From bbb9f5d88e2c26bf9801b514c305f66e1bf9b718 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 18 Jan 2013 16:03:05 +0000 Subject: [PATCH 01/12] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9293 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_tools.html | 12 ++++++++++++ doc/Section_tools.txt | 12 ++++++++++++ 2 files changed, 24 insertions(+) diff --git a/doc/Section_tools.html b/doc/Section_tools.html index cb60dcc14c..991a536ad3 100644 --- a/doc/Section_tools.html +++ b/doc/Section_tools.html @@ -54,6 +54,7 @@ own sub-directories with their own Makefiles.
  • eff
  • emacs
  • ipp +
  • kate
  • lmp2arc
  • lmp2cfg
  • lmp2vmd @@ -224,6 +225,17 @@ tools/createatoms tool's input file.

    +

    kate tool +

    +

    The file in the tools/kate directory is an add-on to the Kate editor +in the KDE suite that allow syntax highlighting of LAMMPS input +scripts. See the README.txt file for details. +

    +

    The file was provided by Alessandro Luigi Sellerio +(alessandro.sellerio at ieni.cnr.it). +

    +
    +

    lmp2arc tool

    The lmp2arc sub-directory contains a tool for converting LAMMPS output diff --git a/doc/Section_tools.txt b/doc/Section_tools.txt index 2d1a1d3fd5..ff9e807613 100644 --- a/doc/Section_tools.txt +++ b/doc/Section_tools.txt @@ -50,6 +50,7 @@ own sub-directories with their own Makefiles. "eff"_#eff "emacs"_#emacs "ipp"_#ipp +"kate"_#kate "lmp2arc"_#arc "lmp2cfg"_#cfg "lmp2vmd"_#vmd @@ -220,6 +221,17 @@ tools/createatoms tool's input file. :line +kate tool :h4,link(kate) + +The file in the tools/kate directory is an add-on to the Kate editor +in the KDE suite that allow syntax highlighting of LAMMPS input +scripts. See the README.txt file for details. + +The file was provided by Alessandro Luigi Sellerio +(alessandro.sellerio at ieni.cnr.it). + +:line + lmp2arc tool :h4,link(arc) The lmp2arc sub-directory contains a tool for converting LAMMPS output From 43e422a6833f1214136258719951f30ff3b6d67b Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 18 Jan 2013 16:04:11 +0000 Subject: [PATCH 02/12] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9294 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- tools/kate/README.txt | 6 + tools/kate/lammps.xml | 878 ++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 884 insertions(+) create mode 100644 tools/kate/README.txt create mode 100644 tools/kate/lammps.xml diff --git a/tools/kate/README.txt b/tools/kate/README.txt new file mode 100644 index 0000000000..7e35f46b57 --- /dev/null +++ b/tools/kate/README.txt @@ -0,0 +1,6 @@ +The lammps.xml file in this dir is for use with the Kate editor +in the KDE suite, to do syntax highlighting for LAMMPS input +scripts. + +The author is Alessandro Luigi Sellerio . +Please contact him with questions. diff --git a/tools/kate/lammps.xml b/tools/kate/lammps.xml new file mode 100644 index 0000000000..0d8ba0fda4 --- /dev/null +++ b/tools/kate/lammps.xml @@ -0,0 +1,878 @@ + + + + +]> + + + + + + angle_coeff + angle_style + atom_modify + atom_style + balance + bond_coeff + bond_style + boundary + box + change_box + clear + communicate + compute + compute_modify + create_atoms + create_box + delete_atoms + delete_bonds + dielectric + dihedral_coeff + dihedral_style + dimension + displace_atoms + dump + dump_image + dump_modify + echo + fix + fix_modify + group + if + improper_coeff + improper_style + include + jump + kspace_modify + kspace_style + label + lattice + log + mass + minimize + min_modify + min_style + neb + neigh_modify + neighbor + newton + next + package + pair_coeff + pair_modify + pair_style + pair_write + partition + prd + print + processors + quit + read_data + read_dump + read_restart + region + replicate + rerun + reset_timestep + restart + run + run_style + set + shell + special_bonds + suffix + tad + temper + thermo + thermo_modify + thermo_style + timestep + uncompute + undump + unfix + units + variable + velocity + write_restart + + + adapt + addforce + append/atoms + aveforce + ave/atom + ave/correlate + ave/histo + ave/spatial + ave/time + balance + bond/break + bond/create + bond/swap + box/relax + deform + deposit + drag + dt/reset + efield + enforce2d + evaporate + external + freeze + gcmc + gravity + heat + indent + langevin + lineforce + momentum + move + msst + neb + nph + nphug + nph/asphere + nph/sphere + npt + npt/asphere + npt/sphere + nve + nve/asphere + nve/asphere/noforce + nve/limit + nve/line + nve/noforce + nve/sphere + nve/tri + nvt + nvt/asphere + nvt/sllod + nvt/sphere + orient/fcc + planeforce + poems + pour + press/berendsen + print + qeq/comb + reax/bonds + recenter + restrain + rigid + rigid/nph + rigid/npt + rigid/nve + rigid/nvt + setforce + shake + spring + spring/rg + spring/self + srd + store/force + store/state + temp/berendsen + temp/rescale + thermal/conductivity + tmd + ttm + viscosity + viscous + wall/colloid + wall/gran + wall/harmonic + wall/lj126 + wall/lj93 + wall/piston + wall/reflect + wall/region + wall/srd + + + addtorque + atc + colvars + imd + langevin/eff + meso + meso/stationary + nph/eff + npt/eff + nve/eff + nvt/eff + nvt/sllod/eff + qeq/reax + reax/c/bonds + smd + temp/rescale/eff + + + freeze/cuda + addforce/cuda + aveforce/cuda + enforce2d/cuda + gravity/cuda + gravity/omp + npt/cuda + nve/cuda + nve/sphere/omp + nvt/cuda + qeq/comb/omp + setforce/cuda + shake/cuda + temp/berendsen/cuda + temp/rescale/cuda + temp/rescale/limit/cuda + viscous/cuda + + + angle/local + atom/molecule + bond/local + centro/atom + cluster/atom + cna/atom + com + com/molecule + contact/atom + coord/atom + damage/atom + dihedral/local + displace/atom + erotate/asphere + erotate/sphere + erotate/sphere/atom + event/displace + group/group + gyration + gyration/molecule + heat/flux + improper/local + ke + ke/atom + msd + msd/molecule + pair + pair/local + pe + pe/atom + pressure + property/atom + property/local + property/molecule + rdf + reduce + reduce/region + slice + stress/atom + temp + temp/asphere + temp/com + temp/deform + temp/partial + temp/profile + temp/ramp + temp/region + temp/sphere + + + ackland/atom + ke/eff + ke/atom/eff + meso_e/atom + meso_rho/atom + meso_t/atom + temp/eff + temp/deform/eff + temp/region/eff + temp/rotate + + + pe/cuda + pressure/cuda + temp/cuda + temp/partial/cuda + + + none + hybrid + hybrid/overlay + adp + airebo + beck + bop + born + born/coul/long + born/coul/wolf + brownian + brownian/poly + buck + buck/coul/cut + buck/coul/long + buck/long/coul/long + colloid + comb + coul/cut + coul/debye + coul/dsf + coul/long + coul/wolf + dipole/cut + dpd + dpd/tstat + dsmc + eam + eam/alloy + eam/fs + eim + gauss + gayberne + gran/hertz/history + gran/hooke + gran/hooke/history + hbond/dreiding/lj + hbond/dreiding/morse + kim + lcbop + line/lj + lj/charmm/coul/charmm + lj/charmm/coul/charmm/implicit + lj/charmm/coul/long + lj/class2 + lj/class2/coul/cut + lj/class2/coul/long + lj/cut + lj/cut/coul/cut + lj/cut/coul/debye + lj/cut/coul/dsf + lj/cut/coul/long + lj/long/coul/long + lj/cut/tip4p/long + lj/long/tip4p/long + lj/expand + lj/gromacs + lj/gromacs/coul/gromacs + lj/smooth + lj/smooth/linear + lj96/cut + lubricate + lubricate/poly + lubricateU + lubricateU/poly + meam + morse + peri/lps + peri/pmb + reax + rebo + resquared + soft + sw + table + tersoff + tersoff/zbl + tri/lj + yukawa + yukawa/colloid + + + awpmd/cut + coul/diel + dipole/sf + eam/cd + edip + eff/cut + gauss/cut + lj/sdk + lj/sdk/coul/long + lj/sf + meam/spline + meam/sw/spline + reax/c + sph/heatconduction + sph/idealgas + sph/lj + sph/rhosum + sph/taitwater + sph/taitwater/morris + tersoff/table + + + adp/omp + airebo/omp + beck/omp + born/coul/long/cuda + born/coul/long/gpu + born/coul/long/omp + born/coul/wolf/gpu + born/coul/wolf/omp + born/gpu + born/omp + brownian/omp + brownian/poly/omp + buck/coul/cut/cuda + buck/coul/cut/gpu + buck/coul/cut/omp + buck/coul/long/cuda + buck/coul/long/gpu + buck/coul/long/omp + buck/cuda + buck/long/coul/long/omp + buck/gpu + buck/omp + colloid/gpu + colloid/omp + comb/omp + coul/cut/omp + coul/debye/omp + coul/dsf/gpu + coul/long/gpu + coul/long/omp + coul/wolf + dipole/cut/gpu + dipole/cut/omp + dipole/sf/gpu + dipole/sf/omp + dpd/omp + dpd/tstat/omp + eam/alloy/cuda + eam/alloy/gpu + eam/alloy/omp + eam/alloy/opt + eam/cd/omp + eam/cuda + eam/fs/cuda + eam/fs/gpu + eam/fs/omp + eam/fs/opt + eam/gpu + eam/omp + eam/opt + edip/omp + eim/omp + gauss/gpu + gauss/omp + gayberne/gpu + gayberne/omp + gran/hertz/history/omp + gran/hooke/cuda + gran/hooke/history/omp + gran/hooke/omp + hbond/dreiding/lj/omp + hbond/dreiding/morse/omp + line/lj/omp + lj/charmm/coul/charmm/cuda + lj/charmm/coul/charmm/omp + lj/charmm/coul/charmm/implicit/cuda + lj/charmm/coul/charmm/implicit/omp + lj/charmm/coul/long/cuda + lj/charmm/coul/long/gpu + lj/charmm/coul/long/omp + lj/charmm/coul/long/opt + lj/charmm/coul/pppm/omp + lj/class2/coul/cut/cuda + lj/class2/coul/cut/omp + lj/class2/coul/long/cuda + lj/class2/coul/long/gpu + lj/class2/coul/pppm/omp + lj/class2/coul/long/omp + lj/class2/cuda + lj/class2/gpu + lj/class2/omp + lj/long/coul/long/omp + lj/cut/coul/cut/cuda + lj/cut/coul/cut/gpu + lj/cut/coul/cut/omp + lj/cut/coul/debye/cuda + lj/cut/coul/debye/gpu + lj/cut/coul/debye/omp + lj/cut/coul/dsf/gpu + lj/cut/coul/long/cuda + lj/cut/coul/long/gpu + lj/cut/coul/long/omp + lj/cut/coul/long/opt + lj/cut/coul/pppm/omp + lj/cut/cuda + lj/cut/experimental/cuda + lj/cut/gpu + lj/cut/omp + lj/cut/opt + lj/cut/tip4p/long/omp + lj/cut/tip4p/long/opt + lj/expand/cuda + lj/expand/gpu + lj/expand/omp + lj/gromacs/coul/gromacs/cuda + lj/gromacs/coul/gromacs/omp + lj/gromacs/cuda + lj/gromacs/omp + lj/sdk/gpu + lj/sdk/omp + lj/sdk/coul/long/gpu + lj/sdk/coul/long/omp + lj/sf/omp + lj/smooth/cuda + lj/smooth/omp + lj/smooth/linear/omp + lj96/cut/cuda + lj96/cut/gpu + lj96/cut/omp + lubricate/omp + lubricate/poly/omp + meam/spline/omp + morse/cuda + morse/gpu + morse/omp + morse/opt + peri/lps/omp + peri/pmb/omp + rebo/omp + resquared/gpu + resquared/omp + soft/omp + sw/cuda + sw/omp + table/gpu + table/omp + tersoff/cuda + tersoff/omp + tersoff/table/omp + tersoff/zbl/omp + tri/lj/omp + yukawa/gpu + yukawa/omp + yukawa/colloid/gpu + yukawa/colloid/omp + + + none + hybrid + class2 + fene + fene/expand + harmonic + morse + nonlinear + quartic + table + + + harmonic/shift + harmonic/shift/cut + + + class2/omp + fene/omp + fene/expand/omp + harmonic/omp + harmonic/shift/omp + harmonic/shift/cut/omp + morse/omp + nonlinear/omp + quartic/omp + table/omp + + + none + hybrid + charmm + class2 + cosine + cosine/delta + cosine/periodic + cosine/squared + harmonic + table + + + sdk + cosine/shift + cosine/shift/exp + dipole + fourier + fourier/simple + quartic + + + charmm/omp + class2/omp + cosine/omp + cosine/delta/omp + cosine/periodic/omp + cosine/shift/omp + cosine/shift/exp/omp + cosine/squared/omp + dipole/ompharmonic/omp + table/omp + + + none + hybrid + charmm + class2 + harmonic + helix + multi/harmonic + opls + + + cosine/shift/exp + fourier + nharmonic + quadratic + table + + + charmm/omp + class2/omp + cosine/shift/exp/omp + harmonic/omp + helix/omp + multi/harmonic/omp + opls/omptable/omp + + + none + hybrid + class2 + cvff + harmonic + umbrella + cossq + ring + class2/omp + cossq/omp + cvff/omp + fourier + harmonic/omp + ring/omp + umbrella/omp + + + ewald + ewald/disp + msm + pppm + pppm/cg + pppm/disp + pppm/disp/tip4p + pppm/tip4p + ewald/omp + pppm/cuda + pppm/gpu + pppm/omp + pppm/cg/omp + pppm/tip4p/omp + + + equal + add + sub + mult + div + + + NULL + EDGE + & + + + if + then + elif + else + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From 7866cd6a293b744c7c83379743e465be2a33c32d Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 18 Jan 2013 16:53:13 +0000 Subject: [PATCH 03/12] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9295 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/FLD/pair_brownian.cpp | 12 ++-- src/FLD/pair_brownian_poly.cpp | 10 +-- src/FLD/pair_lubricate.cpp | 12 ++-- src/FLD/pair_lubricateU.cpp | 20 +++--- src/FLD/pair_lubricateU_poly.cpp | 16 ++--- src/FLD/pair_lubricate_poly.cpp | 12 ++-- src/fix_wall.cpp | 106 +++++++++++++++++++++++-------- src/fix_wall.h | 23 ++++--- 8 files changed, 133 insertions(+), 78 deletions(-) diff --git a/src/FLD/pair_brownian.cpp b/src/FLD/pair_brownian.cpp index b4966dca52..1ff6dc2308 100755 --- a/src/FLD/pair_brownian.cpp +++ b/src/FLD/pair_brownian.cpp @@ -115,8 +115,8 @@ void PairBrownian::compute(int eflag, int vflag) for (int m = 0; m < wallfix->nwall; m++){ int dim = wallfix->wallwhich[m] / 2; int side = wallfix->wallwhich[m] % 2; - if (wallfix->wallstyle[m] == VARIABLE){ - wallcoord = input->variable->compute_equal(wallfix->varindex[m]); + if (wallfix->xstyle[m] == VARIABLE){ + wallcoord = input->variable->compute_equal(wallfix->xindex[m]); } else wallcoord = wallfix->coord0[m]; if (side == 0) walllo[dim] = wallcoord; @@ -503,7 +503,7 @@ void PairBrownian::init_style() flagdeform = 1; else if (strstr(modify->fix[i]->style,"wall") != NULL){ flagwall = 1; // Walls exist - if (((FixWall *) modify->fix[i])->varflag ) { + if (((FixWall *) modify->fix[i])->xflag ) { flagwall = 2; // Moving walls exist wallfix = (FixWall *) modify->fix[i]; } @@ -523,10 +523,10 @@ void PairBrownian::init_style() for (int m = 0; m < wallfix->nwall; m++){ int dim = wallfix->wallwhich[m] / 2; int side = wallfix->wallwhich[m] % 2; - if (wallfix->wallstyle[m] == VARIABLE){ - wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]); + if (wallfix->xstyle[m] == VARIABLE){ + wallfix->xindex[m] = input->variable->find(wallfix->xstr[m]); // Since fix->wall->init happens after pair->init_style - wallcoord = input->variable->compute_equal(wallfix->varindex[m]); + wallcoord = input->variable->compute_equal(wallfix->xindex[m]); } else wallcoord = wallfix->coord0[m]; diff --git a/src/FLD/pair_brownian_poly.cpp b/src/FLD/pair_brownian_poly.cpp index 379f2a7ce9..444ccd7442 100644 --- a/src/FLD/pair_brownian_poly.cpp +++ b/src/FLD/pair_brownian_poly.cpp @@ -101,8 +101,8 @@ void PairBrownianPoly::compute(int eflag, int vflag) for (int m = 0; m < wallfix->nwall; m++){ int dim = wallfix->wallwhich[m] / 2; int side = wallfix->wallwhich[m] % 2; - if (wallfix->wallstyle[m] == VARIABLE){ - wallcoord = input->variable->compute_equal(wallfix->varindex[m]); + if (wallfix->xstyle[m] == VARIABLE){ + wallcoord = input->variable->compute_equal(wallfix->xindex[m]); } else wallcoord = wallfix->coord0[m]; if (side == 0) walllo[dim] = wallcoord; @@ -363,10 +363,10 @@ void PairBrownianPoly::init_style() for (int m = 0; m < wallfix->nwall; m++){ int dim = wallfix->wallwhich[m] / 2; int side = wallfix->wallwhich[m] % 2; - if (wallfix->wallstyle[m] == VARIABLE){ - wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]); + if (wallfix->xstyle[m] == VARIABLE){ + wallfix->xindex[m] = input->variable->find(wallfix->xstr[m]); // Since fix->wall->init happens after pair->init_style - wallcoord = input->variable->compute_equal(wallfix->varindex[m]); + wallcoord = input->variable->compute_equal(wallfix->xindex[m]); } else wallcoord = wallfix->coord0[m]; diff --git a/src/FLD/pair_lubricate.cpp b/src/FLD/pair_lubricate.cpp index 570f6b4eed..0c473e470c 100755 --- a/src/FLD/pair_lubricate.cpp +++ b/src/FLD/pair_lubricate.cpp @@ -181,8 +181,8 @@ void PairLubricate::compute(int eflag, int vflag) for (int m = 0; m < wallfix->nwall; m++){ int dim = wallfix->wallwhich[m] / 2; int side = wallfix->wallwhich[m] % 2; - if (wallfix->wallstyle[m] == VARIABLE){ - wallcoord = input->variable->compute_equal(wallfix->varindex[m]); + if (wallfix->xstyle[m] == VARIABLE){ + wallcoord = input->variable->compute_equal(wallfix->xindex[m]); } else wallcoord = wallfix->coord0[m]; if (side == 0) walllo[dim] = wallcoord; @@ -597,7 +597,7 @@ void PairLubricate::init_style() } if (strstr(modify->fix[i]->style,"wall") != NULL){ flagwall = 1; // Walls exist - if (((FixWall *) modify->fix[i])->varflag ) { + if (((FixWall *) modify->fix[i])->xflag ) { flagwall = 2; // Moving walls exist wallfix = (FixWall *) modify->fix[i]; } @@ -619,10 +619,10 @@ void PairLubricate::init_style() for (int m = 0; m < wallfix->nwall; m++){ int dim = wallfix->wallwhich[m] / 2; int side = wallfix->wallwhich[m] % 2; - if (wallfix->wallstyle[m] == VARIABLE){ - wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]); + if (wallfix->xstyle[m] == VARIABLE){ + wallfix->xindex[m] = input->variable->find(wallfix->xstr[m]); //Since fix->wall->init happens after pair->init_style - wallcoord = input->variable->compute_equal(wallfix->varindex[m]); + wallcoord = input->variable->compute_equal(wallfix->xindex[m]); } else wallcoord = wallfix->coord0[m]; diff --git a/src/FLD/pair_lubricateU.cpp b/src/FLD/pair_lubricateU.cpp index 67c1aeac8b..eb3772451a 100644 --- a/src/FLD/pair_lubricateU.cpp +++ b/src/FLD/pair_lubricateU.cpp @@ -627,8 +627,8 @@ void PairLubricateU::compute_Fh(double **x) for (int m = 0; m < wallfix->nwall; m++){ int dim = wallfix->wallwhich[m] / 2; int side = wallfix->wallwhich[m] % 2; - if (wallfix->wallstyle[m] == VARIABLE){ - wallcoord = input->variable->compute_equal(wallfix->varindex[m]); + if (wallfix->xstyle[m] == VARIABLE){ + wallcoord = input->variable->compute_equal(wallfix->xindex[m]); } else wallcoord = wallfix->coord0[m]; if (side == 0) walllo[dim] = wallcoord; @@ -866,8 +866,8 @@ void PairLubricateU::compute_RU() for (int m = 0; m < wallfix->nwall; m++){ int dim = wallfix->wallwhich[m] / 2; int side = wallfix->wallwhich[m] % 2; - if (wallfix->wallstyle[m] == VARIABLE){ - wallcoord = input->variable->compute_equal(wallfix->varindex[m]); + if (wallfix->xstyle[m] == VARIABLE){ + wallcoord = input->variable->compute_equal(wallfix->xindex[m]); } else wallcoord = wallfix->coord0[m]; if (side == 0) walllo[dim] = wallcoord; @@ -1143,8 +1143,8 @@ void PairLubricateU::compute_RU(double **x) for (int m = 0; m < wallfix->nwall; m++){ int dim = wallfix->wallwhich[m] / 2; int side = wallfix->wallwhich[m] % 2; - if (wallfix->wallstyle[m] == VARIABLE){ - wallcoord = input->variable->compute_equal(wallfix->varindex[m]); + if (wallfix->xstyle[m] == VARIABLE){ + wallcoord = input->variable->compute_equal(wallfix->xindex[m]); } else wallcoord = wallfix->coord0[m]; if (side == 0) walllo[dim] = wallcoord; @@ -1879,7 +1879,7 @@ void PairLubricateU::init_style() flagdeform = 1; else if (strstr(modify->fix[i]->style,"wall") != NULL){ flagwall = 1; // Walls exist - if (((FixWall *) modify->fix[i])->varflag ) { + if (((FixWall *) modify->fix[i])->xflag ) { flagwall = 2; // Moving walls exist wallfix = (FixWall *) modify->fix[i]; } @@ -1899,10 +1899,10 @@ void PairLubricateU::init_style() for (int m = 0; m < wallfix->nwall; m++){ int dim = wallfix->wallwhich[m] / 2; int side = wallfix->wallwhich[m] % 2; - if (wallfix->wallstyle[m] == VARIABLE){ - wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]); + if (wallfix->xstyle[m] == VARIABLE){ + wallfix->xindex[m] = input->variable->find(wallfix->xstr[m]); //Since fix->wall->init happens after pair->init_style - wallcoord = input->variable->compute_equal(wallfix->varindex[m]); + wallcoord = input->variable->compute_equal(wallfix->xindex[m]); } else wallcoord = wallfix->coord0[m]; diff --git a/src/FLD/pair_lubricateU_poly.cpp b/src/FLD/pair_lubricateU_poly.cpp index 19b4ae818c..2a451b3652 100644 --- a/src/FLD/pair_lubricateU_poly.cpp +++ b/src/FLD/pair_lubricateU_poly.cpp @@ -379,8 +379,8 @@ void PairLubricateUPoly::compute_Fh(double **x) for (int m = 0; m < wallfix->nwall; m++){ int dim = wallfix->wallwhich[m] / 2; int side = wallfix->wallwhich[m] % 2; - if (wallfix->wallstyle[m] == VARIABLE){ - wallcoord = input->variable->compute_equal(wallfix->varindex[m]); + if (wallfix->xstyle[m] == VARIABLE){ + wallcoord = input->variable->compute_equal(wallfix->xindex[m]); } else wallcoord = wallfix->coord0[m]; if (side == 0) walllo[dim] = wallcoord; @@ -660,8 +660,8 @@ void PairLubricateUPoly::compute_RU(double **x) for (int m = 0; m < wallfix->nwall; m++){ int dim = wallfix->wallwhich[m] / 2; int side = wallfix->wallwhich[m] % 2; - if (wallfix->wallstyle[m] == VARIABLE){ - wallcoord = input->variable->compute_equal(wallfix->varindex[m]); + if (wallfix->xstyle[m] == VARIABLE){ + wallcoord = input->variable->compute_equal(wallfix->xindex[m]); } else wallcoord = wallfix->coord0[m]; if (side == 0) walllo[dim] = wallcoord; @@ -1212,7 +1212,7 @@ void PairLubricateUPoly::init_style() flagdeform = 1; else if (strstr(modify->fix[i]->style,"wall") != NULL){ flagwall = 1; // Walls exist - if (((FixWall *) modify->fix[i])->varflag ) { + if (((FixWall *) modify->fix[i])->xflag ) { flagwall = 2; // Moving walls exist wallfix = (FixWall *) modify->fix[i]; } @@ -1233,10 +1233,10 @@ void PairLubricateUPoly::init_style() for (int m = 0; m < wallfix->nwall; m++){ int dim = wallfix->wallwhich[m] / 2; int side = wallfix->wallwhich[m] % 2; - if (wallfix->wallstyle[m] == VARIABLE){ - wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]); + if (wallfix->xstyle[m] == VARIABLE){ + wallfix->xindex[m] = input->variable->find(wallfix->xstr[m]); //Since fix->wall->init happens after pair->init_style - wallcoord = input->variable->compute_equal(wallfix->varindex[m]); + wallcoord = input->variable->compute_equal(wallfix->xindex[m]); } else wallcoord = wallfix->coord0[m]; diff --git a/src/FLD/pair_lubricate_poly.cpp b/src/FLD/pair_lubricate_poly.cpp index 47909db667..f2aad523e0 100644 --- a/src/FLD/pair_lubricate_poly.cpp +++ b/src/FLD/pair_lubricate_poly.cpp @@ -165,8 +165,8 @@ void PairLubricatePoly::compute(int eflag, int vflag) for (int m = 0; m < wallfix->nwall; m++){ int dim = wallfix->wallwhich[m] / 2; int side = wallfix->wallwhich[m] % 2; - if (wallfix->wallstyle[m] == VARIABLE){ - wallcoord = input->variable->compute_equal(wallfix->varindex[m]); + if (wallfix->xstyle[m] == VARIABLE){ + wallcoord = input->variable->compute_equal(wallfix->xindex[m]); } else wallcoord = wallfix->coord0[m]; if (side == 0) walllo[dim] = wallcoord; @@ -492,7 +492,7 @@ void PairLubricatePoly::init_style() } if (strstr(modify->fix[i]->style,"wall") != NULL){ flagwall = 1; // Walls exist - if (((FixWall *) modify->fix[i])->varflag ) { + if (((FixWall *) modify->fix[i])->xflag ) { flagwall = 2; // Moving walls exist wallfix = (FixWall *) modify->fix[i]; } @@ -511,10 +511,10 @@ void PairLubricatePoly::init_style() for (int m = 0; m < wallfix->nwall; m++){ int dim = wallfix->wallwhich[m] / 2; int side = wallfix->wallwhich[m] % 2; - if (wallfix->wallstyle[m] == VARIABLE){ - wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]); + if (wallfix->xstyle[m] == VARIABLE){ + wallfix->xindex[m] = input->variable->find(wallfix->xstr[m]); //Since fix->wall->init happens after pair->init_style - wallcoord = input->variable->compute_equal(wallfix->varindex[m]); + wallcoord = input->variable->compute_equal(wallfix->xindex[m]); } else wallcoord = wallfix->coord0[m]; diff --git a/src/fix_wall.cpp b/src/fix_wall.cpp index 4181c2c897..70fcbbea2c 100644 --- a/src/fix_wall.cpp +++ b/src/fix_wall.cpp @@ -49,6 +49,8 @@ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) : fldflag = 0; int pbcflag = 0; + for (int i = 0; i < 6; i++) xstr[i] = estr[i] = sstr[i] = NULL; + int iarg = 3; while (iarg < narg) { if ((strcmp(arg[iarg],"xlo") == 0) || (strcmp(arg[iarg],"xhi") == 0) || @@ -70,23 +72,41 @@ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) : wallwhich[nwall] = newwall; if (strcmp(arg[iarg+1],"EDGE") == 0) { - wallstyle[nwall] = EDGE; + xstyle[nwall] = EDGE; int dim = wallwhich[nwall] / 2; int side = wallwhich[nwall] % 2; if (side == 0) coord0[nwall] = domain->boxlo[dim]; else coord0[nwall] = domain->boxhi[dim]; } else if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) { - wallstyle[nwall] = VARIABLE; + xstyle[nwall] = VARIABLE; int n = strlen(&arg[iarg+1][2]) + 1; - varstr[nwall] = new char[n]; - strcpy(varstr[nwall],&arg[iarg+1][2]); + xstr[nwall] = new char[n]; + strcpy(xstr[nwall],&arg[iarg+1][2]); } else { - wallstyle[nwall] = CONSTANT; + xstyle[nwall] = CONSTANT; coord0[nwall] = atof(arg[iarg+1]); } - epsilon[nwall] = atof(arg[iarg+2]); - sigma[nwall] = atof(arg[iarg+3]); + if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) { + int n = strlen(&arg[iarg+2][2]) + 1; + estr[nwall] = new char[n]; + strcpy(estr[nwall],&arg[iarg+2][2]); + estyle[nwall] = VARIABLE; + } else { + epsilon[nwall] = atof(arg[iarg+2]); + estyle[nwall] = CONSTANT; + } + + if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) { + int n = strlen(&arg[iarg+3][2]) + 1; + sstr[nwall] = new char[n]; + strcpy(sstr[nwall],&arg[iarg+3][2]); + sstyle[nwall] = VARIABLE; + } else { + sigma[nwall] = atof(arg[iarg+3]); + sstyle[nwall] = CONSTANT; + } + cutoff[nwall] = atof(arg[iarg+4]); nwall++; iarg += 5; @@ -136,11 +156,11 @@ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) : } } - // scale factors for CONSTANT and VARIABLE walls + // scale factors for wall position for CONSTANT and VARIABLE walls int flag = 0; for (int m = 0; m < nwall; m++) - if (wallstyle[m] != EDGE) flag = 1; + if (xstyle[m] != EDGE) flag = 1; if (flag) { if (scaleflag && domain->lattice == NULL) @@ -154,18 +174,24 @@ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) : else xscale = yscale = zscale = 1.0; for (int m = 0; m < nwall; m++) { - if (wallstyle[m] != CONSTANT) continue; + if (xstyle[m] != CONSTANT) continue; if (wallwhich[m] < YLO) coord0[m] *= xscale; else if (wallwhich[m] < ZLO) coord0[m] *= yscale; else coord0[m] *= zscale; } } - // set varflag if any wall positions are variable + // set xflag if any wall positions are variable + // set vflag if any wall positions are variable + // set wstyle to VARIABLE if either epsilon or sigma is a variable - varflag = 0; - for (int m = 0; m < nwall; m++) - if (wallstyle[m] == VARIABLE) varflag = 1; + vflag = xflag = 0; + for (int m = 0; m < nwall; m++) { + if (xstyle[m] == VARIABLE) xflag = 1; + if (xflag || estyle[m] == VARIABLE || sstyle[m] == VARIABLE) vflag = 1; + if (estyle[m] == VARIABLE || sstyle[m] == VARIABLE) wstyle[m] = VARIABLE; + else wstyle[m] = CONSTANT; + } eflag = 0; for (int m = 0; m <= nwall; m++) ewall[m] = 0.0; @@ -175,8 +201,11 @@ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) : FixWall::~FixWall() { - for (int m = 0; m < nwall; m++) - if (wallstyle[m] == VARIABLE) delete [] varstr[m]; + for (int m = 0; m < nwall; m++) { + delete [] xstr[m]; + delete [] estr[m]; + delete [] sstr[m]; + } } /* ---------------------------------------------------------------------- */ @@ -203,12 +232,27 @@ void FixWall::init() dt = update->dt; for (int m = 0; m < nwall; m++) { - if (wallstyle[m] != VARIABLE) continue; - varindex[m] = input->variable->find(varstr[m]); - if (varindex[m] < 0) - error->all(FLERR,"Variable name for fix wall does not exist"); - if (!input->variable->equalstyle(varindex[m])) - error->all(FLERR,"Variable for fix wall is invalid style"); + if (xstyle[m] == VARIABLE) { + xindex[m] = input->variable->find(xstr[m]); + if (xindex[m] < 0) + error->all(FLERR,"Variable name for fix wall does not exist"); + if (!input->variable->equalstyle(xindex[m])) + error->all(FLERR,"Variable for fix wall is invalid style"); + } + if (estyle[m] == VARIABLE) { + eindex[m] = input->variable->find(estr[m]); + if (eindex[m] < 0) + error->all(FLERR,"Variable name for fix wall does not exist"); + if (!input->variable->equalstyle(eindex[m])) + error->all(FLERR,"Variable for fix wall is invalid style"); + } + if (sstyle[m] == VARIABLE) { + sindex[m] = input->variable->find(sstr[m]); + if (sindex[m] < 0) + error->all(FLERR,"Variable name for fix wall does not exist"); + if (!input->variable->equalstyle(sindex[m])) + error->all(FLERR,"Variable for fix wall is invalid style"); + } } // setup coefficients @@ -256,23 +300,31 @@ void FixWall::post_force(int vflag) for (int m = 0; m <= nwall; m++) ewall[m] = 0.0; // coord = current position of wall - // evaluate variable if necessary, wrap with clear/add + // evaluate variables if necessary, wrap with clear/add + // for epsilon/sigma variables need to re-invoke precompute() - if (varflag) modify->clearstep_compute(); + if (vflag) modify->clearstep_compute(); double coord; for (int m = 0; m < nwall; m++) { - if (wallstyle[m] == VARIABLE) { - coord = input->variable->compute_equal(varindex[m]); + if (xstyle[m] == VARIABLE) { + coord = input->variable->compute_equal(xindex[m]); if (wallwhich[m] < YLO) coord *= xscale; else if (wallwhich[m] < ZLO) coord *= yscale; else coord *= zscale; } else coord = coord0[m]; + if (wstyle[m] == VARIABLE) { + if (estyle[m] == VARIABLE) + epsilon[m] = input->variable->compute_equal(eindex[m]); + if (sstyle[m] == VARIABLE) + sigma[m] = input->variable->compute_equal(sindex[m]); + precompute(m); + } wall_particle(m,wallwhich[m],coord); } - if (varflag) modify->addstep_compute(update->ntimestep + 1); + if (vflag) modify->addstep_compute(update->ntimestep + 1); } /* ---------------------------------------------------------------------- */ diff --git a/src/fix_wall.h b/src/fix_wall.h index 84f824b6e8..eee3cf6025 100644 --- a/src/fix_wall.h +++ b/src/fix_wall.h @@ -20,6 +20,14 @@ namespace LAMMPS_NS { class FixWall : public Fix { public: + int nwall; + int wallwhich[6]; + double coord0[6]; + int xflag; // 1 if any wall position is a variable + int xstyle[6]; + int xindex[6]; + char *xstr[6]; + FixWall(class LAMMPS *, int, char **); virtual ~FixWall(); int setmask(); @@ -36,20 +44,15 @@ class FixWall : public Fix { virtual void precompute(int) = 0; virtual void wall_particle(int, int, double) = 0; - int nwall; - int wallwhich[6]; - double coord0[6]; - int varflag; - int wallstyle[6]; - int varindex[6]; - char *varstr[6]; - - protected: double epsilon[6],sigma[6],cutoff[6]; double ewall[7],ewall_all[7]; double xscale,yscale,zscale; - int eflag; + int estyle[6],sstyle[6],wstyle[6]; + int eindex[6],sindex[6]; + char *estr[6],*sstr[6]; + int vflag; // 1 if any wall position,epsilon,sigma is a var + int eflag; // per-wall flag for energy summation int nlevels_respa; double dt; int fldflag; From 580cecfd0971b7a5e38cbe4e573e73f42d4521ba Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 18 Jan 2013 16:58:14 +0000 Subject: [PATCH 04/12] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9296 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/fix_adapt.html | 11 +++++++---- doc/fix_adapt.txt | 8 ++++++-- doc/fix_wall.html | 28 +++++++++++++++++++++------- doc/fix_wall.txt | 17 +++++++++++++++-- 4 files changed, 49 insertions(+), 15 deletions(-) diff --git a/doc/fix_adapt.html b/doc/fix_adapt.html index cfbf36373b..28b0d9cb40 100644 --- a/doc/fix_adapt.html +++ b/doc/fix_adapt.html @@ -42,9 +42,8 @@ 

      scale value = no or yes
     no = the variable value is the new setting
-    yes = the variable value multiplies the original setting 
-
    -
      reset value = no or yes
+    yes = the variable value multiplies the original setting
+  reset value = no or yes
     no = values will remain altered at the end of a run
     yes = reset altered values to their original values at the end of a run
    @@ -65,7 +64,11 @@ attributes which can be varied by this fix are discussed below. Many other fixes can also be used to time-vary simulation parameters, e.g. the "fix deform" command will change the simulation box size/shape and the "fix move" command will change atom positions and -velocities in a prescribed manner. +velocities in a prescribed manner. Also note that many commands allow +variables as arguments for specific parameters, if described in that +manner on their doc pages. An equal-style variable can calculate a +time-dependent quantity, so this is another way to vary a simulation +parameter over time.

    If N is specified as 0, the specified attributes are only changed once, before the simulation begins. This is all that is needed if the diff --git a/doc/fix_adapt.txt b/doc/fix_adapt.txt index 6c7b6ef356..bd9bc5a9a7 100644 --- a/doc/fix_adapt.txt +++ b/doc/fix_adapt.txt @@ -31,7 +31,7 @@ zero or more keyword/value pairs may be appended :l keyword = {scale} or {reset} :l {scale} value = {no} or {yes} {no} = the variable value is the new setting - {yes} = the variable value multiplies the original setting :pre + {yes} = the variable value multiplies the original setting {reset} value = {no} or {yes} {no} = values will remain altered at the end of a run {yes} = reset altered values to their original values at the end of a run :pre @@ -52,7 +52,11 @@ attributes which can be varied by this fix are discussed below. Many other fixes can also be used to time-vary simulation parameters, e.g. the "fix deform" command will change the simulation box size/shape and the "fix move" command will change atom positions and -velocities in a prescribed manner. +velocities in a prescribed manner. Also note that many commands allow +variables as arguments for specific parameters, if described in that +manner on their doc pages. An equal-style variable can calculate a +time-dependent quantity, so this is another way to vary a simulation +parameter over time. If {N} is specified as 0, the specified attributes are only changed once, before the simulation begins. This is all that is needed if the diff --git a/doc/fix_wall.html b/doc/fix_wall.html index 5e8f1546d9..281d36a005 100644 --- a/doc/fix_wall.html +++ b/doc/fix_wall.html @@ -29,14 +29,18 @@

  • face = xlo or xhi or ylo or yhi or zlo or zhi -
      args = coord epsilon sigma cutoff
+
  •   args = coord epsilon sigma cutoff
     coord = position of wall = EDGE or constant or variable
       EDGE = current lo or hi edge of simulation box
       constant = number like 0.0 or -30.0 (distance units)
       variable = equal-style variable like v_x or v_wiggle
     epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units)
-    sigma = size factor for wall-particle interaction (distance units)
-    cutoff = distance from wall at which wall-particle interaction is cut off (distance units) 
+      epsilon can be a variable (see below) 
+
+
  •     sigma = size factor for wall-particle interaction (distance units)
+      sigma can be a variable (see below) 
+
+
        cutoff = distance from wall at which wall-particle interaction is cut off (distance units) 
 
    
 
  • zero or more keyword/value pairs may be appended 
 
@@ -47,9 +51,8 @@
     box = the wall position is defined in simulation box units
   fld value = yes or no
     yes = invoke the wall constraint to be compatible with implicit FLD
-    no = invoke the wall constraint in the normal way 
-
    • -
      pbc value = yes or no
+    no = invoke the wall constraint in the normal way
+  pbc value = yes or no
     yes = allow periodic boundary in a wall dimension
     no = require non-perioidic boundaries in any wall dimension
    @@ -144,6 +147,16 @@ constant K, and has units (energy/distance^2). The input parameter spring is at the cutoff. This is a repulsive-only spring since the interaction is truncated at the cutoff

    +

    For any wall, the epsilon and/or sigma parameter can be specified +as an equal-style variable, in which case it should be +specified as v_name, where name is the variable name. As with a +variable wall position, the variable is evaluated each timestep and +the result becomes the current epsilon or sigma of the wall. +Equal-style variables can specify formulas with various mathematical +functions, and include thermo_style command +keywords for the simulation box parameters and timestep and elapsed +time. Thus it is easy to specify a time-dependent wall interaction. +

    IMPORTANT NOTE: For all of the styles, you must insure that r is always > 0 for all particles in the group, or LAMMPS will generate an error. This means you cannot start your simulation with particles at @@ -194,7 +207,8 @@ want.

    Here are examples of variable definitions that move the wall position in a time-dependent fashion using equal-style -variables. +variables. The wall interaction parameters (epsilon, +sigma) could be varied with additional variable definitions. 

    variable ramp equal ramp(0,10)
 fix 1 all wall xlo v_ramp 1.0 1.0 2.5 
diff --git a/doc/fix_wall.txt b/doc/fix_wall.txt
index 3874587bd0..803aff618e 100644
--- a/doc/fix_wall.txt
+++ b/doc/fix_wall.txt
@@ -25,7 +25,9 @@ face = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} :l
       constant = number like 0.0 or -30.0 (distance units)
       variable = "equal-style variable"_variable.html like v_x or v_wiggle
     epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units)
+      epsilon can be a variable (see below) :l
     sigma = size factor for wall-particle interaction (distance units)
+      sigma can be a variable (see below) :l
     cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :pre
 zero or more keyword/value pairs may be appended :l
 keyword = {units} or {fld} :l
@@ -34,7 +36,7 @@ keyword = {units} or {fld} :l
     {box} = the wall position is defined in simulation box units
   {fld} value = {yes} or {no}
     {yes} = invoke the wall constraint to be compatible with implicit FLD
-    {no} = invoke the wall constraint in the normal way :pre
+    {no} = invoke the wall constraint in the normal way
   {pbc} value = {yes} or {no}
     {yes} = allow periodic boundary in a wall dimension
     {no} = require non-perioidic boundaries in any wall dimension :pre
@@ -129,6 +131,16 @@ constant K, and has units (energy/distance^2).  The input parameter
 spring is at the {cutoff}.  This is a repulsive-only spring since the
 interaction is truncated at the {cutoff}
 
+For any wall, the {epsilon} and/or {sigma} parameter can be specified
+as an "equal-style variable"_variable.html, in which case it should be
+specified as v_name, where name is the variable name.  As with a
+variable wall position, the variable is evaluated each timestep and
+the result becomes the current epsilon or sigma of the wall.
+Equal-style variables can specify formulas with various mathematical
+functions, and include "thermo_style"_thermo_style.html command
+keywords for the simulation box parameters and timestep and elapsed
+time.  Thus it is easy to specify a time-dependent wall interaction.
+
 IMPORTANT NOTE: For all of the styles, you must insure that r is
 always > 0 for all particles in the group, or LAMMPS will generate an
 error.  This means you cannot start your simulation with particles at
@@ -179,7 +191,8 @@ want.
 
 Here are examples of variable definitions that move the wall position
 in a time-dependent fashion using equal-style
-"variables"_variable.html.
+"variables"_variable.html.  The wall interaction parameters (epsilon,
+sigma) could be varied with additional variable definitions.
 
 variable ramp equal ramp(0,10)
 fix 1 all wall xlo v_ramp 1.0 1.0 2.5 :pre

From aa62e9b389830676c409d376848dec6a59d58f9f Mon Sep 17 00:00:00 2001
From: sjplimp 
Date: Fri, 18 Jan 2013 16:59:43 +0000
Subject: [PATCH 05/12] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@9297
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 src/version.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/version.h b/src/version.h
index 840d95c190..06f5372acb 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "19 Jan 2013"
+#define LAMMPS_VERSION "20 Jan 2013"

From 2d6d2de507ff921827d4a23f168a819f0abe2a60 Mon Sep 17 00:00:00 2001
From: sjplimp 
Date: Fri, 18 Jan 2013 20:39:12 +0000
Subject: [PATCH 06/12] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@9299
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 src/fix_wall.cpp         | 10 ++++++--
 src/region.cpp           | 34 ++++++++++++++++++++-------
 src/region.h             | 17 ++++++++++----
 src/region_intersect.cpp |  3 ++-
 src/region_sphere.cpp    | 50 +++++++++++++++++++++++++++++++++++++---
 src/region_sphere.h      |  6 +++++
 src/variable.cpp         | 12 +++++-----
 7 files changed, 108 insertions(+), 24 deletions(-)

diff --git a/src/fix_wall.cpp b/src/fix_wall.cpp
index 70fcbbea2c..297f22741c 100644
--- a/src/fix_wall.cpp
+++ b/src/fix_wall.cpp
@@ -314,10 +314,16 @@ void FixWall::post_force(int vflag)
       else coord *= zscale;
     } else coord = coord0[m];
     if (wstyle[m] == VARIABLE) {
-      if (estyle[m] == VARIABLE)
+      if (estyle[m] == VARIABLE) {
         epsilon[m] = input->variable->compute_equal(eindex[m]);
-      if (sstyle[m] == VARIABLE)
+        if (epsilon[m] < 0.0)
+          error->all(FLERR,"Variable evaluation in fix wall gave bad value");
+      }
+      if (sstyle[m] == VARIABLE) {
         sigma[m] = input->variable->compute_equal(sindex[m]);
+        if (sigma[m] < 0.0) 
+          error->all(FLERR,"Variable evaluation in fix wall gave bad value");
+      }
       precompute(m);
     }
 
diff --git a/src/region.cpp b/src/region.cpp
index a9d27e1a38..14f7155e4a 100644
--- a/src/region.cpp
+++ b/src/region.cpp
@@ -36,9 +36,10 @@ Region::Region(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
   style = new char[n];
   strcpy(style,arg[1]);
 
+  varshape = 0;
   xstr = ystr = zstr = tstr = NULL;
   dx = dy = dz = 0.0;
-  laststep = -1;
+  lastshape = lastdynamic = -1;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -100,23 +101,35 @@ int Region::dynamic_check()
    XOR computes 0 if 2 args are the same, 1 if different
    note that inside() returns 1 for points on surface of region
    thus point on surface of exterior region will not match
+   if region has variable shape, invoke shape_update() once per timestep
    if region is dynamic, apply inverse transform to x,y,z
      unmove first, then unrotate, so don't have to change rotation point
+   caller is responsible for wrapping this call with
+     modify->clearstep_compute() and modify->addstep_compute() if needed
 ------------------------------------------------------------------------- */
 
 int Region::match(double x, double y, double z)
 {
-  if (dynamic) inverse_transform(x,y,z);
+  if (varshape && update->ntimestep != lastshape) {
+    shape_update();
+    lastshape = update->ntimestep;
+  }
+
+  if (dynamic && update->ntimestep) inverse_transform(x,y,z);
+
   return !(inside(x,y,z) ^ interior);
 }
 
 /* ----------------------------------------------------------------------
    generate list of contact points for interior or exterior regions
+   if region has variable shape, invoke shape_update() once per timestep
    if region is dynamic:
      before: inverse transform x,y,z (unmove, then unrotate)
      after: forward transform contact point xs,yx,zs (rotate, then move),
             then reset contact delx,dely,delz based on new contact point
             no need to do this if no rotation since delxyz doesn't change
+   caller is responsible for wrapping this call with
+     modify->clearstep_compute() and modify->addstep_compute() if needed
 ------------------------------------------------------------------------- */
 
 int Region::surface(double x, double y, double z, double cutoff)
@@ -125,6 +138,11 @@ int Region::surface(double x, double y, double z, double cutoff)
   double xs,ys,zs;
   double xnear[3],xorig[3];
 
+  if (varshape && update->ntimestep != lastshape) {
+    shape_update();
+    lastshape = update->ntimestep;
+  }
+
   if (dynamic) {
     xorig[0] = x;
     xorig[1] = y;
@@ -179,13 +197,13 @@ void Region::add_contact(int n, double *x, double xp, double yp, double zp)
 void Region::forward_transform(double &x, double &y, double &z)
 {
   if (rotateflag) {
-    if (update->ntimestep != laststep)
+    if (update->ntimestep != lastdynamic)
       theta = input->variable->compute_equal(tvar);
     rotate(x,y,z,theta);
   }
 
   if (moveflag) {
-    if (update->ntimestep != laststep) {
+    if (update->ntimestep != lastdynamic) {
       if (xstr) dx = input->variable->compute_equal(xvar);
       if (ystr) dy = input->variable->compute_equal(yvar);
       if (zstr) dz = input->variable->compute_equal(zvar);
@@ -195,7 +213,7 @@ void Region::forward_transform(double &x, double &y, double &z)
     z += dz;
   }
 
-  laststep = update->ntimestep;
+  lastdynamic = update->ntimestep;
 }
 
 /* ----------------------------------------------------------------------
@@ -206,7 +224,7 @@ void Region::forward_transform(double &x, double &y, double &z)
 void Region::inverse_transform(double &x, double &y, double &z)
 {
   if (moveflag) {
-    if (update->ntimestep != laststep) {
+    if (update->ntimestep != lastdynamic) {
       if (xstr) dx = input->variable->compute_equal(xvar);
       if (ystr) dy = input->variable->compute_equal(yvar);
       if (zstr) dz = input->variable->compute_equal(zvar);
@@ -217,12 +235,12 @@ void Region::inverse_transform(double &x, double &y, double &z)
   }
 
   if (rotateflag) {
-    if (update->ntimestep != laststep)
+    if (update->ntimestep != lastdynamic)
       theta = input->variable->compute_equal(tvar);
     rotate(x,y,z,-theta);
   }
 
-  laststep = update->ntimestep;
+  lastdynamic = update->ntimestep;
 }
 
 /* ----------------------------------------------------------------------
diff --git a/src/region.h b/src/region.h
index 2406dc186f..8f79590258 100644
--- a/src/region.h
+++ b/src/region.h
@@ -40,27 +40,36 @@ class Region : protected Pointers {
 
   Region(class LAMMPS *, int, char **);
   virtual ~Region();
-  void init();
+  virtual void init();
   virtual int dynamic_check();
+
+  // called by other classes to check point versus region
+
   int match(double, double, double);
   int surface(double, double, double, double);
 
+  // implemented by each region, not called by other classes
+
   virtual int inside(double, double, double) = 0;
   virtual int surface_interior(double *, double) = 0;
   virtual int surface_exterior(double *, double) = 0;
+  virtual void shape_update() {}
 
  protected:
+  int varshape;       // 1 if region shape changes over time
+
   void add_contact(int, double *, double, double, double);
   void options(int, char **);
 
  private:
-  int dynamic;                      // 1 if region changes over time
-  int moveflag,rotateflag;
+  int dynamic;        // 1 if region position/orientation changes over time
+  int moveflag,rotateflag;   // 1 if position/orientation changes
+
   double point[3],axis[3],runit[3];
   char *xstr,*ystr,*zstr,*tstr;
   int xvar,yvar,zvar,tvar;
   double dx,dy,dz,theta;
-  bigint laststep;
+  bigint lastshape,lastdynamic;
 
   void forward_transform(double &, double &, double &);
   void inverse_transform(double &, double &, double &);
diff --git a/src/region_intersect.cpp b/src/region_intersect.cpp
index 1d3d78d186..736ec3c6e1 100644
--- a/src/region_intersect.cpp
+++ b/src/region_intersect.cpp
@@ -37,7 +37,8 @@ RegIntersect::RegIntersect(LAMMPS *lmp, int narg, char **arg) :
   int iregion;
   for (int iarg = 0; iarg < n; iarg++) {
     iregion = domain->find_region(arg[iarg+3]);
-    if (iregion == -1) error->all(FLERR,"Region intersect region ID does not exist");
+    if (iregion == -1) 
+      error->all(FLERR,"Region intersect region ID does not exist");
     list[nregion++] = iregion;
   }
 
diff --git a/src/region_sphere.cpp b/src/region_sphere.cpp
index e90704dd74..773fc4cb16 100644
--- a/src/region_sphere.cpp
+++ b/src/region_sphere.cpp
@@ -15,10 +15,15 @@
 #include "stdlib.h"
 #include "string.h"
 #include "region_sphere.h"
+#include "input.h"
+#include "variable.h"
+#include "update.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
 
+enum{CONSTANT,VARIABLE};
+
 /* ---------------------------------------------------------------------- */
 
 RegSphere::RegSphere(LAMMPS *lmp, int narg, char **arg) :
@@ -29,13 +34,23 @@ RegSphere::RegSphere(LAMMPS *lmp, int narg, char **arg) :
   xc = xscale*atof(arg[2]);
   yc = yscale*atof(arg[3]);
   zc = zscale*atof(arg[4]);
-  radius = xscale*atof(arg[5]);
 
-  // error check
+  rstr = NULL;
+  if (strstr(arg[5],"v_") == arg[5]) {
+    int n = strlen(&arg[5][2]) + 1;
+    rstr = new char[n];
+    strcpy(rstr,&arg[5][2]);
+    radius = 0.0;
+    rstyle = VARIABLE;
+    varshape = 1;
+  } else {
+    radius = xscale*atof(arg[5]);
+    rstyle = CONSTANT;
+  }
 
   if (radius < 0.0) error->all(FLERR,"Illegal region sphere command");
 
-  // extent of sphere
+  // extent of sphere, will be 0.0 for variable radius
 
   if (interior) {
     bboxflag = 1;
@@ -55,9 +70,27 @@ RegSphere::RegSphere(LAMMPS *lmp, int narg, char **arg) :
 
 RegSphere::~RegSphere()
 {
+  delete [] rstr;
   delete [] contact;
 }
 
+/* ---------------------------------------------------------------------- */
+
+void RegSphere::init()
+{
+  Region::init();
+
+  // check variable
+
+  if (rstr) {
+    rvar = input->variable->find(rstr);
+    if (rvar < 0)
+      error->all(FLERR,"Variable name for region sphere does not exist");
+    if (!input->variable->equalstyle(rvar))
+      error->all(FLERR,"Variable for region sphere is invalid style");
+  }
+}
+
 /* ----------------------------------------------------------------------
    inside = 1 if x,y,z is inside or on surface
    inside = 0 if x,y,z is outside and not on surface
@@ -124,3 +157,14 @@ int RegSphere::surface_exterior(double *x, double cutoff)
   }
   return 0;
 }
+
+/* ----------------------------------------------------------------------
+   change region shape via variable evaluation
+------------------------------------------------------------------------- */
+
+void RegSphere::shape_update()
+{
+  radius = xscale * input->variable->compute_equal(rvar);
+  if (radius < 0.0)
+    error->one(FLERR,"Variable evaluation in region gave bad value");
+}
diff --git a/src/region_sphere.h b/src/region_sphere.h
index 73556d07c3..ed34369221 100644
--- a/src/region_sphere.h
+++ b/src/region_sphere.h
@@ -28,13 +28,19 @@ class RegSphere : public Region {
  public:
   RegSphere(class LAMMPS *, int, char **);
   ~RegSphere();
+  void init();
   int inside(double, double, double);
   int surface_interior(double *, double);
   int surface_exterior(double *, double);
+  void shape_update();
 
  private:
   double xc,yc,zc;
   double radius;
+  int rstyle,rvar;
+  char *rstr;
+
+  void variable_check();
 };
 
 }
diff --git a/src/variable.cpp b/src/variable.cpp
index 5b9402a731..d60acccc58 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -2159,17 +2159,17 @@ double Variable::eval_tree(Tree *tree, int i)
   }
 
   if (tree->type == RMASK) {
-    if (domain->regions[tree->ivalue1]->inside(atom->x[i][0],
-                                               atom->x[i][1],
-                                               atom->x[i][2])) return 1.0;
+    if (domain->regions[tree->ivalue1]->match(atom->x[i][0],
+                                              atom->x[i][1],
+                                              atom->x[i][2])) return 1.0;
     else return 0.0;
   }
 
   if (tree->type == GRMASK) {
     if ((atom->mask[i] & tree->ivalue1) &&
-        (domain->regions[tree->ivalue2]->inside(atom->x[i][0],
-                                                atom->x[i][1],
-                                                atom->x[i][2]))) return 1.0;
+        (domain->regions[tree->ivalue2]->match(atom->x[i][0],
+                                               atom->x[i][1],
+                                               atom->x[i][2]))) return 1.0;
     else return 0.0;
   }
 

From 746deead15bf42ebc6e89009cc7b56381d986c55 Mon Sep 17 00:00:00 2001
From: sjplimp 
Date: Fri, 18 Jan 2013 20:46:51 +0000
Subject: [PATCH 07/12] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@9300
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 src/region_cylinder.cpp | 60 ++++++++++++++++++++++++++++++++++++++---
 src/region_cylinder.h   |  7 +++++
 src/region_sphere.cpp   | 33 ++++++++++++++---------
 3 files changed, 85 insertions(+), 15 deletions(-)

diff --git a/src/region_cylinder.cpp b/src/region_cylinder.cpp
index d6d71ba9b9..b806ea07ea 100644
--- a/src/region_cylinder.cpp
+++ b/src/region_cylinder.cpp
@@ -15,12 +15,16 @@
 #include "stdlib.h"
 #include "string.h"
 #include "region_cylinder.h"
+#include "update.h"
 #include "domain.h"
+#include "input.h"
+#include "variable.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
 
 #define BIG 1.0e20
+enum{CONSTANT,VARIABLE};
 
 /* ---------------------------------------------------------------------- */
 
@@ -36,15 +40,29 @@ RegCylinder::RegCylinder(LAMMPS *lmp, int narg, char **arg) :
   if (axis == 'x') {
     c1 = yscale*atof(arg[3]);
     c2 = zscale*atof(arg[4]);
-    radius = yscale*atof(arg[5]);
   } else if (axis == 'y') {
     c1 = xscale*atof(arg[3]);
     c2 = zscale*atof(arg[4]);
-    radius = xscale*atof(arg[5]);
   } else if (axis == 'z') {
     c1 = xscale*atof(arg[3]);
     c2 = yscale*atof(arg[4]);
-    radius = xscale*atof(arg[5]);
+  }
+
+  rstr = NULL;
+  if (strstr(arg[5],"v_") == arg[5]) {
+    int n = strlen(&arg[5][2]) + 1;
+    rstr = new char[n];
+    strcpy(rstr,&arg[5][2]);
+    radius = 0.0;
+    rstyle = VARIABLE;
+    varshape = 1;
+    variable_check();
+    shape_update();
+  } else {
+    radius = atof(arg[5]);
+    if (axis == 'x') radius *= xscale;
+    else radius *= xscale;
+    rstyle = CONSTANT;
   }
 
   if (strcmp(arg[6],"INF") == 0 || strcmp(arg[6],"EDGE") == 0) {
@@ -100,6 +118,7 @@ RegCylinder::RegCylinder(LAMMPS *lmp, int narg, char **arg) :
   if (radius <= 0.0) error->all(FLERR,"Illegal region cylinder command");
 
   // extent of cylinder
+  // for variable radius, uses initial radius
 
   if (interior) {
     bboxflag = 1;
@@ -139,9 +158,18 @@ RegCylinder::RegCylinder(LAMMPS *lmp, int narg, char **arg) :
 
 RegCylinder::~RegCylinder()
 {
+  delete [] rstr;
   delete [] contact;
 }
 
+/* ---------------------------------------------------------------------- */
+
+void RegCylinder::init()
+{
+  Region::init();
+  if (rstr) variable_check();
+}
+
 /* ----------------------------------------------------------------------
    inside = 1 if x,y,z is inside or on surface
    inside = 0 if x,y,z is outside and not on surface
@@ -400,3 +428,29 @@ int RegCylinder::surface_exterior(double *x, double cutoff)
     return 0;
   }
 }
+
+/* ----------------------------------------------------------------------
+   change region shape via variable evaluation
+------------------------------------------------------------------------- */
+
+void RegCylinder::shape_update()
+{
+  radius = input->variable->compute_equal(rvar);
+  if (radius < 0.0)
+    error->one(FLERR,"Variable evaluation in region gave bad value");
+  if (axis == 'x') radius *= xscale;
+  else radius *= xscale;
+}
+
+/* ----------------------------------------------------------------------
+   error check on existence of variable
+------------------------------------------------------------------------- */
+
+void RegCylinder::variable_check()
+{
+  rvar = input->variable->find(rstr);
+  if (rvar < 0)
+    error->all(FLERR,"Variable name for region cylinder does not exist");
+  if (!input->variable->equalstyle(rvar))
+    error->all(FLERR,"Variable for region cylinder is invalid style");
+}
diff --git a/src/region_cylinder.h b/src/region_cylinder.h
index 93bb74aaff..07c26ca065 100644
--- a/src/region_cylinder.h
+++ b/src/region_cylinder.h
@@ -30,15 +30,22 @@ class RegCylinder : public Region {
  public:
   RegCylinder(class LAMMPS *, int, char **);
   ~RegCylinder();
+  void init();
   int inside(double, double, double);
   int surface_interior(double *, double);
   int surface_exterior(double *, double);
+  void shape_update();
 
  private:
   char axis;
   double c1,c2;
   double radius;
   double lo,hi;
+  int rstyle,rvar;
+  char *rstr;
+
+  void variable_check();
+
 };
 
 }
diff --git a/src/region_sphere.cpp b/src/region_sphere.cpp
index 773fc4cb16..28436cc171 100644
--- a/src/region_sphere.cpp
+++ b/src/region_sphere.cpp
@@ -15,9 +15,9 @@
 #include "stdlib.h"
 #include "string.h"
 #include "region_sphere.h"
+#include "update.h"
 #include "input.h"
 #include "variable.h"
-#include "update.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
@@ -43,14 +43,19 @@ RegSphere::RegSphere(LAMMPS *lmp, int narg, char **arg) :
     radius = 0.0;
     rstyle = VARIABLE;
     varshape = 1;
+    variable_check();
+    shape_update();
   } else {
     radius = xscale*atof(arg[5]);
     rstyle = CONSTANT;
   }
 
+  // error check
+
   if (radius < 0.0) error->all(FLERR,"Illegal region sphere command");
 
-  // extent of sphere, will be 0.0 for variable radius
+  // extent of sphere
+  // for variable radius, uses initial radius
 
   if (interior) {
     bboxflag = 1;
@@ -79,16 +84,7 @@ RegSphere::~RegSphere()
 void RegSphere::init()
 {
   Region::init();
-
-  // check variable
-
-  if (rstr) {
-    rvar = input->variable->find(rstr);
-    if (rvar < 0)
-      error->all(FLERR,"Variable name for region sphere does not exist");
-    if (!input->variable->equalstyle(rvar))
-      error->all(FLERR,"Variable for region sphere is invalid style");
-  }
+  if (rstr) variable_check();
 }
 
 /* ----------------------------------------------------------------------
@@ -168,3 +164,16 @@ void RegSphere::shape_update()
   if (radius < 0.0)
     error->one(FLERR,"Variable evaluation in region gave bad value");
 }
+
+/* ----------------------------------------------------------------------
+   error check on existence of variable
+------------------------------------------------------------------------- */
+
+void RegSphere::variable_check()
+{
+  rvar = input->variable->find(rstr);
+  if (rvar < 0)
+    error->all(FLERR,"Variable name for region sphere does not exist");
+  if (!input->variable->equalstyle(rvar))
+    error->all(FLERR,"Variable for region sphere is invalid style");
+}

From 35769609d95cc2fa70abb0f68f8c8087129de46e Mon Sep 17 00:00:00 2001
From: sjplimp 
Date: Fri, 18 Jan 2013 20:55:26 +0000
Subject: [PATCH 08/12] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@9301
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 src/region.h             |  3 +--
 src/region_intersect.cpp | 29 +++++++++++++++++++++++++++--
 src/region_intersect.h   |  2 ++
 src/region_union.cpp     | 32 +++++++++++++++++++++++++++++---
 src/region_union.h       |  2 ++
 5 files changed, 61 insertions(+), 7 deletions(-)

diff --git a/src/region.h b/src/region.h
index 8f79590258..0a1d888a98 100644
--- a/src/region.h
+++ b/src/region.h
@@ -28,6 +28,7 @@ class Region : protected Pointers {
   double extent_ylo,extent_yhi;
   double extent_zlo,extent_zhi;
   int bboxflag;                     // 1 if bounding box is computable
+  int varshape;                     // 1 if region shape changes over time
 
   // contact = particle near region surface
 
@@ -56,8 +57,6 @@ class Region : protected Pointers {
   virtual void shape_update() {}
 
  protected:
-  int varshape;       // 1 if region shape changes over time
-
   void add_contact(int, double *, double, double, double);
   void options(int, char **);
 
diff --git a/src/region_intersect.cpp b/src/region_intersect.cpp
index 736ec3c6e1..bae73952d3 100644
--- a/src/region_intersect.cpp
+++ b/src/region_intersect.cpp
@@ -42,10 +42,14 @@ RegIntersect::RegIntersect(LAMMPS *lmp, int narg, char **arg) :
     list[nregion++] = iregion;
   }
 
-  // extent of intersection of regions
-  // has bounding box if interior and any sub-region has bounding box
+  // this region is variable shape if any of sub-regions are
 
   Region **regions = domain->regions;
+  for (int ilist = 0; ilist < nregion; ilist++)
+    if (regions[list[ilist]]->varshape) varshape = 1;
+
+  // extent of intersection of regions
+  // has bounding box if interior and any sub-region has bounding box
 
   bboxflag = 0;
   for (int ilist = 0; ilist < nregion; ilist++)
@@ -91,6 +95,16 @@ RegIntersect::~RegIntersect()
   delete [] contact;
 }
 
+/* ---------------------------------------------------------------------- */
+
+void RegIntersect::init()
+{
+  Region::init();
+  Region **regions = domain->regions;
+  for (int ilist = 0; ilist < nregion; ilist++)
+    regions[list[ilist]]->init();
+}
+
 /* ----------------------------------------------------------------------
    return 1 if region is dynamic, 0 if static
    dynamic if any sub-region is dynamic, else static
@@ -206,3 +220,14 @@ int RegIntersect::surface_exterior(double *x, double cutoff)
 
   return n;
 }
+
+/* ----------------------------------------------------------------------
+   change region shape of all sub-regions
+------------------------------------------------------------------------- */
+
+void RegIntersect::shape_update()
+{
+  Region **regions = domain->regions;
+  for (int ilist = 0; ilist < nregion; ilist++)
+    regions[list[ilist]]->shape_update();
+}
diff --git a/src/region_intersect.h b/src/region_intersect.h
index a8bd460f34..62946a65c0 100644
--- a/src/region_intersect.h
+++ b/src/region_intersect.h
@@ -28,10 +28,12 @@ class RegIntersect : public Region {
  public:
   RegIntersect(class LAMMPS *, int, char **);
   ~RegIntersect();
+  void init();
   int dynamic_check();
   int inside(double, double, double);
   int surface_interior(double *, double);
   int surface_exterior(double *, double);
+  void shape_update();
 
  private:
   int nregion;
diff --git a/src/region_union.cpp b/src/region_union.cpp
index ca1e693f37..3741e8fdd1 100644
--- a/src/region_union.cpp
+++ b/src/region_union.cpp
@@ -38,14 +38,19 @@ RegUnion::RegUnion(LAMMPS *lmp, int narg, char **arg) : Region(lmp, narg, arg)
   int iregion;
   for (int iarg = 0; iarg < n; iarg++) {
     iregion = domain->find_region(arg[iarg+3]);
-    if (iregion == -1) error->all(FLERR,"Region union region ID does not exist");
+    if (iregion == -1) 
+      error->all(FLERR,"Region union region ID does not exist");
     list[nregion++] = iregion;
   }
 
-  // extent of union of regions
-  // has bounding box if interior and all sub-regions have bounding box
+  // this region is variable shape if any of sub-regions are
 
   Region **regions = domain->regions;
+  for (int ilist = 0; ilist < nregion; ilist++)
+    if (regions[list[ilist]]->varshape) varshape = 1;
+
+  // extent of union of regions
+  // has bounding box if interior and all sub-regions have bounding box
 
   bboxflag = 1;
   for (int ilist = 0; ilist < nregion; ilist++)
@@ -82,6 +87,16 @@ RegUnion::~RegUnion()
   delete [] contact;
 }
 
+/* ---------------------------------------------------------------------- */
+
+void RegUnion::init()
+{
+  Region::init();
+  Region **regions = domain->regions;
+  for (int ilist = 0; ilist < nregion; ilist++)
+    regions[list[ilist]]->init();
+}
+
 /* ----------------------------------------------------------------------
    return 1 if region is dynamic, 0 if static
    dynamic if any sub-region is dynamic, else static
@@ -197,3 +212,14 @@ int RegUnion::surface_exterior(double *x, double cutoff)
 
   return n;
 }
+
+/* ----------------------------------------------------------------------
+   change region shape of all sub-regions
+------------------------------------------------------------------------- */
+
+void RegUnion::shape_update()
+{
+  Region **regions = domain->regions;
+  for (int ilist = 0; ilist < nregion; ilist++)
+    regions[list[ilist]]->shape_update();
+}
diff --git a/src/region_union.h b/src/region_union.h
index 44d99375c9..6d0ec063cf 100644
--- a/src/region_union.h
+++ b/src/region_union.h
@@ -28,10 +28,12 @@ class RegUnion : public Region {
  public:
   RegUnion(class LAMMPS *, int, char **);
   ~RegUnion();
+  void init();
   int dynamic_check();
   int inside(double, double, double);
   int surface_interior(double *, double);
   int surface_exterior(double *, double);
+  void shape_update();
 
  private:
   int nregion;

From 6efc2340659c29ed9cba28b2337e9f4af0478721 Mon Sep 17 00:00:00 2001
From: sjplimp 
Date: Fri, 18 Jan 2013 21:00:07 +0000
Subject: [PATCH 09/12] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@9302
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/region.html | 13 +++++++++++++
 doc/region.txt  | 13 +++++++++++++
 2 files changed, 26 insertions(+)

diff --git a/doc/region.html b/doc/region.html
index 58832093d3..1bd4b5392d 100644
--- a/doc/region.html
+++ b/doc/region.html
@@ -31,6 +31,7 @@
     dim = x or y or z = axis of cylinder
     c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
     radius = cylinder radius (distance units)
+      radius can be a variable (see below)
     lo,hi = bounds of cylinder in dim (distance units)
   plane args = px py pz nx ny nz
     px,py,pz = point on the plane (distance units)
@@ -43,6 +44,7 @@
   sphere args = x y z radius
     x,y,z = center of sphere (distance units)
     radius = radius of sphere (distance units)
+      radius can be a variable (see below)
   union args = N reg-ID1 reg-ID2 ...
     N = # of regions to follow, must be 2 or greater
     reg-ID1,reg-ID2, ... = IDs of regions to join together
@@ -175,6 +177,17 @@ since if the maximum tilt factor is 5 (as in this example), then
 configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
 geometrically equivalent.
 
    
+
    The radius value for style sphere and cylinder can be specified
+as an equal-style variable.  If the value is a
+variable, it should be specified as v_name, where name is the variable
+name.  In this case, the variable will be evaluated each timestep, and
+its value used to determine the radius of the region.
+
    
+
    Equal-style variables can specify formulas with various mathematical
+functions, and include thermo_style command
+keywords for the simulation box parameters and timestep and elapsed
+time.  Thus it is easy to specify a time-dependent radius.
+
    
 
    See Section_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
diff --git a/doc/region.txt b/doc/region.txt
index 74744ab501..ff79470846 100644
--- a/doc/region.txt
+++ b/doc/region.txt
@@ -26,6 +26,7 @@ style = {delete} or {block} or {cone} or {cylinder} or {plane} or {prism} or {sp
     dim = {x} or {y} or {z} = axis of cylinder
     c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
     radius = cylinder radius (distance units)
+      radius can be a variable (see below)
     lo,hi = bounds of cylinder in dim (distance units)
   {plane} args = px py pz nx ny nz
     px,py,pz = point on the plane (distance units)
@@ -38,6 +39,7 @@ style = {delete} or {block} or {cone} or {cylinder} or {plane} or {prism} or {sp
   {sphere} args = x y z radius
     x,y,z = center of sphere (distance units)
     radius = radius of sphere (distance units)
+      radius can be a variable (see below)
   {union} args = N reg-ID1 reg-ID2 ...
     N = # of regions to follow, must be 2 or greater
     reg-ID1,reg-ID2, ... = IDs of regions to join together
@@ -166,6 +168,17 @@ since if the maximum tilt factor is 5 (as in this example), then
 configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
 geometrically equivalent.
 
+The {radius} value for style {sphere} and {cylinder} can be specified
+as an equal-style "variable"_variable.html.  If the value is a
+variable, it should be specified as v_name, where name is the variable
+name.  In this case, the variable will be evaluated each timestep, and
+its value used to determine the radius of the region.
+
+Equal-style variables can specify formulas with various mathematical
+functions, and include "thermo_style"_thermo_style.html command
+keywords for the simulation box parameters and timestep and elapsed
+time.  Thus it is easy to specify a time-dependent radius.
+
 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

From fd75622da330831ff6b488764b5475eb7578de95 Mon Sep 17 00:00:00 2001
From: sjplimp 
Date: Fri, 18 Jan 2013 21:02:02 +0000
Subject: [PATCH 10/12] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@9303
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 src/version.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/version.h b/src/version.h
index 06f5372acb..7d81684e82 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "20 Jan 2013"
+#define LAMMPS_VERSION "21 Jan 2013"

From 5b1fe9d76389d7a710104a2cc2cbf9e626bf13fd Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer 
Date: Mon, 21 Jan 2013 03:28:22 -0500
Subject: [PATCH 11/12] update /omp versions of brownian and lubricate pair
 styles for changes in upstream serial variants

---
 src/USER-OMP/pair_brownian_omp.cpp       | 4 ++--
 src/USER-OMP/pair_brownian_poly_omp.cpp  | 4 ++--
 src/USER-OMP/pair_lubricate_omp.cpp      | 4 ++--
 src/USER-OMP/pair_lubricate_poly_omp.cpp | 4 ++--
 4 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/USER-OMP/pair_brownian_omp.cpp b/src/USER-OMP/pair_brownian_omp.cpp
index 561c82abf5..20cc068809 100644
--- a/src/USER-OMP/pair_brownian_omp.cpp
+++ b/src/USER-OMP/pair_brownian_omp.cpp
@@ -91,8 +91,8 @@ void PairBrownianOMP::compute(int eflag, int vflag)
         for (int m = 0; m < wallfix->nwall; m++){
           int dim = wallfix->wallwhich[m] / 2;
           int side = wallfix->wallwhich[m] % 2;
-          if (wallfix->wallstyle[m] == VARIABLE){
-            wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
+          if (wallfix->xstyle[m] == VARIABLE){
+            wallcoord = input->variable->compute_equal(wallfix->xindex[m]);
           }
           else wallcoord = wallfix->coord0[m];
           if (side == 0) walllo[dim] = wallcoord;
diff --git a/src/USER-OMP/pair_brownian_poly_omp.cpp b/src/USER-OMP/pair_brownian_poly_omp.cpp
index 6affbf96cf..0378989fbc 100644
--- a/src/USER-OMP/pair_brownian_poly_omp.cpp
+++ b/src/USER-OMP/pair_brownian_poly_omp.cpp
@@ -91,8 +91,8 @@ void PairBrownianPolyOMP::compute(int eflag, int vflag)
         for (int m = 0; m < wallfix->nwall; m++){
           int dim = wallfix->wallwhich[m] / 2;
           int side = wallfix->wallwhich[m] % 2;
-          if (wallfix->wallstyle[m] == VARIABLE){
-            wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
+          if (wallfix->xstyle[m] == VARIABLE){
+            wallcoord = input->variable->compute_equal(wallfix->xindex[m]);
           }
           else wallcoord = wallfix->coord0[m];
           if (side == 0) walllo[dim] = wallcoord;
diff --git a/src/USER-OMP/pair_lubricate_omp.cpp b/src/USER-OMP/pair_lubricate_omp.cpp
index 22090b2978..877be4bed2 100644
--- a/src/USER-OMP/pair_lubricate_omp.cpp
+++ b/src/USER-OMP/pair_lubricate_omp.cpp
@@ -85,8 +85,8 @@ void PairLubricateOMP::compute(int eflag, int vflag)
          for (int m = 0; m < wallfix->nwall; m++){
            int dim = wallfix->wallwhich[m] / 2;
            int side = wallfix->wallwhich[m] % 2;
-           if (wallfix->wallstyle[m] == VARIABLE){
-             wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
+           if (wallfix->xstyle[m] == VARIABLE){
+             wallcoord = input->variable->compute_equal(wallfix->xindex[m]);
            }
            else wallcoord = wallfix->coord0[m];
            if (side == 0) walllo[dim] = wallcoord;
diff --git a/src/USER-OMP/pair_lubricate_poly_omp.cpp b/src/USER-OMP/pair_lubricate_poly_omp.cpp
index 26339b7749..a9161805b6 100644
--- a/src/USER-OMP/pair_lubricate_poly_omp.cpp
+++ b/src/USER-OMP/pair_lubricate_poly_omp.cpp
@@ -86,8 +86,8 @@ void PairLubricatePolyOMP::compute(int eflag, int vflag)
          for (int m = 0; m < wallfix->nwall; m++){
            int dim = wallfix->wallwhich[m] / 2;
            int side = wallfix->wallwhich[m] % 2;
-           if (wallfix->wallstyle[m] == VARIABLE){
-             wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
+           if (wallfix->xstyle[m] == VARIABLE){
+             wallcoord = input->variable->compute_equal(wallfix->xindex[m]);
            }
            else wallcoord = wallfix->coord0[m];
            if (side == 0) walllo[dim] = wallcoord;

From 7930d8b34f8d547adad3602ee63cd877e89ad730 Mon Sep 17 00:00:00 2001
From: sjplimp 
Date: Mon, 21 Jan 2013 16:35:54 +0000
Subject: [PATCH 12/12] git-svn-id:
 svn://svn.icms.temple.edu/lammps-ro/trunk@9306
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/Section_commands.html | 111 +++++++++++++++++++-------------------
 doc/Section_commands.txt  |  14 +++--
 doc/kspace_style.html     |   4 +-
 doc/kspace_style.txt      |   4 +-
 doc/pair_born.html        |  43 +++++++++------
 doc/pair_born.txt         |  41 ++++++++------
 doc/pair_buck.html        |  36 ++++++++-----
 doc/pair_buck.txt         |  34 +++++++-----
 doc/pair_charmm.html      |  28 +++++++---
 doc/pair_charmm.txt       |  26 ++++++---
 doc/pair_coul.html        |  28 ++++++----
 doc/pair_coul.txt         |  26 +++++----
 doc/pair_lj.html          |  37 ++++++++-----
 doc/pair_lj.txt           |  35 +++++++-----
 14 files changed, 289 insertions(+), 178 deletions(-)

diff --git a/doc/Section_commands.html b/doc/Section_commands.html
index c78886303c..4a8ea4e525 100644
--- a/doc/Section_commands.html
+++ b/doc/Section_commands.html
@@ -419,25 +419,26 @@ potentials.  Click on the style itself for a full description:
 
    
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
    
 
    nonehybridhybrid/overlayadp
    
 
    airebobeckbopborn
    born/coul/longborn/coul/wolfbrownianbrownian/poly
    buckbuck/coul/cutbuck/coul/longbuck/long/coul/long
    colloidcombcoul/cutcoul/debye
    coul/dsfcoul/longcoul/wolfdipole/cut
    dpddpd/tstatdsmceam
    eam/alloyeam/fseimgauss
    gaybernegran/hertz/historygran/hookegran/hooke/history
    hbond/dreiding/ljhbond/dreiding/morsekimlcbop
    line/ljlj/charmm/coul/charmmlj/charmm/coul/charmm/implicitlj/charmm/coul/long
    born/coul/longborn/coul/msmborn/coul/wolfbrownian
    brownian/polybuckbuck/coul/cutbuck/coul/long
    buck/coul/msmbuck/long/coul/longcolloidcomb
    coul/cutcoul/debyecoul/dsfcoul/long
    coul/msmcoul/wolfdipole/cutdpd
    dpd/tstatdsmceameam/alloy
    eam/fseimgaussgayberne
    gran/hertz/historygran/hookegran/hooke/historyhbond/dreiding/lj
    hbond/dreiding/morsekimlcbopline/lj
    lj/charmm/coul/charmmlj/charmm/coul/charmm/implicitlj/charmm/coul/longlj/charmm/coul/msm
    
 
    lj/class2lj/class2/coul/cutlj/class2/coul/longlj/cut
    
 
    lj/cut/coul/cutlj/cut/coul/debyelj/cut/coul/dsflj/cut/coul/long
    lj/long/coul/longlj/cut/tip4p/longlj/long/tip4p/longlj/expand
    lj/gromacslj/gromacs/coul/gromacslj/smoothlj/smooth/linear
    lj96/cutlubricatelubricate/polylubricateU
    lubricateU/polymeammie/cutmorse
    peri/lpsperi/pmbreaxrebo
    resquaredsoftswtable
    tersofftersoff/zbltri/ljyukawa
    yukawa/colloid 
+
    lj/cut/coul/msmlj/long/coul/longlj/cut/tip4p/longlj/long/tip4p/long
    lj/expandlj/gromacslj/gromacs/coul/gromacslj/smooth
    lj/smooth/linearlj96/cutlubricatelubricate/poly
    lubricateUlubricateU/polymeammie/cut
    morseperi/lpsperi/pmbreax
    reboresquaredsoftsw
    tabletersofftersoff/zbltri/lj
    yukawayukawa/colloid 
 
    
 
 
    These are pair styles contributed by users, which can be used if
@@ -458,42 +459,42 @@ package.
 
    
 
    
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
    
 
    adp/ompairebo/ompbeck/ompborn/coul/long/cuda
    born/coul/long/gpuborn/coul/long/ompborn/coul/wolf/gpuborn/coul/wolf/omp
    born/gpuborn/ompbrownian/ompbrownian/poly/omp
    buck/coul/cut/cudabuck/coul/cut/gpubuck/coul/cut/ompbuck/coul/long/cuda
    buck/coul/long/gpubuck/coul/long/ompbuck/cudabuck/long/coul/long/omp
    buck/gpubuck/ompcolloid/gpucolloid/omp
    comb/ompcoul/cut/ompcoul/debye/ompcoul/dsf/gpu
    coul/long/gpucoul/long/ompcoul/wolfdipole/cut/gpu
    dipole/cut/ompdipole/sf/gpudipole/sf/ompdpd/omp
    dpd/tstat/ompeam/alloy/cudaeam/alloy/gpueam/alloy/omp
    eam/alloy/opteam/cd/ompeam/cudaeam/fs/cuda
    eam/fs/gpueam/fs/ompeam/fs/opteam/gpu
    eam/ompeam/optedip/ompeim/omp
    gauss/gpugauss/ompgayberne/gpugayberne/omp
    gran/hertz/history/ompgran/hooke/cudagran/hooke/history/ompgran/hooke/omp
    hbond/dreiding/lj/omphbond/dreiding/morse/ompline/lj/omplj/charmm/coul/charmm/cuda
    lj/charmm/coul/charmm/omplj/charmm/coul/charmm/implicit/cudalj/charmm/coul/charmm/implicit/omplj/charmm/coul/long/cuda
    lj/charmm/coul/long/gpulj/charmm/coul/long/omplj/charmm/coul/long/optlj/charmm/coul/pppm/omp
    lj/class2/coul/cut/cudalj/class2/coul/cut/omplj/class2/coul/long/cudalj/class2/coul/long/gpu
    lj/class2/coul/pppm/omplj/class2/coul/long/omplj/class2/cudalj/class2/gpu
    lj/class2/omplj/long/coul/long/omplj/cut/coul/cut/cudalj/cut/coul/cut/gpu
    lj/cut/coul/cut/omplj/cut/coul/debye/cudalj/cut/coul/debye/gpulj/cut/coul/debye/omp
    lj/cut/coul/dsf/gpulj/cut/coul/long/cudalj/cut/coul/long/gpulj/cut/coul/long/omp
    lj/cut/coul/long/optlj/cut/coul/pppm/omplj/cut/cudalj/cut/experimental/cuda
    lj/cut/gpulj/cut/omplj/cut/optlj/cut/tip4p/long/omp
    lj/cut/tip4p/long/optlj/expand/cudalj/expand/gpulj/expand/omp
    lj/gromacs/coul/gromacs/cudalj/gromacs/coul/gromacs/omplj/gromacs/cudalj/gromacs/omp
    lj/sdk/gpulj/sdk/omplj/sdk/coul/long/gpulj/sdk/coul/long/omp
    lj/sf/omplj/smooth/cudalj/smooth/omplj/smooth/linear/omp
    lj96/cut/cudalj96/cut/gpulj96/cut/omplubricate/omp
    lubricate/poly/ompmeam/spline/ompmorse/cudamorse/gpu
    morse/ompmorse/optperi/lps/ompperi/pmb/omp
    rebo/ompresquared/gpuresquared/ompsoft/omp
    sw/cudasw/omptable/gputable/omp
    tersoff/cudatersoff/omptersoff/table/omptersoff/zbl/omp
    tri/lj/ompyukawa/gpuyukawa/ompyukawa/colloid/gpu
    yukawa/colloid/omp 
+
    born/coul/long/gpuborn/coul/long/ompborn/coul/msm/ompborn/coul/wolf/gpu
    born/coul/wolf/ompborn/gpuborn/ompbrownian/omp
    brownian/poly/ompbuck/coul/cut/cudabuck/coul/cut/gpubuck/coul/cut/omp
    buck/coul/long/cudabuck/coul/long/gpubuck/coul/long/ompbuck/coul/msm/omp
    buck/cudabuck/long/coul/long/ompbuck/gpubuck/omp
    colloid/gpucolloid/ompcomb/ompcoul/cut/omp
    coul/debye/ompcoul/dsf/gpucoul/long/gpucoul/long/omp
    coul/msm/ompcoul/wolfdipole/cut/gpudipole/cut/omp
    dipole/sf/gpudipole/sf/ompdpd/ompdpd/tstat/omp
    eam/alloy/cudaeam/alloy/gpueam/alloy/ompeam/alloy/opt
    eam/cd/ompeam/cudaeam/fs/cudaeam/fs/gpu
    eam/fs/ompeam/fs/opteam/gpueam/omp
    eam/optedip/ompeim/ompgauss/gpu
    gauss/ompgayberne/gpugayberne/ompgran/hertz/history/omp
    gran/hooke/cudagran/hooke/history/ompgran/hooke/omphbond/dreiding/lj/omp
    hbond/dreiding/morse/ompline/lj/omplj/charmm/coul/charmm/cudalj/charmm/coul/charmm/omp
    lj/charmm/coul/charmm/implicit/cudalj/charmm/coul/charmm/implicit/omplj/charmm/coul/long/cudalj/charmm/coul/long/gpu
    lj/charmm/coul/long/omplj/charmm/coul/long/optlj/class2/coul/cut/cudalj/class2/coul/cut/omp
    lj/class2/coul/long/cudalj/class2/coul/long/gpulj/class2/coul/long/omplj/class2/coul/msm/omp
    lj/class2/cudalj/class2/gpulj/class2/omplj/long/coul/long/omp
    lj/cut/coul/cut/cudalj/cut/coul/cut/gpulj/cut/coul/cut/omplj/cut/coul/debye/cuda
    lj/cut/coul/debye/gpulj/cut/coul/debye/omplj/cut/coul/dsf/gpulj/cut/coul/long/cuda
    lj/cut/coul/long/gpulj/cut/coul/long/omplj/cut/coul/long/optlj/cut/coul/msm/opt
    lj/cut/cudalj/cut/experimental/cudalj/cut/gpulj/cut/omp
    lj/cut/optlj/cut/tip4p/long/omplj/cut/tip4p/long/optlj/expand/cuda
    lj/expand/gpulj/expand/omplj/gromacs/coul/gromacs/cudalj/gromacs/coul/gromacs/omp
    lj/gromacs/cudalj/gromacs/omplj/sdk/gpulj/sdk/omp
    lj/sdk/coul/long/gpulj/sdk/coul/long/omplj/sf/omplj/smooth/cuda
    lj/smooth/omplj/smooth/linear/omplj96/cut/cudalj96/cut/gpu
    lj96/cut/omplubricate/omplubricate/poly/ompmeam/spline/omp
    morse/cudamorse/gpumorse/ompmorse/opt
    peri/lps/ompperi/pmb/omprebo/ompresquared/gpu
    resquared/ompsoft/ompsw/cudasw/omp
    table/gputable/omptersoff/cudatersoff/omp
    tersoff/table/omptersoff/zbl/omptri/lj/ompyukawa/gpu
    yukawa/ompyukawa/colloid/gpuyukawa/colloid/omp 
 
    
 
 
    
@@ -637,8 +638,8 @@ built with the appropriate accelerated
 package.
 
    
 
 
 
diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt
index 22b70d6d6b..ceb459d4cc 100644
--- a/doc/Section_commands.txt
+++ b/doc/Section_commands.txt
@@ -636,12 +636,14 @@ potentials.  Click on the style itself for a full description:
 "bop"_pair_bop.html,
 "born"_pair_born.html,
 "born/coul/long"_pair_born.html,
+"born/coul/msm"_pair_born.html,
 "born/coul/wolf"_pair_born.html,
 "brownian"_pair_brownian.html,
 "brownian/poly"_pair_brownian.html,
 "buck"_pair_buck.html,
 "buck/coul/cut"_pair_buck.html,
 "buck/coul/long"_pair_buck.html,
+"buck/coul/msm"_pair_buck.html,
 "buck/long/coul/long"_pair_buck_long.html,
 "colloid"_pair_colloid.html,
 "comb"_pair_comb.html,
@@ -649,6 +651,7 @@ potentials.  Click on the style itself for a full description:
 "coul/debye"_pair_coul.html,
 "coul/dsf"_pair_coul.html,
 "coul/long"_pair_coul.html,
+"coul/msm"_pair_coul.html,
 "coul/wolf"_pair_coul.html,
 "dipole/cut"_pair_dipole.html,
 "dpd"_pair_dpd.html,
@@ -671,6 +674,7 @@ potentials.  Click on the style itself for a full description:
 "lj/charmm/coul/charmm"_pair_charmm.html,
 "lj/charmm/coul/charmm/implicit"_pair_charmm.html,
 "lj/charmm/coul/long"_pair_charmm.html,
+"lj/charmm/coul/msm"_pair_charmm.html,
 "lj/class2"_pair_class2.html,
 "lj/class2/coul/cut"_pair_class2.html,
 "lj/class2/coul/long"_pair_class2.html,
@@ -679,6 +683,7 @@ potentials.  Click on the style itself for a full description:
 "lj/cut/coul/debye"_pair_lj.html,
 "lj/cut/coul/dsf"_pair_lj.html,
 "lj/cut/coul/long"_pair_lj.html,
+"lj/cut/coul/msm"_pair_lj.html,
 "lj/long/coul/long"_pair_lj_long.html,
 "lj/cut/tip4p/long"_pair_lj.html,
 "lj/long/tip4p/long"_pair_lj_long.html,
@@ -744,6 +749,7 @@ package"_Section_accelerate.html.
 "born/coul/long/cuda"_pair_born.html,
 "born/coul/long/gpu"_pair_born.html,
 "born/coul/long/omp"_pair_born.html,
+"born/coul/msm/omp"_pair_born.html,
 "born/coul/wolf/gpu"_pair_born.html,
 "born/coul/wolf/omp"_pair_born.html,
 "born/gpu"_pair_born.html,
@@ -756,6 +762,7 @@ package"_Section_accelerate.html.
 "buck/coul/long/cuda"_pair_buck.html,
 "buck/coul/long/gpu"_pair_buck.html,
 "buck/coul/long/omp"_pair_buck.html,
+"buck/coul/msm/omp"_pair_buck.html,
 "buck/cuda"_pair_buck.html,
 "buck/long/coul/long/omp"_pair_buck_long.html,
 "buck/gpu"_pair_buck.html,
@@ -768,6 +775,7 @@ package"_Section_accelerate.html.
 "coul/dsf/gpu"_pair_coul.html,
 "coul/long/gpu"_pair_coul.html,
 "coul/long/omp"_pair_coul.html,
+"coul/msm/omp"_pair_coul.html,
 "coul/wolf"_pair_coul.html,
 "dipole/cut/gpu"_pair_dipole.html,
 "dipole/cut/omp"_pair_dipole.html,
@@ -809,13 +817,12 @@ package"_Section_accelerate.html.
 "lj/charmm/coul/long/gpu"_pair_charmm.html,
 "lj/charmm/coul/long/omp"_pair_charmm.html,
 "lj/charmm/coul/long/opt"_pair_charmm.html,
-"lj/charmm/coul/pppm/omp"_pair_charmm.html,
 "lj/class2/coul/cut/cuda"_pair_class2.html,
 "lj/class2/coul/cut/omp"_pair_class2.html,
 "lj/class2/coul/long/cuda"_pair_class2.html,
 "lj/class2/coul/long/gpu"_pair_class2.html,
-"lj/class2/coul/pppm/omp"_pair_class2.html,
 "lj/class2/coul/long/omp"_pair_class2.html,
+"lj/class2/coul/msm/omp"_pair_class2.html,
 "lj/class2/cuda"_pair_class2.html,
 "lj/class2/gpu"_pair_class2.html,
 "lj/class2/omp"_pair_class2.html,
@@ -831,7 +838,7 @@ package"_Section_accelerate.html.
 "lj/cut/coul/long/gpu"_pair_lj.html,
 "lj/cut/coul/long/omp"_pair_lj.html,
 "lj/cut/coul/long/opt"_pair_lj.html,
-"lj/cut/coul/pppm/omp"_pair_lj.html,
+"lj/cut/coul/msm/opt"_pair_lj.html,
 "lj/cut/cuda"_pair_lj.html,
 "lj/cut/experimental/cuda"_pair_lj.html,
 "lj/cut/gpu"_pair_lj.html,
@@ -1065,6 +1072,7 @@ built with the "appropriate accelerated
 package"_Section_accelerate.html.
 
 "ewald/omp"_kspace_style.html,
+"msm/omp"_kspace_style.html,
 "pppm/cuda"_kspace_style.html,
 "pppm/gpu"_kspace_style.html,
 "pppm/omp"_kspace_style.html,
diff --git a/doc/kspace_style.html b/doc/kspace_style.html
index c1f33d20c1..0042ff4e95 100644
--- a/doc/kspace_style.html
+++ b/doc/kspace_style.html
@@ -15,7 +15,7 @@
 
    
 
    kspace_style style value 
 
    
-
    • style = none or ewald or ewald/disp or ewald/omp or pppm or pppm/cg or pppm/disp or pppm/tip4p or pppm/disp/tip4p or pppm/gpu or pppm/omp or pppm/cg/omp or pppm/tip4p/omp or msm 
+
      • style = none or ewald or ewald/disp or ewald/omp or pppm or pppm/cg or pppm/disp or pppm/tip4p or pppm/disp/tip4p or pppm/gpu or pppm/omp or pppm/cg/omp or pppm/tip4p/omp or msm or msm/omp 
 
 
          none value = none
   ewald value = accuracy
@@ -44,6 +44,8 @@
   pppm/tip4p/omp value = accuracy
     accuracy = desired relative error in forces
   msm value = accuracy
+    accuracy = desired relative error in forces
+  msm/omp value = accuracy
     accuracy = desired relative error in forces 
 
        
 
diff --git a/doc/kspace_style.txt b/doc/kspace_style.txt
index 5f0bed56ed..863d412a0e 100644
--- a/doc/kspace_style.txt
+++ b/doc/kspace_style.txt
@@ -12,7 +12,7 @@ kspace_style command :h3
 
 kspace_style style value :pre
 
-style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg} or {pppm/disp} or {pppm/tip4p} or {pppm/disp/tip4p} or {pppm/gpu} or {pppm/omp} or {pppm/cg/omp} or {pppm/tip4p/omp} or {msm} :ulb,l
+style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg} or {pppm/disp} or {pppm/tip4p} or {pppm/disp/tip4p} or {pppm/gpu} or {pppm/omp} or {pppm/cg/omp} or {pppm/tip4p/omp} or {msm} or {msm/omp} :ulb,l
   {none} value = none
   {ewald} value = accuracy
     accuracy = desired relative error in forces
@@ -40,6 +40,8 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg}
   {pppm/tip4p/omp} value = accuracy
     accuracy = desired relative error in forces
   {msm} value = accuracy
+    accuracy = desired relative error in forces
+  {msm/omp} value = accuracy
     accuracy = desired relative error in forces :pre
 :ule
 
diff --git a/doc/pair_born.html b/doc/pair_born.html
index bd0f492ce8..c30a7093eb 100644
--- a/doc/pair_born.html
+++ b/doc/pair_born.html
@@ -23,6 +23,10 @@
 
 
        pair_style born/coul/long/omp command 
 
        
+
        pair_style born/coul/msm command 
+
        
+
        pair_style born/coul/msm/omp command 
+
        
 
        pair_style born/coul/wolf command 
 
        
 
        pair_style born/coul/wolf/gpu command 
@@ -33,7 +37,7 @@
 
        
 
        pair_style style args 
 
        
-
        • style = born or born/coul/long or born/coul/wolf
+
          • style = born or born/coul/long or born/coul/msm or born/coul/wolf
 
          • args = list of arguments for a particular style 
 
          
 
            born args = cutoff
@@ -41,6 +45,9 @@
   born/coul/long args = cutoff (cutoff2)
     cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
     cutoff2 = global cutoff for Coulombic (optional) (distance units)
+  born/coul/msm args = cutoff (cutoff2)
+    cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
+    cutoff2 = global cutoff for Coulombic (optional) (distance units)
   born/coul/wolf args = alpha cutoff (cutoff2)
     alpha = damping parameter (inverse distance units)
     cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
@@ -57,6 +64,11 @@ pair_style born/coul/long 10.0 8.0
 pair_coeff * * 6.08 0.317 2.340 24.18 11.51
 pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 
 
          
+
          pair_style born/coul/msm 10.0
+pair_style born/coul/msm 10.0 8.0
+pair_coeff * * 6.08 0.317 2.340 24.18 11.51
+pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 
+
          
 
          pair_style born/coul/wolf 0.25 10.0
 pair_style born/coul/wolf 0.25 10.0 9.0
 pair_coeff * * 6.08 0.317 2.340 24.18 11.51
@@ -72,27 +84,24 @@ potential described in (Fumi and Tosi), given by
 
          where sigma is an interaction-dependent length parameter, rho is an
 ionic-pair dependent length parameter, and Rc is the cutoff.
 
          
-
          The born/coul/long style adds a Coulombic term as described for the
-coul/long pair style.  An additional damping factor
-is applied to the Coulombic term so it can be used in conjunction with
-the kspace_style command and its ewald or pppm
-option.  The Coulombic cutoff specified for this style means that
-pairwise interactions within this distance are computed directly;
-interactions outside that distance are computed in reciprocal space.
+
          The styles with coul/long or coul/msm add a Coulombic term as
+described for the lj/cut pair styles.  An additional
+damping factor is applied to the Coulombic term so it can be used in
+conjunction with the kspace_style command and its
+ewald or pppm of msm option.  The Coulombic cutoff specified for
+this style means that pairwise interactions within this distance are
+computed directly; interactions outside that distance are computed in
+reciprocal space.
 
          
-
          If one cutoff is specified for the born/coul/long style, it is used
-for both the A,C,D and Coulombic terms.  If two cutoffs are specified,
-the first is used as the cutoff for the A,C,D terms, and the second is
-the cutoff for the Coulombic term.
+
          If one cutoff is specified for the born/coul/long and
+born/coul/msm style, it is used for both the A,C,D and Coulombic
+terms.  If two cutoffs are specified, the first is used as the cutoff
+for the A,C,D terms, and the second is the cutoff for the Coulombic
+term.
 
          
 
          The born/coul/wolf style adds a Coulombic term as described for the
 Wolf potential in the coul/wolf pair style.
 
          
-
          If one cutoff is specified for the born/coulk/long style, it is used
-for both the A,C,D and Coulombic terms.  If two cutoffs are specified,
-the first is used as the cutoff for the A,C,D terms, and the second is
-the cutoff for the Coulombic term.
-
          
 
          Note that these potentials are related to the Buckingham
 potential.
 
          
diff --git a/doc/pair_born.txt b/doc/pair_born.txt
index 57fb3471c1..e8cbbb4437 100644
--- a/doc/pair_born.txt
+++ b/doc/pair_born.txt
@@ -14,6 +14,8 @@ pair_style born/coul/long command :h3
 pair_style born/coul/long/cuda command :h3
 pair_style born/coul/long/gpu command :h3
 pair_style born/coul/long/omp command :h3
+pair_style born/coul/msm command :h3
+pair_style born/coul/msm/omp command :h3
 pair_style born/coul/wolf command :h3
 pair_style born/coul/wolf/gpu command :h3
 pair_style born/coul/wolf/omp command :h3
@@ -22,13 +24,16 @@ pair_style born/coul/wolf/omp command :h3
 
 pair_style style args :pre
 
-style = {born} or {born/coul/long} or {born/coul/wolf}
+style = {born} or {born/coul/long} or {born/coul/msm} or {born/coul/wolf}
 args = list of arguments for a particular style :ul
   {born} args = cutoff
     cutoff = global cutoff for non-Coulombic interactions (distance units)
   {born/coul/long} args = cutoff (cutoff2)
     cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
     cutoff2 = global cutoff for Coulombic (optional) (distance units)
+  {born/coul/msm} args = cutoff (cutoff2)
+    cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
+    cutoff2 = global cutoff for Coulombic (optional) (distance units)
   {born/coul/wolf} args = alpha cutoff (cutoff2)
     alpha = damping parameter (inverse distance units)
     cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
@@ -45,6 +50,11 @@ pair_style born/coul/long 10.0 8.0
 pair_coeff * * 6.08 0.317 2.340 24.18 11.51
 pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
 
+pair_style born/coul/msm 10.0
+pair_style born/coul/msm 10.0 8.0
+pair_coeff * * 6.08 0.317 2.340 24.18 11.51
+pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
+
 pair_style born/coul/wolf 0.25 10.0
 pair_style born/coul/wolf 0.25 10.0 9.0
 pair_coeff * * 6.08 0.317 2.340 24.18 11.51
@@ -60,27 +70,24 @@ potential described in "(Fumi and Tosi)"_#FumiTosi, given by
 where sigma is an interaction-dependent length parameter, rho is an
 ionic-pair dependent length parameter, and Rc is the cutoff.
 
-The {born/coul/long} style adds a Coulombic term as described for the
-"coul/long"_pair_coul.html pair style.  An additional damping factor
-is applied to the Coulombic term so it can be used in conjunction with
-the "kspace_style"_kspace_style.html command and its {ewald} or {pppm}
-option.  The Coulombic cutoff specified for this style means that
-pairwise interactions within this distance are computed directly;
-interactions outside that distance are computed in reciprocal space.
+The styles with {coul/long} or {coul/msm} add a Coulombic term as
+described for the "lj/cut"_pair_lj.html pair styles.  An additional
+damping factor is applied to the Coulombic term so it can be used in
+conjunction with the "kspace_style"_kspace_style.html command and its
+{ewald} or {pppm} of {msm} option.  The Coulombic cutoff specified for
+this style means that pairwise interactions within this distance are
+computed directly; interactions outside that distance are computed in
+reciprocal space.
 
-If one cutoff is specified for the {born/coul/long} style, it is used
-for both the A,C,D and Coulombic terms.  If two cutoffs are specified,
-the first is used as the cutoff for the A,C,D terms, and the second is
-the cutoff for the Coulombic term.
+If one cutoff is specified for the {born/coul/long} and
+{born/coul/msm} style, it is used for both the A,C,D and Coulombic
+terms.  If two cutoffs are specified, the first is used as the cutoff
+for the A,C,D terms, and the second is the cutoff for the Coulombic
+term.
 
 The {born/coul/wolf} style adds a Coulombic term as described for the
 Wolf potential in the "coul/wolf"_pair_coul.html pair style.
 
-If one cutoff is specified for the {born/coulk/long} style, it is used
-for both the A,C,D and Coulombic terms.  If two cutoffs are specified,
-the first is used as the cutoff for the A,C,D terms, and the second is
-the cutoff for the Coulombic term.
-
 Note that these potentials are related to the "Buckingham
 potential"_pair_born.html.
 
diff --git a/doc/pair_buck.html b/doc/pair_buck.html
index f3f9737380..84a9ea5813 100644
--- a/doc/pair_buck.html
+++ b/doc/pair_buck.html
@@ -33,11 +33,15 @@
 
        
 
        pair_style buck/coul/long/omp command 
 
        
+
        pair_style buck/coul/msm command 
+
        
+
        pair_style buck/coul/msm/omp command 
+
        
 
        Syntax:
 
        
 
        pair_style style args 
 
        
-
        • style = buck or buck/coul/cut or buck/coul/long
+
          • style = buck or buck/coul/cut or buck/coul/long or buck/coul/msm
 
          • args = list of arguments for a particular style 
 
          
 
            buck args = cutoff
@@ -46,6 +50,9 @@
     cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
     cutoff2 = global cutoff for Coulombic (optional) (distance units)
   buck/coul/long args = cutoff (cutoff2)
+    cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
+    cutoff2 = global cutoff for Coulombic (optional) (distance units)
+  buck/coul/msm args = cutoff (cutoff2)
     cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
     cutoff2 = global cutoff for Coulombic (optional) (distance units) 
 
          
@@ -66,6 +73,11 @@ pair_style buck/coul/long 10.0 8.0
 pair_coeff * * 100.0 1.5 200.0
 pair_coeff 1 1 100.0 1.5 200.0 9.0
    +
    pair_style buck/coul/msm 10.0
+pair_style buck/coul/msm 10.0 8.0
+pair_coeff * * 100.0 1.5 200.0
+pair_coeff 1 1 100.0 1.5 200.0 9.0 
+

    Description:

    The buck style computes a Buckingham potential (exp/6 instead of @@ -76,20 +88,20 @@ Lennard-Jones 12/6) given by

    where rho is an ionic-pair dependent length parameter, and Rc is the cutoff.

    -

    The buck/coul/cut and buck/coul/long styles add a Coulombic term -as described for the lj/cut pair styles. For -buck/coul/long, an additional damping factor is applied to the -Coulombic term so it can be used in conjunction with the -kspace_style command and its ewald or pppm -option. The Coulombic cutoff specified for this style means that -pairwise interactions within this distance are computed directly; +

    The styles with coul/cut or coul/long or coul/msm add a +Coulombic term as described for the lj/cut pair styles. +For buck/coul/long and buc/coul/msm, an additional damping factor +is applied to the Coulombic term so it can be used in conjunction with +the kspace_style command and its ewald or pppm +or msm option. The Coulombic cutoff specified for this style means +that pairwise interactions within this distance are computed directly; interactions outside that distance are computed in reciprocal space.

    If one cutoff is specified for the born/coul/cut and -born/coulk/long styles, it is used for both the A,C and Coulombic -terms. If two cutoffs are specified, the first is used as the cutoff -for the A,C terms, and the second is the cutoff for the Coulombic -term. +born/coul/long and born/coul/msm styles, it is used for both the +A,C and Coulombic terms. If two cutoffs are specified, the first is +used as the cutoff for the A,C terms, and the second is the cutoff for +the Coulombic term.

    Note that these potentials are related to the Born-Mayer-Huggins potential. diff --git a/doc/pair_buck.txt b/doc/pair_buck.txt index f2d2b22650..1b8c02789d 100644 --- a/doc/pair_buck.txt +++ b/doc/pair_buck.txt @@ -18,12 +18,14 @@ pair_style buck/coul/long command :h3 pair_style buck/coul/long/cuda command :h3 pair_style buck/coul/long/gpu command :h3 pair_style buck/coul/long/omp command :h3 +pair_style buck/coul/msm command :h3 +pair_style buck/coul/msm/omp command :h3 [Syntax:] pair_style style args :pre -style = {buck} or {buck/coul/cut} or {buck/coul/long} +style = {buck} or {buck/coul/cut} or {buck/coul/long} or {buck/coul/msm} args = list of arguments for a particular style :ul {buck} args = cutoff cutoff = global cutoff for Buckingham interactions (distance units) @@ -31,6 +33,9 @@ args = list of arguments for a particular style :ul cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units) cutoff2 = global cutoff for Coulombic (optional) (distance units) {buck/coul/long} args = cutoff (cutoff2) + cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) + {buck/coul/msm} args = cutoff (cutoff2) cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units) cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre @@ -51,6 +56,11 @@ pair_style buck/coul/long 10.0 8.0 pair_coeff * * 100.0 1.5 200.0 pair_coeff 1 1 100.0 1.5 200.0 9.0 :pre +pair_style buck/coul/msm 10.0 +pair_style buck/coul/msm 10.0 8.0 +pair_coeff * * 100.0 1.5 200.0 +pair_coeff 1 1 100.0 1.5 200.0 9.0 :pre + [Description:] The {buck} style computes a Buckingham potential (exp/6 instead of @@ -61,20 +71,20 @@ Lennard-Jones 12/6) given by where rho is an ionic-pair dependent length parameter, and Rc is the cutoff. -The {buck/coul/cut} and {buck/coul/long} styles add a Coulombic term -as described for the "lj/cut"_pair_lj.html pair styles. For -{buck/coul/long}, an additional damping factor is applied to the -Coulombic term so it can be used in conjunction with the -"kspace_style"_kspace_style.html command and its {ewald} or {pppm} -option. The Coulombic cutoff specified for this style means that -pairwise interactions within this distance are computed directly; +The styles with {coul/cut} or {coul/long} or {coul/msm} add a +Coulombic term as described for the "lj/cut"_pair_lj.html pair styles. +For {buck/coul/long} and {buc/coul/msm}, an additional damping factor +is applied to the Coulombic term so it can be used in conjunction with +the "kspace_style"_kspace_style.html command and its {ewald} or {pppm} +or {msm} option. The Coulombic cutoff specified for this style means +that pairwise interactions within this distance are computed directly; interactions outside that distance are computed in reciprocal space. If one cutoff is specified for the {born/coul/cut} and -{born/coulk/long} styles, it is used for both the A,C and Coulombic -terms. If two cutoffs are specified, the first is used as the cutoff -for the A,C terms, and the second is the cutoff for the Coulombic -term. +{born/coul/long} and {born/coul/msm} styles, it is used for both the +A,C and Coulombic terms. If two cutoffs are specified, the first is +used as the cutoff for the A,C terms, and the second is the cutoff for +the Coulombic term. Note that these potentials are related to the "Born-Mayer-Huggins potential"_pair_born.html. diff --git a/doc/pair_charmm.html b/doc/pair_charmm.html index 76a844a12d..76081e24c3 100644 --- a/doc/pair_charmm.html +++ b/doc/pair_charmm.html @@ -31,11 +31,15 @@

    pair_style lj/charmm/coul/long/omp command

    +

    pair_style lj/charmm/coul/msm command +

    +

    pair_style lj/charmm/coul/msm/omp command +

    Syntax: 

    pair_style style args
    -