[pull] develop from lammps:develop

doc/src/fix_nh.rst

@@ -71,6 +71,7 @@ Syntax
        *scaleyz* value = *yes* or *no* = scale yz with lz
        *scalexz* value = *yes* or *no* = scale xz with lz
        *flip* value = *yes* or *no* = allow or disallow box flips when it becomes highly skewed
+       *isochoric* = *x* or *y* or *z* or *xy* or *yz* or *xz*
        *fixedpoint* values = x y z
          x,y,z = perform barostat dilation/contraction around this point (distance units)
        *update* value = *dipole* or *dipole/dlm*
@@ -375,6 +376,24 @@ acquire ghost atoms around a processor's irregular-shaped subdomain.
 For extreme values of tilt, LAMMPS may also lose atoms and generate an
 error.
 
+The *isochoric* keyword allows to maintain constant volume when barostating
+up to two dimensions with this fix. The values following the isochoric keyword indicates the
+dimensions to use in that regard: "x" indicates the x dimension, "yz" (no
+space) indicates the y and z dimensions, etc. The selected dimensions are scaled to
+compensate the strain induced by the barostat and keep the system at a constant volume
+(or area in 2d). It is not possible to use this keyword if all the
+dimensions are coupled to barostats. In the case of 2d simulations, only x and
+y dimensions can be used to maintain a constant plane area. If you want to perform
+strain with constant volume, the :doc:`fix deform <fix_deform>` command using
+*volume* keyword is more likely to suit your needs.
+
+.. note::
+   If large strains are caused by the barostat because the initial configuration
+   is far from pressure equilibrium or equilibrated too fast, the system will
+   see large strains on the other dimensions as well. It is recommended to
+   perform preliminary NPT equilibration if necessary using standard NPT
+   simulations.
+
 The *fixedpoint* keyword specifies the fixed point for barostat volume
 changes. By default, it is the center of the box.  Whatever point is
 chosen will not move during the simulation.  For example, if the lower
@@ -702,10 +721,10 @@ Related commands
 Default
 """""""
 
-The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = 1,
-ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none,
-flip = yes, scaleyz = scalexz = scalexy = yes if periodic in second
-dimension and not coupled to barostat, otherwise no.
+The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = 1, ploop =
+1, nreset = 0, drag = 0.0, dilate = all, couple = none, flip = yes, scaleyz =
+scalexz = scalexy = yes if periodic in second dimension and not coupled to
+barostat, otherwise no.
 
 ----------
 

doc/src/labelmap.rst

@@ -10,14 +10,16 @@ Syntax
 
    labelmap option args
 
-* *option* = *atom* or *bond* or *angle* or *dihedral* or *improper* or *clear* or *write*
+* *option* = *atom* or *bond* or *angle* or *dihedral* or *improper* or *clear* or *write* or *check_labels*
 
   .. parsed-literal::
 
      *clear* = no args
      *write* arg = filename
      *atom* or *bond* or *angle* or *dihedral* or *improper*
        args = list of one or more numeric-type/type-label pairs
+     *check_labels* value = string
+       string = string containing any of the following characters: 'b', 'a', 'd', or 'i'
 
 Examples
 """"""""
@@ -54,12 +56,12 @@ or '[' and ']', parenthesis '(' and ')', dash '-', underscore '_', plus
 '+' and equals '=' signs and more.  They must not contain blanks or any
 other whitespace.  Note that type labels must be put in single or double
 quotation marks if they contain the '#' character or if they contain a
-double (") or single quotation mark (').  If the label contains both
-a single and a double quotation mark, then triple quotation (""") must
-be used.  When enclosing a type label with quotation marks, the
-LAMMPS input parser may require adding leading or trailing blanks
-around the type label so it can identify the enclosing quotation
-marks.  Those blanks will be removed when defining the label.
+double (") or single quotation mark (').  If the label contains both a
+single and a double quotation mark, then triple quotation (""") must be
+used.  When enclosing a type label with quotation marks, the LAMMPS
+input parser may require adding leading or trailing blanks around the
+type label so it can identify the enclosing quotation marks.  Those
+blanks will be removed when defining the label.
 
 A *labelmap* command can only modify the label map for one type-kind
 (atom types, bond types, etc).  Any number of numeric-type/type-label
@@ -79,6 +81,29 @@ label mappings to a file as a sequence of *labelmap* commands, so the
 file can be copied into a new LAMMPS input file or read in using the
 :doc:`include <include>` command.
 
+.. versionadded:: TBD
+
+The *check_labels* keyword provides a warning if the type label of a
+bond, angle, dihedral, or improper defined in the simulation is not
+consistent with the atom types of its constituent atoms.  This
+consistency check is performed only once, when the simulation is
+initialized by the first :doc:`run <run>` or :doc:`minimize <minimize>`
+command after this *labelmap* command.  The *check_labels* value is a
+single string that should contain one or more of the characters 'b',
+'a', 'd', and 'i', which correspond to bonds, angles, dihedrals, and
+impropers, respectively.  For example, the keyword/value pair
+'check_labels badi' will check all the type labels of all higher-order
+interactions, while 'check_labels adi' will only check type labels for
+angles, dihedrals, and impropers.  The *check_labels* keyword requires a
+specific :doc:`type label<Howto_type_labels>` format to infer the types
+of higher-order interactions.  Bond, angle, dihedral, and improper type
+labels must contain their constituent atom types delimited by hyphens,
+e.g., 'c2-c2-c2-n' for a dihedral that contains three atoms of type 'c2'
+and one atom of 'n'.  If the constituent atoms do not have these atom
+types in the proper order, a warning will be generated when using this
+*check_types* keyword.  Interactions that have been disabled, e.g., via
+:doc:`fix_shake <fix_shake>`, will not be checked.
+
 ----------
 
 Restrictions
@@ -88,7 +113,7 @@ This command must come after the simulation box is defined by a
 :doc:`read_data <read_data>`, :doc:`read_restart <read_restart>`, or
 :doc:`create_box <create_box>` command.
 
-Label maps are currently not supported when using the KOKKOS package.
+Label maps are considered experimental when using the KOKKOS package.
 
 Related commands
 """"""""""""""""

doc/utils/sphinx-config/false_positives.txt

@@ -37,6 +37,7 @@ Addington
 addstep
 addtorque
 adf
+adi
 Adhikari
 adiam
 adim
@@ -238,6 +239,7 @@ Babaei
 Baconnier
 backcolor
 Baczewski
+badi
 Baer
 Bagchi
 Bagi

src/OPENMP/fix_nh_omp.cpp

@@ -45,6 +45,7 @@ using dbl3_t = struct { double x,y,z; };
 void FixNHOMP::remap()
 {
   double oldlo,oldhi,expfac;
+  double isofac;
 
   double * const * _noalias const x = atom->x;
   const int * _noalias const mask = atom->mask;
@@ -121,36 +122,75 @@ void FixNHOMP::remap()
     }
   }
 
+  if (isochoric) isofac = vol_start;
+
   // scale diagonal components
   // scale tilt factors with cell, if set
 
   if (p_flag[0]) {
     oldlo = domain->boxlo[0];
     oldhi = domain->boxhi[0];
     expfac = exp(dto*omega_dot[0]);
+    isofac /= expfac;
     domain->boxlo[0] = (oldlo-fixedpoint[0])*expfac + fixedpoint[0];
     domain->boxhi[0] = (oldhi-fixedpoint[0])*expfac + fixedpoint[0];
+    if (isochoric) isofac /= domain->boxhi[0] - domain->boxlo[0];
   }
 
   if (p_flag[1]) {
     oldlo = domain->boxlo[1];
     oldhi = domain->boxhi[1];
     expfac = exp(dto*omega_dot[1]);
+    isofac /= expfac;
     domain->boxlo[1] = (oldlo-fixedpoint[1])*expfac + fixedpoint[1];
     domain->boxhi[1] = (oldhi-fixedpoint[1])*expfac + fixedpoint[1];
+    if (isochoric) isofac /= domain->boxhi[1] - domain->boxlo[1];
     if (scalexy) h[5] *= expfac;
   }
 
   if (p_flag[2]) {
     oldlo = domain->boxlo[2];
     oldhi = domain->boxhi[2];
     expfac = exp(dto*omega_dot[2]);
+    isofac /= expfac;
     domain->boxlo[2] = (oldlo-fixedpoint[2])*expfac + fixedpoint[2];
     domain->boxhi[2] = (oldhi-fixedpoint[2])*expfac + fixedpoint[2];
+    if (isochoric) isofac /= domain->boxhi[2] - domain->boxlo[2];
     if (scalexz) h[4] *= expfac;
     if (scaleyz) h[3] *= expfac;
   }
 
+  if (isochoric) {
+    for (int i = 0; i < 3; i++) {
+      if (p_isoch[i] || !p_flag[i]) isofac /= (domain->boxhi[i]-domain->boxlo[i]);
+    }
+    int iso_sum = p_isoch[0] + p_isoch[1] + p_isoch[2];
+    if (iso_sum == 2) isofac = sqrt(isofac);
+    if (p_isoch[0]) {
+      // Scale x
+      oldlo = domain->boxlo[0];
+      oldhi = domain->boxhi[0];
+      domain->boxlo[0] = (oldlo-fixedpoint[0])*isofac + fixedpoint[0];
+      domain->boxhi[0] = (oldhi-fixedpoint[0])*isofac + fixedpoint[0];
+    }
+    if (p_isoch[1]) {
+      // Scale y
+      oldlo = domain->boxlo[1];
+      oldhi = domain->boxhi[1];
+      domain->boxlo[1] = (oldlo-fixedpoint[1])*isofac + fixedpoint[1];
+      domain->boxhi[1] = (oldhi-fixedpoint[1])*isofac + fixedpoint[1];
+      if (scalexy) h[5] *= isofac;
+    }
+    if (p_isoch[2]) {
+      oldlo = domain->boxlo[2];
+      oldhi = domain->boxhi[2];
+      domain->boxlo[2] = (oldlo-fixedpoint[2])*isofac + fixedpoint[2];
+      domain->boxhi[2] = (oldhi-fixedpoint[2])*isofac + fixedpoint[2];
+      if (scalexz) h[4] *= isofac;
+      if (scaleyz) h[3] *= isofac;
+    }
+  }
+
   // off-diagonal components, second half
 
   if (pstyle == TRICLINIC) {