Generally, LAMMPS will print a message to the screen and exit -gracefully when it encounters a fatal error. Sometimes it will print -a WARNING and continue on; you can decide if the WARNING is important -or not. If LAMMPS crashes or hangs without spitting out an error -message first then it could be a bug (see this section) or one -of the following cases: +
Generally, LAMMPS will print a message to the screen and logfile and +exit gracefully when it encounters a fatal error. Sometimes it will +print a WARNING to the screen and logfile and continue on; you can +decide if the WARNING is important or not. A WARNING message that is +generated in the middle of a run is only printed to the screen, not to +the logfile, to avoid cluttering up thermodynamic output. If LAMMPS +crashes or hangs without spitting out an error message first then it +could be a bug (see this section) or one of the following +cases:
LAMMPS runs in the available memory a processor allows to be allocated. Most reasonable MD runs are compute limited, not memory @@ -3144,7 +3147,7 @@ box length.
if $a < $b then & - "print Minimum value = $a" + "print Minimum value = $a" & "run 1000" & else & "print Minimum value = $b" & diff --git a/doc/if.txt b/doc/if.txt index ac7cbbc001..ca823f030c 100644 --- a/doc/if.txt +++ b/doc/if.txt @@ -54,7 +54,7 @@ can be spread across many lines, though it is still a single command: if $a < $b then & - "print Minimum value = $a" + "print Minimum value = $a" & "run 1000" & else & "print Minimum value = $b" & diff --git a/doc/run.html b/doc/run.html index a93d102276..eae351b275 100644 --- a/doc/run.html +++ b/doc/run.html @@ -156,6 +156,16 @@ print Coord = $q particular atom between runs. Note that the variable "$q" will be evaluated afresh each time the print command is executed. +Note that by using the line continuation character "&", the run every +command can be spread across many lines, though it is still a single +command: +
+run 100000 every 1000 & + "print Minimum value = $a" & + "print Maximum value = $b" & + "print Temp = $c" & + "print Press = $d" +If the pre and post options are set to "no" when used with the every keyword, then the 1st run will do the full setup and the last run will print the full timing summary, but these operations will be diff --git a/doc/run.txt b/doc/run.txt index 56f47be800..4e295a3e91 100644 --- a/doc/run.txt +++ b/doc/run.txt @@ -149,6 +149,16 @@ which does 3 runs of 2000 steps and prints the x-coordinate of a particular atom between runs. Note that the variable "$q" will be evaluated afresh each time the print command is executed. +Note that by using the line continuation character "&", the run every +command can be spread across many lines, though it is still a single +command: + +run 100000 every 1000 & + "print Minimum value = $a" & + "print Maximum value = $b" & + "print Temp = $c" & + "print Press = $d" :pre + If the {pre} and {post} options are set to "no" when used with the {every} keyword, then the 1st run will do the full setup and the last run will print the full timing summary, but these operations will be diff --git a/src/CLASS2/dihedral_class2.cpp b/src/CLASS2/dihedral_class2.cpp index 36e826a339..7b03fbbec1 100644 --- a/src/CLASS2/dihedral_class2.cpp +++ b/src/CLASS2/dihedral_class2.cpp @@ -212,7 +212,7 @@ void DihedralClass2::compute(int eflag, int vflag) sprintf(str,"Dihedral problem: %d %d %d %d %d %d", me,update->ntimestep, atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]); - error->warning(str); + error->warning(str,0); fprintf(screen," 1st atom: %d %g %g %g\n", me,x[i1][0],x[i1][1],x[i1][2]); fprintf(screen," 2nd atom: %d %g %g %g\n", diff --git a/src/CLASS2/improper_class2.cpp b/src/CLASS2/improper_class2.cpp index 1f02b25500..37f7f9aeaf 100644 --- a/src/CLASS2/improper_class2.cpp +++ b/src/CLASS2/improper_class2.cpp @@ -159,7 +159,7 @@ void ImproperClass2::compute(int eflag, int vflag) sprintf(str,"Improper problem: %d %d %d %d %d %d", me,update->ntimestep, atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]); - error->warning(str); + error->warning(str,0); fprintf(screen," 1st atom: %d %g %g %g\n", me,x[i1][0],x[i1][1],x[i1][2]); fprintf(screen," 2nd atom: %d %g %g %g\n", diff --git a/src/DSMC/pair_dsmc.cpp b/src/DSMC/pair_dsmc.cpp index 6e8e8a44bc..090f2af796 100644 --- a/src/DSMC/pair_dsmc.cpp +++ b/src/DSMC/pair_dsmc.cpp @@ -158,9 +158,9 @@ void PairDSMC::compute(int eflag, int vflag) convert_double_to_equivalent_int(num_of_collisions_double); if (num_of_collisions > number_of_A) - error->warning("Pair dsmc: num_of_collisions > number_of_A"); + error->warning("Pair dsmc: num_of_collisions > number_of_A",0); if (num_of_collisions > number_of_B) - error->warning("Pair dsmc: num_of_collisions > number_of_B"); + error->warning("Pair dsmc: num_of_collisions > number_of_B",0); // perform collisions on pairs of particles in icell diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp index 69d9e72233..8b00fde01b 100644 --- a/src/GRANULAR/fix_pour.cpp +++ b/src/GRANULAR/fix_pour.cpp @@ -416,7 +416,7 @@ void FixPour::pre_exchange() ninserted += nnear-nprevious; if (nnear - nprevious < nnew && me == 0) - error->warning("Less insertions than requested"); + error->warning("Less insertions than requested",0); // check if new atom is in my sub-box or above it if I'm highest proc // if so, add to my list via create_atom() diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp index 83eebfae7e..96f8159aa7 100644 --- a/src/MANYBODY/pair_comb.cpp +++ b/src/MANYBODY/pair_comb.cpp @@ -1781,14 +1781,14 @@ double PairComb::qfo_self(Param *param, double qi, double selfpot) char str[128]; sprintf(str,"Pair COMB charge %.10f with force %.10f hit min barrier", qi,self_d); - error->warning(str); + error->warning(str,0); self_d += 4.0 * cmin * pow((qi-qmin),3); } if (qi > qmax) { char str[128]; sprintf(str,"Pair COMB charge %.10f with force %.10f hit max barrier", qi,self_d); - error->warning(str); + error->warning(str,0); self_d += 4.0 * cmax * pow((qi-qmax),3); } */ diff --git a/src/MOLECULE/bond_fene.cpp b/src/MOLECULE/bond_fene.cpp index baa147a234..babb22689b 100644 --- a/src/MOLECULE/bond_fene.cpp +++ b/src/MOLECULE/bond_fene.cpp @@ -88,7 +88,7 @@ void BondFENE::compute(int eflag, int vflag) char str[128]; sprintf(str,"FENE bond too long: %d %d %d %g", update->ntimestep,atom->tag[i1],atom->tag[i2],sqrt(rsq)); - error->warning(str); + error->warning(str,0); if (rlogarg <= -3.0) error->one("Bad FENE bond"); rlogarg = 0.1; } @@ -244,7 +244,7 @@ double BondFENE::single(int type, double rsq, int i, int j) if (rlogarg < 0.1) { char str[128]; sprintf(str,"FENE bond too long: %d %g",update->ntimestep,sqrt(rsq)); - error->warning(str); + error->warning(str,0); if (rlogarg <= -3.0) error->one("Bad FENE bond"); rlogarg = 0.1; } diff --git a/src/MOLECULE/bond_fene_expand.cpp b/src/MOLECULE/bond_fene_expand.cpp index 44a9aba998..9607861569 100644 --- a/src/MOLECULE/bond_fene_expand.cpp +++ b/src/MOLECULE/bond_fene_expand.cpp @@ -93,7 +93,7 @@ void BondFENEExpand::compute(int eflag, int vflag) char str[128]; sprintf(str,"FENE bond too long: %d %d %d %g", update->ntimestep,atom->tag[i1],atom->tag[i2],sqrt(rsq)); - error->warning(str); + error->warning(str,0); if (rlogarg <= -3.0) error->one("Bad FENE bond"); rlogarg = 0.1; } @@ -258,7 +258,7 @@ double BondFENEExpand::single(int type, double rsq, int i, int j) if (rlogarg < 0.1) { char str[128]; sprintf(str,"FENE bond too long: %d %g",update->ntimestep,sqrt(rsq)); - error->warning(str); + error->warning(str,0); if (rlogarg <= -3.0) error->one("Bad FENE bond"); rlogarg = 0.1; } diff --git a/src/MOLECULE/dihedral_charmm.cpp b/src/MOLECULE/dihedral_charmm.cpp index 183ee4f1d4..a92d261bc8 100644 --- a/src/MOLECULE/dihedral_charmm.cpp +++ b/src/MOLECULE/dihedral_charmm.cpp @@ -150,7 +150,7 @@ void DihedralCharmm::compute(int eflag, int vflag) sprintf(str,"Dihedral problem: %d %d %d %d %d %d", me,update->ntimestep, atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]); - error->warning(str); + error->warning(str,0); fprintf(screen," 1st atom: %d %g %g %g\n", me,x[i1][0],x[i1][1],x[i1][2]); fprintf(screen," 2nd atom: %d %g %g %g\n", diff --git a/src/MOLECULE/dihedral_harmonic.cpp b/src/MOLECULE/dihedral_harmonic.cpp index 67a7e50e30..17f7dbf9cb 100644 --- a/src/MOLECULE/dihedral_harmonic.cpp +++ b/src/MOLECULE/dihedral_harmonic.cpp @@ -140,7 +140,7 @@ void DihedralHarmonic::compute(int eflag, int vflag) sprintf(str,"Dihedral problem: %d %d %d %d %d %d", me,update->ntimestep, atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]); - error->warning(str); + error->warning(str,0); fprintf(screen," 1st atom: %d %g %g %g\n", me,x[i1][0],x[i1][1],x[i1][2]); fprintf(screen," 2nd atom: %d %g %g %g\n", diff --git a/src/MOLECULE/dihedral_helix.cpp b/src/MOLECULE/dihedral_helix.cpp index b45e956f67..ce12bcca16 100644 --- a/src/MOLECULE/dihedral_helix.cpp +++ b/src/MOLECULE/dihedral_helix.cpp @@ -172,7 +172,7 @@ void DihedralHelix::compute(int eflag, int vflag) sprintf(str,"Dihedral problem: %d %d %d %d %d %d", me,update->ntimestep, atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]); - error->warning(str); + error->warning(str,0); fprintf(screen," 1st atom: %d %g %g %g\n", me,x[i1][0],x[i1][1],x[i1][2]); fprintf(screen," 2nd atom: %d %g %g %g\n", diff --git a/src/MOLECULE/dihedral_multi_harmonic.cpp b/src/MOLECULE/dihedral_multi_harmonic.cpp index 470bebc9cc..4eb323ba85 100644 --- a/src/MOLECULE/dihedral_multi_harmonic.cpp +++ b/src/MOLECULE/dihedral_multi_harmonic.cpp @@ -163,7 +163,7 @@ void DihedralMultiHarmonic::compute(int eflag, int vflag) sprintf(str,"Dihedral problem: %d %d %d %d %d %d", comm->me,update->ntimestep, atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]); - error->warning(str); + error->warning(str,0); fprintf(screen," 1st atom: %d %g %g %g\n", comm->me,x[i1][0],x[i1][1],x[i1][2]); fprintf(screen," 2nd atom: %d %g %g %g\n", diff --git a/src/MOLECULE/dihedral_opls.cpp b/src/MOLECULE/dihedral_opls.cpp index 68c23dcf47..e4d0e5327b 100644 --- a/src/MOLECULE/dihedral_opls.cpp +++ b/src/MOLECULE/dihedral_opls.cpp @@ -169,7 +169,7 @@ void DihedralOPLS::compute(int eflag, int vflag) sprintf(str,"Dihedral problem: %d %d %d %d %d %d", comm->me,update->ntimestep, atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]); - error->warning(str); + error->warning(str,0); fprintf(screen," 1st atom: %d %g %g %g\n", comm->me,x[i1][0],x[i1][1],x[i1][2]); fprintf(screen," 2nd atom: %d %g %g %g\n", diff --git a/src/MOLECULE/fix_bond_create.cpp b/src/MOLECULE/fix_bond_create.cpp index 9af3e5f694..091ac32cd3 100755 --- a/src/MOLECULE/fix_bond_create.cpp +++ b/src/MOLECULE/fix_bond_create.cpp @@ -183,12 +183,14 @@ void FixBondCreate::init() // require special bonds = 0,1,1 - int flag = 0; if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 || - force->special_lj[3] != 1.0) flag = 1; - if (force->special_coul[1] != 0.0 || force->special_coul[2] != 1.0 || - force->special_coul[3] != 1.0) flag = 1; - if (flag) error->all("Fix bond/create requires special_bonds = 0,1,1"); + force->special_lj[3] != 1.0) + error->all("Fix bond/create requires special_bonds lj = 0,1,1"); + + if (atom->q_flag) + if (force->special_coul[1] != 0.0 || force->special_coul[2] != 1.0 || + force->special_coul[3] != 1.0) + error->all("Fix bond/create requires special_bonds coul = 0,1,1"); // warn if angles, dihedrals, impropers are being used diff --git a/src/MOLECULE/improper_cvff.cpp b/src/MOLECULE/improper_cvff.cpp index 09d16071d9..6cbf7e8876 100644 --- a/src/MOLECULE/improper_cvff.cpp +++ b/src/MOLECULE/improper_cvff.cpp @@ -154,7 +154,7 @@ void ImproperCvff::compute(int eflag, int vflag) sprintf(str,"Improper problem: %d %d %d %d %d %d", me,update->ntimestep, atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]); - error->warning(str); + error->warning(str,0); fprintf(screen," 1st atom: %d %g %g %g\n", me,x[i1][0],x[i1][1],x[i1][2]); fprintf(screen," 2nd atom: %d %g %g %g\n", diff --git a/src/MOLECULE/improper_harmonic.cpp b/src/MOLECULE/improper_harmonic.cpp index b7eb2b9190..008b73e8d1 100644 --- a/src/MOLECULE/improper_harmonic.cpp +++ b/src/MOLECULE/improper_harmonic.cpp @@ -125,7 +125,7 @@ void ImproperHarmonic::compute(int eflag, int vflag) sprintf(str,"Improper problem: %d %d %d %d %d %d", me,update->ntimestep, atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]); - error->warning(str); + error->warning(str,0); fprintf(screen," 1st atom: %d %g %g %g\n", me,x[i1][0],x[i1][1],x[i1][2]); fprintf(screen," 2nd atom: %d %g %g %g\n", diff --git a/src/compute_cna_atom.cpp b/src/compute_cna_atom.cpp index 06a51b5844..4416671d5c 100644 --- a/src/compute_cna_atom.cpp +++ b/src/compute_cna_atom.cpp @@ -191,7 +191,7 @@ void ComputeCNAAtom::compute_peratom() if (nerrorall && comm->me == 0) { char str[128]; sprintf(str,"Too many neighbors in CNA for %d atoms",nerrorall); - error->warning(str); + error->warning(str,0); } // compute CNA for each atom in group diff --git a/src/error.cpp b/src/error.cpp index b63b8a895e..c2226c1ab7 100644 --- a/src/error.cpp +++ b/src/error.cpp @@ -106,7 +106,8 @@ void Error::one(const char *str) only write to screen if non-NULL on this proc since could be file ------------------------------------------------------------------------- */ -void Error::warning(const char *str) +void Error::warning(const char *str, int logflag) { if (screen) fprintf(screen,"WARNING: %s\n",str); + if (logflag && logfile) fprintf(logfile,"WARNING: %s\n",str); } diff --git a/src/error.h b/src/error.h index 6b279cbf9a..b578d4ba50 100644 --- a/src/error.h +++ b/src/error.h @@ -27,7 +27,7 @@ class Error : protected Pointers { void all(const char *); void one(const char *); - void warning(const char *); + void warning(const char *, int = 1); }; } diff --git a/src/fix_deposit.cpp b/src/fix_deposit.cpp index 4e02e59d1c..60fc34ed65 100644 --- a/src/fix_deposit.cpp +++ b/src/fix_deposit.cpp @@ -324,7 +324,7 @@ void FixDeposit::pre_exchange() if (comm->me == 0) if (success == 0) - error->warning("Particle deposition was unsuccessful"); + error->warning("Particle deposition was unsuccessful",0); // set tag # of new particle beyond all previous atoms // reset global natoms diff --git a/src/fix_shake.cpp b/src/fix_shake.cpp index d4c6c8abaf..ab38ee793b 100644 --- a/src/fix_shake.cpp +++ b/src/fix_shake.cpp @@ -1345,7 +1345,7 @@ void FixShake::shake2(int m) double determ = b*b - 4.0*a*c; if (determ < 0.0) { - error->warning("Shake determinant < 0.0"); + error->warning("Shake determinant < 0.0",0); determ = 0.0; } diff --git a/src/fix_ttm.cpp b/src/fix_ttm.cpp index 0d5bb506fe..0cc1a191f5 100644 --- a/src/fix_ttm.cpp +++ b/src/fix_ttm.cpp @@ -431,7 +431,7 @@ void FixTTM::end_of_step() num_inner_timesteps = static_cast
(update->dt/inner_dt) + 1; inner_dt = update->dt/double(num_inner_timesteps); if (num_inner_timesteps > 1000000) - error->warning("Too many inner timesteps in fix ttm"); + error->warning("Too many inner timesteps in fix ttm",0); } for (int ith_inner_timestep = 0; ith_inner_timestep < num_inner_timesteps; diff --git a/src/input.cpp b/src/input.cpp index 0a38c3ceb8..e01e2ce0a3 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -237,8 +237,8 @@ char *Input::one(const char *single) // echo the command unless scanning for label if (me == 0 && label_active == 0) { - if (echo_screen && screen) fprintf(screen,"%s",line); - if (echo_log && logfile) fprintf(logfile,"%s",line); + if (echo_screen && screen) fprintf(screen,"%s\n",line); + if (echo_log && logfile) fprintf(logfile,"%s\n",line); } // parse the line diff --git a/src/thermo.cpp b/src/thermo.cpp index aa7ab7eeb6..e31fd8a8e2 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -359,7 +359,7 @@ double Thermo::lost_check() char str[128]; sprintf(str,"Lost atoms: original %.15g current %.15g",atom->natoms,ntotal); - if (me == 0) error->warning(str); + if (me == 0) error->warning(str,0); lostbefore = 1; return ntotal; } diff --git a/src/version.h b/src/version.h index aa41895b15..43394fc066 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "11 Sep 2010" +#define LAMMPS_VERSION "12 Sep 2010"