/doc/pair_style_none.html b/doc/pair_none.html
similarity index 100%
rename from doc/pair_style_none.html
rename to doc/pair_none.html
diff --git a/doc/pair_style_none.txt b/doc/pair_none.txt
similarity index 100%
rename from doc/pair_style_none.txt
rename to doc/pair_none.txt
diff --git a/doc/pair_style_soft.html b/doc/pair_soft.html
similarity index 100%
rename from doc/pair_style_soft.html
rename to doc/pair_soft.html
diff --git a/doc/pair_style_soft.txt b/doc/pair_soft.txt
similarity index 100%
rename from doc/pair_style_soft.txt
rename to doc/pair_soft.txt
diff --git a/doc/pair_style_dipole.html b/doc/pair_style_dipole.html
deleted file mode 100644
index 1ac19e561b..0000000000
--- a/doc/pair_style_dipole.html
+++ /dev/null
@@ -1,66 +0,0 @@
-
-
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands
-
-
-
-
-
-
-
-
-
-pair_style dipole/cut command
-
-Syntax:
-
-pair_style dipole/cut cutoff (cutoff2)
-
-
- cutoff = global cutoff for LJ interactions (and Coulombic if only 1 arg) (distance units)
-
- cutoff2 = global cutoff for Coulombic and dipole interactions (optional) (distance units)
-
-Examples:
-
-pair_style dipole/cut 2.5
-pair_style dipole/cut 2.5 5.0
-pair_coeff * * 100.0 2.0 1.5
-pair_coeff 1 1 100.0 2.0 1.5 3.0
-
-Description:
-
-Style dipole/cut
-
-The dipole styles are not yet implemented in LAMMPS. They will
-enable a point dipole and charge to be assigned to each atom and the
-resulting charge-dipole and dipole-dipole interactions to be computed.
-
- computes pairwise interactions with the formula
-
-
-Rc is the cutoff.
-
-The following coefficients must be defined for each pair of atoms
-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:
-
-- D0 (energy units)
-
- alpha (1/distance units)
-
- r0 (distance units)
-
- cutoff (distance units)
-
-The last coefficient is optional. If not specified, the global morse
-cutoff is used.
-
-Restrictions: none
-
-Must use atom style dipole.
-
-Related commands:
-
-
-Default: none
-
-
diff --git a/doc/pair_style_dipole.txt b/doc/pair_style_dipole.txt
deleted file mode 100644
index 5758693a96..0000000000
--- a/doc/pair_style_dipole.txt
+++ /dev/null
@@ -1,61 +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 dipole/cut command :h3
-
-[Syntax:]
-
-pair_style dipole/cut cutoff (cutoff2) :pre
-
-cutoff = global cutoff for LJ interactions (and Coulombic if only 1 arg) (distance units)
-cutoff2 = global cutoff for Coulombic and dipole interactions (optional) (distance units) :ul
-
-[Examples:]
-
-pair_style dipole/cut 2.5
-pair_style dipole/cut 2.5 5.0
-pair_coeff * * 100.0 2.0 1.5
-pair_coeff 1 1 100.0 2.0 1.5 3.0 :pre
-
-[Description:]
-
-Style {dipole/cut}
-
-The {dipole} styles are not yet implemented in LAMMPS. They will
-enable a point dipole and charge to be assigned to each atom and the
-resulting charge-dipole and dipole-dipole interactions to be computed.
-
- computes pairwise interactions with the formula
-
-:c,image(Eqs/pair_dipole.jpg)
-
-Rc is the cutoff.
-
-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:
-
-D0 (energy units)
-alpha (1/distance units)
-r0 (distance units)
-cutoff (distance units) :ul
-
-The last coefficient is optional. If not specified, the global morse
-cutoff is used.
-
-[Restrictions:] none
-
-Must use atom style dipole.
-
-[Related commands:]
-
-"pair_coeff"_pair_coeff.html
-
-[Default:] none
diff --git a/doc/pair_style_sw.html b/doc/pair_sw.html
similarity index 100%
rename from doc/pair_style_sw.html
rename to doc/pair_sw.html
diff --git a/doc/pair_style_sw.txt b/doc/pair_sw.txt
similarity index 100%
rename from doc/pair_style_sw.txt
rename to doc/pair_sw.txt
diff --git a/doc/pair_style_table.html b/doc/pair_table.html
similarity index 100%
rename from doc/pair_style_table.html
rename to doc/pair_table.html
diff --git a/doc/pair_style_table.txt b/doc/pair_table.txt
similarity index 100%
rename from doc/pair_style_table.txt
rename to doc/pair_table.txt
diff --git a/doc/pair_style_tersoff.html b/doc/pair_tersoff.html
similarity index 100%
rename from doc/pair_style_tersoff.html
rename to doc/pair_tersoff.html
diff --git a/doc/pair_style_tersoff.txt b/doc/pair_tersoff.txt
similarity index 100%
rename from doc/pair_style_tersoff.txt
rename to doc/pair_tersoff.txt
diff --git a/doc/pair_style_yukawa.html b/doc/pair_yukawa.html
similarity index 100%
rename from doc/pair_style_yukawa.html
rename to doc/pair_yukawa.html
diff --git a/doc/pair_style_yukawa.txt b/doc/pair_yukawa.txt
similarity index 100%
rename from doc/pair_style_yukawa.txt
rename to doc/pair_yukawa.txt
diff --git a/doc/temperature.html b/doc/temperature.html
deleted file mode 100644
index 35d995042d..0000000000
--- a/doc/temperature.html
+++ /dev/null
@@ -1,136 +0,0 @@
-
-LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands
-
-
-
-
-
-
-
-
-
-temperature command
-
-Syntax:
-
-temperature ID group-ID style args keyword value ...
-
-- ID = user-assigned name for the temperature
-
-
- group-ID = ID of group of atoms to compute the temperature for
-
-
- style = full or partial or ramp or region
-
-
full args = none
- partial args = x y z
- x,y,z = 0 or 1
- ramp args = vdim vlo vhi dim clo chi
- vdim = vx or vy or vz
- vlo,vhi = subtract velocities between vlo and vhi (velocity units)
- dim = x or y or z
- clo,chi = lower and upper bound of domain to
- subtract from (distance units)
- region args = region-ID
- region-ID = ID of region to use for choosing atoms
-
- - zero or more keyword/value pairs may be appended to the args
-
-
- keyword = units
-
-
units value = lattice or box
-
-
-
-Examples:
-
-temperature mine peptide full
-temperature new flow partial 1 1 0
-temperature mine flow region boundary
-temperature 2nd middle ramp vx 0 8 y 2 12 units lattice
-
-Description:
-
-Define a method for computing the temperature of a group of atoms.
-
-The ID of the temperature can be referred to in other commands, such
-as thermo_modify, velocity,
-fix_modify, temp_modify. Note
-that certain fixes create their own temperatures with the same ID as
-the fix, e.g. fix temp/rescale, fix
-nvt, fix npt, etc.
-
-The style determines how the temperature is computed. The full
-style means KE = dim/2 N k T, where KE = total kinetic energy of the
-group of 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 number of atoms contributing to
-the temperature is assumed to be constant for the duration of the run;
-use the dynamic option of the temp_modify command
-if this is not the case.
-
-The partial style uses the same formula as full, except entire
-dimensions can be eliminated from the kinetic energy computation.
-This can be useful for systems where atoms are flowing, and only the
-thermal temperature in the non-flow directions is desired. A "0"
-means do not use the component of velocity in that dimension when
-computing KE. In the example above with arguments 1 1 0, only x and y
-velocities (not z) would be used in computing KE and temperature.
-
-The ramp style can be used to eliminate an imposed velocity on a
-system before computing thermal KE. The meaning of these arguments is
-the same as for the velocity command which was
-presumably used to impose the velocity.
-
-The region style is the same as full except that only atoms in the
-specified geometric region contribute to the temperature. Since atoms
-can enter/leave a region, this test is performed each time the
-temperature is computed. This can be useful for thermostatting one
-portion of the simulation box. E.g. a McDLT simulation where one side
-is cooled, and the other side is heated.
-
-Note that a region-style temperature can be used to thermostat with
-fix temp/rescale or fix
-langevin, but should probably not be used with
-Nose/Hoover style fixes (>fix nvt, fix
-npt, or fix nph), if the
-degrees-of-freedom included in the computed T varies with time.
-
-The units keyword determines the meaning of the distance units used
-for coordinates (c1,c2) and velocities (vlo,vhi) defined for the
-ramp style. A box value selects standard distance units as
-defined by the units command, e.g. Angstroms for units =
-real or metal. A lattice value means the distance units are in
-lattice spacings; e.g. velocity = lattice spacings / tau. The
-lattice command must have been previously used to
-define the lattice spacing.
-
-LAMMPS defines a temperature with ID = default which computes a
-full style on the all group of atoms. This is the temperature
-used for thermodynamic output of quantities like temperature,
-pressure, kinetic energy (see the thermo_style
-command) unless you change it via the
-thermo_modify command.
-
-All temperature styles (except region) subtract out
-degrees-of-freedom (DOF) due to fixes that constrain molecular motion.
-Currently, these are fix shake and fix
-rigid. DOF is the N * dim factor in the above
-equation for the full style. 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 tweaked using the
-temp_modify command.
-
-Restrictions: none
-
-Related commands:
-
-thermo_modify, velocity,
-fix_modify, temp_modify
-
-Default:
-
-A temperature with ID = default is defined by LAMMPS, as if it had
-been specified as "temperature default all full". The option default
-is units = lattice.
-
-
diff --git a/doc/temperature.txt b/doc/temperature.txt
deleted file mode 100644
index 80d5aade25..0000000000
--- a/doc/temperature.txt
+++ /dev/null
@@ -1,124 +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
-
-temperature command :h3
-
-[Syntax:]
-
-temperature ID group-ID style args keyword value ... :pre
-
-ID = user-assigned name for the temperature :ulb,l
-group-ID = ID of group of atoms to compute the temperature for :l
-style = {full} or {partial} or {ramp} or {region} :l
- {full} args = none
- {partial} args = x y z
- x,y,z = 0 or 1
- {ramp} args = vdim vlo vhi dim clo chi
- vdim = {vx} or {vy} or {vz}
- vlo,vhi = subtract velocities between vlo and vhi (velocity units)
- dim = {x} or {y} or {z}
- clo,chi = lower and upper bound of domain to
- subtract from (distance units)
- {region} args = region-ID
- region-ID = ID of region to use for choosing atoms :pre
-zero or more keyword/value pairs may be appended to the args :l
-keyword = {units} :l
- {units} value = {lattice} or {box} :pre
-:ule
-
-[Examples:]
-
-temperature mine peptide full
-temperature new flow partial 1 1 0
-temperature mine flow region boundary
-temperature 2nd middle ramp vx 0 8 y 2 12 units lattice :pre
-
-[Description:]
-
-Define a method for computing the temperature of a group of atoms.
-
-The ID of the temperature can be referred to in other commands, such
-as "thermo_modify"_thermo_modify.html, "velocity"_velocity.html,
-"fix_modify"_fix_modify.html, "temp_modify"_temp_modify.html. Note
-that certain fixes create their own temperatures with the same ID as
-the fix, e.g. "fix temp/rescale"_fix_temp_rescale.html, "fix
-nvt"_fix_nvt.html, "fix npt"_fix_npt.html, etc.
-
-The style determines how the temperature is computed. The {full}
-style means KE = dim/2 N k T, where KE = total kinetic energy of the
-group of 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 number of atoms contributing to
-the temperature is assumed to be constant for the duration of the run;
-use the {dynamic} option of the "temp_modify"_temp_modify.html command
-if this is not the case.
-
-The {partial} style uses the same formula as {full}, except entire
-dimensions can be eliminated from the kinetic energy computation.
-This can be useful for systems where atoms are flowing, and only the
-thermal temperature in the non-flow directions is desired. A "0"
-means do not use the component of velocity in that dimension when
-computing KE. In the example above with arguments 1 1 0, only x and y
-velocities (not z) would be used in computing KE and temperature.
-
-The {ramp} style can be used to eliminate an imposed velocity on a
-system before computing thermal KE. The meaning of these arguments is
-the same as for the "velocity"_velocity.html command which was
-presumably used to impose the velocity.
-
-The {region} style is the same as {full} except that only atoms in the
-specified geometric region contribute to the temperature. Since atoms
-can enter/leave a region, this test is performed each time the
-temperature is computed. This can be useful for thermostatting one
-portion of the simulation box. E.g. a McDLT simulation where one side
-is cooled, and the other side is heated.
-
-Note that a {region}-style temperature can be used to thermostat with
-"fix temp/rescale"_fix_temp_rescale.html or "fix
-langevin"_fix_langevin.html, but should probably not be used with
-Nose/Hoover style fixes ("fix nvt"_fix_nvt.html, fix
-npt"_fix_npt.html, or "fix nph"_fix_nph.html), if the
-degrees-of-freedom included in the computed T varies with time.
-
-The {units} keyword determines the meaning of the distance units used
-for coordinates (c1,c2) and velocities (vlo,vhi) defined for the
-{ramp} style. A {box} value selects standard distance units as
-defined by the "units"_units.html command, e.g. Angstroms for units =
-real or metal. A {lattice} value means the distance units are in
-lattice spacings; e.g. velocity = lattice spacings / tau. The
-"lattice"_lattice.html command must have been previously used to
-define the lattice spacing.
-
-LAMMPS defines a temperature with ID = {default} which computes a
-{full} style on the {all} group of atoms. This is the temperature
-used for thermodynamic output of quantities like temperature,
-pressure, kinetic energy (see the "thermo_style"_thermo_style.html
-command) unless you change it via the
-"thermo_modify"_thermo_modify.html command.
-
-All temperature styles (except {region}) subtract out
-degrees-of-freedom (DOF) due to fixes that constrain molecular motion.
-Currently, these are "fix shake"_fix_shake.html and "fix
-rigid"_fix_rigid.html. DOF is the N * dim factor in the above
-equation for the {full} style. 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 tweaked using the
-"temp_modify"_temp_modify.html command.
-
-[Restrictions:] none
-
-[Related commands:]
-
-"thermo_modify"_thermo_modify.html, "velocity"_velocity.html,
-"fix_modify"_fix_modify.html, "temp_modify"_temp_modify.html
-
-[Default:]
-
-A temperature with ID = {default} is defined by LAMMPS, as if it had
-been specified as "temperature default all full". The option default
-is units = lattice.
diff --git a/doc/uncompute.html b/doc/uncompute.html
new file mode 100644
index 0000000000..8487f4aac6
--- /dev/null
+++ b/doc/uncompute.html
@@ -0,0 +1,39 @@
+
+LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands
+
+
+
+
+
+
+
+
+
+uncompute command
+
+Syntax:
+
+uncompute compute-ID
+
+- compute-ID = ID of a previously defined compute
+
+Examples:
+
+uncompute 2
+uncompute lower-boundary
+
+Description:
+
+Delete a compute that was previously defined with a compute
+command. This also wipes out any additional changes made to the compute
+via the compute_modify command.
+
+Restrictions: none
+
+Related commands:
+
+compute
+
+Default: none
+
+
diff --git a/doc/uncompute.txt b/doc/uncompute.txt
new file mode 100644
index 0000000000..49b46781d7
--- /dev/null
+++ b/doc/uncompute.txt
@@ -0,0 +1,34 @@
+"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
+
+uncompute command :h3
+
+[Syntax:]
+
+uncompute compute-ID :pre
+
+compute-ID = ID of a previously defined compute :ul
+
+[Examples:]
+
+uncompute 2
+uncompute lower-boundary :pre
+
+[Description:]
+
+Delete a compute that was previously defined with a "compute"_compute.html
+command. This also wipes out any additional changes made to the compute
+via the "compute_modify"_compute_modify.html command.
+
+[Restrictions:] none
+
+[Related commands:]
+
+"compute"_compute.html
+
+[Default:] none