doc page for thermo output difference with triclinic/general

doc/src/thermo_modify.rst

@@ -11,7 +11,7 @@ Syntax
    thermo_modify keyword value ...
 
 * one or more keyword/value pairs may be listed
-* keyword = *lost* or *lost/bond* or *warn* or *norm* or *flush* or *line* or *colname* or *format* or *temp* or *press*
+* keyword = *lost* or *lost/bond* or *warn* or *norm* or *flush* or *line* or *colname* or *format* or *temp* or *press* or *triclinic/general*
 
   .. parsed-literal::
 
@@ -32,6 +32,8 @@ Syntax
               *or* a thermo keyword or reference to compute, fix, property or variable.
        *temp* value = compute ID that calculates a temperature
        *press* value = compute ID that calculates a pressure
+       *triclinic/general* arg = none
+
 
 Examples
 """"""""
@@ -240,6 +242,17 @@ command, thermo output uses a default compute for pressure with ID =
    keyword, then the new pressure compute specified by the *press*
    keyword will be unaffected by the *temp* setting.
 
+The *triclinic/general* keyword can only be used if the simulation box
+was created as a general triclinic box.  See the :doc:`Howto_triclinic
+<Howto_triclinic>` doc page for a detailed explanation of orthogonal,
+restricted triclinic, and general triclinic simulation boxes.
+
+If this keyword is used, the output of pressure tensor components for
+the system is affected.  These components are specified by the
+*pxx,pyy,pzz,pxy,pxz,pyz* keywords of the :doc:`thermo_style
+<thermo_style>` command.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
+
 Restrictions
 """"""""""""
 none

doc/src/thermo_style.rst

@@ -68,7 +68,7 @@ Syntax
            density = mass density of system
            lx,ly,lz = box lengths in x,y,z
            xlo,xhi,ylo,yhi,zlo,zhi = box boundaries
-           xy,xz,yz = box tilt for triclinic (non-orthogonal) simulation boxes
+           xy,xz,yz = box tilt for restricted triclinic (non-orthogonal) simulation boxes
            xlat,ylat,zlat = lattice spacings as calculated by :doc:`lattice <lattice>` command
            bonds,angles,dihedrals,impropers = # of these interactions defined
            pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor
@@ -102,9 +102,12 @@ Examples
 Description
 """""""""""
 
-Set the style and content for printing thermodynamic data to the screen
-and log files.
-
+Set the style and content for printing thermodynamic data to the
+screen and log files.  The units for each column of output
+corresponding to the list of keywords is determined by the :doc:`units
+<units>` command for the simulation.  E.g. energies will be in energy
+units, temperature in temperature units, pressure in pressure units.
+     
 Style *one* prints a single line of thermodynamic info that is the
 equivalent of "thermo_style custom step temp epair emol etotal press".
 The line contains only numeric values.
@@ -319,6 +322,27 @@ thermostatting or barostatting to their coupling reservoirs -- that is,
 the NVT, NPH, or NPT ensembles, the *econserve* quantity should remain
 constant over time even though *etotal* may change.
 
+The *pxx,pyy,pzz,pxy,pxz,pyz* keywords are the 6 components of the
+symmetric pressure tensor for the system.  See the :doc:`compute
+pressure <compute_pressure>` command doc page for details of how it is
+calculated.
+
+If the :doc:`thermo_modify triclinic/general <thermo_modify>` option
+is set and the simulation box was created as a geenral triclinic box,
+then the components will be output as values consistent with the
+orientation of the general triclinic box relative to the standard xyz
+coordinate axes.  If this keyword is not used, the values will be
+consistent with the orientation of the restricted triclinic box (which
+aligns with the xyz coordinate axes).  As explained on the
+:doc:`Howto_triclinic <Howto_triclinic>` doc page, even if the
+simulation box is created as a general triclinic box, internally
+LAMMPS uses a restricted triclinic box.
+
+Note that because the pressure tensor components are computed using
+force vectors and atom coordinates, both of which are rotated in the
+general versus restricted triclinic representation, the values will
+typically be different for the two cases.
+
 The *fmax* and *fnorm* keywords are useful for monitoring the progress
 of an :doc:`energy minimization <minimize>`.  The *fmax* keyword
 calculates the maximum force in any dimension on any atom in the
@@ -338,13 +362,13 @@ to reduce the delay factor to ensure no force interactions are missed
 by atoms moving beyond the neighbor skin distance before a rebuild
 takes place.
 
-The keywords *cella*, *cellb*, *cellc*, *cellalpha*,
-*cellbeta*, *cellgamma*, correspond to the usual crystallographic
-quantities that define the periodic unit cell of a crystal.  See the
-:doc:`Howto triclinic <Howto_triclinic>` page for a geometric
-description of triclinic periodic cells, including a precise
-definition of these quantities in terms of the internal LAMMPS cell
-dimensions *lx*, *ly*, *lz*, *yz*, *xz*, *xy*\ .
+The keywords *cella*, *cellb*, *cellc*, *cellalpha*, *cellbeta*,
+*cellgamma*, correspond to the usual crystallographic quantities that
+define the periodic unit cell of a crystal.  See the :doc:`Howto
+triclinic <Howto_triclinic>` page for a geometric description of
+restricted triclinic periodic cells, including a precise definition of
+these quantities in terms of the internal LAMMPS cell dimensions *lx*,
+*ly*, *lz*, *yz*, *xz*, *xy*\ .
 
 ----------
 

src/thermo.cpp

@@ -579,7 +579,8 @@ void Thermo::modify_params(int narg, char **arg)
       if (iarg + 2 > narg) error->all(FLERR,"Illegal thermo_modify command");
       triclinic_general = utils::logical(FLERR,arg[iarg+1],false,lmp);
       if (triclinic_general && !domain->triclinic_general)
-        error->all(FLERR,"Thermo_modify triclinic/general invalid b/c simulation box is not");
+        error->all(FLERR,"Thermo_modify triclinic/general cannot be used "
+                   "if simulation box is not general triclinic");
       iarg += 2;
 
     } else if (strcmp(arg[iarg], "lost") == 0) {

src/thermo.h

@@ -57,8 +57,8 @@ class Thermo : protected Pointers {
  private:
   int nfield, nfield_initial;
   int *vtype;
+  int triclinic_general;   // set by thermo_modify
 
-  int triclinic_general;              // set by thermo_modify
   std::string line;
   std::vector<std::string> keyword, format, format_column_user, keyword_user;
   std::string format_line_user, format_float_user, format_int_user, format_bigint_user;