git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@99 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/GRANULAR/fix_wall_gran.cpp

@@ -400,7 +400,7 @@ void FixWallGran::history(double rsq, double dx, double dy, double dz,
   double r,vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
   double wr1,wr2,wr3,xmeff,damp,ccel,vtr1,vtr2,vtr3,vrel;
   double fn,fs,fs1,fs2,fs3,ccelx,ccely,ccelz,tor1,tor2,tor3;
-  double shrmag,rsht;
+  double shrmag,rsht,rinv;
 
   r = sqrt(rsq);
 
@@ -507,9 +507,10 @@ void FixWallGran::history(double rsq, double dx, double dy, double dz,
 
   // torques
 
-  tor1 = dy*fs3 - dz*fs2;
-  tor2 = dz*fs1 - dx*fs3;
-  tor3 = dx*fs2 - dy*fs1;
+  rinv = 1/r;
+  tor1 = rinv * (dy*fs3 - dz*fs2);
+  tor2 = rinv * (dz*fs1 - dx*fs3);
+  tor3 = rinv * (dx*fs2 - dy*fs1);
   phia[0] -= radius*tor1;
   phia[1] -= radius*tor2;
   phia[2] -= radius*tor3;

src/MAKE/Makefile.tbird

@@ -5,7 +5,11 @@ SHELL = /bin/sh
 
 # System-specific settings
 
-FFTW =		/apps/libraries/fftw
+# NOTE: you may need to invoke (by typing or in your .cshrc)
+#   module load libraries/fftw-2.1.5-openmpi-1.1.2_rc4-ofed-intel-9.1
+# before building LAMMPS
+
+FFTW =	/apps/x86_64/libraries/fftw/openmpi-1.1.2_rc4-ofed-intel-9.1/fftw-2.1.5
 
 CC =		mpicxx
 CCFLAGS =	-O -DFFT_FFTW -I${FFTW}/include

src/Make.csh

@@ -3,16 +3,16 @@
 
 if ($1 == "Makefile.lib") then
 
-  set list = `ls --width=10000 *.cpp | sed s/main\.cpp//`
+  set list = `ls *.cpp | sed s/^main\.cpp//`
   sed -i -e "s/SRC =\t.*/SRC =\t$list/" Makefile.lib
-  set list = `ls --width=10000 *.h`
+  set list = `ls *.h`
   sed -i -e "s/INC =\t.*/INC =\t$list/" Makefile.lib
 
 else if ($1 == "Makefile.list") then
 
-  set list = `ls --width=10000 *.cpp`
+  set list = `ls *.cpp`
   sed -i -e "s/SRC =\t.*/SRC =\t$list/" Makefile.list
-  set list = `ls --width=10000 *.h`
+  set list = `ls *.h`
   sed -i -e "s/INC =\t.*/INC =\t$list/" Makefile.list
 
 endif

src/Makefile.lib

@@ -7,9 +7,9 @@ SHELL = /bin/sh
 ROOT =	lmp
 EXE =	lib$(ROOT)_$@.a
 
-SRC =	angle.cpp angle_charmm.cpp angle_cosine.cpp angle_cosine_squared.cpp angle_harmonic.cpp angle_hybrid.cpp atom.cpp atom_angle.cpp atom_atomic.cpp atom_bond.cpp atom_charge.cpp atom_full.cpp atom_hybrid.cpp atom_molecular.cpp bond.cpp bond_fene.cpp bond_fene_expand.cpp bond_harmonic.cpp bond_hybrid.cpp bond_morse.cpp bond_nonlinear.cpp bond_quartic.cpp comm.cpp create_atoms.cpp create_box.cpp delete_atoms.cpp delete_bonds.cpp dihedral.cpp dihedral_charmm.cpp dihedral_harmonic.cpp dihedral_helix.cpp dihedral_hybrid.cpp dihedral_multi_harmonic.cpp dihedral_opls.cpp displace_atoms.cpp do dump.cpp dump_atom.cpp dump_bond.cpp dump_custom.cpp dump_dcd.cpp dump_xyz.cpp error.cpp ewald.cpp fft3d.cpp fft3d_wrap.cpp finish.cpp fix.cpp fix_add_force.cpp fix_ave_force.cpp fix_centro.cpp fix_com.cpp fix_drag.cpp fix_efield.cpp fix_energy.cpp fix_enforce2d.cpp fix_gravity.cpp fix_gyration.cpp fix_indent.cpp fix_langevin.cpp fix_line_force.cpp fix_minimize.cpp fix_momentum.cpp fix_msd.cpp fix_nph.cpp fix_npt.cpp fix_nve.cpp fix_nvt.cpp fix_orient_fcc.cpp fix_plane_force.cpp fix_print.cpp fix_rdf.cpp fix_recenter.cpp fix_respa.cpp fix_rigid.cpp fix_set_force.cpp fix_shake.cpp fix_spring.cpp fix_spring_rg.cpp fix_spring_self.cpp fix_stress.cpp fix_temp_rescale.cpp fix_tmd.cpp fix_uniaxial.cpp fix_viscous.cpp fix_volume_rescale.cpp fix_wall_lj93.cpp fix_wall_reflect.cpp fix_wiggle.cpp force.cpp group.cpp improper.cpp improper_cvff.cpp improper_harmonic.cpp improper_hybrid.cpp input.cpp kspace.cpp lammps.cpp library.cpp memory.cpp min.cpp min_cg.cpp min_cg_fr.cpp min_sd.cpp minimize.cpp modify.cpp neigh_bond.cpp neigh_full.cpp neigh_gran.cpp neigh_half.cpp neigh_respa.cpp neighbor.cpp output.cpp pack.cpp pair.cpp pair_buck.cpp pair_buck_coul_cut.cpp pair_buck_coul_long.cpp pair_eam.cpp pair_eam_alloy.cpp pair_eam_fs.cpp pair_hybrid.cpp pair_lj_charmm_coul_charmm.cpp pair_lj_charmm_coul_charmm_implicit.cpp pair_lj_charmm_coul_long.cpp pair_lj_cut.cpp pair_lj_cut_coul_cut.cpp pair_lj_cut_coul_debye.cpp pair_lj_cut_coul_long.cpp pair_lj_cut_coul_long_tip4p.cpp pair_lj_expand.cpp pair_lj_smooth.cpp pair_morse.cpp pair_soft.cpp pair_table.cpp pair_yukawa.cpp pppm.cpp pppm_tip4p.cpp pressure.cpp random_mars.cpp random_park.cpp read_data.cpp read_restart.cpp region.cpp region_block.cpp region_cylinder.cpp region_intersect.cpp region_sphere.cpp region_union.cpp remap.cpp remap_wrap.cpp replicate.cpp respa.cpp run.cpp set.cpp shell.cpp special.cpp system.cpp temp_full.cpp temp_partial.cpp temp_ramp.cpp temp_region.cpp temper.cpp temperature.cpp thermo.cpp timer.cpp universe.cpp update.cpp variable.cpp velocity.cpp verlet.cpp write_restart.cpp
+SRC =	angle.cpp angle_charmm.cpp angle_class2.cpp angle_cosine.cpp angle_cosine_squared.cpp angle_harmonic.cpp angle_hybrid.cpp atom.cpp atom_angle.cpp atom_atomic.cpp atom_bond.cpp atom_charge.cpp atom_dpd.cpp atom_full.cpp atom_granular.cpp atom_hybrid.cpp atom_molecular.cpp bond.cpp bond_class2.cpp bond_fene.cpp bond_fene_expand.cpp bond_harmonic.cpp bond_hybrid.cpp bond_morse.cpp bond_nonlinear.cpp bond_quartic.cpp comm.cpp create_atoms.cpp create_box.cpp delete_atoms.cpp delete_bonds.cpp dihedral.cpp dihedral_charmm.cpp dihedral_class2.cpp dihedral_harmonic.cpp dihedral_helix.cpp dihedral_hybrid.cpp dihedral_multi_harmonic.cpp dihedral_opls.cpp displace_atoms.cpp domain.cpp dump.cpp dump_atom.cpp dump_bond.cpp dump_custom.cpp dump_dcd.cpp dump_xyz.cpp error.cpp ewald.cpp fft3d.cpp fft3d_wrap.cpp finish.cpp fix.cpp fix_add_force.cpp fix_ave_force.cpp fix_centro.cpp fix_com.cpp fix_drag.cpp fix_efield.cpp fix_energy.cpp fix_enforce2d.cpp fix_freeze.cpp fix_gran_diag.cpp fix_gravity.cpp fix_gyration.cpp fix_indent.cpp fix_insert.cpp fix_langevin.cpp fix_line_force.cpp fix_minimize.cpp fix_momentum.cpp fix_msd.cpp fix_nph.cpp fix_npt.cpp fix_nve.cpp fix_nve_gran.cpp fix_nvt.cpp fix_orient_fcc.cpp fix_plane_force.cpp fix_print.cpp fix_rdf.cpp fix_recenter.cpp fix_respa.cpp fix_rigid.cpp fix_set_force.cpp fix_shake.cpp fix_shear_history.cpp fix_spring.cpp fix_spring_rg.cpp fix_spring_self.cpp fix_stress.cpp fix_temp_rescale.cpp fix_tmd.cpp fix_uniaxial.cpp fix_viscous.cpp fix_volume_rescale.cpp fix_wall_gran.cpp fix_wall_lj93.cpp fix_wall_reflect.cpp fix_wiggle.cpp force.cpp group.cpp improper.cpp improper_class2.cpp improper_cvff.cpp improper_harmonic.cpp improper_hybrid.cpp input.cpp kspace.cpp lammps.cpp library.cpp memory.cpp min.cpp min_cg.cpp min_cg_fr.cpp min_sd.cpp minimize.cpp modify.cpp neigh_bond.cpp neigh_full.cpp neigh_gran.cpp neigh_half.cpp neigh_respa.cpp neighbor.cpp output.cpp pack.cpp pair.cpp pair_buck.cpp pair_buck_coul_cut.cpp pair_buck_coul_long.cpp pair_dpd.cpp pair_eam.cpp pair_eam_alloy.cpp pair_eam_fs.cpp pair_gran_hertzian.cpp pair_gran_history.cpp pair_gran_no_history.cpp pair_hybrid.cpp pair_lj_charmm_coul_charmm.cpp pair_lj_charmm_coul_charmm_implicit.cpp pair_lj_charmm_coul_long.cpp pair_lj_class2.cpp pair_lj_class2_coul_cut.cpp pair_lj_class2_coul_long.cpp pair_lj_cut.cpp pair_lj_cut_coul_cut.cpp pair_lj_cut_coul_debye.cpp pair_lj_cut_coul_long.cpp pair_lj_cut_coul_long_tip4p.cpp pair_lj_cut_fast.cpp pair_lj_expand.cpp pair_lj_smooth.cpp pair_morse.cpp pair_soft.cpp pair_sw.cpp pair_table.cpp pair_tersoff.cpp pair_yukawa.cpp pppm.cpp pppm_tip4p.cpp pressure.cpp random_mars.cpp random_park.cpp read_data.cpp read_restart.cpp region.cpp region_block.cpp region_cylinder.cpp region_intersect.cpp region_prism.cpp region_sphere.cpp region_union.cpp remap.cpp remap_wrap.cpp replicate.cpp respa.cpp run.cpp set.cpp shell.cpp special.cpp system.cpp temp_full.cpp temp_partial.cpp temp_ramp.cpp temp_region.cpp temper.cpp temperature.cpp thermo.cpp timer.cpp universe.cpp update.cpp variable.cpp velocity.cpp verlet.cpp write_restart.cpp
 
-INC =	angle.h angle_charmm.h angle_cosine.h angle_cosine_squared.h angle_harmonic.h angle_hybrid.h atom.h atom_angle.h atom_atomic.h atom_bond.h atom_charge.h atom_full.h atom_hybrid.h atom_molecular.h bond.h bond_fene.h bond_fene_expand.h bond_harmonic.h bond_hybrid.h bond_morse.h bond_nonlinear.h bond_quartic.h comm.h create_atoms.h create_box.h delete_atoms.h delete_bonds.h dihedral.h dihedral_charmm.h dihedral_harmonic.h dihedral_helix.h dihedral_hybrid.h dihedral_multi_harmonic.h dihedral_opls.h displace_atoms.h domain.h dump.h dump_atom.h dump_bond.h dump_custom.h dump_dcd.h dump_xyz.h error.h ewald.h fft3d.h fft3d_wrap.h finish.h fix.h fix_add_force.h fix_ave_force.h fix_centro.h fix_com.h fix_drag.h fix_efield.h fix_energy.h fix_enforce2d.h fix_gravity.h fix_gyration.h fix_indent.h fix_langevin.h fix_line_force.h fix_minimize.h fix_momentum.h fix_msd.h fix_nph.h fix_npt.h fix_nve.h fix_nvt.h fix_orient_fcc.h fix_plane_force.h fix_print.h fix_rdf.h fix_recenter.h fix_respa.h fix_rigid.h fix_set_force.h fix_shake.h fix_shear_history.h fix_spring.h fix_spring_rg.h fix_spring_self.h fix_stress.h fix_temp_rescale.h fix_tmd.h fix_uniaxial.h fix_viscous.h fix_volume_rescale.h fix_wall_lj93.h fix_wall_reflect.h fix_wiggle.h force.h group.h improper.h improper_cvff.h improper_harmonic.h improper_hybrid.h input.h integrate.h kspace.h lammps.h library.h memory.h memory.hold.h min.h min_cg.h min_cg_fr.h min_sd.h minimize.h modify.h neighbor.h output.h pack.h pair.h pair_buck.h pair_buck_coul_cut.h pair_buck_coul_long.h pair_eam.h pair_eam_alloy.h pair_eam_fs.h pair_hybrid.h pair_lj_charmm_coul_charmm.h pair_lj_charmm_coul_charmm_implicit.h pair_lj_charmm_coul_long.h pair_lj_class2_coul_long.h pair_lj_cut.h pair_lj_cut_coul_cut.h pair_lj_cut_coul_debye.h pair_lj_cut_coul_long.h pair_lj_cut_coul_long_tip4p.h pair_lj_expand.h pair_lj_smooth.h pair_morse.h pair_soft.h pair_table.h pair_yukawa.h pppm.h pppm_tip4p.h pressure.h random_mars.h random_park.h read_data.h read_restart.h region.h region_block.h region_cylinder.h region_intersect.h region_sphere.h region_union.h remap.h remap_wrap.h replicate.h respa.h run.h set.h shell.h special.h style.h style_class2.h style_dpd.h style_granular.h style_kspace.h style_manybody.h style_molecule.h style_poems.h style_user.h style_xtc.h system.h temp_full.h temp_partial.h temp_ramp.h temp_region.h temper.h temperature.h thermo.h timer.h universe.h update.h variable.h velocity.h verlet.h write_restart.h
+INC =	angle.h angle_charmm.h angle_class2.h angle_cosine.h angle_cosine_squared.h angle_harmonic.h angle_hybrid.h atom.h atom_angle.h atom_atomic.h atom_bond.h atom_charge.h atom_dpd.h atom_full.h atom_granular.h atom_hybrid.h atom_molecular.h bond.h bond_class2.h bond_fene.h bond_fene_expand.h bond_harmonic.h bond_hybrid.h bond_morse.h bond_nonlinear.h bond_quartic.h comm.h create_atoms.h create_box.h delete_atoms.h delete_bonds.h dihedral.h dihedral_charmm.h dihedral_class2.h dihedral_harmonic.h dihedral_helix.h dihedral_hybrid.h dihedral_multi_harmonic.h dihedral_opls.h displace_atoms.h domain.h dump.h dump_atom.h dump_bond.h dump_custom.h dump_dcd.h dump_xyz.h error.h ewald.h fft3d.h fft3d_wrap.h finish.h fix.h fix_add_force.h fix_ave_force.h fix_centro.h fix_com.h fix_drag.h fix_efield.h fix_energy.h fix_enforce2d.h fix_freeze.h fix_gran_diag.h fix_gravity.h fix_gyration.h fix_indent.h fix_insert.h fix_langevin.h fix_line_force.h fix_minimize.h fix_momentum.h fix_msd.h fix_nph.h fix_npt.h fix_nve.h fix_nve_gran.h fix_nvt.h fix_orient_fcc.h fix_plane_force.h fix_print.h fix_rdf.h fix_recenter.h fix_respa.h fix_rigid.h fix_set_force.h fix_shake.h fix_shear_history.h fix_spring.h fix_spring_rg.h fix_spring_self.h fix_stress.h fix_temp_rescale.h fix_tmd.h fix_uniaxial.h fix_viscous.h fix_volume_rescale.h fix_wall_gran.h fix_wall_lj93.h fix_wall_reflect.h fix_wiggle.h force.h group.h improper.h improper_class2.h improper_cvff.h improper_harmonic.h improper_hybrid.h input.h integrate.h kspace.h lammps.h library.h memory.h memory.hold.h min.h min_cg.h min_cg_fr.h min_sd.h minimize.h modify.h neighbor.h output.h pack.h pair.h pair_buck.h pair_buck_coul_cut.h pair_buck_coul_long.h pair_dpd.h pair_eam.h pair_eam_alloy.h pair_eam_fs.h pair_gran_hertzian.h pair_gran_history.h pair_gran_no_history.h pair_hybrid.h pair_lj_charmm_coul_charmm.h pair_lj_charmm_coul_charmm_implicit.h pair_lj_charmm_coul_long.h pair_lj_class2.h pair_lj_class2_coul_cut.h pair_lj_class2_coul_long.h pair_lj_cut.h pair_lj_cut_coul_cut.h pair_lj_cut_coul_debye.h pair_lj_cut_coul_long.h pair_lj_cut_coul_long_tip4p.h pair_lj_cut_fast.h pair_lj_expand.h pair_lj_smooth.h pair_morse.h pair_soft.h pair_sw.h pair_table.h pair_tersoff.h pair_yukawa.h pppm.h pppm_tip4p.h pressure.h random_mars.h random_park.h read_data.h read_restart.h region.h region_block.h region_cylinder.h region_intersect.h region_prism.h region_sphere.h region_union.h remap.h remap_wrap.h replicate.h respa.h run.h set.h shell.h special.h style.h style_class2.h style_dpd.h style_granular.h style_kspace.h style_manybody.h style_molecule.h style_poems.h style_user.h style_xtc.h system.h temp_full.h temp_partial.h temp_ramp.h temp_region.h temper.h temperature.h thermo.h timer.h universe.h update.h variable.h velocity.h verlet.h write_restart.h
 
 OBJ = 	$(SRC:.cpp=.o)
 

src/Makefile.list

@@ -7,9 +7,9 @@ SHELL = /bin/sh
 ROOT =	lmp
 EXE =	$(ROOT)_$@
 
-SRC =	angle.cpp angle_charmm.cpp angle_cosine.cpp angle_cosine_squared.cpp angle_harmonic.cpp angle_hybrid.cpp atom.cpp atom_angle.cpp atom_atomic.cpp atom_bond.cpp atom_charge.cpp atom_full.cpp atom_hybrid.cpp atom_molecular.cpp bond.cpp bond_fene.cpp bond_fene_expand.cpp bond_harmonic.cpp bond_hybrid.cpp bond_morse.cpp bond_nonlinear.cpp bond_quartic.cpp comm.cpp create_atoms.cpp create_box.cpp delete_atoms.cpp delete_bonds.cpp dihedral.cpp dihedral_charmm.cpp dihedral_harmonic.cpp dihedral_helix.cpp dihedral_hybrid.cpp dihedral_multi_harmonic.cpp dihedral_opls.cpp displace_atoms.cpp domain.cpp dump.cpp dump_atom.cpp dump_bond.cpp dump_custom.cpp dump_dcd.cpp dump_xyz.cpp error.cpp ewald.cpp fft3d.cpp fft3d_wrap.cpp finish.cpp fix.cpp fix_add_force.cpp fix_ave_force.cpp fix_centro.cpp fix_com.cpp fix_drag.cpp fix_efield.cpp fix_energy.cpp fix_enforce2d.cpp fix_gravity.cpp fix_gyration.cpp fix_indent.cpp fix_langevin.cpp fix_line_force.cpp fix_minimize.cpp fix_momentum.cpp fix_msd.cpp fix_nph.cpp fix_npt.cpp fix_nve.cpp fix_nvt.cpp fix_orient_fcc.cpp fix_plane_force.cpp fix_print.cpp fix_rdf.cpp fix_recenter.cpp fix_respa.cpp fix_rigid.cpp fix_set_force.cpp fix_shake.cpp fix_spring.cpp fix_spring_rg.cpp fix_spring_self.cpp fix_stress.cpp fix_temp_rescale.cpp fix_tmd.cpp fix_uniaxial.cpp fix_viscous.cpp fix_volume_rescale.cpp fix_wall_lj93.cpp fix_wall_reflect.cpp fix_wiggle.cpp force.cpp group.cpp improper.cpp improper_cvff.cpp improper_harmonic.cpp improper_hybrid.cpp input.cpp kspace.cpp lammps.cpp library.cpp main.cpp memory.cpp min.cpp min_cg.cpp min_cg_fr.cpp min_sd.cpp minimize.cpp modify.cpp neigh_bond.cpp neigh_full.cpp neigh_gran.cpp neigh_half.cpp neigh_respa.cpp neighbor.cpp output.cpp pack.cpp pair.cpp pair_buck.cpp pair_buck_coul_cut.cpp pair_buck_coul_long.cpp pair_eam.cpp pair_eam_alloy.cpp pair_eam_fs.cpp pair_hybrid.cpp pair_lj_charmm_coul_charmm.cpp pair_lj_charmm_coul_charmm_implicit.cpp pair_lj_charmm_coul_long.cpp pair_lj_cut.cpp pair_lj_cut_coul_cut.cpp pair_lj_cut_coul_debye.cpp pair_lj_cut_coul_long.cpp pair_lj_cut_coul_long_tip4p.cpp pair_lj_expand.cpp pair_lj_smooth.cpp pair_morse.cpp pair_soft.cpp pair_table.cpp pair_yukawa.cpp pppm.cpp pppm_tip4p.cpp pressure.cpp random_mars.cpp random_park.cpp read_data.cpp read_restart.cpp region.cpp region_block.cpp region_cylinder.cpp region_intersect.cpp region_sphere.cpp region_union.cpp remap.cpp remap_wrap.cpp replicate.cpp respa.cpp run.cpp set.cpp shell.cpp special.cpp system.cpp temp_full.cpp temp_partial.cpp temp_ramp.cpp temp_region.cpp temper.cpp temperature.cpp thermo.cpp timer.cpp universe.cpp update.cpp variable.cpp velocity.cpp verlet.cpp write_restart.cpp
+SRC =	angle.cpp angle_charmm.cpp angle_class2.cpp angle_cosine.cpp angle_cosine_squared.cpp angle_harmonic.cpp angle_hybrid.cpp atom.cpp atom_angle.cpp atom_atomic.cpp atom_bond.cpp atom_charge.cpp atom_dpd.cpp atom_full.cpp atom_granular.cpp atom_hybrid.cpp atom_molecular.cpp bond.cpp bond_class2.cpp bond_fene.cpp bond_fene_expand.cpp bond_harmonic.cpp bond_hybrid.cpp bond_morse.cpp bond_nonlinear.cpp bond_quartic.cpp comm.cpp create_atoms.cpp create_box.cpp delete_atoms.cpp delete_bonds.cpp dihedral.cpp dihedral_charmm.cpp dihedral_class2.cpp dihedral_harmonic.cpp dihedral_helix.cpp dihedral_hybrid.cpp dihedral_multi_harmonic.cpp dihedral_opls.cpp displace_atoms.cpp domain.cpp dump.cpp dump_atom.cpp dump_bond.cpp dump_custom.cpp dump_dcd.cpp dump_xyz.cpp error.cpp ewald.cpp fft3d.cpp fft3d_wrap.cpp finish.cpp fix.cpp fix_add_force.cpp fix_ave_force.cpp fix_centro.cpp fix_com.cpp fix_drag.cpp fix_efield.cpp fix_energy.cpp fix_enforce2d.cpp fix_freeze.cpp fix_gran_diag.cpp fix_gravity.cpp fix_gyration.cpp fix_indent.cpp fix_insert.cpp fix_langevin.cpp fix_line_force.cpp fix_minimize.cpp fix_momentum.cpp fix_msd.cpp fix_nph.cpp fix_npt.cpp fix_nve.cpp fix_nve_gran.cpp fix_nvt.cpp fix_orient_fcc.cpp fix_plane_force.cpp fix_print.cpp fix_rdf.cpp fix_recenter.cpp fix_respa.cpp fix_rigid.cpp fix_set_force.cpp fix_shake.cpp fix_shear_history.cpp fix_spring.cpp fix_spring_rg.cpp fix_spring_self.cpp fix_stress.cpp fix_temp_rescale.cpp fix_tmd.cpp fix_uniaxial.cpp fix_viscous.cpp fix_volume_rescale.cpp fix_wall_gran.cpp fix_wall_lj93.cpp fix_wall_reflect.cpp fix_wiggle.cpp force.cpp group.cpp improper.cpp improper_class2.cpp improper_cvff.cpp improper_harmonic.cpp improper_hybrid.cpp input.cpp kspace.cpp lammps.cpp library.cpp main.cpp memory.cpp min.cpp min_cg.cpp min_cg_fr.cpp min_sd.cpp minimize.cpp modify.cpp neigh_bond.cpp neigh_full.cpp neigh_gran.cpp neigh_half.cpp neigh_respa.cpp neighbor.cpp output.cpp pack.cpp pair.cpp pair_buck.cpp pair_buck_coul_cut.cpp pair_buck_coul_long.cpp pair_dpd.cpp pair_eam.cpp pair_eam_alloy.cpp pair_eam_fs.cpp pair_gran_hertzian.cpp pair_gran_history.cpp pair_gran_no_history.cpp pair_hybrid.cpp pair_lj_charmm_coul_charmm.cpp pair_lj_charmm_coul_charmm_implicit.cpp pair_lj_charmm_coul_long.cpp pair_lj_class2.cpp pair_lj_class2_coul_cut.cpp pair_lj_class2_coul_long.cpp pair_lj_cut.cpp pair_lj_cut_coul_cut.cpp pair_lj_cut_coul_debye.cpp pair_lj_cut_coul_long.cpp pair_lj_cut_coul_long_tip4p.cpp pair_lj_cut_fast.cpp pair_lj_expand.cpp pair_lj_smooth.cpp pair_morse.cpp pair_soft.cpp pair_sw.cpp pair_table.cpp pair_tersoff.cpp pair_yukawa.cpp pppm.cpp pppm_tip4p.cpp pressure.cpp random_mars.cpp random_park.cpp read_data.cpp read_restart.cpp region.cpp region_block.cpp region_cylinder.cpp region_intersect.cpp region_prism.cpp region_sphere.cpp region_union.cpp remap.cpp remap_wrap.cpp replicate.cpp respa.cpp run.cpp set.cpp shell.cpp special.cpp system.cpp temp_full.cpp temp_partial.cpp temp_ramp.cpp temp_region.cpp temper.cpp temperature.cpp thermo.cpp timer.cpp universe.cpp update.cpp variable.cpp velocity.cpp verlet.cpp write_restart.cpp
 
-INC =	angle.h angle_charmm.h angle_cosine.h angle_cosine_squared.h angle_harmonic.h angle_hybrid.h atom.h atom_angle.h atom_atomic.h atom_bond.h atom_charge.h atom_full.h atom_hybrid.h atom_molecular.h bond.h bond_fene.h bond_fene_expand.h bond_harmonic.h bond_hybrid.h bond_morse.h bond_nonlinear.h bond_quartic.h comm.h create_atoms.h create_box.h delete_atoms.h delete_bonds.h dihedral.h dihedral_charmm.h dihedral_harmonic.h dihedral_helix.h dihedral_hybrid.h dihedral_multi_harmonic.h dihedral_opls.h displace_atoms.h domain.h dump.h dump_atom.h dump_bond.h dump_custom.h dump_dcd.h dump_xyz.h error.h ewald.h fft3d.h fft3d_wrap.h finish.h fix.h fix_add_force.h fix_ave_force.h fix_centro.h fix_com.h fix_drag.h fix_efield.h fix_energy.h fix_enforce2d.h fix_gravity.h fix_gyration.h fix_indent.h fix_langevin.h fix_line_force.h fix_minimize.h fix_momentum.h fix_msd.h fix_nph.h fix_npt.h fix_nve.h fix_nvt.h fix_orient_fcc.h fix_plane_force.h fix_print.h fix_rdf.h fix_recenter.h fix_respa.h fix_rigid.h fix_set_force.h fix_shake.h fix_shear_history.h fix_spring.h fix_spring_rg.h fix_spring_self.h fix_stress.h fix_temp_rescale.h fix_tmd.h fix_uniaxial.h fix_viscous.h fix_volume_rescale.h fix_wall_lj93.h fix_wall_reflect.h fix_wiggle.h force.h group.h improper.h improper_cvff.h improper_harmonic.h improper_hybrid.h input.h integrate.h kspace.h lammps.h library.h memory.h memory.hold.h min.h min_cg.h min_cg_fr.h min_sd.h minimize.h modify.h neighbor.h output.h pack.h pair.h pair_buck.h pair_buck_coul_cut.h pair_buck_coul_long.h pair_eam.h pair_eam_alloy.h pair_eam_fs.h pair_hybrid.h pair_lj_charmm_coul_charmm.h pair_lj_charmm_coul_charmm_implicit.h pair_lj_charmm_coul_long.h pair_lj_class2_coul_long.h pair_lj_cut.h pair_lj_cut_coul_cut.h pair_lj_cut_coul_debye.h pair_lj_cut_coul_long.h pair_lj_cut_coul_long_tip4p.h pair_lj_expand.h pair_lj_smooth.h pair_morse.h pair_soft.h pair_table.h pair_yukawa.h pppm.h pppm_tip4p.h pressure.h random_mars.h random_park.h read_data.h read_restart.h region.h region_block.h region_cylinder.h region_intersect.h region_sphere.h region_union.h remap.h remap_wrap.h replicate.h respa.h run.h set.h shell.h special.h style.h style_class2.h style_dpd.h style_granular.h style_kspace.h style_manybody.h style_molecule.h style_poems.h style_user.h style_xtc.h system.h temp_full.h temp_partial.h temp_ramp.h temp_region.h temper.h temperature.h thermo.h timer.h universe.h update.h variable.h velocity.h verlet.h write_restart.h
+INC =	angle.h angle_charmm.h angle_class2.h angle_cosine.h angle_cosine_squared.h angle_harmonic.h angle_hybrid.h atom.h atom_angle.h atom_atomic.h atom_bond.h atom_charge.h atom_dpd.h atom_full.h atom_granular.h atom_hybrid.h atom_molecular.h bond.h bond_class2.h bond_fene.h bond_fene_expand.h bond_harmonic.h bond_hybrid.h bond_morse.h bond_nonlinear.h bond_quartic.h comm.h create_atoms.h create_box.h delete_atoms.h delete_bonds.h dihedral.h dihedral_charmm.h dihedral_class2.h dihedral_harmonic.h dihedral_helix.h dihedral_hybrid.h dihedral_multi_harmonic.h dihedral_opls.h displace_atoms.h domain.h dump.h dump_atom.h dump_bond.h dump_custom.h dump_dcd.h dump_xyz.h error.h ewald.h fft3d.h fft3d_wrap.h finish.h fix.h fix_add_force.h fix_ave_force.h fix_centro.h fix_com.h fix_drag.h fix_efield.h fix_energy.h fix_enforce2d.h fix_freeze.h fix_gran_diag.h fix_gravity.h fix_gyration.h fix_indent.h fix_insert.h fix_langevin.h fix_line_force.h fix_minimize.h fix_momentum.h fix_msd.h fix_nph.h fix_npt.h fix_nve.h fix_nve_gran.h fix_nvt.h fix_orient_fcc.h fix_plane_force.h fix_print.h fix_rdf.h fix_recenter.h fix_respa.h fix_rigid.h fix_set_force.h fix_shake.h fix_shear_history.h fix_spring.h fix_spring_rg.h fix_spring_self.h fix_stress.h fix_temp_rescale.h fix_tmd.h fix_uniaxial.h fix_viscous.h fix_volume_rescale.h fix_wall_gran.h fix_wall_lj93.h fix_wall_reflect.h fix_wiggle.h force.h group.h improper.h improper_class2.h improper_cvff.h improper_harmonic.h improper_hybrid.h input.h integrate.h kspace.h lammps.h library.h memory.h memory.hold.h min.h min_cg.h min_cg_fr.h min_sd.h minimize.h modify.h neighbor.h output.h pack.h pair.h pair_buck.h pair_buck_coul_cut.h pair_buck_coul_long.h pair_dpd.h pair_eam.h pair_eam_alloy.h pair_eam_fs.h pair_gran_hertzian.h pair_gran_history.h pair_gran_no_history.h pair_hybrid.h pair_lj_charmm_coul_charmm.h pair_lj_charmm_coul_charmm_implicit.h pair_lj_charmm_coul_long.h pair_lj_class2.h pair_lj_class2_coul_cut.h pair_lj_class2_coul_long.h pair_lj_cut.h pair_lj_cut_coul_cut.h pair_lj_cut_coul_debye.h pair_lj_cut_coul_long.h pair_lj_cut_coul_long_tip4p.h pair_lj_cut_fast.h pair_lj_expand.h pair_lj_smooth.h pair_morse.h pair_soft.h pair_sw.h pair_table.h pair_tersoff.h pair_yukawa.h pppm.h pppm_tip4p.h pressure.h random_mars.h random_park.h read_data.h read_restart.h region.h region_block.h region_cylinder.h region_intersect.h region_prism.h region_sphere.h region_union.h remap.h remap_wrap.h replicate.h respa.h run.h set.h shell.h special.h style.h style_class2.h style_dpd.h style_granular.h style_kspace.h style_manybody.h style_molecule.h style_poems.h style_user.h style_xtc.h system.h temp_full.h temp_partial.h temp_ramp.h temp_region.h temper.h temperature.h thermo.h timer.h universe.h update.h variable.h velocity.h verlet.h write_restart.h
 
 OBJ = 	$(SRC:.cpp=.o)
 

src/dump_custom.cpp

@@ -65,6 +65,8 @@ DumpCustom::DumpCustom(int narg, char **arg) : Dump(narg, arg)
       pack_choice[i] = &DumpCustom::pack_tag;
       vtype[i] = INT;
     } else if (strcmp(arg[iarg],"mol") == 0) {
+      if (atom->molecule == NULL)
+	error->all("Dumping an atom quantity that isn't allocated");
       pack_choice[i] = &DumpCustom::pack_molecule;
       vtype[i] = INT;
     } else if (strcmp(arg[iarg],"type") == 0) {
@@ -125,24 +127,38 @@ DumpCustom::DumpCustom(int narg, char **arg) : Dump(narg, arg)
       pack_choice[i] = &DumpCustom::pack_fz;
       vtype[i] = DOUBLE;
     } else if (strcmp(arg[iarg],"q") == 0) {
+      if (atom->q == NULL)
+	error->all("Dumping an atom quantity that isn't allocated");
       pack_choice[i] = &DumpCustom::pack_q;
       vtype[i] = DOUBLE;
     } else if (strcmp(arg[iarg],"mux") == 0) {
+      if (atom->mu == NULL)
+	error->all("Dumping an atom quantity that isn't allocated");
       pack_choice[i] = &DumpCustom::pack_mux;
       vtype[i] = DOUBLE;
     } else if (strcmp(arg[iarg],"muy") == 0) {
+      if (atom->mu == NULL)
+	error->all("Dumping an atom quantity that isn't allocated");
       pack_choice[i] = &DumpCustom::pack_muy;
       vtype[i] = DOUBLE;
     } else if (strcmp(arg[iarg],"muz") == 0) {
+      if (atom->mu == NULL)
+	error->all("Dumping an atom quantity that isn't allocated");
       pack_choice[i] = &DumpCustom::pack_muz;
       vtype[i] = DOUBLE;
     } else if (strcmp(arg[iarg],"tqx") == 0) {
+      if (atom->torque == NULL)
+	error->all("Dumping an atom quantity that isn't allocated");
       pack_choice[i] = &DumpCustom::pack_tqx;
       vtype[i] = DOUBLE;
     } else if (strcmp(arg[iarg],"tqy") == 0) {
+      if (atom->torque == NULL)
+	error->all("Dumping an atom quantity that isn't allocated");
       pack_choice[i] = &DumpCustom::pack_tqy;
       vtype[i] = DOUBLE;
     } else if (strcmp(arg[iarg],"tqz") == 0) {
+      if (atom->torque == NULL)
+	error->all("Dumping an atom quantity that isn't allocated");
       pack_choice[i] = &DumpCustom::pack_tqz;
       vtype[i] = DOUBLE;
     } else if (strcmp(arg[iarg],"centro") == 0) {

src/fix_nve.h

@@ -27,7 +27,7 @@ class FixNVE : public Fix {
   void initial_integrate_respa(int, int);
   void final_integrate_respa(int);
 
- protected:
+ private:
   double dtv,dtf;
   double *step_respa;
   int mass_require;

src/library.cpp

@@ -93,7 +93,7 @@ void lammps_get_coords(double *coords)
 
 /* ---------------------------------------------------------------------- */
 
-void lammps_put_coords(const double *coords)
+void lammps_put_coords(double *coords)
 {
   int natoms = static_cast<int> (lammps->atom->natoms);
 

src/region.cpp

@@ -21,48 +21,13 @@
 
 Region::Region(int narg, char **arg)
 {
-  // region ID
-
   int n = strlen(arg[0]) + 1;
   id = new char[n];
   strcpy(id,arg[0]);
 
-  // set option defaults
-
-  interior = 1;
-  scaleflag = 1;
-
-  // read style and options from end of input line
-
   n = strlen(arg[1]) + 1;
   style = new char[n];
   strcpy(style,arg[1]);
-
-  if (strcmp(style,"block") == 0) options(narg-8,&arg[8]);
-  else if (strcmp(style,"sphere") == 0) options(narg-6,&arg[6]);
-  else if (strcmp(arg[1],"cylinder") == 0) options(narg-8,&arg[8]);
-  else if (strcmp(style,"prism") == 0) options(narg-11,&arg[11]);
-  else if (strcmp(arg[1],"union") == 0) {
-    if (narg < 5) error->all("Illegal region command");
-    n = atoi(arg[2]);
-    options(narg-(n+3),&arg[n+3]);
-  } else if (strcmp(arg[1],"intersect") == 0) {
-    if (narg < 5) error->all("Illegal region command");
-    n = atoi(arg[2]);
-    options(narg-(n+3),&arg[n+3]);
-  } else error->all("Illegal region command");
-
-  // setup scaling
-
-  if (scaleflag && strcmp(domain->lattice_style,"none") == 0)
-    error->all("Use of region with undefined lattice");
-
-  if (scaleflag) {
-    xscale = domain->xlattice;
-    yscale = domain->ylattice;
-    zscale = domain->zlattice;
-  }
-  else xscale = yscale = zscale = 1.0;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -81,6 +46,11 @@ void Region::options(int narg, char **arg)
 {
   if (narg < 0) error->all("Illegal region command");
 
+  // option defaults
+
+  interior = 1;
+  scaleflag = 1;
+
   int iarg = 0;
   while (iarg < narg) {
     if (strcmp(arg[iarg],"units") == 0) {
@@ -97,4 +67,16 @@ void Region::options(int narg, char **arg)
       iarg += 2;
     } else error->all("Illegal region command");
   }
+
+  // setup scaling
+
+  if (scaleflag && strcmp(domain->lattice_style,"none") == 0)
+    error->all("Use of region with undefined lattice");
+
+  if (scaleflag) {
+    xscale = domain->xlattice;
+    yscale = domain->ylattice;
+    zscale = domain->zlattice;
+  }
+  else xscale = yscale = zscale = 1.0;
 }

src/region.h

@@ -30,7 +30,7 @@ class Region : public LAMMPS {
   virtual ~Region();
   virtual int match(double, double, double) = 0;
 
- private:
+ protected:
   void options(int, char **);
 };
 

src/region_block.cpp

@@ -21,6 +21,8 @@
 
 RegBlock::RegBlock(int narg, char **arg) : Region(narg, arg)
 {
+  options(narg-8,&arg[8]);
+
   if (strcmp(arg[2],"INF") == 0) {
     if (domain->box_exist == 0) 
       error->all("Cannot use region INF when box does not exist");

src/region_cylinder.cpp

@@ -22,6 +22,8 @@
 
 RegCylinder::RegCylinder(int narg, char **arg) : Region(narg, arg)
 {
+  options(narg-8,&arg[8]);
+
   if (strcmp(arg[2],"x") && strcmp(arg[2],"y") && strcmp(arg[2],"z")) 
     error->all("Illegal region cylinder command");
   axis = arg[2][0];

src/region_intersect.cpp

@@ -24,9 +24,13 @@
 
 RegIntersect::RegIntersect(int narg, char **arg) : Region(narg, arg)
 {
+  if (narg < 5) error->all("Illegal region command");
+  int n = atoi(arg[2]);
+  if (n < 2) error->all("Illegal region command");
+  options(narg-(n+3),&arg[n+3]);
+
   // build list of regions to intersect
 
-  int n = atoi(arg[2]);
   list = new int[n];
   nregion = 0;
 

src/region_prism.cpp

@@ -29,6 +29,8 @@
 
 RegPrism::RegPrism(int narg, char **arg) : Region(narg, arg)
 {
+  options(narg-11,&arg[11]);
+
   if (strcmp(arg[2],"INF") == 0) {
     if (domain->box_exist == 0) 
       error->all("Cannot use region INF when box does not exist");

src/region_sphere.cpp

@@ -21,6 +21,8 @@
 
 RegSphere::RegSphere(int narg, char **arg) : Region(narg, arg)
 {
+  options(narg-6,&arg[6]);
+
   xc = xscale*atof(arg[2]);
   yc = yscale*atof(arg[3]);
   zc = zscale*atof(arg[4]);

src/region_union.cpp

@@ -26,9 +26,13 @@
 
 RegUnion::RegUnion(int narg, char **arg) : Region(narg, arg)
 {
+  if (narg < 5) error->all("Illegal region command");
+  int n = atoi(arg[2]);
+  if (n < 2) error->all("Illegal region command");
+  options(narg-(n+3),&arg[n+3]);
+
   // build list of regions to union
 
-  int n = atoi(arg[2]);
   list = new int[n];
   nregion = 0;