Merge pull request #1354 from akohlmey/collected-small-fixes

Collected small fixes and updates for the next patch release

src/USER-ADIOS/dump_custom_adios.cpp

@@ -154,6 +154,7 @@ DumpCustomADIOS::~DumpCustomADIOS()
         internal->fh.Close();
     }
     delete internal->ad;
+    delete internal;
 }
 
 /* ---------------------------------------------------------------------- */

src/USER-PHONON/dynamical_matrix.cpp

@@ -316,9 +316,10 @@ void DynamicalMatrix::calculateMatrix()
 
 void DynamicalMatrix::writeMatrix(double **dynmat)
 {
-    if (me != 0)
-        return;
+    if (me != 0 || fp == NULL) return;
+
     // print file comment lines
+
     if (!binaryflag && fp) {
         clearerr(fp);
         for (int i = 0; i < 3; i++) {

src/USER-PHONON/dynamical_matrix.h

@@ -54,10 +54,10 @@ namespace LAMMPS_NS {
         double conv_mass;
         double del;
         int igroup,groupbit;
-        int gcount;  // number of atoms in group
+        bigint gcount;             // number of atoms in group
+        bigint dynlen;             // rank of dynamical matrix
         int scaleflag;
         int me;
-        bigint dynlen;
         int *groupmap;
 
         int compressed;            // 1 if dump file is written compressed, 0 no
@@ -71,4 +71,4 @@ namespace LAMMPS_NS {
 
 
 #endif //LMP_DYNAMICAL_MATRIX_H
-#endif
+#endif

src/USER-PTM/compute_ptm_atom.h

@@ -35,7 +35,7 @@ class ComputePTMAtom : public Compute {
 
  private:
   int nmax;
-  int32_t input_flags;
+  smallint input_flags;
   double rmsd_threshold;
   class NeighList *list;
   double **output;

src/USER-PTM/ptm_neighbour_ordering.h

@@ -11,6 +11,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 #define PTM_NEIGHBOUR_ORDERING_H
 
 #include <cstddef>
+#include <stdint.h>
 
 namespace ptm {