From f6bdf5662ec9af4f0eefcfc31fe4c61ba1d1bd10 Mon Sep 17 00:00:00 2001
From: "Jibril B. Coulibaly"
 <43829860+jibril-b-coulibaly@users.noreply.github.com>
Date: Fri, 6 Dec 2019 10:40:04 -0600
Subject: [PATCH 01/14] Update pair_granular.rst

Correct formula for tangent stiffness, consistent with `PairGranular::mix_stiffnessG()`
---
 doc/src/pair_granular.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/src/pair_granular.rst b/doc/src/pair_granular.rst
index d5f522462d..294bec9b8c 100644
--- a/doc/src/pair_granular.rst
+++ b/doc/src/pair_granular.rst
@@ -432,7 +432,7 @@ option by an additional factor of *a*\ , the radius of the contact region. The t
 Here, *a* is the radius of the contact region, given by :math:`a =\sqrt{R\delta}`
 for all normal contact models, except for *jkr*\ , where it is given
 implicitly by :math:`\delta = a^2/R - 2\sqrt{\pi \gamma a/E}`, see
-discussion above. To match the Mindlin solution, one should set :math:`k_t = 8G`, where :math:`G` is the shear modulus, related to Young's modulus
+discussion above. To match the Mindlin solution, one should set :math:`k_t = 4G/(2-\nu)`, where :math:`G` is the shear modulus, related to Young's modulus
 :math:`E` by :math:`G = E/(2(1+\nu))`, where :math:`\nu` is Poisson's ratio. This
 can also be achieved by specifying *NULL* for :math:`k_t`, in which case a
 normal contact model that specifies material parameters :math:`E` and

From 5859b18d2f7b1d63b45a9e541a6908f598b0a16b Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Fri, 6 Dec 2019 11:04:50 -0700
Subject: [PATCH 02/14] enable fix rigid commands to add gravity to COM of
 rigid bodies

---
 src/RIGID/fix_rigid.cpp       | 62 +++++++++++++++++++++++++++++------
 src/RIGID/fix_rigid.h         |  6 +++-
 src/RIGID/fix_rigid_small.cpp | 40 ++++++++++++++++++++--
 src/RIGID/fix_rigid_small.h   |  3 ++
 src/fix_gravity.cpp           | 52 +++++++++++++++++++++++++----
 src/fix_gravity.h             |  5 ++-
 6 files changed, 146 insertions(+), 22 deletions(-)

diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp
index 3e6130ac7c..5e994810ac 100644
--- a/src/RIGID/fix_rigid.cpp
+++ b/src/RIGID/fix_rigid.cpp
@@ -52,8 +52,8 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
   torque(NULL), quat(NULL), imagebody(NULL), fflag(NULL),
   tflag(NULL), langextra(NULL), sum(NULL), all(NULL),
   remapflag(NULL), xcmimage(NULL), eflags(NULL), orient(NULL),
-  dorient(NULL), id_dilate(NULL), random(NULL), avec_ellipsoid(NULL),
-  avec_line(NULL), avec_tri(NULL)
+  dorient(NULL), id_dilate(NULL), id_gravity(NULL), random(NULL), 
+  avec_ellipsoid(NULL), avec_line(NULL), avec_tri(NULL)
 {
   int i,ibody;
 
@@ -124,14 +124,17 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
     if (custom_flag) {
       if (narg < 5) error->all(FLERR,"Illegal fix rigid command");
 
-      // determine whether atom-style variable or atom property is used.
+      // determine whether atom-style variable or atom property is used
+
       if (strstr(arg[4],"i_") == arg[4]) {
         int is_double=0;
         int custom_index = atom->find_custom(arg[4]+2,is_double);
         if (custom_index == -1)
-          error->all(FLERR,"Fix rigid custom requires previously defined property/atom");
+          error->all(FLERR,"Fix rigid custom requires "
+                     "previously defined property/atom");
         else if (is_double)
-          error->all(FLERR,"Fix rigid custom requires integer-valued property/atom");
+          error->all(FLERR,"Fix rigid custom requires "
+                     "integer-valued property/atom");
         int minval = INT_MAX;
         int *value = atom->ivector[custom_index];
         for (i = 0; i < nlocal; i++)
@@ -163,12 +166,15 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
           if (mask[i] & groupbit)
             molecule[i] = (tagint)((tagint)value[i] - minval + 1);
         delete[] value;
+
       } else error->all(FLERR,"Unsupported fix rigid custom property");
+
     } else {
       if (atom->molecule_flag == 0)
         error->all(FLERR,"Fix rigid molecule requires atom attribute molecule");
       molecule = atom->molecule;
     }
+
     iarg = 4 + custom_flag;
 
     tagint maxmol_tag = -1;
@@ -297,6 +303,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
   }
 
   // number of linear rigid bodies is counted later
+
   nlinear = 0;
 
   // parse optional args
@@ -308,12 +315,14 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
   tstat_flag = 0;
   pstat_flag = 0;
   allremap = 1;
-  id_dilate = NULL;
   t_chain = 10;
   t_iter = 1;
   t_order = 3;
   p_chain = 10;
+
   inpfile = NULL;
+  id_gravity = NULL;
+  id_dilate = NULL;
 
   pcouple = NONE;
   pstyle = ANISO;
@@ -543,12 +552,20 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
       iarg += 2;
 
     } else if (strcmp(arg[iarg],"reinit") == 0) {
-      if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid/small command");
+      if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid command");
       if (strcmp("yes",arg[iarg+1]) == 0) reinitflag = 1;
       else if  (strcmp("no",arg[iarg+1]) == 0) reinitflag = 0;
       else error->all(FLERR,"Illegal fix rigid command");
       iarg += 2;
 
+    } else if (strcmp(arg[iarg],"gravity") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid command");
+      delete [] id_gravity;
+      int n = strlen(arg[iarg+1]) + 1;
+      id_gravity = new char[n];
+      strcpy(id_gravity,arg[iarg+1]);
+      iarg += 2;
+
     } else error->all(FLERR,"Illegal fix rigid command");
   }
 
@@ -621,6 +638,9 @@ FixRigid::~FixRigid()
 
   delete random;
   delete [] inpfile;
+  delete [] id_dilate;
+  delete [] id_gravity;
+
   memory->destroy(mol2body);
   memory->destroy(body2mol);
 
@@ -687,7 +707,7 @@ void FixRigid::init()
   avec_tri = (AtomVecTri *) atom->style_match("tri");
 
   // warn if more than one rigid fix
-  // if earlyflag, warn if any post-force fixes come after POEMS fix
+  // if earlyflag, warn if any post-force fixes come after a rigid fix
 
   int count = 0;
   for (i = 0; i < modify->nfix; i++)
@@ -701,7 +721,8 @@ void FixRigid::init()
       if (rflag && (modify->fmask[i] & POST_FORCE) &&
           !modify->fix[i]->rigid_flag) {
         char str[128];
-        snprintf(str,128,"Fix %s alters forces after fix rigid",modify->fix[i]->id);
+        snprintf(str,128,"Fix %s alters forces after fix rigid",
+                 modify->fix[i]->id);
         error->warning(FLERR,str);
       }
     }
@@ -713,12 +734,24 @@ void FixRigid::init()
     if (strcmp(modify->fix[i]->style,"npt") == 0) break;
     if (strcmp(modify->fix[i]->style,"nph") == 0) break;
   }
+
   if (i < modify->nfix) {
     for (int j = i; j < modify->nfix; j++)
       if (strcmp(modify->fix[j]->style,"rigid") == 0)
         error->all(FLERR,"Rigid fix must come before NPT/NPH fix");
   }
 
+  // add gravity forces based on gravity vector from fix
+
+  if (id_gravity) {
+    int ifix = modify->find_fix(id_gravity);
+    if (ifix < 0) error->all(FLERR,"Fix rigid cannot find fix gravity ID");
+    if (strcmp(modify->fix[ifix]->style,"gravity") != 0) 
+      error->all(FLERR,"Fix rigid gravity fix is invalid");
+    int tmp;
+    gvec = (double *) modify->fix[ifix]->extract("gvec",tmp);
+  }
+
   // timestep info
 
   dtv = update->dt;
@@ -1061,8 +1094,17 @@ void FixRigid::compute_forces_and_torques()
     torque[ibody][1] = all[ibody][4] + langextra[ibody][4];
     torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
   }
-}
 
+  // add gravity force to COM of each body
+
+  if (id_gravity) {
+    for (ibody = 0; ibody < nbody; ibody++) {
+      fcm[ibody][0] += gvec[0]*masstotal[ibody];
+      fcm[ibody][1] += gvec[1]*masstotal[ibody];
+      fcm[ibody][2] += gvec[2]*masstotal[ibody];
+    }
+  }
+}
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/RIGID/fix_rigid.h b/src/RIGID/fix_rigid.h
index 8c4ab9ed49..c261d89cce 100644
--- a/src/RIGID/fix_rigid.h
+++ b/src/RIGID/fix_rigid.h
@@ -66,7 +66,8 @@ class FixRigid : public Fix {
   double *step_respa;
   int triclinic;
 
-  char *inpfile;             // file to read rigid body attributes from
+  char *inpfile;            // file to read rigid body attributes from
+
   int rstyle;               // SINGLE,MOLECULE,GROUP
   int setupflag;            // 1 if body properties are setup, else 0
   int earlyflag;            // 1 if forces/torques computed at post_force()
@@ -131,6 +132,9 @@ class FixRigid : public Fix {
   int dilate_group_bit;      // mask for dilation group
   char *id_dilate;           // group name to dilate
 
+  char *id_gravity;         // ID of fix gravity command to add gravity forces
+  double *gvec;             // ptr to gravity vector inside the fix
+
   class RanMars *random;
   class AtomVecEllipsoid *avec_ellipsoid;
   class AtomVecLine *avec_line;
diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp
index ba570d5840..4d2776b9ff 100644
--- a/src/RIGID/fix_rigid_small.cpp
+++ b/src/RIGID/fix_rigid_small.cpp
@@ -57,7 +57,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
   xcmimage(NULL), displace(NULL), eflags(NULL), orient(NULL), dorient(NULL),
   avec_ellipsoid(NULL), avec_line(NULL), avec_tri(NULL), counts(NULL),
   itensor(NULL), mass_body(NULL), langextra(NULL), random(NULL),
-  id_dilate(NULL), onemols(NULL)
+  id_dilate(NULL), id_gravity(NULL), onemols(NULL)
 {
   int i;
 
@@ -107,7 +107,8 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
       bodyID = new tagint[nlocal];
       customflag = 1;
 
-      // determine whether atom-style variable or atom property is used.
+      // determine whether atom-style variable or atom property is used
+
       if (strstr(arg[4],"i_") == arg[4]) {
         int is_double=0;
         int custom_index = atom->find_custom(arg[4]+2,is_double);
@@ -356,6 +357,13 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
       p_chain = force->numeric(FLERR,arg[iarg+1]);
       iarg += 2;
 
+    } else if (strcmp(arg[iarg],"gravity") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid/small command");
+      delete [] id_gravity;
+      int n = strlen(arg[iarg+1]) + 1;
+      id_gravity = new char[n];
+      strcpy(id_gravity,arg[iarg+1]);
+      iarg += 2;
 
     } else error->all(FLERR,"Illegal fix rigid/small command");
   }
@@ -515,6 +523,8 @@ FixRigidSmall::~FixRigidSmall()
 
   delete random;
   delete [] inpfile;
+  delete [] id_dilate;
+  delete [] id_gravity;
 
   memory->destroy(langextra);
   memory->destroy(mass_body);
@@ -543,6 +553,7 @@ void FixRigidSmall::init()
   triclinic = domain->triclinic;
 
   // warn if more than one rigid fix
+  // if earlyflag, warn if any post-force fixes come after a rigid fix
 
   int count = 0;
   for (i = 0; i < modify->nfix; i++)
@@ -575,6 +586,17 @@ void FixRigidSmall::init()
         error->all(FLERR,"Rigid fix must come before NPT/NPH fix");
   }
 
+  // add gravity forces based on gravity vector from fix
+
+  if (id_gravity) {
+    int ifix = modify->find_fix(id_gravity);
+    if (ifix < 0) error->all(FLERR,"Fix rigid/small cannot find fix gravity ID");
+    if (strcmp(modify->fix[ifix]->style,"gravity") != 0) 
+      error->all(FLERR,"Fix rigid/small gravity fix is invalid");
+    int tmp;
+    gvec = (double *) modify->fix[ifix]->extract("gvec",tmp);
+  }
+
   // timestep info
 
   dtv = update->dt;
@@ -954,8 +976,20 @@ void FixRigidSmall::compute_forces_and_torques()
       tcm[2] += langextra[ibody][5];
     }
   }
-}
 
+  // add gravity force to COM of each body
+
+  if (id_gravity) {
+    double mass;
+    for (ibody = 0; ibody < nlocal_body; ibody++) {
+      mass = body[ibody].mass;
+      fcm = body[ibody].fcm;
+      fcm[0] += gvec[0]*mass;
+      fcm[1] += gvec[1]*mass;
+      fcm[2] += gvec[2]*mass;
+    }
+  }
+}
 
 /* ---------------------------------------------------------------------- */
 
diff --git a/src/RIGID/fix_rigid_small.h b/src/RIGID/fix_rigid_small.h
index 0d1cdb5963..974f5711e2 100644
--- a/src/RIGID/fix_rigid_small.h
+++ b/src/RIGID/fix_rigid_small.h
@@ -164,6 +164,9 @@ class FixRigidSmall : public Fix {
   int dilate_group_bit;      // mask for dilation group
   char *id_dilate;           // group name to dilate
 
+  char *id_gravity;         // ID of fix gravity command to add gravity forces
+  double *gvec;             // ptr to gravity vector inside the fix
+
   double p_current[3],p_target[3];
 
   // molecules added on-the-fly as rigid bodies
diff --git a/src/fix_gravity.cpp b/src/fix_gravity.cpp
index 14ba913c01..c36d2230c5 100644
--- a/src/fix_gravity.cpp
+++ b/src/fix_gravity.cpp
@@ -37,7 +37,8 @@ enum{CONSTANT,EQUAL};
 
 FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg),
-  mstr(NULL), vstr(NULL), pstr(NULL), tstr(NULL), xstr(NULL), ystr(NULL), zstr(NULL)
+  mstr(NULL), vstr(NULL), pstr(NULL), tstr(NULL), 
+  xstr(NULL), ystr(NULL), zstr(NULL)
 {
   if (narg < 5) error->all(FLERR,"Illegal fix gravity command");
 
@@ -61,8 +62,10 @@ FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
     mstyle = CONSTANT;
   }
 
+  int iarg;
+
   if (strcmp(arg[4],"chute") == 0) {
-    if (narg != 6) error->all(FLERR,"Illegal fix gravity command");
+    if (narg < 6) error->all(FLERR,"Illegal fix gravity command");
     style = CHUTE;
     if (strstr(arg[5],"v_") == arg[5]) {
       int n = strlen(&arg[5][2]) + 1;
@@ -73,9 +76,10 @@ FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
       vert = force->numeric(FLERR,arg[5]);
       vstyle = CONSTANT;
     }
+    iarg = 6;
 
   } else if (strcmp(arg[4],"spherical") == 0) {
-    if (narg != 7) error->all(FLERR,"Illegal fix gravity command");
+    if (narg < 7) error->all(FLERR,"Illegal fix gravity command");
     style = SPHERICAL;
     if (strstr(arg[5],"v_") == arg[5]) {
       int n = strlen(&arg[5][2]) + 1;
@@ -95,9 +99,10 @@ FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
       theta = force->numeric(FLERR,arg[6]);
       tstyle = CONSTANT;
     }
+    iarg = 7;
 
   } else if (strcmp(arg[4],"vector") == 0) {
-    if (narg != 8) error->all(FLERR,"Illegal fix gravity command");
+    if (narg < 8) error->all(FLERR,"Illegal fix gravity command");
     style = VECTOR;
     if (strstr(arg[5],"v_") == arg[5]) {
       int n = strlen(&arg[5][2]) + 1;
@@ -126,9 +131,23 @@ FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
       zdir = force->numeric(FLERR,arg[7]);
       zstyle = CONSTANT;
     }
+    iarg = 8;
 
   } else error->all(FLERR,"Illegal fix gravity command");
 
+  // optional keywords
+
+  disable = 0;
+
+  while (iarg < narg) {
+    if (strcmp(arg[iarg],"disable") == 0) {
+      disable = 1;
+      iarg++;
+    } else error->all(FLERR,"Illegal fix gravity command");
+  }
+
+  // initializations
+
   degree2rad = MY_PI/180.0;
   time_origin = update->ntimestep;
 
@@ -266,6 +285,12 @@ void FixGravity::post_force(int /*vflag*/)
     set_acceleration();
   }
 
+  // just exit if application of force is disabled
+
+  if (disable) return;
+
+  // apply gravity force to each particle
+
   double **x = atom->x;
   double **f = atom->f;
   double *rmass = atom->rmass;
@@ -338,9 +363,9 @@ void FixGravity::set_acceleration()
     }
   }
 
-  xacc = magnitude*xgrav;
-  yacc = magnitude*ygrav;
-  zacc = magnitude*zgrav;
+  gvec[0] = xacc = magnitude*xgrav;
+  gvec[1] = yacc = magnitude*ygrav;
+  gvec[2] = zacc = magnitude*zgrav;
 }
 
 /* ----------------------------------------------------------------------
@@ -357,3 +382,16 @@ double FixGravity::compute_scalar()
   }
   return egrav_all;
 }
+
+/* ----------------------------------------------------------------------
+   extract current gravity direction vector
+------------------------------------------------------------------------- */
+
+void *FixGravity::extract(const char *name, int &dim)
+{
+  if (strcmp(name,"gvec") == 0) {
+    dim = 1;
+    return (void *) gvec;
+  }
+  return NULL;
+}
diff --git a/src/fix_gravity.h b/src/fix_gravity.h
index 1f18ee274b..ba6a61ee0d 100644
--- a/src/fix_gravity.h
+++ b/src/fix_gravity.h
@@ -36,9 +36,10 @@ class FixGravity : public Fix {
   virtual void post_force(int);
   virtual void post_force_respa(int, int, int);
   double compute_scalar();
+  void *extract(const char *, int &);
 
  protected:
-  int style;
+  int style,disable;
   double magnitude;
   double vert,phi,theta;
   double xdir,ydir,zdir;
@@ -46,6 +47,8 @@ class FixGravity : public Fix {
   double degree2rad;
   int ilevel_respa;
   int time_origin;
+  double gvec[3];
+
   int eflag;
   double egrav,egrav_all;
 

From a11b886b5c39e42c51686e31945b1fdf5394f85f Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Thu, 19 Dec 2019 16:17:14 -0700
Subject: [PATCH 03/14] add warning if gravity is used incorrectly with
 overlapped rigid bodies

---
 src/RIGID/fix_rigid.cpp       | 17 +++++++++++++++++
 src/RIGID/fix_rigid_small.cpp | 17 +++++++++++++++++
 2 files changed, 34 insertions(+)

diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp
index 5e994810ac..d852a47381 100644
--- a/src/RIGID/fix_rigid.cpp
+++ b/src/RIGID/fix_rigid.cpp
@@ -728,6 +728,23 @@ void FixRigid::init()
     }
   }
 
+  // warn if body properties are read from inpfile
+  //   and the gravity keyword is not set and a gravity fix exists
+  // this could mean body particles are overlapped
+  //   and gravity is not applied correctly
+
+  if (inpfile && !id_gravity) {
+    for (i = 0; i < modify->nfix; i++) {
+      if (strcmp(modify->fix[i]->style,"gravity") == 0) {
+        if (comm->me == 0) 
+          error->warning(FLERR,"Gravity may not be correctly applied "
+                         "to rigid bodies if they consist of "
+                         "overlapped particles");
+        break;
+      }
+    }
+  }
+
   // error if npt,nph fix comes before rigid fix
 
   for (i = 0; i < modify->nfix; i++) {
diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp
index 4d2776b9ff..cbdc877d09 100644
--- a/src/RIGID/fix_rigid_small.cpp
+++ b/src/RIGID/fix_rigid_small.cpp
@@ -574,6 +574,23 @@ void FixRigidSmall::init()
     }
   }
 
+  // warn if body properties are read from inpfile or a mol template file
+  //   and the gravity keyword is not set and a gravity fix exists
+  // this could mean body particles are overlapped
+  //   and gravity is not applied correctly
+
+  if ((inpfile || onemols) && !id_gravity) {
+    for (i = 0; i < modify->nfix; i++) {
+      if (strcmp(modify->fix[i]->style,"gravity") == 0) {
+        if (comm->me == 0) 
+          error->warning(FLERR,"Gravity may not be correctly applied "
+                         "to rigid bodies if they consist of "
+                         "overlapped particles");
+        break;
+      }
+    }
+  }
+
   // error if npt,nph fix comes before rigid fix
 
   for (i = 0; i < modify->nfix; i++) {

From c8a53d560a55748744d6f7c5f468976843663232 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20H=C3=B6rmann?=
 <johannes.hoermann@imtek.uni-freiburg.de>
Date: Wed, 18 Dec 2019 12:09:21 +0100
Subject: [PATCH 04/14] Find parallel NetCDF with cmake for USER-NETCDF

Conflicts:
	cmake/presets/forhlr2-gnu.cmake
---
 cmake/Modules/FindNetCDF.cmake           |  6 ++-
 cmake/Modules/FindPNetCDF.cmake          | 55 ++++++++++++++++++++++++
 cmake/Modules/Packages/USER-NETCDF.cmake | 26 +++++++++--
 3 files changed, 82 insertions(+), 5 deletions(-)
 create mode 100644 cmake/Modules/FindPNetCDF.cmake

diff --git a/cmake/Modules/FindNetCDF.cmake b/cmake/Modules/FindNetCDF.cmake
index a28c959acf..3d4aed947d 100644
--- a/cmake/Modules/FindNetCDF.cmake
+++ b/cmake/Modules/FindNetCDF.cmake
@@ -46,10 +46,14 @@ endif()
 find_path (NETCDF_INCLUDE_DIR netcdf.h
   HINTS "${NETCDF_DIR}/include")
 mark_as_advanced (NETCDF_INCLUDE_DIR)
+
 set (NETCDF_C_INCLUDE_DIRS ${NETCDF_INCLUDE_DIR})
 
+string(REGEX REPLACE "/include/?$" "/lib"
+  NETCDF_LIB_HINT ${NETCDF_INCLUDE_DIR})
+
 find_library (NETCDF_LIBRARY NAMES netcdf
-  HINTS "${NETCDF_DIR}/lib")
+  HINTS "${NETCDF_DIR}/lib" "${NETCDF_LIB_HINT}")
 mark_as_advanced (NETCDF_LIBRARY)
 
 set (NETCDF_C_LIBRARIES ${NETCDF_LIBRARY})
diff --git a/cmake/Modules/FindPNetCDF.cmake b/cmake/Modules/FindPNetCDF.cmake
new file mode 100644
index 0000000000..0cc2c1faa8
--- /dev/null
+++ b/cmake/Modules/FindPNetCDF.cmake
@@ -0,0 +1,55 @@
+# source: https://ftp.space.dtu.dk/pub/Ioana/pism0.6.1-10/CMake/FindPNetCDF.cmake
+# license: GPL v3 (https://ftp.space.dtu.dk/pub/Ioana/pism0.6.1-10/COPYING)
+#
+# - Find PNetCDF
+# Find the native PNetCDF includes and library
+#
+#  PNETCDF_INCLUDES    - where to find netcdf.h, etc
+#  PNETCDF_LIBRARIES   - Link these libraries when using NetCDF
+#  PNETCDF_FOUND       - True if PNetCDF was found
+#
+# Normal usage would be:
+#  find_package (PNetCDF REQUIRED)
+#  target_link_libraries (uses_pnetcdf ${PNETCDF_LIBRARIES})
+
+if (PNETCDF_INCLUDES AND PNETCDF_LIBRARIES)
+  # Already in cache, be silent
+  set (PNETCDF_FIND_QUIETLY TRUE)
+endif (PNETCDF_INCLUDES AND PNETCDF_LIBRARIES)
+
+find_path (PNETCDF_INCLUDES pnetcdf.h
+  HINTS "${PNETCDF_ROOT}/include" "$ENV{PNETCDF_ROOT}/include")
+
+string(REGEX REPLACE "/include/?$" "/lib"
+  PNETCDF_LIB_HINT ${PNETCDF_INCLUDES})
+
+find_library (PNETCDF_LIBRARIES
+  NAMES pnetcdf
+  HINTS ${PNETCDF_LIB_HINT})
+
+if ((NOT PNETCDF_LIBRARIES) OR (NOT PNETCDF_INCLUDES))
+  message(STATUS "Trying to find PNetCDF using LD_LIBRARY_PATH (we're desperate)...")
+
+  file(TO_CMAKE_PATH "$ENV{LD_LIBRARY_PATH}" LD_LIBRARY_PATH)
+
+  find_library(PNETCDF_LIBRARIES
+    NAMES pnetcdf
+    HINTS ${LD_LIBRARY_PATH})
+
+  if (PNETCDF_LIBRARIES)
+    get_filename_component(PNETCDF_LIB_DIR ${PNETCDF_LIBRARIES} PATH)
+    string(REGEX REPLACE "/lib/?$" "/include"
+      PNETCDF_H_HINT ${PNETCDF_LIB_DIR})
+
+    find_path (PNETCDF_INCLUDES pnetcdf.h
+      HINTS ${PNETCDF_H_HINT}
+      DOC "Path to pnetcdf.h")
+  endif()
+endif()
+
+# handle the QUIETLY and REQUIRED arguments and set PNETCDF_FOUND to TRUE if
+# all listed variables are TRUE
+include (FindPackageHandleStandardArgs)
+find_package_handle_standard_args (PNetCDF DEFAULT_MSG PNETCDF_LIBRARIES PNETCDF_INCLUDES)
+
+mark_as_advanced (PNETCDF_LIBRARIES PNETCDF_INCLUDES)
diff --git a/cmake/Modules/Packages/USER-NETCDF.cmake b/cmake/Modules/Packages/USER-NETCDF.cmake
index a90725bbbc..f60c046ab9 100644
--- a/cmake/Modules/Packages/USER-NETCDF.cmake
+++ b/cmake/Modules/Packages/USER-NETCDF.cmake
@@ -1,6 +1,24 @@
 if(PKG_USER-NETCDF)
-  find_package(NetCDF REQUIRED)
-  include_directories(${NETCDF_INCLUDE_DIRS})
-  list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARIES})
-  add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
+  # USER-NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.
+  # NetCDF library enables dump sytle "netcdf", while PNetCDF enables dump style "netcdf/mpiio"
+  find_package(NetCDF)
+  if(NETCDF_FOUND)
+    find_package(PNetCDF)
+  else(NETCDF_FOUND)
+    find_package(PNetCDF REQUIRED)
+  endif(NETCDF_FOUND)
+
+  if(NETCDF_FOUND)
+    include_directories(${NETCDF_INCLUDE_DIRS})
+    list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARIES})
+    add_definitions(-DLMP_HAS_NETCDF)
+  endif(NETCDF_FOUND)
+
+  if(PNETCDF_FOUND)
+    include_directories(${PNETCDF_INCLUDES})
+    list(APPEND LAMMPS_LINK_LIBS ${PNETCDF_LIBRARIES})
+    add_definitions(-DLMP_HAS_PNETCDF)
+  endif(PNETCDF_FOUND)
+
+  add_definitions(-DNC_64BIT_DATA=0x0020)
 endif()

From 3b76ab56f05c705fc71952a1709e97a1898b4ddc Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 20 Dec 2019 12:09:50 -0500
Subject: [PATCH 05/14] port gravity changes to rigid fixes to USER-OMP package
 versions

---
 src/USER-OMP/fix_rigid_nh_omp.cpp    | 13 +++++++++++++
 src/USER-OMP/fix_rigid_omp.cpp       | 13 +++++++++++++
 src/USER-OMP/fix_rigid_small_omp.cpp | 15 +++++++++++++++
 3 files changed, 41 insertions(+)

diff --git a/src/USER-OMP/fix_rigid_nh_omp.cpp b/src/USER-OMP/fix_rigid_nh_omp.cpp
index d92a82a6bf..da512cb428 100644
--- a/src/USER-OMP/fix_rigid_nh_omp.cpp
+++ b/src/USER-OMP/fix_rigid_nh_omp.cpp
@@ -383,6 +383,19 @@ void FixRigidNHOMP::compute_forces_and_torques()
     torque[ibody][1] = all[ibody][4] + langextra[ibody][4];
     torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
   }
+
+  // add gravity force to COM of each body
+
+  if (id_gravity) {
+#if defined(_OPENMP)
+#pragma omp parallel for default(none) private(ibody) schedule(static)
+#endif
+    for (ibody = 0; ibody < nbody; ibody++) {
+      fcm[ibody][0] += gvec[0]*masstotal[ibody];
+      fcm[ibody][1] += gvec[1]*masstotal[ibody];
+      fcm[ibody][2] += gvec[2]*masstotal[ibody];
+    }
+  }
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/USER-OMP/fix_rigid_omp.cpp b/src/USER-OMP/fix_rigid_omp.cpp
index 20d3009d40..1cdf1018b2 100644
--- a/src/USER-OMP/fix_rigid_omp.cpp
+++ b/src/USER-OMP/fix_rigid_omp.cpp
@@ -256,6 +256,19 @@ void FixRigidOMP::compute_forces_and_torques()
     torque[ibody][1] = all[ibody][4] + langextra[ibody][4];
     torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
   }
+
+  // add gravity force to COM of each body
+
+  if (id_gravity) {
+#if defined(_OPENMP)
+#pragma omp parallel for default(none) private(ibody) schedule(static)
+#endif
+    for (int ibody = 0; ibody < nbody; ibody++) {
+      fcm[ibody][0] += gvec[0]*masstotal[ibody];
+      fcm[ibody][1] += gvec[1]*masstotal[ibody];
+      fcm[ibody][2] += gvec[2]*masstotal[ibody];
+    }
+  }
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/USER-OMP/fix_rigid_small_omp.cpp b/src/USER-OMP/fix_rigid_small_omp.cpp
index 705f0e6bd0..bdd10b0ca7 100644
--- a/src/USER-OMP/fix_rigid_small_omp.cpp
+++ b/src/USER-OMP/fix_rigid_small_omp.cpp
@@ -196,6 +196,21 @@ void FixRigidSmallOMP::compute_forces_and_torques()
       tcm[2] += langextra[ibody][5];
     }
   }
+
+  // add gravity force to COM of each body
+
+  if (id_gravity) {
+#if defined(_OPENMP)
+#pragma omp parallel for default(none) private(ibody) schedule(static)
+#endif
+    for (int ibody = 0; ibody < nbody; ibody++) {
+      double * _noalias const fcm = body[ibody].fcm;
+      const double mass = body[ibody].mass;
+      fcm[0] += gvec[0]*mass;
+      fcm[1] += gvec[1]*mass;
+      fcm[2] += gvec[2]*mass;
+    }
+  }
 }
 
 /* ---------------------------------------------------------------------- */

From a88a00dbbb86fdcc2b4ed7bde34f50180bbaa89d Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 20 Dec 2019 15:08:51 -0500
Subject: [PATCH 06/14] remove trailing whitespace

---
 src/RIGID/fix_rigid.cpp       | 6 +++---
 src/RIGID/fix_rigid_small.cpp | 4 ++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp
index d852a47381..101b94c2a4 100644
--- a/src/RIGID/fix_rigid.cpp
+++ b/src/RIGID/fix_rigid.cpp
@@ -52,7 +52,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
   torque(NULL), quat(NULL), imagebody(NULL), fflag(NULL),
   tflag(NULL), langextra(NULL), sum(NULL), all(NULL),
   remapflag(NULL), xcmimage(NULL), eflags(NULL), orient(NULL),
-  dorient(NULL), id_dilate(NULL), id_gravity(NULL), random(NULL), 
+  dorient(NULL), id_dilate(NULL), id_gravity(NULL), random(NULL),
   avec_ellipsoid(NULL), avec_line(NULL), avec_tri(NULL)
 {
   int i,ibody;
@@ -736,7 +736,7 @@ void FixRigid::init()
   if (inpfile && !id_gravity) {
     for (i = 0; i < modify->nfix; i++) {
       if (strcmp(modify->fix[i]->style,"gravity") == 0) {
-        if (comm->me == 0) 
+        if (comm->me == 0)
           error->warning(FLERR,"Gravity may not be correctly applied "
                          "to rigid bodies if they consist of "
                          "overlapped particles");
@@ -763,7 +763,7 @@ void FixRigid::init()
   if (id_gravity) {
     int ifix = modify->find_fix(id_gravity);
     if (ifix < 0) error->all(FLERR,"Fix rigid cannot find fix gravity ID");
-    if (strcmp(modify->fix[ifix]->style,"gravity") != 0) 
+    if (strcmp(modify->fix[ifix]->style,"gravity") != 0)
       error->all(FLERR,"Fix rigid gravity fix is invalid");
     int tmp;
     gvec = (double *) modify->fix[ifix]->extract("gvec",tmp);
diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp
index cbdc877d09..33105418ff 100644
--- a/src/RIGID/fix_rigid_small.cpp
+++ b/src/RIGID/fix_rigid_small.cpp
@@ -582,7 +582,7 @@ void FixRigidSmall::init()
   if ((inpfile || onemols) && !id_gravity) {
     for (i = 0; i < modify->nfix; i++) {
       if (strcmp(modify->fix[i]->style,"gravity") == 0) {
-        if (comm->me == 0) 
+        if (comm->me == 0)
           error->warning(FLERR,"Gravity may not be correctly applied "
                          "to rigid bodies if they consist of "
                          "overlapped particles");
@@ -608,7 +608,7 @@ void FixRigidSmall::init()
   if (id_gravity) {
     int ifix = modify->find_fix(id_gravity);
     if (ifix < 0) error->all(FLERR,"Fix rigid/small cannot find fix gravity ID");
-    if (strcmp(modify->fix[ifix]->style,"gravity") != 0) 
+    if (strcmp(modify->fix[ifix]->style,"gravity") != 0)
       error->all(FLERR,"Fix rigid/small gravity fix is invalid");
     int tmp;
     gvec = (double *) modify->fix[ifix]->extract("gvec",tmp);

From 4e7bcee8e386dd6c467aa8cd9ef04214a227be22 Mon Sep 17 00:00:00 2001
From: jotelha <johannes.hoermann@imtek.uni-freiburg.de>
Date: Sun, 22 Dec 2019 13:24:34 +0100
Subject: [PATCH 07/14] Update cmake/Modules/FindNetCDF.cmake

Co-Authored-By: Christoph Junghans <christoph.junghans@gmail.com>
---
 cmake/Modules/FindNetCDF.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cmake/Modules/FindNetCDF.cmake b/cmake/Modules/FindNetCDF.cmake
index 3d4aed947d..4181e3f027 100644
--- a/cmake/Modules/FindNetCDF.cmake
+++ b/cmake/Modules/FindNetCDF.cmake
@@ -53,7 +53,7 @@ string(REGEX REPLACE "/include/?$" "/lib"
   NETCDF_LIB_HINT ${NETCDF_INCLUDE_DIR})
 
 find_library (NETCDF_LIBRARY NAMES netcdf
-  HINTS "${NETCDF_DIR}/lib" "${NETCDF_LIB_HINT}")
+  HINTS "${NETCDF_DIR}" "${NETCDF_LIB_HINT}" PATH_SUFFIXES lib lib64)
 mark_as_advanced (NETCDF_LIBRARY)
 
 set (NETCDF_C_LIBRARIES ${NETCDF_LIBRARY})

From 0c7d6a01e8f93669f94170acbc335c128058f7fe Mon Sep 17 00:00:00 2001
From: jotelha <johannes.hoermann@imtek.uni-freiburg.de>
Date: Sun, 22 Dec 2019 13:25:08 +0100
Subject: [PATCH 08/14] Update cmake/Modules/FindNetCDF.cmake

Co-Authored-By: Christoph Junghans <christoph.junghans@gmail.com>
---
 cmake/Modules/FindNetCDF.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cmake/Modules/FindNetCDF.cmake b/cmake/Modules/FindNetCDF.cmake
index 4181e3f027..2a992b6b3b 100644
--- a/cmake/Modules/FindNetCDF.cmake
+++ b/cmake/Modules/FindNetCDF.cmake
@@ -49,7 +49,7 @@ mark_as_advanced (NETCDF_INCLUDE_DIR)
 
 set (NETCDF_C_INCLUDE_DIRS ${NETCDF_INCLUDE_DIR})
 
-string(REGEX REPLACE "/include/?$" "/lib"
+string(REGEX REPLACE "/include/?$" ""
   NETCDF_LIB_HINT ${NETCDF_INCLUDE_DIR})
 
 find_library (NETCDF_LIBRARY NAMES netcdf

From 3f24144abd499042720c8d1f200a10e843f5b69a Mon Sep 17 00:00:00 2001
From: jotelha <johannes.hoermann@imtek.uni-freiburg.de>
Date: Sun, 22 Dec 2019 13:25:24 +0100
Subject: [PATCH 09/14] Update cmake/Modules/FindPNetCDF.cmake

Co-Authored-By: Christoph Junghans <christoph.junghans@gmail.com>
---
 cmake/Modules/FindPNetCDF.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cmake/Modules/FindPNetCDF.cmake b/cmake/Modules/FindPNetCDF.cmake
index 0cc2c1faa8..e95ed4e559 100644
--- a/cmake/Modules/FindPNetCDF.cmake
+++ b/cmake/Modules/FindPNetCDF.cmake
@@ -38,7 +38,7 @@ if ((NOT PNETCDF_LIBRARIES) OR (NOT PNETCDF_INCLUDES))
 
   if (PNETCDF_LIBRARIES)
     get_filename_component(PNETCDF_LIB_DIR ${PNETCDF_LIBRARIES} PATH)
-    string(REGEX REPLACE "/lib/?$" "/include"
+    string(REGEX REPLACE "/(lib|lib64)/?$" "/include"
       PNETCDF_H_HINT ${PNETCDF_LIB_DIR})
 
     find_path (PNETCDF_INCLUDES pnetcdf.h

From 6aa4f4caf644398b17722f546be19dd91030b0f3 Mon Sep 17 00:00:00 2001
From: "Dan S. Bolintineanu" <dsbolin@sandia.gov>
Date: Mon, 6 Jan 2020 21:18:00 -0700
Subject: [PATCH 10/14] Added example script and input data file showing
 benefits of new fix gravity and fix rigid options

---
 examples/rigid/in.rigid.gravity | 62 +++++++++++++++++++++++++++++++++
 examples/rigid/molecule.data    | 41 ++++++++++++++++++++++
 2 files changed, 103 insertions(+)
 create mode 100644 examples/rigid/in.rigid.gravity
 create mode 100644 examples/rigid/molecule.data

diff --git a/examples/rigid/in.rigid.gravity b/examples/rigid/in.rigid.gravity
new file mode 100644
index 0000000000..22abb0740e
--- /dev/null
+++ b/examples/rigid/in.rigid.gravity
@@ -0,0 +1,62 @@
+#Pour composite granular particles on flat wall
+
+newton		on
+atom_style	sphere
+atom_modify	map array sort 0 0
+
+thermo_modify	flush yes
+units 		si  
+
+variable	minrad equal 0.5
+variable	maxrad equal 1.4
+
+variable 	skin equal 0.3*${maxrad}
+
+boundary	p p f
+region		reg block 0 20 0 20 0 200 units box
+create_box	1 reg
+
+fix             prop all property/atom mol ghost yes
+
+variable	dumpfreq equal 1000
+variable	logfreq equal 1000
+
+pair_style	gran/hooke/history 4e5 NULL 1e2 NULL 0.5 0
+pair_coeff	* *
+
+timestep 	0.0001
+
+group		particles type 1
+atom_modify     first particles
+
+neighbor        ${skin} bin
+group		rigid type 1
+neigh_modify	every 1 delay 0 check yes exclude molecule/intra all 
+
+thermo 		${logfreq}
+thermo_style	custom step cpu atoms ke
+thermo_modify	flush yes lost warn
+
+comm_modify	vel yes cutoff 3
+
+molecule	mymol molecule.data
+region		pourreg block 5 15 5 15 80 100 side in units box
+
+#Note: in versions prior to 1/2020, the 'disable' keyword to fix/gravity
+# and the 'gravity' keyword to fix rigid/small were not available.
+# These settings produce undesirable behavior, where gravity can induce
+# torque on rigid bodies.
+#fix		gravfix all gravity 9.8 vector 0 0 -1 #disable
+#fix		rigidfix all rigid/small molecule mol mymol #gravity gravfix
+
+#The correct behavior is recovered with the following settings:
+fix		gravfix all gravity 9.8 vector 0 0 -1 disable
+fix		rigidfix all rigid/small molecule mol mymol gravity gravfix
+fix		pourfix all pour 5 0 1234 region pourreg mol mymol rigid rigidfix
+
+fix		zwall all wall/gran hooke/history 4000.0 NULL 100.0 NULL 0.5 0 zplane 0.1 NULL
+
+dump		1 all custom 1000 molecule_pour.dump id type mass radius x y z fx fy fz
+
+run		100000
+
diff --git a/examples/rigid/molecule.data b/examples/rigid/molecule.data
new file mode 100644
index 0000000000..e0677b0f63
--- /dev/null
+++ b/examples/rigid/molecule.data
@@ -0,0 +1,41 @@
+LAMMPS data file created for rigid body molecule template
+
+5 atoms
+
+2.3388800000000005 mass
+
+6.002239704473936 4.99 4.989999999999999 com
+
+116.79265620480001 144.26721336320003 144.26721336320006 -70.05220681600004 -70.05220681600002 -58.238345888000005 inertia
+
+Coords
+
+1 5 5 5
+2 5.1 5.0 5.0
+3 5.2 5.0 5.0
+4 6.2 5.0 5.0
+5 7.2 5.0 5.0
+
+Types
+
+1 1
+2 1
+3 1
+4 1
+5 1
+
+Diameters
+
+1 1.0
+2 0.9
+3 1.2
+4 1.2
+5 1.0
+
+Masses
+
+1 0.5235987755982988
+2 0.3817035074111599
+3 0.9047786842338602
+4 0.9047786842338602
+5 0.5235987755982988

From 7bc8c8e9d8e200a5303377836a94b1106dac096f Mon Sep 17 00:00:00 2001
From: "Dan S. Bolintineanu" <dsbolin@sandia.gov>
Date: Mon, 6 Jan 2020 21:26:34 -0700
Subject: [PATCH 11/14] Minor tweaks to in.rigid.gravity example

---
 examples/rigid/in.rigid.gravity | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/examples/rigid/in.rigid.gravity b/examples/rigid/in.rigid.gravity
index 22abb0740e..1094681f18 100644
--- a/examples/rigid/in.rigid.gravity
+++ b/examples/rigid/in.rigid.gravity
@@ -52,11 +52,12 @@ region		pourreg block 5 15 5 15 80 100 side in units box
 #The correct behavior is recovered with the following settings:
 fix		gravfix all gravity 9.8 vector 0 0 -1 disable
 fix		rigidfix all rigid/small molecule mol mymol gravity gravfix
+
 fix		pourfix all pour 5 0 1234 region pourreg mol mymol rigid rigidfix
 
 fix		zwall all wall/gran hooke/history 4000.0 NULL 100.0 NULL 0.5 0 zplane 0.1 NULL
 
-dump		1 all custom 1000 molecule_pour.dump id type mass radius x y z fx fy fz
+#dump		1 all custom 1000 molecule_pour.dump id type mass radius x y z fx fy fz
 
 run		100000
 

From 24ef36dd4dc5671546dc74335ef54644c51c88df Mon Sep 17 00:00:00 2001
From: jotelha <johannes.hoermann@imtek.uni-freiburg.de>
Date: Tue, 7 Jan 2020 13:25:54 +0100
Subject: [PATCH 12/14] Update cmake/Modules/FindPNetCDF.cmake

Co-Authored-By: Christoph Junghans <christoph.junghans@gmail.com>
---
 cmake/Modules/FindPNetCDF.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cmake/Modules/FindPNetCDF.cmake b/cmake/Modules/FindPNetCDF.cmake
index e95ed4e559..8778335f62 100644
--- a/cmake/Modules/FindPNetCDF.cmake
+++ b/cmake/Modules/FindPNetCDF.cmake
@@ -20,7 +20,7 @@ endif (PNETCDF_INCLUDES AND PNETCDF_LIBRARIES)
 find_path (PNETCDF_INCLUDES pnetcdf.h
   HINTS "${PNETCDF_ROOT}/include" "$ENV{PNETCDF_ROOT}/include")
 
-string(REGEX REPLACE "/include/?$" "/lib"
+string(REGEX REPLACE "/include/?$" ""
   PNETCDF_LIB_HINT ${PNETCDF_INCLUDES})
 
 find_library (PNETCDF_LIBRARIES

From 46584d45201f43d42e9fc396db6f47d38907881b Mon Sep 17 00:00:00 2001
From: jotelha <johannes.hoermann@imtek.uni-freiburg.de>
Date: Tue, 7 Jan 2020 13:26:01 +0100
Subject: [PATCH 13/14] Update cmake/Modules/FindPNetCDF.cmake

Co-Authored-By: Christoph Junghans <christoph.junghans@gmail.com>
---
 cmake/Modules/FindPNetCDF.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cmake/Modules/FindPNetCDF.cmake b/cmake/Modules/FindPNetCDF.cmake
index 8778335f62..bc3a5f9538 100644
--- a/cmake/Modules/FindPNetCDF.cmake
+++ b/cmake/Modules/FindPNetCDF.cmake
@@ -25,7 +25,7 @@ string(REGEX REPLACE "/include/?$" ""
 
 find_library (PNETCDF_LIBRARIES
   NAMES pnetcdf
-  HINTS ${PNETCDF_LIB_HINT})
+  HINTS ${PNETCDF_LIB_HINT} PATH_SUFFIXES lib lib64)
 
 if ((NOT PNETCDF_LIBRARIES) OR (NOT PNETCDF_INCLUDES))
   message(STATUS "Trying to find PNetCDF using LD_LIBRARY_PATH (we're desperate)...")

From f1a23b1ea24187b3ab22f52d8a41d70a57cf1e9f Mon Sep 17 00:00:00 2001
From: tabedzki2 <59632999+tabedzki2@users.noreply.github.com>
Date: Tue, 7 Jan 2020 21:47:43 -0500
Subject: [PATCH 14/14] Updated Makefile.stampede: replacement options icc

The default options for Makefile.stampede did not compile. They had to be updated to include the `q` replacement options.
---
 src/MAKE/MACHINES/Makefile.stampede | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/MAKE/MACHINES/Makefile.stampede b/src/MAKE/MACHINES/Makefile.stampede
index 69da22c9c9..ecd0810d1d 100644
--- a/src/MAKE/MACHINES/Makefile.stampede
+++ b/src/MAKE/MACHINES/Makefile.stampede
@@ -6,13 +6,13 @@ SHELL = /bin/sh
 # compiler/linker settings
 # specify flags and libraries needed for your compiler
 
-CC =		mpicc -openmp -DLMP_INTEL_OFFLOAD -DLAMMPS_MEMALIGN=64
-MIC_OPT =       -offload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs=\"gather_scatter_loop_unroll=4\""
-CCFLAGS =	-O3 -xhost -fp-model precise -restrict -override-limits $(MIC_OPT)
+CC =		mpicc -qopenmp -DLMP_INTEL_OFFLOAD -DLAMMPS_MEMALIGN=64
+MIC_OPT =       -qoffload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs=\"gather_scatter_loop_unroll=4\""
+CCFLAGS =	-O3 -xhost -fp-model precise -restrict -qoverride-limits $(MIC_OPT)
 SHFLAGS =	-fPIC
 DEPFLAGS =	-M
 
-LINK =		mpicc -openmp
+LINK =		mpicc -qopenmp
 LINKFLAGS =	-O3 -xhost
 LIB =           -ltbbmalloc
 SIZE =		size