small bug fixes

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15527 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/README.md

@@ -14,8 +14,8 @@ make clean-all    # remove entire build folder and any cached data
 
 ## Installing prerequisites
 
-To run the documention build toolchain Python 3 and virtualenv have to be
+To run the documention build toolchain, Python 3 and virtualenv have
-installed. Here are instructions for common setups:
+to be installed. Here are instructions for common setups:
 
 ### Ubuntu
 
@@ -23,10 +23,16 @@ installed. Here are instructions for common setups:
 sudo apt-get install python-virtualenv
 ```
 
-### Fedora
+### Fedora (up to version 21), Red Hat Enterprise Linux or CentOS (up to version 7.x)
 
+```bash
+sudo yum install python3-virtualenv
 ```
-sudo yum install python-virtualenv
+
+### Fedora (since version 22)
+
+```bash
+sudo dnf install python3-virtualenv
 ```
 
 ### MacOS X

doc/html/Section_howto.html

@@ -2339,14 +2339,14 @@ velocity:</p>
 <ol class="arabic simple" start="4">
 <li>Total force on each molecule and ave/max across all molecules:</li>
 </ol>
-<pre class="literal-block">
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
-compute cc1 all chunk/atom molecule
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">1000</span> <span class="mi">1</span> <span class="mi">1000</span> <span class="n">cc1</span> <span class="n">fx</span> <span class="n">fy</span> <span class="n">fz</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span>
-fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out
+<span class="n">variable</span> <span class="n">xave</span> <span class="n">equal</span> <span class="n">ave</span><span class="p">(</span><span class="n">f_1</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
-variable xave equal ave(f_1<strong>2</strong>)
+<span class="n">variable</span> <span class="n">xmax</span> <span class="n">equal</span> <span class="nb">max</span><span class="p">(</span><span class="n">f_1</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
-variable xmax equal max(f_1<strong>2</strong>)
+<span class="n">thermo</span> <span class="mi">1000</span>
-thermo 1000
+<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">v_xave</span> <span class="n">v_xmax</span>
-thermo_style custom step temp v_xave v_xmax
+</pre></div>
-</pre>
+</div>
 <ol class="arabic simple" start="5">
 <li>Histogram of cluster sizes:</li>
 </ol>

doc/html/compute_omega_chunk.html

@@ -178,11 +178,11 @@ how they are set for each atom.  You can reset the image flags
 <p>The simplest way to output the results of the compute omega/chunk
 calculation to a file is to use the <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>
 command, for example:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
+<pre class="literal-block">
-<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">omega</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
+compute cc1 all chunk/atom molecule
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myChunk</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="n">mode</span> <span class="n">vector</span>
+compute myChunk all omega/chunk cc1
-</pre></div>
+fix 1 all ave/time 100 1 100 c_myChunk<strong>*</strong> file tmp.out mode vector
-</div>
+</pre>
 <p><strong>Output info:</strong></p>
 <p>This compute calculates a global array where the number of rows = the
 number of chunks <em>Nchunk</em> as calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command.  The number of columns =

doc/html/fix_nve_manifold_rattle.html

@@ -158,7 +158,7 @@ keyword = <em>every</em>
 <p>Perform constant NVE integration to update position and velocity for
 atoms constrained to a curved surface (manifold) in the group each timestep. The constraint
 is handled by RATTLE <a class="reference internal" href="fix_shake.html#andersen"><span class="std std-ref">(Andersen)</span></a> written out for the special case of
-single-particle constraints as explained in <a class="reference internal" href="manifolds.html#paquay"><span class="std std-ref">(Paquay)</span></a>.
+single-particle constraints as explained in <a class="reference internal" href="fix_nvt_manifold_rattle.html#paquay"><span class="std std-ref">(Paquay)</span></a>.
 V is volume; E is energy. This way, the dynamics of particles constrained to
 curved surfaces can be studied. If combined with <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>, this generates
 Brownian motion of particles constrained to a curved surface. For a list of currently supported

doc/html/fix_nvt_manifold_rattle.html

@@ -157,7 +157,7 @@ keyword = <em>temp</em> or <em>tchain</em> or <em>every</em>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
-<p>This fix combines the RATTLE-based <a class="reference internal" href="fix_shake.html#andersen"><span class="std std-ref">(Andersen)</span></a> time integrator of <a class="reference internal" href="fix_nve_manifold_rattle.html"><span class="doc">fix nve/manifold/rattle</span></a> <a class="reference internal" href="manifolds.html#paquay"><span class="std std-ref">(Paquay)</span></a> with a Nose-Hoover-chain thermostat to sample the
+<p>This fix combines the RATTLE-based <a class="reference internal" href="fix_shake.html#andersen"><span class="std std-ref">(Andersen)</span></a> time integrator of <a class="reference internal" href="fix_nve_manifold_rattle.html"><span class="doc">fix nve/manifold/rattle</span></a> <a class="reference internal" href="#paquay"><span class="std std-ref">(Paquay)</span></a> with a Nose-Hoover-chain thermostat to sample the
 canonical ensemble of particles constrained to a curved surface (manifold). This sampling does suffer from discretization bias of O(dt).
 For a list of currently supported manifolds and their parameters, see <a class="reference internal" href="manifolds.html"><span class="doc">manifolds</span></a></p>
 </div>

doc/src/compute_omega_chunk.txt

@@ -64,7 +64,7 @@ command, for example:
 
 compute cc1 all chunk/atom molecule
 compute myChunk all omega/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector :pre
+fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector :pre
 
 [Output info:]
 

lib/meam/meam_setup_done.F

@@ -438,9 +438,17 @@ c     use precomputed values
           rho0_2 = rho0_meam(b)*Z2*G2
         endif
         Gam1 = (t11av*rho11+t21av*rho21+t31av*rho31)
+        if (rho01 < 1.0d-14) then
+          Gam1 = 0.0d0
+        else
           Gam1 = Gam1/(rho01*rho01)
+        endif
         Gam2 = (t12av*rho12+t22av*rho22+t32av*rho32)
+        if (rho02 < 1.0d-14) then
+          Gam2 = 0.0d0
+        else
           Gam2 = Gam2/(rho02*rho02)
+        endif
         call G_gam(Gam1,ibar_meam(a),gsmooth_factor,G1,errorflag)
         call G_gam(Gam2,ibar_meam(b),gsmooth_factor,G2,errorflag)
         if (mix_ref_t.eq.1) then

src/BODY/compute_body_local.h

@@ -37,8 +37,6 @@ class ComputeBodyLocal : public Compute {
   int *which,*index;
 
   int nmax;
-  double *vector;
-  double **array;
 
   class AtomVecBody *avec;
   class Body *bptr;

src/RIGID/compute_rigid_local.h

@@ -41,8 +41,6 @@ class ComputeRigidLocal : public Compute {
   class FixRigidSmall *fixrigid;
 
   int nmax;
-  double *vector;
-  double **array;
 
   int compute_rigid(int);
   void reallocate(int);

src/USER-REAXC/compute_spec_atom.h

@@ -36,8 +36,6 @@ class ComputeSpecAtom : public Compute {
  private:
   int nvalues;
   int nmax;
-  double *vector;
-  double **array;
   double *buf;
   double *vbuf;
 

src/atom.cpp

@@ -1589,6 +1589,7 @@ void Atom::add_molecule(int narg, char **arg)
 
 int Atom::find_molecule(char *id)
 {
+  if(id == NULL) return -1;
   int imol;
   for (imol = 0; imol < nmolecule; imol++)
     if (strcmp(id,molecules[imol]->id) == 0) return imol;
@@ -1913,6 +1914,8 @@ void Atom::add_callback(int flag)
 
 void Atom::delete_callback(const char *id, int flag)
 {
+  if(id==NULL) return;
+
   int ifix;
   for (ifix = 0; ifix < modify->nfix; ifix++)
     if (strcmp(id,modify->fix[ifix]->id) == 0) break;
@@ -1968,6 +1971,8 @@ void Atom::update_callback(int ifix)
 
 int Atom::find_custom(const char *name, int &flag)
 {
+  if(name == NULL) return -1;
+
   for (int i = 0; i < nivector; i++)
     if (iname[i] && strcmp(iname[i],name) == 0) {
       flag = 0;

src/compute_angle_local.cpp

@@ -33,8 +33,7 @@ using namespace MathConst;
 /* ---------------------------------------------------------------------- */
 
 ComputeAngleLocal::ComputeAngleLocal(LAMMPS *lmp, int narg, char **arg) :
-  Compute(lmp, narg, arg),
+  Compute(lmp, narg, arg)
-  vector(NULL), array(NULL)
 {
   if (narg < 4) error->all(FLERR,"Illegal compute angle/local command");
 

src/compute_angle_local.h

@@ -37,8 +37,6 @@ class ComputeAngleLocal : public Compute {
   int ncount;
 
   int nmax;
-  double *vector;
-  double **array;
 
   int compute_angles(int);
   void reallocate(int);

src/compute_bond_local.cpp

@@ -34,7 +34,7 @@ enum{DIST,ENG,FORCE};
 
 ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg),
-  bstyle(NULL), vector(NULL), array(NULL)
+  bstyle(NULL)
 {
   if (narg < 4) error->all(FLERR,"Illegal compute bond/local command");
 

src/compute_bond_local.h

@@ -39,8 +39,6 @@ class ComputeBondLocal : public Compute {
   int singleflag;
 
   int nmax;
-  double *vector;
-  double **array;
 
   int compute_bonds(int);
   void reallocate(int);

src/compute_chunk_atom.cpp

@@ -57,9 +57,10 @@ ComputeChunkAtom *ComputeChunkAtom::cptr;
 
 ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg),
-  id_fix(NULL), chunk(NULL), ichunk(NULL), exclude(NULL),
+  chunk_volume_vec(NULL), coord(NULL), ichunk(NULL), chunkID(NULL),
-  chunk_volume_vec(NULL), coord(NULL), chunkID(NULL), idregion(NULL), cfvid(NULL), 
+  cfvid(NULL), idregion(NULL), region(NULL), cchunk(NULL), fchunk(NULL),
-  hash(NULL), varatom(NULL)
+  varatom(NULL), id_fix(NULL), fixstore(NULL), lockfix(NULL), chunk(NULL),
+  exclude(NULL), hash(NULL)
 {
   if (narg < 4) error->all(FLERR,"Illegal compute chunk/atom command");
 

src/compute_cna_atom.cpp

@@ -279,7 +279,7 @@ void ComputeCNAAtom::compute_peratom()
       for (n = 0; n < ncommon; n++) bonds[n] = 0;
 
       nbonds = 0;
-      for (jj = 0; jj < ncommon; jj++) {
+      for (jj = 0; jj < ncommon-1; jj++) {
         j = common[jj];
         xtmp = x[j][0];
         ytmp = x[j][1];

src/compute_dihedral_local.cpp

@@ -34,8 +34,7 @@ using namespace MathConst;
 /* ---------------------------------------------------------------------- */
 
 ComputeDihedralLocal::ComputeDihedralLocal(LAMMPS *lmp, int narg, char **arg) :
-  Compute(lmp, narg, arg),
+  Compute(lmp, narg, arg)
-  vector(NULL), array(NULL)
 {
   if (narg < 4) error->all(FLERR,"Illegal compute dihedral/local command");
 

src/compute_dihedral_local.h

@@ -37,8 +37,6 @@ class ComputeDihedralLocal : public Compute {
   int ncount;
 
   int nmax;
-  double *vector;
-  double **array;
 
   int compute_dihedrals(int);
   void reallocate(int);

src/compute_displace_atom.cpp

@@ -30,7 +30,7 @@ using namespace LAMMPS_NS;
 
 ComputeDisplaceAtom::ComputeDisplaceAtom(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg),
-  id_fix(NULL), displace(NULL)
+  displace(NULL), id_fix(NULL)
 {
   if (narg != 3) error->all(FLERR,"Illegal compute displace/atom command");
 

src/compute_improper_local.cpp

@@ -35,8 +35,7 @@ using namespace MathConst;
 /* ---------------------------------------------------------------------- */
 
 ComputeImproperLocal::ComputeImproperLocal(LAMMPS *lmp, int narg, char **arg) :
-  Compute(lmp, narg, arg),
+  Compute(lmp, narg, arg)
-  vector(NULL), array(NULL)
 {
   if (narg < 4) error->all(FLERR,"Illegal compute improper/local command");
 

src/compute_improper_local.h

@@ -37,8 +37,6 @@ class ComputeImproperLocal : public Compute {
   int ncount;
 
   int nmax;
-  double *vector;
-  double **array;
 
   int compute_impropers(int);
   void reallocate(int);

src/compute_omega_chunk.cpp

@@ -28,7 +28,7 @@ using namespace LAMMPS_NS;
 ComputeOmegaChunk::ComputeOmegaChunk(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg),
   idchunk(NULL),massproc(NULL),masstotal(NULL),com(NULL),comall(NULL),
-  angmom(NULL), angmomall(NULL)
+  inertia(NULL),inertiaall(NULL),angmom(NULL),angmomall(NULL),omega(NULL)
 {
   if (narg != 4) error->all(FLERR,"Illegal compute omega/chunk command");
 
@@ -64,6 +64,9 @@ ComputeOmegaChunk::~ComputeOmegaChunk()
   memory->destroy(comall);
   memory->destroy(angmom);
   memory->destroy(angmomall);
+  memory->destroy(inertia);
+  memory->destroy(inertiaall);
+  memory->destroy(omega);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -83,7 +86,7 @@ void ComputeOmegaChunk::init()
 
 void ComputeOmegaChunk::compute_array()
 {
-  int i,j,m,index;
+  int i,j,index;
   double dx,dy,dz,massone;
   double unwrap[3];
 

src/compute_pair_local.cpp

@@ -37,7 +37,7 @@ enum{TYPE,RADIUS};
 
 ComputePairLocal::ComputePairLocal(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg),
-  pstyle(NULL), pindex(NULL), vector(NULL), array(NULL)
+  pstyle(NULL), pindex(NULL)
 {
   if (narg < 4) error->all(FLERR,"Illegal compute pair/local command");
 

src/compute_pair_local.h

@@ -41,8 +41,6 @@ class ComputePairLocal : public Compute {
   int singleflag;
 
   int nmax;
-  double *vector;
-  double **array;
 
   class NeighList *list;
 

src/compute_property_atom.cpp

@@ -33,7 +33,7 @@ using namespace LAMMPS_NS;
 
 ComputePropertyAtom::ComputePropertyAtom(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg),
-  index(NULL), vector(NULL), array(NULL), pack_choice(NULL)
+  index(NULL), pack_choice(NULL)
 {
   if (narg < 4) error->all(FLERR,"Illegal compute property/atom command");
 

src/compute_property_atom.h

@@ -36,8 +36,6 @@ class ComputePropertyAtom : public Compute {
   int nvalues;
   int nmax;
   int *index;
-  double *vector;
-  double **array;
   double *buf;
   class AtomVecEllipsoid *avec_ellipsoid;
   class AtomVecLine *avec_line;

src/compute_property_local.cpp

@@ -35,7 +35,7 @@ enum{TYPE,RADIUS};
 
 ComputePropertyLocal::ComputePropertyLocal(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg),
-  vector(NULL), array(NULL), indices(NULL), pack_choice(NULL)
+  indices(NULL), pack_choice(NULL)
 {
   if (narg < 4) error->all(FLERR,"Illegal compute property/local command");
 

src/compute_property_local.h

@@ -37,8 +37,6 @@ class ComputePropertyLocal : public Compute {
   int nvalues,kindflag,cutstyle;
 
   int nmax;
-  double *vector;
-  double **array;
   double *buf;
 
   class NeighList *list;

src/create_box.cpp

@@ -158,7 +158,7 @@ void CreateBox::command(int narg, char **arg)
       iarg += 2;
     } else if (strcmp(arg[iarg],"extra/special/per/atom") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal create_box command");
-      atom->maxspecial = force->inumeric(FLERR,arg[iarg+1]);
+      force->special_extra = force->inumeric(FLERR,arg[iarg+1]);
       iarg += 2;
     } else error->all(FLERR,"Illegal create_box command");
   }

src/fix_ave_chunk.cpp

@@ -40,7 +40,14 @@ enum{ONE,RUNNING,WINDOW};
 /* ---------------------------------------------------------------------- */
 
 FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
-  Fix(lmp, narg, arg)
+  Fix(lmp, narg, arg),
+  nvalues(0), nrepeat(0),
+  which(NULL), argindex(NULL), value2index(NULL), ids(NULL),
+  fp(NULL), idchunk(NULL), varatom(NULL),
+  count_one(NULL), count_many(NULL), count_sum(NULL),
+  values_one(NULL), values_many(NULL), values_sum(NULL),
+  count_total(NULL), count_list(NULL),
+  values_total(NULL), values_list(NULL)
 {
   if (narg < 7) error->all(FLERR,"Illegal fix ave/chunk command");
 
@@ -72,7 +79,6 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
   argindex = new int[nargnew];
   ids = new char*[nargnew];
   value2index = new int[nargnew];
-  nvalues = 0;
 
   int iarg = 0;
   while (iarg < nargnew) {
@@ -149,7 +155,6 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
   normflag = ALL;
   scaleflag = ATOM;
   ave = ONE;
-  fp = NULL;
   nwindow = 0;
   biasflag = 0;
   id_bias = NULL;
@@ -433,7 +438,6 @@ FixAveChunk::~FixAveChunk()
   if (fp && me == 0) fclose(fp);
 
   memory->destroy(varatom);
-
   memory->destroy(count_one);
   memory->destroy(count_many);
   memory->destroy(count_sum);
@@ -457,6 +461,24 @@ FixAveChunk::~FixAveChunk()
   }
 
   delete [] idchunk;
+  which = NULL;
+  argindex = NULL;
+  ids = NULL;
+  value2index = NULL;
+  fp = NULL;
+  varatom = NULL;
+  count_one = NULL;
+  count_many = NULL;
+  count_sum = NULL;
+  count_total = NULL;
+  count_list = NULL;
+  values_one = NULL;
+  values_many = NULL;
+  values_sum = NULL;
+  values_total = NULL;
+  values_list = NULL;
+  idchunk = NULL;
+  cchunk = NULL;
 }
 
 /* ---------------------------------------------------------------------- */

src/modify.cpp

@@ -911,6 +911,7 @@ void Modify::delete_fix(const char *id)
 
 int Modify::find_fix(const char *id)
 {
+  if(id==NULL) return -1;
   int ifix;
   for (ifix = 0; ifix < nfix; ifix++)
     if (strcmp(id,fix[ifix]->id) == 0) break;
@@ -1040,6 +1041,7 @@ void Modify::delete_compute(const char *id)
 
 int Modify::find_compute(const char *id)
 {
+  if(id==NULL) return -1;
   int icompute;
   for (icompute = 0; icompute < ncompute; icompute++)
     if (strcmp(id,compute[icompute]->id) == 0) break;

src/variable.cpp

@@ -710,6 +710,7 @@ int Variable::next(int narg, char **arg)
 
 int Variable::find(char *name)
 {
+  if(name==NULL) return -1;
   for (int i = 0; i < nvar; i++)
     if (strcmp(name,names[i]) == 0) return i;
   return -1;