git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13467 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/Depend.sh

@@ -77,6 +77,7 @@ if (test $1 = "KSPACE") then
   depend USER-OMP
   depend USER-INTEL
   depend USER-PHONON
+  depend USER-FEP
 fi
 
 if (test $1 = "MANYBODY") then
@@ -94,6 +95,7 @@ if (test $1 = "MOLECULE") then
   depend USER-CUDA
   depend USER-MISC
   depend USER-OMP
+  depend USER-FEP
   depend USER-INTEL
 fi
 
@@ -112,6 +114,10 @@ if (test $1 = "USER-CG-CMM") then
   depend USER-OMP
 fi
 
+if (test $1 = "USER-FEP") then
+  depend USER-OMP
+fi
+
 if (test $1 = "USER-MISC") then
   depend GPU
   depend USER-OMP

src/KSPACE/pppm.cpp

@@ -385,6 +385,16 @@ void PPPM::setup()
     return;
   }
 
+  // perform some checks to avoid illegal boundaries with read_data
+
+  if (slabflag == 0 && domain->nonperiodic > 0)
+    error->all(FLERR,"Cannot use nonperiodic boundaries with PPPM");
+  if (slabflag) {
+    if (domain->xperiodic != 1 || domain->yperiodic != 1 ||
+        domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1)
+      error->all(FLERR,"Incorrect boundaries with slab PPPM");
+  }
+
   int i,j,k,n;
   double *prd;
 

src/KSPACE/pppm_disp.cpp

@@ -603,6 +603,15 @@ void PPPMDisp::init()
 
 void PPPMDisp::setup()
 {
+
+  if (slabflag == 0 && domain->nonperiodic > 0)
+    error->all(FLERR,"Cannot use nonperiodic boundaries with PPPMDisp");
+  if (slabflag == 1) {
+    if (domain->xperiodic != 1 || domain->yperiodic != 1 || 
+	domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1)
+      error->all(FLERR,"Incorrect boundaries with slab PPPMDisp");
+  }
+ 
   double *prd;
 
   // volume-dependent factors

src/USER-MISC/pair_meam_spline.h

@@ -74,8 +74,8 @@ protected:
                 }
 
                 /// Initialization of spline function.
-                void init(int _N, double _deriv0, double _derivN) {
-                        N = _N;
+                void init(int _n, double _deriv0, double _derivN) {
+                        N = _n;
                         deriv0 = _deriv0;
                         derivN = _derivN;
                         delete[] X;

src/USER-MISC/pair_meam_sw_spline.h

@@ -74,8 +74,8 @@ protected:
                 }
 
                 /// Initialization of spline function.
-                void init(int _N, double _deriv0, double _derivN) {
-                        N = _N;
+                void init(int _n, double _deriv0, double _derivN) {
+                        N = _n;
                         deriv0 = _deriv0;
                         derivN = _derivN;
                         delete[] X;

src/compute.cpp

@@ -89,6 +89,7 @@ Compute::Compute(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
 
   extra_dof = domain->dimension;
   dynamic_user = 0;
+  fix_dof = 0;
 
   // setup list of timesteps
 

src/fix_langevin.cpp

@@ -174,6 +174,8 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
     }
   }
 
+  if (tallyflag && zeroflag && comm->me == 0)
+    error->warning(FLERR,"Energy tally does not account for 'zero yes'");
 }
 
 /* ---------------------------------------------------------------------- */

src/fix_langevin.h

@@ -103,6 +103,12 @@ E: Fix langevin period must be > 0.0
 
 The time window for temperature relaxation must be > 0
 
+W: Energy tally does not account for 'zero yes'
+
+The energy removed by using the 'zero yes' flag is not accounted
+for in the energy tally and thus energy conservation cannot be
+monitored in this case.
+
 E: Fix langevin omega requires atom style sphere
 
 Self-explanatory.

src/fix_move.cpp

@@ -51,6 +51,9 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
   peratom_freq = 1;
   time_integrate = 1;
   create_attribute = 1;
+  displaceflag = 0;
+  velocityflag = 0;
+  maxatom = 0;
 
   // parse args
 

src/fix_nve_limit.cpp

@@ -71,9 +71,10 @@ void FixNVELimit::init()
   // warn if using fix shake, which will lead to invalid constraint forces
 
   for (int i = 0; i < modify->nfix; i++)
-    if (strcmp(modify->fix[i]->style,"shake") == 0) {
+    if ((strcmp(modify->fix[i]->style,"shake") == 0)
+        || (strcmp(modify->fix[i]->style,"rattle") == 0)) {
       if (comm->me == 0)
-        error->warning(FLERR,"Should not use fix nve/limit with fix shake");
+        error->warning(FLERR,"Should not use fix nve/limit with fix shake or fix rattle");
     }
 }
 

src/fix_temp_csvr.cpp

@@ -13,7 +13,7 @@
 
 /* ----------------------------------------------------------------------
    Contributing author: Axel Kohlmeyer (Temple U)
-   Based on code by Paulo Raiteri (Curtin U) and Giovanni Bussi (SISSA)
+   Based on code by Paolo Raiteri (Curtin U) and Giovanni Bussi (SISSA)
 ------------------------------------------------------------------------- */
 
 #include "string.h"

src/pair.cpp

@@ -191,6 +191,10 @@ void Pair::init()
     error->all(FLERR,"Cannot use pair tail corrections with 2d simulations");
   if (tail_flag && domain->nonperiodic && comm->me == 0)
     error->warning(FLERR,"Using pair tail corrections with nonperiodic system");
+  if (!compute_flag && tail_flag)
+    error->warning(FLERR,"Using pair tail corrections with compute set to no");
+  if (!compute_flag && offset_flag)
+    error->warning(FLERR,"Using pair potential shift with compute set to no");
 
   // for manybody potentials
   // check if bonded exclusions could invalidate the neighbor list

src/special.cpp

@@ -68,7 +68,15 @@ void Special::build()
   tagint **bond_atom = atom->bond_atom;
   int **nspecial = atom->nspecial;
 
-  if (me == 0 && screen) fprintf(screen,"Finding 1-2 1-3 1-4 neighbors ...\n");
+  if (me == 0 && screen) {
+    const double * const special_lj   = force->special_lj;
+    const double * const special_coul = force->special_coul;
+    fprintf(screen,"Finding 1-2 1-3 1-4 neighbors ...\n"
+                   " Special bond factors lj:   %-10g %-10g %-10g\n"
+                   " Special bond factors coul: %-10g %-10g %-10g\n",
+                   special_lj[1],special_lj[2],special_lj[3],
+                   special_coul[1],special_coul[2],special_coul[3]);
+  }
 
   // initialize nspecial counters to 0