From 0e7ce194eb7a68e1b4e14e6808d30159fe1f4c9c Mon Sep 17 00:00:00 2001 From: Anders Hafreager Date: Wed, 24 Aug 2016 15:57:06 +0200 Subject: [PATCH 01/11] Fixed initialization of arrays in computes --- src/compute.cpp | 15 ++++++--------- src/compute_angle.cpp | 3 ++- src/compute_angle_local.cpp | 5 ++--- src/compute_angmom_chunk.cpp | 6 ++---- src/compute_bond.cpp | 3 ++- src/compute_bond_local.cpp | 5 ++--- src/compute_centro_atom.cpp | 7 ++----- src/compute_chunk_atom.cpp | 5 ++++- 8 files changed, 22 insertions(+), 27 deletions(-) diff --git a/src/compute.cpp b/src/compute.cpp index 153116e4d5..20cb88ad8a 100644 --- a/src/compute.cpp +++ b/src/compute.cpp @@ -38,10 +38,13 @@ int Compute::instance_total = 0; /* ---------------------------------------------------------------------- */ -Compute::Compute(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) +Compute::Compute(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp), + id(NULL), style(NULL), + vector(NULL), array(NULL), vector_atom(NULL), array_atom(NULL), vector_local(NULL), array_local(NULL), + tlist(NULL) { instance_me = instance_total++; - + if (narg < 3) error->all(FLERR,"Illegal compute command"); // compute ID, group, and style @@ -93,8 +96,7 @@ Compute::Compute(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) // setup list of timesteps ntime = maxtime = 0; - tlist = NULL; - + // data masks datamask = ALL_MASK; @@ -105,11 +107,6 @@ Compute::Compute(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) datamask_modify = ALL_MASK; copymode = 0; - - // force init to zero in case these are used as logicals - - vector = vector_atom = vector_local = NULL; - array = array_atom = array_local = NULL; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_angle.cpp b/src/compute_angle.cpp index 9301d3ed7d..a9fe0f817e 100644 --- a/src/compute_angle.cpp +++ b/src/compute_angle.cpp @@ -24,7 +24,8 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputeAngle::ComputeAngle(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + emine(NULL) { if (narg != 3) error->all(FLERR,"Illegal compute angle command"); diff --git a/src/compute_angle_local.cpp b/src/compute_angle_local.cpp index 031d4856b5..2ea78311a2 100644 --- a/src/compute_angle_local.cpp +++ b/src/compute_angle_local.cpp @@ -33,7 +33,8 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ ComputeAngleLocal::ComputeAngleLocal(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + vector(NULL), array(NULL) { if (narg < 4) error->all(FLERR,"Illegal compute angle/local command"); @@ -55,8 +56,6 @@ ComputeAngleLocal::ComputeAngleLocal(LAMMPS *lmp, int narg, char **arg) : } nmax = 0; - vector = NULL; - array = NULL; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_angmom_chunk.cpp b/src/compute_angmom_chunk.cpp index 5e88f5bc25..98c6ea0441 100644 --- a/src/compute_angmom_chunk.cpp +++ b/src/compute_angmom_chunk.cpp @@ -26,7 +26,8 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputeAngmomChunk::ComputeAngmomChunk(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + idchunk(NULL), massproc(NULL), masstotal(NULL), com(NULL), comall(NULL), angmom(NULL), angmomall(NULL) { if (narg != 4) error->all(FLERR,"Illegal compute angmom/chunk command"); @@ -48,9 +49,6 @@ ComputeAngmomChunk::ComputeAngmomChunk(LAMMPS *lmp, int narg, char **arg) : nchunk = 1; maxchunk = 0; - massproc = masstotal = NULL; - com = comall = NULL; - angmom = angmomall = NULL; allocate(); } diff --git a/src/compute_bond.cpp b/src/compute_bond.cpp index 241702d672..29869713e7 100644 --- a/src/compute_bond.cpp +++ b/src/compute_bond.cpp @@ -24,7 +24,8 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputeBond::ComputeBond(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + emine(NULL) { if (narg != 3) error->all(FLERR,"Illegal compute bond command"); diff --git a/src/compute_bond_local.cpp b/src/compute_bond_local.cpp index 9cea55de58..f7917acd2b 100644 --- a/src/compute_bond_local.cpp +++ b/src/compute_bond_local.cpp @@ -33,7 +33,8 @@ enum{DIST,ENG,FORCE}; /* ---------------------------------------------------------------------- */ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + bstyle(NULL), vector(NULL), array(NULL) { if (narg < 4) error->all(FLERR,"Illegal compute bond/local command"); @@ -62,8 +63,6 @@ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) : if (bstyle[i] != DIST) singleflag = 1; nmax = 0; - vector = NULL; - array = NULL; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_centro_atom.cpp b/src/compute_centro_atom.cpp index 3640b11269..3f88095d77 100644 --- a/src/compute_centro_atom.cpp +++ b/src/compute_centro_atom.cpp @@ -36,7 +36,8 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputeCentroAtom::ComputeCentroAtom(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + distsq(NULL), nearest(NULL), centro(NULL) { if (narg < 4 || narg > 6) error->all(FLERR,"Illegal compute centro/atom command"); @@ -69,11 +70,7 @@ ComputeCentroAtom::ComputeCentroAtom(LAMMPS *lmp, int narg, char **arg) : else size_peratom_cols = 10; nmax = 0; - centro = NULL; maxneigh = 0; - distsq = NULL; - nearest = NULL; - array_atom = NULL; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_chunk_atom.cpp b/src/compute_chunk_atom.cpp index b9286ea482..7b578611f0 100644 --- a/src/compute_chunk_atom.cpp +++ b/src/compute_chunk_atom.cpp @@ -56,7 +56,10 @@ ComputeChunkAtom *ComputeChunkAtom::cptr; /* ---------------------------------------------------------------------- */ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + id_fix(NULL), chunk(NULL), ichunk(NULL), exclude(NULL), + chunk_volume_vec(NULL), coord(NULL), chunkID(NULL), idregion(NULL), cfvid(NULL), + hash(NULL), varatom(NULL) { if (narg < 4) error->all(FLERR,"Illegal compute chunk/atom command"); From d09a85733bce19a61ae79a4cca858fcc8fc23ce6 Mon Sep 17 00:00:00 2001 From: Anders Hafreager Date: Wed, 24 Aug 2016 16:03:44 +0200 Subject: [PATCH 02/11] Fixed initialization of arrays in computes --- src/compute_cluster_atom.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/compute_cluster_atom.cpp b/src/compute_cluster_atom.cpp index c81785f215..80c002d39f 100644 --- a/src/compute_cluster_atom.cpp +++ b/src/compute_cluster_atom.cpp @@ -34,7 +34,8 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputeClusterAtom::ComputeClusterAtom(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + clusterID(NULL) { if (narg != 4) error->all(FLERR,"Illegal compute cluster/atom command"); @@ -46,7 +47,6 @@ ComputeClusterAtom::ComputeClusterAtom(LAMMPS *lmp, int narg, char **arg) : comm_forward = 1; nmax = 0; - clusterID = NULL; } /* ---------------------------------------------------------------------- */ From 95dde5c04128d0e3d0d0ec1b20158d83f3fc1f55 Mon Sep 17 00:00:00 2001 From: Anders Hafreager Date: Wed, 24 Aug 2016 16:06:58 +0200 Subject: [PATCH 03/11] Fixed initialization of arrays in computes --- src/compute_cna_atom.cpp | 6 ++---- src/compute_com_chunk.cpp | 5 ++--- src/compute_contact_atom.cpp | 4 ++-- src/compute_coord_atom.cpp | 5 ++--- 4 files changed, 8 insertions(+), 12 deletions(-) diff --git a/src/compute_cna_atom.cpp b/src/compute_cna_atom.cpp index 46c6726b00..024a95d9d1 100644 --- a/src/compute_cna_atom.cpp +++ b/src/compute_cna_atom.cpp @@ -42,7 +42,8 @@ enum{NCOMMON,NBOND,MAXBOND,MINBOND}; /* ---------------------------------------------------------------------- */ ComputeCNAAtom::ComputeCNAAtom(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + nearest(NULL), nnearest(NULL), pattern(NULL) { if (narg != 4) error->all(FLERR,"Illegal compute cna/atom command"); @@ -54,9 +55,6 @@ ComputeCNAAtom::ComputeCNAAtom(LAMMPS *lmp, int narg, char **arg) : cutsq = cutoff*cutoff; nmax = 0; - nearest = NULL; - nnearest = NULL; - pattern = NULL; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_com_chunk.cpp b/src/compute_com_chunk.cpp index ebf2b30f6e..3eb686783b 100644 --- a/src/compute_com_chunk.cpp +++ b/src/compute_com_chunk.cpp @@ -28,7 +28,8 @@ enum{ONCE,NFREQ,EVERY}; /* ---------------------------------------------------------------------- */ ComputeCOMChunk::ComputeCOMChunk(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + idchunk(NULL), masstotal(NULL), massproc(NULL), com(NULL), comall(NULL) { if (narg != 4) error->all(FLERR,"Illegal compute com/chunk command"); @@ -50,8 +51,6 @@ ComputeCOMChunk::ComputeCOMChunk(LAMMPS *lmp, int narg, char **arg) : nchunk = 1; maxchunk = 0; - massproc = masstotal = NULL; - com = comall = NULL; allocate(); firstflag = massneed = 1; diff --git a/src/compute_contact_atom.cpp b/src/compute_contact_atom.cpp index 99c4766b6b..c86829bc14 100644 --- a/src/compute_contact_atom.cpp +++ b/src/compute_contact_atom.cpp @@ -32,7 +32,8 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputeContactAtom::ComputeContactAtom(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + contact(NULL) { if (narg != 3) error->all(FLERR,"Illegal compute contact/atom command"); @@ -41,7 +42,6 @@ ComputeContactAtom::ComputeContactAtom(LAMMPS *lmp, int narg, char **arg) : comm_reverse = 1; nmax = 0; - contact = NULL; // error checks diff --git a/src/compute_coord_atom.cpp b/src/compute_coord_atom.cpp index c6aa561eb6..5747c869dc 100644 --- a/src/compute_coord_atom.cpp +++ b/src/compute_coord_atom.cpp @@ -32,7 +32,8 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + typelo(NULL), typehi(NULL), cvec(NULL), carray(NULL) { if (narg < 4) error->all(FLERR,"Illegal compute coord/atom command"); @@ -65,8 +66,6 @@ ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) : else size_peratom_cols = ncol; nmax = 0; - cvec = NULL; - carray = NULL; } /* ---------------------------------------------------------------------- */ From 3e793d6eb7489c665aff38e447a5345e90c43a83 Mon Sep 17 00:00:00 2001 From: Anders Hafreager Date: Wed, 24 Aug 2016 16:16:03 +0200 Subject: [PATCH 04/11] Fixed initialization of arrays in computes --- src/compute_dihedral.cpp | 3 ++- src/compute_dihedral_local.cpp | 5 ++--- src/compute_dipole_chunk.cpp | 8 +++----- src/compute_displace_atom.cpp | 4 ++-- src/compute_erotate_sphere_atom.cpp | 4 ++-- src/compute_group_group.cpp | 3 ++- src/compute_gyration_chunk.cpp | 8 +++----- src/compute_heat_flux.cpp | 3 ++- 8 files changed, 18 insertions(+), 20 deletions(-) diff --git a/src/compute_dihedral.cpp b/src/compute_dihedral.cpp index c6cb97c0dd..bbd7fe2038 100644 --- a/src/compute_dihedral.cpp +++ b/src/compute_dihedral.cpp @@ -24,7 +24,8 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputeDihedral::ComputeDihedral(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + emine(NULL) { if (narg != 3) error->all(FLERR,"Illegal compute dihedral command"); diff --git a/src/compute_dihedral_local.cpp b/src/compute_dihedral_local.cpp index 66523d00a1..f50f49fa11 100644 --- a/src/compute_dihedral_local.cpp +++ b/src/compute_dihedral_local.cpp @@ -34,7 +34,8 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ ComputeDihedralLocal::ComputeDihedralLocal(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + vector(NULL), array(NULL) { if (narg < 4) error->all(FLERR,"Illegal compute dihedral/local command"); @@ -56,8 +57,6 @@ ComputeDihedralLocal::ComputeDihedralLocal(LAMMPS *lmp, int narg, char **arg) : } nmax = 0; - vector = NULL; - array = NULL; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_dipole_chunk.cpp b/src/compute_dipole_chunk.cpp index cb618055f6..4bdf23e273 100644 --- a/src/compute_dipole_chunk.cpp +++ b/src/compute_dipole_chunk.cpp @@ -30,7 +30,9 @@ enum { MASSCENTER, GEOMCENTER }; /* ---------------------------------------------------------------------- */ ComputeDipoleChunk::ComputeDipoleChunk(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + idchunk(NULL), massproc(NULL), masstotal(NULL), chrgproc(NULL), chrgtotal(NULL), com(NULL), + comall(NULL), dipole(NULL), dipoleall(NULL) { if ((narg != 4) && (narg != 5)) error->all(FLERR,"Illegal compute dipole/chunk command"); @@ -60,10 +62,6 @@ ComputeDipoleChunk::ComputeDipoleChunk(LAMMPS *lmp, int narg, char **arg) : nchunk = 1; maxchunk = 0; - massproc = masstotal = NULL; - chrgproc = chrgtotal = NULL; - com = comall = NULL; - dipole = dipoleall = NULL; allocate(); } diff --git a/src/compute_displace_atom.cpp b/src/compute_displace_atom.cpp index f274c32f5d..03a56b2bc4 100644 --- a/src/compute_displace_atom.cpp +++ b/src/compute_displace_atom.cpp @@ -29,7 +29,8 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputeDisplaceAtom::ComputeDisplaceAtom(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + id_fix(NULL), displace(NULL) { if (narg != 3) error->all(FLERR,"Illegal compute displace/atom command"); @@ -76,7 +77,6 @@ ComputeDisplaceAtom::ComputeDisplaceAtom(LAMMPS *lmp, int narg, char **arg) : // per-atom displacement array nmax = 0; - displace = NULL; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_erotate_sphere_atom.cpp b/src/compute_erotate_sphere_atom.cpp index ed6946e8c8..b29c18c1e3 100644 --- a/src/compute_erotate_sphere_atom.cpp +++ b/src/compute_erotate_sphere_atom.cpp @@ -29,7 +29,8 @@ using namespace LAMMPS_NS; ComputeErotateSphereAtom:: ComputeErotateSphereAtom(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + erot(NULL) { if (narg != 3) error->all(FLERR,"Illegal compute erotate/sphere//atom command"); @@ -43,7 +44,6 @@ ComputeErotateSphereAtom(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Compute erotate/sphere/atom requires atom style sphere"); nmax = 0; - erot = NULL; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_group_group.cpp b/src/compute_group_group.cpp index 741d4a667b..4b5e6ad05b 100644 --- a/src/compute_group_group.cpp +++ b/src/compute_group_group.cpp @@ -42,7 +42,8 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ ComputeGroupGroup::ComputeGroupGroup(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + group2(NULL) { if (narg < 4) error->all(FLERR,"Illegal compute group/group command"); diff --git a/src/compute_gyration_chunk.cpp b/src/compute_gyration_chunk.cpp index 58fe33bc3c..f7e774566b 100644 --- a/src/compute_gyration_chunk.cpp +++ b/src/compute_gyration_chunk.cpp @@ -27,7 +27,9 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputeGyrationChunk::ComputeGyrationChunk(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + idchunk(NULL), massproc(NULL), masstotal(NULL), com(NULL), comall(NULL), rg(NULL), + rgall(NULL), rgt(NULL), rgtall(NULL) { if (narg < 4) error->all(FLERR,"Illegal compute gyration/chunk command"); @@ -67,10 +69,6 @@ ComputeGyrationChunk::ComputeGyrationChunk(LAMMPS *lmp, int narg, char **arg) : nchunk = 1; maxchunk = 0; - massproc = masstotal = NULL; - com = comall = NULL; - rg = rgall = NULL; - rgt = rgtall = NULL; allocate(); } diff --git a/src/compute_heat_flux.cpp b/src/compute_heat_flux.cpp index 33e7f7a449..108691aec2 100644 --- a/src/compute_heat_flux.cpp +++ b/src/compute_heat_flux.cpp @@ -33,7 +33,8 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputeHeatFlux::ComputeHeatFlux(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + id_ke(NULL), id_pe(NULL), id_stress(NULL) { if (narg != 6) error->all(FLERR,"Illegal compute heat/flux command"); From 1f3ef8e0ee5e09e8f345bb423de688e2108f5e23 Mon Sep 17 00:00:00 2001 From: Anders Hafreager Date: Wed, 24 Aug 2016 16:24:20 +0200 Subject: [PATCH 05/11] Fixed initialization of arrays in computes --- src/compute_hexorder_atom.cpp | 6 ++---- src/compute_improper.cpp | 3 ++- src/compute_improper_local.cpp | 5 ++--- src/compute_inertia_chunk.cpp | 7 +++---- src/compute_ke_atom.cpp | 4 ++-- src/compute_msd.cpp | 3 ++- src/compute_msd_chunk.cpp | 7 ++----- src/compute_omega_chunk.cpp | 6 ++---- 8 files changed, 17 insertions(+), 24 deletions(-) diff --git a/src/compute_hexorder_atom.cpp b/src/compute_hexorder_atom.cpp index cf9bd6d09f..93b84080bc 100644 --- a/src/compute_hexorder_atom.cpp +++ b/src/compute_hexorder_atom.cpp @@ -44,7 +44,8 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ ComputeHexOrderAtom::ComputeHexOrderAtom(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + distsq(NULL), nearest(NULL), qnarray(NULL) { if (narg < 3 ) error->all(FLERR,"Illegal compute hexorder/atom command"); @@ -87,10 +88,7 @@ ComputeHexOrderAtom::ComputeHexOrderAtom(LAMMPS *lmp, int narg, char **arg) : size_peratom_cols = ncol; nmax = 0; - qnarray = NULL; maxneigh = 0; - distsq = NULL; - nearest = NULL; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_improper.cpp b/src/compute_improper.cpp index 961ddb2c1e..32c5811af1 100644 --- a/src/compute_improper.cpp +++ b/src/compute_improper.cpp @@ -24,7 +24,8 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputeImproper::ComputeImproper(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + emine(NULL) { if (narg != 3) error->all(FLERR,"Illegal compute improper command"); diff --git a/src/compute_improper_local.cpp b/src/compute_improper_local.cpp index 3c0af24a10..b9d69dc5b8 100644 --- a/src/compute_improper_local.cpp +++ b/src/compute_improper_local.cpp @@ -35,7 +35,8 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ ComputeImproperLocal::ComputeImproperLocal(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + vector(NULL), array(NULL) { if (narg < 4) error->all(FLERR,"Illegal compute improper/local command"); @@ -57,8 +58,6 @@ ComputeImproperLocal::ComputeImproperLocal(LAMMPS *lmp, int narg, char **arg) : } nmax = 0; - vector = NULL; - array = NULL; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_inertia_chunk.cpp b/src/compute_inertia_chunk.cpp index c4e83fa4a1..1e3c595ed1 100644 --- a/src/compute_inertia_chunk.cpp +++ b/src/compute_inertia_chunk.cpp @@ -26,7 +26,9 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputeInertiaChunk::ComputeInertiaChunk(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + idchunk(NULL), massproc(NULL), masstotal(NULL), com(NULL), comall(NULL), + inertia(NULL), inertiaall(NULL) { if (narg != 4) error->all(FLERR,"Illegal compute inertia/chunk command"); @@ -48,9 +50,6 @@ ComputeInertiaChunk::ComputeInertiaChunk(LAMMPS *lmp, int narg, char **arg) : nchunk = 1; maxchunk = 0; - massproc = masstotal = NULL; - com = comall = NULL; - inertia = inertiaall = NULL; allocate(); } diff --git a/src/compute_ke_atom.cpp b/src/compute_ke_atom.cpp index aa893981a4..da159669de 100644 --- a/src/compute_ke_atom.cpp +++ b/src/compute_ke_atom.cpp @@ -26,7 +26,8 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputeKEAtom::ComputeKEAtom(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + ke(NULL) { if (narg != 3) error->all(FLERR,"Illegal compute ke/atom command"); @@ -34,7 +35,6 @@ ComputeKEAtom::ComputeKEAtom(LAMMPS *lmp, int narg, char **arg) : size_peratom_cols = 0; nmax = 0; - ke = NULL; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_msd.cpp b/src/compute_msd.cpp index 7f005d2759..f2e82fe239 100644 --- a/src/compute_msd.cpp +++ b/src/compute_msd.cpp @@ -26,7 +26,8 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputeMSD::ComputeMSD(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + id_fix(NULL) { if (narg < 3) error->all(FLERR,"Illegal compute msd command"); diff --git a/src/compute_msd_chunk.cpp b/src/compute_msd_chunk.cpp index 30eee1d64a..bc5a374fad 100644 --- a/src/compute_msd_chunk.cpp +++ b/src/compute_msd_chunk.cpp @@ -28,7 +28,8 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputeMSDChunk::ComputeMSDChunk(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + idchunk(NULL), id_fix(NULL), massproc(NULL), masstotal(NULL), com(NULL), comall(NULL), msd(NULL) { if (narg != 4) error->all(FLERR,"Illegal compute msd/chunk command"); @@ -47,10 +48,6 @@ ComputeMSDChunk::ComputeMSDChunk(LAMMPS *lmp, int narg, char **arg) : firstflag = 1; init(); - massproc = masstotal = NULL; - com = comall = NULL; - msd = NULL; - // create a new fix STORE style for reference positions // id = compute-ID + COMPUTE_STORE, fix group = compute group // do not know size of array at this point, just allocate 1x3 array diff --git a/src/compute_omega_chunk.cpp b/src/compute_omega_chunk.cpp index 54e0b8f906..58acc19c37 100644 --- a/src/compute_omega_chunk.cpp +++ b/src/compute_omega_chunk.cpp @@ -26,7 +26,8 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputeOmegaChunk::ComputeOmegaChunk(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + idchunk(NULL), massproc(NULL), masstotal(NULL), com(NULL), comall(NULL), angmom(NULL), angmomall(NULL) { if (narg != 4) error->all(FLERR,"Illegal compute omega/chunk command"); @@ -48,9 +49,6 @@ ComputeOmegaChunk::ComputeOmegaChunk(LAMMPS *lmp, int narg, char **arg) : nchunk = 1; maxchunk = 0; - massproc = masstotal = NULL; - com = comall = NULL; - angmom = angmomall = NULL; allocate(); } From fcd54f02e6b73c2030bea9dbbb34b58ea3d3a161 Mon Sep 17 00:00:00 2001 From: Anders Hafreager Date: Wed, 24 Aug 2016 16:38:30 +0200 Subject: [PATCH 06/11] Fixed initialization of arrays in computes --- src/compute_orientorder_atom.cpp | 9 ++------- src/compute_pair.cpp | 3 ++- src/compute_pair_local.cpp | 5 ++--- src/compute_pe_atom.cpp | 4 ++-- src/compute_pressure.cpp | 3 ++- 5 files changed, 10 insertions(+), 14 deletions(-) diff --git a/src/compute_orientorder_atom.cpp b/src/compute_orientorder_atom.cpp index fd3493cd7e..6c5a2c0c0e 100644 --- a/src/compute_orientorder_atom.cpp +++ b/src/compute_orientorder_atom.cpp @@ -45,7 +45,8 @@ using namespace std; /* ---------------------------------------------------------------------- */ ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + distsq(NULL), nearest(NULL), rlist(NULL), qlist(NULL), qnarray(NULL), qnm_r(NULL), qnm_i(NULL) { if (narg < 3 ) error->all(FLERR,"Illegal compute orientorder/atom command"); @@ -109,13 +110,7 @@ ComputeOrientOrderAtom::ComputeOrientOrderAtom(LAMMPS *lmp, int narg, char **arg size_peratom_cols = ncol; nmax = 0; - qnarray = NULL; maxneigh = 0; - distsq = NULL; - nearest = NULL; - rlist = NULL; - qnm_r = NULL; - qnm_i = NULL; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_pair.cpp b/src/compute_pair.cpp index 62661b43e6..b00944e1bc 100644 --- a/src/compute_pair.cpp +++ b/src/compute_pair.cpp @@ -26,7 +26,8 @@ enum{EPAIR,EVDWL,ECOUL}; /* ---------------------------------------------------------------------- */ ComputePair::ComputePair(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + pstyle(NULL), pair(NULL), one(NULL) { if (narg < 4 || narg > 5) error->all(FLERR,"Illegal compute pair command"); diff --git a/src/compute_pair_local.cpp b/src/compute_pair_local.cpp index 13dccc5787..6ba4b75728 100644 --- a/src/compute_pair_local.cpp +++ b/src/compute_pair_local.cpp @@ -36,7 +36,8 @@ enum{TYPE,RADIUS}; /* ---------------------------------------------------------------------- */ ComputePairLocal::ComputePairLocal(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + pstyle(NULL), pindex(NULL), vector(NULL), array(NULL) { if (narg < 4) error->all(FLERR,"Illegal compute pair/local command"); @@ -96,8 +97,6 @@ ComputePairLocal::ComputePairLocal(LAMMPS *lmp, int narg, char **arg) : if (pstyle[i] != DIST) singleflag = 1; nmax = 0; - vector = NULL; - array = NULL; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_pe_atom.cpp b/src/compute_pe_atom.cpp index c04edb09f5..f83c91b94c 100755 --- a/src/compute_pe_atom.cpp +++ b/src/compute_pe_atom.cpp @@ -33,7 +33,8 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputePEAtom::ComputePEAtom(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + energy(NULL) { if (narg < 3) error->all(FLERR,"Illegal compute pe/atom command"); @@ -68,7 +69,6 @@ ComputePEAtom::ComputePEAtom(LAMMPS *lmp, int narg, char **arg) : } nmax = 0; - energy = NULL; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_pressure.cpp b/src/compute_pressure.cpp index ca493e46fd..fde19a277a 100644 --- a/src/compute_pressure.cpp +++ b/src/compute_pressure.cpp @@ -34,7 +34,8 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + vptr(NULL), id_temp(NULL) { if (narg < 4) error->all(FLERR,"Illegal compute pressure command"); if (igroup) error->all(FLERR,"Compute pressure must use group all"); From 5e811f16e87d6ecf8191010a6d1d75d8c4a14434 Mon Sep 17 00:00:00 2001 From: Anders Hafreager Date: Wed, 24 Aug 2016 16:50:11 +0200 Subject: [PATCH 07/11] Fixed initialization of arrays in computes --- src/compute_property_atom.cpp | 5 ++--- src/compute_property_chunk.cpp | 6 ++---- src/compute_property_local.cpp | 6 ++---- src/compute_rdf.cpp | 4 +++- src/compute_reduce.cpp | 4 +++- src/compute_slice.cpp | 3 ++- 6 files changed, 14 insertions(+), 14 deletions(-) diff --git a/src/compute_property_atom.cpp b/src/compute_property_atom.cpp index c9575dba5f..2ce10fdb68 100644 --- a/src/compute_property_atom.cpp +++ b/src/compute_property_atom.cpp @@ -32,7 +32,8 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputePropertyAtom::ComputePropertyAtom(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + index(NULL), vector(NULL), array(NULL), pack_choice(NULL) { if (narg < 4) error->all(FLERR,"Illegal compute property/atom command"); @@ -352,8 +353,6 @@ ComputePropertyAtom::ComputePropertyAtom(LAMMPS *lmp, int narg, char **arg) : } nmax = 0; - vector = NULL; - array = NULL; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_property_chunk.cpp b/src/compute_property_chunk.cpp index 9567748918..1461a83ad2 100644 --- a/src/compute_property_chunk.cpp +++ b/src/compute_property_chunk.cpp @@ -25,7 +25,8 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputePropertyChunk::ComputePropertyChunk(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + idchunk(NULL), count_one(NULL), count_all(NULL) { if (narg < 5) error->all(FLERR,"Illegal compute property/chunk command"); @@ -78,9 +79,6 @@ ComputePropertyChunk::ComputePropertyChunk(LAMMPS *lmp, int narg, char **arg) : nchunk = 1; maxchunk = 0; - vector = NULL; - array = NULL; - count_one = count_all = NULL; allocate(); if (nvalues == 1) { diff --git a/src/compute_property_local.cpp b/src/compute_property_local.cpp index 60460f271a..b9472cb45b 100644 --- a/src/compute_property_local.cpp +++ b/src/compute_property_local.cpp @@ -34,7 +34,8 @@ enum{TYPE,RADIUS}; /* ---------------------------------------------------------------------- */ ComputePropertyLocal::ComputePropertyLocal(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + vector(NULL), array(NULL), indices(NULL), pack_choice(NULL) { if (narg < 4) error->all(FLERR,"Illegal compute property/local command"); @@ -253,9 +254,6 @@ ComputePropertyLocal::ComputePropertyLocal(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Compute property/local requires atom attribute radius"); nmax = 0; - vector = NULL; - array = NULL; - indices = NULL; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_rdf.cpp b/src/compute_rdf.cpp index 14a12bb5c6..8624508017 100644 --- a/src/compute_rdf.cpp +++ b/src/compute_rdf.cpp @@ -38,7 +38,9 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + rdfpair(NULL), nrdfpair(NULL), ilo(NULL), ihi(NULL), jlo(NULL), jhi(NULL), + hist(NULL), histall(NULL), typecount(NULL), icount(NULL), jcount(NULL), duplicates(NULL) { if (narg < 4 || (narg-4) % 2) error->all(FLERR,"Illegal compute rdf command"); diff --git a/src/compute_reduce.cpp b/src/compute_reduce.cpp index 7ea3c2aafe..dc6896f27b 100644 --- a/src/compute_reduce.cpp +++ b/src/compute_reduce.cpp @@ -43,7 +43,9 @@ enum{PERATOM,LOCAL}; /* ---------------------------------------------------------------------- */ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + nvalues(0), which(NULL), argindex(NULL), flavor(NULL), value2index(NULL), ids(NULL), + onevec(NULL), replace(NULL), indices(NULL), owner(NULL), idregion(NULL), varatom(NULL) { int iarg = 0; if (strcmp(style,"reduce") == 0) { diff --git a/src/compute_slice.cpp b/src/compute_slice.cpp index d2c3c18de4..da077ddfc0 100644 --- a/src/compute_slice.cpp +++ b/src/compute_slice.cpp @@ -34,7 +34,8 @@ enum{COMPUTE,FIX,VARIABLE}; /* ---------------------------------------------------------------------- */ ComputeSlice::ComputeSlice(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + nvalues(0), which(NULL), argindex(NULL), value2index(NULL), ids(NULL) { if (narg < 7) error->all(FLERR,"Illegal compute slice command"); From 7d43f349e6d8ba4d856bb39af788b81f02929990 Mon Sep 17 00:00:00 2001 From: Anders Hafreager Date: Wed, 24 Aug 2016 17:06:58 +0200 Subject: [PATCH 08/11] Fixed initialization of arrays in computes --- src/compute.cpp | 2 +- src/compute_stress_atom.cpp | 4 ++-- src/compute_temp_chunk.cpp | 11 ++++------- src/compute_temp_profile.cpp | 4 ++-- src/compute_temp_region.cpp | 3 ++- src/compute_temp_sphere.cpp | 4 ++-- src/compute_torque_chunk.cpp | 6 ++---- src/compute_vacf.cpp | 3 ++- src/compute_vcm_chunk.cpp | 5 ++--- 9 files changed, 19 insertions(+), 23 deletions(-) diff --git a/src/compute.cpp b/src/compute.cpp index 20cb88ad8a..96bf6ceb54 100644 --- a/src/compute.cpp +++ b/src/compute.cpp @@ -41,7 +41,7 @@ int Compute::instance_total = 0; Compute::Compute(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp), id(NULL), style(NULL), vector(NULL), array(NULL), vector_atom(NULL), array_atom(NULL), vector_local(NULL), array_local(NULL), - tlist(NULL) + tlist(NULL), vbiasall(NULL) { instance_me = instance_total++; diff --git a/src/compute_stress_atom.cpp b/src/compute_stress_atom.cpp index 3455d9eb08..46ee2ec3c5 100644 --- a/src/compute_stress_atom.cpp +++ b/src/compute_stress_atom.cpp @@ -36,7 +36,8 @@ enum{NOBIAS,BIAS}; /* ---------------------------------------------------------------------- */ ComputeStressAtom::ComputeStressAtom(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + id_temp(NULL), stress(NULL) { if (narg < 4) error->all(FLERR,"Illegal compute stress/atom command"); @@ -98,7 +99,6 @@ ComputeStressAtom::ComputeStressAtom(LAMMPS *lmp, int narg, char **arg) : } nmax = 0; - stress = NULL; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_temp_chunk.cpp b/src/compute_temp_chunk.cpp index 87d6e11864..8daaeb0621 100644 --- a/src/compute_temp_chunk.cpp +++ b/src/compute_temp_chunk.cpp @@ -29,7 +29,9 @@ enum{TEMP,KECOM,INTERNAL}; /* ---------------------------------------------------------------------- */ ComputeTempChunk::ComputeTempChunk(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + which(NULL), idchunk(NULL), id_bias(NULL), sum(NULL), sumall(NULL), count(NULL), + countall(NULL), massproc(NULL), masstotal(NULL), vcm(NULL), vcmall(NULL) { if (narg < 4) error->all(FLERR,"Illegal compute temp/chunk command"); @@ -129,12 +131,7 @@ ComputeTempChunk::ComputeTempChunk(LAMMPS *lmp, int narg, char **arg) : nchunk = 1; maxchunk = 0; - sum = sumall = NULL; - count = countall = NULL; - massproc = masstotal = NULL; - vcm = vcmall = NULL; - array = NULL; - + if (nvalues) { array_flag = 1; size_array_cols = nvalues; diff --git a/src/compute_temp_profile.cpp b/src/compute_temp_profile.cpp index 654bea7ebe..1c6e56359d 100644 --- a/src/compute_temp_profile.cpp +++ b/src/compute_temp_profile.cpp @@ -31,7 +31,8 @@ enum{TENSOR,BIN}; /* ---------------------------------------------------------------------- */ ComputeTempProfile::ComputeTempProfile(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + bin(NULL), vbin(NULL), binave(NULL), tbin(NULL), tbinall(NULL) { if (narg < 7) error->all(FLERR,"Illegal compute temp/profile command"); @@ -138,7 +139,6 @@ ComputeTempProfile::ComputeTempProfile(LAMMPS *lmp, int narg, char **arg) : } maxatom = 0; - bin = NULL; } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_temp_region.cpp b/src/compute_temp_region.cpp index 33e07bfb1e..e636669344 100644 --- a/src/compute_temp_region.cpp +++ b/src/compute_temp_region.cpp @@ -28,7 +28,8 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputeTempRegion::ComputeTempRegion(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + idregion(NULL) { if (narg != 4) error->all(FLERR,"Illegal compute temp/region command"); diff --git a/src/compute_temp_sphere.cpp b/src/compute_temp_sphere.cpp index 64b23308e2..50995dfa84 100644 --- a/src/compute_temp_sphere.cpp +++ b/src/compute_temp_sphere.cpp @@ -33,7 +33,8 @@ enum{ROTATE,ALL}; /* ---------------------------------------------------------------------- */ ComputeTempSphere::ComputeTempSphere(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + id_bias(NULL) { if (narg < 3) error->all(FLERR,"Illegal compute temp/sphere command"); @@ -44,7 +45,6 @@ ComputeTempSphere::ComputeTempSphere(LAMMPS *lmp, int narg, char **arg) : tempflag = 1; tempbias = 0; - id_bias = NULL; mode = ALL; int iarg = 3; diff --git a/src/compute_torque_chunk.cpp b/src/compute_torque_chunk.cpp index 5462debcfc..25386ad40d 100644 --- a/src/compute_torque_chunk.cpp +++ b/src/compute_torque_chunk.cpp @@ -26,7 +26,8 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputeTorqueChunk::ComputeTorqueChunk(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + idchunk(NULL), massproc(NULL), masstotal(NULL), com(NULL), comall(NULL), torque(NULL), torqueall(NULL) { if (narg != 4) error->all(FLERR,"Illegal compute torque/chunk command"); @@ -48,9 +49,6 @@ ComputeTorqueChunk::ComputeTorqueChunk(LAMMPS *lmp, int narg, char **arg) : nchunk = 1; maxchunk = 0; - massproc = masstotal = NULL; - com = comall = NULL; - torque = torqueall = NULL; allocate(); } diff --git a/src/compute_vacf.cpp b/src/compute_vacf.cpp index c06113a770..6ba272e579 100755 --- a/src/compute_vacf.cpp +++ b/src/compute_vacf.cpp @@ -25,7 +25,8 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputeVACF::ComputeVACF(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + id_fix(NULL) { if (narg < 3) error->all(FLERR,"Illegal compute vacf command"); diff --git a/src/compute_vcm_chunk.cpp b/src/compute_vcm_chunk.cpp index cd864b2aa8..0661bf4457 100644 --- a/src/compute_vcm_chunk.cpp +++ b/src/compute_vcm_chunk.cpp @@ -28,7 +28,8 @@ enum{ONCE,NFREQ,EVERY}; /* ---------------------------------------------------------------------- */ ComputeVCMChunk::ComputeVCMChunk(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + idchunk(NULL), massproc(NULL), masstotal(NULL), vcm(NULL), vcmall(NULL) { if (narg != 4) error->all(FLERR,"Illegal compute vcm/chunk command"); @@ -50,8 +51,6 @@ ComputeVCMChunk::ComputeVCMChunk(LAMMPS *lmp, int narg, char **arg) : nchunk = 1; maxchunk = 0; - massproc = masstotal = NULL; - vcm = vcmall = NULL; allocate(); firstflag = massneed = 1; From ea368919f3b535331f72e8fbcebfb5ec21a13057 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 26 Aug 2016 00:01:34 -0400 Subject: [PATCH 09/11] Remove sha1sum dependency for doc generation On MacOS X there is no sha1sum. So to simplify doc generation on those systems use a Python script instead to generate a unique string from the repository path. --- doc/Makefile | 2 +- doc/utils/sha1sum.py | 7 +++++++ 2 files changed, 8 insertions(+), 1 deletion(-) create mode 100755 doc/utils/sha1sum.py diff --git a/doc/Makefile b/doc/Makefile index 198fffda22..8ee8379c58 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -1,5 +1,5 @@ # Makefile for LAMMPS documentation -SHA1 = $(shell echo $USER-$PWD | sha1sum | cut -f1 -d" ") +SHA1 = $(shell echo $USER-$PWD | python utils/sha1sum.py) BUILDDIR = /tmp/lammps-docs-$(SHA1) RSTDIR = $(BUILDDIR)/rst VENV = $(BUILDDIR)/docenv diff --git a/doc/utils/sha1sum.py b/doc/utils/sha1sum.py new file mode 100755 index 0000000000..d4842ecf1a --- /dev/null +++ b/doc/utils/sha1sum.py @@ -0,0 +1,7 @@ +#!/bin/env python +# simple utility which reimplements sha1sum using Python +import hashlib +import sys +s = hashlib.sha1() +s.update(sys.stdin.read().encode()) +print(s.hexdigest()) From 95aabdf51a96e79e2ff1d797bff47de38831802a Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 26 Aug 2016 10:08:22 -0400 Subject: [PATCH 10/11] Add MacOS X instructions to doc generation README --- doc/README.md | 20 +++++++++++++++----- 1 file changed, 15 insertions(+), 5 deletions(-) diff --git a/doc/README.md b/doc/README.md index fb130b35b9..26a51c13ab 100644 --- a/doc/README.md +++ b/doc/README.md @@ -15,18 +15,28 @@ make clean-all # remove entire build folder and any cached data ## Installing prerequisites To run the documention build toolchain Python 3 and virtualenv have to be -installed. The following are instructions for common Linux distributions: +installed. Here are instructions for common setups: -### virtualenv - -#### Ubuntu +### Ubuntu ```bash sudo apt-get install python-virtualenv ``` -#### Fedora +### Fedora ``` sudo yum install python-virtualenv ``` + +### MacOS X + +## Python 3 + +Download the latest Python 3 MacOS X package from https://www.python.org and install it. +This will install both Python 3 and pip3. + +## virtualenv + +Once Python 3 is installed, open a Terminal and type `pip3 install virtualenv`. This will +install virtualenv from the Python Package Index. From 3a1397dc7c364f88c8554ba80fd28a05a02354bd Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Sat, 27 Aug 2016 17:11:16 -0600 Subject: [PATCH 11/11] sync with SVN --- doc/html/Manual.html | 2 +- doc/html/fix_flow_gauss.html | 98 +++++++++++++-------------- doc/html/genindex.html | 8 ++- doc/html/searchindex.js | 2 +- doc/src/Manual.txt | 4 +- doc/src/fix_flow_gauss.txt | 109 ++++++++++++++++--------------- src/USER-MISC/README | 2 +- src/USER-MISC/fix_flow_gauss.cpp | 10 ++- src/version.h | 2 +- 9 files changed, 125 insertions(+), 112 deletions(-) diff --git a/doc/html/Manual.html b/doc/html/Manual.html index 963ee9cacd..5c7ec2f31d 100644 --- a/doc/html/Manual.html +++ b/doc/html/Manual.html @@ -135,7 +135,7 @@

LAMMPS Documentation

-

23 Aug 2016 version

+

27 Aug 2016 version

Version info:

diff --git a/doc/html/fix_flow_gauss.html b/doc/html/fix_flow_gauss.html index 64869110c6..ca10c2d38d 100644 --- a/doc/html/fix_flow_gauss.html +++ b/doc/html/fix_flow_gauss.html @@ -159,64 +159,65 @@

Description

-

This fix implements the Gaussian dynamics (GD) method to simulate a system at -constant mass flux (Strong). GD is a nonequilibrium molecular -dynamics simulation method that can be used to study fluid flows through -pores, pipes, and channels. In its original implementation GD was used to -compute the pressure required to achieve a fixed mass flux through an opening. -The flux can be conserved in any combination of the directions, x, y, or z, -using xflag,yflag,zflag. This fix does not initialize a net flux through -a system, it only conserves the center-of-mass momentum that is present -when the fix is declared in the input script. Use the velocity -command to generate an initial center-of-mass momentum.

-

GD applies an external fluctuating gravitational field that acts as a driving -force to keep the system away from equilibrium. To maintain steady state, a -profile-unbiased thermostat must be implemented to dissipate the heat that is -added by the driving force. Compute temp/profile -can be used to implement a profile-unbiased thermostat.

-

A common use of this fix is to compute a pressure drop across a pipe, pore, or -membrane. The pressure profile can be computed in LAMMPS with compute stress/atom and fix ave/chunk, -or with the hardy method in fix atc. Note that the simple -compute stress/atom method is only accurate away -from inhomogeneities in the fluid, such as fixed wall atoms. Further, the -computed pressure profile must be corrected for the acceleration applied by -GD before computing a pressure drop or comparing it to other methods, such as -the pump method (Zhu). The pressure correction is discussed and -described in (Strong).

+

This fix implements the Gaussian dynamics (GD) method to simulate a +system at constant mass flux (Strong). GD is a +nonequilibrium molecular dynamics simulation method that can be used +to study fluid flows through pores, pipes, and channels. In its +original implementation GD was used to compute the pressure required +to achieve a fixed mass flux through an opening. The flux can be +conserved in any combination of the directions, x, y, or z, using +xflag,yflag,zflag. This fix does not initialize a net flux through a +system, it only conserves the center-of-mass momentum that is present +when the fix is declared in the input script. Use the +velocity command to generate an initial center-of-mass +momentum.

+

GD applies an external fluctuating gravitational field that acts as a +driving force to keep the system away from equilibrium. To maintain +steady state, a profile-unbiased thermostat must be implemented to +dissipate the heat that is added by the driving force. Compute temp/profile can be used to implement a +profile-unbiased thermostat.

+

A common use of this fix is to compute a pressure drop across a pipe, +pore, or membrane. The pressure profile can be computed in LAMMPS with +compute stress/atom and fix ave/chunk, or with the hardy method in fix atc. Note that the simple compute stress/atom method is only accurate away +from inhomogeneities in the fluid, such as fixed wall atoms. Further, +the computed pressure profile must be corrected for the acceleration +applied by GD before computing a pressure drop or comparing it to +other methods, such as the pump method (Zhu). The pressure +correction is discussed and described in (Strong).

Note

-

For a complete example including the considerations discussed above, see -the examples/USER/flow_gauss directory.

+

For a complete example including the considerations discussed +above, see the examples/USER/flow_gauss directory.

Note

Only the flux of the atoms in group-ID will be conserved. If the -velocities of the group-ID atoms are coupled to the velocities of other atoms -in the simulation, the flux will not be conserved. For example, in a -simulation with fluid atoms and harmonically constrained wall atoms, if a -single thermostat is applied to group all, the fluid atom velocities will be -coupled to the wall atom velocities, and the flux will not be conserved. This -issue can be avoided by thermostatting the fluid and wall groups separately.

+velocities of the group-ID atoms are coupled to the velocities of +other atoms in the simulation, the flux will not be conserved. For +example, in a simulation with fluid atoms and harmonically constrained +wall atoms, if a single thermostat is applied to group all, the +fluid atom velocities will be coupled to the wall atom velocities, and +the flux will not be conserved. This issue can be avoided by +thermostatting the fluid and wall groups separately.

-
-
Adding an acceleration to atoms does work on the system. This added energy
-
can be optionally subtracted from the potential energy for the thermodynamic
-
-

output (see below) to check that the timestep is small enough to conserve -energy. Since the applied acceleration is fluctuating in time, the work cannot -be computed from a potential. As a result, computing the work is slightly more -computationally expensive than usual, so it is not performed by default. To -invoke the work calculation, use the energy keyword. The +

Adding an acceleration to atoms does work on the system. This added +energy can be optionally subtracted from the potential energy for the +thermodynamic output (see below) to check that the timestep is small +enough to conserve energy. Since the applied acceleration is +fluctuating in time, the work cannot be computed from a potential. As +a result, computing the work is slightly more computationally +expensive than usual, so it is not performed by default. To invoke the +work calculation, use the energy keyword. The fix_modify energy option also invokes the work -calculation, and overrides an energy no setting here. If neither energy yes -or fix_modify energy yes are set, the global scalar computed by the fix -will return zero.

+calculation, and overrides an energy no setting here. If neither +energy yes or fix_modify energy yes are set, the global scalar +computed by the fix will return zero.

Note

-

In order to check energy conservation, any other fixes that do work on -the system must have fix_modify energy yes set as well. This includes -thermostat fixes and any constraints that hold the positions of wall atoms -fixed, such as fix spring/self.

+

In order to check energy conservation, any other fixes that do +work on the system must have fix_modify energy yes set as well. This +includes thermostat fixes and any constraints that hold the positions +of wall atoms fixed, such as fix spring/self.

@@ -252,7 +253,6 @@ the run(Strong) Strong and Eaves, J. Phys. Chem. Lett. 7, 1907 (2016).

(Evans) Evans and Morriss, Phys. Rev. Lett. 56, 2172 (1986).

(Zhu) Zhu, Tajkhorshid, and Schulten, Biophys. J. 83, 154 (2002).

-
diff --git a/doc/html/genindex.html b/doc/html/genindex.html index 2a8af45337..a4ece0112b 100644 --- a/doc/html/genindex.html +++ b/doc/html/genindex.html @@ -1094,6 +1094,10 @@ +
fix flow/gauss +
+ +
fix freeze
@@ -1241,12 +1245,12 @@
fix nve/eff
+ +
fix nve/limit
-
-
fix nve/line
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js index 622bf39e1a..655458bf7d 100644 --- a/doc/html/searchindex.js +++ b/doc/html/searchindex.js @@ -1 +1 @@ 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r:147,buffer:57,bufi:57,bug:0,bui:57,build:[0,1,2],built:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,37,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,56,60,63,64,65,66,67,68,69,70,71,72,74,75,77,78,79,82,83,84,85,86,87,88,89,90,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],bulatov:[135,136],bulk:[2,29,67,70,106,134,137,147],bundl:[57,162],button:162,bypass:2,c11:134,c_0:[79,94,151,152],c_1:[40,43,66],c_2:[40,43],c_cluster:2,c_cstherm:2,c_doubl:3,c_e:79,c_flux:35,c_gauss:116,c_hb:120,c_i:65,c_id:[2,32,62],c_ij:2,c_ijkl:2,c_k:66,c_mychunk:[2,34],c_n_k:66,c_p:42,c_peratom:42,c_pi:97,c_prop:2,c_sigma:97,c_size:2,c_thermo_temp:62,ca2:43,cach:4,cacul:75,calcforc:67,calclat:35,calcluat:[37,39,42,105],calcualt:35,calcul:[0,1],caldwel:[2,45],calhoun:71,call:[1,2,3,4,71,94,103,160,162],callabl:3,callback:3,caltech:[2,113],calucl:2,calul:[3,29],can:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],cannot:[1,2,3,4,19,28,57,59,60,61,66,68,72,79,80,81,91,92,99,100,102,111,117,119,122,126,128,130,143,145,146,153],canon:[68,71,78,137],cao1:71,cao2:71,cao:71,capabl:[3,4,94,102],capac:[64,79,150],capolungo:[40,43],captur:[2,94,100,113,118,126,134],carbid:105,carbon:[57,89,94,104,134],card:[4,32,120],care:[2,44,55,67,68,96],carefulli:[3,28],carlo:[2,60],caro:111,carri:[4,79,118],carrillo:4,cartesian:[2,93],cascad:79,cat:[4,57],cate:67,categori:[0,94],cation:[114,147],caus:[1,2,4,44,61,68,70,74,75,80,81,91,92,120,122,128,131,132],caution:1,cautious:94,caveat:94,cbecker:[93,111],cc1:[2,34],ccc:[112,154,155,157,158],ccflag:4,ccflags:4,ccm6:111,ccsi:[112,154,155,157,158],ccu:97,cd2:43,cdeam:111,cdll:3,cdof:2,cdte:97,cdte_bop:97,cdtese:97,cdzn:97,cdznte:97,ce3:43,ce4:43,cell:[2,40,43,44,61,68,69,72,79,113,137],cella:2,cellalpha:2,cellb:2,cellbeta:2,cellc:2,cellgamma:2,center:[2,9,33,34,37,40,44,57,61,66,68,76,78,80,81,83,96,112,113,117,118,131,132,134,135,136,154,155,156,157,158],centr:63,central:[29,36,38,41,70,75,76,86,137,142,158],centro:2,centroid:71,centrosymmetri:29,certain:[1,2,57,60,62],cfg:[2,57],cg_type:146,ch2:75,ch2lmp:[0,2],ch3:75,chain:[0,2,13,28,60,68,69,71,75,78,89,108,109,153],challeng:2,champaign:131,chan:137,chandler:[93,111],chandrasekhar:[2,122],chang:[1,2,3,4,19,22,32,44,57,58,59,60,61,62,67,68,69,70,72,73,74,75,77,78,79,81,91,92,109,113,118,131,132,134,137,147,153,162],change_box:2,chapter:71,charact:[2,19,57,59,65,74,113,115,121,140,141,144,147],character:[2,29,38,41,148],characterist:77,charg:[1,2,3,32,40,43,44,98,99,104,105,107,108,111,113,114,122,126,130,143,147,157,158,160,161],charl:62,charmm:0,cheaper:[117,145],check:[2,3,19,35,59,73,75,78,91,92,121],checkout:162,chem:[2,5,6,9,20,21,22,32,38,39,42,45,46,53,63,66,67,68,71,72,77,78,80,83,89,90,92,94,98,101,102,104,105,106,108,109,110,113,116,117,119,120,122,126,127,130,134,138,140,141,143,147,153],chemic:[31,40,43,58,115,141],chemistri:[72,94,97,113],chen:79,cheng:104,chi:[70,114,117],chiral:89,chmod:3,cho:134,choic:[2,4,19,28,29,32,42,55,59,60,67,68,71,92,130],choos:[1,2,13,28,32,57,60,61,62,67,68,69],chose:[155,157],chosen:[2,41,44,50,57,61,62,66,67,68,69,71,110,113,118,121,124,146,155],chunk:0,chunkid:34,ciccotti:75,cieplak:[2,45],circular:2,circumv:[36,38],citat:[0,67],cite:147,cl1:43,clarendon:[13,108],clarifi:[155,157],clark:143,classic:[0,2,4,71,72,79,90,113],classifi:158,clean:2,clear:[2,3,62],clebsch:41,click:[3,44,56,57,92,162],climb:92,clockwis:45,clone:162,close:[2,3,19,42,60,61,67,68,75,81,92,94,97,105,106,134,140,141,157,162],closer:[19,59,61,77,92],closest:[70,117,145,153],cloud:147,cluster:[2,4,42,63,75],cmax:134,cmd:[3,71],cmdarg:3,cmin:134,cmm:[18,146],cna:29,co2:[43,74,75,115],coars:[13,18,28,50,65,74,115,119,141,146],coarsest:41,code:[0,1],coeff:[6,45,46,55,83,121,149],coeffici:0,coefficienct:109,coefficient0:111,coefficient1:111,coeffieci:[2,95],coeffincientn:111,coexist:113,cohes:[2,114,134],coincid:[81,101,131,132],cold:2,coleman:[40,43],collect:[2,34,44,103],colliex:43,collis:[67,118,161],colloid:2,color:[19,57,59,66,72],column:[2,29,34,36,38,41,42,43,72,79,94,116,120],colvar:0,com:[2,37,63,96,162],comand:60,combiant:106,combin:[2,3,18,32,55,57,58,63,68,71,81,83,103,105,106,110,113,114,115,129,130,148,154,155,157,158,160],come:[0,2,13,61,62,68,77,78,154,155,157,158,162],comit:162,comm:[0,3,30,92,109],comm_modifi:[2,97,103,109,113,118],comm_styl:[19,59],comm_world:3,command:[0,1],comment:[3,45,65,74,79,92,93,111,112,114,115,121,134,140,141,142,147,148,154,155,156,157,158,162],commit:162,commmand:2,common:[0,1,2,3,4,30,61,71,81,83,118,120,154,155,157],commonli:[2,9,37,38,57,90,119,124,148,155,157],commun:[1,2,3,4,19,57,59,61,67,68,79,110],comp:[75,92,113,145,152,156],compar:[1,2,4,40,43,56,91,92,134,147],comparison:0,compass:[6,20,46,56,83,102],compat:[3,19,49,59,62,63,80,137],compens:[2,113],compil:[4,57,137],complain:3,complement:134,complementari:[105,122],complet:[2,3,19,59,71,92,114],complex:[2,3,9,36,38,41,44,67,81,92,113,137],complic:2,compon:[2,29,30,33,34,35,36,37,38,39,41,42,57,60,61,62,63,67,68,69,71,75,81,91,92,109,113,118,131,132,147,148],componenet:2,composit:[2,67,111],compound:[104,113,114,158],compress:[2,57,69,72],compris:[81,115,145],compton:[40,43],comput:[0,1],computation:[2,79,97],compute_modifi:[60,61,68,69],compute_sa:40,compute_xrd:43,concav:81,concentr:[65,74,111,115,141],concept:2,conceptu:[2,61,92,105,134],concern:[2,30,32,66],concis:3,concurr:4,conden:[79,155,157],condens:[2,79,94,107,111,122,158],condit:[2,39,40,42,43,57,58,67,69,70,72,75,76,79,110,113,119],conducit:2,conduct:0,confer:[4,137],configur:[1,2,4,57,61,71,91,92,94,97,112,134,137,154,155,157,158,162],conflict:162,conform:[2,60,61,73,89,92,113],confus:158,conjuct:109,conjug:113,conjunct:[2,32,44,67,92,98,99,105,109,113,120,122,143,146],connect:[2,32,60,75,92,106,118,153,157],conner:94,connor:94,consecut:[3,44,105,122,126],consequ:[1,2,79,121],conserv:[13,60,66,67,68,74,75,92,108,109,110,118,128,147],consid:[2,29,32,59,60,79,113,145,147,153],consider:2,consist:[2,3,39,44,50,62,66,68,69,72,73,74,82,92,94,97,103,105,113,117,131,132,134,137,140,141,145,147],consistent_fe_initi:58,constant:0,constantli:63,constitu:[2,80,81,103,145],constrain:[2,63,66,75,76,91,113],constraint:[19,39,42,59,63,75,76,80,91,132],construct:[2,28,29,30,36,38,40,41,43,61,68,73,74,81,108,137,153,154],constructor:3,consult:4,consum:1,contact:[0,106,112,114,117,118,145],contain:[0,1,2,3,19,32,35,40,41,43,44,45,56,57,58,59,62,65,67,70,72,74,79,81,92,93,94,97,104,105,108,111,112,113,115,134,137,140,141,142,144,148,154,155,156,157,158,162],context:[2,4,160],contibut:29,contin:4,continu:[0,2,19,59,60,61,62,63,66,68,69,72,77,78,79,81,97,109,124,127,145,156],continuum:[2,58,79],contour_integr:58,contract:[61,68],contrain:75,contrast:[1,2,160],contrib:79,contribut:[2,29,32,33,34,35,39,41,42,61,67,75,91,92,109,111,113,131,132,137,147,162],control:[2,3,4,11,13,19,32,35,41,47,57,58,59,61],control_typ:58,convect:35,conveni:[2,13,148,162],convent:[13,49,54,56,73,111,113],converg:[2,19,57,59,60,61,69,72,73,75,91,92,104,105,122,147],convers:[41,57,105,106,107,113,122,126,130,143],convert:[2,5,6,8,12,16,17,18,35,44,46,57,83,84,88,89,92,93,111,137,155,157,161],convex:81,cool:63,coord:[2,3,36,38,70,80,92],coordb:147,coordbb:147,coordiat:91,coordin:[1,2,3,19,32,33,34,41,44,57,59,60,61,63,68,70,75,76,78,79,91,92,93,94,96,112,147],coords:147,copi:[0,3,57,79,92,162],copper:161,coprocessor:[1,4],core:[0,1],coreshel:2,coreshell:[2,99,105,107],cornel:[2,45],corner:[2,57,81,162],corpor:4,corr:104,correct:[2,3,32,45,57,63,68,72,80,81,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,111,112,113,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],correction_max_iter:58,correctli:[3,68,75,81,92,107,132,137,162],correl:[2,35,36,41,66,71],correpond:65,correspond:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,29,32,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,57,61,62,63,65,67,68,69,70,71,74,75,80,81,82,83,84,85,87,88,89,90,92,93,94,95,98,99,100,101,102,103,104,105,108,109,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,134,135,137,139,141,142,143,144,145,146,147,148,149,154,155,156,157,158,159,160,161],correspondingli:[131,132],cosin:2,cosineshift:11,cost:[1,2,3,19,40,42,43,57,59,68,74,79,105,122,126,137,154],costheta0:[154,155,157,158],costheta:144,costli:[3,4],coul:[2,4,18,21,22,32,45,91],could:[2,3,19,32,34,35,39,57,59,62,72,79,80,81,91,94,116,120],coulomb:[2,42,91,98,99,100,101,102,104,105,106,107,108,113,118,119,122,126,130,133,143,146,147,157,158,160],coulommb:2,count:[1,2,3,19,35,45,59,61,68,75,81,91,92,116,120],counteract:62,counterbal:63,counterbalanc:13,counterclockwis:45,coupl:0,couple:[2,3],cours:[4,66,73,80,131,149],cov:147,coval:[2,13,113,134,147],cover:[2,58,67,113],cpp:[1,2,3,32,75],cpu:[1,4],cpuinfo:4,cr2:43,cr3:43,creat:[0,1,2,3,19,35,39,40,44,57,58,59,60,61,65,68,69,70,71,73,79,82,92,94,97,104,111,112,130,139,140,141,144,147,154,155,156,157,158,162],create_atom:[2,19,35],create_box:[2,19,35,44,61,68,153],create_elementset:58,create_faceset:58,create_nodeset:58,createatom:0,creation:44,criteria:[57,60,91],criterion:[19,44,59,60,91,92,104,113,118,147],critic:[2,24,25,79,91],cross:[4,33,57,92,101,109,111,119,120,122,124,126,144,146,155,157,161],crossov:1,crozier:0,crucial:72,crystal:[2,4,29,30,38,70,78],crystallin:[2,156],crystallogr:[40,43],crystallographi:[40,43],cs1:43,cs_chunk:2,csanyi:[41,148],cscl:134,csequ:2,csh:[3,4],cshrc:3,csic:[112,154,155,157,158],csinfo:2,csisi:[112,154,155,157,158],cst:111,cstherm:2,csvr:2,ctcm:[93,111],ctype:3,cu1:43,cu2:43,cu3au:134,cube:[2,81],cubes:[19,59],cubic:[38,67,70,111],cuda:1,cuh:97,cummul:[2,60,120],cumul:[2,68,69,92],currenlti:62,current:[0,1,2,3,4,19,30,32,42,57,58,59,60,61,62,63,68,73,74,75,76,79,80,91,92,97,104,108,111,113,114,118,121,131,132,134,135,136,144,149,155,157,162],curv:[2,44],curvatur:[117,145,161],custom:[0,2,3,33,34,35,42,57,60,61,68,69,72,91,94,116,120],cut:[1,2,4,19],cuthi:70,cutinn:[131,132],cutlo:70,cutmax:144,cutoff1:[102,108,122,126,130,133,143,146],cutoff2:[98,99,100,102,107,108,122,126,130,133,143,146],cutoff:[2,4,21,22,28,29,30,32,36,38,41,60,65,70,72,80,81,91,93,94,95,96,97,98,99,100,101,102,103,105,106,107,108,109,110,111,112,113,114,115,116,117,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],cutoffa:112,cutoffc:112,cuu3:111,cval:43,cvar:62,cvff:4,cwiggl:80,cyan:57,cycl:[68,69],cyclic:45,cylind:[57,81],cylindr:2,cyrot:97,d3q15:67,d3q19:67,d_e:79,daan:78,damp:[2,68,69,72,91,92,98,99,101,105,108,113,118,122,130,143,146],dampflag:118,danger:109,darden:108,darken:57,dash:118,dat:[2,35,58],data2xmovi:0,data:1,databas:0,date:[0,2],datum:2,davenport:133,davi:80,david:[155,157],daw:[111,144],dcd:[2,57,71],deactiv:130,debug:[2,3,40,43,44,71],decai:[36,105,161],decid:[2,4,162],decod:57,decompos:[32,148],decomposit:[58,71],decoupl:2,decreas:[4,60,63],dedic:4,defect:[2,29,137],defin:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,64,65,67,68,69,70,71,74,75,76,77,78,79,80,81,83,84,85,86,87,88,89,90,91,92,94,95,96,98,99,100,101,102,103,105,106,108,109,110,112,113,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,133,137,138,139,140,141,142,143,144,145,146,148,149,150,151,152,153,154,155,156,157,158,159,160,161],definit:[2,41,62,64,69,80,97,103,110,113,144,148],deform:[2,42,61,68,131,132],deg2theta:43,degre:[2,5,6,8,12,13,16,17,18,36,38,39,43,44,45,46,48,49,54,55,57,60,68,69,71,73,75,78,83,84,88,89,90,91,108,111,120],delai:2,delet:[28,60,68,153,162],delete_atom:44,delete_bond:[20,21,22,23,24,25,26,27,28],delete_el:58,delimit:74,dellago:[2,63],deloc:[113,147],delr:134,delta_1:97,delta_3:97,delta_7:97,delta_ij:[134,144],delta_pi:97,delta_r:144,delta_sigma:97,deltah_f:65,demo:3,demonstr:[72,134],dendrim:120,denniston:67,denot:[40,63,105,119],dens:[60,74,113],densiti:[2,19,41,44,58,59,67,79,80,93,94,97,111,134,135,136,140,141,144,145,147,150,151,152],depart:0,departur:72,depend:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,36,39,41,44,45,46,47,48,49,50,51,52,53,54,56,57,59,61,65,67,68,69,70,74,75,77,79,80,81,82,83,84,85,87,88,89,90,91,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,134,135,137,138,139,140,141,142,143,144,145,146,147,148,149,154,155,156,157,158,159,160,161],dependend:2,deposit:[68,75],depth:[26,57,79,115,117,145],der:[32,103,104,130,160],deriv:[2,32,41,61,62,63,68,69,70,77,78,79,80,81,94,97,103,108,113,114,119,124,128,129,134,137,160],derjagin:160,derlet:70,descib:57,describ:[0,1,2,3,4,19,29,30,40,41,42,43,44,50,53,59,60,61,62,65,66,67,68,69,70,71,72,74,77,78,80,91,92,94,96,98,99,101,102,103,104,105,108,111,113,114,115,117,118,119,122,123,124,125,126,127,128,129,130,131,132,133,134,137,138,140,141,144,145,146,147,148,149,153,154,155,156,157,158,159,160,161,162],descript:[2,3],descriptor:41,design:[0,2,3,40,43,58,60,68,70,79,95,96,101,105,107,113,130,131,132,135,136,144],desir:[2,3,4,35,39,42,44,61,62,66,68,75,91,92,109,111,120,131,132,154,155,157],desktop:[2,57],destabil:97,destre:89,destroi:3,detail:[1,2,3,4,19,34,35,39,41,42,44,56,57,58,59,60,61,62,63,66,67,68,69,72,75,78,79,91,93,94,96,97,100,101,102,103,104,105,108,109,113,114,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,133,134,138,140,141,145,147,148,149,159,160,162],detect:[36,92,104,120,121],determin:[1,2,4,26,32,39,40,42,43,44,57,59,61,65,68,70,71,72,73,74,80,81,94,100,104,108,111,115,116,118,126,134,137,141,145,147,153,160],devan:146,devanathan:157,develop:[0,2,3,4,62,69,72,94,97,113,136,137,147,158],deviat:[69,70,116],devic:1,devin:104,devis:136,dfactor:57,dft:137,dhug:72,dhugoniot:72,dia:134,diag:74,diagnost:[4,60,74],diagon:[2,41,42,61,68],diagonalstyl:148,diagram:[19,40,43,56,59,71],diallo:120,diam:57,diamet:[2,44,57,103,117,118,124,145,160],diamond:[113,134],dick:2,dicken:62,did:[91,109,111,118,155,157],dielectr:[101,105,106,107,122,126,130,143],diff:[2,4],differ:[1,2,3,4,19,28,29,32,36,41,44,56,57,59,60,61,62,63,66,67,68,70,71,72,75,76,77,78,79,80,81,83,92,93,94,97,100,101,103,104,109,110,111,113,115,117,118,119,122,123,125,126,133,134,135,136,138,139,140,141,142,144,145,146,147,148,149,154,155,157,158,160],differenti:[1,2,13,74,105,144,156],difficult:[61,62,71,120],difficulti:[36,38,75],diffract:[40,43],diffraction:[40,43],diffus:0,diffuse:2,digit:137,dihedr:[0,4,28,36,38,39,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,60,73,84,85,86,88,91,94,97,101],dihedral_coeff:[45,46,47,48,49,50,51,52,53,54,55,56],dihedral_cosine_shift_exp:11,dihedral_styl:[0,2,42],dihydrid:113,dij:75,dilat:[61,68,69],dim:[44,134],dimens:[1,2,19,35,42,44,57,59,61,67,68,69,72,80,92],dimension:[36,39,40,41,43,79,92,144],dimensionless:[37,41,62,79,148,160],dimer:[2,134],dimstr:[19,59],dintel_offload_noaffinity:4,dipol:0,dipolar:13,dipole:108,dir:[1,3,70,72,144],dirac:41,direc:144,direct:[2,4,13,29,38,40,41,43,44,45,57,67,69,70,72,77,78,79,80,81,91,92,109,110,118,132],directli:[2,3,32,41,44,57,62,67,74,81,93,94,98,99,100,105,108,111,113,122,126,143,146,153],directori:[0,1,2,3,4,62,77,78,92,93,94,97,104,105,111,112,114,130,134,135,136,137,142,144,147,148,154,155,156,157,158],disabl:[4,79,121],disadvantag:[2,59],disallow:68,discard:[19,59,81],discontinu:[91,128],discourag:134,discret:[2,57,62,67],discuss:[0,1],disk:[2,36],disloc:[29,137],disord:[29,137],disp:0,dispar:145,disperion:[108,126],dispers:[2,100,108,126,131,158],displac:[2,37,61,68,70,118],displai:[3,56,57],disregard:137,dissip:[2,31,64,66,77,78,109,110,118,131,132],dist:[2,35,71,73,153],distanc:[2,5,6,20,21,22,23,24,25,26,27,28,30,33,34,36,37,38,40,41,44,46,57,60,61,63,67,68,69,70,72,73,75,76,78,79,80,81,83],distinct:[2,145],distinguish:[2,41,113],distort:93,distrbut:93,distribut:[0,2,3,19,32,41,56,59,66,67,68,93,97,105,111,112,114,134,135,136,142,144,145,154,155,156,157,158],distro:144,ditto:161,div:4,diverg:[78,94],divid:[2,4,19,35,39,42,56,59,70,91,92,114,147,158],divis:[2,55,67,97,130],dl_poly:2,dlammps_ffmpeg:57,dlammps_gzip:57,dlammps_jpeg:57,dlammps_memalign:4,dlammps_png:57,dlm:68,dlmp_intel_offload:4,dlopen:2,dlvo:[103,160],dm_lb:67,doc:[0,1,2,3,32,34,37,39,42,44,56,57,62,68,81,91,92,93,94,96,104,105,111,112,114,120,134,135,136,142,144,148,154,155,157,158,162],docuement:145,doe:[0,1,2,3,19,28,29,32,35,40,43,44,45,56,57,58,59,60,61,62,63,65,66,67,68,79,80,81,84,85,86,88,89,92,93,94,95,96,97,100,101,102,103,104,105,106,108,109,111,112,113,115,116,117,118,119,121,124,125,127,128,129,131,132,134,135,136,137,140,141,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],doesn:[44,94,104,112,154,155,156,157,158],dof:39,doi:[2,70],domain:[2,19,40,43,57,59,61,67,68,71,79,80,92],domin:[1,113],don:[0,4,81,134,147,162],done:[1,2,19,44,55,57,58,59,60,61,62,65,68,71,75,77,78,91,92,94,100,111,126,132,133,134,140,141,153,162],donor:120,dot:42,doti:[97,144],doubl:[1,2,3,4,32,45,61,81,97,114,119,137],dover:58,down:[2,3,61,113,147],download:3,downsid:2,dpd:2,dpdtheta:[31,110],dpdtheta_i:[64,65],dr_ewald:40,drag:[2,35,68,69,76],dragforc:67,drai:[57,72],drain:91,dramat:[60,61,68,147],drautz:97,draw:57,drawn:[57,66],drayleigh:72,dreid:2,dreiding:0,drfourth:37,drho:[93,111,140,141],drift:[2,37,63,66],drive:[3,61,68,70,92],driven:[2,50],driver:2,drop:109,drsquar:37,drude:0,dt_collis:67,dt_lb:67,dt_md:67,dtqm:72,dudarev:43,due:[1,2,4,28,29,33,34,37,40,41,42,43,44,57,60,61,66,67,68,69,70,73,77,78,79,80,81,91,92,106,109,110,111,116,117,131,132,144,145,146,153,155,157,160,161],duffi:79,dullweb:68,dummi:[13,156],dump:[0,1],dump_modifi:[2,57],dunbrack:[2,5,45,101],duplic:[19,59,70],durat:[56,79,118],dure:[2,4,19,32,45,58,59,60,61,62,63,65,66,67,68,69,70,71,72,73,75,76,77,78,79,80,81,82,91,92,109,130,137,139,140,141],dvlo:160,dvx:2,dx_lb:67,dy3:43,dyanam:2,dynam:[0,2,3,4,19,31,37,44,57,58,59,60,62,64,66,68,69,71,72,73,77,78,79,91,92,109,110,113,131,132,152],dynamo:[93,111,134],dyre:127,e28637:13,e_1:97,e_2:97,e_a:74,e_b:114,e_ee:113,e_hbond:120,e_i:[2,97,114],e_j:[2,97],e_k:97,e_ke:113,e_kl:2,e_lj:[94,108],e_n:[62,97],e_ne:113,e_nn:113,e_pr:113,e_rebo:94,e_torsion:94,e_tot:137,e_vol:137,eaa:83,eaat:46,each:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,32,33,34,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,65,66,67,68,69,70,71,74,75,76,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,157,158,159,160,161],eacn:[19,59],eam:[0,93,105],earli:[19,59],earlier:[92,118,134],earth:113,easi:[2,3,32,42,80],easier:[4,57],easili:[3,57,92],eat:46,eaxmpl:2,eba:6,ebb13:46,ebb:6,ebt:46,ec_ii:134,ec_ij:134,ec_jj:134,echo:[3,40,43],ecp:113,edg:[2,19,40,43,57,80,81],edge:80,edit:[4,162],edition:4,edu:[3,111,131],eebt:46,eff:0,effect:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,33,34,37,39,42,45,46,47,48,49,50,51,52,53,54,56,57,58,60,61,63,66,68,69,70,71,72,73,75,78,79,80,81,82,83,84,85,87,88,89,90,91,92,93,94,95,97,98,99,100,101,102,103,104,105,108,109,111,112,113,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,137,139,140,141,142,143,145,146,147,149,154,155,156,157,158,159,160,161],effici:[0,1,2,4,39,55,57,61,68,71,75,97,103,105,122,126,137,140,141,145],efficienc:4,efield:[75,91],eggebrecht:[105,147],ehex:2,eigenvalu:71,einstein:[2,78],either:[1,2,3,4,19,29,40,41,42,43,44,57,59,60,61,62,63,67,68,69,70,74,75,81,91,97,103,111,115,118,131,132,134,137,141,144,153,155,157],ejtehadi:[103,117,145],elaps:[80,149],elast:[2,21,22,92,118,156],elastic:0,elba:13,electr:[2,58,114,161],electric:4,electrolyt:160,electron:[2,40,58,79,93,104,108,111,113,114,134,137,144,147,157,158,161],electron_integr:58,electron_temperatur:58,electron_unit:113,electroneg:[2,104,114,147],electroneg_compon:147,electrostat:[2,4,103,108,113,122,130,132,147,160],elem1:[114,134,148],elem2:[114,134,148],elem:147,element1:[93,111,147],element2:[93,111,147],element:[2,33,37,39,41,42,57,58,93,94,97,104,111,112,113,114,134,135,136,137,142,144,147,148,154,155,156,157,158],elementn:[93,111],elementset:58,elif:41,elig:120,elimin:[2,66,75,77,78],elj:108,ellips:2,ellipsoid:[2,44,91,117,132,145],els:[57,62,68,79],elsewher:134,elt:134,emac:0,email:[0,3,114],emb:81,emb_lin_neg:134,embed:[3,13,79,93,111,114,130,134,135,136,144],embt:46,emin:61,emphas:118,empir:[58,113],empiric:94,emploi:[63,156],empti:121,enabl:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,31,32,37,39,40,41,43,45,46,47,48,49,50,51,52,53,54,56,60,62,63,64,65,66,67,68,69,70,71,72,73,74,75,77,78,79,80,81,82,83,84,85,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,134,135,136,137,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161],enclos:[2,134,147],encod:57,encompass:2,encount:38,encourag:[74,76],end:[1,2,3,4,19,46,57,60,61,63,66,68,73,74,79,92,109,111,117,133,137,145,148,149],endbondtors:46,energet:[60,94],energi:[0,1,2,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,35,39,42,44,45,46,47,48,49,50,51,52,53,54,55,56,58,59,60,61,62,63,64,65,66,67,68,69,70,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109],energy_compon:147,enforc:[2,57,60,68,75,122],enforce2d:[2,91],eng:[3,104,136],engineer:[58,77,111],enginer:135,enhanc:[58,63],enlarg:57,enough:[44,59,72,80,81,105],enpub:111,ensembl:[2,32,35,68,71,72,82,109,147],ensight:2,ensur:[2,41,61,66,68,97,130,154,158],enter:[114,137,158],enthalpi:[74,111],entir:[0,2,3,19,31,39,40,42,43,44,59,60,63,66,68,69,70,71,74,76,79,108,126],entiti:2,entri:[40,65,72,97,112,134,140,141,142,148,154,155,156,157,158],entry1:[140,141],enumuer:2,environ:[1,2,3,4,57,70,93,97,104,112,113,144,155],eos:65,epair:[94,116,120],epp:108,epq:108,eps0:160,eps14:130,epsilon0:157,epsilon:[2,18,21,22,27,28,32,45,80,81,91,96,101,102,103,105,106,107,108,115,117,119,120,121,122,123,124,125,126,127,128,129,130,133,138,143,145,146,154,159,160],epsilon_0:161,epsilon_14:101,epsilon_:145,epsilon_d:106,epsilon_i:[117,145],epsilon_i_:145,epsilon_i_a:[117,145],epsilon_i_b:[117,145],epsilon_i_c:[117,145],epsilon_j:[117,145],epsilon_j_:145,epsilon_j_a:[117,145],epsilon_j_b:[117,145],epsilon_j_c:[117,145],epsilon_lj:145,eqp:108,eqq:108,equal:[2,3,19,28,32,35,42,44,57,59,61,62,66,67,69,70,71,72,73,74,77,78,79,80,91,92,94,104,109,110,116,117,120,131,137,138,144,145,147,148,149,158,161],equat:[2,35,38,39,40,43,56,61,62,63,64,65,67,68,69,70,71,72,74,75,79,80,103,108,109,110,113,114,115,118,131,132,134,141,145,150,151,152,161],equation:[70,89],equilibr:[2,35,44,60,61,68,72,77,78,104,105],equilibrium:[1,2,6,8,10,11,12,13,16,17,18,20,23,24,25,26,27,46,47,61,66,67,68,69,72,73,75,78,83,84,88,89,104,134,142,147],equilibrium_start:58,equival:[2,13,61,68,73,94,109,113,147,155,157],equlibrium:2,er3:43,eradiu:113,eras:77,erat:132,erc:105,erfc:[105,122],erhart:[111,155,157],eros:134,erose_form:134,erot:2,errata:[155,157],erratum:80,error:[0,1,2,3,11,47,57,61,62,63,65,68,74,79,80,81,91,105,122,145,153,155,157],erta:118,especi:[4,44,59,72,73],essenti:[3,11,47,94,105,122,157],essential:69,essex:13,establish:32,estim:[1,2,19,29,35,42,58,59,74],esub:134,eta:[2,67,68,72,112,114,117,144,156,158],eta_dot:68,eta_ij:144,eta_ji:114,etap:68,etap_dot:68,etc:[1,2,3,4,28,33,34,35,42,44,57,58,66,68,79,81,91,92,111,112,130,132,137,154,155,157,158],etol:[91,92],etot0:72,etot:[2,42,72],eu2:43,eu3:43,euler:[74,91,92],eulerian:58,europhi:67,evalu:[3,32,35,41,44,45,57,58,62,66,74,80,91,137,140,141,144,147],evanseck:[2,5,45,101],evaul:91,even:[2,4,19,29,55,59,61,63,68,79,80,81,91,92,96,113,114,118,145,158],evenli:[19,42,59,67],event:[2,68,79],eventu:2,ever:28,everaer:[103,117,145],everi:[0,1,2,3,4,19,35,57,58,59,60,61,62,63,67,68,69,70,72,74,75,79,92,109,130,147,162],everyth:162,everywher:124,eviri:113,evolut:[63,67,71],evolv:[67,71],ewald:[2,40,42,91,98,99,100,105,108,113,122,126,143,146],ewald_disp:108,exact:[19,59,60,66,79],exactli:[2,19,35,44,59,66,72,109,111,118,131,140,141],examin:[2,60,74],exampl:[0,1],exce:[2,4,19,59,61,68,91],exceed:[19,59,68],excel:113,except:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,33,34,39,42,44,45,46,47,48,49,50,51,52,53,54,56,59,61,68,69,71,75,79,82,83,84,85,87,88,89,90,92,93,94,95,98,99,100,101,102,103,104,105,107,108,109,111,112,113,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,135,139,142,143,145,146,149,154,155,156,157,158,159,160,161],excess:113,exchang:[2,58,63,79,113],excit:113,excite:113,exclud:[2,4,39,41,91,118,131,132,153],exclus:[1,4,32,45,104,137],excurs:68,execut:[1,2,3,57],exempl:147,exemplari:66,exemplifi:113,exert:[2,81],exhaust:58,exhibit:[36,63,68,113],exist:[2,3,29,44,56,57,61,83,84,85,86,88,110,153,162],exit:[3,19,59],expans:[41,55],expect:[1,4,19,59,70,72,134,137],expens:[2,70,79],experi:[2,73,92,109],experienc:[2,4],explain:[1,2,3,19,30,57,59,61,68,70,92,96,111,147,149,162],explan:[2,41,70],explic:138,explicit:[2,3,32,74,94,97,101,111,113,121,131,162],explicitli:[2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,44,45,46,47,48,49,50,51,52,53,54,61,66,68,69,72,75,79,82,83,84,85,87,88,89,90,93,94,95,98,99,100,101,102,103,104,105,106,108,109,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,135,137,139,140,141,142,143,145,146,149,150,151,152,154,155,156,157,158,159,160,161,162],explictli:4,exploit:71,explor:[40,43],expon:[74,111,115,117,120,130,138,146],exponenti:[32,74,115,144,154,158,161],expos:3,exposit:[58,109],express:[2,41,44,61,70,74,79,97,111,113,124,134,147,148],expressiont:97,extend:[0,2],extens:[2,4,21,22,27,32,35,62,63,68,69,70,73,77,78,79,80,81,117,134,137,145,148],extent:[1,19,21,59,94],exterior:[2,81],extern:[32,57,61,66,67,68,69,79,91,135,136],extra:[2,3,4,19,22,39,40,42,43,44,59,68,72,91,108,118,134],extract:[2,3,18,32,92,105,114,134,148],extract_atom:3,extract_comput:3,extract_fix:3,extract_glob:3,extract_vari:3,extrapol:1,extrem:[1,2,57,61,68,78,113,156],extrema:130,extreme:113,extrins:58,f_1:[2,61],f_a:[155,156,157],f_c:156,f_f:157,f_fix_id:72,f_harm:78,f_i:[13,144],f_id:[2,62],f_ij:144,f_int:77,f_j:13,f_jj:35,f_k:144,f_langevin:79,f_max:72,f_r:[155,156,157],f_sigma:97,f_solid:78,f_ss:2,face:[2,80,81,117,134,145],facil:0,facilit:2,fact:[2,4,78,118,147],factor:[1,2,8,12,16,17,18,19,22,23,32,35,40,41,43,45,53,57,59,61,63,67,68,69,71,73,74,75,80,81,88,94,97,98,99,101,105,106,107,109,110,113,118,121,122,134,137,140,141,142,143,146,149,154],fail:[3,61,91,92,107],fairli:[3,162],faken:30,fall:2,fals:147,famili:158,familiar:[0,3,162],fan:144,far:[2,59,61,68,70,73,80,84,88,92],farrel:[155,157],fashion:[2,19,44,59,62,68,69,72,78,79,80,92,131],fast:[2,4,62,72,74,131,132,137],faster:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,37,39,45,46,47,48,49,50,51,52,53,54,59,68,69,75,77,79,82,83,84,85,87,88,89,90,93,94,95,97,98,99,100,101,102,103,104,105,108,109,111,112,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,139,142,143,145,146,149,154,155,156,157,158,159,160,161],fastest:[1,2,79],fault:29,fava:117,favor:60,fcc:[2,29,30,35,38],fcold:63,fdt:[64,65,74],fdti:32,fe2:43,fe3:43,fe_md_boundari:58,featur:[0,2,3,41,57,60,66,71,81,91,162],fecr:111,feedback:62,feel:[70,81,92],fehlberg:74,felling:136,felt:81,fene:[2,4],fennel:[105,122],fep:0,ferguson:[2,45],fermi:[1,157],fermion:113,fernando:133,few:[1,2,3,63,68,75,91,92,94,147],fewer:[1,3,4],feynman:71,ffield:[104,114,147],fflag1:57,fflag2:57,ffmpeg:57,ffplai:57,fft:[1,3,42],fhot:63,ficiti:153,fictiti:[2,71,73,105,122,126,153],field:0,fifth:[2,115,142],figshar:70,figur:[1,4,72,162],fij:108,file0:70,file1:[3,65,70],file2:[3,65],file:[0,1],filenam:[4,19,57,58,59,65,70,74,79,92,93,94,97,105,111,112,114,115,134,135,136,140,141,142,144,147,148,154,155,156,157,158],fill:[44,57,79,97,137,162],filter:58,finchham:[2,107],find:[0,2,3,4,30,32,60,61,62,65,70,73,91,92,105,122,126,134,140,141,147,162],fine:[4,78,162],finer:[41,44],finger:44,finish:[2,3,19,59],finit:0,finni:111,fire:[91,92],first:[0,1,2,3,4,6,19,21,22,28,29,35,37,38,39,42,43,46,57,59,60,62,65,66,67,68,70,71,72,75,76,77,78,79,83,91,92,93,94,96,97,98,99,101,104,105,111,113,114,115,118,119,121,122,126,131,132,134,136,137,140,141,142,144,147,148,153,154,155,156,157,158,161,162],fischer:[2,5,45,101],fit:[2,73,94,97,134,140,141,156,162],five:[30,72,97,135],fix:[0,1],fix_flux:58,fix_heat:63,fix_id:[61,68,69,72],fix_manifoldforc:162,fix_modifi:2,fix_nv:162,fix_rattl:75,fix_shak:75,fixedpoint:[61,68],fixid:[57,58],fji:108,flag:[3,4,33,34,40,43,57,60,94,120,121,134,137,153,162],flag_buck:100,flag_coul:[100,108,126],flag_lj:[108,126],flagfld:[131,132],flaghi:[131,132],flaglog:[131,132],flagvf:[131,132],flat:[2,4,79,80],fld:[80,131,132],flexibl:[2,57,113,156],flip:[2,68],fluctuat:[2,32,61,66,67,68,69,70,78,79,89,110],fluid:[2,61],flux:2,flv:57,fly:[19,57,58,75,97,137],fmass:71,fmax:91,fmsec:68,fno:4,fnorm:91,fnve:63,focu:75,foil:[41,70,148],fold:[4,76],follow:[0,1,2,3,4,5,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,35,36,38,41,42,44,45,47,48,49,50,51,52,53,54,55,57,58,59,62,64,65,66,67,68,69,71,72,73,74,75,77,78,79,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],foo:[3,57,74],foo_species:74,foot:2,forc:[0,1],forcefield:[73,120],forcegroup:67,ford:108,forgiv:68,fork:162,form:[2,28,32,33,34,36,41,42,62,66,73,74,79,80,81,83,86,89,92,94,97,110,111,113,116,120,121,133,134,136,137,140,141,142,143,144,145,147,148,149,155,156,157,160],formal:[2,35,66,68,71,147],format:[2,19,57,59,65,74,79,92,93,94,97,111,114,115,121,134,136,140,141,146,148,158],formation:65,former:[2,19,59,79,97],formul:[1,2,42,68,73,75,94,97,111,113,117,134],formula:[2,6,28,29,30,32,33,34,35,39,40,42,43,46,56,62,70,76,80,83,85,94,96,97,101,102,103,108,109,111,112,117,118,119,120,121,122,124,125,126,128,129,131,132,134,138,139,145,146,149,154,155,156,157,158,159,160],forth:[1,2,3],fortran:[2,3,111,134],forward:[32,92],foster:[97,144],found:[2,30,60,63,67,105,108],four:[2,3,28,41,62,79,89,92,137],fourier:2,fourth:[2,4,37,73,101,115,142,147],fox:[2,40,45,152],fqq:108,fraction:[1,2,4,19,42,57,60,61,72,74,92,97,115,118,131,132],frame:[41,58,72,117],framer:57,framework:[93,148],frattl:63,free:[2,13,29,32,70,77,78,79,92,113,130,137,139,144,160],freedom:[2,39,60,68,69,71,75,78,91,108],freeli:[0,2,57],freez:2,frenkel:[2,63,78],frequenc:[2,4,71,72,74,109,113,147],frequent:[29,30,36,38,41,63],fri:72,friction:[2,72,79,118],from:[0,1],front:72,frontend:57,frozen:[2,39,66,116],fs2:[2,35],ftol:[91,92],fuction:105,fudg:75,fulfil:2,full:[1,2,4,35,57,63,67,70,74,97,111,113,114,117],fuller:91,fulli:[2,70,91,92,105,144,162],fulton:111,fumi:98,funcfl:111,fund:0,funrol:137,further:[2,37,57,67,71,79,91,92,93,96,104,137,147],furthermor:[11,47,63,74,110,113],futur:[0,2,59,66,92,135,136],g_jik:144,g_p:79,ga3:43,gaa:97,gai:117,gain:[4,62],galindo:138,gamma0:13,gamma:[2,13,67,72,109,110,112,117,134,138,150,151,152,154,155,157,158],gamma_:79,gamma_ijk:155,gamma_n:118,gamma_p:79,gamma_t:118,gammaa:138,gammafactor:67,gammar:138,gan:[144,154,155,157,158],gan_sw:144,gan_tersoff:144,gao:[2,5,45,101],gap:[131,132,148],gather:3,gather_atom:3,gathert_atom:3,gauch:50,gauss:106,gaussian:[2,35,37,66,71,73,109,113,116],gavhan:4,gaybern:[2,4,91],gd3:43,gdot:132,ge4:43,gec:[155,157],gen:68,gener:0,gentler:80,gentli:112,geom:2,geometr:[2,44,59,68,81,92,96,102,103,105,108,113,115,117,119,122,123,124,125,126,127,128,129,130,131,132,133,138,141,145,149,159,160],geometri:[2,9,19,44,59,61],gerber:130,germann:[69,124],germano:117,get:[0,1,2,3,4,19,35,41,44,57,59,61,81,92,105,158,162],get_natom:3,get_rank:3,get_siz:3,gewald:2,gezelt:[105,122],ghost:[2,4,30,61,68,109,110,113,118,121],gif:57,gifsicl:57,gillan:148,gingold:[150,151],git:162,give:[0,1,2,3,4,28,36,38,44,61,68,70,91,94,97,113,120,134,137,145,155,156,157],given:[2,3,4,11,38,41,42,47,56,61,63,66,67,68,69,70,71,72,73,74,75,76,79,80,81,93,94,97,98,99,100,102,103,104,105,106,109,110,111,113,114,115,117,118,120,122,123,124,126,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,161],glosli:137,glotzer:109,glue:3,gnu:0,gnuplot:3,goal:62,goddard:[2,9,90,113,120],goe:[28,41,44,63,91,108,112,119,124,127,149,161],gold:29,goldman:72,good:[1,2,4,19,30,40,43,59,62,68,75,92,93,103,111,137,158,162],gordan:41,gordon:2,got:162,gould:[2,45],gov:[0,93,111,114],govern:67,gpa:94,gpl:0,gpt:137,gpu:[1,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,68,69,75,82,83,84,85,87,88,89,90,93,94],grab:2,grad:2,gradient:[2,61,63,79,92,132,140,141],graft:60,grain:[2,13,18,28,44,50,65,70,74,115,119,137,141,146],gram:111,gran:[2,80,81],granular:0,graph:3,graphic:3,graviti:2,grdient:58,great:[72,162],greater:[1,61,66,68,70,96,98,99,100],greatli:[40,63],green:[2,35,57,71,97,162],green_kubo:2,grest:[21,22,60,100,118,126],grid:[19,40,43,59,67,79],grigera:2,gromac:91,gromacs:[2,91,119],groot:109,ground:[2,31,64,113],group:[2,3,4,19,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,92,147,158],group_id:3,grow:[2,68,70,74,118],growth:2,gsmooth_factor:134,guarante:44,guess:162,gui:[3,162],guid:[1,150,151,152],guidelin:1,gullet:134,gulp:2,gunnel:137,gunsteren:130,guo:[2,5,45,50,101],gyrat:2,gzip:[57,92],h12:117,h2o:[115,141],had:[2,3,60,61,66,68,69,79,109,118,153],hafskjold:[2,63],half:[1,2,4,19,57,59,68,79,80,81,97,103,113,137],halfwai:[19,57,162],halperin:36,h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Documentation","5. Accelerating LAMMPS performance","6. How-to discussions","11. Python interface to LAMMPS","5.USER-INTEL package","angle_style charmm command","angle_style class2 command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style quartic command","angle_style sdk command","balance command","bond_style class2 command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style morse command","bond_style nonlinear command","bond_style quartic command","compute centro/atom command","compute cna/atom command","compute dpd command","compute fep command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute msd/nongauss command","compute orientorder/atom command","compute pressure command","compute saed command","compute sna/atom command","compute stress/atom command","compute xrd command","create_atoms command","dihedral_style charmm command","dihedral_style class2 command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style spherical command","dihedral_style command","dump image command","fix atc command","fix balance command","fix bond/swap command","fix box/relax command","fix controller command","fix ehex command","fix eos/cv command","fix eos/table/rx command","fix gld command","fix lb/fluid command","fix nvt command","fix nphug command","fix orient/fcc command","fix pimd command","fix qbmsst command","fix restrain command","fix rx command","fix shake command","fix spring/rg command","fix ti/rs command","fix ti/spring command","fix ttm command","fix wall/lj93 command","fix wall/region command","fix nve command","improper_style class2 command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style ring command","improper_style umbrella command","minimize command","neb command","pair_style adp command","pair_style airebo command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style exp6/rx command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_style morse command","pair_style multi/lucy command","pair_style multi/lucy/rx command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style polymorphic command","pair_style resquared command","pair_style lj/sdk command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/idealgas command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style sw command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style vashishta command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","LAMMPS GitHub 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,133],brows:0,browser:57,bryantsev:121,btype:[106,123,127,131,154],buc:100,buck:[2,4,32,99],buckingham:[99,100,101,108,134],buckplusattr:148,buffer:57,bufi:57,bug:0,bui:57,build:[0,1,2],built:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,37,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,56,60,63,64,65,66,67,68,69,70,71,72,73,74,76,77,79,80,81,84,85,86,87,88,89,90,91,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],bulatov:[136,137],bulk:[2,29,67,72,107,135,138,148],bundl:[57,163],button:163,bypass:2,c11:135,c_0:[81,95,152,153],c_1:[40,43,66],c_2:[40,43],c_cluster:2,c_cstherm:2,c_doubl:3,c_e:81,c_flux:35,c_gauss:117,c_hb:121,c_i:65,c_id:[2,32,62],c_ij:2,c_ijkl:2,c_k:66,c_mychunk:[2,34],c_n_k:66,c_p:42,c_peratom:42,c_pi:98,c_prop:2,c_sigma:98,c_size:2,c_thermo_temp:62,ca2:43,cach:4,cacul:77,calcforc:67,calclat:35,calcluat:[37,39,42,106],calcualt:35,calcul:[0,1],caldwel:[2,45],calhoun:73,call:[1,2,3,4,73,95,104,161,163],callabl:3,callback:3,caltech:[2,114],calucl:2,calul:[3,29],can:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],cannot:[1,2,3,4,19,28,57,59,60,61,66,68,74,81,82,83,92,93,100,101,103,112,118,120,123,127,129,131,144,146,147,154],canon:[68,71,73,80,138],cao1:73,cao2:73,cao:73,capabl:[3,4,95,103],capac:[64,81,151],capolungo:[40,43],captur:[2,95,101,114,119,127,135],carbid:106,carbon:[57,90,95,105,135],card:[4,32,121],care:[2,44,55,67,68,97],carefulli:[3,28],carlo:[2,60],caro:112,carri:[4,81,119],carrillo:4,cartesian:[2,94],cascad:81,cat:[4,57],cate:67,categori:[0,95],cation:[115,148],caus:[1,2,4,44,61,68,72,76,77,82,83,92,93,121,123,129,132,133],caution:1,cautious:95,caveat:95,cbecker:[94,112],cc1:[2,34],ccc:[113,155,156,158,159],ccflag:4,ccflags:4,ccm6:112,ccsi:[113,155,156,158,159],ccu:98,cd2:43,cdeam:112,cdll:3,cdof:2,cdte:98,cdte_bop:98,cdtese:98,cdzn:98,cdznte:98,ce3:43,ce4:43,cell:[2,40,43,44,61,68,69,74,81,114,138],cella:2,cellalpha:2,cellb:2,cellbeta:2,cellc:2,cellgamma:2,center:[2,9,33,34,37,40,44,57,61,66,68,78,80,82,83,84,97,113,114,118,119,132,133,135,136,137,155,156,157,158,159],centr:63,central:[29,36,38,41,72,77,78,87,138,143,159],centro:2,centroid:73,centrosymmetri:29,certain:[1,2,57,60,62],cfg:[2,57],cg_type:147,ch2:77,ch2lmp:[0,2],ch3:77,chain:[0,2,13,28,60,68,69,71,73,77,80,90,109,110,154],challeng:2,champaign:132,chan:138,chandler:[94,112],chandrasekhar:[2,123],chang:[1,2,3,4,19,22,32,44,57,58,59,60,61,62,67,68,69,70,72,74,75,76,77,79,80,81,83,92,93,110,114,119,132,133,135,138,148,154,163],change_box:2,chapter:73,charact:[2,19,57,59,65,76,114,116,122,141,142,145,148],character:[2,29,38,41,149],characterist:79,charg:[1,2,3,32,40,43,44,99,100,105,106,108,109,112,114,115,123,127,131,144,148,158,159,161,162],charl:62,charmm:0,cheaper:[118,146],check:[2,3,19,35,59,75,77,80,92,93,122],checkout:163,chem:[2,5,6,9,20,21,22,32,38,39,42,45,46,53,63,66,67,68,73,74,79,80,82,84,90,91,93,95,99,102,103,105,106,107,109,110,111,114,117,118,120,121,123,127,128,131,135,139,141,142,144,148,154],chemic:[31,40,43,58,116,142],chemistri:[74,95,98,114],chen:81,cheng:105,chi:[72,115,118],chiral:90,chmod:3,cho:135,choic:[2,4,19,28,29,32,42,55,59,60,67,68,73,93,131],choos:[1,2,13,28,32,57,60,61,62,67,68,69],chose:[156,158],chosen:[2,41,44,50,57,61,62,66,67,68,69,73,111,114,119,122,125,147,156],chunk:0,chunkid:34,ciccotti:77,cieplak:[2,45],circular:2,circumv:[36,38],citat:[0,67],cite:148,cl1:43,clarendon:[13,109],clarifi:[156,158],clark:144,classic:[0,2,4,73,74,81,91,114],classifi:159,clean:2,clear:[2,3,62],clebsch:41,click:[3,44,56,57,93,163],climb:93,clockwis:45,clone:163,close:[2,3,19,42,60,61,67,68,70,77,83,93,95,98,106,107,135,141,142,158,163],closer:[19,59,61,79,93],closest:[72,118,146,154],cloud:148,cluster:[2,4,42,63,77],cmax:135,cmd:[3,73],cmdarg:3,cmin:135,cmm:[18,147],cna:29,co2:[43,76,77,116],coars:[13,18,28,50,65,76,116,120,142,147],coarsest:41,code:[0,1],coeff:[6,45,46,55,84,122,150],coeffici:0,coefficienct:110,coefficient0:112,coefficient1:112,coeffieci:[2,96],coeffincientn:112,coexist:114,cohes:[2,115,135],coincid:[83,102,132,133],cold:2,coleman:[40,43],collect:[2,34,44,104],colliex:43,collis:[67,119,162],colloid:2,color:[19,57,59,66,74],column:[2,29,34,36,38,41,42,43,74,81,95,117,121],colvar:0,com:[2,37,63,97,163],comand:60,combiant:107,combin:[2,3,18,32,55,57,58,63,68,70,71,73,83,84,104,106,107,111,114,115,116,130,131,149,155,156,158,159,161],come:[0,2,13,61,62,68,79,80,155,156,158,159,163],comit:163,comm:[0,3,30,93,110],comm_modifi:[2,98,104,110,114,119],comm_styl:[19,59],comm_world:3,command:[0,1],comment:[3,45,65,76,81,93,94,112,113,115,116,122,135,141,142,143,148,149,155,156,157,158,159,163],commit:163,commmand:2,common:[0,1,2,3,4,30,61,73,83,84,119,121,155,156,158],commonli:[2,9,37,38,57,91,120,125,149,156,158],commun:[1,2,3,4,19,57,59,61,67,68,81,111],comp:[70,71,77,93,114,146,153,157],compar:[1,2,4,40,43,56,92,93,135,148],comparison:0,compass:[6,20,46,56,84,103],compat:[3,19,49,59,62,63,82,138],compens:[2,114],compil:[4,57,138],complain:3,complement:135,complementari:[106,123],complet:[2,3,19,59,73,93,115],complex:[2,3,9,36,38,41,44,67,70,83,93,114,138],complic:2,compon:[2,29,30,33,34,35,36,37,38,39,41,42,57,60,61,62,63,67,68,69,73,77,83,92,93,110,114,119,132,133,148,149],componenet:2,composit:[2,67,112],compound:[105,114,115,159],compress:[2,57,69,74],compris:[83,116,146],compton:[40,43],comput:[0,1],computation:[2,81,98],compute_modifi:[60,61,68,69],compute_sa:40,compute_xrd:43,concav:83,concentr:[65,76,112,116,142],concept:2,conceptu:[2,61,93,106,135],concern:[2,30,32,66],concis:3,concurr:4,conden:[81,156,158],condens:[2,81,95,108,112,123,159],condit:[2,39,40,42,43,57,58,67,69,72,74,77,78,81,111,114,120],conducit:2,conduct:0,confer:[4,138],configur:[1,2,4,57,61,73,92,93,95,98,113,135,138,155,156,158,159,163],conflict:163,conform:[2,60,61,75,90,93,114],confus:159,conjuct:110,conjug:114,conjunct:[2,32,44,67,93,99,100,106,110,114,121,123,144,147],connect:[2,32,60,77,93,107,119,154,158],conner:95,connor:95,consecut:[3,44,106,123,127],consequ:[1,2,81,122],conserv:[13,60,66,67,68,70,76,77,93,109,110,111,119,129,148],consid:[2,29,32,59,60,81,114,146,148,154],consider:2,consist:[2,3,39,44,50,62,66,68,69,74,75,76,93,95,98,104,106,114,118,132,133,135,138,141,142,146,148],consistent_fe_initi:58,constant:0,constantli:63,constitu:[2,82,83,104,146],constrain:[2,63,66,70,71,77,78,92,114],constraint:[19,39,42,59,63,70,77,78,82,92,133],construct:[2,28,29,30,36,38,40,41,43,61,68,75,76,83,109,138,154,155],constructor:3,consult:4,consum:1,contact:[0,107,113,115,118,119,146],contain:[0,1,2,3,19,32,35,40,41,43,44,45,56,57,58,59,62,65,67,72,74,76,81,83,93,94,95,98,105,106,109,112,113,114,116,135,138,141,142,143,145,149,155,156,157,158,159,163],context:[2,4,161],contibut:29,contin:4,continu:[0,2,19,59,60,61,62,63,66,68,69,74,79,80,81,83,98,110,125,128,146,157],continuum:[2,58,81],contour_integr:58,contract:[61,68],contrain:77,contrast:[1,2,161],contrib:81,contribut:[2,29,32,33,34,35,39,41,42,61,67,77,92,93,110,112,114,132,133,138,148,163],control:[2,3,4,11,13,19,32,35,41,47,57,58,59,61],control_typ:58,convect:35,conveni:[2,13,149,163],convent:[13,49,54,56,75,112,114],converg:[2,19,57,59,60,61,69,70,71,74,75,77,92,93,105,106,123,148],convers:[41,57,106,107,108,114,123,127,131,144],convert:[2,5,6,8,12,16,17,18,35,44,46,57,84,85,89,90,93,94,112,138,156,158,162],convex:83,cool:63,coord:[2,3,36,38,72,82,93],coordb:148,coordbb:148,coordiat:92,coordin:[1,2,3,19,32,33,34,41,44,57,59,60,61,63,68,72,77,78,80,81,92,93,94,95,97,113,148],coords:148,copi:[0,3,57,81,93,163],copper:162,coprocessor:[1,4],core:[0,1],coreshel:2,coreshell:[2,100,106,108],cornel:[2,45],corner:[2,57,83,163],corpor:4,corr:105,correct:[2,3,32,45,57,63,68,74,82,83,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,112,113,114,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],correction_max_iter:58,correctli:[3,68,77,83,93,108,133,138,163],correl:[2,35,36,41,66,73],correpond:65,correspond:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,29,32,39,40,41,43,45,46,47,48,49,50,51,52,53,54,55,57,61,62,63,65,67,68,69,72,73,76,77,82,83,84,85,86,88,89,90,91,93,94,95,96,99,100,101,102,103,104,105,106,109,110,112,113,114,115,116,117,118,119,120,121,123,124,125,126,127,128,129,130,131,132,135,136,138,140,142,143,144,145,146,147,148,149,150,155,156,157,158,159,160,161,162],correspondingli:[132,133],cosin:2,cosineshift:11,cost:[1,2,3,19,40,42,43,57,59,68,76,81,106,123,127,138,155],costheta0:[155,156,158,159],costheta:145,costli:[3,4],coul:[2,4,18,21,22,32,45,92],could:[2,3,19,32,34,35,39,57,59,62,74,81,82,83,92,95,117,121],coulomb:[2,42,92,99,100,101,102,103,105,106,107,108,109,114,119,120,123,127,131,134,144,147,148,158,159,161],coulommb:2,count:[1,2,3,19,35,45,59,61,68,77,83,92,93,117,121],counteract:62,counterbal:63,counterbalanc:13,counterclockwis:45,coupl:0,couple:[2,3],cours:[4,66,75,82,132,150],cov:148,coval:[2,13,114,135,148],cover:[2,58,67,114],cpp:[1,2,3,32,77],cpu:[1,4],cpuinfo:4,cr2:43,cr3:43,creat:[0,1,2,3,19,35,39,40,44,57,58,59,60,61,65,68,69,72,73,75,81,93,95,98,105,112,113,131,140,141,142,145,148,155,156,157,158,159,163],create_atom:[2,19,35],create_box:[2,19,35,44,61,68,154],create_elementset:58,create_faceset:58,create_nodeset:58,createatom:0,creation:44,criteria:[57,60,92],criterion:[19,44,59,60,92,93,105,114,119,148],critic:[2,24,25,81,92],cross:[4,33,57,93,102,110,112,120,121,123,125,127,145,147,156,158,162],crossov:1,crozier:0,crucial:74,crystal:[2,4,29,30,38,72,80],crystallin:[2,157],crystallogr:[40,43],crystallographi:[40,43],cs1:43,cs_chunk:2,csanyi:[41,149],cscl:135,csequ:2,csh:[3,4],cshrc:3,csic:[113,155,156,158,159],csinfo:2,csisi:[113,155,156,158,159],cst:112,cstherm:2,csvr:2,ctcm:[94,112],ctype:3,cu1:43,cu2:43,cu3au:135,cube:[2,83],cubes:[19,59],cubic:[38,67,72,112],cuda:1,cuh:98,cummul:[2,60,121],cumul:[2,68,69,93],currenlti:62,current:[0,1,2,3,4,19,30,32,42,57,58,59,60,61,62,63,68,70,71,75,76,77,78,81,82,92,93,98,105,109,112,114,115,119,122,132,133,135,136,137,145,150,156,158,163],curv:[2,44,70,71],curvatur:[118,146,162],custom:[0,2,3,33,34,35,42,57,60,61,68,69,74,92,95,117,121],cut:[1,2,4,19],cuthi:72,cutinn:[132,133],cutlo:72,cutmax:145,cutoff1:[103,109,123,127,131,134,144,147],cutoff2:[99,100,101,103,108,109,123,127,131,134,144,147],cutoff:[2,4,21,22,28,29,30,32,36,38,41,60,65,72,74,82,83,92,94,95,96,97,98,99,100,101,102,103,104,106,107,108,109,110,111,112,113,114,115,116,117,118,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],cutoffa:113,cutoffc:113,cuu3:112,cval:43,cvar:62,cvff:4,cwiggl:82,cyan:57,cycl:[68,69],cyclic:45,cylind:[57,71,83],cylindr:2,cyrot:98,d3q15:67,d3q19:67,d_e:81,daan:80,damp:[2,68,69,71,74,92,93,99,100,102,106,109,114,119,123,131,144,147],dampflag:119,danger:110,darden:109,darken:57,dash:119,dat:[2,35,58],data2xmovi:0,data:1,databas:0,date:[0,2],datum:2,davenport:134,davi:82,david:[156,158],daw:[112,145],dcd:[2,57,73],deactiv:131,debug:[2,3,40,43,44,73],decai:[36,106,162],decid:[2,4,163],decod:57,decompos:[32,149],decomposit:[58,73],decoupl:2,decreas:[4,60,63],dedic:4,defect:[2,29,138],defin:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,64,65,67,68,69,72,73,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,95,96,97,99,100,101,102,103,104,106,107,109,110,111,113,114,116,117,118,119,120,121,123,124,125,126,127,128,129,130,131,132,133,134,138,139,140,141,142,143,144,145,146,147,149,150,151,152,153,154,155,156,157,158,159,160,161,162],definit:[2,41,62,64,69,82,98,104,111,114,145,149],deform:[2,42,61,68,132,133],deg2theta:43,degre:[2,5,6,8,12,13,16,17,18,36,38,39,43,44,45,46,48,49,54,55,57,60,68,69,73,75,77,80,84,85,89,90,91,92,109,112,121],delai:2,delet:[28,60,68,154,163],delete_atom:44,delete_bond:[20,21,22,23,24,25,26,27,28],delete_el:58,delimit:76,dellago:[2,63],deloc:[114,148],delr:135,delta_1:98,delta_3:98,delta_7:98,delta_ij:[135,145],delta_pi:98,delta_r:145,delta_sigma:98,deltah_f:65,demo:3,demonstr:[74,135],dendrim:121,denniston:67,denot:[40,63,106,120],dens:[60,76,114],densiti:[2,19,41,44,58,59,67,81,82,94,95,98,112,135,136,137,141,142,145,146,148,151,152,153],depart:0,departur:74,depend:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,36,39,41,44,45,46,47,48,49,50,51,52,53,54,56,57,59,61,65,67,68,69,72,76,77,79,81,82,83,84,85,86,88,89,90,91,92,94,95,96,97,98,99,100,101,102,103,104,105,106,107,109,110,112,113,114,115,116,117,118,119,120,121,123,124,125,126,127,128,129,130,131,132,135,136,138,139,140,141,142,143,144,145,146,147,148,149,150,155,156,157,158,159,160,161,162],dependend:2,deposit:[68,77],depth:[26,57,81,116,118,146],der:[32,104,105,131,161],deriv:[2,32,41,61,62,63,68,69,72,79,80,81,82,83,95,98,104,109,114,115,120,125,129,130,135,138,161],derjagin:161,derlet:72,descib:57,describ:[0,1,2,3,4,19,29,30,40,41,42,43,44,50,53,59,60,61,62,65,66,67,68,69,72,73,74,76,79,80,82,92,93,95,97,99,100,102,103,104,105,106,109,112,114,115,116,118,119,120,123,124,125,126,127,128,129,130,131,132,133,134,135,138,139,141,142,145,146,147,148,149,150,154,155,156,157,158,159,160,161,162,163],descript:[2,3],descriptor:41,design:[0,2,3,40,43,58,60,68,72,81,96,97,102,106,108,114,131,132,133,136,137,145],desir:[2,3,4,35,39,42,44,61,62,66,68,77,92,93,110,112,121,132,133,155,156,158],desktop:[2,57],destabil:98,destre:90,destroi:3,detail:[1,2,3,4,19,34,35,39,41,42,44,56,57,58,59,60,61,62,63,66,67,68,69,74,77,80,81,92,94,95,97,98,101,102,103,104,105,106,109,110,114,115,118,119,120,121,123,124,125,126,127,128,129,130,131,132,133,134,135,139,141,142,146,148,149,150,160,161,163],detect:[36,93,105,121,122],determin:[1,2,4,26,32,39,40,42,43,44,57,59,61,65,68,72,73,74,75,76,82,83,95,101,105,109,112,116,117,119,127,135,138,142,146,148,154,161],devan:147,devanathan:158,develop:[0,2,3,4,62,69,74,95,98,114,137,138,148,159],deviat:[69,72,117],devic:1,devin:105,devis:137,dfactor:57,dft:138,dhug:74,dhugoniot:74,dia:135,diag:76,diagnost:[4,60,76],diagon:[2,41,42,61,68],diagonalstyl:149,diagram:[19,40,43,56,59,73],diallo:121,diam:57,diamet:[2,44,57,104,118,119,125,146,161],diamond:[114,135],dick:2,dicken:62,did:[92,110,112,119,156,158],dielectr:[102,106,107,108,123,127,131,144],diff:[2,4],differ:[1,2,3,4,19,28,29,32,36,41,44,56,57,59,60,61,62,63,66,67,68,72,73,74,77,78,79,80,81,82,83,84,93,94,95,98,101,102,104,105,110,111,112,114,116,118,119,120,123,124,126,127,134,135,136,137,139,140,141,142,143,145,146,147,148,149,150,155,156,158,159,161],differenti:[1,2,13,76,106,145,157],difficult:[61,62,73,121],difficulti:[36,38,77],diffract:[40,43],diffraction:[40,43],diffus:0,diffuse:2,digit:138,dihedr:[0,4,28,36,38,39,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,60,75,85,86,87,89,92,95,98,102],dihedral_coeff:[45,46,47,48,49,50,51,52,53,54,55,56],dihedral_cosine_shift_exp:11,dihedral_styl:[0,2,42],dihydrid:114,dij:77,dilat:[61,68,69],dim:[44,135],dimens:[1,2,19,35,42,44,57,59,61,67,68,69,74,82,93],dimension:[36,39,40,41,43,81,93,145],dimensionless:[37,41,62,81,149,161],dimer:[2,135],dimstr:[19,59],dintel_offload_noaffinity:4,dipol:0,dipolar:13,dipole:109,dir:[1,3,72,74,145],dirac:41,direc:145,direct:[2,4,13,29,38,40,41,43,44,45,57,67,69,72,74,79,80,81,82,83,92,93,110,111,119,133],directli:[2,3,32,41,44,57,62,67,76,83,94,95,99,100,101,106,109,112,114,123,127,144,147,154],directori:[0,1,2,3,4,62,79,80,93,94,95,98,105,106,112,113,115,131,135,136,137,138,143,145,148,149,155,156,157,158,159],disabl:[4,81,122],disadvantag:[2,59],disallow:68,discard:[19,59,83],discontinu:[92,129],discourag:135,discret:[2,57,62,67,71],discuss:[0,1],disk:[2,36],disloc:[29,138],disord:[29,138],disp:0,dispar:146,disperion:[109,127],dispers:[2,101,109,127,132,159],displac:[2,37,61,68,72,119],displai:[3,56,57],disregard:138,dissip:[2,31,64,66,79,80,110,111,119,132,133],dist:[2,35,73,75,154],distanc:[2,5,6,20,21,22,23,24,25,26,27,28,30,33,34,36,37,38,40,41,44,46,57,60,61,63,67,68,69,72,74,75,77,78,80,81,82,83,84],distinct:[2,146],distinguish:[2,41,114],distort:94,distrbut:94,distribut:[0,2,3,19,32,41,56,59,66,67,68,94,98,106,112,113,115,135,136,137,143,145,146,155,156,157,158,159],distro:145,ditto:162,div:4,diverg:[80,95],divid:[2,4,19,35,39,42,56,59,72,92,93,115,148,159],divis:[2,55,67,98,131],dl_poly:2,dlammps_ffmpeg:57,dlammps_gzip:57,dlammps_jpeg:57,dlammps_memalign:4,dlammps_png:57,dlm:68,dlmp_intel_offload:4,dlopen:2,dlvo:[104,161],dm_lb:67,doc:[0,1,2,3,32,34,37,39,42,44,56,57,62,68,83,92,93,94,95,97,105,106,112,113,115,121,135,136,137,143,145,149,155,156,158,159,163],docuement:146,doe:[0,1,2,3,19,28,29,32,35,40,43,44,45,56,57,58,59,60,61,62,63,65,66,67,68,71,81,82,83,85,86,87,89,90,93,94,95,96,97,98,101,102,103,104,105,106,107,109,110,112,113,114,116,117,118,119,120,122,125,126,128,129,130,132,133,135,136,137,138,141,142,145,146,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],doesn:[44,95,105,113,155,156,157,158,159],dof:39,doi:[2,72],domain:[2,19,40,43,57,59,61,67,68,73,81,82,93],domin:[1,114],don:[0,4,83,135,148,163],done:[1,2,19,44,55,57,58,59,60,61,62,65,68,73,77,79,80,92,93,95,101,112,127,133,134,135,141,142,154,163],donor:121,dot:42,doti:[98,145],doubl:[1,2,3,4,32,45,61,83,98,115,120,138],dover:58,down:[2,3,61,114,148],download:3,downsid:2,dpd:2,dpdtheta:[31,111],dpdtheta_i:[64,65],dr_ewald:40,drag:[2,35,68,69,78],dragforc:67,drai:[57,74],drain:92,dramat:[60,61,68,148],drautz:98,draw:57,drawn:[57,66],drayleigh:74,dreid:2,dreiding:0,drfourth:37,drho:[94,112,141,142],drift:[2,37,63,66],drive:[3,61,68,72,93],driven:[2,50],driver:2,drop:110,drsquar:37,drude:0,dt_collis:67,dt_lb:67,dt_md:67,dtqm:74,dudarev:43,due:[1,2,4,28,29,33,34,37,40,41,42,43,44,57,60,61,66,67,68,69,72,75,79,80,81,82,83,92,93,107,110,111,112,117,118,132,133,145,146,147,154,156,158,161,162],duffi:81,dullweb:68,dummi:[13,157],dump:[0,1],dump_modifi:[2,57],dunbrack:[2,5,45,102],duplic:[19,59,72],durat:[56,81,119],dure:[2,4,19,32,45,58,59,60,61,62,63,65,66,67,68,69,70,71,72,73,74,75,77,78,79,80,81,82,83,92,93,110,131,138,140,141,142],dvlo:161,dvx:2,dx_lb:67,dy3:43,dyanam:2,dynam:[0,2,3,4,19,31,37,44,57,58,59,60,62,64,66,68,69,70,73,74,75,79,80,81,92,93,110,111,114,132,133,153],dynamo:[94,112,135],dyre:128,e28637:13,e_1:98,e_2:98,e_a:76,e_b:115,e_ee:114,e_hbond:121,e_i:[2,98,115],e_j:[2,98],e_k:98,e_ke:114,e_kl:2,e_lj:[95,109],e_n:[62,98],e_ne:114,e_nn:114,e_pr:114,e_rebo:95,e_torsion:95,e_tot:138,e_vol:138,eaa:84,eaat:46,each:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,32,33,34,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,65,66,67,68,69,70,72,73,76,77,78,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,158,159,160,161,162],eacn:[19,59],eam:[0,94,106],earli:[19,59],earlier:[93,119,135],earth:114,easi:[2,3,32,42,82],easier:[4,57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lerian:58,europhi:67,evalu:[3,32,35,41,44,45,57,58,62,66,76,82,92,138,141,142,145,148],evanseck:[2,5,45,102],evaul:92,even:[2,4,19,29,55,59,61,63,68,81,82,83,92,93,97,114,115,119,146,159],evenli:[19,42,59,67],event:[2,68,81],eventu:2,ever:28,everaer:[104,118,146],everi:[0,1,2,3,4,19,35,57,58,59,60,61,62,63,67,68,69,70,71,72,74,76,77,81,93,110,131,148,163],everyth:163,everywher:125,eviri:114,evolut:[63,67,73],evolv:[67,73],ewald:[2,40,42,92,99,100,101,106,109,114,123,127,144,147],ewald_disp:109,exact:[19,59,60,66,81],exactli:[2,19,35,44,59,66,74,110,112,119,132,141,142],examin:[2,60,76],exampl:[0,1],exce:[2,4,19,59,61,68,92],exceed:[19,59,68],excel:114,except:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,33,34,39,42,44,45,46,47,48,49,50,51,52,53,54,56,59,61,68,69,73,77,81,84,85,86,88,89,90,91,93,94,95,96,99,100,101,102,103,104,105,106,108,109,110,112,113,114,115,117,118,119,120,121,123,124,125,126,127,128,129,130,131,132,133,136,140,143,144,146,147,150,155,156,157,158,159,160,161,162],excess:114,exchang:[2,58,63,81,114],excit:114,excite:114,exclud:[2,4,39,41,92,119,132,133,154],exclus:[1,4,32,45,105,138],excurs:68,execut:[1,2,3,57],exempl:148,exemplari:66,exemplifi:114,exert:[2,70,83],exhaust:58,exhibit:[36,63,68,114],exist:[2,3,29,44,56,57,61,84,85,86,87,89,111,154,163],exit:[3,19,59],expans:[41,55],expect:[1,4,19,59,72,74,135,138],expens:[2,72,81],experi:[2,75,93,110],experienc:[2,4],explain:[1,2,3,19,30,57,59,61,68,70,72,93,97,112,148,150,163],explan:[2,41,72],explic:139,explicit:[2,3,32,76,95,98,102,112,114,122,132,163],explicitli:[2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,44,45,46,47,48,49,50,51,52,53,54,61,66,68,69,74,77,81,84,85,86,88,89,90,91,94,95,96,99,100,101,102,103,104,105,106,107,109,110,112,113,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,136,138,140,141,142,143,144,146,147,150,151,152,153,155,156,157,158,159,160,161,162,163],explictli:4,exploit:73,explor:[40,43],expon:[76,112,116,118,121,131,139,147],exponenti:[32,76,116,145,155,159,162],expos:3,exposit:[58,110],express:[2,41,44,61,72,76,81,98,112,114,125,135,148,149],expressiont:98,extend:[0,2],extens:[2,4,21,22,27,32,35,62,63,68,69,72,75,79,80,81,82,83,118,135,138,146,149],extent:[1,19,21,59,95],exterior:[2,83],extern:[32,57,61,66,67,68,69,71,81,92,136,137],extra:[2,3,4,19,22,39,40,42,43,44,59,68,74,92,109,119,135],extract:[2,3,18,32,93,106,115,135,149],extract_atom:3,extract_comput:3,extract_fix:3,extract_glob:3,extract_vari:3,extrapol:1,extrem:[1,2,57,61,68,80,114,157],extrema:131,extreme:114,extrins:58,f_1:[2,61],f_a:[156,157,158],f_c:157,f_f:158,f_fix_id:74,f_harm:80,f_i:[13,145],f_id:[2,62],f_ij:145,f_int:79,f_j:13,f_jj:35,f_k:145,f_langevin:81,f_max:74,f_r:[156,157,158],f_sigma:98,f_solid:80,f_ss:2,face:[2,82,83,118,135,146],facil:0,facilit:2,fact:[2,4,80,119,148],factor:[1,2,8,12,16,17,18,19,22,23,32,35,40,41,43,45,53,57,59,61,63,67,68,69,73,75,76,77,82,83,89,95,98,99,100,102,106,107,108,110,111,114,119,122,123,135,138,141,142,143,144,147,150,155],fail:[3,61,92,93,108],fairli:[3,163],faken:30,fall:2,fals:148,famili:159,familiar:[0,3,163],fan:145,far:[2,59,61,68,72,75,82,85,89,93],farrel:[156,158],fashion:[2,19,44,59,62,68,69,74,80,81,82,93,132],fast:[2,4,62,74,76,132,133,138],faster:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,37,39,45,46,47,48,49,50,51,52,53,54,59,68,69,77,79,81,84,85,86,88,89,90,91,94,95,96,98,99,100,101,102,103,104,105,106,109,110,112,113,115,117,118,119,120,121,123,124,125,126,127,128,129,130,131,132,136,140,143,144,146,147,150,155,156,157,158,159,160,161,162],fastest:[1,2,81],fault:29,fava:118,favor:60,fcc:[2,29,30,35,38],fcold:63,fdt:[64,65,76],fdti:32,fe2:43,fe3:43,fe_md_boundari:58,featur:[0,2,3,41,57,60,66,73,83,92,163],fecr:112,feedback:62,feel:[72,83,93],fehlberg:76,felling:137,felt:83,fene:[2,4],fennel:[106,123],fep:0,ferguson:[2,45],fermi:[1,158],fermion:114,fernando:134,few:[1,2,3,63,68,77,92,93,95,148],fewer:[1,3,4],feynman:73,ffield:[105,115,148],fflag1:57,fflag2:57,ffmpeg:57,ffplai:57,fft:[1,3,42],fhot:63,ficiti:154,fictiti:[2,73,75,106,123,127,154],field:0,fifth:[2,116,143],figshar:72,figur:[1,4,74,163],fij:109,file0:72,file1:[3,65,72],file2:[3,65],file:[0,1],filenam:[4,19,57,58,59,65,72,76,81,93,94,95,98,106,112,113,115,116,135,136,137,141,142,143,145,148,149,155,156,157,158,159],fill:[44,57,81,98,138,163],filter:58,finchham:[2,108],find:[0,2,3,4,30,32,60,61,62,65,72,75,92,93,106,123,127,135,141,142,148,163],fine:[4,80,163],finer:[41,44],finger:44,finish:[2,3,19,59],finit:0,finni:112,fire:[92,93],first:[0,1,2,3,4,6,19,21,22,28,29,35,37,38,39,42,43,46,57,59,60,62,65,66,67,68,72,73,74,77,78,79,80,81,84,92,93,94,95,97,98,99,100,102,105,106,112,114,115,116,119,120,122,123,127,132,133,135,137,138,141,142,143,145,148,149,154,155,156,157,158,159,162,163],fischer:[2,5,45,102],fit:[2,75,95,98,135,141,142,157,163],five:[30,74,98,136],fix:[0,1],fix_flux:58,fix_heat:63,fix_id:[61,68,69,74],fix_manifoldforc:163,fix_modifi:2,fix_nv:163,fix_rattl:77,fix_shak:77,fixedpoint:[61,68],fixid:[57,58],fji:109,flag:[3,4,33,34,40,43,57,60,95,121,122,135,138,154,163],flag_buck:101,flag_coul:[101,109,127],flag_lj:[109,127],flagfld:[132,133],flaghi:[132,133],flaglog:[132,133],flagvf:[132,133],flat:[2,4,81,82],fld:[82,132,133],flexibl:[2,57,114,157],flip:[2,68],fluctuat:[2,32,61,66,67,68,69,72,80,81,90,111],fluid:[2,61],flux:2,flv:57,fly:[19,57,58,77,98,138],fmass:73,fmax:92,fmsec:68,fno:4,fnorm:92,fnve:63,focu:77,foil:[41,72,149],fold:[4,78],follow:[0,1,2,3,4,5,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,35,36,38,41,42,44,45,47,48,49,50,51,52,53,54,55,57,58,59,62,64,65,66,67,68,69,73,74,75,76,77,79,80,81,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],foo:[3,57,76],foo_species:76,foot:2,forc:[0,1],forcefield:[75,121],forcegroup:67,ford:109,forgiv:68,fork:163,form:[2,28,32,33,34,36,41,42,62,66,75,76,81,82,83,84,87,90,93,95,98,111,112,114,117,121,122,134,135,137,138,141,142,143,144,145,146,148,149,150,156,157,158,161],formal:[2,35,66,68,73,148],format:[2,19,57,59,65,76,81,93,94,95,98,112,115,116,122,135,137,141,142,147,149,159],formation:65,former:[2,19,59,81,98],formul:[1,2,42,68,75,77,95,98,112,114,118,135],formula:[2,6,28,29,30,32,33,34,35,39,40,42,43,46,56,62,72,78,82,84,86,95,97,98,102,103,104,109,110,112,113,118,119,120,121,122,123,125,126,127,129,130,132,133,135,139,140,146,147,150,155,156,157,158,159,160,161],forth:[1,2,3],fortran:[2,3,112,135],forward:[32,93],foster:[98,145],found:[2,30,60,63,67,106,109],four:[2,3,28,41,62,81,90,93,138],fourier:2,fourth:[2,4,37,75,102,116,143,148],fox:[2,40,45,153],fqq:109,fraction:[1,2,4,19,42,57,60,61,74,76,93,98,116,119,132,133],frame:[41,58,74,118],framer:57,framework:[94,149],frattl:63,free:[2,13,29,32,72,79,80,81,93,114,131,138,140,145,161],freedom:[2,39,60,68,69,73,77,80,92,109],freeli:[0,2,57],freez:2,frenkel:[2,63,80],frequenc:[2,4,73,74,76,110,114,148],frequent:[29,30,36,38,41,63],fri:74,friction:[2,74,81,119],from:[0,1],front:74,frontend:57,frozen:[2,39,66,117],fs2:[2,35],ftol:[92,93],fuction:106,fudg:77,fulfil:2,full:[1,2,4,35,57,63,67,72,76,98,112,114,115,118],fuller:92,fulli:[2,72,92,93,106,145,163],fulton:112,fumi:99,funcfl:112,fund:0,funrol:138,further:[2,37,57,67,73,81,92,93,94,97,105,138,148],furthermor:[11,47,63,76,111,114],futur:[0,2,59,66,93,136,137],g_jik:145,g_p:81,ga3:43,gaa:98,gai:118,gain:[4,62],galindo:139,gamma0:13,gamma:[2,13,67,74,110,111,113,118,135,139,151,152,153,155,156,158,159],gamma_:81,gamma_ijk:156,gamma_n:119,gamma_p:81,gamma_t:119,gammaa:139,gammafactor:67,gammar:139,gan:[145,155,156,158,159],gan_sw:145,gan_tersoff:145,gao:[2,5,45,102],gap:[132,133,149],gather:3,gather_atom:3,gathert_atom:3,gauch:50,gauss:107,gaussian:[2,35,37,66,73,75,110,114,117],gavhan:4,gaybern:[2,4,92],gd3:43,gdot:133,ge4:43,gec:[156,158],gen:68,gener:0,gentler:82,gentli:113,geom:2,geometr:[2,44,59,68,83,93,97,103,104,106,109,114,116,118,120,123,124,125,126,127,128,129,130,131,132,133,134,139,142,146,150,160,161],geometri:[2,9,19,44,59,61],gerber:131,germann:[69,125],germano:118,get:[0,1,2,3,4,19,35,41,44,57,59,61,83,93,106,159,163],get_natom:3,get_rank:3,get_siz:3,gewald:2,gezelt:[106,123],ghost:[2,4,30,61,68,110,111,114,119,122],gif:57,gifsicl:57,gillan:149,gingold:[151,152],git:163,give:[0,1,2,3,4,28,36,38,44,61,68,72,92,95,98,114,121,135,138,146,156,157,158],given:[2,3,4,11,38,41,42,47,56,61,63,66,67,68,69,72,73,74,75,76,77,78,81,82,83,94,95,98,99,100,101,103,104,105,106,107,110,111,112,114,115,116,118,119,121,123,124,125,127,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,162],glosli:138,glotzer:110,glue:3,gnu:0,gnuplot:3,goal:62,goddard:[2,9,91,114,121],goe:[28,41,44,63,92,109,113,120,125,128,150,162],gold:29,goldman:74,good:[1,2,4,19,30,40,43,59,62,68,77,93,94,104,112,138,159,163],gordan:41,gordon:2,got:163,gould:[2,45],gov:[0,94,112,115],govern:67,gpa:95,gpl:0,gpt:138,gpu:[1,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,68,69,77,84,85,86,88,89,90,91,94,95],grab:2,grad:2,gradient:[2,61,63,81,93,133,141,142],graft:60,grain:[2,13,18,28,44,50,65,72,76,116,120,138,142,147],gram:112,gran:[2,82,83],granular:0,graph:3,graphic:3,graviti:2,grdient:58,great:[74,163],greater:[1,61,66,68,72,97,99,100,101],greatli:[40,63],green:[2,35,57,73,98,163],green_kubo:2,grest:[21,22,60,101,119,127],grid:[19,40,43,59,67,81],grigera:2,gromac:92,gromacs:[2,92,120],groot:110,ground:[2,31,64,114],group:[2,3,4,19,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,93,148,159],group_id:3,grow:[2,68,72,76,119],growth:2,gsmooth_factor:135,guarante:44,guess:163,gui:[3,163],guid:[1,151,152,153],gu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Documentation","5. Accelerating LAMMPS performance","6. How-to discussions","11. Python interface to LAMMPS","5.USER-INTEL package","angle_style charmm command","angle_style class2 command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style quartic command","angle_style sdk command","balance command","bond_style class2 command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style morse command","bond_style nonlinear command","bond_style quartic command","compute centro/atom command","compute cna/atom command","compute dpd command","compute fep command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute msd/nongauss command","compute orientorder/atom command","compute pressure command","compute saed command","compute sna/atom command","compute stress/atom command","compute xrd command","create_atoms command","dihedral_style charmm command","dihedral_style class2 command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style spherical command","dihedral_style command","dump image command","fix atc command","fix balance command","fix bond/swap command","fix box/relax command","fix controller command","fix ehex command","fix eos/cv command","fix eos/table/rx command","fix gld command","fix lb/fluid command","fix nvt command","fix nphug command","fix nve/manifold/rattle command","fix nvt/manifold/rattle command","fix orient/fcc command","fix pimd command","fix qbmsst command","fix restrain command","fix rx command","fix shake command","fix spring/rg command","fix ti/rs command","fix ti/spring command","fix ttm command","fix wall/lj93 command","fix wall/region command","improper_style class2 command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style ring command","improper_style umbrella command","minimize command","neb command","pair_style adp command","pair_style airebo command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style exp6/rx command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_style morse command","pair_style multi/lucy command","pair_style multi/lucy/rx command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style polymorphic command","pair_style resquared command","pair_style lj/sdk command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/idealgas command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style sw command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style vashishta command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","LAMMPS GitHub 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\ No newline at end of file diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index 6ea54ae222..adf6b5c47e 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@

LAMMPS Documentation :c,h3 -23 Aug 2016 version :c,h4 +27 Aug 2016 version :c,h4 Version info: :h4 diff --git a/doc/src/fix_flow_gauss.txt b/doc/src/fix_flow_gauss.txt index 617c65b798..2a0ec4f548 100644 --- a/doc/src/fix_flow_gauss.txt +++ b/doc/src/fix_flow_gauss.txt @@ -31,61 +31,67 @@ fix GD fluid flow/gauss 1 1 1 energy yes :pre [Description:] -This fix implements the Gaussian dynamics (GD) method to simulate a system at -constant mass flux "(Strong)"_#Strong. GD is a nonequilibrium molecular -dynamics simulation method that can be used to study fluid flows through -pores, pipes, and channels. In its original implementation GD was used to -compute the pressure required to achieve a fixed mass flux through an opening. -The flux can be conserved in any combination of the directions, x, y, or z, -using xflag,yflag,zflag. This fix does not initialize a net flux through -a system, it only conserves the center-of-mass momentum that is present -when the fix is declared in the input script. Use the "velocity"_velocity.html -command to generate an initial center-of-mass momentum. +This fix implements the Gaussian dynamics (GD) method to simulate a +system at constant mass flux "(Strong)"_#Strong. GD is a +nonequilibrium molecular dynamics simulation method that can be used +to study fluid flows through pores, pipes, and channels. In its +original implementation GD was used to compute the pressure required +to achieve a fixed mass flux through an opening. The flux can be +conserved in any combination of the directions, x, y, or z, using +xflag,yflag,zflag. This fix does not initialize a net flux through a +system, it only conserves the center-of-mass momentum that is present +when the fix is declared in the input script. Use the +"velocity"_velocity.html command to generate an initial center-of-mass +momentum. -GD applies an external fluctuating gravitational field that acts as a driving -force to keep the system away from equilibrium. To maintain steady state, a -profile-unbiased thermostat must be implemented to dissipate the heat that is -added by the driving force. "Compute temp/profile"_compute_temp_profile.html -can be used to implement a profile-unbiased thermostat. +GD applies an external fluctuating gravitational field that acts as a +driving force to keep the system away from equilibrium. To maintain +steady state, a profile-unbiased thermostat must be implemented to +dissipate the heat that is added by the driving force. "Compute +temp/profile"_compute_temp_profile.html can be used to implement a +profile-unbiased thermostat. -A common use of this fix is to compute a pressure drop across a pipe, pore, or -membrane. The pressure profile can be computed in LAMMPS with "compute -stress/atom"_compute_stress_atom.html and "fix ave/chunk"_fix_ave_chunk.html, -or with the hardy method in "fix atc"_fix_atc.html. Note that the simple -"compute stress/atom"_compute_stress_atom.html method is only accurate away -from inhomogeneities in the fluid, such as fixed wall atoms. Further, the -computed pressure profile must be corrected for the acceleration applied by -GD before computing a pressure drop or comparing it to other methods, such as -the pump method "(Zhu)"_#Zhu. The pressure correction is discussed and -described in "(Strong)"_#Strong. +A common use of this fix is to compute a pressure drop across a pipe, +pore, or membrane. The pressure profile can be computed in LAMMPS with +"compute stress/atom"_compute_stress_atom.html and "fix +ave/chunk"_fix_ave_chunk.html, or with the hardy method in "fix +atc"_fix_atc.html. Note that the simple "compute +stress/atom"_compute_stress_atom.html method is only accurate away +from inhomogeneities in the fluid, such as fixed wall atoms. Further, +the computed pressure profile must be corrected for the acceleration +applied by GD before computing a pressure drop or comparing it to +other methods, such as the pump method "(Zhu)"_#Zhu. The pressure +correction is discussed and described in "(Strong)"_#Strong. -NOTE: For a complete example including the considerations discussed above, see -the examples/USER/flow_gauss directory. +NOTE: For a complete example including the considerations discussed +above, see the examples/USER/flow_gauss directory. -NOTE: Only the flux of the atoms in group-ID will be conserved. If the -velocities of the group-ID atoms are coupled to the velocities of other atoms -in the simulation, the flux will not be conserved. For example, in a -simulation with fluid atoms and harmonically constrained wall atoms, if a -single thermostat is applied to group {all}, the fluid atom velocities will be -coupled to the wall atom velocities, and the flux will not be conserved. This -issue can be avoided by thermostatting the fluid and wall groups separately. +NOTE: Only the flux of the atoms in group-ID will be conserved. If the +velocities of the group-ID atoms are coupled to the velocities of +other atoms in the simulation, the flux will not be conserved. For +example, in a simulation with fluid atoms and harmonically constrained +wall atoms, if a single thermostat is applied to group {all}, the +fluid atom velocities will be coupled to the wall atom velocities, and +the flux will not be conserved. This issue can be avoided by +thermostatting the fluid and wall groups separately. -Adding an acceleration to atoms does work on the system. This added energy - can be optionally subtracted from the potential energy for the thermodynamic -output (see below) to check that the timestep is small enough to conserve -energy. Since the applied acceleration is fluctuating in time, the work cannot -be computed from a potential. As a result, computing the work is slightly more -computationally expensive than usual, so it is not performed by default. To -invoke the work calculation, use the {energy} keyword. The -"fix_modify"_fix_modify.html {energy} option also invokes the work -calculation, and overrides an {energy no} setting here. If neither {energy yes} -or {fix_modify energy yes} are set, the global scalar computed by the fix -will return zero. +Adding an acceleration to atoms does work on the system. This added +energy can be optionally subtracted from the potential energy for the +thermodynamic output (see below) to check that the timestep is small +enough to conserve energy. Since the applied acceleration is +fluctuating in time, the work cannot be computed from a potential. As +a result, computing the work is slightly more computationally +expensive than usual, so it is not performed by default. To invoke the +work calculation, use the {energy} keyword. The +"fix_modify"_fix_modify.html {energy} option also invokes the work +calculation, and overrides an {energy no} setting here. If neither +{energy yes} or {fix_modify energy yes} are set, the global scalar +computed by the fix will return zero. -NOTE: In order to check energy conservation, any other fixes that do work on -the system must have {fix_modify energy yes} set as well. This includes -thermostat fixes and any constraints that hold the positions of wall atoms -fixed, such as "fix spring/self"_fix_spring_self.html. +NOTE: In order to check energy conservation, any other fixes that do +work on the system must have {fix_modify energy yes} set as well. This +includes thermostat fixes and any constraints that hold the positions +of wall atoms fixed, such as "fix spring/self"_fix_spring_self.html. :line @@ -117,7 +123,8 @@ the "run"_run.html command. [Related commands:] -"fix addforce"_fix_addforce.html, "compute temp/profile"_compute_temp_profile.html, "velocity"_velocity.html +"fix addforce"_fix_addforce.html, "compute +temp/profile"_compute_temp_profile.html, "velocity"_velocity.html [Default:] @@ -133,5 +140,3 @@ The option default for the {energy} keyword is energy = no. :link(Zhu) [(Zhu)] Zhu, Tajkhorshid, and Schulten, Biophys. J. 83, 154 (2002). - -:line diff --git a/src/USER-MISC/README b/src/USER-MISC/README index c461544ff2..d60e2c85c8 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -37,7 +37,7 @@ dihedral_style spherical, Andrew Jewett, jewett.aij@gmail.com, 15 Jul 16 dihedral_style table, Andrew Jewett, jewett.aij@gmail.com, 10 Jan 12 fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11 fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015 -fix flow/gauss, Joel D. Eaves (CU Boulder), Joel.Eaves@Colorado.edu, 23 Aug 2016 +fix flow/gauss, Joel Eaves (CU Boulder), Joel.Eaves@Colorado.edu, 23 Aug 2016 fix gle, Michele Ceriotti (EPFL Lausanne), michele.ceriotti at gmail.com, 24 Nov 2014 fix imd, Axel Kohlmeyer, akohlmey at gmail.com, 9 Nov 2009 fix ipi, Michele Ceriotti (EPFL Lausanne), michele.ceriotti at gmail.com, 24 Nov 2014 diff --git a/src/USER-MISC/fix_flow_gauss.cpp b/src/USER-MISC/fix_flow_gauss.cpp index b7d271735d..e5c319c395 100644 --- a/src/USER-MISC/fix_flow_gauss.cpp +++ b/src/USER-MISC/fix_flow_gauss.cpp @@ -9,10 +9,12 @@ the GNU General Public License. See the README file in the top-level LAMMPS directory. + ------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- Contributing authors: Steven E. Strong and Joel D. Eaves Joel.Eaves@Colorado.edu - ------------------------------------------------------------------------- */ +------------------------------------------------------------------------- */ #include #include @@ -45,7 +47,8 @@ static const char cite_flow_gauss[] = "pages = {1907--1912}\n" "}\n\n"; -FixFlowGauss::FixFlowGauss(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) +FixFlowGauss::FixFlowGauss(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) { if (lmp->citeme) lmp->citeme->add(cite_flow_gauss); @@ -83,7 +86,8 @@ FixFlowGauss::FixFlowGauss(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, a if ( strcmp(arg[iarg],"energy") == 0 ) { if ( iarg+2 > narg ) error->all(FLERR,"Illegal energy keyword"); if ( strcmp(arg[iarg+1],"yes") == 0 ) workflag = 1; - else if ( strcmp(arg[iarg+1],"no") == 1 ) error->all(FLERR,"Illegal energy keyword"); + else if ( strcmp(arg[iarg+1],"no") == 1 ) + error->all(FLERR,"Illegal energy keyword"); iarg += 2; } else error->all(FLERR,"Illegal fix flow/gauss command"); } diff --git a/src/version.h b/src/version.h index 32ceacc47b..9725014aa4 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "23 Aug 2016" +#define LAMMPS_VERSION "27 Aug 2016"