Merge pull request #1448 from akohlmey/collected-small-changes

Collected small changes and bugfixes

doc/src/Eqs/pair_mdf-6.tex

@@ -1,9 +1,9 @@
 \documentclass[12pt]{article}
-
+\pagestyle{empty}
 \begin{document}
 
 $$
-   E(r) = \frac{A}{r^{12}} - \frac{A}{r^{6}}
+   E(r) = \frac{A}{r^{12}} - \frac{B}{r^{6}}
 $$
 
 \end{document}

doc/src/pair_mdf.txt

@@ -30,16 +30,16 @@ args = list of arguments for a particular style :l
 [Examples:]
 
 pair_style lj/mdf 2.5 3.0
-pair_coeff * * 1 1
-pair_coeff 1 1 1 1.1 2.8 3.0 3.2 :pre
+pair_coeff * * 1.0 1.0
+pair_coeff 1 1 1.1 2.8 3.0 3.2 :pre
 
 pair_style buck 2.5 3.0
 pair_coeff * * 100.0 1.5 200.0
 pair_coeff * * 100.0 1.5 200.0 3.0 3.5 :pre
 
 pair_style lennard/mdf 2.5 3.0
-pair_coeff * * 1 1
-pair_coeff 1 1 1 1.1 2.8 3.0 3.2 :pre
+pair_coeff * * 1.0 1.0
+pair_coeff 1 1 1021760.3664 2120.317338 3.0 3.2 :pre
 
 [Description:]
 
@@ -69,11 +69,12 @@ standard 12-6 Lennard-Jones written in the epsilon/sigma form:
 
 :c,image(Eqs/pair_mdf-4.jpg)
 
-The following coefficients must be defined for each pair of atoms
-types via the pair_coeff command as in the examples above, or in the
-data file or restart files read by the "read_data"_read_data.html or
-"read_restart commands"_read_restart.html, or by mixing as described
-below:
+Either the first two or all of the following coefficients must be
+defined for each pair of atoms types via the pair_coeff command as
+in the examples above, or in the data file read by the
+"read_data"_read_data.html. The two cutoffs default to the global
+values and epsilon and sigma can also be determined by mixing as
+described below:
 
 epsilon (energy units)
 sigma (distance units)
@@ -83,7 +84,9 @@ r_{cut} (distance units) :ul
 :line
 
 For the {buck/mdf} pair_style, the potential energy, {E(r)}, is the
-standard Buckingham potential:
+standard Buckingham potential with three required coefficients.
+The two cutoffs can be omitted and default to the corresponding
+global values:
 
 :c,image(Eqs/pair_mdf-5.jpg)
 
@@ -91,19 +94,20 @@ A (energy units)
 \rho (distance units)
 C (energy-distance^6 units)
 r_m (distance units)
-r_{cut}$ (distance units) :ul
+r_{cut} (distance units) :ul
 
 :line
 
 For the {lennard/mdf} pair_style, the potential energy, {E(r)}, is the
-standard 12-6 Lennard-Jones written in the $A/B$ form:
+standard 12-6 Lennard-Jones written in the A/B form:
 
 :c,image(Eqs/pair_mdf-6.jpg)
 
 The following coefficients must be defined for each pair of atoms
 types via the pair_coeff command as in the examples above, or in the
-data file or restart files read by the read_data or read_restart
-commands, or by mixing as described below:
+data file read by the read_data commands, or by mixing as described below.
+The two cutoffs default to their global values and must be either both
+given or both left out:
 
 A (energy-distance^12 units)
 B (energy-distance^6 units)
@@ -115,33 +119,23 @@ r_{cut} (distance units) :ul
 [Mixing, shift, table, tail correction, restart, rRESPA info]:
 
 For atom type pairs I,J and I != J, the epsilon and sigma coefficients
-and cutoff distance for all of the lj/cut pair styles can be mixed.
+and cutoff distances for the lj/mdf pair style can be mixed.
 The default mix value is {geometric}.  See the "pair_modify" command
-for details.
+for details. The other two pair styles buck/mdf and lennard/mdf do not
+support mixing, so all I,J pairs of coefficients must be specified
+explicitly.
 
-All of the {lj/cut} pair styles support the
-"pair_modify"_pair_modify.html shift option for the energy of the
-Lennard-Jones portion of the pair interaction.
+None of the lj/mdf, buck/mdf, or lennard/mdf pair styles supports
+the "pair_modify"_pair_modify.html shift option or long-range
+tail corrections to pressure and energy.
 
-The {lj/cut/coul/long} and {lj/cut/tip4p/long} pair styles support the
-"pair_modify"_pair_modify.html table option since they can tabulate
-the short-range portion of the long-range Coulombic interaction.
+These styles write their information to "binary restart
+files"_restart.html, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
 
-All of the {lj/cut} pair styles support the
-"pair_modify"_pair_modify.html tail option for adding a long-range
-tail correction to the energy and pressure for the Lennard-Jones
-portion of the pair interaction.
-
-All of the {lj/cut} pair styles write their information to "binary
-restart files"_restart.html, so pair_style and pair_coeff commands do
-not need to be specified in an input script that reads a restart file.
-
-The {lj/cut} and {lj/cut/coul/long} pair styles support the use of the
-{inner}, {middle}, and {outer} keywords of the "run_style
-respa"_run_style.html command, meaning the pairwise forces can be
-partitioned by distance at different levels of the rRESPA hierarchy.
-The other styles only support the {pair} keyword of run_style respa.
-See the "run_style"_run_style.html command for details.
+These styles can only be used via the {pair} keyword of the "run_style
+respa"_run_style.html command.  They do not support the {inner},
+{middle}, {outer} keywords.
 
 :line
 

doc/src/write_coeff.txt

@@ -26,11 +26,9 @@ coefficients in a way, that it can be read by LAMMPS with the
 option of "write_data"_write_data.html this can be used to move
 the Coeffs sections from a data file into a separate file.
 
-NOTE: The write_coeff command is not yet fully implemented in two
-respects.  First, some pair styles do not yet write their coefficient
-information into the coeff file.  This means you will need to specify
-that information in your input script that reads the data file, via
-the "pair_coeff"_pair_coeff.html command.
+NOTE: The write_coeff command is not yet fully implemented as
+some pair styles do not output their coefficient information.
+This means you will need to add/copy this information manually.
 
 :line
 

src/SPIN/fix_nve_spin.cpp

@@ -573,7 +573,7 @@ void FixNVESpin::AdvanceSingleSpin(int i)
   int *sametag = atom->sametag;
   double **sp = atom->sp;
   double **fm = atom->fm;
-  double msq,scale,fm2,energy,dts2;
+  double fm2,energy,dts2;
   double cp[3],g[3];
 
   cp[0] = cp[1] = cp[2] = 0.0;

src/SPIN/fix_setforce_spin.cpp

@@ -126,7 +126,6 @@ void FixSetForceSpin::single_setforce_spin(int i, double fmi[3])
 {
   double **x = atom->x;
   int *mask = atom->mask;
-  int nlocal = atom->nlocal;
 
   // update region if necessary
 

src/USER-MISC/pair_buck_mdf.cpp

@@ -52,7 +52,6 @@ PairBuckMDF::~PairBuckMDF()
     memory->destroy(rhoinv);
     memory->destroy(buck1);
     memory->destroy(buck2);
-    memory->destroy(offset);
   }
 }
 
@@ -177,7 +176,6 @@ void PairBuckMDF::allocate()
   memory->create(rhoinv,n+1,n+1,"pair:rhoinv");
   memory->create(buck1,n+1,n+1,"pair:buck1");
   memory->create(buck2,n+1,n+1,"pair:buck2");
-  memory->create(offset,n+1,n+1,"pair:offset");
 }
 
 /* ----------------------------------------------------------------------
@@ -207,7 +205,8 @@ void PairBuckMDF::settings(int narg, char **arg)
 
 void PairBuckMDF::coeff(int narg, char **arg)
 {
-  if (narg != 5 && narg != 7) error->all(FLERR,"Incorrect args for pair coefficients");
+  if (narg != 5 && narg != 7)
+    error->all(FLERR,"Incorrect args for pair coefficients");
   if (!allocated) allocate();
 
   int ilo,ihi,jlo,jhi;
@@ -258,11 +257,6 @@ double PairBuckMDF::init_one(int i, int j)
   buck1[i][j] = a[i][j]/rho[i][j];
   buck2[i][j] = 6.0*c[i][j];
 
-  if (offset_flag && (cut[i][j] > 0.0)) {
-    double rexp = exp(-cut[i][j]/rho[i][j]);
-    offset[i][j] = a[i][j]*rexp - c[i][j]/pow(cut[i][j],6.0);
-  } else offset[i][j] = 0.0;
-
   cut_inner[j][i] = cut_inner[i][j];
   cut_inner_sq[i][j] = cut_inner[i][j]*cut_inner[i][j];
   cut_inner_sq[j][i] = cut_inner_sq[i][j];
@@ -272,36 +266,6 @@ double PairBuckMDF::init_one(int i, int j)
   rhoinv[j][i] = rhoinv[i][j];
   buck1[j][i] = buck1[i][j];
   buck2[j][i] = buck2[i][j];
-  offset[j][i] = offset[i][j];
-
-  // compute I,J contribution to long-range tail correction
-  // count total # of atoms of type I and J via Allreduce
-
-  if (tail_flag) {
-    int *type = atom->type;
-    int nlocal = atom->nlocal;
-
-    double count[2],all[2];
-    count[0] = count[1] = 0.0;
-    for (int k = 0; k < nlocal; k++) {
-      if (type[k] == i) count[0] += 1.0;
-      if (type[k] == j) count[1] += 1.0;
-    }
-    MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
-
-    double rho1 = rho[i][j];
-    double rho2 = rho1*rho1;
-    double rho3 = rho2*rho1;
-    double rc = cut[i][j];
-    double rc2 = rc*rc;
-    double rc3 = rc2*rc;
-    etail_ij = 2.0*MY_PI*all[0]*all[1]*
-      (a[i][j]*exp(-rc/rho1)*rho1*(rc2 + 2.0*rho1*rc + 2.0*rho2) -
-       c[i][j]/(3.0*rc3));
-    ptail_ij = (-1/3.0)*2.0*MY_PI*all[0]*all[1]*
-      (-a[i][j]*exp(-rc/rho1)*
-       (rc3 + 3.0*rho1*rc2 + 6.0*rho2*rc + 6.0*rho3) + 2.0*c[i][j]/rc3);
-  }
 
   return cut[i][j];
 }

src/USER-MISC/pair_lennard_mdf.cpp

@@ -251,13 +251,7 @@ void PairLJ_AB_MDF::coeff(int narg, char **arg)
 
 double PairLJ_AB_MDF::init_one(int i, int j)
 {
-  if (setflag[i][j] == 0) {
-    aparm[i][j] = mix_energy(aparm[i][i],aparm[j][j],
-                               bparm[i][i],bparm[j][j]);
-    bparm[i][j] = mix_distance(bparm[i][i],bparm[j][j]);
-    cut_inner[i][j] = mix_distance(cut_inner[i][i],cut_inner[j][j]);
-    cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
-  }
+  if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
 
   cut_inner_sq[i][j] = cut_inner[i][j]*cut_inner[i][j];
 

src/USER-MISC/pair_lj_mdf.cpp

@@ -33,7 +33,9 @@ using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-PairLJMDF::PairLJMDF(LAMMPS *lmp) : Pair(lmp) {}
+PairLJMDF::PairLJMDF(LAMMPS *lmp) : Pair(lmp) {
+  writedata = 1;
+}
 
 /* ---------------------------------------------------------------------- */
 
@@ -349,6 +351,29 @@ void PairLJMDF::read_restart_settings(FILE *fp)
   MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
 }
 
+/* ----------------------------------------------------------------------
+   proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void PairLJMDF::write_data(FILE *fp)
+{
+  for (int i = 1; i <= atom->ntypes; i++)
+    fprintf(fp,"%d %g %g\n",i,epsilon[i][i],sigma[i][i]);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes all pairs to data file
+------------------------------------------------------------------------- */
+
+void PairLJMDF::write_data_all(FILE *fp)
+{
+  for (int i = 1; i <= atom->ntypes; i++)
+    for (int j = i; j <= atom->ntypes; j++)
+      fprintf(fp,"%d %d %g %g %g %g\n",
+              i,j,epsilon[i][j],sigma[i][j],
+              cut_inner[i][j],cut[i][j]);
+}
+
 /* ---------------------------------------------------------------------- */
 
 double PairLJMDF::single(int /*i*/, int /*j*/, int itype, int jtype,

src/USER-MISC/pair_lj_mdf.h

@@ -37,6 +37,8 @@ class PairLJMDF : public Pair {
   void read_restart(FILE *);
   void write_restart_settings(FILE *);
   void read_restart_settings(FILE *);
+  void write_data(FILE *);
+  void write_data_all(FILE *);
   double single(int, int, int, int, double, double, double, double &);
   void *extract(const char *, int &);
 

src/domain.cpp

@@ -57,6 +57,7 @@ Domain::Domain(LAMMPS *lmp) : Pointers(lmp)
 {
   box_exist = 0;
   box_change = 0;
+  deform_flag = deform_vremap = deform_groupbit = 0;
 
   dimension = 3;
   nonperiodic = 0;

src/output.cpp

@@ -675,8 +675,13 @@ void Output::set_thermo(int narg, char **arg)
 {
   if (narg != 1) error->all(FLERR,"Illegal thermo command");
 
+  // always reset var_thermo, so it is possible to switch back from
+  // variable spaced thermo outputs to constant spaced ones.
+
+  delete [] var_thermo;
+  var_thermo = NULL;
+
   if (strstr(arg[0],"v_") == arg[0]) {
-    delete [] var_thermo;
     int n = strlen(&arg[0][2]) + 1;
     var_thermo = new char[n];
     strcpy(var_thermo,&arg[0][2]);