Merge pull request #330 from akohlmey/collected-small-bugfixes

Collected small bugfixes

doc/src/Section_packages.txt

@@ -1153,7 +1153,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
 "USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
 "USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surface, Stefan Paquay (Eindhoven U of Technology), "fix manifoldforce"_fix_manifoldforce.html, USER/manifold, "manifold"_manifold, -
 "USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE
-"USER-NC-DUMP"_#USER-NC-DUMP, dump output via NetCDF, Lars Pastewka (Karlsruhe Institute of Technology, KIT), "dump nc, dump nc/mpiio"_dump_nc.html, -, -, lib/netcdf
+"USER-NC-DUMP"_#USER-NC-DUMP, dump output via NetCDF, Lars Pastewka (Karlsruhe Institute of Technology, KIT), "dump nc / dump nc/mpiio"_dump_nc.html, -, -, lib/netcdf
 "USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section 5.3.4"_accelerate_omp.html, -, -, -
 "USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -
 "USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm
@@ -1610,11 +1610,12 @@ and a "dump nc/mpiio"_dump_nc.html command to output LAMMPS snapshots
 in this format.  See src/USER-NC-DUMP/README for more details.
 
 NetCDF files can be directly visualized with the following tools:
+
 Ovito (http://www.ovito.org/). Ovito supports the AMBER convention
-  and all of the above extensions. :ulb,l
+and all of the above extensions. :ulb,l
 VMD (http://www.ks.uiuc.edu/Research/vmd/) :l
 AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye contains
-  a NetCDF reader that is not present in the standard distribution of AtomEye :l,ule
+a NetCDF reader that is not present in the standard distribution of AtomEye :l,ule
 
 The person who created these files is Lars Pastewka at
 Karlsruhe Institute of Technology (lars.pastewka at kit.edu).

doc/src/Section_start.txt

@@ -1727,7 +1727,7 @@ thermodynamic state and a total run time for the simulation.  It then
 appends statistics about the CPU time and storage requirements for the
 simulation.  An example set of statistics is shown here:
 
-Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms
+Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms :pre
 
 Performance: 18.436 ns/day  1.302 hours/ns  106.689 timesteps/s
 97.0% CPU use with 4 MPI tasks x no OpenMP threads :pre
@@ -1757,14 +1757,14 @@ Ave special neighs/atom = 2.34032
 Neighbor list builds = 26
 Dangerous builds = 0 :pre
 
-The first section provides a global loop timing summary. The loop time
+The first section provides a global loop timing summary. The {loop time}
 is the total wall time for the section.  The {Performance} line is
 provided for convenience to help predicting the number of loop
-continuations required and for comparing performance with other
+continuations required and for comparing performance with other,
-similar MD codes.  The CPU use line provides the CPU utilzation per
+similar MD codes.  The {CPU use} line provides the CPU utilzation per
 MPI task; it should be close to 100% times the number of OpenMP
-threads (or 1). Lower numbers correspond to delays due to file I/O or
+threads (or 1 of no OpenMP). Lower numbers correspond to delays due
-insufficient thread utilization.
+to file I/O or insufficient thread utilization.
 
 The MPI task section gives the breakdown of the CPU run time (in
 seconds) into major categories:
@@ -1791,7 +1791,7 @@ is present that also prints the CPU utilization in percent. In
 addition, when using {timer full} and the "package omp"_package.html
 command are active, a similar timing summary of time spent in threaded
 regions to monitor thread utilization and load balance is provided. A
-new entry is the {Reduce} section, which lists the time spend in
+new entry is the {Reduce} section, which lists the time spent in
 reducing the per-thread data elements to the storage for non-threaded
 computation. These thread timings are taking from the first MPI rank
 only and and thus, as the breakdown for MPI tasks can change from MPI

doc/src/commands.txt

@@ -91,6 +91,7 @@ Commands :h1
    suffix
    tad
    temper
+   temper_grem
    thermo
    thermo_modify
    thermo_style

doc/src/computes.txt

@@ -35,6 +35,7 @@ Computes :h1
    compute_erotate_sphere_atom
    compute_event_displace
    compute_fep
+   compute_global_atom
    compute_group_group
    compute_gyration
    compute_gyration_chunk

doc/src/fix_grem.txt

@@ -29,7 +29,7 @@ fix             fxgREM all grem 502 -0.15 -80000 fxnvt :pre
 [Description:]
 
 This fix implements the molecular dynamics version of the generalized
-replica exchange method (gREM) originally developed by "(Kim)"_#Kim,
+replica exchange method (gREM) originally developed by "(Kim)"_#Kim2010,
 which uses non-Boltzmann ensembles to sample over first order phase
 transitions. The is done by defining replicas with an enthalpy
 dependent effective temperature
@@ -103,7 +103,7 @@ npt"_fix_nh.html, "thermo_modify"_thermo_modify.html
 
 :line
 
-:link(Kim)
+:link(Kim2010)
 [(Kim)] Kim, Keyes, Straub, J Chem. Phys, 132, 224107 (2010).
 
 :link(Malolepsza)

doc/src/lammps.book

@@ -23,6 +23,7 @@ Section_history.html
 
 tutorial_drude.html
 tutorial_github.html
+tutorial_pylammps.html
 
 body.html
 manifolds.html
@@ -113,6 +114,7 @@ special_bonds.html
 suffix.html
 tad.html
 temper.html
+temper_grem.html
 thermo.html
 thermo_modify.html
 thermo_style.html

doc/src/temper_grem.txt

@@ -32,7 +32,7 @@ Run a parallel tempering or replica exchange simulation in LAMMPS
 partition mode using multiple generalized replicas (ensembles) of a
 system defined by "fix grem"_fix_grem.html, which stands for the
 generalized replica exchange method (gREM) originally developed by
-"(Kim)"_#Kim.  It uses non-Boltzmann ensembles to sample over first
+"(Kim)"_#KimStraub.  It uses non-Boltzmann ensembles to sample over first
 order phase transitions. The is done by defining replicas with an
 enthalpy dependent effective temperature
 
@@ -105,5 +105,5 @@ This command must be used with "fix grem"_fix_grem.html.
 
 [Default:] none
 
-:link(Kim)
+:link(KimStraub)
 [(Kim)] Kim, Keyes, Straub, J Chem Phys, 132, 224107 (2010).

doc/src/timer.txt

@@ -33,14 +33,14 @@ timer loop :pre
 Select the level of detail at which LAMMPS performs its CPU timings.
 Multiple keywords can be specified with the {timer} command.  For
 keywords that are mutually exclusive, the last one specified takes
-effect.
+precedence.
 
 During a simulation run LAMMPS collects information about how much
 time is spent in different sections of the code and thus can provide
 information for determining performance and load imbalance problems.
 This can be done at different levels of detail and accuracy.  For more
 information about the timing output, see this "discussion of screen
-output"_Section_start.html#start_8.
+output in Section 2.8"_Section_start.html#start_8.
 
 The {off} setting will turn all time measurements off. The {loop}
 setting will only measure the total time for a run and not collect any
@@ -52,20 +52,22 @@ procsessors.  The {full} setting adds information about CPU
 utilization and thread utilization, when multi-threading is enabled.
 
 With the {sync} setting, all MPI tasks are synchronized at each timer
-call which meaures load imbalance more accuractly, though it can also
+call which measures load imbalance for each section more accuractly,
-slow down the simulation.  Using the {nosync} setting (which is the
+though it can also slow down the simulation by prohibiting overlapping
-default) turns off this synchronization.
+independent computations on different MPI ranks  Using the {nosync}
+setting (which is the default) turns this synchronization off.
 
-With the {timeout} keyword a walltime limit can be imposed that
+With the {timeout} keyword a walltime limit can be imposed, that
 affects the "run"_run.html and "minimize"_minimize.html commands.
-This can be convenient when runs have to confirm to time limits,
+This can be convenient when calculations have to comply with execution
-e.g. when running under a batch system and you want to maximize
+time limits, e.g. when running under a batch system when you want to
-the utilization of the batch time slot, especially when the time
+maximize the utilization of the batch time slot, especially for runs
-per timestep varies and is thus difficult to predict how many
+where the time per timestep varies much and thus it becomes difficult
-steps a simulation can perform, or for difficult to converge
+to predict how many steps a simulation can perform for a given walltime
-minimizations. The timeout {elapse} value should be somewhat smaller
+limit. This also applies for difficult to converge minimizations.
-than the time requested from the batch system, as there is usually
+The timeout {elapse} value should be somewhat smaller than the maximum
-some overhead to launch jobs, and it may be advisable to write
+wall time requested from the batch system, as there is usually
+some overhead to launch jobs, and it is advisable to write
 out a restart after terminating a run due to a timeout.
 
 The timeout timer starts when the command is issued. When the time

src/.gitignore

@@ -374,6 +374,8 @@
 /fix_meso.h
 /fix_meso_stationary.cpp
 /fix_meso_stationary.h
+/fix_mscg.cpp
+/fix_mscg.h
 /fix_msst.cpp
 /fix_msst.h
 /fix_neb.cpp
@@ -394,6 +396,8 @@
 /fix_nph_body.h
 /fix_npt_body.cpp
 /fix_npt_body.h
+/fix_nvk.cpp
+/fix_nvk.h
 /fix_nvt_body.cpp
 /fix_nvt_body.h
 /fix_nve_body.cpp

src/GRANULAR/fix_wall_gran.cpp

@@ -149,7 +149,7 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
     if (narg < iarg+2) error->all(FLERR,"Illegal fix wall/gran command");
     wallstyle = ZCYLINDER;
     lo = hi = 0.0;
-    cylradius = force->numeric(FLERR,arg[iarg+3]);
+    cylradius = force->numeric(FLERR,arg[iarg+1]);
     iarg += 2;
   } else if (strcmp(arg[iarg],"region") == 0) {
     if (narg < iarg+2) error->all(FLERR,"Illegal fix wall/gran command");

src/KSPACE/pair_buck_long_coul_long.cpp

@@ -51,6 +51,8 @@ PairBuckLongCoulLong::PairBuckLongCoulLong(LAMMPS *lmp) : Pair(lmp)
   dispersionflag = ewaldflag = pppmflag = 1;
   respa_enable = 1;
   writedata = 1;
+  ftable = NULL;
+  fdisptable = NULL;
 }
 
 /* ----------------------------------------------------------------------
@@ -230,7 +232,27 @@ void PairBuckLongCoulLong::init_style()
   // require an atom style with charge defined
 
   if (!atom->q_flag && (ewald_order&(1<<1)))
-    error->all(FLERR,"Pair style buck/long/coul/long requires atom attribute q");
+    error->all(FLERR,
+        "Invoking coulombic in pair style buck/long/coul/long requires atom attribute q");
+
+  // ensure use of KSpace long-range solver, set two g_ewalds
+
+  if (force->kspace == NULL)
+    error->all(FLERR,"Pair style requires a KSpace style");
+  if (ewald_order&(1<<1)) g_ewald = force->kspace->g_ewald;
+  if (ewald_order&(1<<6)) g_ewald_6 = force->kspace->g_ewald_6;
+
+  // set rRESPA cutoffs
+
+  if (strstr(update->integrate_style,"respa") &&
+      ((Respa *) update->integrate)->level_inner >= 0)
+    cut_respa = ((Respa *) update->integrate)->cutoff;
+  else cut_respa = NULL;
+
+  // setup force tables
+
+  if (ncoultablebits && (ewald_order&(1<<1))) init_tables(cut_coul,cut_respa);
+  if (ndisptablebits && (ewald_order&(1<<6))) init_tables_disp(cut_buck_global);
 
   // request regular or rRESPA neighbor lists if neighrequest_flag != 0
 
@@ -271,24 +293,6 @@ void PairBuckLongCoulLong::init_style()
   }
 
   cut_coulsq = cut_coul * cut_coul;
-
-  // set rRESPA cutoffs
-
-  if (strstr(update->integrate_style,"respa") &&
-      ((Respa *) update->integrate)->level_inner >= 0)
-    cut_respa = ((Respa *) update->integrate)->cutoff;
-  else cut_respa = NULL;
-
-  // ensure use of KSpace long-range solver, set two g_ewalds
-
-  if (force->kspace == NULL)
-    error->all(FLERR,"Pair style requires a KSpace style");
-  if (ewald_order&(1<<1)) g_ewald = force->kspace->g_ewald;
-  if (ewald_order&(1<<6)) g_ewald_6 = force->kspace->g_ewald_6;
-  // setup force tables
-
-  if (ncoultablebits && (ewald_order&(1<<1))) init_tables(cut_coul,cut_respa);
-  if (ndisptablebits && (ewald_order&(1<<6))) init_tables_disp(cut_buck_global);
 }
 
 /* ----------------------------------------------------------------------

src/KSPACE/pair_lj_long_coul_long.cpp

@@ -81,10 +81,12 @@ void PairLJLongCoulLong::settings(int narg, char **arg)
 {
   if (narg != 3 && narg != 4) error->all(FLERR,"Illegal pair_style command");
 
-  ewald_off = 0;
   ewald_order = 0;
-  options(arg, 6);
+  ewald_off = 0;
-  options(++arg, 1);
+
+  options(arg,6);
+  options(++arg,1);
+
   if (!comm->me && ewald_order == ((1<<1) | (1<<6)))
     error->warning(FLERR,"Using largest cutoff for lj/long/coul/long");
   if (!*(++arg))
@@ -226,7 +228,26 @@ void PairLJLongCoulLong::init_style()
 
   if (!atom->q_flag && (ewald_order&(1<<1)))
     error->all(FLERR,
-        "Invoking coulombic in pair style lj/coul requires atom attribute q");
+        "Invoking coulombic in pair style lj/long/coul/long requires atom attribute q");
+
+  // ensure use of KSpace long-range solver, set two g_ewalds
+
+  if (force->kspace == NULL)
+    error->all(FLERR,"Pair style requires a KSpace style");
+  if (ewald_order&(1<<1)) g_ewald = force->kspace->g_ewald;
+  if (ewald_order&(1<<6)) g_ewald_6 = force->kspace->g_ewald_6;
+
+  // set rRESPA cutoffs
+
+  if (strstr(update->integrate_style,"respa") &&
+      ((Respa *) update->integrate)->level_inner >= 0)
+    cut_respa = ((Respa *) update->integrate)->cutoff;
+  else cut_respa = NULL;
+
+  // setup force tables
+
+  if (ncoultablebits && (ewald_order&(1<<1))) init_tables(cut_coul,cut_respa);
+  if (ndisptablebits && (ewald_order&(1<<6))) init_tables_disp(cut_lj_global);
 
   // request regular or rRESPA neighbor lists if neighrequest_flag != 0
 
@@ -265,27 +286,8 @@ void PairLJLongCoulLong::init_style()
 
     } else irequest = neighbor->request(this,instance_me);
   }
+
   cut_coulsq = cut_coul * cut_coul;
-
-  // set rRESPA cutoffs
-
-  if (strstr(update->integrate_style,"respa") &&
-      ((Respa *) update->integrate)->level_inner >= 0)
-    cut_respa = ((Respa *) update->integrate)->cutoff;
-  else cut_respa = NULL;
-
-  // ensure use of KSpace long-range solver, set g_ewald
-
-  if (force->kspace == NULL)
-    error->all(FLERR,"Pair style requires a KSpace style");
-  if (force->kspace) g_ewald = force->kspace->g_ewald;
-  if (force->kspace) g_ewald_6 = force->kspace->g_ewald_6;
-
-  // setup force tables
-
-  if (ncoultablebits && (ewald_order&(1<<1))) init_tables(cut_coul,cut_respa);
-  if (ndisptablebits && (ewald_order&(1<<6))) init_tables_disp(cut_lj_global);
-
 }
 
 /* ----------------------------------------------------------------------

src/MAKE/OPTIONS/Makefile.intel_cpu

@@ -54,7 +54,7 @@ MPI_LIB =
 
 FFT_INC =       -DFFT_MKL -DFFT_SINGLE
 FFT_PATH = 
-FFT_LIB =       -L$MKLROOT/lib/intel64/ -lmkl_intel_ilp64 \
+FFT_LIB =       -L$(MKLROOT)/lib/intel64/ -lmkl_intel_ilp64 \
                 -lmkl_sequential -lmkl_core	
 
 # JPEG and/or PNG library

src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi

@@ -54,7 +54,7 @@ MPI_LIB =
 
 FFT_INC =       -DFFT_MKL -DFFT_SINGLE
 FFT_PATH = 
-FFT_LIB =       -L$MKLROOT/lib/intel64/ -lmkl_intel_ilp64 \
+FFT_LIB =       -L$(MKLROOT)/lib/intel64/ -lmkl_intel_ilp64 \
                 -lmkl_sequential -lmkl_core	
 
 # JPEG and/or PNG library

src/MAKE/OPTIONS/Makefile.knl

@@ -54,7 +54,7 @@ MPI_LIB =
 
 FFT_INC =       -DFFT_MKL -DFFT_SINGLE
 FFT_PATH = 
-FFT_LIB =       -L$MKLROOT/lib/intel64/ -lmkl_intel_ilp64 \
+FFT_LIB =       -L$(MKLROOT)/lib/intel64/ -lmkl_intel_ilp64 \
                 -lmkl_sequential -lmkl_core	
 
 # JPEG and/or PNG library

src/compute_chunk_atom.cpp

@@ -493,7 +493,7 @@ ComputeChunkAtom::~ComputeChunkAtom()
 {
   // check nfix in case all fixes have already been deleted
 
-  if (modify->nfix) modify->delete_fix(id_fix);
+  if (id_fix && modify->nfix) modify->delete_fix(id_fix);
   delete [] id_fix;
 
   memory->destroy(chunk);

src/finish.cpp

@@ -247,7 +247,7 @@ void Finish::end(int flag)
     }
   }
 
-  // PRD stats using PAIR,BOND,KSPACE for dephase,dynamics,quench
+  // PRD stats
 
   if (prdflag) {
     if (me == 0) {
@@ -329,7 +329,7 @@ void Finish::end(int flag)
     }
   }
 
-  // TAD stats using PAIR,BOND,KSPACE for neb,dynamics,quench
+  // TAD stats
 
   if (tadflag) {
     if (me == 0) {
@@ -415,7 +415,7 @@ void Finish::end(int flag)
     }
   }
 
-  // HYPER stats using PAIR,BOND,KSPACE for dynamics,quench
+  // HYPER stats
 
   if (hyperflag) {
     if (me == 0) {
@@ -912,7 +912,7 @@ void mpi_timings(const char *label, Timer *t, enum Timer::ttype tt,
   time_cpu = tmp/nprocs*100.0;
 
   // % variance from the average as measure of load imbalance
-  if ((time_sq/time - time) > 1.0e-10)
+  if ((time > 0.001) && ((time_sq/time - time) > 1.0e-10))
     time_sq = sqrt(time_sq/time - time)*100.0;
   else
     time_sq = 0.0;
@@ -964,7 +964,7 @@ void omp_times(FixOMP *fix, const char *label, enum Timer::ttype which,
   time_std /= nthreads;
   time_total /= nthreads;
 
-  if ((time_std/time_avg -time_avg) > 1.0e-10)
+  if ((time_avg > 0.001) && ((time_std/time_avg -time_avg) > 1.0e-10))
     time_std = sqrt(time_std/time_avg - time_avg)*100.0;
   else
     time_std = 0.0;