Merge branch 'master' into lammps-icms
Resolved Conflicts: doc/Section_commands.html src/displace_box.h
This commit is contained in:
Axel Kohlmeyer
@ -290,7 +290,7 @@ in the command's documentation.
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</P>
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<P><A HREF = "delete_atoms.html">delete_atoms</A>, <A HREF = "delete_bonds.html">delete_bonds</A>,
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<A HREF = "displace_atoms.html">displace_atoms</A>,
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<A HREF = "displace_box.html">displace_box</A>, <A HREF = "minimize.html">minimize</A>,
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<A HREF = "change_box.html">change_box</A>, <A HREF = "minimize.html">minimize</A>,
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<A HREF = "neb.html">neb</A> <A HREF = "prd.html">prd</A>, <A HREF = "run.html">run</A>, <A HREF = "temper.html">temper</A>
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</P>
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<P>Miscellaneous:
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@ -317,17 +317,17 @@ in the command's documentation.
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<TR ALIGN="center"><TD ><A HREF = "angle_coeff.html">angle_coeff</A></TD><TD ><A HREF = "angle_style.html">angle_style</A></TD><TD ><A HREF = "atom_modify.html">atom_modify</A></TD><TD ><A HREF = "atom_style.html">atom_style</A></TD><TD ><A HREF = "bond_coeff.html">bond_coeff</A></TD><TD ><A HREF = "bond_style.html">bond_style</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "boundary.html">boundary</A></TD><TD ><A HREF = "change_box.html">change_box</A></TD><TD ><A HREF = "clear.html">clear</A></TD><TD ><A HREF = "communicate.html">communicate</A></TD><TD ><A HREF = "compute.html">compute</A></TD><TD ><A HREF = "compute_modify.html">compute_modify</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "create_atoms.html">create_atoms</A></TD><TD ><A HREF = "create_box.html">create_box</A></TD><TD ><A HREF = "delete_atoms.html">delete_atoms</A></TD><TD ><A HREF = "delete_bonds.html">delete_bonds</A></TD><TD ><A HREF = "dielectric.html">dielectric</A></TD><TD ><A HREF = "dihedral_coeff.html">dihedral_coeff</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "dihedral_style.html">dihedral_style</A></TD><TD ><A HREF = "dimension.html">dimension</A></TD><TD ><A HREF = "displace_atoms.html">displace_atoms</A></TD><TD ><A HREF = "displace_box.html">displace_box</A></TD><TD ><A HREF = "dump.html">dump</A></TD><TD ><A HREF = "dump_image.html">dump image</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "dump_modify.html">dump_modify</A></TD><TD ><A HREF = "echo.html">echo</A></TD><TD ><A HREF = "fix.html">fix</A></TD><TD ><A HREF = "fix_modify.html">fix_modify</A></TD><TD ><A HREF = "group.html">group</A></TD><TD ><A HREF = "if.html">if</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "improper_coeff.html">improper_coeff</A></TD><TD ><A HREF = "improper_style.html">improper_style</A></TD><TD ><A HREF = "include.html">include</A></TD><TD ><A HREF = "jump.html">jump</A></TD><TD ><A HREF = "kspace_modify.html">kspace_modify</A></TD><TD ><A HREF = "kspace_style.html">kspace_style</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "label.html">label</A></TD><TD ><A HREF = "lattice.html">lattice</A></TD><TD ><A HREF = "loadbalance.html">loadbalance</A></TD><TD ><A HREF = "log.html">log</A></TD><TD ><A HREF = "mass.html">mass</A></TD><TD ><A HREF = "minimize.html">minimize</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "min_modify.html">min_modify</A></TD><TD ><A HREF = "min_style.html">min_style</A></TD><TD ><A HREF = "neb.html">neb</A></TD><TD ><A HREF = "neigh_modify.html">neigh_modify</A></TD><TD ><A HREF = "neighbor.html">neighbor</A></TD><TD ><A HREF = "newton.html">newton</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "next.html">next</A></TD><TD ><A HREF = "package.html">package</A></TD><TD ><A HREF = "pair_coeff.html">pair_coeff</A></TD><TD ><A HREF = "pair_modify.html">pair_modify</A></TD><TD ><A HREF = "pair_style.html">pair_style</A></TD><TD ><A HREF = "pair_write.html">pair_write</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "partition.html">partition</A></TD><TD ><A HREF = "prd.html">prd</A></TD><TD ><A HREF = "print.html">print</A></TD><TD ><A HREF = "processors.html">processors</A></TD><TD ><A HREF = "quit.html">quit</A></TD><TD ><A HREF = "read_data.html">read_data</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "read_restart.html">read_restart</A></TD><TD ><A HREF = "region.html">region</A></TD><TD ><A HREF = "replicate.html">replicate</A></TD><TD ><A HREF = "reset_timestep.html">reset_timestep</A></TD><TD ><A HREF = "restart.html">restart</A></TD><TD ><A HREF = "run.html">run</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "run_style.html">run_style</A></TD><TD ><A HREF = "set.html">set</A></TD><TD ><A HREF = "shell.html">shell</A></TD><TD ><A HREF = "special_bonds.html">special_bonds</A></TD><TD ><A HREF = "suffix.html">suffix</A></TD><TD ><A HREF = "tad.html">tad</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "temper.html">temper</A></TD><TD ><A HREF = "thermo.html">thermo</A></TD><TD ><A HREF = "thermo_modify.html">thermo_modify</A></TD><TD ><A HREF = "thermo_style.html">thermo_style</A></TD><TD ><A HREF = "timestep.html">timestep</A></TD><TD ><A HREF = "uncompute.html">uncompute</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "undump.html">undump</A></TD><TD ><A HREF = "unfix.html">unfix</A></TD><TD ><A HREF = "units.html">units</A></TD><TD ><A HREF = "variable.html">variable</A></TD><TD ><A HREF = "velocity.html">velocity</A></TD><TD ><A HREF = "write_restart.html">write_restart</A>
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<TR ALIGN="center"><TD ><A HREF = "dihedral_style.html">dihedral_style</A></TD><TD ><A HREF = "dimension.html">dimension</A></TD><TD ><A HREF = "displace_atoms.html">displace_atoms</A></TD><TD ><A HREF = "dump.html">dump</A></TD><TD ><A HREF = "dump_image.html">dump image</A></TD><TD ><A HREF = "dump_modify.html">dump_modify</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "echo.html">echo</A></TD><TD ><A HREF = "fix.html">fix</A></TD><TD ><A HREF = "fix_modify.html">fix_modify</A></TD><TD ><A HREF = "group.html">group</A></TD><TD ><A HREF = "if.html">if</A></TD><TD ><A HREF = "improper_coeff.html">improper_coeff</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "improper_style.html">improper_style</A></TD><TD ><A HREF = "include.html">include</A></TD><TD ><A HREF = "jump.html">jump</A></TD><TD ><A HREF = "kspace_modify.html">kspace_modify</A></TD><TD ><A HREF = "kspace_style.html">kspace_style</A></TD><TD ><A HREF = "label.html">label</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "lattice.html">lattice</A></TD><TD ><A HREF = "loadbalance.html">loadbalance</A></TD><TD ><A HREF = "log.html">log</A></TD><TD ><A HREF = "mass.html">mass</A></TD><TD ><A HREF = "minimize.html">minimize</A></TD><TD ><A HREF = "min_modify.html">min_modify</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "min_style.html">min_style</A></TD><TD ><A HREF = "neb.html">neb</A></TD><TD ><A HREF = "neigh_modify.html">neigh_modify</A></TD><TD ><A HREF = "neighbor.html">neighbor</A></TD><TD ><A HREF = "newton.html">newton</A></TD><TD ><A HREF = "next.html">next</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "package.html">package</A></TD><TD ><A HREF = "pair_coeff.html">pair_coeff</A></TD><TD ><A HREF = "pair_modify.html">pair_modify</A></TD><TD ><A HREF = "pair_style.html">pair_style</A></TD><TD ><A HREF = "pair_write.html">pair_write</A></TD><TD ><A HREF = "partition.html">partition</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "prd.html">prd</A></TD><TD ><A HREF = "print.html">print</A></TD><TD ><A HREF = "processors.html">processors</A></TD><TD ><A HREF = "quit.html">quit</A></TD><TD ><A HREF = "read_data.html">read_data</A></TD><TD ><A HREF = "read_restart.html">read_restart</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "region.html">region</A></TD><TD ><A HREF = "replicate.html">replicate</A></TD><TD ><A HREF = "reset_timestep.html">reset_timestep</A></TD><TD ><A HREF = "restart.html">restart</A></TD><TD ><A HREF = "run.html">run</A></TD><TD ><A HREF = "run_style.html">run_style</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "set.html">set</A></TD><TD ><A HREF = "shell.html">shell</A></TD><TD ><A HREF = "special_bonds.html">special_bonds</A></TD><TD ><A HREF = "suffix.html">suffix</A></TD><TD ><A HREF = "tad.html">tad</A></TD><TD ><A HREF = "temper.html">temper</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "thermo.html">thermo</A></TD><TD ><A HREF = "thermo_modify.html">thermo_modify</A></TD><TD ><A HREF = "thermo_style.html">thermo_style</A></TD><TD ><A HREF = "timestep.html">timestep</A></TD><TD ><A HREF = "uncompute.html">uncompute</A></TD><TD ><A HREF = "undump.html">undump</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "unfix.html">unfix</A></TD><TD ><A HREF = "units.html">units</A></TD><TD ><A HREF = "variable.html">variable</A></TD><TD ><A HREF = "velocity.html">velocity</A></TD><TD ><A HREF = "write_restart.html">write_restart</A>
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</TD></TR></TABLE></DIV>
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<HR>
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@ -453,40 +453,40 @@ built with the <A HREF = "Section_accelerate.html">appropriate accelerated
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package</A>.
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</P>
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR ALIGN="center"><TD ><A HREF = "pair_adp.html">adp/omp</A></TD><TD ><A HREF = "pair_airebo.html">airebo/omp</A></TD><TD ><A HREF = "pair_born.html">born/coul/long/cuda</A></TD><TD ><A HREF = "pair_born.html">born/coul/long/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_born.html">born/coul/wolf/omp</A></TD><TD ><A HREF = "pair_born.html">born/omp</A></TD><TD ><A HREF = "pair_brownian.html">brownian/omp</A></TD><TD ><A HREF = "pair_brownian.html">brownian/poly/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/coul/cut/cuda</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/cut/gpu</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/cut/omp</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long/cuda</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/coul/long/gpu</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long/omp</A></TD><TD ><A HREF = "pair_buck_coul.html">buck/coul/omp</A></TD><TD ><A HREF = "pair_buck.html">buck/cuda</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/gpu</A></TD><TD ><A HREF = "pair_buck.html">buck/omp</A></TD><TD ><A HREF = "pair_colloid.html">colloid/omp</A></TD><TD ><A HREF = "pair_comb.html">comb/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/cut/omp</A></TD><TD ><A HREF = "pair_coul.html">coul/debye/omp</A></TD><TD ><A HREF = "pair_coul.html">coul/long/gpu</A></TD><TD ><A HREF = "pair_coul.html">coul/long/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/wolf</A></TD><TD ><A HREF = "pair_dipole.html">dipole/cut/omp</A></TD><TD ><A HREF = "pair_dipole.html">dipole/sf/omp</A></TD><TD ><A HREF = "pair_dpd.html">dpd/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_dpd.html">dpd/tstat/omp</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/cuda</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/gpu</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/omp</A></TD></TR>
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||||
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/alloy/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/cd/omp</A></TD><TD ><A HREF = "pair_eam.html">eam/cuda</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/cuda</A></TD></TR>
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||||
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/fs/gpu</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/omp</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/gpu</A></TD></TR>
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||||
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/omp</A></TD><TD ><A HREF = "pair_eam.html">eam/opt</A></TD><TD ><A HREF = "pair_edip.html">edip/omp</A></TD><TD ><A HREF = "pair_eim.html">eim/omp</A></TD></TR>
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||||
<TR ALIGN="center"><TD ><A HREF = "pair_gauss.html">gauss/omp</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne/gpu</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne/omp</A></TD><TD ><A HREF = "pair_gran.html">gran/hertz/history/omp</A></TD></TR>
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||||
<TR ALIGN="center"><TD ><A HREF = "pair_gran.html">gran/hooke/cuda</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/history/omp</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/omp</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/lj/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/morse/omp</A></TD><TD ><A HREF = "pair_line_lj.html">line/lj/omp</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/cuda</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit/cuda</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit/omp</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/cuda</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/gpu</A></TD></TR>
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||||
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/omp</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/opt</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/pppm/omp</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut/cuda</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut/omp</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/cuda</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/gpu</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/pppm/omp</A></TD></TR>
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||||
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/omp</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/cuda</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/gpu</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/omp</A></TD></TR>
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||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj_coul.html">lj/coul/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/omp</A></TD></TR>
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||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/gpu</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/opt</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p/opt</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/pppm/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/pppm/tip4p/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/experimental/cuda</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/cuda</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj_expand.html">lj/expand/gpu</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/omp</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs/cuda</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs/cuda</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/omp</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/gpu</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/long/gpu</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/long/omp</A></TD><TD ><A HREF = "pair_lj_sf.html">lj/sf/omp</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth/cuda</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj_smooth.html">lj/smooth/omp</A></TD><TD ><A HREF = "pair_lj_smooth_linear.html">lj/smooth/linear/omp</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut/cuda</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut/gpu</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj96.html">lj96/cut/omp</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate/omp</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate/poly/omp</A></TD><TD ><A HREF = "pair_morse.html">morse/cuda</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_morse.html">morse/gpu</A></TD><TD ><A HREF = "pair_morse.html">morse/omp</A></TD><TD ><A HREF = "pair_morse.html">morse/opt</A></TD><TD ><A HREF = "pair_peri.html">peri/lps/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_peri.html">peri/pmb/omp</A></TD><TD ><A HREF = "pair_airebo.html">rebo/omp</A></TD><TD ><A HREF = "pair_resquared.html">resquared/gpu</A></TD><TD ><A HREF = "pair_resquared.html">resquared/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_soft.html">soft/omp</A></TD><TD ><A HREF = "pair_sw.html">sw/cuda</A></TD><TD ><A HREF = "pair_sw.html">sw/omp</A></TD><TD ><A HREF = "pair_table.html">table/gpu</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_table.html">table/omp</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/cuda</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/omp</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/table/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl/omp</A></TD><TD ><A HREF = "pair_tri_lj.html">tri/lj/omp</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa/gpu</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid/omp</A>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_adp.html">adp/omp</A></TD><TD ><A HREF = "pair_airebo.html">airebo/omp</A></TD><TD ><A HREF = "pair_beck.html">beck/omp</A></TD><TD ><A HREF = "pair_born.html">born/coul/long/cuda</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_born.html">born/coul/long/omp</A></TD><TD ><A HREF = "pair_born.html">born/coul/wolf/omp</A></TD><TD ><A HREF = "pair_born.html">born/omp</A></TD><TD ><A HREF = "pair_brownian.html">brownian/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_brownian.html">brownian/poly/omp</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/cut/cuda</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/cut/gpu</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/cut/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/coul/long/cuda</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long/gpu</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long/omp</A></TD><TD ><A HREF = "pair_buck_coul.html">buck/coul/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/cuda</A></TD><TD ><A HREF = "pair_buck.html">buck/gpu</A></TD><TD ><A HREF = "pair_buck.html">buck/omp</A></TD><TD ><A HREF = "pair_colloid.html">colloid/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_comb.html">comb/omp</A></TD><TD ><A HREF = "pair_coul.html">coul/cut/omp</A></TD><TD ><A HREF = "pair_coul.html">coul/debye/omp</A></TD><TD ><A HREF = "pair_coul.html">coul/long/gpu</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/long/omp</A></TD><TD ><A HREF = "pair_coul.html">coul/wolf</A></TD><TD ><A HREF = "pair_dipole.html">dipole/cut/omp</A></TD><TD ><A HREF = "pair_dipole.html">dipole/sf/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_dpd.html">dpd/omp</A></TD><TD ><A HREF = "pair_dpd.html">dpd/tstat/omp</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/cuda</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/gpu</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/alloy/omp</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/cd/omp</A></TD><TD ><A HREF = "pair_eam.html">eam/cuda</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/fs/cuda</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/gpu</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/omp</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/opt</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/gpu</A></TD><TD ><A HREF = "pair_eam.html">eam/omp</A></TD><TD ><A HREF = "pair_eam.html">eam/opt</A></TD><TD ><A HREF = "pair_edip.html">edip/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_eim.html">eim/omp</A></TD><TD ><A HREF = "pair_gauss.html">gauss/omp</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne/gpu</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_gran.html">gran/hertz/history/omp</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/cuda</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/history/omp</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/lj/omp</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/morse/omp</A></TD><TD ><A HREF = "pair_line_lj.html">line/lj/omp</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/cuda</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/omp</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit/cuda</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit/omp</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/cuda</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/gpu</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/omp</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/opt</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/pppm/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut/cuda</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut/omp</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/cuda</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/gpu</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/pppm/omp</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/omp</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/cuda</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/gpu</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/omp</A></TD><TD ><A HREF = "pair_lj_coul.html">lj/coul/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/gpu</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/cuda</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/opt</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p/opt</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/pppm/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/pppm/tip4p/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/cuda</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/experimental/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj_expand.html">lj/expand/cuda</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/gpu</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/omp</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs/cuda</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs/omp</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/cuda</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/omp</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/gpu</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_sdk.html">lj/sdk/omp</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/long/gpu</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/long/omp</A></TD><TD ><A HREF = "pair_lj_sf.html">lj/sf/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj_smooth.html">lj/smooth/cuda</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth/omp</A></TD><TD ><A HREF = "pair_lj_smooth_linear.html">lj/smooth/linear/omp</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut/cuda</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj96.html">lj96/cut/gpu</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut/omp</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate/omp</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate/poly/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_meam_spline.html">meam/spline/omp</A></TD><TD ><A HREF = "pair_morse.html">morse/cuda</A></TD><TD ><A HREF = "pair_morse.html">morse/gpu</A></TD><TD ><A HREF = "pair_morse.html">morse/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_morse.html">morse/opt</A></TD><TD ><A HREF = "pair_peri.html">peri/lps/omp</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb/omp</A></TD><TD ><A HREF = "pair_airebo.html">rebo/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_resquared.html">resquared/gpu</A></TD><TD ><A HREF = "pair_resquared.html">resquared/omp</A></TD><TD ><A HREF = "pair_soft.html">soft/omp</A></TD><TD ><A HREF = "pair_sw.html">sw/cuda</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_sw.html">sw/omp</A></TD><TD ><A HREF = "pair_table.html">table/gpu</A></TD><TD ><A HREF = "pair_table.html">table/omp</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/cuda</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_tersoff.html">tersoff/omp</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/table/omp</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl/omp</A></TD><TD ><A HREF = "pair_tri_lj.html">tri/lj/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_yukawa.html">yukawa/gpu</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa/omp</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid/omp</A>
|
||||
</TD></TR></TABLE></DIV>
|
||||
|
||||
<HR>
|
||||
|
||||
@ -286,7 +286,7 @@ Actions:
|
||||
|
||||
"delete_atoms"_delete_atoms.html, "delete_bonds"_delete_bonds.html,
|
||||
"displace_atoms"_displace_atoms.html,
|
||||
"displace_box"_displace_box.html, "minimize"_minimize.html,
|
||||
"change_box"_change_box.html, "minimize"_minimize.html,
|
||||
"neb"_neb.html "prd"_prd.html, "run"_run.html, "temper"_temper.html
|
||||
|
||||
Miscellaneous:
|
||||
@ -330,7 +330,6 @@ in the command's documentation.
|
||||
"dihedral_style"_dihedral_style.html,
|
||||
"dimension"_dimension.html,
|
||||
"displace_atoms"_displace_atoms.html,
|
||||
"displace_box"_displace_box.html,
|
||||
"dump"_dump.html,
|
||||
"dump image"_dump_image.html,
|
||||
"dump_modify"_dump_modify.html,
|
||||
|
||||
@ -1660,8 +1660,8 @@ derivative w.r.t. e_i, it follows that C_ij is also symmetric, with at
|
||||
most 7*6/2 = 21 distinct elements.
|
||||
</P>
|
||||
<P>At zero temperature, it is easy to estimate these derivatives by
|
||||
deforming the cell in one of the six directions using the command
|
||||
<A HREF = "displace_box.html">displace_box</A> and measuring the change in the
|
||||
deforming the simulation box in one of the six directions using the
|
||||
<A HREF = "change_box.html">change_box</A> command and measuring the change in the
|
||||
stress tensor. A general-purpose script that does this is given in the
|
||||
examples/elastic directory described in <A HREF = "Section_example.html">this
|
||||
section</A>.
|
||||
|
||||
@ -1647,8 +1647,8 @@ derivative w.r.t. e_i, it follows that C_ij is also symmetric, with at
|
||||
most 7*6/2 = 21 distinct elements.
|
||||
|
||||
At zero temperature, it is easy to estimate these derivatives by
|
||||
deforming the cell in one of the six directions using the command
|
||||
"displace_box"_displace_box.html and measuring the change in the
|
||||
deforming the simulation box in one of the six directions using the
|
||||
"change_box"_change_box.html command and measuring the change in the
|
||||
stress tensor. A general-purpose script that does this is given in the
|
||||
examples/elastic directory described in "this
|
||||
section"_Section_example.html.
|
||||
|
||||
@ -77,7 +77,10 @@ triclinic representations.
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>This command cannot be used after the simulation box is defined by a
|
||||
<A HREF = "read_data.html">read_data</A> or <A HREF = "create_box.html">create_box</A> command.
|
||||
<A HREF = "read_data.html">read_data</A> or <A HREF = "create_box.html">create_box</A> command or
|
||||
<A HREF = "read_restart.html">read_restart</A> command. See the
|
||||
<A HREF = "change_box.html">change_box</A> command for how to change the simulation
|
||||
box boundaries after it has been defined.
|
||||
</P>
|
||||
<P>For 2d simulations, the z dimension must be periodic.
|
||||
</P>
|
||||
|
||||
@ -72,7 +72,10 @@ triclinic representations.
|
||||
[Restrictions:]
|
||||
|
||||
This command cannot be used after the simulation box is defined by a
|
||||
"read_data"_read_data.html or "create_box"_create_box.html command.
|
||||
"read_data"_read_data.html or "create_box"_create_box.html command or
|
||||
"read_restart"_read_restart.html command. See the
|
||||
"change_box"_change_box.html command for how to change the simulation
|
||||
box boundaries after it has been defined.
|
||||
|
||||
For 2d simulations, the z dimension must be periodic.
|
||||
|
||||
|
||||
@ -13,51 +13,298 @@
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>change_box style
|
||||
<PRE>change_box group-ID parameter args ... keyword args ...
|
||||
</PRE>
|
||||
<LI>style = <I>ortho</I> or <I>triclinic</I>
|
||||
<UL><LI>group-ID = ID of group of atoms to (optionally) displace
|
||||
|
||||
<PRE> <I>ortho</I> = convert simulation box from non-orthogonal (triclinic) to orthogonal
|
||||
<I>triclinic</I> = convert simulation box from orthogonal to non-orthogonal (triclinic)
|
||||
<LI>one or more parameter/arg pairs may be appended
|
||||
|
||||
<PRE>parameter = <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>xz</I> or <I>yz</I> or <I>boundary</I> or <I>ortho</I> or <I>triclinic</I> or <I>set</I> or <I>remap</I>
|
||||
<I>x</I>, <I>y</I>, <I>z</I> args = style value(s)
|
||||
style = <I>final</I> or <I>delta</I> or <I>scale</I> or <I>volume</I>
|
||||
<I>final</I> values = lo hi
|
||||
lo hi = box boundaries after displacement (distance units)
|
||||
<I>delta</I> values = dlo dhi
|
||||
dlo dhi = change in box boundaries after displacement (distance units)
|
||||
<I>scale</I> values = factor
|
||||
factor = multiplicative factor for change in box length after displacement
|
||||
<I>volume</I> value = none = adjust this dim to preserve volume of system
|
||||
<I>xy</I>, <I>xz</I>, <I>yz</I> args = style value
|
||||
style = <I>final</I> or <I>delta</I>
|
||||
<I>final</I> value = tilt
|
||||
tilt = tilt factor after displacement (distance units)
|
||||
<I>delta</I> value = dtilt
|
||||
dtilt = change in tilt factor after displacement (distance units)
|
||||
<I>boundary</I> args = x y z
|
||||
x,y,z = <I>p</I> or <I>s</I> or <I>f</I> or <I>m</I>, one or two letters
|
||||
<I>p</I> is periodic
|
||||
<I>f</I> is non-periodic and fixed
|
||||
<I>s</I> is non-periodic and shrink-wrapped
|
||||
<I>m</I> is non-periodic and shrink-wrapped with a minimum value
|
||||
<I>ortho</I> args = none = change box to orthogonal
|
||||
(triclinic</I> args = none = change box to triclinic
|
||||
<I>set</I> args = none = store state of current box
|
||||
<I>remap</I> args = none = remap atom coords from last saved state to current box
|
||||
</PRE>
|
||||
<LI>zero or more keyword/value pairs may be appended
|
||||
|
||||
<LI>keyword = <I>units</I>
|
||||
|
||||
<PRE> <I>units</I> value = <I>lattice</I> or <I>box</I>
|
||||
lattice = distances are defined in lattice units
|
||||
box = distances are defined in simulation box units
|
||||
</PRE>
|
||||
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>change_box ortho
|
||||
change_box triclinic
|
||||
<PRE>change_box all xy final -2.0 z final 0.0 5.0 boundary p p f remap units box
|
||||
change_box all x scale 1.1 y volume z volume remap
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>By default LAMMPS runs a simulation in an orthogonal, axis-aligned
|
||||
simulation box. LAMMPS can also run simulations in <A HREF = "Section_howto.html#howto_12">non-orthogonal
|
||||
(triclinic) simulation boxes</A>. A box is
|
||||
defined as either orthogonal or non-orthogonal when it is created via
|
||||
the <A HREF = "create_box.html">create_box</A>, <A HREF = "read_data.html">read_data</A>, or
|
||||
<A HREF = "read_restart.html">read_restart</A> commands.
|
||||
<P>Change the volume and/or shape and/or boundary conditions for the
|
||||
simulation box. Orthogonal simulation boxes have 3 adjustable size
|
||||
parameters (x,y,z). Triclinic (non-orthogonal) simulation boxes have
|
||||
6 adjustable size/shape parameters (x,y,z,xy,xz,yz). Any or all of
|
||||
them can be adjusted independently by this command. Thus it can be
|
||||
used to expand or contract a box, or to apply a shear strain to a
|
||||
non-orthogonal box. It can also be used to change the boundary
|
||||
conditions for the simulation box, similar to the
|
||||
<A HREF = "boundary.html">boundary</A> command.
|
||||
</P>
|
||||
<P>This command allows you to toggle the existing simulation box from
|
||||
orthogonal to non-orthogonal and vice versa. For example, an initial
|
||||
<P>The size and shape of the initial simulation box are specified by the
|
||||
<A HREF = "create_box.html">create_box</A> or <A HREF = "read_data.html">read_data</A> or
|
||||
<A HREF = "read_restart.html">read_restart</A> command used to setup the simulation.
|
||||
The size and shape may be altered by subsequent runs, e.g. by use of
|
||||
the <A HREF = "fix_nh.html">fix npt</A> or <A HREF = "fix_deform.html">fix deform</A> commands.
|
||||
The <A HREF = "create_box.html">create_box</A>, <A HREF = "read_data.html">read data</A>, and
|
||||
<A HREF = "read_restart.html">read_restart</A> commands also determine whether the
|
||||
simulation box is orthogonal or triclinic and their doc pages explain
|
||||
the meaning of the xy,xz,yz tilt factors.
|
||||
</P>
|
||||
<P>See <A HREF = "Section_howto.html#howto_12">Section_howto 12</A> of the doc pages
|
||||
for a geometric description of triclinic boxes, as defined by LAMMPS,
|
||||
and how to transform these parameters to and from other commonly used
|
||||
triclinic representations.
|
||||
</P>
|
||||
<P>The keywords used in this command are applied sequentially to the
|
||||
simulation box and the atoms in it, in the order specified.
|
||||
</P>
|
||||
<P>Before the sequence of keywords are invoked, the current box
|
||||
size/shape are stored, in case a <I>remap</I> keyword is used to map the
|
||||
atom coordinates from the previous box size/shape to the current one.
|
||||
</P>
|
||||
<P>After all the keywords have been processed, any shrink-wrap boundary
|
||||
conditions are invoked (see the <A HREF = "boundary.html">boundary</A> command)
|
||||
which may change simulation box boundaries, and atoms are migrated to
|
||||
new owning processors.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: It is possible to lose atoms with this command.
|
||||
E.g. by changing the box without remapping the atoms, and having atoms
|
||||
end up outside of non-periodic boundaries. It is also possible when
|
||||
remapping atoms to put them (nearly) on top of each other which will
|
||||
lead to bad dynamics. E.g. by converting a boundary from non-periodic
|
||||
to periodic.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: The simulation box size/shape can be changed by
|
||||
arbitrarily large amounts by this command. This is not a problem,
|
||||
except that the mapping of processors to the simulation box is not
|
||||
changed from its initial 3d configuration; see the
|
||||
<A HREF = "processors.html">processors</A> command. Thus, if the box size/shape
|
||||
changes dramatically, the mapping of processors to the simulation box
|
||||
may not end up as optimal as the initial mapping attempted to be.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>For the <I>x</I>, <I>y</I>, and <I>z</I> parameters, this is the meaning of their
|
||||
styles and values.
|
||||
</P>
|
||||
<P>For style <I>final</I>, the final lo and hi box boundaries of a dimension
|
||||
are specified. The values can be in lattice or box distance units.
|
||||
See the discussion of the units keyword below.
|
||||
</P>
|
||||
<P>For style <I>delta</I>, plus or minus changes in the lo/hi box boundaries
|
||||
of a dimension are specified. The values can be in lattice or box
|
||||
distance units. See the discussion of the units keyword below.
|
||||
</P>
|
||||
<P>For style <I>scale</I>, a multiplicative factor to apply to the box length
|
||||
of a dimension is specified. For example, if the initial box length
|
||||
is 10, and the factor is 1.1, then the final box length will be 11. A
|
||||
factor less than 1.0 means compression.
|
||||
</P>
|
||||
<P>The <I>volume</I> style changes the specified dimension in such a way that
|
||||
the overall box volume remains constant with respect to the operation
|
||||
performed by the preceding keyword. The <I>volume</I> style can only be
|
||||
used following a keyword that changed the volume, which is any of the
|
||||
<I>x</I>, <I>y</I>, <I>z</I> keywords. If the preceding keyword "key" had a <I>volume</I>
|
||||
style, then both it and the current keyword apply to the keyword
|
||||
preceding "key". I.e. this sequence of keywords is allowed:
|
||||
</P>
|
||||
<PRE>change_box all x scale 1.1 y volume z volume
|
||||
</PRE>
|
||||
<P>The <I>volume</I> style changes the associated dimension so that the
|
||||
overall box volume is unchanged relative to its value before the
|
||||
preceding keyword was invoked.
|
||||
</P>
|
||||
<P>If the following command is used, then the z box length will shrink by
|
||||
the same 1.1 factor the x box length was increased by:
|
||||
</P>
|
||||
<PRE>change_box all x scale 1.1 z volume
|
||||
</PRE>
|
||||
<P>If the following command is used, then the y,z box lengths will each
|
||||
shrink by sqrt(1.1) to keep the volume constant. In this case, the
|
||||
y,z box lengths shrink so as to keep their relative aspect ratio
|
||||
constant:
|
||||
</P>
|
||||
<PRE>change_box all"x scale 1.1 y volume z volume
|
||||
</PRE>
|
||||
<P>If the following command is used, then the final box will be a factor
|
||||
of 10% larger in x and y, and a factor of 21% smaller in z, so as to
|
||||
keep the volume constant:
|
||||
</P>
|
||||
<PRE>change_box all x scale 1.1 z volume y scale 1.1 z volume
|
||||
</PRE>
|
||||
<P>IMPORTANT NOTE: For solids or liquids, when one dimension of the box
|
||||
is expanded, it may be physically undesirable to hold the other 2 box
|
||||
lengths constant since that implies a density change. For solids,
|
||||
adjusting the other dimensions via the <I>volume</I> style may make
|
||||
physical sense (just as for a liquid), but may not be correct for
|
||||
materials and potentials whose Poisson ratio is not 0.5.
|
||||
</P>
|
||||
<P>For the <I>scale</I> and <I>volume</I> styles, the box length is expanded or
|
||||
compressed around its mid point.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>For the <I>xy</I>, <I>xz</I>, and <I>yz</I> parameters, this is the meaning of their
|
||||
styles and values. Note that changing the tilt factors of a triclinic
|
||||
box does not change its volume.
|
||||
</P>
|
||||
<P>For style <I>final</I>, the final tilt factor is specified. The value
|
||||
can be in lattice or box distance units. See the discussion of the
|
||||
units keyword below.
|
||||
</P>
|
||||
<P>For style <I>delta</I>, a plus or minus change in the tilt factor is
|
||||
specified. The value can be in lattice or box distance units. See
|
||||
the discussion of the units keyword below.
|
||||
</P>
|
||||
<P>All of these styles change the xy, xz, yz tilt factors. In LAMMPS,
|
||||
tilt factors (xy,xz,yz) for triclinic boxes are required to be no more
|
||||
than half the distance of the parallel box length. For example, if
|
||||
xlo = 2 and xhi = 12, then the x box length is 10 and the xy tilt
|
||||
factor must be between -5 and 5. Similarly, both xz and yz must be
|
||||
between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a
|
||||
limitation, since if the maximum tilt factor is 5 (as in this
|
||||
example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
|
||||
... are all equivalent. Any tilt factor specified by this command
|
||||
must be within these limits.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The <I>boundary</I> keyword takes arguments that have exactly the same
|
||||
meaning as they do for the <A HREF = "boundary.html">boundary</A> command. In each
|
||||
dimension, a single letter assigns the same style to both the lower
|
||||
and upper face of the box. Two letters assigns the first style to the
|
||||
lower face and the second style to the upper face.
|
||||
</P>
|
||||
<P>The style <I>p</I> means the box is periodic; the other styles mean
|
||||
non-periodic. For style <I>f</I>, the position of the face is fixed. For
|
||||
style <I>s</I>, the position of the face is set so as to encompass the
|
||||
atoms in that dimension (shrink-wrapping), no matter how far they
|
||||
move. For style <I>m</I>, shrink-wrapping occurs, but is bounded by the
|
||||
current box edge in that dimension, so that the box will become no
|
||||
smaller. See the <A HREF = "boundary.html">boundary</A> command for more
|
||||
explanation of these style options.
|
||||
</P>
|
||||
<P>Note that the "boundary" command itself can only be used before the
|
||||
simulation box is defined via a <A HREF = "read_data.html">read_data</A> or
|
||||
<A HREF = "create_box.html">create_box</A> or <A HREF = "read_restart.html">read_restart</A>
|
||||
command. This command allows the boundary conditions to be changed
|
||||
later in your input script. Also note that the
|
||||
<A HREF = "read_restart.html">read_restart</A> will change boundary conditions to
|
||||
match what is stored in the restart file. So if you wish to change
|
||||
them, you should use the change_box command after the read_restart
|
||||
command.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The <I>ortho</I> and <I>triclinic</I> keywords convert the simulation box to be
|
||||
orthogonal or triclinic (non-orthongonal). See <A HREF = "Section_howto#howto_13">this
|
||||
section</A> for a discussion of how non-orthongal
|
||||
boxes are represented in LAMMPS.
|
||||
</P>
|
||||
<P>The simulation box is defined as either orthogonal or triclinic when
|
||||
it is created via the <A HREF = "create_box.html">create_box</A>,
|
||||
<A HREF = "read_data.html">read_data</A>, or <A HREF = "read_restart.html">read_restart</A>
|
||||
commands.
|
||||
</P>
|
||||
<P>These keywords allow you to toggle the existing simulation box from
|
||||
orthogonal to triclinic and vice versa. For example, an initial
|
||||
equilibration simulation can be run in an orthogonal box, the box can
|
||||
be toggled to non-orthogonal, and then a <A HREF = "Section_howto.html#howto_13">non-equilibrium MD (NEMD)
|
||||
be toggled to triclinic, and then a <A HREF = "Section_howto.html#howto_13">non-equilibrium MD (NEMD)
|
||||
simulation</A> can be run with deformation
|
||||
via the <A HREF = "fix_deform.html">fix deform</A> command.
|
||||
</P>
|
||||
<P>Note that if the simulation box is currently non-orthogonal and has
|
||||
non-zero tilt in xy, yz, or xz, then it cannot be converted to an
|
||||
orthogonal box.
|
||||
<P>If the simulation box is currently triclinic and has non-zero tilt in
|
||||
xy, yz, or xz, then it cannot be converted to an orthogonal box.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The <I>set</I> keyword saves the current box size/shape. This can be
|
||||
useful if you wish to use the <I>remap</I> keyword more than once or if you
|
||||
wish it to be applied to an intermediate box size/shape in a sequence
|
||||
of keyword operations. Note that the box size/shape is saved before
|
||||
any of the keywords are processed, i.e. the box size/shape at the time
|
||||
the create_box command is encountered in the input script.
|
||||
</P>
|
||||
<P>The <I>remap</I> keyword remaps atom coordinates from the last saved box
|
||||
size/shape to the current box state. For example, if you stretch the
|
||||
box in the x dimension or tilt it in the xy plane via the <I>x</I> and <I>xy</I>
|
||||
keywords, then the <I>remap</I> commmand will dilate or tilt the atoms to
|
||||
conform to the new box size/shape, as if the atoms moved with the box
|
||||
as it deformed.
|
||||
</P>
|
||||
<P>Note that this operation is performed without regard to periodic
|
||||
boundaries. Any shrink-wrapping of non-periodic boundaries (see the
|
||||
<A HREF = "boundary.html">boundary</A> command occurs after all keywords, including
|
||||
this one, have been processed.
|
||||
</P>
|
||||
<P>Only atoms in the specified group are remapped.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: If you do not explicitly specify the <I>remap</I> keyword,
|
||||
atom coordinates will not be changed even though the box size/shape
|
||||
changes. This may be the behavior you desire, but can also cause
|
||||
atoms to be lost.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The <I>units</I> keyword determines the meaning of the distance units used
|
||||
to define various arguments. A <I>box</I> value selects standard distance
|
||||
units as defined by the <A HREF = "units.html">units</A> command, e.g. Angstroms for
|
||||
units = real or metal. A <I>lattice</I> value means the distance units are
|
||||
in lattice spacings. The <A HREF = "lattice.html">lattice</A> command must have
|
||||
been previously used to define the lattice spacing.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>At the point in the input script when this command is issued, no
|
||||
<A HREF = "dump.html">dumps</A> can be active, nor can a <A HREF = "fix_ave_spatial.html">fix
|
||||
ave/spatial</A> or <A HREF = "fix_deform.html">fix deform</A> be
|
||||
active. This is because these commands test whether the simulation
|
||||
box is orthogonal when they are first issued. Note that these
|
||||
commands can appear in your script before a change_box command is
|
||||
issued, so long as an <A HREF = "undump.html">undump</A> or <A HREF = "unfix.html">unfix</A>
|
||||
command is also used to turn them off.
|
||||
<P>If you use the <I>ortho</I> or <I>triclinic</I> keywords, then at the point in
|
||||
the input script when this command is issued, no <A HREF = "dump.html">dumps</A> can
|
||||
be active, nor can a <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> or <A HREF = "fix_deform.html">fix
|
||||
deform</A> be active. This is because these commands
|
||||
test whether the simulation box is orthogonal when they are first
|
||||
issued. Note that these commands can be used in your script before a
|
||||
change_box command is issued, so long as an <A HREF = "undump.html">undump</A> or
|
||||
<A HREF = "unfix.html">unfix</A> command is also used to turn them off.
|
||||
</P>
|
||||
<P><B>Related commands:</B> none
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
<P><A HREF = "fix_deform.html">fix deform</A>, <A HREF = "boundary.html">boundary</A>
|
||||
</P>
|
||||
<P><B>Default:</B>
|
||||
</P>
|
||||
<P>The option default is units = lattice.
|
||||
</P>
|
||||
</HTML>
|
||||
|
||||
@ -10,48 +10,291 @@ change_box command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
change_box style :pre
|
||||
change_box group-ID parameter args ... keyword args ... :pre
|
||||
|
||||
style = {ortho} or {triclinic} :l
|
||||
{ortho} = convert simulation box from non-orthogonal (triclinic) to orthogonal
|
||||
{triclinic} = convert simulation box from orthogonal to non-orthogonal (triclinic) :pre
|
||||
group-ID = ID of group of atoms to (optionally) displace :ulb,l
|
||||
one or more parameter/arg pairs may be appended :l
|
||||
parameter = {x} or {y} or {z} or {xy} or {xz} or {yz} or {boundary} or {ortho} or {triclinic} or {set} or {remap}
|
||||
{x}, {y}, {z} args = style value(s)
|
||||
style = {final} or {delta} or {scale} or {volume}
|
||||
{final} values = lo hi
|
||||
lo hi = box boundaries after displacement (distance units)
|
||||
{delta} values = dlo dhi
|
||||
dlo dhi = change in box boundaries after displacement (distance units)
|
||||
{scale} values = factor
|
||||
factor = multiplicative factor for change in box length after displacement
|
||||
{volume} value = none = adjust this dim to preserve volume of system
|
||||
{xy}, {xz}, {yz} args = style value
|
||||
style = {final} or {delta}
|
||||
{final} value = tilt
|
||||
tilt = tilt factor after displacement (distance units)
|
||||
{delta} value = dtilt
|
||||
dtilt = change in tilt factor after displacement (distance units)
|
||||
{boundary} args = x y z
|
||||
x,y,z = {p} or {s} or {f} or {m}, one or two letters
|
||||
{p} is periodic
|
||||
{f} is non-periodic and fixed
|
||||
{s} is non-periodic and shrink-wrapped
|
||||
{m} is non-periodic and shrink-wrapped with a minimum value
|
||||
{ortho} args = none = change box to orthogonal
|
||||
(triclinic} args = none = change box to triclinic
|
||||
{set} args = none = store state of current box
|
||||
{remap} args = none = remap atom coords from last saved state to current box :pre
|
||||
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {units} :l
|
||||
{units} value = {lattice} or {box}
|
||||
lattice = distances are defined in lattice units
|
||||
box = distances are defined in simulation box units :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
change_box ortho
|
||||
change_box triclinic :pre
|
||||
change_box all xy final -2.0 z final 0.0 5.0 boundary p p f remap units box
|
||||
change_box all x scale 1.1 y volume z volume remap :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
By default LAMMPS runs a simulation in an orthogonal, axis-aligned
|
||||
simulation box. LAMMPS can also run simulations in "non-orthogonal
|
||||
(triclinic) simulation boxes"_Section_howto.html#howto_12. A box is
|
||||
defined as either orthogonal or non-orthogonal when it is created via
|
||||
the "create_box"_create_box.html, "read_data"_read_data.html, or
|
||||
"read_restart"_read_restart.html commands.
|
||||
Change the volume and/or shape and/or boundary conditions for the
|
||||
simulation box. Orthogonal simulation boxes have 3 adjustable size
|
||||
parameters (x,y,z). Triclinic (non-orthogonal) simulation boxes have
|
||||
6 adjustable size/shape parameters (x,y,z,xy,xz,yz). Any or all of
|
||||
them can be adjusted independently by this command. Thus it can be
|
||||
used to expand or contract a box, or to apply a shear strain to a
|
||||
non-orthogonal box. It can also be used to change the boundary
|
||||
conditions for the simulation box, similar to the
|
||||
"boundary"_boundary.html command.
|
||||
|
||||
This command allows you to toggle the existing simulation box from
|
||||
orthogonal to non-orthogonal and vice versa. For example, an initial
|
||||
The size and shape of the initial simulation box are specified by the
|
||||
"create_box"_create_box.html or "read_data"_read_data.html or
|
||||
"read_restart"_read_restart.html command used to setup the simulation.
|
||||
The size and shape may be altered by subsequent runs, e.g. by use of
|
||||
the "fix npt"_fix_nh.html or "fix deform"_fix_deform.html commands.
|
||||
The "create_box"_create_box.html, "read data"_read_data.html, and
|
||||
"read_restart"_read_restart.html commands also determine whether the
|
||||
simulation box is orthogonal or triclinic and their doc pages explain
|
||||
the meaning of the xy,xz,yz tilt factors.
|
||||
|
||||
See "Section_howto 12"_Section_howto.html#howto_12 of the doc pages
|
||||
for a geometric description of triclinic boxes, as defined by LAMMPS,
|
||||
and how to transform these parameters to and from other commonly used
|
||||
triclinic representations.
|
||||
|
||||
The keywords used in this command are applied sequentially to the
|
||||
simulation box and the atoms in it, in the order specified.
|
||||
|
||||
Before the sequence of keywords are invoked, the current box
|
||||
size/shape are stored, in case a {remap} keyword is used to map the
|
||||
atom coordinates from the previous box size/shape to the current one.
|
||||
|
||||
After all the keywords have been processed, any shrink-wrap boundary
|
||||
conditions are invoked (see the "boundary"_boundary.html command)
|
||||
which may change simulation box boundaries, and atoms are migrated to
|
||||
new owning processors.
|
||||
|
||||
IMPORTANT NOTE: It is possible to lose atoms with this command.
|
||||
E.g. by changing the box without remapping the atoms, and having atoms
|
||||
end up outside of non-periodic boundaries. It is also possible when
|
||||
remapping atoms to put them (nearly) on top of each other which will
|
||||
lead to bad dynamics. E.g. by converting a boundary from non-periodic
|
||||
to periodic.
|
||||
|
||||
IMPORTANT NOTE: The simulation box size/shape can be changed by
|
||||
arbitrarily large amounts by this command. This is not a problem,
|
||||
except that the mapping of processors to the simulation box is not
|
||||
changed from its initial 3d configuration; see the
|
||||
"processors"_processors.html command. Thus, if the box size/shape
|
||||
changes dramatically, the mapping of processors to the simulation box
|
||||
may not end up as optimal as the initial mapping attempted to be.
|
||||
|
||||
:line
|
||||
|
||||
For the {x}, {y}, and {z} parameters, this is the meaning of their
|
||||
styles and values.
|
||||
|
||||
For style {final}, the final lo and hi box boundaries of a dimension
|
||||
are specified. The values can be in lattice or box distance units.
|
||||
See the discussion of the units keyword below.
|
||||
|
||||
For style {delta}, plus or minus changes in the lo/hi box boundaries
|
||||
of a dimension are specified. The values can be in lattice or box
|
||||
distance units. See the discussion of the units keyword below.
|
||||
|
||||
For style {scale}, a multiplicative factor to apply to the box length
|
||||
of a dimension is specified. For example, if the initial box length
|
||||
is 10, and the factor is 1.1, then the final box length will be 11. A
|
||||
factor less than 1.0 means compression.
|
||||
|
||||
The {volume} style changes the specified dimension in such a way that
|
||||
the overall box volume remains constant with respect to the operation
|
||||
performed by the preceding keyword. The {volume} style can only be
|
||||
used following a keyword that changed the volume, which is any of the
|
||||
{x}, {y}, {z} keywords. If the preceding keyword "key" had a {volume}
|
||||
style, then both it and the current keyword apply to the keyword
|
||||
preceding "key". I.e. this sequence of keywords is allowed:
|
||||
|
||||
change_box all x scale 1.1 y volume z volume :pre
|
||||
|
||||
The {volume} style changes the associated dimension so that the
|
||||
overall box volume is unchanged relative to its value before the
|
||||
preceding keyword was invoked.
|
||||
|
||||
If the following command is used, then the z box length will shrink by
|
||||
the same 1.1 factor the x box length was increased by:
|
||||
|
||||
change_box all x scale 1.1 z volume :pre
|
||||
|
||||
If the following command is used, then the y,z box lengths will each
|
||||
shrink by sqrt(1.1) to keep the volume constant. In this case, the
|
||||
y,z box lengths shrink so as to keep their relative aspect ratio
|
||||
constant:
|
||||
|
||||
change_box all"x scale 1.1 y volume z volume :pre
|
||||
|
||||
If the following command is used, then the final box will be a factor
|
||||
of 10% larger in x and y, and a factor of 21% smaller in z, so as to
|
||||
keep the volume constant:
|
||||
|
||||
change_box all x scale 1.1 z volume y scale 1.1 z volume :pre
|
||||
|
||||
IMPORTANT NOTE: For solids or liquids, when one dimension of the box
|
||||
is expanded, it may be physically undesirable to hold the other 2 box
|
||||
lengths constant since that implies a density change. For solids,
|
||||
adjusting the other dimensions via the {volume} style may make
|
||||
physical sense (just as for a liquid), but may not be correct for
|
||||
materials and potentials whose Poisson ratio is not 0.5.
|
||||
|
||||
For the {scale} and {volume} styles, the box length is expanded or
|
||||
compressed around its mid point.
|
||||
|
||||
:line
|
||||
|
||||
For the {xy}, {xz}, and {yz} parameters, this is the meaning of their
|
||||
styles and values. Note that changing the tilt factors of a triclinic
|
||||
box does not change its volume.
|
||||
|
||||
For style {final}, the final tilt factor is specified. The value
|
||||
can be in lattice or box distance units. See the discussion of the
|
||||
units keyword below.
|
||||
|
||||
For style {delta}, a plus or minus change in the tilt factor is
|
||||
specified. The value can be in lattice or box distance units. See
|
||||
the discussion of the units keyword below.
|
||||
|
||||
All of these styles change the xy, xz, yz tilt factors. In LAMMPS,
|
||||
tilt factors (xy,xz,yz) for triclinic boxes are required to be no more
|
||||
than half the distance of the parallel box length. For example, if
|
||||
xlo = 2 and xhi = 12, then the x box length is 10 and the xy tilt
|
||||
factor must be between -5 and 5. Similarly, both xz and yz must be
|
||||
between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a
|
||||
limitation, since if the maximum tilt factor is 5 (as in this
|
||||
example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
|
||||
... are all equivalent. Any tilt factor specified by this command
|
||||
must be within these limits.
|
||||
|
||||
:line
|
||||
|
||||
The {boundary} keyword takes arguments that have exactly the same
|
||||
meaning as they do for the "boundary"_boundary.html command. In each
|
||||
dimension, a single letter assigns the same style to both the lower
|
||||
and upper face of the box. Two letters assigns the first style to the
|
||||
lower face and the second style to the upper face.
|
||||
|
||||
The style {p} means the box is periodic; the other styles mean
|
||||
non-periodic. For style {f}, the position of the face is fixed. For
|
||||
style {s}, the position of the face is set so as to encompass the
|
||||
atoms in that dimension (shrink-wrapping), no matter how far they
|
||||
move. For style {m}, shrink-wrapping occurs, but is bounded by the
|
||||
current box edge in that dimension, so that the box will become no
|
||||
smaller. See the "boundary"_boundary.html command for more
|
||||
explanation of these style options.
|
||||
|
||||
Note that the "boundary" command itself can only be used before the
|
||||
simulation box is defined via a "read_data"_read_data.html or
|
||||
"create_box"_create_box.html or "read_restart"_read_restart.html
|
||||
command. This command allows the boundary conditions to be changed
|
||||
later in your input script. Also note that the
|
||||
"read_restart"_read_restart.html will change boundary conditions to
|
||||
match what is stored in the restart file. So if you wish to change
|
||||
them, you should use the change_box command after the read_restart
|
||||
command.
|
||||
|
||||
:line
|
||||
|
||||
The {ortho} and {triclinic} keywords convert the simulation box to be
|
||||
orthogonal or triclinic (non-orthongonal). See "this
|
||||
section"_Section_howto#howto_13 for a discussion of how non-orthongal
|
||||
boxes are represented in LAMMPS.
|
||||
|
||||
The simulation box is defined as either orthogonal or triclinic when
|
||||
it is created via the "create_box"_create_box.html,
|
||||
"read_data"_read_data.html, or "read_restart"_read_restart.html
|
||||
commands.
|
||||
|
||||
These keywords allow you to toggle the existing simulation box from
|
||||
orthogonal to triclinic and vice versa. For example, an initial
|
||||
equilibration simulation can be run in an orthogonal box, the box can
|
||||
be toggled to non-orthogonal, and then a "non-equilibrium MD (NEMD)
|
||||
be toggled to triclinic, and then a "non-equilibrium MD (NEMD)
|
||||
simulation"_Section_howto.html#howto_13 can be run with deformation
|
||||
via the "fix deform"_fix_deform.html command.
|
||||
|
||||
Note that if the simulation box is currently non-orthogonal and has
|
||||
non-zero tilt in xy, yz, or xz, then it cannot be converted to an
|
||||
orthogonal box.
|
||||
If the simulation box is currently triclinic and has non-zero tilt in
|
||||
xy, yz, or xz, then it cannot be converted to an orthogonal box.
|
||||
|
||||
:line
|
||||
|
||||
The {set} keyword saves the current box size/shape. This can be
|
||||
useful if you wish to use the {remap} keyword more than once or if you
|
||||
wish it to be applied to an intermediate box size/shape in a sequence
|
||||
of keyword operations. Note that the box size/shape is saved before
|
||||
any of the keywords are processed, i.e. the box size/shape at the time
|
||||
the create_box command is encountered in the input script.
|
||||
|
||||
The {remap} keyword remaps atom coordinates from the last saved box
|
||||
size/shape to the current box state. For example, if you stretch the
|
||||
box in the x dimension or tilt it in the xy plane via the {x} and {xy}
|
||||
keywords, then the {remap} commmand will dilate or tilt the atoms to
|
||||
conform to the new box size/shape, as if the atoms moved with the box
|
||||
as it deformed.
|
||||
|
||||
Note that this operation is performed without regard to periodic
|
||||
boundaries. Any shrink-wrapping of non-periodic boundaries (see the
|
||||
"boundary"_boundary.html command occurs after all keywords, including
|
||||
this one, have been processed.
|
||||
|
||||
Only atoms in the specified group are remapped.
|
||||
|
||||
IMPORTANT NOTE: If you do not explicitly specify the {remap} keyword,
|
||||
atom coordinates will not be changed even though the box size/shape
|
||||
changes. This may be the behavior you desire, but can also cause
|
||||
atoms to be lost.
|
||||
|
||||
:line
|
||||
|
||||
The {units} keyword determines the meaning of the distance units used
|
||||
to define various arguments. A {box} value selects standard distance
|
||||
units as defined by the "units"_units.html command, e.g. Angstroms for
|
||||
units = real or metal. A {lattice} value means the distance units are
|
||||
in lattice spacings. The "lattice"_lattice.html command must have
|
||||
been previously used to define the lattice spacing.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
At the point in the input script when this command is issued, no
|
||||
"dumps"_dump.html can be active, nor can a "fix
|
||||
ave/spatial"_fix_ave_spatial.html or "fix deform"_fix_deform.html be
|
||||
active. This is because these commands test whether the simulation
|
||||
box is orthogonal when they are first issued. Note that these
|
||||
commands can appear in your script before a change_box command is
|
||||
issued, so long as an "undump"_undump.html or "unfix"_unfix.html
|
||||
command is also used to turn them off.
|
||||
If you use the {ortho} or {triclinic} keywords, then at the point in
|
||||
the input script when this command is issued, no "dumps"_dump.html can
|
||||
be active, nor can a "fix ave/spatial"_fix_ave_spatial.html or "fix
|
||||
deform"_fix_deform.html be active. This is because these commands
|
||||
test whether the simulation box is orthogonal when they are first
|
||||
issued. Note that these commands can be used in your script before a
|
||||
change_box command is issued, so long as an "undump"_undump.html or
|
||||
"unfix"_unfix.html command is also used to turn them off.
|
||||
|
||||
[Related commands:] none
|
||||
[Related commands:]
|
||||
|
||||
[Default:] none
|
||||
"fix deform"_fix_deform.html, "boundary"_boundary.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The option default is units = lattice.
|
||||
|
||||
@ -76,29 +76,29 @@ define the lattice spacing.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>Care should be taken not to move atoms on top of other atoms. After
|
||||
the move, atoms are remapped into the periodic simulation box if
|
||||
needed.
|
||||
<P>IMPORTANT NOTE: Care should be taken not to move atoms on top of other
|
||||
atoms. After the move, atoms are remapped into the periodic
|
||||
simulation box if needed, and any shrink-wrap boundary conditions (see
|
||||
the <A HREF = "boundary.html">boundary</A> command) are enforced which may change
|
||||
the box size. Other than this effect, this command does not change
|
||||
the size or shape of the simulation box. See the
|
||||
<A HREF = "change_box.html">change_box</A> command if that effect is desired.
|
||||
</P>
|
||||
<P>Atoms can be moved arbitrarily long distances by this command. If the
|
||||
simulation box is non-periodic, this can change its size or shape.
|
||||
This is not a problem, except that the mapping of processors to the
|
||||
simulation box is not changed by this command from its initial 3d
|
||||
configuration; see the <A HREF = "processors.html">processors</A> command. Thus, if
|
||||
the box size or shape changes dramatically, the simulation may not be
|
||||
as well load-balanced (atoms per processor) as the initial mapping
|
||||
tried to achieve.
|
||||
<P>IMPORTANT NOTE: Atoms can be moved arbitrarily long distances by this
|
||||
command. If the simulation box is non-periodic and shrink-wrapped
|
||||
(see the <A HREF = "boundary.html">boundary</A> command), this can change its size
|
||||
or shape. This is not a problem, except that the mapping of
|
||||
processors to the simulation box is not changed by this command from
|
||||
its initial 3d configuration; see the <A HREF = "processors.html">processors</A>
|
||||
command. Thus, if the box size/shape changes dramatically, the
|
||||
mapping of processors to the simulation box may not end up as optimal
|
||||
as the initial mapping attempted to be.
|
||||
</P>
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>This command requires inter-processor communication to migrate atoms
|
||||
once they have been displaced. This means that your system must be
|
||||
ready to perform a simulation before using this command (force fields
|
||||
are setup, atom masses are set, etc).
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "lattice.html">lattice</A>
|
||||
<P><A HREF = "lattice.html">lattice</A>, <A HREF = "change_box.html">change_box</A>
|
||||
</P>
|
||||
<P><B>Default:</B>
|
||||
</P>
|
||||
|
||||
@ -68,29 +68,29 @@ define the lattice spacing.
|
||||
|
||||
:line
|
||||
|
||||
Care should be taken not to move atoms on top of other atoms. After
|
||||
the move, atoms are remapped into the periodic simulation box if
|
||||
needed.
|
||||
IMPORTANT NOTE: Care should be taken not to move atoms on top of other
|
||||
atoms. After the move, atoms are remapped into the periodic
|
||||
simulation box if needed, and any shrink-wrap boundary conditions (see
|
||||
the "boundary"_boundary.html command) are enforced which may change
|
||||
the box size. Other than this effect, this command does not change
|
||||
the size or shape of the simulation box. See the
|
||||
"change_box"_change_box.html command if that effect is desired.
|
||||
|
||||
Atoms can be moved arbitrarily long distances by this command. If the
|
||||
simulation box is non-periodic, this can change its size or shape.
|
||||
This is not a problem, except that the mapping of processors to the
|
||||
simulation box is not changed by this command from its initial 3d
|
||||
configuration; see the "processors"_processors.html command. Thus, if
|
||||
the box size or shape changes dramatically, the simulation may not be
|
||||
as well load-balanced (atoms per processor) as the initial mapping
|
||||
tried to achieve.
|
||||
IMPORTANT NOTE: Atoms can be moved arbitrarily long distances by this
|
||||
command. If the simulation box is non-periodic and shrink-wrapped
|
||||
(see the "boundary"_boundary.html command), this can change its size
|
||||
or shape. This is not a problem, except that the mapping of
|
||||
processors to the simulation box is not changed by this command from
|
||||
its initial 3d configuration; see the "processors"_processors.html
|
||||
command. Thus, if the box size/shape changes dramatically, the
|
||||
mapping of processors to the simulation box may not end up as optimal
|
||||
as the initial mapping attempted to be.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This command requires inter-processor communication to migrate atoms
|
||||
once they have been displaced. This means that your system must be
|
||||
ready to perform a simulation before using this command (force fields
|
||||
are setup, atom masses are set, etc).
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"lattice"_lattice.html
|
||||
"lattice"_lattice.html, "change_box"_change_box.html
|
||||
|
||||
[Default:]
|
||||
|
||||
|
||||
@ -1,191 +0,0 @@
|
||||
<HTML>
|
||||
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
|
||||
</CENTER>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<HR>
|
||||
|
||||
<H3>displace_box command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>displace_box group-ID parameter args ... keyword value ...
|
||||
</PRE>
|
||||
<UL><LI>group-ID = ID of group of atoms to displace
|
||||
|
||||
<LI>one or more parameter/arg pairs may be appended
|
||||
|
||||
<PRE>parameter = <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>xz</I> or <I>yz</I>
|
||||
<I>x</I>, <I>y</I>, <I>z</I> args = style value(s)
|
||||
style = <I>final</I> or <I>delta</I> or <I>scale</I> or <I>volume</I>
|
||||
<I>final</I> values = lo hi
|
||||
lo hi = box boundaries at end of run (distance units)
|
||||
<I>delta</I> values = dlo dhi
|
||||
dlo dhi = change in box boundaries at end of run (distance units)
|
||||
<I>scale</I> values = factor
|
||||
factor = multiplicative factor for change in box length at end of run
|
||||
<I>volume</I> value = none = adjust this dim to preserve volume of system
|
||||
<I>xy</I>, <I>xz</I>, <I>yz</I> args = style value
|
||||
style = <I>final</I> or <I>delta</I>
|
||||
<I>final</I> value = tilt
|
||||
tilt = tilt factor at end of run (distance units)
|
||||
<I>delta</I> value = dtilt
|
||||
dtilt = change in tilt factor at end of run (distance units)
|
||||
</PRE>
|
||||
<LI>zero or more keyword/value pairs may be appended
|
||||
|
||||
<LI>keyword = <I>remap</I> or <I>units</I>
|
||||
|
||||
<PRE> <I>remap</I> value = <I>x</I> or <I>none</I>
|
||||
x = remap coords of atoms in group into deforming box
|
||||
none = no remapping of coords
|
||||
<I>units</I> value = <I>lattice</I> or <I>box</I>
|
||||
lattice = distances are defined in lattice units
|
||||
box = distances are defined in simulation box units
|
||||
</PRE>
|
||||
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>displace_box all xy final -2.0 z final 0.0 5.0 units box
|
||||
displace_box all x scale 1.1 y volume z volume
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Change the volume and/or shape of the simulation box. Orthogonal
|
||||
simulation boxes have 3 adjustable parameters (x,y,z). Triclinic
|
||||
(non-orthogonal) simulation boxes have 6 adjustable parameters
|
||||
(x,y,z,xy,xz,yz). Any or all of them can be adjusted independently
|
||||
and simultaneously by this command. This fix can be used to expand or
|
||||
contract a box, or to apply a shear strain to a non-orthogonal box.
|
||||
</P>
|
||||
<P>Any parameter varied by this command must refer to a periodic
|
||||
dimension - see the <A HREF = "boundary.html">boundary</A> command. For parameters
|
||||
"xy", "xz", and "yz" this means both affected dimensions must be
|
||||
periodic, e.g. x and y for "xy". Dimensions not varied by this
|
||||
command can be periodic or non-periodic.
|
||||
</P>
|
||||
<P>The size and shape of the initial simulation box are specified by the
|
||||
<A HREF = "create_box.html">create_box</A> or <A HREF = "read_data.html">read_data</A> or
|
||||
<A HREF = "read_restart.html">read_restart</A> command used to setup the simulation,
|
||||
or they are the values from the end of the previous run. The
|
||||
<A HREF = "create_box.html">create_box</A>, <A HREF = "read_data.html">read data</A>, and
|
||||
<A HREF = "read_restart.html">read_restart</A> commands also determine whether the
|
||||
simulation box is orthogonal or triclinic and their doc pages explain
|
||||
the meaning of the xy,xz,yz tilt factors. If the displace_box command
|
||||
changes the xy,xz,yz tilt factors, then the simulation box must be
|
||||
triclinic, even if its initial tilt factors are 0.0.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>For the <I>x</I>, <I>y</I>, and <I>z</I> parameters, this is the meaning of their
|
||||
styles and values.
|
||||
</P>
|
||||
<P>For style <I>final</I>, the final lo and hi box boundaries of a dimension
|
||||
are specified. The values can be in lattice or box distance units.
|
||||
See the discussion of the units keyword below.
|
||||
</P>
|
||||
<P>For style <I>delta</I>, plus or minus changes in the lo/hi box boundaries
|
||||
of a dimension are specified. The values can be in lattice or box
|
||||
distance units. See the discussion of the units keyword below.
|
||||
</P>
|
||||
<P>For style <I>scale</I>, a multiplicative factor to apply to the box length
|
||||
of a dimension is specified. For example, if the initial box length
|
||||
is 10, and the factor is 1.1, then the final box length will be 11. A
|
||||
factor less than 1.0 means compression.
|
||||
</P>
|
||||
<P>The <I>volume</I> style changes the specified dimension in such a way that
|
||||
the box volume remains constant while other box dimensions are changed
|
||||
explicitly via the styles discussed above. For example, "x scale 1.1
|
||||
y scale 1.1 z volume" will shrink the z box length as the x,y box
|
||||
lengths increase, to keep the volume constant (product of x,y,z
|
||||
lengths). If "x scale 1.1 z volume" is specified and parameter <I>y</I> is
|
||||
unspecified, then the z box length will shrink as x increases to keep
|
||||
the product of x,z lengths constant. If "x scale 1.1 y volume z
|
||||
volume" is specified, then both the y,z box lengths will shrink as x
|
||||
increases to keep the volume constant (product of x,y,z lengths). In
|
||||
this case, the y,z box lengths shrink so as to keep their relative
|
||||
aspect ratio constant.
|
||||
</P>
|
||||
<P>For solids or liquids, note that when one dimension of the box is
|
||||
expanded by this command, it may be physically undesirable to hold the
|
||||
other 2 box lengths constant (unspecified by this command) since that
|
||||
implies a density change. Using the <I>volume</I> style for those 2
|
||||
dimensions to keep the box volume constant may make more physical
|
||||
sense, but may also not be correct for materials and potentials whose
|
||||
Poisson ratio is not 0.5.
|
||||
</P>
|
||||
<P>For the <I>scale</I> and <I>volume</I> styles, the box length is expanded or
|
||||
compressed around its mid point.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>For the <I>xy</I>, <I>xz</I>, and <I>yz</I> parameters, this is the meaning of their
|
||||
styles and values. Note that changing the tilt factors of a triclinic
|
||||
box does not change its volume.
|
||||
</P>
|
||||
<P>For style <I>final</I>, the final tilt factor is specified. The value
|
||||
can be in lattice or box distance units. See the discussion of the
|
||||
units keyword below.
|
||||
</P>
|
||||
<P>For style <I>delta</I>, a plus or minus change in the tilt factor is
|
||||
specified. The value can be in lattice or box distance units. See
|
||||
the discussion of the units keyword below.
|
||||
</P>
|
||||
<P>All of these styles change the xy, xz, yz tilt factors. In LAMMPS,
|
||||
tilt factors (xy,xz,yz) for triclinic boxes are always bounded by half
|
||||
the distance of the parallel box length. For example, if xlo = 2 and
|
||||
xhi = 12, then the x box length is 10 and the xy tilt factor must be
|
||||
between -5 and 5. Similarly, both xz and yz must be between
|
||||
-(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation,
|
||||
since if the maximum tilt factor is 5 (as in this example), then
|
||||
configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
|
||||
equivalent. Any tilt factor specified by this command must be within
|
||||
these limits.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The <I>remap</I> keyword determines whether atom positions are re-mapped to
|
||||
the new box. If <I>remap</I> is set to <I>x</I> (the default), atoms in the fix
|
||||
group are re-mapped; otherwise they are not. If <I>remap</I> is set to
|
||||
<I>none</I>, then this remapping does not take place.
|
||||
</P>
|
||||
<P>The <I>units</I> keyword determines the meaning of the distance units used
|
||||
to define various arguments. A <I>box</I> value selects standard distance
|
||||
units as defined by the <A HREF = "units.html">units</A> command, e.g. Angstroms for
|
||||
units = real or metal. A <I>lattice</I> value means the distance units are
|
||||
in lattice spacings. The <A HREF = "lattice.html">lattice</A> command must have
|
||||
been previously used to define the lattice spacing.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The simulation box size or shape can be changed by arbitrarily large
|
||||
amounts by this command. This is not a problem, except that the
|
||||
mapping of processors to the simulation box is not changed by this
|
||||
command from its initial 3d configuration; see the
|
||||
<A HREF = "processors.html">processors</A> command. Thus, if the box size or shape
|
||||
changes dramatically, the simulation may not be as well load-balanced
|
||||
(atoms per processor) as the initial mapping tried to achieve.
|
||||
</P>
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>Any box dimension varied by this fix must be periodic.
|
||||
</P>
|
||||
<P>This command requires inter-processor communication to migrate atoms
|
||||
once they have moved. This means that your system must be ready to
|
||||
perform a simulation before using this command (force fields are
|
||||
setup, atom masses are set, etc).
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "fix_deform.html">fix deform</A>
|
||||
</P>
|
||||
<P><B>Default:</B>
|
||||
</P>
|
||||
<P>The option defaults are remap = x and units = lattice.
|
||||
</P>
|
||||
</HTML>
|
||||
@ -1,181 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
displace_box command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
displace_box group-ID parameter args ... keyword value ... :pre
|
||||
|
||||
group-ID = ID of group of atoms to displace :ulb,l
|
||||
one or more parameter/arg pairs may be appended :l
|
||||
parameter = {x} or {y} or {z} or {xy} or {xz} or {yz}
|
||||
{x}, {y}, {z} args = style value(s)
|
||||
style = {final} or {delta} or {scale} or {volume}
|
||||
{final} values = lo hi
|
||||
lo hi = box boundaries at end of run (distance units)
|
||||
{delta} values = dlo dhi
|
||||
dlo dhi = change in box boundaries at end of run (distance units)
|
||||
{scale} values = factor
|
||||
factor = multiplicative factor for change in box length at end of run
|
||||
{volume} value = none = adjust this dim to preserve volume of system
|
||||
{xy}, {xz}, {yz} args = style value
|
||||
style = {final} or {delta}
|
||||
{final} value = tilt
|
||||
tilt = tilt factor at end of run (distance units)
|
||||
{delta} value = dtilt
|
||||
dtilt = change in tilt factor at end of run (distance units) :pre
|
||||
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {remap} or {units} :l
|
||||
{remap} value = {x} or {none}
|
||||
x = remap coords of atoms in group into deforming box
|
||||
none = no remapping of coords
|
||||
{units} value = {lattice} or {box}
|
||||
lattice = distances are defined in lattice units
|
||||
box = distances are defined in simulation box units :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
displace_box all xy final -2.0 z final 0.0 5.0 units box
|
||||
displace_box all x scale 1.1 y volume z volume :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Change the volume and/or shape of the simulation box. Orthogonal
|
||||
simulation boxes have 3 adjustable parameters (x,y,z). Triclinic
|
||||
(non-orthogonal) simulation boxes have 6 adjustable parameters
|
||||
(x,y,z,xy,xz,yz). Any or all of them can be adjusted independently
|
||||
and simultaneously by this command. This fix can be used to expand or
|
||||
contract a box, or to apply a shear strain to a non-orthogonal box.
|
||||
|
||||
Any parameter varied by this command must refer to a periodic
|
||||
dimension - see the "boundary"_boundary.html command. For parameters
|
||||
"xy", "xz", and "yz" this means both affected dimensions must be
|
||||
periodic, e.g. x and y for "xy". Dimensions not varied by this
|
||||
command can be periodic or non-periodic.
|
||||
|
||||
The size and shape of the initial simulation box are specified by the
|
||||
"create_box"_create_box.html or "read_data"_read_data.html or
|
||||
"read_restart"_read_restart.html command used to setup the simulation,
|
||||
or they are the values from the end of the previous run. The
|
||||
"create_box"_create_box.html, "read data"_read_data.html, and
|
||||
"read_restart"_read_restart.html commands also determine whether the
|
||||
simulation box is orthogonal or triclinic and their doc pages explain
|
||||
the meaning of the xy,xz,yz tilt factors. If the displace_box command
|
||||
changes the xy,xz,yz tilt factors, then the simulation box must be
|
||||
triclinic, even if its initial tilt factors are 0.0.
|
||||
|
||||
:line
|
||||
|
||||
For the {x}, {y}, and {z} parameters, this is the meaning of their
|
||||
styles and values.
|
||||
|
||||
For style {final}, the final lo and hi box boundaries of a dimension
|
||||
are specified. The values can be in lattice or box distance units.
|
||||
See the discussion of the units keyword below.
|
||||
|
||||
For style {delta}, plus or minus changes in the lo/hi box boundaries
|
||||
of a dimension are specified. The values can be in lattice or box
|
||||
distance units. See the discussion of the units keyword below.
|
||||
|
||||
For style {scale}, a multiplicative factor to apply to the box length
|
||||
of a dimension is specified. For example, if the initial box length
|
||||
is 10, and the factor is 1.1, then the final box length will be 11. A
|
||||
factor less than 1.0 means compression.
|
||||
|
||||
The {volume} style changes the specified dimension in such a way that
|
||||
the box volume remains constant while other box dimensions are changed
|
||||
explicitly via the styles discussed above. For example, "x scale 1.1
|
||||
y scale 1.1 z volume" will shrink the z box length as the x,y box
|
||||
lengths increase, to keep the volume constant (product of x,y,z
|
||||
lengths). If "x scale 1.1 z volume" is specified and parameter {y} is
|
||||
unspecified, then the z box length will shrink as x increases to keep
|
||||
the product of x,z lengths constant. If "x scale 1.1 y volume z
|
||||
volume" is specified, then both the y,z box lengths will shrink as x
|
||||
increases to keep the volume constant (product of x,y,z lengths). In
|
||||
this case, the y,z box lengths shrink so as to keep their relative
|
||||
aspect ratio constant.
|
||||
|
||||
For solids or liquids, note that when one dimension of the box is
|
||||
expanded by this command, it may be physically undesirable to hold the
|
||||
other 2 box lengths constant (unspecified by this command) since that
|
||||
implies a density change. Using the {volume} style for those 2
|
||||
dimensions to keep the box volume constant may make more physical
|
||||
sense, but may also not be correct for materials and potentials whose
|
||||
Poisson ratio is not 0.5.
|
||||
|
||||
For the {scale} and {volume} styles, the box length is expanded or
|
||||
compressed around its mid point.
|
||||
|
||||
:line
|
||||
|
||||
For the {xy}, {xz}, and {yz} parameters, this is the meaning of their
|
||||
styles and values. Note that changing the tilt factors of a triclinic
|
||||
box does not change its volume.
|
||||
|
||||
For style {final}, the final tilt factor is specified. The value
|
||||
can be in lattice or box distance units. See the discussion of the
|
||||
units keyword below.
|
||||
|
||||
For style {delta}, a plus or minus change in the tilt factor is
|
||||
specified. The value can be in lattice or box distance units. See
|
||||
the discussion of the units keyword below.
|
||||
|
||||
All of these styles change the xy, xz, yz tilt factors. In LAMMPS,
|
||||
tilt factors (xy,xz,yz) for triclinic boxes are always bounded by half
|
||||
the distance of the parallel box length. For example, if xlo = 2 and
|
||||
xhi = 12, then the x box length is 10 and the xy tilt factor must be
|
||||
between -5 and 5. Similarly, both xz and yz must be between
|
||||
-(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation,
|
||||
since if the maximum tilt factor is 5 (as in this example), then
|
||||
configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
|
||||
equivalent. Any tilt factor specified by this command must be within
|
||||
these limits.
|
||||
|
||||
:line
|
||||
|
||||
The {remap} keyword determines whether atom positions are re-mapped to
|
||||
the new box. If {remap} is set to {x} (the default), atoms in the fix
|
||||
group are re-mapped; otherwise they are not. If {remap} is set to
|
||||
{none}, then this remapping does not take place.
|
||||
|
||||
The {units} keyword determines the meaning of the distance units used
|
||||
to define various arguments. A {box} value selects standard distance
|
||||
units as defined by the "units"_units.html command, e.g. Angstroms for
|
||||
units = real or metal. A {lattice} value means the distance units are
|
||||
in lattice spacings. The "lattice"_lattice.html command must have
|
||||
been previously used to define the lattice spacing.
|
||||
|
||||
:line
|
||||
|
||||
The simulation box size or shape can be changed by arbitrarily large
|
||||
amounts by this command. This is not a problem, except that the
|
||||
mapping of processors to the simulation box is not changed by this
|
||||
command from its initial 3d configuration; see the
|
||||
"processors"_processors.html command. Thus, if the box size or shape
|
||||
changes dramatically, the simulation may not be as well load-balanced
|
||||
(atoms per processor) as the initial mapping tried to achieve.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
Any box dimension varied by this fix must be periodic.
|
||||
|
||||
This command requires inter-processor communication to migrate atoms
|
||||
once they have moved. This means that your system must be ready to
|
||||
perform a simulation before using this command (force fields are
|
||||
setup, atom masses are set, etc).
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix deform"_fix_deform.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The option defaults are remap = x and units = lattice.
|
||||
@ -533,7 +533,7 @@ xy) that is shrink-wrapped via the <A HREF = "boundary.html">boundary</A> comamn
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "displace_box.html">displace_box</A>
|
||||
<P><A HREF = "change_box.html">change_box</A>
|
||||
</P>
|
||||
<P><B>Default:</B>
|
||||
</P>
|
||||
|
||||
@ -523,7 +523,7 @@ xy) that is shrink-wrapped via the "boundary"_boundary.html comamnd.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"displace_box"_displace_box.html
|
||||
"change_box"_change_box.html
|
||||
|
||||
[Default:]
|
||||
|
||||
|
||||
@ -33,8 +33,8 @@ class lammps:
|
||||
except:
|
||||
try:
|
||||
self.lib = CDLL("_lammps_serial.so")
|
||||
#except:
|
||||
# raise OSError,"Could not load LAMMPS dynamic library"
|
||||
except:
|
||||
raise OSError,"Could not load LAMMPS dynamic library"
|
||||
|
||||
# create an instance of LAMMPS
|
||||
# don't know how to pass an MPI communicator from PyPar
|
||||
|
||||
@ -874,7 +874,7 @@ void PPPM::set_grid()
|
||||
acons[7][5] = 1755948832039.0 / 36229939200000.0;
|
||||
acons[7][6] = 4887769399.0 / 37838389248.0;
|
||||
|
||||
double q2 = qsqsum / force->dielectric;
|
||||
double q2 = qsqsum * force->qqrd2e / force->dielectric;
|
||||
bigint natoms = atom->natoms;
|
||||
|
||||
// use xprd,yprd,zprd even if triclinic so grid size is the same
|
||||
|
||||
@ -111,7 +111,8 @@ FixBondCreate::FixBondCreate(LAMMPS *lmp, int narg, char **arg) :
|
||||
error->all(FLERR,"Cannot use fix bond/create with non-molecular systems");
|
||||
if (iatomtype == jatomtype &&
|
||||
((imaxbond != jmaxbond) || (inewtype != jnewtype)))
|
||||
error->all(FLERR,"Inconsistent iparam/jparam values in fix bond/create command");
|
||||
error->all(FLERR,
|
||||
"Inconsistent iparam/jparam values in fix bond/create command");
|
||||
|
||||
// initialize Marsaglia RNG with processor-unique seed
|
||||
|
||||
@ -249,7 +250,8 @@ void FixBondCreate::setup(int vflag)
|
||||
if (newton_bond) {
|
||||
m = atom->map(bond_atom[i][j]);
|
||||
if (m < 0)
|
||||
error->one(FLERR,"Could not count initial bonds in fix bond/create");
|
||||
error->one(FLERR,
|
||||
"Could not count initial bonds in fix bond/create");
|
||||
bondcount[m]++;
|
||||
}
|
||||
}
|
||||
@ -422,7 +424,8 @@ void FixBondCreate::post_integrate()
|
||||
n1 = nspecial[i][0];
|
||||
n3 = nspecial[i][2];
|
||||
if (n3 == atom->maxspecial)
|
||||
error->one(FLERR,"New bond exceeded special list size in fix bond/create");
|
||||
error->one(FLERR,
|
||||
"New bond exceeded special list size in fix bond/create");
|
||||
for (m = n3; m > n1; m--) slist[m+1] = slist[m];
|
||||
slist[n1] = tag[j];
|
||||
nspecial[i][0]++;
|
||||
|
||||
@ -195,9 +195,9 @@ void PairEAMCuda::array2spline()
|
||||
memory->destroy(rhor_spline);
|
||||
memory->destroy(z2r_spline);
|
||||
|
||||
memory->create(frho_spline,nfrho,nrho+1,7,"pair:frho");
|
||||
memory->create(rhor_spline,nrhor,nr+1,7,"pair:rhor");
|
||||
memory->create(z2r_spline,nz2r,nr+1,7,"pair:z2r");
|
||||
memory->create(frho_spline,nfrho,nrho+1,8,"pair:frho");
|
||||
memory->create(rhor_spline,nrhor,nr+1,8,"pair:rhor");
|
||||
memory->create(z2r_spline,nz2r,nr+1,8,"pair:z2r");
|
||||
|
||||
for (int i = 0; i < nfrho; i++){
|
||||
interpolate(nrho,drho,frho[i],frho_spline[i]);
|
||||
|
||||
@ -11,17 +11,28 @@
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "lmptype.h"
|
||||
#include "mpi.h"
|
||||
#include "math.h"
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "change_box.h"
|
||||
#include "domain.h"
|
||||
#include "atom.h"
|
||||
#include "modify.h"
|
||||
#include "fix.h"
|
||||
#include "domain.h"
|
||||
#include "lattice.h"
|
||||
#include "comm.h"
|
||||
#include "irregular.h"
|
||||
#include "output.h"
|
||||
#include "group.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
enum{ORTHO,TRICLINIC};
|
||||
enum{XYZ,TILT,BOUNDARY,ORTHO,TRICLINIC,SET,REMAP};
|
||||
enum{FINAL,DELTA,SCALE};
|
||||
enum{X,Y,Z,YZ,XZ,XY};
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -31,34 +42,412 @@ ChangeBox::ChangeBox(LAMMPS *lmp) : Pointers(lmp) {}
|
||||
|
||||
void ChangeBox::command(int narg, char **arg)
|
||||
{
|
||||
int i;
|
||||
|
||||
if (domain->box_exist == 0)
|
||||
error->all(FLERR,"Change_box command before simulation box is defined");
|
||||
if (narg != 1) error->all(FLERR,"Illegal change_box command");
|
||||
if (narg < 2) error->all(FLERR,"Illegal change_box command");
|
||||
if (modify->nfix_restart_peratom)
|
||||
error->all(FLERR,"Cannot change_box after "
|
||||
"reading restart file with per-atom info");
|
||||
|
||||
int style;
|
||||
if (strcmp(arg[0],"ortho") == 0) style = ORTHO;
|
||||
else if (strcmp(arg[0],"triclinic") == 0) style = TRICLINIC;
|
||||
else error->all(FLERR,"Illegal change_box command");
|
||||
if (comm->me == 0 && screen) fprintf(screen,"Changing box ...\n");
|
||||
|
||||
if (style == ORTHO && domain->triclinic == 0)
|
||||
error->all(FLERR,"Change_box operation is invalid");
|
||||
if (style == TRICLINIC && domain->triclinic == 1)
|
||||
error->all(FLERR,"Change_box operation is invalid");
|
||||
if (style == ORTHO &&
|
||||
(domain->xy != 0.0 || domain->yz != 0.0 || domain->xz != 0.0))
|
||||
error->all(FLERR,"Cannot change box to orthogonal when tilt is non-zero");
|
||||
// group
|
||||
|
||||
if (output->ndump)
|
||||
error->all(FLERR,"Cannot change box with dumps defined");
|
||||
for (int i = 0; i < modify->nfix; i++)
|
||||
if (modify->fix[i]->no_change_box)
|
||||
error->all(FLERR,"Cannot change box with certain fixes defined");
|
||||
int igroup = group->find(arg[0]);
|
||||
if (igroup == -1) error->all(FLERR,"Could not find change_box group ID");
|
||||
int groupbit = group->bitmask[igroup];
|
||||
|
||||
if (style == ORTHO) domain->triclinic = 0;
|
||||
else domain->triclinic = 1;
|
||||
domain->xy = domain->yz = domain->xz = 0.0;
|
||||
// parse operation arguments
|
||||
// allocate ops to max possible length
|
||||
// volume option does not increment nops
|
||||
|
||||
domain->set_global_box();
|
||||
if (style == TRICLINIC) domain->set_lamda_box();
|
||||
domain->set_local_box();
|
||||
int dimension = domain->dimension;
|
||||
|
||||
ops = new Operation[narg-1];
|
||||
nops = 0;
|
||||
|
||||
int index;
|
||||
int iarg = 1;
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg],"x") == 0 || strcmp(arg[iarg],"y") == 0 ||
|
||||
strcmp(arg[iarg],"z") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal change_box command");
|
||||
ops[nops].style = XYZ;
|
||||
if (strcmp(arg[iarg],"x") == 0) ops[nops].dim = X;
|
||||
else if (strcmp(arg[iarg],"y") == 0) ops[nops].dim = Y;
|
||||
else if (strcmp(arg[iarg],"z") == 0) ops[nops].dim = Z;
|
||||
|
||||
if (dimension == 2 && ops[nops].dim == Z)
|
||||
error->all(FLERR,"Cannot change_box in z dimension for 2d simulation");
|
||||
|
||||
if (strcmp(arg[iarg+1],"final") == 0) {
|
||||
if (iarg+4 > narg) error->all(FLERR,"Illegal change_box command");
|
||||
ops[nops].flavor = FINAL;
|
||||
ops[nops].flo = atof(arg[iarg+2]);
|
||||
ops[nops].fhi = atof(arg[iarg+3]);
|
||||
ops[nops].vdim1 = ops[nops].vdim2 = -1;
|
||||
nops++;
|
||||
iarg += 4;
|
||||
} else if (strcmp(arg[iarg+1],"delta") == 0) {
|
||||
if (iarg+4 > narg) error->all(FLERR,"Illegal change_box command");
|
||||
ops[nops].flavor = DELTA;
|
||||
ops[nops].dlo = atof(arg[iarg+2]);
|
||||
ops[nops].dhi = atof(arg[iarg+3]);
|
||||
ops[nops].vdim1 = ops[nops].vdim2 = -1;
|
||||
nops++;
|
||||
iarg += 4;
|
||||
} else if (strcmp(arg[iarg+1],"scale") == 0) {
|
||||
if (iarg+3 > narg) error->all(FLERR,"Illegal change_box command");
|
||||
ops[nops].flavor = SCALE;
|
||||
ops[nops].scale = atof(arg[iarg+2]);
|
||||
ops[nops].vdim1 = ops[nops].vdim2 = -1;
|
||||
nops++;
|
||||
iarg += 3;
|
||||
} else if (strcmp(arg[iarg+1],"volume") == 0) {
|
||||
if (nops == 0 || ops[nops-1].style != XYZ ||
|
||||
ops[nops].dim == ops[nops-1].dim)
|
||||
error->all(FLERR,"Change_box volume used incorrectly");
|
||||
if (ops[nops-1].vdim2 >= 0)
|
||||
error->all(FLERR,"Change_box volume used incorrectly");
|
||||
else if (ops[nops-1].vdim1 >= 0) ops[nops-1].vdim2 = ops[nops].dim;
|
||||
else ops[nops-1].vdim1 = ops[nops].dim;
|
||||
iarg += 2;
|
||||
|
||||
} else error->all(FLERR,"Illegal change_box command");
|
||||
|
||||
} else if (strcmp(arg[iarg],"xy") == 0 || strcmp(arg[iarg],"xz") == 0 ||
|
||||
strcmp(arg[iarg],"yz") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal change_box command");
|
||||
ops[nops].style = TILT;
|
||||
if (strcmp(arg[iarg],"xy") == 0) ops[nops].dim = XY;
|
||||
else if (strcmp(arg[iarg],"xz") == 0) ops[nops].dim = XZ;
|
||||
else if (strcmp(arg[iarg],"yz") == 0) ops[nops].dim = YZ;
|
||||
|
||||
if (dimension == 2 && (ops[nops].dim == XZ || ops[nops].dim == YZ))
|
||||
error->all(FLERR,"Cannot change_box in xz or yz for 2d simulation");
|
||||
|
||||
if (strcmp(arg[iarg+1],"final") == 0) {
|
||||
if (iarg+3 > narg) error->all(FLERR,"Illegal change_box command");
|
||||
ops[nops].flavor = FINAL;
|
||||
ops[nops].ftilt = atof(arg[iarg+2]);
|
||||
nops++;
|
||||
iarg += 3;
|
||||
} else if (strcmp(arg[iarg+1],"delta") == 0) {
|
||||
if (iarg+3 > narg) error->all(FLERR,"Illegal change_box command");
|
||||
ops[nops].flavor = DELTA;
|
||||
ops[nops].dtilt = atof(arg[iarg+2]);
|
||||
nops++;
|
||||
iarg += 3;
|
||||
} else error->all(FLERR,"Illegal change_box command");
|
||||
|
||||
} else if (strcmp(arg[iarg],"boundary") == 0) {
|
||||
if (iarg+4 > narg) error->all(FLERR,"Illegal change_box command");
|
||||
ops[nops].style = BOUNDARY;
|
||||
ops[nops].boundindex = iarg+1;
|
||||
nops++;
|
||||
iarg += 4;
|
||||
|
||||
} else if (strcmp(arg[iarg],"ortho") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal change_box command");
|
||||
ops[nops].style = ORTHO;
|
||||
nops++;
|
||||
iarg += 1;
|
||||
|
||||
} else if (strcmp(arg[iarg],"triclinic") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal change_box command");
|
||||
ops[nops].style = TRICLINIC;
|
||||
nops++;
|
||||
iarg += 1;
|
||||
|
||||
} else if (strcmp(arg[iarg],"set") == 0) {
|
||||
if (iarg+1 > narg) error->all(FLERR,"Illegal change_box command");
|
||||
ops[nops].style = SET;
|
||||
nops++;
|
||||
iarg += 1;
|
||||
|
||||
} else if (strcmp(arg[iarg],"remap") == 0) {
|
||||
if (iarg+1 > narg) error->all(FLERR,"Illegal change_box command");
|
||||
ops[nops].style = REMAP;
|
||||
nops++;
|
||||
iarg += 1;
|
||||
|
||||
} else break;
|
||||
}
|
||||
|
||||
if (nops == 0) error->all(FLERR,"Illegal change_box command");
|
||||
|
||||
// read options from end of input line
|
||||
|
||||
options(narg-iarg,&arg[iarg]);
|
||||
|
||||
// compute scale factors if FINAL,DELTA used since they have distance units
|
||||
|
||||
int flag = 0;
|
||||
for (int i = 0; i < nops; i++)
|
||||
if (ops[i].style == FINAL || ops[i].style == DELTA) flag = 1;
|
||||
|
||||
if (flag && scaleflag && domain->lattice == NULL)
|
||||
error->all(FLERR,"Use of change_box with undefined lattice");
|
||||
|
||||
if (flag && scaleflag) {
|
||||
scale[0] = domain->lattice->xlattice;
|
||||
scale[1] = domain->lattice->ylattice;
|
||||
scale[2] = domain->lattice->zlattice;
|
||||
}
|
||||
else scale[0] = scale[1] = scale[2] = 1.0;
|
||||
|
||||
// perform sequence of operations
|
||||
// first insure atoms are in current box & update box via shrink-wrap
|
||||
// then save current box state so can remap atoms from it
|
||||
|
||||
domain->pbc();
|
||||
domain->reset_box();
|
||||
save_box_state();
|
||||
|
||||
for (int i = 0; i < nops; i++) {
|
||||
if (ops[i].style == XYZ) {
|
||||
double volume;
|
||||
if (domain->dimension == 2) volume = domain->xprd * domain->yprd;
|
||||
else volume = domain->xprd * domain->yprd * domain->zprd;
|
||||
|
||||
if (ops[i].flavor == FINAL) {
|
||||
domain->boxlo[ops[i].dim] = scale[ops[i].dim]*ops[i].flo;
|
||||
domain->boxhi[ops[i].dim] = scale[ops[i].dim]*ops[i].fhi;
|
||||
if (ops[i].vdim1)
|
||||
volume_preserve(ops[i].vdim1,ops[i].vdim2,volume);
|
||||
domain->set_initial_box();
|
||||
domain->set_global_box();
|
||||
domain->set_local_box();
|
||||
domain->print_box(" ");
|
||||
|
||||
} else if (ops[i].flavor == DELTA) {
|
||||
domain->boxlo[ops[i].dim] += scale[ops[i].dim]*ops[i].dlo;
|
||||
domain->boxhi[ops[i].dim] += scale[ops[i].dim]*ops[i].dhi;
|
||||
if (ops[i].vdim1)
|
||||
volume_preserve(ops[i].vdim1,ops[i].vdim2,volume);
|
||||
domain->set_initial_box();
|
||||
domain->set_global_box();
|
||||
domain->set_local_box();
|
||||
domain->print_box(" ");
|
||||
|
||||
} else if (ops[i].flavor == SCALE) {
|
||||
double mid = 0.5 *
|
||||
(domain->boxlo[ops[i].dim] + domain->boxhi[ops[i].dim]);
|
||||
double delta = domain->boxlo[ops[i].dim] - mid;
|
||||
domain->boxlo[ops[i].dim] = mid + ops[i].scale*delta;
|
||||
delta = domain->boxhi[ops[i].dim] - mid;
|
||||
domain->boxhi[ops[i].dim] = mid + ops[i].scale*delta;
|
||||
if (ops[i].vdim1)
|
||||
volume_preserve(ops[i].vdim1,ops[i].vdim2,volume);
|
||||
domain->set_initial_box();
|
||||
domain->set_global_box();
|
||||
domain->set_local_box();
|
||||
domain->print_box(" ");
|
||||
}
|
||||
|
||||
} else if (ops[i].style == TILT) {
|
||||
if (domain->triclinic == 0)
|
||||
error->all(FLERR,"Cannot change box tilt factors for orthogonal box");
|
||||
|
||||
if (ops[i].flavor == FINAL) {
|
||||
if (ops[i].dim == XY) domain->xy = scale[X]*ops[i].ftilt;
|
||||
else if (ops[i].dim == XZ) domain->xz = scale[X]*ops[i].ftilt;
|
||||
else if (ops[i].dim == YZ) domain->yz = scale[Y]*ops[i].ftilt;
|
||||
domain->set_initial_box();
|
||||
domain->set_global_box();
|
||||
domain->set_local_box();
|
||||
domain->print_box(" ");
|
||||
|
||||
} else if (ops[i].flavor == DELTA) {
|
||||
if (ops[i].dim == XY) domain->xy += scale[X]*ops[i].dtilt;
|
||||
else if (ops[i].dim == XZ) domain->xz += scale[X]*ops[i].dtilt;
|
||||
else if (ops[i].dim == YZ) domain->yz += scale[Y]*ops[i].dtilt;
|
||||
domain->set_initial_box();
|
||||
domain->set_global_box();
|
||||
domain->set_local_box();
|
||||
domain->print_box(" ");
|
||||
}
|
||||
|
||||
} else if (ops[i].style == BOUNDARY) {
|
||||
domain->set_boundary(3,&arg[ops[i].boundindex],1);
|
||||
if (domain->dimension == 2 && domain->zperiodic == 0)
|
||||
error->all(FLERR,
|
||||
"Cannot run 2d simulation with nonperiodic Z dimension");
|
||||
domain->set_initial_box();
|
||||
domain->set_global_box();
|
||||
domain->set_local_box();
|
||||
|
||||
} else if (ops[i].style == ORTHO) {
|
||||
if (domain->xy != 0.0 || domain->yz != 0.0 || domain->xz != 0.0)
|
||||
error->all(FLERR,
|
||||
"Cannot change box to orthogonal when tilt is non-zero");
|
||||
if (output->ndump)
|
||||
error->all(FLERR,
|
||||
"Cannot change box ortho/triclinic with dumps defined");
|
||||
for (int i = 0; i < modify->nfix; i++)
|
||||
if (modify->fix[i]->no_change_box)
|
||||
error->all(FLERR,
|
||||
"Cannot change box ortho/triclinic with "
|
||||
"certain fixes defined");
|
||||
domain->triclinic = 0;
|
||||
domain->set_initial_box();
|
||||
domain->set_global_box();
|
||||
domain->set_local_box();
|
||||
domain->print_box(" ");
|
||||
|
||||
} else if (ops[i].style == TRICLINIC) {
|
||||
if (output->ndump)
|
||||
error->all(FLERR,
|
||||
"Cannot change box ortho/triclinic with dumps defined");
|
||||
for (int i = 0; i < modify->nfix; i++)
|
||||
if (modify->fix[i]->no_change_box)
|
||||
error->all(FLERR,
|
||||
"Cannot change box ortho/triclinic with "
|
||||
"certain fixes defined");
|
||||
domain->triclinic = 1;
|
||||
domain->set_lamda_box();
|
||||
domain->set_initial_box();
|
||||
domain->set_global_box();
|
||||
domain->set_local_box();
|
||||
domain->print_box(" ");
|
||||
|
||||
} else if (ops[i].style == SET) {
|
||||
save_box_state();
|
||||
|
||||
} else if (ops[i].style == REMAP) {
|
||||
|
||||
// convert atoms to lamda coords, using last box state
|
||||
// convert atoms back to box coords, using current box state
|
||||
// save current box state
|
||||
|
||||
double **x = atom->x;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit)
|
||||
domain->x2lamda(x[i],x[i],boxlo,h_inv);
|
||||
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit)
|
||||
domain->lamda2x(x[i],x[i]);
|
||||
|
||||
save_box_state();
|
||||
}
|
||||
}
|
||||
|
||||
// clean up
|
||||
|
||||
delete [] ops;
|
||||
|
||||
// apply shrink-wrap boundary conditions
|
||||
|
||||
if (domain->nonperiodic == 2) domain->reset_box();
|
||||
|
||||
// move atoms back inside simulation box and to new processors
|
||||
// use remap() instead of pbc()
|
||||
// in case box moved a long distance relative to atoms
|
||||
// use irregular() in case box moved a long distance relative to atoms
|
||||
|
||||
double **x = atom->x;
|
||||
int *image = atom->image;
|
||||
int nlocal = atom->nlocal;
|
||||
for (i = 0; i < nlocal; i++) domain->remap(x[i],image[i]);
|
||||
|
||||
if (domain->triclinic) domain->x2lamda(atom->nlocal);
|
||||
domain->reset_box();
|
||||
Irregular *irregular = new Irregular(lmp);
|
||||
irregular->migrate_atoms();
|
||||
delete irregular;
|
||||
if (domain->triclinic) domain->lamda2x(atom->nlocal);
|
||||
|
||||
// check if any atoms were lost
|
||||
|
||||
bigint natoms;
|
||||
bigint nblocal = atom->nlocal;
|
||||
MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
|
||||
if (natoms != atom->natoms) {
|
||||
char str[128];
|
||||
sprintf(str,"Lost atoms via change_box: original " BIGINT_FORMAT
|
||||
" current " BIGINT_FORMAT,atom->natoms,natoms);
|
||||
error->warning(FLERR,str);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
parse optional parameters
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ChangeBox::options(int narg, char **arg)
|
||||
{
|
||||
if (narg < 0) error->all(FLERR,"Illegal change_box command");
|
||||
|
||||
scaleflag = 1;
|
||||
|
||||
int iarg = 0;
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg],"units") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal change_box command");
|
||||
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
|
||||
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
|
||||
else error->all(FLERR,"Illegal change_box command");
|
||||
iarg += 2;
|
||||
} else error->all(FLERR,"Illegal change_box command");
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
save current box state for converting atoms to lamda coords
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ChangeBox::save_box_state()
|
||||
{
|
||||
boxlo[0] = domain->boxlo[0];
|
||||
boxlo[1] = domain->boxlo[1];
|
||||
boxlo[2] = domain->boxlo[2];
|
||||
|
||||
for (int i = 0; i < 6; i++)
|
||||
h_inv[i] = domain->h_inv[i];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
reset box lengths of dim1/2 to preserve old volume
|
||||
which changed due to change in 3rd dim
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ChangeBox::volume_preserve(int dim1, int dim2, double oldvol)
|
||||
{
|
||||
double newvol;
|
||||
if (domain->dimension == 2) newvol = domain->xprd * domain->yprd;
|
||||
else newvol = domain->xprd * domain->yprd * domain->zprd;
|
||||
|
||||
double scale = oldvol/newvol;
|
||||
double mid,delta;
|
||||
|
||||
// change dim1 only
|
||||
|
||||
if (dim2 < 0) {
|
||||
mid = 0.5 * (domain->boxlo[dim1] + domain->boxhi[dim1]);
|
||||
delta = domain->boxlo[dim1] - mid;
|
||||
domain->boxlo[dim1] = mid + scale*delta;
|
||||
delta = domain->boxhi[dim1] - mid;
|
||||
domain->boxhi[dim1] = mid + scale*delta;
|
||||
|
||||
// change dim1 and dim2, keeping their relative aspect constant
|
||||
// means both are scaled by sqrt(scale)
|
||||
|
||||
} else {
|
||||
mid = 0.5 * (domain->boxlo[dim1] + domain->boxhi[dim1]);
|
||||
delta = domain->boxlo[dim1] - mid;
|
||||
domain->boxlo[dim1] = mid + sqrt(scale)*delta;
|
||||
delta = domain->boxhi[dim1] - mid;
|
||||
domain->boxhi[dim1] = mid + sqrt(scale)*delta;
|
||||
mid = 0.5 * (domain->boxlo[dim2] + domain->boxhi[dim2]);
|
||||
delta = domain->boxlo[dim2] - mid;
|
||||
domain->boxlo[dim2] = mid + sqrt(scale)*delta;
|
||||
delta = domain->boxhi[dim2] - mid;
|
||||
domain->boxhi[dim2] = mid + sqrt(scale)*delta;
|
||||
}
|
||||
}
|
||||
|
||||
@ -28,6 +28,28 @@ class ChangeBox : protected Pointers {
|
||||
public:
|
||||
ChangeBox(class LAMMPS *);
|
||||
void command(int, char **);
|
||||
|
||||
private:
|
||||
int scaleflag;
|
||||
double scale[3];
|
||||
|
||||
struct Operation {
|
||||
int style,flavor;
|
||||
int dim,boundindex;
|
||||
int vdim1,vdim2;
|
||||
double flo,fhi,ftilt;
|
||||
double dlo,dhi,dtilt;
|
||||
double scale;
|
||||
};
|
||||
|
||||
Operation *ops;
|
||||
int nops;
|
||||
|
||||
double boxlo[3],h_inv[6];
|
||||
|
||||
void options(int, char **);
|
||||
void save_box_state();
|
||||
void volume_preserve(int, int, double);
|
||||
};
|
||||
|
||||
}
|
||||
@ -37,7 +59,7 @@ class ChangeBox : protected Pointers {
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Change_box command before simulation box is defined
|
||||
E: Displace_box command before simulation box is defined
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
@ -47,22 +69,41 @@ Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Change_box operation is invalid
|
||||
E: Cannot displace_box after reading restart file with per-atom info
|
||||
|
||||
Cannot change orthogonal box to orthogonal or a triclinic box to
|
||||
triclinic.
|
||||
This is because the restart file info cannot be migrated with the
|
||||
atoms. You can get around this by performing a 0-timestep run which
|
||||
will assign the restart file info to actual atoms.
|
||||
|
||||
E: Cannot change box to orthogonal when tilt is non-zero
|
||||
E: Could not find displace_box group ID
|
||||
|
||||
Self-explanatory
|
||||
Group ID used in the displace_box command does not exist.
|
||||
|
||||
E: Cannot change box with dumps defined
|
||||
E: Displace_box tilt factors require triclinic box
|
||||
|
||||
Cannot use tilt factors unless the simulation box is
|
||||
non-orthogonal.
|
||||
|
||||
E: Cannot displace_box on a non-periodic boundary
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Cannot change box with certain fixes defined
|
||||
E: Use of displace_box with undefined lattice
|
||||
|
||||
The change_box command cannot be used when fix ave/spatial or
|
||||
fix/deform are defined .
|
||||
Must use lattice command with displace_box command if units option is
|
||||
set to lattice.
|
||||
|
||||
E: Fix deform volume setting is invalid
|
||||
|
||||
Cannot use volume style unless other dimensions are being controlled.
|
||||
|
||||
E: Induced tilt by displace_box is too large
|
||||
|
||||
The final tilt value must be between -1/2 and 1/2 of the perpendicular
|
||||
box length.
|
||||
|
||||
E: Lost atoms via displace_box: original %ld current %ld
|
||||
|
||||
UNDOCUMENTED
|
||||
|
||||
*/
|
||||
|
||||
@ -1,418 +0,0 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "lmptype.h"
|
||||
#include "mpi.h"
|
||||
#include "math.h"
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "displace_box.h"
|
||||
#include "atom.h"
|
||||
#include "modify.h"
|
||||
#include "domain.h"
|
||||
#include "lattice.h"
|
||||
#include "comm.h"
|
||||
#include "irregular.h"
|
||||
#include "group.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
enum{NONE,FINAL,DELTA,SCALE,VOLUME};
|
||||
enum{ONE_FROM_ONE,ONE_FROM_TWO,TWO_FROM_ONE};
|
||||
enum{NO_REMAP,X_REMAP};
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
DisplaceBox::DisplaceBox(LAMMPS *lmp) : Pointers(lmp) {}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DisplaceBox::command(int narg, char **arg)
|
||||
{
|
||||
int i;
|
||||
|
||||
if (domain->box_exist == 0)
|
||||
error->all(FLERR,"Displace_box command before simulation box is defined");
|
||||
if (narg < 2) error->all(FLERR,"Illegal displace_box command");
|
||||
if (modify->nfix_restart_peratom)
|
||||
error->all(FLERR,"Cannot displace_box after "
|
||||
"reading restart file with per-atom info");
|
||||
|
||||
if (comm->me == 0 && screen) fprintf(screen,"Displacing box ...\n");
|
||||
|
||||
// group
|
||||
|
||||
int igroup = group->find(arg[0]);
|
||||
if (igroup == -1) error->all(FLERR,"Could not find displace_box group ID");
|
||||
int groupbit = group->bitmask[igroup];
|
||||
|
||||
// set defaults
|
||||
|
||||
set = new Set[6];
|
||||
set[0].style = set[1].style = set[2].style =
|
||||
set[3].style = set[4].style = set[5].style = NONE;
|
||||
|
||||
// parse arguments
|
||||
|
||||
int triclinic = domain->triclinic;
|
||||
|
||||
int index;
|
||||
int iarg = 1;
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg],"x") == 0 || strcmp(arg[iarg],"y") == 0 ||
|
||||
strcmp(arg[iarg],"z") == 0) {
|
||||
if (strcmp(arg[iarg],"x") == 0) index = 0;
|
||||
else if (strcmp(arg[iarg],"y") == 0) index = 1;
|
||||
else if (strcmp(arg[iarg],"z") == 0) index = 2;
|
||||
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal displace_box command");
|
||||
if (strcmp(arg[iarg+1],"final") == 0) {
|
||||
if (iarg+4 > narg) error->all(FLERR,"Illegal displace_box command");
|
||||
set[index].style = FINAL;
|
||||
set[index].flo = atof(arg[iarg+2]);
|
||||
set[index].fhi = atof(arg[iarg+3]);
|
||||
iarg += 4;
|
||||
} else if (strcmp(arg[iarg+1],"delta") == 0) {
|
||||
if (iarg+4 > narg) error->all(FLERR,"Illegal displace_box command");
|
||||
set[index].style = DELTA;
|
||||
set[index].dlo = atof(arg[iarg+2]);
|
||||
set[index].dhi = atof(arg[iarg+3]);
|
||||
iarg += 4;
|
||||
} else if (strcmp(arg[iarg+1],"scale") == 0) {
|
||||
if (iarg+3 > narg) error->all(FLERR,"Illegal displace_box command");
|
||||
set[index].style = SCALE;
|
||||
set[index].scale = atof(arg[iarg+2]);
|
||||
iarg += 3;
|
||||
} else if (strcmp(arg[iarg+1],"volume") == 0) {
|
||||
set[index].style = VOLUME;
|
||||
iarg += 2;
|
||||
} else error->all(FLERR,"Illegal displace_box command");
|
||||
|
||||
} else if (strcmp(arg[iarg],"xy") == 0 || strcmp(arg[iarg],"xz") == 0 ||
|
||||
strcmp(arg[iarg],"yz") == 0) {
|
||||
if (triclinic == 0)
|
||||
error->all(FLERR,"Displace_box tilt factors require triclinic box");
|
||||
if (strcmp(arg[iarg],"xy") == 0) index = 5;
|
||||
else if (strcmp(arg[iarg],"xz") == 0) index = 4;
|
||||
else if (strcmp(arg[iarg],"yz") == 0) index = 3;
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal displace_box command");
|
||||
if (strcmp(arg[iarg+1],"final") == 0) {
|
||||
if (iarg+3 > narg) error->all(FLERR,"Illegal displace_box command");
|
||||
set[index].style = FINAL;
|
||||
set[index].ftilt = atof(arg[iarg+2]);
|
||||
iarg += 3;
|
||||
} else if (strcmp(arg[iarg+1],"delta") == 0) {
|
||||
if (iarg+3 > narg) error->all(FLERR,"Illegal displace_box command");
|
||||
set[index].style = DELTA;
|
||||
set[index].dtilt = atof(arg[iarg+2]);
|
||||
iarg += 3;
|
||||
} else error->all(FLERR,"Illegal displace_box command");
|
||||
|
||||
} else break;
|
||||
}
|
||||
|
||||
// read options from end of input line
|
||||
|
||||
options(narg-iarg,&arg[iarg]);
|
||||
|
||||
// check periodicity
|
||||
|
||||
if ((set[0].style && domain->xperiodic == 0) ||
|
||||
(set[1].style && domain->yperiodic == 0) ||
|
||||
(set[2].style && domain->zperiodic == 0))
|
||||
error->all(FLERR,"Cannot displace_box on a non-periodic boundary");
|
||||
|
||||
if (set[3].style && (domain->yperiodic == 0 || domain->zperiodic == 0))
|
||||
error->all(FLERR,"Cannot displace_box on a non-periodic boundary");
|
||||
if (set[4].style && (domain->xperiodic == 0 || domain->zperiodic == 0))
|
||||
error->all(FLERR,"Cannot displace_box on a non-periodic boundary");
|
||||
if (set[5].style && (domain->xperiodic == 0 || domain->yperiodic == 0))
|
||||
error->all(FLERR,"Cannot displace_box on a non-periodic boundary");
|
||||
|
||||
// apply scaling to FINAL,DELTA since they have distance units
|
||||
|
||||
int flag = 0;
|
||||
for (int i = 0; i < 6; i++)
|
||||
if (set[i].style == FINAL || set[i].style == DELTA) flag = 1;
|
||||
|
||||
if (flag && scaleflag && domain->lattice == NULL)
|
||||
error->all(FLERR,"Use of displace_box with undefined lattice");
|
||||
|
||||
double xscale,yscale,zscale;
|
||||
if (flag && scaleflag) {
|
||||
xscale = domain->lattice->xlattice;
|
||||
yscale = domain->lattice->ylattice;
|
||||
zscale = domain->lattice->zlattice;
|
||||
}
|
||||
else xscale = yscale = zscale = 1.0;
|
||||
|
||||
// for 3,4,5 scaling is in 1st dimension, e.g. x for xz
|
||||
|
||||
double map[6];
|
||||
map[0] = xscale; map[1] = yscale; map[2] = zscale;
|
||||
map[3] = yscale; map[4] = xscale; map[5] = xscale;
|
||||
|
||||
for (int i = 0; i < 3; i++) {
|
||||
if (set[i].style == FINAL) {
|
||||
set[i].flo *= map[i];
|
||||
set[i].fhi *= map[i];
|
||||
} else if (set[i].style == DELTA) {
|
||||
set[i].dlo *= map[i];
|
||||
set[i].dhi *= map[i];
|
||||
}
|
||||
}
|
||||
|
||||
for (int i = 3; i < 6; i++) {
|
||||
if (set[i].style == FINAL) set[i].ftilt *= map[i];
|
||||
else if (set[i].style == DELTA) set[i].dtilt *= map[i];
|
||||
}
|
||||
|
||||
// set initial/final values for box size and shape
|
||||
// final = initial if no setting
|
||||
|
||||
for (int i = 0; i < 3; i++) {
|
||||
set[i].lo_stop = set[i].lo_start = domain->boxlo[i];
|
||||
set[i].hi_stop = set[i].hi_start = domain->boxhi[i];
|
||||
|
||||
if (set[i].style == FINAL) {
|
||||
set[i].lo_stop = set[i].flo;
|
||||
set[i].hi_stop = set[i].fhi;
|
||||
} else if (set[i].style == DELTA) {
|
||||
set[i].lo_stop = set[i].lo_start + set[i].dlo;
|
||||
set[i].hi_stop = set[i].hi_start + set[i].dhi;
|
||||
} else if (set[i].style == SCALE) {
|
||||
set[i].lo_stop = 0.5*(set[i].lo_start+set[i].hi_start) -
|
||||
0.5*set[i].scale*(set[i].hi_start-set[i].lo_start);
|
||||
set[i].hi_stop = 0.5*(set[i].lo_start+set[i].hi_start) +
|
||||
0.5*set[i].scale*(set[i].hi_start-set[i].lo_start);
|
||||
}
|
||||
}
|
||||
|
||||
for (int i = 3; i < 6; i++) {
|
||||
if (i == 5) set[i].tilt_start = domain->xy;
|
||||
else if (i == 4) set[i].tilt_start = domain->xz;
|
||||
else if (i == 3) set[i].tilt_start = domain->yz;
|
||||
set[i].tilt_stop = set[i].tilt_start;
|
||||
|
||||
if (set[i].style == FINAL) {
|
||||
set[i].tilt_stop = set[i].ftilt;
|
||||
} else if (set[i].style == DELTA) {
|
||||
set[i].tilt_stop = set[i].tilt_start + set[i].dtilt;
|
||||
}
|
||||
}
|
||||
|
||||
// for VOLUME, setup links to other dims
|
||||
// fixed, dynamic1,2, vol_start
|
||||
|
||||
for (int i = 0; i < 3; i++) {
|
||||
set[i].vol_start = domain->xprd * domain->yprd * domain->zprd;
|
||||
|
||||
if (set[i].style != VOLUME) continue;
|
||||
int other1 = (i+1) % 3;
|
||||
int other2 = (i+2) % 3;
|
||||
|
||||
if (set[other1].style == NONE) {
|
||||
if (set[other2].style == NONE || set[other2].style == VOLUME)
|
||||
error->all(FLERR,"Fix deform volume setting is invalid");
|
||||
set[i].substyle = ONE_FROM_ONE;
|
||||
set[i].fixed = other1;
|
||||
set[i].dynamic1 = other2;
|
||||
} else if (set[other2].style == NONE) {
|
||||
if (set[other1].style == NONE || set[other1].style == VOLUME)
|
||||
error->all(FLERR,"Fix deform volume setting is invalid");
|
||||
set[i].substyle = ONE_FROM_ONE;
|
||||
set[i].fixed = other2;
|
||||
set[i].dynamic1 = other1;
|
||||
} else if (set[other1].style == VOLUME) {
|
||||
if (set[other2].style == NONE || set[other2].style == VOLUME)
|
||||
error->all(FLERR,"Fix deform volume setting is invalid");
|
||||
set[i].substyle = TWO_FROM_ONE;
|
||||
set[i].fixed = other1;
|
||||
set[i].dynamic1 = other2;
|
||||
} else if (set[other2].style == VOLUME) {
|
||||
if (set[other1].style == NONE || set[other1].style == VOLUME)
|
||||
error->all(FLERR,"Fix deform volume setting is invalid");
|
||||
set[i].substyle = TWO_FROM_ONE;
|
||||
set[i].fixed = other2;
|
||||
set[i].dynamic1 = other1;
|
||||
} else {
|
||||
set[i].substyle = ONE_FROM_TWO;
|
||||
set[i].dynamic2 = other1;
|
||||
set[i].dynamic2 = other2;
|
||||
}
|
||||
}
|
||||
|
||||
// set new box size for VOLUME dims that are linked to other dims
|
||||
|
||||
for (int i = 0; i < 3; i++) {
|
||||
if (set[i].style != VOLUME) continue;
|
||||
|
||||
if (set[i].substyle == ONE_FROM_ONE) {
|
||||
set[i].lo_stop = 0.5*(set[i].lo_start+set[i].hi_start) -
|
||||
0.5*(set[i].vol_start /
|
||||
(set[set[i].dynamic1].hi_stop -
|
||||
set[set[i].dynamic1].lo_stop) /
|
||||
(set[set[i].fixed].hi_start-set[set[i].fixed].lo_start));
|
||||
set[i].hi_stop = 0.5*(set[i].lo_start+set[i].hi_start) +
|
||||
0.5*(set[i].vol_start /
|
||||
(set[set[i].dynamic1].hi_stop -
|
||||
set[set[i].dynamic1].lo_stop) /
|
||||
(set[set[i].fixed].hi_start-set[set[i].fixed].lo_start));
|
||||
|
||||
} else if (set[i].substyle == ONE_FROM_TWO) {
|
||||
set[i].lo_stop = 0.5*(set[i].lo_start+set[i].hi_start) -
|
||||
0.5*(set[i].vol_start /
|
||||
(set[set[i].dynamic1].hi_stop -
|
||||
set[set[i].dynamic1].lo_stop) /
|
||||
(set[set[i].dynamic2].hi_stop -
|
||||
set[set[i].dynamic2].lo_stop));
|
||||
set[i].hi_stop = 0.5*(set[i].lo_start+set[i].hi_start) +
|
||||
0.5*(set[i].vol_start /
|
||||
(set[set[i].dynamic1].hi_stop -
|
||||
set[set[i].dynamic1].lo_stop) /
|
||||
(set[set[i].dynamic2].hi_stop -
|
||||
set[set[i].dynamic2].lo_stop));
|
||||
|
||||
} else if (set[i].substyle == TWO_FROM_ONE) {
|
||||
set[i].lo_stop = 0.5*(set[i].lo_start+set[i].hi_start) -
|
||||
0.5*sqrt(set[i].vol_start /
|
||||
(set[set[i].dynamic1].hi_stop -
|
||||
set[set[i].dynamic1].lo_stop) /
|
||||
(set[set[i].fixed].hi_start -
|
||||
set[set[i].fixed].lo_start) *
|
||||
(set[i].hi_start - set[i].lo_start));
|
||||
set[i].hi_stop = 0.5*(set[i].lo_start+set[i].hi_start) +
|
||||
0.5*sqrt(set[i].vol_start /
|
||||
(set[set[i].dynamic1].hi_stop -
|
||||
set[set[i].dynamic1].lo_stop) /
|
||||
(set[set[i].fixed].hi_start -
|
||||
set[set[i].fixed].lo_start) *
|
||||
(set[i].hi_start - set[i].lo_start));
|
||||
}
|
||||
}
|
||||
|
||||
// check that final tilt is not illegal value
|
||||
|
||||
double xprd_stop = set[0].hi_stop - set[0].lo_stop;
|
||||
double yprd_stop = set[0].hi_stop - set[0].lo_stop;
|
||||
|
||||
if (set[3].tilt_stop < -0.5*yprd_stop || set[3].tilt_stop > 0.5*yprd_stop ||
|
||||
set[4].tilt_stop < -0.5*xprd_stop || set[4].tilt_stop > 0.5*xprd_stop ||
|
||||
set[5].tilt_stop < -0.5*xprd_stop || set[5].tilt_stop > 0.5*xprd_stop)
|
||||
error->all(FLERR,"Induced tilt by displace_box is too large");
|
||||
|
||||
// convert atoms to lamda coords
|
||||
|
||||
if (remapflag == X_REMAP) {
|
||||
double **x = atom->x;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit)
|
||||
domain->x2lamda(x[i],x[i]);
|
||||
}
|
||||
|
||||
// reset global and local box to new size/shape
|
||||
|
||||
domain->boxlo[0] = set[0].lo_stop;
|
||||
domain->boxlo[1] = set[1].lo_stop;
|
||||
domain->boxlo[2] = set[2].lo_stop;
|
||||
domain->boxhi[0] = set[0].hi_stop;
|
||||
domain->boxhi[1] = set[1].hi_stop;
|
||||
domain->boxhi[2] = set[2].hi_stop;
|
||||
|
||||
if (triclinic) {
|
||||
domain->yz = set[3].tilt_stop;
|
||||
domain->xz = set[4].tilt_stop;
|
||||
domain->xy = set[5].tilt_stop;
|
||||
}
|
||||
|
||||
domain->set_global_box();
|
||||
domain->set_local_box();
|
||||
|
||||
// convert atoms back to box coords
|
||||
|
||||
if (remapflag == X_REMAP) {
|
||||
double **x = atom->x;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit)
|
||||
domain->lamda2x(x[i],x[i]);
|
||||
}
|
||||
|
||||
// move atoms back inside simulation box and to new processors
|
||||
// use remap() instead of pbc()
|
||||
// in case box moved a long distance relative to atoms
|
||||
// use irregular() in case box moved a long distance relative to atoms
|
||||
|
||||
double **x = atom->x;
|
||||
int *image = atom->image;
|
||||
int nlocal = atom->nlocal;
|
||||
for (i = 0; i < nlocal; i++) domain->remap(x[i],image[i]);
|
||||
|
||||
if (domain->triclinic) domain->x2lamda(atom->nlocal);
|
||||
domain->reset_box();
|
||||
Irregular *irregular = new Irregular(lmp);
|
||||
irregular->migrate_atoms();
|
||||
delete irregular;
|
||||
if (domain->triclinic) domain->lamda2x(atom->nlocal);
|
||||
|
||||
// clean up
|
||||
|
||||
delete [] set;
|
||||
|
||||
// check if any atoms were lost
|
||||
|
||||
bigint natoms;
|
||||
bigint nblocal = atom->nlocal;
|
||||
MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
|
||||
if (natoms != atom->natoms) {
|
||||
char str[128];
|
||||
sprintf(str,"Lost atoms via displace_box: original " BIGINT_FORMAT
|
||||
" current " BIGINT_FORMAT,atom->natoms,natoms);
|
||||
error->all(FLERR,str);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
parse optional parameters at end of displace_box input line
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void DisplaceBox::options(int narg, char **arg)
|
||||
{
|
||||
if (narg < 0) error->all(FLERR,"Illegal displace_box command");
|
||||
|
||||
remapflag = X_REMAP;
|
||||
scaleflag = 1;
|
||||
|
||||
int iarg = 0;
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg],"remap") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal displace_box command");
|
||||
if (strcmp(arg[iarg+1],"x") == 0) remapflag = X_REMAP;
|
||||
else if (strcmp(arg[iarg+1],"none") == 0) remapflag = NO_REMAP;
|
||||
else error->all(FLERR,"Illegal displace_box command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"units") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal displace_box command");
|
||||
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
|
||||
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
|
||||
else error->all(FLERR,"Illegal displace_box command");
|
||||
iarg += 2;
|
||||
} else error->all(FLERR,"Illegal displace_box command");
|
||||
}
|
||||
}
|
||||
@ -1,105 +0,0 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef COMMAND_CLASS
|
||||
|
||||
CommandStyle(displace_box,DisplaceBox)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_DISPLACE_BOX_H
|
||||
#define LMP_DISPLACE_BOX_H
|
||||
|
||||
#include "pointers.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class DisplaceBox : protected Pointers {
|
||||
public:
|
||||
DisplaceBox(class LAMMPS *);
|
||||
void command(int, char **);
|
||||
|
||||
private:
|
||||
int remapflag,scaleflag;
|
||||
|
||||
struct Set {
|
||||
int style,substyle;
|
||||
double flo,fhi,ftilt;
|
||||
double dlo,dhi,dtilt;
|
||||
double scale;
|
||||
double lo_start,hi_start;
|
||||
double lo_stop,hi_stop;
|
||||
double tilt_start,tilt_stop;
|
||||
double vol_start;
|
||||
int fixed,dynamic1,dynamic2;
|
||||
};
|
||||
Set *set;
|
||||
|
||||
void options(int, char **);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Displace_box command before simulation box is defined
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Cannot displace_box after reading restart file with per-atom info
|
||||
|
||||
This is because the restart file info cannot be migrated with the
|
||||
atoms. You can get around this by performing a 0-timestep run which
|
||||
will assign the restart file info to actual atoms.
|
||||
|
||||
E: Could not find displace_box group ID
|
||||
|
||||
Group ID used in the displace_box command does not exist.
|
||||
|
||||
E: Displace_box tilt factors require triclinic box
|
||||
|
||||
Cannot use tilt factors unless the simulation box is
|
||||
non-orthogonal.
|
||||
|
||||
E: Cannot displace_box on a non-periodic boundary
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Use of displace_box with undefined lattice
|
||||
|
||||
Must use lattice command with displace_box command if units option is
|
||||
set to lattice.
|
||||
|
||||
E: Fix deform volume setting is invalid
|
||||
|
||||
Cannot use volume style unless other dimensions are being controlled.
|
||||
|
||||
E: Induced tilt by displace_box is too large
|
||||
|
||||
The final tilt value must be between -1/2 and 1/2 of the perpendicular
|
||||
box length.
|
||||
|
||||
E: Lost atoms via displace_box: original %ld current %ld
|
||||
|
||||
UNDOCUMENTED
|
||||
|
||||
*/
|
||||
@ -1121,10 +1121,12 @@ int Domain::find_region(char *name)
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
boundary settings from the input script
|
||||
(re)set boundary settings
|
||||
flag = 0, called from the input script
|
||||
flag = 1, called from change box command
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Domain::set_boundary(int narg, char **arg)
|
||||
void Domain::set_boundary(int narg, char **arg, int flag)
|
||||
{
|
||||
if (narg != 3) error->all(FLERR,"Illegal boundary command");
|
||||
|
||||
@ -1139,7 +1141,10 @@ void Domain::set_boundary(int narg, char **arg)
|
||||
else if (c == 'f') boundary[idim][iside] = 1;
|
||||
else if (c == 's') boundary[idim][iside] = 2;
|
||||
else if (c == 'm') boundary[idim][iside] = 3;
|
||||
else error->all(FLERR,"Illegal boundary command");
|
||||
else {
|
||||
if (flag == 0) error->all(FLERR,"Illegal boundary command");
|
||||
if (flag == 1) error->all(FLERR,"Illegal change_box command");
|
||||
}
|
||||
}
|
||||
|
||||
for (int idim = 0; idim < 3; idim++)
|
||||
@ -1269,6 +1274,26 @@ void Domain::x2lamda(double *x, double *lamda)
|
||||
lamda[2] = h_inv[2]*delta[2];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
convert box coords to triclinic 0-1 lamda coords for one atom
|
||||
use my_boxlo & my_h_inv stored by caller for previous state of box
|
||||
lamda = H^-1 (x - x0)
|
||||
x and lamda can point to same 3-vector
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Domain::x2lamda(double *x, double *lamda,
|
||||
double *my_boxlo, double *my_h_inv)
|
||||
{
|
||||
double delta[3];
|
||||
delta[0] = x[0] - my_boxlo[0];
|
||||
delta[1] = x[1] - my_boxlo[1];
|
||||
delta[2] = x[2] - my_boxlo[2];
|
||||
|
||||
lamda[0] = my_h_inv[0]*delta[0] + my_h_inv[5]*delta[1] + my_h_inv[4]*delta[2];
|
||||
lamda[1] = my_h_inv[1]*delta[1] + my_h_inv[3]*delta[2];
|
||||
lamda[2] = my_h_inv[2]*delta[2];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
convert 8 lamda corner pts of lo/hi box to box coords
|
||||
return bboxlo/hi = bounding box around 8 corner pts in box coords
|
||||
|
||||
@ -107,7 +107,7 @@ class Domain : protected Pointers {
|
||||
void add_region(int, char **);
|
||||
void delete_region(int, char **);
|
||||
int find_region(char *);
|
||||
void set_boundary(int, char **);
|
||||
void set_boundary(int, char **, int);
|
||||
void print_box(const char *);
|
||||
|
||||
// load balancing
|
||||
@ -118,6 +118,7 @@ class Domain : protected Pointers {
|
||||
virtual void x2lamda(int);
|
||||
void lamda2x(double *, double *);
|
||||
void x2lamda(double *, double *);
|
||||
void x2lamda(double *, double *, double *, double *);
|
||||
void bbox(double *, double *, double *, double *);
|
||||
void box_corners();
|
||||
|
||||
|
||||
@ -930,7 +930,7 @@ void Input::boundary()
|
||||
{
|
||||
if (domain->box_exist)
|
||||
error->all(FLERR,"Boundary command after simulation box is defined");
|
||||
domain->set_boundary(narg,arg);
|
||||
domain->set_boundary(narg,arg,0);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -16,6 +16,7 @@
|
||||
#include "string.h"
|
||||
#include "ctype.h"
|
||||
#include "pair_hybrid.h"
|
||||
#include "style_pair.h"
|
||||
#include "atom.h"
|
||||
#include "force.h"
|
||||
#include "pair.h"
|
||||
@ -763,4 +764,3 @@ double PairHybrid::memory_usage()
|
||||
for (int m = 0; m < nstyles; m++) bytes += styles[m]->memory_usage();
|
||||
return bytes;
|
||||
}
|
||||
|
||||
|
||||
@ -622,8 +622,8 @@ void PairTable::compute_table(Table *tb)
|
||||
|
||||
// ep0,epn = dE/dr at inner and at cut
|
||||
|
||||
double ep0 = - tb->f[0];
|
||||
double epn = - tb->f[tlm1];
|
||||
double ep0 = - tb->f[0] / (2.0 * sqrt(tb->innersq));
|
||||
double epn = - tb->f[tlm1] / (2.0 * tb->cut);
|
||||
spline(tb->rsq,tb->e,tablength,ep0,epn,tb->e2);
|
||||
|
||||
// fp0,fpn = dh/dg at inner and at cut
|
||||
|
||||
@ -464,7 +464,8 @@ void ReadRestart::header()
|
||||
if (flag == VERSION) {
|
||||
char *version = read_char();
|
||||
if (strcmp(version,universe->version) != 0 && me == 0) {
|
||||
error->warning(FLERR,"Restart file version does not match LAMMPS version");
|
||||
error->warning(FLERR,
|
||||
"Restart file version does not match LAMMPS version");
|
||||
if (screen) fprintf(screen," restart file = %s, LAMMPS = %s\n",
|
||||
version,universe->version);
|
||||
}
|
||||
@ -581,7 +582,8 @@ void ReadRestart::header()
|
||||
boundary[2][0] != domain->boundary[2][0] ||
|
||||
boundary[2][1] != domain->boundary[2][1]) {
|
||||
if (me == 0)
|
||||
error->warning(FLERR,"Restart file used different boundary settings, "
|
||||
error->warning(FLERR,
|
||||
"Restart file used different boundary settings, "
|
||||
"using restart file values");
|
||||
}
|
||||
}
|
||||
|
||||
@ -1 +1 @@
|
||||
#define LAMMPS_VERSION "8 Feb 2012"
|
||||
#define LAMMPS_VERSION "10 Feb 2012"
|
||||
|
||||
Reference in New Issue
Block a user