Merge pull request #1544 from akohlmey/collected-small-fixes

Collected small changes and bugfixes for the next patch release

doc/src/if.txt

@@ -57,8 +57,7 @@ Boolean expression is FALSE, then no commands are executed.
 The syntax for Boolean expressions is described below.
 
 Each command (t1, f1, e1, etc) can be any valid LAMMPS input script
-command, except an "include"_include.html command, which is not
-allowed.  If the command is more than one word, it must enclosed in
+command.  If the command is more than one word, it must enclosed in
 quotes, so it will be treated as a single argument, as in the examples
 above.
 

src/ASPHERE/compute_temp_asphere.cpp

@@ -78,7 +78,7 @@ ComputeTempAsphere::ComputeTempAsphere(LAMMPS *lmp, int narg, char **arg) :
 
   if (mode == ROTATE) extra_dof = 0;
 
-  vector = new double[6];
+  vector = new double[size_vector];
 
 }
 

src/BODY/compute_temp_body.cpp

@@ -71,7 +71,7 @@ ComputeTempBody::ComputeTempBody(LAMMPS *lmp, int narg, char **arg) :
     } else error->all(FLERR,"Illegal compute temp/body command");
   }
 
-  vector = new double[6];
+  vector = new double[size_vector];
 
 }
 

src/CORESHELL/compute_temp_cs.cpp

@@ -101,7 +101,7 @@ ComputeTempCS::ComputeTempCS(LAMMPS *lmp, int narg, char **arg) :
 
   // allocate memory
 
-  vector = new double[6];
+  vector = new double[size_vector];
   maxatom = 0;
   vint = NULL;
 

src/QEQ/fix_qeq_shielded.cpp

@@ -80,7 +80,7 @@ void FixQEqShielded::init()
 
 void FixQEqShielded::extract_reax()
 {
-  Pair *pair = force->pair_match("reax/c",1);
+  Pair *pair = force->pair_match("^reax/c",0);
   if (pair == NULL) error->all(FLERR,"No pair reax/c for fix qeq/shielded");
   int tmp;
   chi = (double *) pair->extract("chi",tmp);

src/SPIN/compute_spin.cpp

@@ -149,6 +149,6 @@ void ComputeSpin::compute_vector()
 
 void ComputeSpin::allocate()
 {
-  memory->create(vector,6,"compute/spin:vector");
+  memory->create(vector,size_vector,"compute/spin:vector");
 }
 

src/USER-BOCS/compute_pressure_bocs.cpp

@@ -106,9 +106,9 @@ ComputePressureBocs::ComputePressureBocs(LAMMPS *lmp, int narg, char **arg) :
 
   if (keflag && id_temp == NULL)
     error->all(FLERR,"Compute pressure/bocs requires temperature ID "
-	       "to include kinetic energy");
+               "to include kinetic energy");
 
-  vector = new double[6];
+  vector = new double[size_vector];
   nvirial = 0;
   vptr = NULL;
 }
@@ -365,7 +365,7 @@ void ComputePressureBocs::compute_vector()
 
   if (force->kspace && kspace_virial && force->kspace->scalar_pressure_flag)
     error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' for "
-	       "tensor components with kspace_style msm");
+               "tensor components with kspace_style msm");
 
   // invoke temperature if it hasn't been already
 

src/USER-DRUDE/compute_temp_drude.cpp

@@ -46,7 +46,7 @@ ComputeTempDrude::ComputeTempDrude(LAMMPS *lmp, int narg, char **arg) :
   extlist[2] = extlist[3] = extlist[4] = extlist[5] = 1;
   tempflag = 0; // because does not compute a single temperature (scalar and vector)
 
-  vector = new double[6];
+  vector = new double[size_vector];
   fix_drude = NULL;
   id_temp = NULL;
   temperature = NULL;

src/USER-EFF/compute_temp_deform_eff.cpp

@@ -54,7 +54,7 @@ ComputeTempDeformEff::ComputeTempDeformEff(LAMMPS *lmp, int narg, char **arg) :
 
   maxbias = 0;
   vbiasall = NULL;
-  vector = new double[6];
+  vector = new double[size_vector];
 }
 
 /* ---------------------------------------------------------------------- */

src/USER-EFF/compute_temp_region_eff.cpp

@@ -58,7 +58,7 @@ ComputeTempRegionEff::ComputeTempRegionEff(LAMMPS *lmp, int narg, char **arg) :
 
   maxbias = 0;
   vbiasall = NULL;
-  vector = new double[6];
+  vector = new double[size_vector];
 }
 
 /* ---------------------------------------------------------------------- */

src/USER-FEP/compute_fep.cpp

@@ -53,7 +53,7 @@ ComputeFEP::ComputeFEP(LAMMPS *lmp, int narg, char **arg) :
   size_vector = 3;
   extvector = 0;
 
-  vector = new double[3];
+  vector = new double[size_vector];
 
   fepinitflag = 0;    // avoid init to run entirely when called by write_data
 

src/USER-MISC/compute_temp_rotate.cpp

@@ -46,7 +46,7 @@ ComputeTempRotate::ComputeTempRotate(LAMMPS *lmp, int narg, char **arg) :
 
   maxbias = 0;
   vbiasall = NULL;
-  vector = new double[6];
+  vector = new double[size_vector];
 }
 
 /* ---------------------------------------------------------------------- */

src/USER-REAXC/fix_qeq_reax.cpp

@@ -124,7 +124,7 @@ FixQEqReax::FixQEqReax(LAMMPS *lmp, int narg, char **arg) :
   // register with Atom class
 
   reaxc = NULL;
-  reaxc = (PairReaxC *) force->pair_match("reax/c",0);
+  reaxc = (PairReaxC *) force->pair_match("^reax/c",0);
 
   s_hist = t_hist = NULL;
   grow_arrays(atom->nmax);

src/compute_com.cpp

@@ -29,7 +29,7 @@ ComputeCOM::ComputeCOM(LAMMPS *lmp, int narg, char **arg) :
   size_vector = 3;
   extvector = 0;
 
-  vector = new double[3];
+  vector = new double[size_vector];
 }
 
 /* ---------------------------------------------------------------------- */

src/compute_group_group.cpp

@@ -105,7 +105,7 @@ ComputeGroupGroup::ComputeGroupGroup(LAMMPS *lmp, int narg, char **arg) :
     } else error->all(FLERR,"Illegal compute group/group command");
   }
 
-  vector = new double[3];
+  vector = new double[size_vector];
 }
 
 /* ---------------------------------------------------------------------- */

src/compute_gyration.cpp

@@ -33,7 +33,7 @@ ComputeGyration::ComputeGyration(LAMMPS *lmp, int narg, char **arg) :
   extscalar = 0;
   extvector = 0;
 
-  vector = new double[6];
+  vector = new double[size_vector];
 }
 
 /* ---------------------------------------------------------------------- */

src/compute_heat_flux.cpp

@@ -70,7 +70,7 @@ ComputeHeatFlux::ComputeHeatFlux(LAMMPS *lmp, int narg, char **arg) :
     error->all(FLERR,
                "Compute heat/flux compute ID does not compute stress/atom");
 
-  vector = new double[6];
+  vector = new double[size_vector];
 }
 
 /* ---------------------------------------------------------------------- */

src/compute_msd.cpp

@@ -115,7 +115,7 @@ ComputeMSD::ComputeMSD(LAMMPS *lmp, int narg, char **arg) :
 
   // displacement vector
 
-  vector = new double[4];
+  vector = new double[size_vector];
 }
 
 /* ---------------------------------------------------------------------- */

src/compute_pressure.cpp

@@ -101,7 +101,7 @@ ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) :
     error->all(FLERR,"Compute pressure requires temperature ID "
                "to include kinetic energy");
 
-  vector = new double[6];
+  vector = new double[size_vector];
   nvirial = 0;
   vptr = NULL;
 }

src/compute_temp.cpp

@@ -37,7 +37,7 @@ ComputeTemp::ComputeTemp(LAMMPS *lmp, int narg, char **arg) :
   extvector = 1;
   tempflag = 1;
 
-  vector = new double[6];
+  vector = new double[size_vector];
 }
 
 /* ---------------------------------------------------------------------- */

src/compute_temp_chunk.cpp

@@ -125,7 +125,7 @@ ComputeTempChunk::ComputeTempChunk(LAMMPS *lmp, int narg, char **arg) :
 
   // vector data
 
-  vector = new double[6];
+  vector = new double[size_vector];
 
   // chunk-based data
 

src/compute_temp_com.cpp

@@ -39,7 +39,7 @@ ComputeTempCOM::ComputeTempCOM(LAMMPS *lmp, int narg, char **arg) :
   tempflag = 1;
   tempbias = 1;
 
-  vector = new double[6];
+  vector = new double[size_vector];
 }
 
 /* ---------------------------------------------------------------------- */

src/compute_temp_deform.cpp

@@ -48,7 +48,7 @@ ComputeTempDeform::ComputeTempDeform(LAMMPS *lmp, int narg, char **arg) :
 
   maxbias = 0;
   vbiasall = NULL;
-  vector = new double[6];
+  vector = new double[size_vector];
 }
 
 /* ---------------------------------------------------------------------- */

src/compute_temp_partial.cpp

@@ -49,7 +49,7 @@ ComputeTempPartial::ComputeTempPartial(LAMMPS *lmp, int narg, char **arg) :
 
   maxbias = 0;
   vbiasall = NULL;
-  vector = new double[6];
+  vector = new double[size_vector];
 }
 
 /* ---------------------------------------------------------------------- */

src/compute_temp_ramp.cpp

@@ -101,7 +101,7 @@ ComputeTempRamp::ComputeTempRamp(LAMMPS *lmp, int narg, char **arg) :
 
   maxbias = 0;
   vbiasall = NULL;
-  vector = new double[6];
+  vector = new double[size_vector];
 }
 
 /* ---------------------------------------------------------------------- */

src/compute_temp_region.cpp

@@ -49,7 +49,7 @@ ComputeTempRegion::ComputeTempRegion(LAMMPS *lmp, int narg, char **arg) :
 
   maxbias = 0;
   vbiasall = NULL;
-  vector = new double[6];
+  vector = new double[size_vector];
 }
 
 /* ---------------------------------------------------------------------- */

src/compute_temp_sphere.cpp

@@ -72,7 +72,7 @@ ComputeTempSphere::ComputeTempSphere(LAMMPS *lmp, int narg, char **arg) :
 
   if (mode == ROTATE) extra_dof = 0;
 
-  vector = new double[6];
+  vector = new double[size_vector];
 
   // error checks
 

src/compute_vacf.cpp

@@ -75,7 +75,7 @@ ComputeVACF::ComputeVACF(LAMMPS *lmp, int narg, char **arg) :
 
   // displacement vector
 
-  vector = new double[4];
+  vector = new double[size_vector];
 }
 
 /* ---------------------------------------------------------------------- */

src/input.cpp

@@ -82,7 +82,6 @@ Input::Input(LAMMPS *lmp, int argc, char **argv) : Pointers(lmp)
   label_active = 0;
   labelstr = NULL;
   jump_skip = 0;
-  ifthenelse_flag = 0;
 
   if (me == 0) {
     nfile = 1;
@@ -959,11 +958,10 @@ void Input::ifthenelse()
       ncommands++;
     }
 
-    ifthenelse_flag = 1;
-    for (int i = 0; i < ncommands; i++) one(commands[i]);
-    ifthenelse_flag = 0;
-
-    for (int i = 0; i < ncommands; i++) delete [] commands[i];
+    for (int i = 0; i < ncommands; i++) {
+      one(commands[i]);
+      delete [] commands[i];
+    }
     delete [] commands;
 
     return;
@@ -1015,13 +1013,10 @@ void Input::ifthenelse()
 
     // execute the list of commands
 
-    ifthenelse_flag = 1;
-    for (int i = 0; i < ncommands; i++) one(commands[i]);
-    ifthenelse_flag = 0;
-
-    // clean up
-
-    for (int i = 0; i < ncommands; i++) delete [] commands[i];
+    for (int i = 0; i < ncommands; i++) {
+      one(commands[i]);
+      delete [] commands[i];
+    }
     delete [] commands;
 
     return;
@@ -1034,13 +1029,6 @@ void Input::include()
 {
   if (narg != 1) error->all(FLERR,"Illegal include command");
 
-  // do not allow include inside an if command
-  // NOTE: this check will fail if a 2nd if command was inside the if command
-  //       and came before the include
-
-  if (ifthenelse_flag)
-    error->all(FLERR,"Cannot use include command within an if command");
-
   if (me == 0) {
     if (nfile == maxfile)
       error->one(FLERR,"Too many nested levels of input scripts");

src/input.h

@@ -54,7 +54,6 @@ class Input : protected Pointers {
   int label_active;            // 0 = no label, 1 = looking for label
   char *labelstr;              // label string being looked for
   int jump_skip;               // 1 if skipping next jump, 0 otherwise
-  int ifthenelse_flag;         // 1 if executing commands inside an if-then-else
 
   FILE **infiles;              // list of open input files
 

src/thermo.cpp

@@ -406,8 +406,9 @@ void Thermo::compute(int flag)
    call function to compute property
 ------------------------------------------------------------------------- */
 
-void Thermo::call_vfunc(int ifield)
+void Thermo::call_vfunc(int ifield_in)
 {
+  ifield = ifield_in;
   (this->*vfunc[ifield])();
 }