The tools/eff directory contains various scripts for generating +structures and post-processing output for simulations using the +electron force field (EFF). +
+These tools were provided by Andres Jaramillo-Botero at CalTech +(ajaramil at wag.caltech.edu). +
+The lmp2arc sub-directory contains a tool for converting LAMMPS output diff --git a/doc/Section_tools.txt b/doc/Section_tools.txt index a672c23a72..238af10a5f 100644 --- a/doc/Section_tools.txt +++ b/doc/Section_tools.txt @@ -45,6 +45,7 @@ own sub-directories with their own Makefiles. "chain"_#chain "data2xmovie"_#data "eam generate"_#eam +"eff_#eff "lmp2arc"_#arc "lmp2cfg"_#cfg "lmp2traj"_#traj @@ -148,6 +149,17 @@ The source files and potentials were provided by Gerolf Ziegenhain :line +eff tool :h4,link(eff) + +The tools/eff directory contains various scripts for generating +structures and post-processing output for simulations using the +electron force field (EFF). + +These tools were provided by Andres Jaramillo-Botero at CalTech +(ajaramil at wag.caltech.edu). + +:line + lmp2arc tool :h4,link(arc) The lmp2arc sub-directory contains a tool for converting LAMMPS output diff --git a/doc/atom_style.html b/doc/atom_style.html index 915ca00711..bc90773587 100644 --- a/doc/atom_style.html +++ b/doc/atom_style.html @@ -15,7 +15,7 @@
atom_style style args-
args = none for any style except hybrid hybrid args = list of one or more sub-styles @@ -59,6 +59,7 @@ quantities.charge charge atomic system with charges colloid angular velocity extended spherical particles + dipole charge and dipole moment atomic system with dipoles electron spin and eradius electronic force field ellipsoid quaternion for particle orientation, angular momentum extended aspherical particles full molecular + charge bio-molecules @@ -67,15 +68,18 @@ quantities. granular diameter, density, angular velocity granular models All of the styles define point particles, except the colloid, -dipole, ellipsoid, granular, and peri styles, which define -finite-size particles. For colloid, dipole, and ellipsoid -systems, the shape command is used to specify the size -and shape of particles on a per-type basis, which is spherical for -colloid and dipole particles and spherical or aspherical for -ellipsoid particles. For granular systems, the particles are -spherical and each has a per-particle specified diameter. For peri -systems, the particles are spherical and each has a per-particle -specified volume. +dipole, electron, ellipsoid, granular, and peri styles, +which define finite-size particles. For colloid, dipole, and +ellipsoid systems, the shape command is used to specify +the size and shape of particles on a per-type basis, which is +spherical for colloid and dipole particles and spherical or +aspherical for ellipsoid particles. For granular systems, the +particles are spherical and each has a per-particle specified +diameter. For peri systems, the particles are spherical and each +has a per-particle specified volume. For electron systems, the +particles are three dimensional Gaussians with a specified position +and bandwidth or uncertainty in position, which is described as the +eradius = electron size.
All of the styles assign mass to particles on a per-type basis, using the mass command, except the granular and peri styles @@ -113,9 +117,10 @@ section. package. The colloid style is part of the "colloid" package. The dipole style is part of the "dipole" package. The ellipsoid style is part of the "asphere" package. The peri style is part of the -"peri" package for Peridynamics. They are only enabled if LAMMPS was -built with that package. See the Making -LAMMPS section for more info. +"peri" package for Peridynamics. The electron style is part of the +"user-eff" package for electronic force fields. They +are only enabled if LAMMPS was built with that package. See the +Making LAMMPS section for more info.
Related commands:
diff --git a/doc/atom_style.txt b/doc/atom_style.txt index f8e44046b6..466cc3b296 100644 --- a/doc/atom_style.txt +++ b/doc/atom_style.txt @@ -13,7 +13,7 @@ atom_style command :h3 atom_style style args :pre style = {angle} or {atomic} or {bond} or {charge} or {colloid} or {dipole} or \ - {ellipsoid} or {full} or {granular} or {molecular} or \ + {electron} or {ellipsoid} or {full} or {granular} or {molecular} or \ {peri} or {hybrid} :ul args = none for any style except {hybrid} {hybrid} args = list of one or more sub-styles :pre @@ -56,6 +56,7 @@ quantities. {charge} | charge | atomic system with charges | {colloid} | angular velocity | extended spherical particles | {dipole} | charge and dipole moment | atomic system with dipoles | +{electron} | spin and eradius | electronic force field | {ellipsoid} | quaternion for particle orientation, angular momentum | extended aspherical particles | {full} | molecular + charge | bio-molecules | {granular} | diameter, density, angular velocity | granular models | @@ -63,15 +64,18 @@ quantities. {peri} | density, volume | mesocopic Peridynamic models :tb(c=3,s=|) All of the styles define point particles, except the {colloid}, -{dipole}, {ellipsoid}, {granular}, and {peri} styles, which define -finite-size particles. For {colloid}, {dipole}, and {ellipsoid} -systems, the "shape"_shape.html command is used to specify the size -and shape of particles on a per-type basis, which is spherical for -{colloid} and {dipole} particles and spherical or aspherical for -{ellipsoid} particles. For {granular} systems, the particles are -spherical and each has a per-particle specified diameter. For {peri} -systems, the particles are spherical and each has a per-particle -specified volume. +{dipole}, {electron}, {ellipsoid}, {granular}, and {peri} styles, +which define finite-size particles. For {colloid}, {dipole}, and +{ellipsoid} systems, the "shape"_shape.html command is used to specify +the size and shape of particles on a per-type basis, which is +spherical for {colloid} and {dipole} particles and spherical or +aspherical for {ellipsoid} particles. For {granular} systems, the +particles are spherical and each has a per-particle specified +diameter. For {peri} systems, the particles are spherical and each +has a per-particle specified volume. For {electron} systems, the +particles are three dimensional Gaussians with a specified position +and bandwidth or uncertainty in position, which is described as the +eradius = electron size. All of the styles assign mass to particles on a per-type basis, using the "mass"_mass.html command, except the {granular} and {peri} styles @@ -109,9 +113,10 @@ The {angle}, {bond}, {full}, and {molecular} styles are part of the package. The {colloid} style is part of the "colloid" package. The {dipole} style is part of the "dipole" package. The {ellipsoid} style is part of the "asphere" package. The {peri} style is part of the -"peri" package for Peridynamics. They are only enabled if LAMMPS was -built with that package. See the "Making -LAMMPS"_Section_start.html#2_3 section for more info. +"peri" package for Peridynamics. The {electron} style is part of the +"user-eff" package for "electronic force fields"_pair_eff.html. They +are only enabled if LAMMPS was built with that package. See the +"Making LAMMPS"_Section_start.html#2_3 section for more info. [Related commands:] diff --git a/doc/dump.html b/doc/dump.html index ed14199987..2af36363f9 100644 --- a/doc/dump.html +++ b/doc/dump.html @@ -49,6 +49,7 @@ radius, omegax, omegay, omegaz, angmomx, angmomy, angmomz, quatw, quati, quatj, quatk, tqx, tqy, tqz, + spin, eradius, evel, eforce, c_ID, c_ID[N], f_ID, f_ID[N], v_name
id = atom ID
@@ -68,6 +69,10 @@
angmomx,angmomy,angmomz = angular momentum of extended particle
quatw,quati,quatj,quatk = quaternion components for aspherical particles
tqx,tqy,tqz = torque on extended particles
+ spin = electron spin
+ eradius = electron radius
+ evel = electron radial velocity
+ eforce = electron radial force
c_ID = per-atom vector calculated by a compute with ID
c_ID[N] = Nth column of per-atom array calculated by a compute with ID
f_ID = per-atom vector calculated by a fix with ID
@@ -84,7 +89,8 @@ dump 4a all custom 100 dump.myforce.* id type x y vx fx
dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
dump 2 inner cfg 10 dump.snap.*.cfg id type xs ys zs vx vy vz
dump snap all cfg 100 dump.config.*.cfg id type xs ys zs id type c_Stress2
-dump 1 all xtc 1000 file.xtc
+dump 1 all xtc 1000 file.xtc
+dump e_data all custom 100 dump.eff id type x y z spin eradius fx fy fz eforce
Description:
@@ -374,6 +380,12 @@ particle. aspherical particles that can sustain a rotational torque due to interactions with other particles. +The spin, eradius, evel, and eforce attributes are for +particles that represent nuclei and electrons modeled with the +electronic force field (EFF). See atom_style +electron and pair_style eff for more +details. +
The c_ID and c_ID[N] attributes allow per-atom vectors or arrays calculated by a compute to be output. The ID in the attribute should be replaced by the actual ID of the compute that has diff --git a/doc/dump.txt b/doc/dump.txt index 263510ac29..ce63b853df 100644 --- a/doc/dump.txt +++ b/doc/dump.txt @@ -40,6 +40,7 @@ args = list of arguments for a particular style :l radius, omegax, omegay, omegaz, angmomx, angmomy, angmomz, quatw, quati, quatj, quatk, tqx, tqy, tqz, + spin, eradius, evel, eforce, c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre id = atom ID @@ -59,6 +60,10 @@ args = list of arguments for a particular style :l angmomx,angmomy,angmomz = angular momentum of extended particle quatw,quati,quatj,quatk = quaternion components for aspherical particles tqx,tqy,tqz = torque on extended particles + spin = electron spin + eradius = electron radius + evel = electron radial velocity + eforce = electron radial force c_ID = per-atom vector calculated by a compute with ID c_ID\[N\] = Nth column of per-atom array calculated by a compute with ID f_ID = per-atom vector calculated by a fix with ID @@ -74,7 +79,8 @@ dump 4a all custom 100 dump.myforce.* id type x y vx fx dump 4b flow custom 100 dump.%.myforce id type c_myF\[3\] v_ke dump 2 inner cfg 10 dump.snap.*.cfg id type xs ys zs vx vy vz dump snap all cfg 100 dump.config.*.cfg id type xs ys zs id type c_Stress[2] -dump 1 all xtc 1000 file.xtc :pre +dump 1 all xtc 1000 file.xtc +dump e_data all custom 100 dump.eff id type x y z spin eradius fx fy fz eforce :pre [Description:] @@ -364,6 +370,12 @@ The {tqx}, {tqy}, {tqz} attributes are for extended spherical or aspherical particles that can sustain a rotational torque due to interactions with other particles. +The {spin}, {eradius}, {evel}, and {eforce} attributes are for +particles that represent nuclei and electrons modeled with the +electronic force field (EFF). See "atom_style +electron"_atom_style.html and "pair_style eff"_pair_eff.html for more +details. + The {c_ID} and {c_ID\[N\]} attributes allow per-atom vectors or arrays calculated by a "compute"_compute.html to be output. The ID in the attribute should be replaced by the actual ID of the compute that has diff --git a/doc/read_data.html b/doc/read_data.html index 2e3ae89c3c..ef4f22242f 100644 --- a/doc/read_data.html +++ b/doc/read_data.html @@ -280,6 +280,7 @@ of analysis.
The units for these quantities depend on the unit style; see the units command for details. @@ -692,6 +695,7 @@ style dipole or ellipsoid.
| all styles except those listed | atom-ID vx vy vz |
| dipole | atom-ID vx vy vz wx wy wz |
| electron | atom-ID vx vy vz evel |
| ellipsoid | atom-ID vx vy vz lx ly lz |
| granular | atom-ID vx vy vz wx wy wz |
The velocity lines can appear in any order. This section can only be used after an Atoms section. This is because the Atoms section must have assigned a unique atom ID to each atom so that velocities can be assigned to them.
-Vx,vy,vz are in units of velocity. Lx, ly, lz are in -units of angular momentum (distance-velocity-mass). Wx,Wy,Wz are in -units of angular velocity (radians/time). +
Vx, vy, vz, and evel are in units of velocity. Lx, ly, +lz are in units of angular momentum (distance-velocity-mass). Wx, Wy, +Wz are in units of angular velocity (radians/time).
Translational velocities can also be set by the velocity command in the input script. diff --git a/doc/read_data.txt b/doc/read_data.txt index f5aed7c4c8..386a69ebad 100644 --- a/doc/read_data.txt +++ b/doc/read_data.txt @@ -260,6 +260,7 @@ bond: atom-ID molecule-ID atom-type x y z charge: atom-ID atom-type q x y z colloid: atom-ID atom-type x y z dipole: atom-ID atom-type q x y z mux muy muz +electron: atom-ID atom-type spin eradius x y z ellipsoid: atom-ID atom-type x y z quatw quati quatj quatk full: atom-ID molecule-ID atom-type q x y z granular: atom-ID atom-type diameter density x y z @@ -278,7 +279,9 @@ density = density of atom (mass/distance^3 units) volume = volume of atom (distance^3 units) x,y,z = coordinates of atom mux,muy,muz = direction of dipole moment of atom -quatw,quati,quatj,quatk = quaternion components for orientation of atom :ul +quatw,quati,quatj,quatk = quaternion components for orientation of atom +spin = electron spin (+1/-1) +eradius = electron radius :ul The units for these quantities depend on the unit style; see the "units"_units.html command for details. @@ -605,6 +608,7 @@ line syntax: depends on atom style :ul all styles except those listed: atom-ID vx vy vz dipole: atom-ID vx vy vz wx wy wz +electron: atom-ID vx vy vz evel ellipsoid: atom-ID vx vy vz lx ly lz granular: atom-ID vx vy vz wx wy wz :tb(s=:) @@ -612,16 +616,17 @@ where the keywords have these meanings: vx,vy,vz = translational velocity of atom lx,ly,lz = angular momentum of aspherical atom -wx,wy,wz = angular velocity of granular atom :ul +wx,wy,wz = angular velocity of granular atom +evel = electron radial velocity :ul The velocity lines can appear in any order. This section can only be used after an {Atoms} section. This is because the {Atoms} section must have assigned a unique atom ID to each atom so that velocities can be assigned to them. -Vx,vy,vz are in "units"_units.html of velocity. Lx, ly, lz are in -units of angular momentum (distance-velocity-mass). Wx,Wy,Wz are in -units of angular velocity (radians/time). +Vx, vy, vz, and evel are in "units"_units.html of velocity. Lx, ly, +lz are in units of angular momentum (distance-velocity-mass). Wx, Wy, +Wz are in units of angular velocity (radians/time). Translational velocities can also be set by the "velocity"_velocity.html command in the input script. diff --git a/doc/units.html b/doc/units.html index 0f21dbff8d..75d86116db 100644 --- a/doc/units.html +++ b/doc/units.html @@ -15,7 +15,7 @@
units style-
Examples:
@@ -126,14 +126,30 @@ results from a unitless LJ simulation into physical quantities.The units command also sets the timestep size and neighbor skin -distance to default values for each style. For style lj these are -dt = 0.005 tau and skin = 0.3 sigma. For style real these are dt = -1.0 fmsec and skin = 2.0 Angstroms. For style metal these are dt = -0.001 psec and skin = 2.0 Angstroms. For style si these are dt = -1.0e-8 sec and skin = 0.001 meters. For style cgs these are dt = -1.0e-8 sec and skin = 0.1 cm. +
For style electron, these are the units:
+The units command also sets the timestep size and neighbor skin +distance to default values for each style: +
+Restrictions:
This command cannot be used after the simulation box is defined by a diff --git a/doc/units.txt b/doc/units.txt index 119d24f5ca..b3b6650e0c 100644 --- a/doc/units.txt +++ b/doc/units.txt @@ -12,7 +12,7 @@ units command :h3 units style :pre -style = {lj} or {real} or {metal} or {si} or {cgs} :ul +style = {lj} or {real} or {metal} or {si} or {cgs} or {electron} :ul [Examples:] @@ -123,13 +123,29 @@ dipole = statcoul-cm = 10^18 debye electric field = statvolt/cm or dyne/esu density = grams/cm^dim :ul +For style {electron}, these are the units: + +mass = atomic mass units +distance = Bohr +time = femtoseconds +energy = Kcal/mole +velocity = Bohr/atomic time units [1.03275e-15 seconds] +force = Hartrees*Bohr +temperature = degrees K +pressure = Pascals +charge = multiple of electron charge (+1.0 is a proton) +dipole moment = Debye +electric field = volts/cm :ul + The units command also sets the timestep size and neighbor skin -distance to default values for each style. For style {lj} these are -dt = 0.005 tau and skin = 0.3 sigma. For style {real} these are dt = -1.0 fmsec and skin = 2.0 Angstroms. For style {metal} these are dt = -0.001 psec and skin = 2.0 Angstroms. For style {si} these are dt = -1.0e-8 sec and skin = 0.001 meters. For style {cgs} these are dt = -1.0e-8 sec and skin = 0.1 cm. +distance to default values for each style: + +For style {lj} these are dt = 0.005 tau and skin = 0.3 sigma. +For style {real} these are dt = 1.0 fmsec and skin = 2.0 Angstroms. +For style {metal} these are dt = 0.001 psec and skin = 2.0 Angstroms. +For style {si} these are dt = 1.0e-8 sec and skin = 0.001 meters. +For style {cgs} these are dt = 1.0e-8 sec and skin = 0.1 cm. +For style {electron} these are dt = 0.001 fmsec and skin = 2.0 Bohr. :ul [Restrictions:]