IMPORTANT NOTE: The per-atom energy does NOT include contributions due +to long-range Coulombic interactions (via the +kspace_style command). It's not clear this +contribution can easily be computed. There are also a few pair styles +for manybody potentials that are not yet instrumented to yield +per-atom energy. See the Restrictions below. +
Output info:
This compute calculates a scalar quantity for each atom, which can be @@ -62,7 +69,11 @@ this section for an overview of LAMMPS output options.
-Restrictions: none +
Restrictions: +
+These pair styles do not yet tabulate per-atom energies to allow them +to work with this compute: airebo, +meam, and TIP4P.
Related commands:
diff -Naur lammps-12Jan08/doc/compute_pe_atom.txt lammps-16Jan08/doc/compute_pe_atom.txt --- lammps-12Jan08/doc/compute_pe_atom.txt 2008-01-03 17:56:10.000000000 -0700 +++ lammps-16Jan08/doc/compute_pe_atom.txt 2008-01-10 08:50:00.000000000 -0700 @@ -52,6 +52,13 @@ pairwise interactions between 1-4 atoms. The energy contribution of these terms is included in the pair energy, not the dihedral energy. +IMPORTANT NOTE: The per-atom energy does NOT include contributions due +to long-range Coulombic interactions (via the +"kspace_style"_kspace_style.html command). It's not clear this +contribution can easily be computed. There are also a few pair styles +for manybody potentials that are not yet instrumented to yield +per-atom energy. See the Restrictions below. + [Output info:] This compute calculates a scalar quantity for each atom, which can be @@ -59,7 +66,11 @@ "this section"_Section_howto.html#4_15 for an overview of LAMMPS output options. -[Restrictions:] none +[Restrictions:] + +These pair styles do not yet tabulate per-atom energies to allow them +to work with this compute: "airebo"_pair_airebo.html, +"meam"_pair_meam.html, and "TIP4P"_pair_lj.html. [Related commands:] diff -Naur lammps-12Jan08/doc/compute_stress_atom.html lammps-16Jan08/doc/compute_stress_atom.html --- lammps-12Jan08/doc/compute_stress_atom.html 2008-01-09 14:59:42.000000000 -0700 +++ lammps-16Jan08/doc/compute_stress_atom.html 2008-01-16 12:17:20.000000000 -0700 @@ -91,8 +91,8 @@ last 2 columns of thermo output will be the same:compute peratom all stress/atom -compute p all sum c_peratom1 c_peratom2 c_peratom3 -variable press equal -(c_p1+c_p2+c_p3)/(3*vol) +compute p all sum c_peratom[1] c_peratom[2] c_peratom[3] +variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol) thermo_style custom step temp etotal press v_press
IMPORTANT NOTE: The per-atom stress does NOT include contributions due @@ -112,8 +112,8 @@
Restrictions:
-These pair styles do not yet tabulate per-atom virial information to -allow them to work with this compute: airebo, +
These pair styles do not yet tabulate per-atom virials to allow them +to work with this compute: airebo, meam, and TIP4P.
Related commands: diff -Naur lammps-12Jan08/doc/compute_stress_atom.txt lammps-16Jan08/doc/compute_stress_atom.txt --- lammps-12Jan08/doc/compute_stress_atom.txt 2008-01-09 14:59:42.000000000 -0700 +++ lammps-16Jan08/doc/compute_stress_atom.txt 2008-01-16 12:17:20.000000000 -0700 @@ -87,8 +87,8 @@ last 2 columns of thermo output will be the same: compute peratom all stress/atom -compute p all sum c_peratom[1] c_peratom[2] c_peratom[3] -variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol) +compute p all sum c_peratom\[1\] c_peratom\[2\] c_peratom\[3\] +variable press equal -(c_p\[1\]+c_p\[2\]+c_p\[3\])/(3*vol) thermo_style custom step temp etotal press v_press :pre IMPORTANT NOTE: The per-atom stress does NOT include contributions due @@ -108,8 +108,8 @@ [Restrictions:] -These pair styles do not yet tabulate per-atom virial information to -allow them to work with this compute: "airebo"_pair_airebo.html, +These pair styles do not yet tabulate per-atom virials to allow them +to work with this compute: "airebo"_pair_airebo.html, "meam"_pair_meam.html, and "TIP4P"_pair_lj.html. [Related commands:] diff -Naur lammps-12Jan08/doc/dump.html lammps-16Jan08/doc/dump.html --- lammps-12Jan08/doc/dump.html 2008-01-03 16:28:08.000000000 -0700 +++ lammps-16Jan08/doc/dump.html 2008-01-16 12:17:20.000000000 -0700 @@ -80,7 +80,7 @@ included. Not all styles support all these options; see details below.
-IMPORTANT NOTE: Vecause periodic boundary conditions are enforced only +
IMPORTANT NOTE: Because periodic boundary conditions are enforced only on timesteps when neighbor lists are rebuilt, the coordinates of an atom written to a dump file may be slightly outside the simulation box. diff -Naur lammps-12Jan08/doc/dump.txt lammps-16Jan08/doc/dump.txt --- lammps-12Jan08/doc/dump.txt 2008-01-03 16:28:08.000000000 -0700 +++ lammps-16Jan08/doc/dump.txt 2008-01-16 12:17:20.000000000 -0700 @@ -70,7 +70,7 @@ included. Not all styles support all these options; see details below. -IMPORTANT NOTE: Vecause periodic boundary conditions are enforced only +IMPORTANT NOTE: Because periodic boundary conditions are enforced only on timesteps when neighbor lists are rebuilt, the coordinates of an atom written to a dump file may be slightly outside the simulation box. diff -Naur lammps-12Jan08/doc/fix_rigid.html lammps-16Jan08/doc/fix_rigid.html --- lammps-12Jan08/doc/fix_rigid.html 2007-10-10 16:28:11.000000000 -0600 +++ lammps-16Jan08/doc/fix_rigid.html 2008-01-09 16:22:14.000000000 -0700 @@ -68,24 +68,22 @@ includes all the desired rigid bodies. LAMMPS will allow multiple rigid fixes to be defined, but it is more expensive.
+This fix uses constant-energy integration, so you may need to impose +additional constraints to control the temperature of an ensemble of +rigid bodies. You can use fix langevin for this +purpose to treat the system as effectively immersed in an implicit +solvent, i.e. a Brownian dynamics model. Or you can thermostat +additional atoms of an explicit solvent directly. +
The degrees-of-freedom removed by rigid bodies are accounted for in -temperature and pressure computations. Similary, the rigid body -contribution to the pressure virial is also accounted for. The latter -is only correct if forces within the bodies have been turned off, and -there is only a single fix rigid defined. For each linear rigid body -of three or more atoms, one degree-of-freedom must be subtracted using -a compute_modify command (i.e. for a simulation -of 10 such rigid bodies, use "compute_modify thermo_temp extra 13", -after the thermo_style command, where 3 is the default setting and -an additional 10 degrees-of-freedom are subtracted). -
-Note that this fix uses constant-energy integration, so you may need -to impose additional constraints to control the temperature of an -ensemble of rigid bodies. You can use fix -langevin for this purpose to treat the system as -effectively immersed in an implicit solvent, i.e. a Brownian dynamics -model. Or you can thermostat additional atoms of an explicit solvent -directly. +temperature and pressure computations. Similarly, the rigid body +contribution to the pressure of the system (virial) is also accounted +for. For linear rigid bodies of three or more atoms, one additional +degree-of-freedom must be subtracted manually using the +compute_modify command. E.g. for a simulation +of 10 such rigid bodies, use "compute_modify thermo_temp extra 13", +after the thermo_style command, where 3 is the default setting and an +additional 10 degrees-of-freedom are subtracted.
IMPORTANT NOTE: The periodic image flags of atoms in rigid bodies are modified when the center-of-mass of the rigid body moves across a diff -Naur lammps-12Jan08/doc/fix_rigid.txt lammps-16Jan08/doc/fix_rigid.txt --- lammps-12Jan08/doc/fix_rigid.txt 2007-10-10 16:28:11.000000000 -0600 +++ lammps-16Jan08/doc/fix_rigid.txt 2008-01-09 16:22:14.000000000 -0700 @@ -61,24 +61,22 @@ includes all the desired rigid bodies. LAMMPS will allow multiple rigid fixes to be defined, but it is more expensive. +This fix uses constant-energy integration, so you may need to impose +additional constraints to control the temperature of an ensemble of +rigid bodies. You can use "fix langevin"_fix_langevin.html for this +purpose to treat the system as effectively immersed in an implicit +solvent, i.e. a Brownian dynamics model. Or you can thermostat +additional atoms of an explicit solvent directly. + The degrees-of-freedom removed by rigid bodies are accounted for in -temperature and pressure computations. Similary, the rigid body -contribution to the pressure virial is also accounted for. The latter -is only correct if forces within the bodies have been turned off, and -there is only a single fix rigid defined. For each linear rigid body -of three or more atoms, one degree-of-freedom must be subtracted using -a "compute_modify"_compute_modify.html command (i.e. for a simulation -of 10 such rigid bodies, use "compute_modify thermo_temp extra 13", -after the thermo_style command, where 3 is the default setting and -an additional 10 degrees-of-freedom are subtracted). - -Note that this fix uses constant-energy integration, so you may need -to impose additional constraints to control the temperature of an -ensemble of rigid bodies. You can use "fix -langevin"_fix_langevin.html for this purpose to treat the system as -effectively immersed in an implicit solvent, i.e. a Brownian dynamics -model. Or you can thermostat additional atoms of an explicit solvent -directly. +temperature and pressure computations. Similarly, the rigid body +contribution to the pressure of the system (virial) is also accounted +for. For linear rigid bodies of three or more atoms, one additional +degree-of-freedom must be subtracted manually using the +"compute_modify"_compute_modify.html command. E.g. for a simulation +of 10 such rigid bodies, use "compute_modify thermo_temp extra 13", +after the thermo_style command, where 3 is the default setting and an +additional 10 degrees-of-freedom are subtracted. IMPORTANT NOTE: The periodic image flags of atoms in rigid bodies are modified when the center-of-mass of the rigid body moves across a diff -Naur lammps-12Jan08/doc/fix_shake.html lammps-16Jan08/doc/fix_shake.html --- lammps-12Jan08/doc/fix_shake.html 2007-10-10 16:28:11.000000000 -0600 +++ lammps-16Jan08/doc/fix_shake.html 2008-01-10 08:50:00.000000000 -0700 @@ -83,7 +83,8 @@
The degrees-of-freedom removed by SHAKE bonds and angles are accounted for in temperature and pressure computations. Similarly, the SHAKE -contribution to the pressure virial is also accounted for. +contribution to the pressure of the system (virial) is also accounted +for.
Restart, fix_modify, output, run start/stop, minimize info:
diff -Naur lammps-12Jan08/doc/fix_shake.txt lammps-16Jan08/doc/fix_shake.txt --- lammps-12Jan08/doc/fix_shake.txt 2007-10-10 16:28:11.000000000 -0600 +++ lammps-16Jan08/doc/fix_shake.txt 2008-01-10 08:50:00.000000000 -0700 @@ -72,7 +72,8 @@ The degrees-of-freedom removed by SHAKE bonds and angles are accounted for in temperature and pressure computations. Similarly, the SHAKE -contribution to the pressure virial is also accounted for. +contribution to the pressure of the system (virial) is also accounted +for. [Restart, fix_modify, output, run start/stop, minimize info:] diff -Naur lammps-12Jan08/tools/xmovie/read.c lammps-16Jan08/tools/xmovie/read.c --- lammps-12Jan08/tools/xmovie/read.c 2006-09-27 13:51:49.000000000 -0600 +++ lammps-16Jan08/tools/xmovie/read.c 2008-01-16 16:53:52.000000000 -0700 @@ -703,14 +703,16 @@ PRIVATE void NewData(void) { int i; - DATA *last_data; + DATA *last_data,*olddataptr; + olddataptr = Common.dataptr; last_data = current_data; if (Common.ndata >= Common.maxdata) { /* need to realloc */ Common.maxdata += 256; - Common.dataptr = (DATA *) XtRealloc((char *) Common.dataptr, - Common.maxdata * sizeof(DATA)); + Common.dataptr = (DATA *) + XtMalloc(Common.maxdata * sizeof(DATA)); + memcpy(Common.dataptr,olddataptr,Common.ndata*sizeof(DATA)); } current_data = Common.dataptr + Common.ndata; @@ -764,6 +766,8 @@ current_data->bonds = NULL; current_data->maxbonds = 0; } + + if (olddataptr != Common.dataptr) XtFree((char *) olddataptr); } PRIVATE void add_point(int index, int type, float x, float y, float z)