Adding arguments to doc page

doc/src/Howto_rheo.rst

@@ -1,3 +1,4 @@
 Reproducing hydrodynamics and elastic objects (RHEO)
 ======================
 
+Text

doc/src/fix_rheo.rst

@@ -8,26 +8,38 @@ Syntax
 
 .. parsed-literal::
 
-   fix ID group-ID rheo
+   fix ID group-ID rheo cut kstyle keyword values...
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
 * rheo = style name of this fix command
+* cut = *quintic* or *CRK0* or *CRK1* or *CRK2*
+* zero or more keyword/value pairs may be appended to args
+* keyword = *shift* or *thermal* or *surface/detection* or *interface/reconstruction* or *rho/sum* or *density* or *sound/squared*
+
+  .. parsed-literal::
+
+       *shift* values = none, turns on velocity shifting
+       *thermal* values = none, turns on thermal evolution
+       *surface/detection* values = *sdstyle* *limit*
+         *sdstyle* = *coordination* or *divergence*
+         *limit* = threshold for surface particles (unitless)
+       *interface/reconstruction* values = none, reconstructs interfaces with solid particles
+       *rho/sum* values = none, uses the kernel to compute the density of particles
+       *density* values = *rho0* (density)
+       *sound/squared* values = *csq* (velocity\^2)
 
 Examples
 """"""""
 
 .. code-block:: LAMMPS
 
-   fix 1 all rheo 1.0 CRK1 shift
+   fix 1 all rheo 1.0 quintic thermal density 0.1 sound/squared 10.0
+   fix 1 all rheo 1.0 CRK1 shift surface/detection coordination 40
 
 Description
 """""""""""
 
-Perform time integration to update position, velocity, internal energy
+Fix description...
-and local density for atoms in the group each timestep. This fix is
-needed to time-integrate SPH systems where particles carry internal
-variables such as internal energy.  SPH stands for Smoothed Particle
-Hydrodynamics.
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@@ -41,6 +53,14 @@ the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minim
 Restrictions
 """"""""""""
 
+This fix must be used with an atom style that includes density
+such as atom_style rheo or rheo/thermal. This fix must be used in
+conjuction with :doc:`fix rheo/pressure <fix_rheo_pressure>`. and
+:doc:`fix rheo/viscosity <fix_rheo_viscosity>`, If the *thermal*
+setting is used, there must also be an instance of
+:doc:`fix rheo/thermal <fix_rheo_thermal>`. The fix group must be
+set to all.
+
 This fix is part of the RHEO package.  It is only enabled if
 LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
 
@@ -56,4 +76,4 @@ Related commands
 Default
 """""""
 
-none
+*rho0* and *csq* are set to 1.0.

doc/src/fix_rheo_pressure.rst

@@ -1,6 +1,6 @@
-.. index:: fix rheo
+.. index:: fix rheo/pressure
 
-fix rheo command
+fix rheo/pressure command
 ===============
 
 Syntax
@@ -8,26 +8,33 @@ Syntax
 
 .. parsed-literal::
 
-   fix ID group-ID rheo
+   fix ID group-ID rheo/pressure pstyle args
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
-* rheo = style name of this fix command
+* rheo/pressure = style name of this fix command
+* pstyle = *linear* or *taitwater* or *cubic*
+
+  .. parsed-literal::
+
+       *linear* args = none
+       *taitwater* args = none
+       *cubic* args = cubic term prefactor :math:`A_3` (pressure/density\^2)
 
 Examples
 """"""""
 
 .. code-block:: LAMMPS
 
-   fix 1 all rheo 1.0 CRK1 shift
+   fix 1 all rheo/pressure linear
+   fix 1 all rheo/pressure cubic 10.0
 
 Description
 """""""""""
 
-Perform time integration to update position, velocity, internal energy
+This fix...
-and local density for atoms in the group each timestep. This fix is
+
-needed to time-integrate SPH systems where particles carry internal
+Only one instance of fix rheo/pressure can be defined and the fix group must be set to all.
-variables such as internal energy.  SPH stands for Smoothed Particle
+
-Hydrodynamics.
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@@ -41,6 +48,11 @@ the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minim
 Restrictions
 """"""""""""
 
+This fix must be used with an atom style that includes density
+such as atom_style rheo or rheo/thermal. This fix must be used in
+conjuction with :doc:`fix rheo <fix_rheo>`. The fix group must be
+set to all.
+
 This fix is part of the RHEO package.  It is only enabled if
 LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
 
@@ -48,7 +60,6 @@ Related commands
 """"""""""""""""
 
 :doc:`fix rheo/viscosity <fix_rheo_viscosity>`,
-:doc:`fix rheo/pressure <fix_rheo_pressure>`,
 :doc:`fix rheo/thermal <fix_rheo_thermal>`,
 :doc:`pair rheo <pair_rheo>`,
 :doc:`compute rheo/property/atom <compute_rheo_property_atom>`

doc/src/fix_rheo_thermal.rst

@@ -1,6 +1,6 @@
-.. index:: fix rheo
+.. index:: fix rheo/thermal
 
-fix rheo command
+fix rheo/thermal command
 ===============
 
 Syntax
@@ -8,26 +8,49 @@ Syntax
 
 .. parsed-literal::
 
-   fix ID group-ID rheo
+   fix ID group-ID rheo/thermal keyword values ...
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
-* rheo = style name of this fix command
+* rheo/viscosity = style name of this fix command
+* one or more attributes may be appended
+* attribute = *conductivity* or *specific/heat* or *Tfreeze*
+
+  .. parsed-literal::
+
+       *conductivity* args = style param
+         style = *constant* or *type*
+           *constant* arg = conductivity (power/temperature)
+           *type* args = list of conductivity values, one per type (power/temperature)
+       *specific/heat* args = style param
+         style = *constant* or *type*
+           *constant* arg = specific heat (energy/(mass*temperature))
+           *type* args = list of specific heat values, one per atom type (energy/(mass*temperature))
+       *Tfreeze* args = style param
+         style = *constant* or *type*
+           *constant* arg = freezing temperature (temperature)
+           *type* args = list of freezing temperature values, one per type (temperature)
 
 Examples
 """"""""
 
 .. code-block:: LAMMPS
 
-   fix 1 all rheo 1.0 CRK1 shift
+   fix 1 all rheo/thermal conductivity constant 1.0 specific/heat constant 1.0 Tfreeze constant 1.0
+   fix 1 all rheo/pressure conductivity constant 1.0 specific/heat type 1.0 2.0
 
 Description
 """""""""""
 
-Perform time integration to update position, velocity, internal energy
+This fix...
-and local density for atoms in the group each timestep. This fix is
+
-needed to time-integrate SPH systems where particles carry internal
+While the *Tfreeze* keyword is optional, the *conducitivity* and
-variables such as internal energy.  SPH stands for Smoothed Particle
+*specific/heat* keywords are mandatory.
-Hydrodynamics.
+
+Multiple instances of this fix may be defined to apply different
+properties to different groups. However, the union of fix groups
+across all instances of fix rheo/thermal must cover all atoms.
+If there are multiple instances of this fix, any intersections in
+the fix groups will lead to incorrect thermal integration.
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@@ -41,15 +64,20 @@ the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minim
 Restrictions
 """"""""""""
 
+This fix must be used with an atom style that includes temperature,
+heatflow, and conductivity such as atom_tyle rheo/thermal This fix
+must be used in conjuction with :doc:`fix rheo <fix_rheo>` with the
+*thermal* setting.
+
 This fix is part of the RHEO package.  It is only enabled if
 LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
 
 Related commands
 """"""""""""""""
 
+:doc:`fix rheo <fix_rheo>`,
 :doc:`fix rheo/viscosity <fix_rheo_viscosity>`,
 :doc:`fix rheo/pressure <fix_rheo_pressure>`,
-:doc:`fix rheo/thermal <fix_rheo_thermal>`,
 :doc:`pair rheo <pair_rheo>`,
 :doc:`compute rheo/property/atom <compute_rheo_property_atom>`
 

doc/src/fix_rheo_viscosity.rst

@@ -1,6 +1,6 @@
-.. index:: fix rheo
+.. index:: fix rheo/viscosity
 
-fix rheo command
+fix rheo/viscosity command
 ===============
 
 Syntax
@@ -8,26 +8,43 @@ Syntax
 
 .. parsed-literal::
 
-   fix ID group-ID rheo
+   fix ID group-ID rheo/viscosity vstyle args
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
-* rheo = style name of this fix command
+* rheo/viscosity = style name of this fix command
+* vstyle = *constant* or *type* or *power*
+
+  .. parsed-literal::
+
+       *constant* arg = viscosity (mass/(length*time))
+       *type* args = list of viscosity values, one per atom type (mass/(length*time))
+       *power* args = *eta* *gd0* *K* *npow* *tau0*
+         *eta* = (units)
+         *gd0* = (units)
+         *K* = (units)
+         *npow* = (units)
+         *tau0* = (units)
 
 Examples
 """"""""
 
 .. code-block:: LAMMPS
 
-   fix 1 all rheo 1.0 CRK1 shift
+   fix 1 all rheo/viscosity constant 1.0
+   fix 1 all rheo/viscosity power 0.1 1e-2 0.5 0.01
 
 Description
 """""""""""
 
-Perform time integration to update position, velocity, internal energy
+This fix...
-and local density for atoms in the group each timestep. This fix is
+
-needed to time-integrate SPH systems where particles carry internal
+Multiple instances of this fix may be defined to apply different
-variables such as internal energy.  SPH stands for Smoothed Particle
+properties to different groups. However, the union of fix groups
-Hydrodynamics.
+across all instances of fix rheo/viscosity must cover all atoms.
+If there are multiple instances of this fix, any intersection
+between fix groups will cause the viscosity for the affected atoms
+to be calculated multiple times. Any such affected atoms will enabled
+up with a viscosity calculated by the latest defined fix.
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@@ -41,13 +58,17 @@ the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minim
 Restrictions
 """"""""""""
 
+This fix must be used with an atom style that includes viscosity
+such as atom_style rheo or rheo/thermal. This fix must be used in
+conjuction with :doc:`fix rheo <fix_rheo>`.
+
 This fix is part of the RHEO package.  It is only enabled if
 LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
 
 Related commands
 """"""""""""""""
 
-:doc:`fix rheo/viscosity <fix_rheo_viscosity>`,
+:doc:`fix rheo <fix_rheo>`,
 :doc:`fix rheo/pressure <fix_rheo_pressure>`,
 :doc:`fix rheo/thermal <fix_rheo_thermal>`,
 :doc:`pair rheo <pair_rheo>`,

doc/src/pair_rheo.rst

@@ -1,6 +1,6 @@
 .. index:: pair_style sph/lj
 
-pair_style sph/lj command
+pair_style rheo command
 =========================
 
 Syntax
@@ -8,79 +8,63 @@ Syntax
 
 .. code-block:: LAMMPS
 
-   pair_style sph/lj
+   pair_style rheo cut keyword values
+
+* cut = *quintic* or *CRK0* or *CRK1* or *CRK2*
+* zero or more keyword/value pairs may be appended to args
+* keyword = *rho/damp* or *artificial/visc*
+
+.. parsed-literal::
+
+     *rho/damp* args = density damping prefactor :math:`\xi` (units?)
+     *artificial/visc* args = artificial viscosity prefactor :math:`\zeta` (units?)
 
 Examples
 """"""""
 
 .. code-block:: LAMMPS
 
-   pair_style sph/lj
+   pair_style rheo 1.0 quintic rho/damp 1.0 artificial/visc 2.0
-   pair_coeff * * 1.0 2.4
+   pair_coeff * *
 
 Description
 """""""""""
 
-The sph/lj style computes pressure forces between particles according
+pair style...
-to the Lennard-Jones equation of state, which is computed according to
-Ree's 1980 polynomial fit :ref:`(Ree) <Ree>`. The Lennard-Jones parameters
-epsilon and sigma are set to unity.  This pair style also computes
-Monaghan's artificial viscosity to prevent particles from
-interpenetrating :ref:`(Monaghan) <Monoghan>`.
 
-See `this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
+No coefficients are defined for each pair of atoms types via the
-LAMMPS.
+:doc:`pair_coeff <pair_coeff>` command as in the examples
-
-The following coefficients must be defined for each pair of atoms
-types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
 above.
 
-* :math:`\nu` artificial viscosity (no units)
-* h kernel function cutoff (distance units)
-
 ----------
 
 Mixing, shift, table, tail correction, restart, rRESPA info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This style does not support mixing.  Thus, coefficients for all
-I,J pairs must be specified explicitly.
-
 This style does not support the :doc:`pair_modify <pair_modify>`
 shift, table, and tail options.
 
 This style does not write information to :doc:`binary restart files <restart>`.  Thus, you need to re-specify the pair_style and
 pair_coeff commands in an input script that reads a restart file.
 
-This style can only be used via the *pair* keyword of the :doc:`run_style respa <run_style>` command.  It does not support the *inner*,
+This style can only be used via the *pair* keyword of the :doc:`run_style respa <run_style>` command.  It does not support the *inner*, *middle*, *outer* keywords.
-*middle*, *outer* keywords.
 
 Restrictions
 """"""""""""
 
-As noted above, the Lennard-Jones parameters epsilon and sigma are set
+This fix is part of the RHEO package.  It is only enabled if
-to unity.
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
-
-This pair style is part of the SPH package.  It is only enabled
-if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
 
 Related commands
 """"""""""""""""
 
-:doc:`pair_coeff <pair_coeff>`, pair_sph/rhosum
+:doc:`fix rheo <fix_rheo>`,
+:doc:`fix rheo/pressure <fix_rheo_pressure>`,
+:doc:`fix rheo/thermal <fix_rheo_thermal>`,
+:doc:`fix rheo/viscosity <fix_rheo_viscosity>`,
+:doc:`compute rheo/property/atom <compute_rheo_property_atom>`
 
 Default
 """""""
 
-none
+No density damping or artificial viscous forces are calculated.
-
-----------
-
-.. _Ree:
-
-**(Ree)** Ree, Journal of Chemical Physics, 73, 5401 (1980).
-
-.. _Monoghan:
-
-**(Monaghan)** Monaghan and Gingold, Journal of Computational Physics,
-52, 374-389 (1983).

src/RHEO/fix_rheo.cpp

@@ -74,7 +74,7 @@ FixRHEO::FixRHEO(LAMMPS *lmp, int narg, char **arg) :
 
   h = utils::numeric(FLERR,arg[3],false,lmp);
   cut = h;
-  if (strcmp(arg[4],"Quintic") == 0) {
+  if (strcmp(arg[4],"quintic") == 0) {
       kernel_style = QUINTIC;
   } else if (strcmp(arg[4],"CRK0") == 0) {
       kernel_style = CRK0;
@@ -109,11 +109,11 @@ FixRHEO::FixRHEO(LAMMPS *lmp, int narg, char **arg) :
       interface_flag = 1;
     } else if (strcmp(arg[iarg],"rho/sum") == 0) {
       rhosum_flag = 1;
-    } else if (strcmp(arg[iarg],"rho0") == 0) {
+    } else if (strcmp(arg[iarg],"density") == 0) {
       if(iarg + 1 >= narg) error->all(FLERR,"Illegal rho0 option in fix rheo");
       rho0 = utils::numeric(FLERR,arg[iarg + 1],false,lmp);
       iarg += 1;
-    } else if (strcmp(arg[iarg],"csq") == 0) {
+    } else if (strcmp(arg[iarg],"sound/squared") == 0) {
       if(iarg+1 >= narg) error->all(FLERR,"Illegal csq option in fix rheo");
       csq = utils::numeric(FLERR,arg[iarg + 1],false,lmp);
       iarg += 1;

src/RHEO/fix_rheo_thermal.cpp

@@ -72,7 +72,7 @@ FixRHEOThermal::FixRHEOThermal(LAMMPS *lmp, int narg, char **arg) :
       } else {
         error->all(FLERR,"Illegal fix command, {}", arg[iarg + 1]);
       }
-    } else if (strcmp(arg[iarg],"cv") == 0) {
+    } else if (strcmp(arg[iarg],"specific/heat") == 0) {
       // Cv arguments
       if (iarg + 1 >= narg) error->all(FLERR,"Insufficient arguments for cv option");
       if (strcmp(arg[iarg + 1],"constant") == 0) {

src/RHEO/pair_rheo.cpp

@@ -357,7 +357,7 @@ void PairRHEO::settings(int narg, char **arg)
   if (narg < 1) error->all(FLERR,"Illegal pair_style command");
 
   h = utils::numeric(FLERR,arg[0],false,lmp);
-printf("settings\n");
+
   int iarg = 1;
   while (iarg < narg) {
     if (strcmp(arg[iarg], "rho/damp") == 0) {
@@ -423,7 +423,7 @@ void PairRHEO::setup()
   thermal_flag = fix_rheo->thermal_flag;
   csq = fix_rheo->csq;
   rho0 = fix_rheo->rho0;
-printf("setup\n");
+
   if (h != fix_rheo->h)
     error->all(FLERR, "Pair rheo cutoff {} does not agree with fix rheo cutoff {}", h, fix_rheo->h);
 
@@ -455,6 +455,6 @@ double PairRHEO::init_one(int i, int j)
   if (setflag[i][j] == 0) {
       error->all(FLERR,"All pair rheo coeffs are not set");
   }
-printf("init one\n");
+
   return h;
 }