From e09f40c9d0a1fa2286413c62a18c83aab0ec7d79 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 27 May 2014 14:02:43 +0000 Subject: [PATCH 1/8] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12028 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/fix_wall_region.html | 12 +++++++++++- doc/fix_wall_region.txt | 12 +++++++++++- 2 files changed, 22 insertions(+), 2 deletions(-) diff --git a/doc/fix_wall_region.html b/doc/fix_wall_region.html index 4bea6c7103..b6a215362e 100644 --- a/doc/fix_wall_region.html +++ b/doc/fix_wall_region.html @@ -76,11 +76,21 @@ points suffer from inaccuracies. The basic problem is that the outward normal of the surface is not continuous at these points. This can cause particles to feel no force (they don't "see" the wall) when in one location, then move a distance epsilon, and suddenly feel a -large force because they now "see" the wall. In the worst-case +large force because they now "see" the wall. In a worst-case scenario, this can blow particles out of the simulation box. Thus, as a general rule you should not use the fix wall/region command with union or interesect regions that have convex points or edges.

+

IMPORTANT NOTE: Similarly, you should not define union or +intersert regions for use with this command that share a common +face, even if the face is smooth. E.g. two regions of style block in +a union region, where the two blocks have the same face. This is +because LAMMPS discards points that are part of multiple sub-regions +when calculating wall/particle interactions, to avoid double-counting +the interaction. Having two coincident faces could cause the face to +become invisible to the particles. The solution is to make the two +faces differ by epsilon in their position. +

The energy of wall-particle interactions depends on the specified style.

diff --git a/doc/fix_wall_region.txt b/doc/fix_wall_region.txt index 0c13cf3b44..607e60374c 100644 --- a/doc/fix_wall_region.txt +++ b/doc/fix_wall_region.txt @@ -73,11 +73,21 @@ points suffer from inaccuracies. The basic problem is that the outward normal of the surface is not continuous at these points. This can cause particles to feel no force (they don't "see" the wall) when in one location, then move a distance epsilon, and suddenly feel a -large force because they now "see" the wall. In the worst-case +large force because they now "see" the wall. In a worst-case scenario, this can blow particles out of the simulation box. Thus, as a general rule you should not use the fix wall/region command with {union} or {interesect} regions that have convex points or edges. +IMPORTANT NOTE: Similarly, you should not define {union} or +{intersert} regions for use with this command that share a common +face, even if the face is smooth. E.g. two regions of style block in +a {union} region, where the two blocks have the same face. This is +because LAMMPS discards points that are part of multiple sub-regions +when calculating wall/particle interactions, to avoid double-counting +the interaction. Having two coincident faces could cause the face to +become invisible to the particles. The solution is to make the two +faces differ by epsilon in their position. + The energy of wall-particle interactions depends on the specified style. From 2da52d8d9d0dab818b84f9747c59576e1afe218a Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 27 May 2014 14:25:40 +0000 Subject: [PATCH 2/8] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12029 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/input.cpp | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/input.cpp b/src/input.cpp index 4ed825a941..c3b265180b 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -1164,6 +1164,11 @@ void Input::comm_style() "Cannot switch to comm style brick from " "irregular tiling of proc domains"); comm = new CommBrick(lmp); + // NOTE: this will lose load balancing info in old CommBrick + if (domain->box_exist) { + comm->set_proc_grid(); + domain->set_local_box(); + } } else if (strcmp(arg[0],"tiled") == 0) { error->all(FLERR,"Comm_style tiled not yet supported"); comm = new CommTiled(lmp); From 0d2f6d9db4ebfc108e4761b28dd71b40db926c8d Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 27 May 2014 14:35:49 +0000 Subject: [PATCH 3/8] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12030 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/fix_adapt.cpp | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp index ce6b4bd64c..22e718dd76 100644 --- a/src/fix_adapt.cpp +++ b/src/fix_adapt.cpp @@ -45,6 +45,8 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) nevery = force->inumeric(FLERR,arg[3]); if (nevery < 0) error->all(FLERR,"Illegal fix adapt command"); + dynamic_group_allow = 1; + // count # of adaptations nadapt = 0; @@ -266,6 +268,13 @@ void FixAdapt::init() { int i,j; + // allow a dynamic group only if ATOM attribute not used + + if (group->dynamic[igroup]) + for (int i = 0; i < nadapt; i++) + if (adapt[i].which == ATOM) + error->all(FLERR,"Cannot use dynamic group with fix adapt atom"); + // setup and error checks anypair = 0; From 58a7b4748e0d0d7e852ae0b4ab794ae6741110d5 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 27 May 2014 17:04:19 +0000 Subject: [PATCH 4/8] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12031 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/fix_rigid.html | 18 ++++++++++++++---- doc/fix_rigid.txt | 18 ++++++++++++++---- 2 files changed, 28 insertions(+), 8 deletions(-) diff --git a/doc/fix_rigid.html b/doc/fix_rigid.html index a71ffde390..88ff880c02 100644 --- a/doc/fix_rigid.html +++ b/doc/fix_rigid.html @@ -103,12 +103,12 @@ fix 1 particles rigid/npt/small molecule temp 1.0 1.0 1.0 iso 0.5 0.5 1.0

Treat one or more sets of atoms as independent rigid bodies. This means that each timestep the total force and torque on each rigid body is computed as the sum of the forces and torques on its constituent -particles and the coordinates, velocities, and orientations of the -atoms in each body are updated so that the body moves and rotates as a +particles. The coordinates, velocities, and orientations of the atoms +in each body are then updated so that the body moves and rotates as a single entity.

-

Examples of large rigid bodies are a large colloidal particle, or -portions of a large biomolecule such as a protein. +

Examples of large rigid bodies are a colloidal particle, or portions +of a biomolecule such as a protein.

Example of small rigid bodies are patchy nanoparticles, such as those modeled in this paper by Sharon Glotzer's group, clumps of @@ -183,6 +183,16 @@ command), setting the force on them to 0.0 (via the fix nve command).

+

IMPORTANT NOTE: The aggregate properties of each rigid body are +calculated at the start of each simulation run. These include its +center of mass, moments of inertia, and net velocity and angular +momentum. This means that before or between runs, per-atom properties +can be changed, e.g. via the set or +velocity command, which will affect the bodies. An +exception is if the infile keyword is used, then all the body +properties (except net velocity and angular momentum) are only +calculated once so that values from the file are valid. +

Each rigid body must have two or more atoms. An atom can belong to at diff --git a/doc/fix_rigid.txt b/doc/fix_rigid.txt index 62bd5e2ee3..66a6c7bd67 100644 --- a/doc/fix_rigid.txt +++ b/doc/fix_rigid.txt @@ -85,12 +85,12 @@ fix 1 particles rigid/npt/small molecule temp 1.0 1.0 1.0 iso 0.5 0.5 1.0 :pre Treat one or more sets of atoms as independent rigid bodies. This means that each timestep the total force and torque on each rigid body is computed as the sum of the forces and torques on its constituent -particles and the coordinates, velocities, and orientations of the -atoms in each body are updated so that the body moves and rotates as a +particles. The coordinates, velocities, and orientations of the atoms +in each body are then updated so that the body moves and rotates as a single entity. -Examples of large rigid bodies are a large colloidal particle, or -portions of a large biomolecule such as a protein. +Examples of large rigid bodies are a colloidal particle, or portions +of a biomolecule such as a protein. Example of small rigid bodies are patchy nanoparticles, such as those modeled in "this paper"_#Zhang by Sharon Glotzer's group, clumps of @@ -165,6 +165,16 @@ command), setting the force on them to 0.0 (via the "fix setforce"_fix_setforce.html command), and integrating them as usual (e.g. via the "fix nve"_fix_nve.html command). +IMPORTANT NOTE: The aggregate properties of each rigid body are +calculated at the start of each simulation run. These include its +center of mass, moments of inertia, and net velocity and angular +momentum. This means that before or between runs, per-atom properties +can be changed, e.g. via the "set"_set.html or +"velocity"_velocity.html command, which will affect the bodies. An +exception is if the {infile} keyword is used, then all the body +properties (except net velocity and angular momentum) are only +calculated once so that values from the file are valid. + :line Each rigid body must have two or more atoms. An atom can belong to at From 53ae7f08c3224f8418fdec747eba313c9cc47bae Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 27 May 2014 17:04:25 +0000 Subject: [PATCH 5/8] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12032 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/RIGID/fix_rigid.cpp | 65 +++++++++++++++++++++-------------- src/RIGID/fix_rigid.h | 2 +- src/RIGID/fix_rigid_small.cpp | 46 ++++++++++++++----------- src/RIGID/fix_rigid_small.h | 2 +- 4 files changed, 67 insertions(+), 48 deletions(-) diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index 8f965ffc2d..75080ec833 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -523,6 +523,13 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) : MINUSPI = -MY_PI; TWOPI = 2.0*MY_PI; + // if infile set, only setup rigid bodies once, using info from file + // this means users cannot change atom properties like mass between runs + // if they do, bodies will not reflect the changes + + staticflag = 0; + if (infile) setup_bodies_static(); + // print statistics int nsum = 0; @@ -532,10 +539,6 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) : if (screen) fprintf(screen,"%d rigid bodies with %d atoms\n",nbody,nsum); if (logfile) fprintf(logfile,"%d rigid bodies with %d atoms\n",nbody,nsum); } - - // firstflag = 1 triggers one-time initialization of rigid body attributes - - firstflag = 1; } /* ---------------------------------------------------------------------- */ @@ -640,15 +643,11 @@ void FixRigid::init() if (strstr(update->integrate_style,"respa")) step_respa = ((Respa *) update->integrate)->step; - // one-time initialization of rigid body attributes - // setup_bodies_static = extended flags, masstotal, COM, inertia tensor - // setup_bodies_dynamic = vcm and angmom + // setup rigid bodies, using current atom info + // allows resetting of atom properties like mass between runs + // only do this if not using an infile, else was called in constructor - if (firstflag) { - firstflag = 0; - setup_bodies_static(); - setup_bodies_dynamic(); - } + if (!infile) setup_bodies_static(); // temperature scale factor @@ -670,6 +669,12 @@ void FixRigid::setup(int vflag) { int i,n,ibody; + // setup_bodies_dynamic sets vcm and angmom + // so angmom_to_omega() and set_v() below will set per-atom vels correctly + // re-calling it every run allows reset of body/atom velocities between runs + + setup_bodies_dynamic(); + // fcm = force on center-of-mass of each rigid body double **f = atom->f; @@ -1113,10 +1118,10 @@ int FixRigid::dof(int tgroup) { // cannot count DOF correctly unless setup_bodies_static() has been called - if (firstflag) { + if (!staticflag) { if (comm->me == 0) error->warning(FLERR,"Cannot count rigid body degrees-of-freedom " - "before bodies are fully initialized"); + "before bodies are initialized"); return 0; } @@ -1522,10 +1527,12 @@ void FixRigid::set_v() } /* ---------------------------------------------------------------------- - one-time initialization of static rigid body attributes - extended flags, masstotal, center-of-mass - Cartesian and diagonalized inertia tensor - read per-body attributes from infile if specified + initialization of static rigid body attributes + called from init() so body/atom properties can be changed between runs + unless reading from infile, in which case called once from constructor + sets extended flags, masstotal, center-of-mass + sets Cartesian and diagonalized inertia tensor + sets body image flags, but only on first call ------------------------------------------------------------------------- */ void FixRigid::setup_bodies_static() @@ -1682,10 +1689,13 @@ void FixRigid::setup_bodies_static() // set image flags for each rigid body to default values // then remap the xcm of each body back into simulation box if needed + // staticflag check insures this in only done once, not on successive runs - for (ibody = 0; ibody < nbody; ibody++) - imagebody[ibody] = ((imageint) IMGMAX << IMG2BITS) | - ((imageint) IMGMAX << IMGBITS) | IMGMAX; + if (!staticflag) { + for (ibody = 0; ibody < nbody; ibody++) + imagebody[ibody] = ((imageint) IMGMAX << IMG2BITS) | + ((imageint) IMGMAX << IMGBITS) | IMGMAX; + } pre_neighbor(); @@ -2018,13 +2028,18 @@ void FixRigid::setup_bodies_static() } if (infile) memory->destroy(inbody); + + // static properties have now been initialized once + // used to prevent re-initialization which would re-read infile + + staticflag = 1; } /* ---------------------------------------------------------------------- - one-time initialization of dynamic rigid body attributes - Vcm and angmom, computed explicitly from constituent particles - even if wrong for overlapping particles, is OK, - since is just setting initial time=0 Vcm and angmom of the body + initialization of dynamic rigid body attributes + set vcm and angmom, computed explicitly from constituent particles + OK if wrong for overlapping particles, + since is just setting vcm/angmom at start of run, which can be estimated value ------------------------------------------------------------------------- */ diff --git a/src/RIGID/fix_rigid.h b/src/RIGID/fix_rigid.h index 62adce6e03..e984825049 100644 --- a/src/RIGID/fix_rigid.h +++ b/src/RIGID/fix_rigid.h @@ -67,7 +67,7 @@ class FixRigid : public Fix { char *infile; // file to read rigid body attributes from int rstyle; // SINGLE,MOLECULE,GROUP - int firstflag; // 1 for first-time setup of rigid bodies + int staticflag; // 1 if static body properties are setup, else 0 int dimension; // # of dimensions int nbody; // # of rigid bodies diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index 0033a62475..18e4a51715 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -421,9 +421,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) : mass_body = NULL; nmax_mass = 0; - // firstflag = 1 triggers one-time initialization of rigid body attributes - - firstflag = 1; + staticflag = 1; } /* ---------------------------------------------------------------------- */ @@ -505,19 +503,16 @@ void FixRigidSmall::init() } /* ---------------------------------------------------------------------- - one-time initialization of rigid body attributes via local comm - extended flags, mass, COM, inertia tensor, displacement of each atom - performed after init() b/c requires communication stencil - has been setup by comm->borders() + setup static/dynamic properties of rigid bodies, using current atom info + allows resetting of atom properties like mass between runs + only do static initialization once if using an infile + cannot do this until now, b/c requires comm->setup() to have setup stencil ------------------------------------------------------------------------- */ void FixRigidSmall::setup_pre_neighbor() { - if (firstflag) { - firstflag = 0; - setup_bodies_static(); - setup_bodies_dynamic(); - } else pre_neighbor(); + if (!staticflag || !infile) setup_bodies_static(); + setup_bodies_dynamic(); } /* ---------------------------------------------------------------------- @@ -972,7 +967,7 @@ int FixRigidSmall::dof(int tgroup) // cannot count DOF correctly unless setup_bodies_static() has been called - if (firstflag) { + if (!staticflag) { if (comm->me == 0) error->warning(FLERR,"Cannot count rigid body degrees-of-freedom " "before bodies are fully initialized"); @@ -1672,10 +1667,12 @@ void FixRigidSmall::ring_farthest(int n, char *cbuf) } /* ---------------------------------------------------------------------- - one-time initialization of rigid body attributes - extended flags, mass, center-of-mass - Cartesian and diagonalized inertia tensor - read per-body attributes from infile if specified + initialization of rigid body attributes + called at setup, so body/atom properties can be changed between runs + unless reading from infile, in which case only called once + sets extended flags, masstotal, center-of-mass + sets Cartesian and diagonalized inertia tensor + sets body image flags, but only on first call ------------------------------------------------------------------------- */ void FixRigidSmall::setup_bodies_static() @@ -1838,10 +1835,12 @@ void FixRigidSmall::setup_bodies_static() // set image flags for each rigid body to default values // then remap the xcm of each body back into simulation box if needed + // staticflag check insures this in only done once, not on successive runs - for (ibody = 0; ibody < nlocal_body; ibody++) - body[ibody].image = ((imageint) IMGMAX << IMG2BITS) | - ((imageint) IMGMAX << IMGBITS) | IMGMAX; + if (!staticflag) + for (ibody = 0; ibody < nlocal_body; ibody++) + body[ibody].image = ((imageint) IMGMAX << IMG2BITS) | + ((imageint) IMGMAX << IMGBITS) | IMGMAX; pre_neighbor(); @@ -2175,6 +2174,11 @@ void FixRigidSmall::setup_bodies_static() memory->destroy(itensor); if (infile) memory->destroy(inbody); + + // static properties have now been initialized once + // used to prevent re-initialization which would re-read infile + + staticflag = 1; } /* ---------------------------------------------------------------------- @@ -2418,7 +2422,7 @@ void FixRigidSmall::write_restart_file(char *file) // do not write file if bodies have not yet been intialized - if (firstflag) return; + if (!staticflag) return; // proc 0 opens file and writes header diff --git a/src/RIGID/fix_rigid_small.h b/src/RIGID/fix_rigid_small.h index 3cdc2fb9f1..2346c78937 100644 --- a/src/RIGID/fix_rigid_small.h +++ b/src/RIGID/fix_rigid_small.h @@ -78,7 +78,7 @@ class FixRigidSmall : public Fix { double MINUSPI,TWOPI; char *infile; // file to read rigid body attributes from - int firstflag; // 1 for first-time setup of rigid bodies + int staticflag; // 1 if static body properties are setup, else 0 int commflag; // various modes of forward/reverse comm int nbody; // total # of rigid bodies tagint maxmol; // max mol-ID From 3cf8560b941084e07b63618ea896100736d3c061 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 27 May 2014 19:21:49 +0000 Subject: [PATCH 6/8] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12033 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/RIGID/fix_rigid_small.cpp | 1 - 1 file changed, 1 deletion(-) diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index 18e4a51715..93c4144140 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -1738,7 +1738,6 @@ void FixRigidSmall::setup_bodies_static() if (atom->line_flag) orientflag = 1; if (atom->tri_flag) orientflag = 4; if (atom->mu_flag) dorientflag = 1; - grow_arrays(atom->nmax); for (i = 0; i < nlocal; i++) { eflags[i] = 0; From 3b6deb5005bb4f732ecb1c85d31d1766e1244be4 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 27 May 2014 19:22:06 +0000 Subject: [PATCH 7/8] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12034 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/version.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/version.h b/src/version.h index f0f6c2230e..535898f618 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "23 May 2014" +#define LAMMPS_VERSION "27 May 2014" From 21141894f74935d765004c2499676166aff11317 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 27 May 2014 19:22:07 +0000 Subject: [PATCH 8/8] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12035 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Manual.html | 4 ++-- doc/Manual.txt | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/Manual.html b/doc/Manual.html index c0342b048a..f19aa6ab31 100644 --- a/doc/Manual.html +++ b/doc/Manual.html @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -22,7 +22,7 @@

LAMMPS Documentation

-

23 May 2014 version +

27 May 2014 version

Version info:

diff --git a/doc/Manual.txt b/doc/Manual.txt index 94f85fe2af..36263db5ed 100644 --- a/doc/Manual.txt +++ b/doc/Manual.txt @@ -1,6 +1,6 @@ LAMMPS Users Manual - + @@ -18,7 +18,7 @@

LAMMPS Documentation :c,h3 -23 May 2014 version :c,h4 +27 May 2014 version :c,h4 Version info: :h4