`
+
+**Default:** none
+
+
+----------
+
+
+.. _Israilev:
+
+
+
+**(Izrailev)** Izrailev, Stepaniants, Isralewitz, Kosztin, Lu, Molnar,
+Wriggers, Schulten. Computational Molecular Dynamics: Challenges,
+Methods, Ideas, volume 4 of Lecture Notes in Computational Science and
+Engineering, pp. 39-65. Springer-Verlag, Berlin, 1998.
+
+**(Park)**
+Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)
+
+**(Jarzynski)**
+Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Section_commands.html#comm
diff --git a/doc/fix_smd_adjust_dt.html b/doc/fix_smd_adjust_dt.html
new file mode 100644
index 0000000000..c3eeb9930d
--- /dev/null
+++ b/doc/fix_smd_adjust_dt.html
@@ -0,0 +1,240 @@
+
+
+
+
+
+
+ fix smd/adjust_dt command — LAMMPS 15 May 2015 version documentation
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ LAMMPS
+
+
+
+
+
+
+
+
+
+
+
+
fix smd/adjust_dt command
+
+
Syntax
+
fix ID group-ID smd/adjust_dt arg
+
+
+
+ID, group-ID are documented in fix
+smd/adjust_dt = style name of this fix command
+arg = s_fact
+
+
+s_fact = safety factor
+
+
+
+
Examples
+
fix 1 all smd/adjust_dt 0.1
+
+
+
+
+
Description
+
The fix calculates a new stable time increment for use with the SMD time integrators.
+
The stable time increment is based on multiple conditions. For the SPH pair styles, a
+CFL criterion (Courant, Friedrichs & Lewy, 1928) is evaluated, which determines the the speed of
+sound cannot propagate further than a typical spacing between particles within a single time step to ensure
+no information is lost. For the contact pair styles, a linear analysis of the pair potential determines a
+stable maximum time step.
+
This fix inquires the minimum stable time increment across all particles contained in the group for which this
+fix is defined. An additional safety factor s_fact is applied to the time increment.
+
See this PDF guide to use Smooth Mach Dynamics in LAMMPS.
+
+
+
Restart, fix_modify, output, run start/stop, minimize info
+
Currently, no part of USER-SMD supports restarting nor minimization.
+
+
+
Restrictions
+
This fix is part of the USER-SMD package. It is only enabled if
+LAMMPS was built with that package. See the Making LAMMPS
+
+
+
+
+
+
+
+
+
+
+
+
+
fix smd/integrate_tlsph command — LAMMPS 15 May 2015 version documentation
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ LAMMPS
+
+
+
+
+
+
+
+
+
+
+
+
fix smd/integrate_tlsph command
+
+
Syntax
+
fix ID group-ID smd/integrate_tlsph keyword values
+
+
+
+ID, group-ID are documented in fix
+smd/integrate_tlsph = style name of this fix command
+zero or more keyword/value pairs may be appended
+keyword = limit_velocity
+
+
+limit_velocity value = max_vel
+ max_vel = maximum allowed velocity
+
+
+
+
Examples
+
fix 1 all smd/integrate_tlsph
+fix 1 all smd/integrate_tlsph limit_velocity 1000
+
+
+
+
+
Description
+
The fix performs explicit time integration for particles which interact according with the Total-Lagrangian SPH pair style.
+
See this PDF guide to using Smooth Mach Dynamics in LAMMPS.
+
The limit_velocity keyword will control the velocity, scaling the norm of
+the velocity vector to max_vel in case it exceeds this velocity limit.
+
+
+
Restart, fix_modify, output, run start/stop, minimize info
+
Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.
+
+
+
Restrictions
+
This fix is part of the USER-SMD package. It is only enabled if
+LAMMPS was built with that package. See the Making LAMMPS
+
+
+
+
+
+
+
+
+
+
+
+
+
fix smd/integrate_ulsph command — LAMMPS 15 May 2015 version documentation
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ LAMMPS
+
+
+
+
+
+
+
+
+
+
+
+
fix smd/integrate_ulsph command
+
+
Syntax
+
fix ID group-ID smd/integrate_ulsph keyword
+
+
+
+ID, group-ID are documented in fix
+smd/integrate_ulsph = style name of this fix command
+zero or more keyword/value pairs may be appended
+
+
keyword = adjust_radius or limit_velocity
+
+adjust_radius values = adjust_radius_factor min_nn max_nn
+adjust_radius_factor = factor which scale the smooth/kernel radius
+min_nn = minimum number of neighbors
+max_nn = maximum number of neighbors
+limit_velocity values = max_velocity
+max_velocity = maximum allowed velocity.
+
+
+
+
Examples
+
fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50
+
+
+
fix 1 all smd/integrate_ulsph limit_velocity 1000
+
+
+
+
+
Description
+
The fix performs explicit time integration for particles which interact with the updated Lagrangian SPH pair style.
+See this PDF guide to using Smooth Mach Dynamics in LAMMPS.
+
The adjust_radius keyword activates dynamic adjustment of the per-particle SPH smoothing kernel radius such that the number of neighbors per particles remains
+within the interval min_nn to max_nn . The parameter adjust_radius_factor determines the amount of adjustment per timestep. Typical values are
+* * *
+
The limit_velocity keyword will control the velocity, scaling the norm of
+the velocity vector to max_vel in case it exceeds this velocity limit.
+
+
+
Restart, fix_modify, output, run start/stop, minimize info
+
Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.
+
+
+
Restrictions
+
This fix is part of the USER-SMD package. It is only enabled if
+LAMMPS was built with that package. See the Making LAMMPS
+
+
+
+
+
+
+
+
+
+
+
+
+
fix smd/move_tri_surf command — LAMMPS 15 May 2015 version documentation
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ LAMMPS
+
+
+
+
+
+
+
+
+
+
+
+
fix smd/move_tri_surf command
+
+
Syntax
+
fix ID group-ID smd/move_tri_surf keyword
+
+
+
+ID, group-ID are documented in fix
+smd/move_tri_surf keyword = style name of this fix command
+keyword = ** ** **
+
+
**LINEAR* args = Vx Vy Vz
+ Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL
+**WIGGLE* args = Vx Vy Vz max_travel
+ vx,vy,vz = components of velocity vector (velocity units), any component can be specified as NULL
+ max_travel = wiggle amplitude
+**ROTATE* args = Px Py Pz Rx Ry Rz period
+ Px,Py,Pz = origin point of axis of rotation (distance units)
+ Rx,Ry,Rz = axis of rotation vector
+ period = period of rotation (time units)
+
+
+
+
+
Examples
+
fix 1 tool smd/move_tri_surf *LINEAR 20 20 10
+fix 2 tool smd/move_tri_surf *WIGGLE 20 20 10
+fix 2 tool smd/move_tri_surf *ROTATE 0 0 0 5 2 1
+
+
+
+
+
Description
+
This fix applies only to rigid surfaces read from .STL files via fix smd/wall_surface
+
The **
+
The **
+
The **
+
See this PDF guide to using Smooth Mach Dynamics in LAMMPS.
+
+
+
Restart, fix_modify, output, run start/stop, minimize info
+
Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.
+
+
+
Restrictions
+
This fix is part of the USER-SMD package. It is only enabled if
+LAMMPS was built with that package. See the Making LAMMPS
+
+
+
+
+
+
+
+
+
+
+
+
+
fix smd/setvel command — LAMMPS 15 May 2015 version documentation
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ LAMMPS
+
+
+
+
+
+
+
+
+
+
+
+
fix smd/setvel command
+
+
Syntax
+
fix ID group-ID smd/setvel vx vy vz keyword value ...
+
+
+
+ID, group-ID are documented in fix
+smd/setvel = style name of this fix command
+vx,vy,vz = velocity component values
+any of vx,vy,vz can be a variable (see below)
+zero or more keyword/value pairs may be appended to args
+keyword = region
+
+
+region value = region-ID
+ region-ID = ID of region particles must be in to have their velocities set
+
+
+
+
Examples
+
fix top_velocity top_group setvel 1.0 0.0 0.0
+
+
+
+
+
Description
+
Set each component of velocity on each particle in the group to the specified
+values vx,vy,vz, regardless of the forces acting on the particle. This command can
+be used to impose velocity boundary conditions.
+
Any of the vx,vy,vz values can be specified as NULL which means do not
+alter the velocity component in that dimension.
+
This fix is indented to be used together with a time integration fix.
+
Any of the 3 quantities defining the velocity components can be specified
+as an equal-style or atom-style variable vx ,
+vy , vz . If the value is a variable, it should be specified as
+v_name, where name is the variable name. In this case, the variable
+will be evaluated each timestep, and its value used to determine the
+force component.
+
Equal-style variables can specify formulas with various mathematical
+functions, and include thermo_style
+
Atom-style variables can specify the same formulas as equal-style
+variables but can also include per-atom values, such as atom
+coordinates. Thus it is easy to specify a spatially-dependent velocity
+field with optional time-dependence as well.
+
If the region keyword is used, the particle must also be in the
+specified geometric region
+
+
+
+
Restart, fix_modify, output, run start/stop, minimize info
+
Currently, no part of USER-SMD supports restarting nor minimization
+None of the fix_modify
+
This fix computes a global 3-vector of forces, which can be accessed
+by various output commands
+
No parameter of this fix can be used with the start/stop keywords of
+the run
+
+
+
Restrictions
+
This fix is part of the USER-SMD package. It is only enabled if
+LAMMPS was built with that package. See the Making LAMMPS
+
Related commands: none
+
Default: none
+
+
+
+
+
+
+
+
+
+
+
+
<no title> — LAMMPS 15 May 2015 version documentation
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ LAMMPS
+
+
+
+
+
+
+
+
+
fix smd/wall_surface command — LAMMPS 15 May 2015 version documentation
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ LAMMPS
+
+
+
+
+
+
+
+
+
+
+
+
fix smd/wall_surface command
+
+
Syntax
+
fix ID group-ID smd/wall_surface arg type mol-ID
+
+
+
+ID, group-ID are documented in fix
+smd/wall_surface = style name of this fix command
+arg = file
+
+
+file = file name of a triangular mesh in stl format
+
+
+type = particle type to be given to the new particles created by this fix
+mol-ID = molecule-ID to be given to the new particles created by this fix (must be >= 65535)
+
+
+
+
Examples
+
fix stl_surf all smd/wall_surface tool.stl 2 65535
+
+
+
+
+
Description
+
This fix creates reads a traingulated surface from a file in .STL format.
+For each triangle, a new particle is created which stores the barycenter of the triangle and the vertex positions.
+The radius of the new particle is that of the minimum circle which encompasses the triangle vertices.
+
The triangulated surface can be used as a complex rigid wall via the smd/tri_surface smd/move_tri_surf
+
Immediately after a .STL file has been read, the simulation needs to be run for 0 timesteps in order to properly register the new particles
+in the system. See the “funnel_flow” example in the USER-SMD examples directory.
+
See this PDF guide to use Smooth Mach Dynamics in LAMMPS.
+
+
+
Restart, fix_modify, output, run start/stop, minimize info
+
Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.
+
+
+
Restrictions
+
This fix is part of the USER-SMD package. It is only enabled if
+LAMMPS was built with that package. See the Making LAMMPS
+
Within each .STL file, only a single triangulated object must be present, even though the STL format allows for the possibility of multiple objects in one file.
+
+
+
+
+
+
+
+
+
+
+
+
+
compute msd
compute msd/chunk
compute property/atom
compute property/chunk
compute smd/contact_radius
+ compute smd/damage
+ compute smd/hourglass_error
+ compute smd/internal_energy
+ compute smd/plastic_strain
+ compute smd/plastic_strain_rate
+ compute smd/rho
+ compute smd/tlsph_defgrad
+ compute smd/tlsph_dt
+ compute smd/tlsph_num_neighs
+ compute smd/tlsph_shape
+ compute smd/tlsph_strain
+ compute smd/tlsph_strain_rate
+ compute smd/tlsph_stress
+ compute smd/ulsph_num_neighs
+ compute smd/ulsph_strain
+ compute smd/ulsph_strain_rate
+ compute smd/ulsph_stress
+ compute smd/vol
+ compute sna/atom
fix nve/asphere/noforce
fix nve/body
fix nve/limit
fix nve/line
fix smd/adjust_dt
+ fix smd/integrate_tlsph
+ fix smd/integrate_ulsph
+ fix smd/move_tri_surf
+ fix smd/setvel
+ fix smd/wall_surface
+ fix spring
pair_style lj/sdk
pair_style lj/sf
pair_style lj/smooth
pair_style lj/smooth/linear
pair_style smd/hertz
+ pair_style smd/tlsph
+ pair_style smd/tri_surface
+ pair_style smd/ulsph
+ pair_style snap
pair_style smd/hertz command — LAMMPS 15 May 2015 version documentation
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ LAMMPS
+
+
+
+
+
+
+
+
+
+
+
+
pair_style smd/hertz command
+
+
Syntax
+
pair_style smd/hertz scale_factor
+
+
+
+
+
Examples
+
pair_style smd/hertz 1.0
+pair_coeff 1 1 <contact_stiffness>
+
+
+
Description
+
The smd/hertz style calculates contact forces between SPH particles belonging to different physical bodies.
+
The contact forces are calculated using a Hertz potential, which evaluates the overlap between two particles
+(whose spatial extents are defined via its contact radius).
+The effect is that a particles cannot penetrate into each other.
+The parameter <contact_stiffness> has units of pressure and should equal roughly one half
+of the Young’s modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particles.
+
The parameter scale_factor can be used to scale the particles’ contact radii. This can be useful to control how close
+particles can approach each other. Usually, *
+
+
Mixing, shift, table, tail correction, restart, rRESPA info :
+
No mixing is performed automatically.
+Currently, no part of USER-SMD supports restarting nor minimization.
+rRESPA does not apply to this pair style.
+
+
+
+
Restrictions
+
This fix is part of the USER-SMD package. It is only enabled if
+LAMMPS was built with that package. See the Making LAMMPS
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+[Description:]
+
+The {smd/hertz} style calculates contact forces between SPH particles belonging to different physical bodies.
+
+The contact forces are calculated using a Hertz potential, which evaluates the overlap between two particles
+(whose spatial extents are defined via its contact radius).
+The effect is that a particles cannot penetrate into each other.
+The parameter has units of pressure and should equal roughly one half
+of the Young's modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particles.
+
+The parameter {scale_factor} can be used to scale the particles' contact radii. This can be useful to control how close
+particles can approach each other. Usually, {scale_factor}=1.0.
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+No mixing is performed automatically.
+Currently, no part of USER-SMD supports restarting nor minimization.
+rRESPA does not apply to this pair style.
+
+:line
+
+[Restrictions:]
+
+This fix is part of the USER-SMD package. It is only enabled if
+LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
+section for more info.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html
+
+[Default:] none
+
+:line
+
diff --git a/doc/pair_smd_tlsph.html b/doc/pair_smd_tlsph.html
new file mode 100644
index 0000000000..7a32ec3900
--- /dev/null
+++ b/doc/pair_smd_tlsph.html
@@ -0,0 +1,243 @@
+
+
+
+
+
+
+ pair_style smd/tlsph command — LAMMPS 15 May 2015 version documentation
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ LAMMPS
+
+
+
+
+
+
+
+
+
+
+
+
pair_style smd/tlsph command
+
+
Syntax
+
pair_style smd/tlsph args
+
+
+
+
+
Examples
+
pair_style smd/tlsph
+
+
+
Description
+
The smd/tlsph style computes particle interactions according to continuum mechanics constitutive laws and a Total-Lagrangian Smooth-Particle Hydrodynamics algorithm.
+
This pair style is invoked with the following command:
+
pair_style smd/tlsph
+pair_coeff i j *COMMON rho0 E nu Q1 Q2 hg Cp &
+ *END
+
+
+
Here, i and j denote the LAMMPS particle types for which this pair style is
+defined. Note that i and j must be equal, i.e., no tlsph cross interactions
+between different particle types are allowed.
+In contrast to the usual LAMMPS pair coeff definitions, which are given solely a
+number of floats and integers, the tlsph pair coeff definition is organised using
+keywords. These keywords mark the beginning of different sets of parameters for particle properties,
+material constitutive models, and damage models. The pair coeff line must be terminated with
+the ** & is recommended. A typical
+invocation of the tlsph for a solid body would consist of an equation of state for computing
+the pressure (the diagonal components of the stress tensor), and a material model to compute shear
+stresses (the off-diagonal components of the stress tensor). Damage and failure models can also be added.
+
Please see the SMD user guide for a complete listing of the possible keywords and material models.
+
+
Mixing, shift, table, tail correction, restart, rRESPA info :
+
No mixing is performed automatically.
+Currently, no part of USER-SMD supports restarting nor minimization.
+rRESPA does not apply to this pair style.
+
+
+
+
Restrictions
+
This fix is part of the USER-SMD package. It is only enabled if
+LAMMPS was built with that package. See the Making LAMMPS
+
+
+
+
+
+
+
+
+
+
+
+
+
pair_style smd/tri_surface command — LAMMPS 15 May 2015 version documentation
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ LAMMPS
+
+
+
+
+
+
+
+
+
+
+
+
pair_style smd/tri_surface command
+
+
Syntax
+
pair_style smd/tri_surface scale_factor
+
+
+
+
+
Examples
+
pair_style smd/tri_surface 1.0
+pair_coeff 1 1 <contact_stiffness>
+
+
+
Description
+
The smd/tri_surface style calculates contact forces between SPH particles and a rigid wall boundary defined via the
+smd/wall_surface
+
The contact forces are calculated using a Hertz potential, which evaluates the overlap between a particle
+(whose spatial extents are defined via its contact radius) and the triangle.
+The effect is that a particle cannot penetrate into the triangular surface.
+The parameter <contact_stiffness> has units of pressure and should equal roughly one half
+of the Young’s modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particle
+
The parameter scale_factor can be used to scale the particles’ contact radii. This can be useful to control how close
+particles can approach the triangulated surface. Usually, *
+
+
Mixing, shift, table, tail correction, restart, rRESPA info :
+
No mixing is performed automatically.
+Currently, no part of USER-SMD supports restarting nor minimization.
+rRESPA does not apply to this pair style.
+
+
+
+
Restrictions
+
This fix is part of the USER-SMD package. It is only enabled if
+LAMMPS was built with that package. See the Making LAMMPS
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+[Description:]
+
+The {smd/tri_surface} style calculates contact forces between SPH particles and a rigid wall boundary defined via the
+"smd/wall_surface"_fix_smd_wall_surface.html fix.
+
+The contact forces are calculated using a Hertz potential, which evaluates the overlap between a particle
+(whose spatial extents are defined via its contact radius) and the triangle.
+The effect is that a particle cannot penetrate into the triangular surface.
+The parameter has units of pressure and should equal roughly one half
+of the Young's modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particle
+
+The parameter {scale_factor} can be used to scale the particles' contact radii. This can be useful to control how close
+particles can approach the triangulated surface. Usually, {scale_factor}=1.0.
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+No mixing is performed automatically.
+Currently, no part of USER-SMD supports restarting nor minimization.
+rRESPA does not apply to this pair style.
+
+:line
+
+[Restrictions:]
+
+This fix is part of the USER-SMD package. It is only enabled if
+LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
+section for more info.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html
+
+[Default:] none
+
+:line
+
diff --git a/doc/pair_smd_ulsph.html b/doc/pair_smd_ulsph.html
new file mode 100644
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+ pair_style smd/ulsph command — LAMMPS 15 May 2015 version documentation
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+ LAMMPS
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+
pair_style smd/ulsph command
+
+
Syntax
+
pair_style smd/ulsph args
+
+
+
+these keywords must be given
+
+
keyword = ** ** ** ** ** **
+
+
+
Examples
+
pair_style smd/ulsph * * *
+
+
+
Description
+
The smd/ulsph style computes particle interactions according to continuum mechanics constitutive laws and an updated Lagrangian Smooth-Particle Hydrodynamics algorithm.
+
This pair style is invoked similar to the following command:
+
pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION
+pair_coeff i j *COMMON rho0 c0 Q1 Cp hg &
+ *END
+
+
+
Here, i and j denote the LAMMPS particle types for which this pair style is
+defined. Note that i and j can be different, i.e., ulsph cross interactions
+between different particle types are allowed. However, i –i respectively j –j pair_coeff lines have to preceed a cross interaction.
+In contrast to the usual LAMMPS pair coeff definitions, which are given solely a
+number of floats and integers, the ulsph pair coeff definition is organised using
+keywords. These keywords mark the beginning of different sets of parameters for particle properties,
+material constitutive models, and damage models. The pair coeff line must be terminated with
+the ** & is recommended. A typical
+invocation of the ulsph for a solid body would consist of an equation of state for computing
+the pressure (the diagonal components of the stress tensor), and a material model to compute shear
+stresses (the off-diagonal components of the stress tensor).
+
Note that the use of * *
+
Please see the SMD user guide for a complete listing of the possible keywords and material models.
+
+
Mixing, shift, table, tail correction, restart, rRESPA info :
+
No mixing is performed automatically.
+Currently, no part of USER-SMD supports restarting nor minimization.
+rRESPA does not apply to this pair style.
+
+
+
+
Restrictions
+
This fix is part of the USER-SMD package. It is only enabled if
+LAMMPS was built with that package. See the Making LAMMPS
+
+
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+
vel values = loop dist
loop = all or local or geom , used in dephasing
dist = uniform or gaussian , used in dephasing
-time value = step or clock
- step = simulation runs for N timesteps on each replica (default)
+time value = steps or clock
+ steps = simulation runs for N timesteps on each replica (default)
clock = simulation runs for N timesteps across all replicas
@@ -171,11 +171,11 @@ prd 5000 100 10 10 100 1 54982 min 0.1 0.1 100 200
replicas of a system. One or more replicas can be used. The total
number of steps N to run can be interpreted in one of two ways; see
discussion of the time keyword below.
-PRD is described in this paper
PRD is described in this paper this review paper this review paper N only includes the
dynamics of stages 2 and 3, not the steps taken during dephasing or
the minimization iterations of quenching. The specified N is
interpreted in one of two ways, depending on the time keyword. If
-the time value is step , which is the default, then each replica
+the time value is steps , which is the default, then each replica
runs for N timesteps. If the time value is clock , then the
simulation runs until N aggregate timesteps across all replicas have
elapsed. This aggregate time is the “clock” time defined below, which
@@ -392,7 +392,7 @@ include the “ave” fixes such as
Default
The option defaults are min = 0.1 0.1 40 50, no temp setting, vel =
-geom gaussian, and time = step.
+geom gaussian, and time = steps.
(Voter) Voter, Phys Rev B, 57, 13985 (1998).
(Voter2) Voter, Montalenti, Germann, Annual Review of Materials
diff --git a/doc/read_data.html b/doc/read_data.html
index 01d1b92d48..0ffe97755e 100644
--- a/doc/read_data.html
+++ b/doc/read_data.html
@@ -610,8 +610,8 @@ box the atom is in. These may be important to include for some kinds
of analysis.
-
angle
@@ -653,19 +653,22 @@ of analysis.
peri
atom-ID atom-type volume density x y z
sphere
+smd
+atom-ID atom-type molecule volume mass kernel_radius contact_radius x y z
+sphere
atom-ID atom-type diameter density x y z
template
+template
atom-ID molecule-ID template-index template-atom atom-type x y z
tri
+tri
atom-ID molecule-ID atom-type triangleflag density x y z
wavepacket
+wavepacket
atom-ID atom-type charge spin eradius etag cs_re cs_im x y z
hybrid
+hybrid
atom-ID atom-type x y z sub-style1 sub-style2 ...
@@ -695,6 +698,8 @@ of analysis.
eradius = electron radius (or fixed-core radius)
etag = integer ID of electron that each wavepacket belongs to
cs_re,cs_im = real/imaginary parts of wavepacket coefficients
+kernel_radius = ??? (distance units)
+contact_radius = ??? (distance units)
The units for these quantities depend on the unit style; see the
units
diff --git a/doc/read_data.txt b/doc/read_data.txt
index 2483699664..f3bd1e5f3f 100644
--- a/doc/read_data.txt
+++ b/doc/read_data.txt
@@ -535,6 +535,7 @@ line: atom-ID molecule-ID atom-type lineflag density x y z
meso: atom-ID atom-type rho e cv x y z
molecular: atom-ID molecule-ID atom-type x y z
peri: atom-ID atom-type volume density x y z
+smd: atom-ID atom-type molecule volume mass kernel_radius contact_radius x y z
sphere: atom-ID atom-type diameter density x y z
template: atom-ID molecule-ID template-index template-atom atom-type x y z
tri: atom-ID molecule-ID atom-type triangleflag density x y z
@@ -565,7 +566,9 @@ cv = heat capacity (need units) for SPH particles
spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
eradius = electron radius (or fixed-core radius)
etag = integer ID of electron that each wavepacket belongs to
-cs_re,cs_im = real/imaginary parts of wavepacket coefficients :ul
+cs_re,cs_im = real/imaginary parts of wavepacket coefficients
+kernel_radius = ??? (distance units)
+contact_radius = ??? (distance units) :ul
The units for these quantities depend on the unit style; see the
"units"_units.html command for details.
diff --git a/doc/searchindex.js b/doc/searchindex.js
index d5e26d2199..e390711443 100644
--- a/doc/searchindex.js
+++ b/doc/searchindex.js
@@ -1 +1 @@
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check:[3,6,8,11,12,15,17,39,41,71,91,164,179,184,188,189,190,195,202,205,211,212,269,273,278,286,288,293,301,303,317,326,327,328,329,330,333,354,365,368,384,393,404,418,420,421,423,431,437,440,441],checkf:164,checkqeq:393,checku:164,chem:[6,13,20,21,25,39,40,43,45,46,87,88,112,121,150,151,161,193,198,206,207,214,216,228,229,230,247,248,253,257,260,262,270,274,278,281,282,285,286,287,288,295,304,312,314,318,319,325,328,335,340,344,345,348,349,350,352,353,357,359,360,362,363,369,373,374,377,380,383,384,387,404,411,432,435,437,443],chemic:[9,118,138,143,167,178,179,205,261,266,267,285,319,392,393,400],chemistri:[9,260,261,263,339,357,392,393],chen:290,cheng:348,chenoweth:[392,393],chenoweth_2008:[392,393],chi:[92,133,166,251,261,263,358,360,449],chiefli:391,child:8,chip:[7,12,17,333,436],chipot:193,chiral:312,chmod:[11,12],cho:380,chocol:[7,169],choic:[3,6,12,15,16,18,40,41,54,87,121,123,137,148,164,181,184,185,188,191,194,195,207,213,216,227,229,253,261,270,285,313,319,324,325,328,330,333,364,377,384,388,423,432,433,436,437,442,443,447],choos:[1,3,6,7,8,12,16,17,18,29,39,54,87,117,134,135,168,189,190,191,192,195,202,213,216,227,229,231,232,233,234,235,257,278,282,296,318,319,325,413,418,420,432,438],chose:[408,410],chosen:[2,3,6,12,17,120,144,147,156,164,168,174,179,192,195,202,205,206,214,216,227,229,233,253,256,267,278,282,285,286,291,293,294,300,319,320,325,333,357,361,367,368,371,395,408,418,432,437,443],chri:142,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[66,75,90,93,104,106,114,124,139,141,181],chute:[4,10,208],ciccotti:273,cieplak:[6,150,435],cii:182,cij:182,circular:[3,6,123,165],circumst:18,circumv:265,citat:[],cite:[3,7,8,12,213],cko:2,cl1:143,clarendon:[29,352],clarifi:[7,408,410],clariti:303,clark:387,class2:[],classic:[0,3,5,6,7,8,9,203,253,260,265,290,314,357],classifi:[9,405],claus:421,clean:[6,12,14,15,17,431],cleanli:[422,451],clear:[],clearli:7,clebsch:120,clermont:[9,13],clever:427,click:[2,11,22,37,44,55,144,152,163,168,210,305,313,328,346,405],client:[210,212],climb:[228,328,437],clinic:[7,13],clo:[133,166,449],clock:[12,418,437],clockwis:296,close:[3,6,11,12,13,39,41,67,121,147,167,190,191,192,207,214,216,229,247,270,273,296,299,317,319,322,324,325,328,333,335,339,349,350,380,384,410,427,433,443,445],closer:[3,41,116,142,166,167,188,192,196,287,328],closest:[190,251,270,293,360,394,404,413],cloud:443,clovertown:18,clsuter:72,clump1:[255,270],clump2:[255,270],clump3:[255,270],clump:270,cluster:[],clutter:[3,9],cmap:423,cmatrix:207,cmax:380,cmd:[11,12,253,434],cmin:380,cmm:[],cn1:182,cn2:182,cna:[],cnn:182,cnr:[9,13],cnt:[364,427],co2:[40,143,273,327],coars:[7,9,29,36,40,54,156,255,270,278,362,395,435],coarser:[319,448],coarsest:120,code:[],coeff:[3,7,8,12,21,22,33,44,50,150,151,152,157,304,305,310,346,364,368,384,397,423,425],coeffcient:423,coeffici:[],coefficienct:353,coefficient0:355,coefficient1:355,coeffieci:[6,337],coeffincientn:355,coexist:[9,205,357],cohes:[6,358,380],coincid:[205,299,344,378,379,418],cold:[6,129,209,329,443],coldest:286,coleman8:9,coleman:[9,118,143,271],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,93,98,104,106,114,124,132,139,141,144,167,169,181,193,219,225,255,265,268,270,301,318,327,329,347,367,423,430,436,452],collid:[199,278,300],colliex:143,collinear:[3,255],collis:[3,216,278,296,300,354,361,416],colllis:278,colloid:[],colombo:39,colon:[170,301,424],color1:169,color2:169,color:[3,9,41,167,168,169,188,206,260,265],column:[3,6,9,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,104,106,108,110,113,114,115,116,117,119,120,121,124,132,139,141,142,143,164,167,169,172,180,181,182,183,184,185,186,219,226,227,260,270,279,280,290,300,359,363,392,393,424,438,440,448],colvar:[],colvarmodul:12,com:[],comamnd:194,comand:[191,425],comannd:333,comb3:[],comb:[],comb_1:262,comb_2:262,combiant:350,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,92,108,115,123,137,167,168,178,183,210,219,229,253,259,282,291,299,302,304,318,319,321,325,333,347,349,350,357,358,364,376,377,396,406,408,410,415,426,431,443,448],come:[],comfort:[12,13],comm:[0,3,12,61,73,210,212,213,319,328,333,353,384,389,407],comm_modifi:[],comm_styl:[],command:[],comment:[2,7,11,12,38,56,150,164,167,214,270,290,327,328,334,355,356,358,368,380,386,393,396,406,407,408,409,410,420,421,423,443,448],commerci:7,commmand:[3,6,12,59,107,248,417,418,420,437,451],common:[],commonli:[3,6,12,17,25,57,59,105,146,167,168,170,314,362,371,396,408,410,423,426,435],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,147,148,168,169,188,189,190,192,193,194,210,212,216,218,219,220,229,252,259,261,262,263,270,278,290,301,318,329,330,331,333,354,388,420,421,425,432,433,450,452],communc:318,comp:[7,212,213,273,319,328,357,384,389,394,403,407,409],compact:[63,172,346,405],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,110,118,127,142,143,152,163,169,198,261,301,303,318,319,326,328,380,418,437,438,443,447],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,151,152,163,304,305,313,345,405],compat:[3,5,7,8,9,11,12,13,17,18,41,71,117,119,155,167,170,174,180,181,182,183,184,185,186,188,252,264,282,285,292,295,298,318,333,365,384,407,420,421,448],compens:[6,189,190,268,329,357],compet:289,competit:319,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,142,167,168,170,210,289,319,333,423,424,428],compl:17,complain:[12,17],complement:380,complementari:[7,349,369],complet:[3,6,9,12,15,41,59,71,169,184,188,193,219,253,256,259,278,289,291,303,317,328,333,358,412,418,423,428,431,435,437,440,443,448],complex:[6,8,11,12,13,25,40,42,62,120,132,144,145,216,299,316,328,357,407,421,423,426,448],compli:[285,289],complic:[6,7,9,12,13,179,205,421],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,93,94,97,104,105,106,107,108,109,110,112,113,117,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,136,137,139,140,141,167,168,169,175,176,180,181,182,183,184,185,186,187,191,192,194,195,200,203,208,212,213,216,219,221,225,226,228,229,230,233,234,235,246,247,249,250,252,253,254,257,268,270,272,273,274,275,278,281,282,283,285,292,293,298,299,300,318,321,325,326,327,328,333,353,357,361,378,379,396,423,424,433,441,448,449],componenet:6,composit:[6,179,216,355],compound:[348,357,358],compres:[71,114,181],compress:[3,6,59,71,114,147,167,168,169,181,194,227,233,257,260],compris:[40,299,367,394,412],compton:[118,143],comptu:[3,6],compuat:319,comput:[],computation:[3,6,189,190,290,339],computational:443,compute_arrai:8,compute_fep:[174,377],compute_group_group:205,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[118,271],compute_scalar:8,compute_temp:8,compute_ti:174,compute_vector:8,compute_xrd:143,concaten:[2,3,451],concav:299,concentr:355,concept:[6,124,134,181,432],conceptu:[3,6,71,132,192,194,328,349,364,380,428],concern:[6,73,87,206],concis:[11,289],conclud:12,concret:8,concurr:[9,16,319],conden:[290,408,410],condens:[6,126,290,335,351,355,369],condit:[],conducit:6,conduct:[],cone:426,confid:[3,437],config:[12,167,420],configfil:193,configur:[1,6,12,15,17,38,59,146,164,166,167,168,172,192,193,194,195,199,205,212,213,241,253,261,289,316,326,328,335,339,356,380,406,408,410,418,423,425,426,437],confin:[423,437],conflict:[3,40,384,421],conform:[3,6,13,59,191,192,228,269,274,289,312,328,357,435],confus:3,conjuct:353,conjug:[7,8,213,325,357,392,393],conjunct:[6,7,71,86,87,114,127,132,138,144,148,169,173,174,213,216,220,241,256,257,261,262,263,265,270,278,286,293,298,318,319,328,340,342,346,349,353,357,363,369,384,387,395,411,423,426,430,443,452],connect:[3,6,87,129,147,191,210,255,270,273,275,328,350,361,404,410,420,421,427,443],conput:3,consecut:[3,11,12,39,71,144,169,173,174,195,210,211,349,369,373,418,424,426],consequ:[1,6,290,368,437],conserv:[3,172,179,191,198,199,206,209,213,215,216,220,225,227,229,241,270,273,281,282,286,293,294,298,328,352,353,361,375,432,437],consid:[6,9,70,71,78,87,115,129,130,147,167,169,173,174,180,182,184,188,190,191,195,217,230,252,270,285,286,289,290,293,319,346,357,364,393,394,404,418,419,421,424,425,426,428,431,433,441,443,448],consider:[6,8,213,214,281,282,283,333,432],consist:[3,6,8,9,11,12,40,42,65,69,79,92,104,108,111,112,115,124,127,129,144,156,166,170,175,176,181,194,195,198,200,203,206,213,214,215,226,229,231,232,233,234,235,236,237,239,240,241,242,244,245,246,247,248,249,257,260,265,267,269,270,281,282,283,284,294,318,319,321,327,328,333,335,339,341,347,349,357,360,364,378,379,380,384,394,407,413,421,423,424,426,427,428,435,443,448],consistent_fe_initi:178,consit:270,constant:[],constitu:[3,6,219,270,295,299,347,394],constrain:[3,6,8,122,123,124,125,127,130,131,132,133,134,136,137,172,181,195,205,206,211,219,223,255,256,268,270,273,276,286,293,326,327,357,428,435,443],constraint:[],construct:[6,8,14,38,54,56,61,64,67,70,72,73,77,118,120,143,192,229,252,269,299,329,333,352,384,404,406,407,426,427,448],constructor:8,consult:393,consum:[1,265,388,448],consumpt:316,contact:[],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,116,118,120,124,132,142,143,144,146,150,152,163,164,167,168,169,170,172,173,174,178,180,181,182,183,184,185,186,188,193,195,200,207,211,212,213,214,216,227,241,251,252,255,256,258,260,263,267,270,271,278,285,289,290,299,300,303,317,319,327,328,331,332,334,335,336,339,348,349,352,355,356,357,364,365,380,386,390,391,392,393,396,406,407,408,409,410,411,418,419,420,421,423,424,425,426,428,430,432,435,437,440,441,443,448,450,452],content:[12,18,393,439,441],context:[3,6,8,12,17,117,169,189,190,195,255,267,294,325,415,423,430,439,447,448,449],contibut:70,contigu:420,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,103,104,140,169,172,173,174,179,181,182,183,184,185,186,188,191,192,193,194,195,205,206,207,209,210,211,213,214,215,221,226,227,229,231,232,233,234,235,246,247,248,249,254,256,259,260,270,271,274,277,278,280,287,288,290,296,299,303,317,332,333,339,353,354,371,374,392,393,394,409,418,421,423,425,426,431,437,440,441,448,450],continuum:[6,7,9,178,290],contour_integr:178,contract:[59,192,194,229,257,270],contradictori:3,contrain:273,contraint:241,contrari:[207,214],contrast:[1,6,42,55,64,129,194,301,415,451],contrib:290,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,93,102,104,106,107,108,109,110,112,114,117,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,174,179,180,181,182,183,184,185,186,192,205,213,216,219,220,224,230,247,248,255,256,264,267,270,271,273,292,318,326,328,336,353,354,355,357,364,378,379,384,392,393,435,441,443],contributor:12,control:[3,5,6,7,8,11,13,16,27,29,41,87,91,120,153,167,168,172,178,179,188,192,193,194,209,210,213,214,229,231,232,233,234,235,257,262,270,281,282,283,290,294,316,318,330,357,360,392,393,406,410,418,420,432,438,439],control_typ:178,controlfil:393,convect:91,conveni:[6,12,29,167,170,186,271,321,396,448],convent:[3,8,9,29,155,162,163,169,269,275,302,355,357,448],converg:[3,6,41,88,167,168,170,175,188,191,192,200,203,233,260,262,265,269,273,324,325,326,328,348,349,369,418,430,437],convers:[3,8,120,168,169,179,182,257,318,349,350,351,357,369,373,377,387,421,437,447],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,144,151,167,168,169,186,227,301,304,306,309,312,321,328,334,355,408,410,416,421,423,424,425,430,440,443,447,448,450,452],convex:299,convinc:[7,12],cooki:7,cool:[7,134,209,268],cooordin:167,cooper:[5,7],coord123:114,coord1:[3,114,181,184,185],coord2:[3,114,181,184,185],coord3:[3,114,181,184,185],coord:[],coordiat:326,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,93,103,104,106,113,114,116,120,127,133,139,141,142,144,148,166,167,168,169,170,172,175,180,181,183,184,185,188,189,190,191,192,193,194,195,198,200,201,203,205,208,209,210,211,212,213,214,226,228,229,231,232,234,235,247,250,251,252,255,256,257,267,268,270,272,273,274,275,276,277,278,280,288,289,290,297,298,300,301,321,326,327,328,333,334,335,338,356,418,423,424,426,428,431,433,437,443,448,449],coordn:[114,181],coorind:104,copi:[0,3,4,8,11,12,15,17,40,119,168,290,328,346,392,421],copper:416,coproccesor:16,coprocessor:[1,4,7,9,16,17,333,436],coproprocessor:17,copy_arrai:8,copyright:[7,8,255],coral:169,core:[],core_shel:126,coreshel:[6,9,342,349,351],cornel:[6,150,435],corner123i:113,corner123x:113,corner123z:113,corner1i:113,corner1x:113,corner1z:113,corner2i:113,corner2x:113,corner2z:113,corner3i:113,corner3x:113,corner3z:113,corner:[3,6,40,113,168,299,300,321,412,423],cornflowerblu:169,cornsilk:169,corpor:16,corr:348,correct:[3,6,9,11,12,16,17,59,87,88,102,110,116,126,131,138,168,194,207,213,229,230,247,255,257,260,289,295,299,318,328,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,351,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,414,415,416,423,438,441,443],correction_max_iter:178,correctli:[3,8,9,11,17,71,81,102,103,122,123,125,127,129,130,131,132,133,136,137,140,167,169,175,195,200,203,214,223,229,230,263,270,273,275,277,296,299,328,329,333,351,379,420,421,423,447,449],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,96,97,109,112,113,114,115,118,119,120,122,123,131,138,143,150,151,152,153,154,155,156,158,159,161,162,164,167,168,169,173,174,175,181,183,184,185,187,190,192,194,201,203,204,208,213,216,217,225,226,227,229,231,232,233,234,235,236,241,244,246,247,249,252,253,257,262,270,272,273,281,283,285,294,295,296,298,299,300,302,304,305,306,307,308,309,312,314,319,323,325,327,328,334,335,337,340,341,342,343,344,345,346,347,348,349,352,353,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,380,381,384,385,386,387,389,390,392,393,394,395,396,397,406,407,408,409,410,412,414,415,416,418,420,421,423,424,426,436,437,438,440,441,443,448],correspondingli:[378,379,432],cosin:[],cosineshift:27,cosmo:[207,212],cossq:[],cost:[1,6,10,11,12,17,39,41,71,109,118,121,143,168,169,181,184,185,188,189,190,202,229,262,290,318,319,331,349,369,373,384,406,420,432],costheta0:[406,408,410],costheta:390,costli:[11,88,207,329],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,93,104,106,109,112,114,124,134,139,141,157,167,168,169,173,174,179,181,182,184,188,194,203,212,259,260,261,265,268,270,272,278,279,285,289,290,291,295,299,301,303,310,315,317,324,326,329,333,336,359,363,364,392,393,419,420,421,423,425,427,430,431,439,443,448,449],coulomb:[3,5,6,7,8,9,10,12,14,15,18,88,107,108,121,145,149,261,263,291,318,319,326,333,340,342,343,344,345,348,349,350,351,352,357,361,362,364,369,373,377,384,387,392,393,395,405,410,411,415,428,435,441,443,447],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,41,63,68,77,91,114,116,117,132,142,148,175,176,179,181,183,184,185,187,188,195,200,202,205,211,229,241,256,273,281,282,299,319,326,327,328,330,333,359,363,384,441,448],counter:[296,418,429,431,437],counterbal:209,counterpart:[167,270,418],counterproduct:18,coupl:[],cours:[3,8,138,167,173,174,206,269,275,289,295,297,298,300,301,319,378,397,420,423,436,443,448,450],coval:[6,29,357,380,443],covari:207,cover:[6,71,164,169,178,216,357,367,412],coverag:[71,184],cpc:212,cpp:[1,3,6,8,9,11,12,13,87,167,173,174,203,273],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,169,172,198,214,291,316,319,333,346,405,418,436,437,440,441],cpuremain:441,cr2:143,cr3:143,crack:[4,329],crada:[5,7],crai:[5,7,13,18,167],crash:[3,329,443],craympi:333,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:178,create_faceset:178,create_nodeset:178,createatom:[],creation:[],crimson:169,critchlei:255,criteria:[3,116,145,168,169,189,190,191,224,326,389,412,425,428,448],criterion:[41,142,144,147,179,188,191,205,241,262,296,301,326,328,348,357,361,428,437,438],criterioni:437,critic:[48,49,227,285,290,326],cross:[3,12,22,71,89,123,152,167,168,180,184,190,194,226,228,247,270,275,277,286,293,305,321,328,344,353,354,355,362,363,364,369,371,373,390,395,408,410,423,427,433,450],crossov:1,crossterm:423,crozier:[0,7,13],crucial:260,crystal:[4,6,13,73,251,252,288,329,427,441,443],crystallin:[6,252,321,409,443],crystallis:285,crystallogr:[118,143],crystallograph:[321,441],crystallographi:[118,143,321],cs1:143,cs_chunk:6,cs_im:[40,423],cs_re:[40,423],csanyi:[120,391,396],cscl:380,csequ:6,csh:[11,12,346],cshrc:[11,12],csic:[356,406,408,410],csinfo:6,csisi:[356,406,408,410],csld:[],cst:355,cstherm:6,cstyle:420,csvr:[],ctcm:[334,355],ctemp_cor:198,cterm:274,ctr:9,ctype:11,cu1:143,cu2:143,cu3au:380,cube:[6,41,142,147,188,198,299,321,443],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:339,cummul:[3,6,186,189,190,191,193,202,207,213,215,278,281,282,283,284,286,293,363,441],cumul:[6,179,181,183,184,185,199,205,213,227,229,233,241,270,271,328],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,102,108,116,117,121,124,132,140,142,145,148,167,168,169,170,173,174,178,179,181,184,185,186,188,189,190,191,192,193,194,195,199,200,203,205,207,210,211,213,219,226,229,230,234,235,241,246,247,249,255,261,262,264,267,268,269,270,273,274,276,277,278,281,282,283,289,290,293,294,295,296,297,298,300,301,303,316,317,318,319,322,323,325,326,327,328,333,339,346,348,352,355,357,358,361,365,368,378,379,380,381,382,384,390,392,393,397,408,410,411,413,418,419,420,421,423,424,425,426,427,429,430,431,433,435,437,438,440,441,448,449,450,451,452],curv:[6,144,205,252],curvatur:[360,394,416],custom:[],cut0:421,cut1:432,cut2:432,cut:[],cuthi:[251,263],cutinn:[341,378,379],cutlo:[251,263],cutmax:390,cutoff1:[345,352,369,373,377,387,395],cutoff2:[340,342,343,345,351,352,369,373,377,387,395],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,108,115,116,120,142,145,147,190,191,196,251,260,261,263,265,267,270,278,291,295,299,301,318,319,326,329,330,331,333,334,335,336,337,338,339,340,341,342,343,344,345,347,349,350,351,352,353,354,355,356,357,358,359,360,362,363,364,365,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,392,393,394,395,396,397,398,399,400,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,421,425,428,432,443],cutoffa:356,cutoffc:356,cuu3:355,cval:143,cvd:285,cvel:274,cvff:[],cwiggl:[3,226,295,298,300,448],cyan:[2,168,169],cycl:[3,205,227,229,230,233],cyclic:[3,164],cygwin:12,cylind:[3,4,168,211,256,296,299,426],cylindr:[6,211,275,296],cypress:333,cyrot:339,cyrstal:252,d3q15:216,d3q19:216,d_double_doubl:15,d_e:290,d_flag2:259,d_flag:259,d_name:[113,167,259,280,433],d_single_doubl:15,d_single_singl:15,d_sx:259,d_sy:259,d_sz:259,daan:288,dai:12,daili:12,daivi:247,damag:[],dammak:265,damp:[3,6,172,177,213,214,215,220,229,230,233,257,260,265,270,281,282,294,296,297,325,326,328,340,342,344,349,352,357,361,369,377,387,395,405,411,437,443],damp_com:214,damp_drud:214,dampen:[270,443],dampflag:[296,361],dan:17,danger:[3,12,205,301,353,441],dangl:147,daniel:9,darden:[319,352],darkblu:169,darkcyan:169,darken:168,darkgoldenrod:169,darkgrai:169,darkgreen:169,darkkhaki:169,darkmagenta:169,darkolivegreen:169,darkorang:169,darkorchid:169,darkr:169,darksalmon:169,darkseagreen:169,darkslateblu:169,darkslategrai:169,darkturquois:169,darkviolet:169,dasgupta:261,dash:[361,440],dat:[6,91,164,178,419],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,271],dataset:271,datatyp:3,date:[0,6,12,13,392,393,448],datom1:115,datom2:115,datom3:115,datom4:115,datum:[3,6,42,65,68,69,79,92,108,115,167,182],davi:295,david:[9,19,318,319,408,410],daw:[355,390],dbg:14,dcd:[3,6,7,167,168,169,170,253,424,428],ddim:166,deactiv:377,dealt:212,debug:[6,7,11,12,13,14,17,118,143,144,253,258,316,318,333,365,384,413,421,422,425,430,433,440,448],deby:[],decai:[349,416],decid:[3,6,12,16,71,226,259,270,291,438],decipher:321,declin:278,decod:168,decompos:[87,396],decomposit:[3,5,7,18,62,178,253],decoupl:[6,443],decreas:[3,167,175,176,191,194,200,203,213,289,318],decrement:274,deepli:315,deeppink:169,deepskyblu:169,def:[12,13,421],defaul:61,defect:[6,70,142],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,150,151,152,153,154,155,156,158,159,161,162,163,164,165,166,167,168,169,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,198,199,200,203,204,205,208,211,212,213,214,215,216,224,226,228,229,230,231,232,233,234,235,237,238,239,242,244,245,246,247,248,249,251,252,253,255,256,257,259,261,263,268,270,271,272,273,276,278,280,281,282,283,284,286,287,288,290,292,293,295,296,297,298,299,300,301,303,304,305,306,307,308,309,312,313,314,316,318,319,321,323,325,326,327,328,329,330,331,332,333,335,336,337,338,340,341,342,343,344,345,346,347,349,350,352,353,354,356,357,359,360,361,362,363,364,365,367,369,370,371,372,373,374,375,376,377,378,379,383,384,385,386,387,389,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,420,421,423,424,426,427,428,429,432,433,434,435,437,438,440,441,443,444,445,446,447,448,449],definit:[2,3,6,8,12,13,78,80,116,120,169,181,182,183,184,185,186,194,211,233,271,280,292,295,298,300,302,313,316,327,336,339,347,357,367,390,396,412,421,423,425,432,434,447,448],defint:441,deform:[],deg2theta:143,deg:443,degener:[3,255],degrad:[8,18,252,319,432],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,94,96,97,99,101,102,112,122,123,124,125,126,127,128,129,130,131,132,133,134,136,137,143,144,150,151,154,155,162,164,166,168,181,191,198,205,207,208,213,214,219,229,230,233,234,235,246,247,249,253,255,269,270,273,281,282,283,288,304,306,309,312,314,326,352,355,363,433,441,443,449],degress:[124,181],del:437,delai:[3,6,12,329,354,441],deleg:364,delet:[2,3,7,8,12,54,57,60,63,142,147,148,172,181,182,183,184,185,186,189,191,202,205,229,271,281,282,301,303,317,327,329,332,384,423,424,426,434,435,440,444,446,448,449],delete_atom:[],delete_bond:[],delete_el:178,deli:166,delimit:[421,448],deloc:[230,357],delr:380,delt_lo:437,delta:[],delta_1:339,delta_3:339,delta_7:339,delta_conf:3,delta_ij:[380,390],delta_mu:[3,179],delta_pi:339,delta_r:390,delta_sigma:339,delx:166,delz:166,demand:265,demo:11,demon:250,demonstr:[260,380],den:256,dendrim:363,denniston:[9,216,218,219,220,252],denomin:[7,149],denot:[118,198,214,252,263,265,349,362,364,393],dens:[71,191,357],densiti:[3,6,7,9,18,40,41,59,100,116,120,130,142,144,173,174,178,181,184,185,188,194,203,216,219,222,223,252,256,257,261,290,295,321,323,327,334,339,355,380,381,382,390,394,399,401,402,403,423,432,433,441,447],depart:[0,7],departur:[227,260],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,108,109,112,113,114,115,119,120,122,127,131,132,138,144,145,150,151,152,153,154,155,156,158,159,161,162,163,164,166,167,168,169,172,173,174,175,176,179,181,183,184,186,187,188,190,192,200,201,204,207,208,209,211,213,214,216,218,219,226,229,231,232,233,234,235,236,244,246,247,249,251,262,265,267,270,272,273,278,281,282,283,285,287,289,290,292,294,295,298,299,300,301,303,304,305,306,307,308,309,312,314,319,321,326,327,329,330,331,333,334,335,337,338,339,340,341,342,343,344,345,346,347,348,349,350,352,353,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,380,381,383,385,386,387,389,390,392,393,394,395,396,397,405,406,407,408,409,410,411,412,414,415,416,418,420,423,425,426,429,433,435,437,440,441,442,448,449],dependend:6,depflag:12,dephas:[418,437],depos:195,deposit:[],deprec:261,depth:[51,123,168,290,360,394],dequidt:9,der:[87,107,347,348,377,392,393,415,443],deriv:[6,7,8,38,56,63,87,120,138,164,182,192,194,205,213,226,229,231,232,233,234,235,251,257,261,265,287,288,290,295,296,299,325,327,335,339,347,352,357,358,362,371,375,376,380,392,393,405,407,415,443],derjagin:415,derlet:251,descend:169,descent:[7,325],descib:[40,261],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,110,113,116,118,120,121,123,124,128,129,132,135,137,138,142,143,144,146,147,156,161,164,167,172,173,174,181,182,183,184,185,186,188,191,192,193,194,195,197,198,206,207,210,211,212,213,214,215,216,218,219,220,224,228,229,230,233,240,248,251,253,258,259,260,261,262,263,270,274,275,278,279,280,281,282,283,284,285,286,287,288,293,295,296,298,303,318,319,321,324,325,326,327,328,332,335,336,338,340,341,342,344,345,346,347,348,349,352,355,357,358,360,361,362,364,369,370,371,372,373,374,375,376,377,378,379,380,383,389,390,391,392,393,394,395,396,397,404,405,406,407,408,409,410,411,414,415,416,418,420,421,423,424,426,427,433,436,437,440,448,449,450],descript:[],descriptor:[120,167,365],deserno:319,design:[0,3,6,7,8,11,13,14,15,17,118,126,129,143,178,191,197,198,229,230,251,252,271,285,290,336,337,338,341,344,349,351,357,377,378,379,381,382,390,393,407,432],desir:[2,3,6,7,11,12,14,15,16,18,33,40,50,59,71,88,91,112,117,121,126,144,157,166,179,192,194,203,205,206,213,214,215,219,229,247,255,256,257,258,261,265,270,273,278,281,282,283,284,289,296,310,315,318,319,321,324,326,327,328,353,355,363,378,379,406,408,410,419,420,421,423,427,432,437,438,440,441,448,449,450],desk:7,desktop:[4,6,7,10,12,17,168],despit:443,destabil:339,destre:312,destroi:[11,39,189,190],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,93,102,104,106,107,109,111,112,114,117,119,120,121,122,123,124,127,137,138,139,141,144,145,148,149,152,163,167,168,169,172,173,174,178,181,182,183,184,186,188,190,191,192,193,194,195,203,205,206,207,208,210,211,213,215,216,220,226,227,228,229,230,231,232,233,234,235,239,241,246,247,248,249,252,255,256,257,259,260,262,263,264,270,273,278,281,282,283,284,285,286,288,289,290,291,292,293,294,301,303,305,313,318,319,322,326,327,329,330,333,334,335,336,338,339,341,343,344,345,346,347,348,349,352,353,357,358,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,379,380,383,384,389,392,393,394,396,397,405,412,414,415,421,423,424,425,426,428,429,432,433,435,438,441,448,449,452],detect:[2,3,12,61,63,86,204,256,289,328,348,363,368,418,420,423,434,437,448],determ:333,determin:[1,3,6,8,12,15,39,40,42,51,57,58,59,61,62,68,71,87,102,107,109,112,118,119,121,132,133,142,143,144,166,167,168,169,170,171,175,176,177,180,181,182,183,184,185,186,187,188,192,194,195,198,200,205,208,209,211,213,214,219,224,226,227,229,234,235,246,247,249,251,253,257,260,267,268,269,270,271,272,278,281,282,283,285,291,292,295,296,297,298,299,300,301,313,318,319,321,327,329,330,333,335,336,343,348,352,354,355,359,361,364,365,373,380,384,393,394,404,407,411,415,420,423,424,426,428,430,433,437,439,440,447,448,449],detil:108,devan:[9,395],devanathan:410,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,210,233,255,260,261,264,335,339,357,382,425],devemi:9,deviat:[227,233,251,359],devic:[1,3,12,15,17,210,333],device_typ:333,devin:[262,348],devis:382,dfactor:168,dff:443,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,319],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,264],dhi:[59,166,194,256],dhug:[227,260],dhugoniot:[227,260],dia:380,diagnost:[],diagon:[3,6,83,120,121,192,229,257,270,293],diagonalstyl:396,diagram:[41,118,143,163,188,253],diallo:363,diam:[168,169,256,327],diamet:[3,6,40,113,144,167,168,169,173,174,213,256,270,278,294,296,327,347,360,361,367,371,394,412,415,423,424,433],diamond:[321,357,380],diamter:[40,256],dick:6,dicsuss:226,dictat:[179,227],did:[3,12,326,353,354,355,361,384,408,410,431],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,140,292,318],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,94,96,97,120,122,123,124,125,127,130,131,132,133,134,136,137,138,144,145,147,152,163,164,166,167,168,169,172,174,177,179,181,183,188,189,190,191,192,193,194,198,204,205,206,207,208,209,210,213,214,216,226,229,230,231,232,234,235,237,239,242,244,245,246,249,251,253,255,257,260,261,262,265,268,270,273,274,275,276,278,281,282,283,286,287,288,290,293,294,295,296,299,303,304,313,315,317,318,319,321,322,324,325,327,328,330,331,332,333,334,335,339,343,344,346,347,348,353,355,357,360,361,362,364,367,369,370,372,373,380,381,382,383,384,386,390,392,393,394,395,396,397,405,406,407,408,410,412,415,416,417,418,420,421,423,425,426,427,428,431,432,433,435,437,438,440,441,443,447,448,449,450],differenti:[1,3,6,29,164,318,349,390,409],difficult:[192,253,333,363,432],difficulti:[273,392],diffract:[],diffus:[],digit:[2,3,169,303],dih_table1:164,dih_table2:164,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:190,dihydrid:357,dij:273,dilat:[],dim1:3,dim2:3,dim:[3,59,71,122,125,126,127,130,131,132,133,134,136,144,166,184,194,211,296,321,380,426,447,448,449],dimdim:448,dimems:252,dimens:[],dimension:[3,39,112,118,120,122,124,125,126,127,130,131,132,133,134,136,143,165,181,184,228,252,290,321,324,328,390,423,433],dimensionless:[105,120,290,319,396,415],dimer:[6,270,380],dimgrai:169,dimstr:[41,188],dinola:[257,281],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,167,280,443],dir1:434,dir2:434,dir:[1,3,4,8,11,12,227,251,260,277,390,392,393,421,434,448],dirac:120,direc:390,direct:[],directli:[3,6,8,9,11,12,87,113,120,167,168,175,200,207,211,216,252,271,282,294,296,297,298,299,321,325,333,334,335,340,342,343,349,352,355,357,369,373,384,387,395,404,421,433,434,435,441,448],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,60,170,193,212,255,261,264,278,287,288,328,332,334,335,339,346,348,349,355,356,358,365,366,377,380,381,382,386,390,391,392,393,396,406,408,409,410,421,423,424,425,434,448],disabl:[3,12,16,290,368,421,436],disadvantag:[6,188],disallow:[194,229],disappear:425,discard:[2,3,41,71,184,188,291,299,420,425,426],discontinu:[9,164,326,375],discourag:380,discov:[13,291],discret:[6,8,40,42,168,169,213,216],discuss:[],disk:[6,84,85,137,165,195,205,256,421],disloc:70,disord:[39,70],disp:[],dispar:394,disperion:[352,373],dispers:[3,6,7,9,142,252,318,319,343,352,373,378,384,393,407],displac:[],displace_atom:[],displace_box:59,displacemet:426,displai:[11,13,22,37,44,55,152,163,167,168,305,313,346,405],dispters:3,dissip:[6,206,213,252,287,288,341,353,361,378,379,405],dissolut:189,dist:[6,69,91,108,117,167,253,269,354,404,418,449],distanc:[3,6,7,9,12,20,21,29,39,43,45,46,47,48,49,51,53,54,55,56,58,59,61,63,64,66,69,71,72,73,74,75,76,77,81,86,89,90,93,103,104,105,106,108,114,115,116,117,118,120,133,139,142,144,145,146,147,151,166,167,168,169,177,181,184,185,189,190,191,192,194,195,196,199,205,211,216,226,227,228,229,233,241,251,252,256,260,261,268,269,270,273,274,275,276,277,278,285,286,288,289,290,293,295,296,297,298,299,300,304,318,319,321,324,326,328,329,330,333,336,337,338,339,340,341,342,343,344,345,347,349,350,351,352,353,354,355,356,357,359,360,361,362,363,367,368,369,370,371,372,373,374,375,376,377,378,379,380,383,384,385,386,387,388,389,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,421,423,426,432,433,437,441,443,447,449],distinct:[6,198,267,318,394],distinguish:[6,86,120,219,357],distort:334,distrbut:334,distribut:[],distro:[111,346,389,390],ditto:[8,11,12,14,15,16,17,18,115,190,421],div:8,divd:117,diverg:[3,12,39,270,288,425,443,450],divid:[3,6,16,41,91,112,117,121,141,142,152,163,169,181,182,183,188,194,251,286,293,298,318,326,328,358,393,432,440,448],divis:[6,216,339,367,377,420,423,441,448],dl_poli:7,dlambda:138,dlammps_async_imd:210,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,168],dlammps_gzip:[3,12,167,168,289,423,424,428],dlammps_jpeg:[3,12,168],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,168],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,167],dlen:433,dlmp_intel_offload:[12,16],dlo:[59,166,194,256],dlvo:[7,347,415],dm_lb:216,dmax:[278,324],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,93,102,104,105,106,107,109,111,112,114,117,119,121,123,124,137,139,141,144,145,146,152,163,167,168,169,170,172,173,174,179,180,181,182,183,184,185,186,195,205,213,214,224,229,230,234,235,239,246,247,248,249,256,259,270,275,278,281,282,283,292,296,299,301,303,305,313,317,326,327,328,333,334,335,338,346,348,349,355,356,358,363,364,366,367,380,381,382,384,386,389,390,391,396,405,406,408,410,412,421,423,424,425,426,428,431,432,433,440,441,448,449,450,451],docuement:394,dodgerblu:169,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,29,33,38,39,41,50,54,56,59,62,63,67,70,71,87,88,91,104,110,117,118,123,124,127,132,134,138,143,144,145,146,148,150,152,157,163,164,166,167,168,169,172,178,179,181,184,187,188,190,191,192,194,198,200,202,205,206,209,211,213,214,216,219,225,229,230,231,232,234,235,246,247,248,249,257,258,259,263,265,268,270,278,281,283,285,286,290,293,294,295,298,299,300,301,306,307,309,310,312,317,318,319,320,321,327,328,329,334,335,336,337,338,339,341,343,344,345,347,348,349,350,352,353,354,355,356,357,359,360,361,362,364,365,366,367,368,371,372,374,375,376,378,379,380,381,382,384,390,391,392,393,394,396,397,398,399,400,401,402,403,404,406,407,408,409,410,411,412,414,415,416,418,419,420,421,423,424,425,426,427,430,431,433,434,435,436,437,440,441,443,448,452],doegenomestolif:7,doesn:[3,7,8,12,144,167,179,184,185,275,327,329,333,335,348,356,366,392,393,406,408,409,410,423,425],dof:[3,8,112,123,124,137,181,270,449],dof_per_atom:[124,181],dof_per_chunk:[124,181],doff:[327,423],doi:[6,193],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,118,133,143,146,166,168,169,172,179,188,192,194,195,209,212,216,229,230,253,265,270,290,295,296,318,319,328,333,354,384,418,420,423,427,440],domin:[1,357,437],don:[0,8,11,12,13,116,147,175,200,214,259,299,380,421,423],donadio:282,done:[1,3,6,7,8,12,14,15,16,17,18,19,38,39,41,56,59,62,71,138,141,144,147,164,168,169,178,179,181,183,184,185,186,188,189,190,191,192,194,195,203,205,210,211,213,214,221,229,234,235,246,247,249,250,252,253,254,259,267,270,271,273,278,281,282,283,285,287,288,301,303,317,318,319,326,328,329,332,333,335,343,355,364,365,366,373,379,380,384,392,404,407,412,418,419,420,421,424,427,428,431,441,443,448,449],donor:363,dot:[121,140,175,200,208,228],doti:[339,390],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,39,87,194,203,258,299,303,317,319,332,333,339,358,362,392,393,419,423,427,431,436,448,449],dover:178,down:[3,6,7,8,11,39,71,192,213,278,294,333,357,384,422],downhil:[324,325],download:[5,7,8,9,11,12,13,17,210,365,391],downsid:6,downward:267,dozen:[8,12,107,172,392,393],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:222,dproduct:336,dr_ewald:[118,271],drag:[],dragforc:216,drai:[227,260],drain:[209,294,326],dramat:[59,166,189,190,191,192,194,229,278,281,282,319,333,384,420],drautz:339,draw:168,drawback:259,drawn:[167,168,169,206,418],drayleigh:[227,260],dreid:[],drfourth:105,drho:[113,334,355],drift:[6,103,105,206,207,213,214,225,268,278,432,440,443],drive:[11,12,176,192,194,208,229,251,257,270,297,328],driven:[6,156],driver:[6,12,14,15,172,203,210],drop:[3,169,353],droplet:364,drsquar:105,drude:[],dry:202,dsecriptor:365,dsf:[],dsmc:[],dstyle:256,dt_collis:216,dt_lb:216,dt_md:216,dt_srd:278,dtilt:[59,194],dtneb:437,dtqm:260,dtype:[115,190],dual:[17,278,333],dudarev:143,due:[1,3,6,9,10,12,16,17,19,40,54,57,58,61,66,70,71,74,75,81,86,88,89,90,93,102,103,104,105,106,110,116,118,120,121,122,123,125,127,130,131,132,133,134,136,137,139,143,144,147,148,167,168,172,175,176,183,187,189,190,191,192,193,194,195,200,201,202,203,206,207,210,211,213,214,215,216,219,220,221,225,226,227,228,229,233,241,251,254,256,268,269,270,272,275,277,278,279,281,282,283,284,285,287,288,290,294,295,297,298,299,301,319,324,326,328,329,330,350,353,355,359,360,364,378,379,384,390,392,394,395,404,407,408,410,413,415,416,418,420,423,424,425,432,437,440,441,443,448,449],duffi:290,duin:[9,261,266,392,393],duke:319,dummi:[12,29,409],dump1:428,dump2:428,dump:[],dump_atom:8,dump_custom:8,dump_modifi:[],dumpcustom:8,dumptimestep:428,dunbrack:[6,20,150,344,435],dunweg:[213,215],duplic:[2,3,14,15,16,17,18,19,41,42,145,188,207,251,423,447],dupont:[5,7,13],durat:[37,55,122,123,125,126,127,129,130,131,132,133,136,137,163,169,181,205,265,290,313,361,405],dure:[2,3,6,8,9,12,16,17,38,39,41,56,71,87,126,145,148,164,167,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,196,199,200,201,202,203,204,205,206,207,208,209,210,211,213,214,215,216,217,218,219,220,221,222,223,225,226,228,229,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,319,326,328,332,333,353,377,384,393,407,418,419,421,423,426,428,430,431,433,435,437,438,441,448,451,452],dvector:8,dvlo:415,dvx:6,dx_lb:216,dy3:143,dyamic:12,dyanam:6,dyanmic:437,dynam:[],dynamo:[5,334,355,380],dyne:447,dyre:374,dysam:426,e28637:29,e_1:339,e_2:339,e_b:358,e_e:357,e_hbond:363,e_i:[6,339,358],e_j:[6,339],e_k:[339,357],e_kl:6,e_lj:[335,352],e_n:[339,357],e_nn:357,e_pr:357,e_rebo:335,e_tors:335,eaa:304,eaat:151,each:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,66,67,68,70,71,72,73,74,75,76,77,78,80,81,83,85,87,89,90,93,94,95,96,97,98,99,100,101,102,103,104,105,106,109,110,111,112,113,114,115,116,117,118,119,120,121,123,124,125,126,127,128,131,132,133,134,136,137,138,139,140,141,142,143,144,147,148,150,151,152,153,154,155,156,157,158,159,161,162,163,164,166,167,168,169,170,171,172,173,174,175,176,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,205,206,207,208,209,210,211,212,213,214,215,216,217,219,220,221,222,223,225,226,227,228,229,231,232,233,234,235,236,237,238,239,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,261,262,263,265,267,270,271,272,273,274,275,276,277,278,279,280,281,282,283,285,288,289,290,291,292,293,294,295,296,298,299,300,301,303,304,306,307,308,309,310,312,313,314,317,318,319,321,325,326,327,328,329,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,357,358,359,360,361,362,363,364,367,368,369,370,371,372,373,374,375,376,377,378,379,380,383,384,385,386,387,389,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,410,411,412,413,414,415,416,417,418,420,421,423,424,425,426,427,428,430,431,432,433,435,437,438,440,441,443,447,448,449,450,452],eacn:[41,188],eam0d:252,eam3d:252,eam:[],eam_databas:13,eam_gener:13,eangl:441,earli:[41,181,183,184,185,186,188,264,271],earlier:[7,8,12,59,169,328,361,380,384,437],earliest:437,earth:357,easi:[6,7,8,11,13,87,121,167,173,174,175,176,184,187,200,208,209,211,213,214,272,281,282,283,295,298,300,327,423,426,431,433,449],easier:[8,9,13,16,167,168,252],easili:[8,11,168,169,294,328,420,430,439,448],eastwood:[318,319],eat:151,eatom:301,eaxmpl:6,eba:21,ebb13:151,ebb:21,ebond:[198,214,440,441],ebt:151,ec_ii:380,ec_ij:380,ec_jj:380,echo:[],eco:[392,393],ecoa:[392,393],ecoul:[107,198,214,392,393,441],ecp:[357,423],edg:[2,3,6,41,59,71,118,142,143,146,147,168,177,184,211,272,295,298,299,300,301,321,423,426,433],edge_histo:142,edge_threshold:142,edih:441,edim:286,edip:[],edit:[3,8,12,13,14,15,16,17,18,19,443],editor:13,edu:[7,9,11,13,355,378,389,392,393],edward:[9,17],eebt:151,eff:[],effect:[1,2,3,6,8,9,11,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,43,45,46,47,48,49,51,53,54,56,66,71,74,75,8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0,274,278,281,282,283,284,286,289,290,293,297,300,301,317,318,327,328,332,333,353,355,360,394,396,397,411,413,418,421,423,424,425,426,428,430,431,435,439,441,443,448,452],end_of_step:8,endbondtors:[3,151,157,423],endif:8,energet:[191,335,393],energi:[0,1,2,3,4,5,6,7,8,9,12,13,20,21,23,24,25,26,27,28,29,30,31,32,35,36,38,40,43,45,46,47,48,49,51,53,54,56,63,65,69,82,83,84,85,86,87,88,91,94,95,96,97,98,99,101,102,107,108,109,110,112,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,144,148,150,151,152,153,154,155,156,158,159,161,162,163,164,167,169,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,304,306,307,308,309,312,314,318,319,324,325,326,328,329,333,334,335,337,338,339,340,341,342,343,344,345,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,389,390,392,393,394,395,396,397,398,399,404,405,406,407,408,409,410,412,413,414,415,416,418,421,423,428,432,433,435,437,439,440,441,443,447,448,451],energy_update_freq:393,enforc:[6,57,58,104,166,167,168,170,172,179,191,194,229,250,252,262,270,273,303,318,369,420,448,449],enforce2d:[],eng:[11,65,69,108,167,203,301,303,348,382],eng_previ:303,engin:[178,194,255,274,287,355,381],engr:[392,393],enhanc:[174,178,418],enlarg:[59,168],enough:[3,40,61,86,144,145,147,188,214,256,260,265,270,291,295,296,299,329,333,349,388,423,427,428],enpub:355,ensembl:[],ensight:6,ensur:[3,6,120,167,179,192,205,206,229,289,319,339,354,377,404,406],enter:[57,134,358,437],enthalpi:[231,232,355,440,441,448],entir:[0,2,3,6,11,14,15,41,42,63,88,109,110,112,116,118,121,124,143,144,169,172,173,174,181,184,185,188,191,193,202,205,206,209,213,214,225,229,231,232,233,234,235,251,253,255,268,270,276,290,292,303,333,352,373,384,407,423,431,432],entireti:[367,412],entiti:[6,8,40,42,167,270],entri:[3,8,38,42,56,65,69,79,92,108,115,118,142,164,169,183,184,185,193,260,301,327,339,356,380,386,393,396,406,407,408,409,410],entropi:437,entry1:[38,56,169,346,407],entry2:169,entryn:169,enumer:[145,167],enumuer:6,env:333,environ:[1,3,6,11,12,16,17,18,168,207,212,251,333,334,339,346,348,356,357,390,408,420,434,448],epair:[107,169,359,363,392,393,441],epen:[392,393],epfl:[207,212],epp:352,epq:352,eps0:415,eps14:377,epsilon0:410,epsilon:[3,6,36,45,46,50,53,54,87,150,173,174,205,270,278,295,299,324,326,338,344,345,347,349,350,351,352,360,362,363,364,367,368,369,370,371,372,373,374,375,376,377,383,387,394,395,400,406,412,414,415,432,443,447],epsilon_0:416,epsilon_14:344,epsilon_:394,epsilon_d:350,epsilon_i:[360,384,394],epsilon_i_:394,epsilon_i_a:[360,394],epsilon_i_b:[360,394],epsilon_i_c:[360,394],epsilon_ij:384,epsilon_j:[360,384,394],epsilon_j_:394,epsilon_j_a:[360,394],epsilon_j_b:[360,394],epsilon_j_c:[360,394],epsilon_lj:394,epton:389,eqch:139,eqeq:[392,393],eqp:352,eqq:352,equal:[2,3,6,8,11,12,17,39,41,54,63,65,68,69,76,79,86,87,91,92,108,110,115,117,119,121,123,138,140,144,168,169,172,173,174,175,176,179,182,183,186,187,188,192,194,195,200,205,206,208,209,211,213,214,216,219,220,226,227,233,243,251,253,256,258,260,261,262,265,267,269,270,272,274,281,282,283,286,287,288,290,292,293,295,298,300,301,303,317,326,328,329,330,332,333,348,353,359,360,363,378,383,390,392,393,394,396,397,407,412,416,419,420,421,423,425,426,430,431,434,437,439,441,448,449],equat:[3,6,7,8,9,91,112,118,143,152,163,172,192,198,199,207,213,214,216,219,227,228,229,230,233,247,251,253,260,261,265,273,278,286,290,293,295,296,298,300,312,318,319,347,352,353,357,358,361,366,378,379,380,384,394,399,400,402,403,411,416,443],equi:230,equidist:228,equil:[3,261,322,430,452],equilater:433,equilibr:[3,4,5,6,7,9,59,91,144,172,179,182,191,192,205,227,229,230,247,248,260,261,262,263,286,287,288,293,348,349,392,393,419,433],equilibria:293,equilibribum:[189,190],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,127,128,151,153,192,194,205,206,207,214,216,229,233,247,260,265,269,273,274,275,278,285,286,288,293,304,306,309,312,348,380,386,443],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:178,equival:[6,12,13,59,142,146,169,183,186,192,194,205,213,229,247,257,269,270,298,353,357,408,410,423,426,431,432,441,443],equlibrium:6,equliibr:[261,263],er3:143,eradiu:[40,113,357,423],eras:[272,287],erat:[194,379],erc:349,erfc:[349,369,384],erforc:113,erg:447,erhart:[179,355,408,410],ermscal:336,ernst:9,eror:3,eros:380,erose_form:380,erot:[],errata:[408,410],erratum:295,erron:3,error:[],erta:361,ervel:[113,423],escap:[195,443],especi:[8,11,16,132,144,172,179,188,205,260,265,268,269,333,420],espresso:[9,264],essenti:[8,11,12,27,88,125,126,127,130,131,132,133,134,136,153,182,233,252,294,319,335,349,369,410,428,441],essex:29,establish:[87,209],estim:[1,3,6,10,12,38,41,56,91,121,178,188,199,227,278,285,318,319,324,384,393,407,437,441],esu:447,esub:380,eta:[6,216,229,260,261,263,294,356,358,360,390,409,447],eta_dot:229,eta_ij:390,eta_ji:358,etag:[40,423],etail:441,etap:229,etap_dot:229,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,17,39,40,42,54,61,68,89,90,91,94,109,110,113,115,121,122,124,125,126,127,128,130,131,132,133,134,136,138,144,146,147,148,157,167,168,169,172,178,179,180,181,183,184,185,186,189,190,194,195,203,205,206,213,229,256,267,271,290,291,299,303,317,318,326,327,328,329,331,355,356,364,377,379,388,392,393,406,408,410,418,421,423,424,425,430,432,433,437,439,440,441,443,447,448,450,452],ethernet:18,etol:[326,328,418,437],etot0:260,etot:[6,94,96,97,110,121,130,169,198,214,227,260,440,441],eu2:143,eu3:143,euler:[326,328],eulerian:178,euqat:398,europhi:216,evalu:[2,3,11,12,38,56,71,87,88,91,107,117,120,124,134,142,144,167,168,169,173,174,175,176,178,180,181,182,183,184,185,186,187,194,200,206,208,209,211,212,213,214,252,258,261,272,281,282,283,292,295,298,300,301,303,318,319,324,326,333,384,390,407,418,419,421,425,426,428,430,431,432,433,437,439,441,448,449],evalut:[303,421],evan:[132,247],evanseck:[6,20,150,344,435],evapor:[],evaul:[8,326],evdwl:[107,392,393,441],even:[3,6,8,12,15,16,17,18,34,39,41,52,57,59,61,63,70,71,119,145,146,160,164,167,169,172,173,174,179,180,181,183,184,185,186,188,189,190,192,194,195,198,211,214,227,229,230,252,265,267,270,271,278,286,290,293,295,299,301,311,318,324,326,328,333,338,357,358,361,364,384,394,413,423,424,426,428,429,430,432,433,435,438,440,441,443,452],evenli:[3,41,121,164,188,216,367,413,423],event:[],eventu:[3,6,12,15,146,261,437],ever:[54,56,212,278],evera:[347,360,394,405],everi:[0,1,2,3,6,8,11,12,15,16,39,41,71,72,91,113,119,132,147,167,168,169,170,172,173,174,175,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,199,202,203,205,207,209,210,211,216,217,225,229,230,233,250,251,252,256,257,258,259,260,261,262,263,265,267,268,270,271,273,274,278,280,281,282,283,284,285,286,289,290,291,292,293,301,303,317,319,328,329,330,333,353,354,364,377,392,393,401,417,418,419,423,425,427,428,430,431,432,437,438,439,441,448,452],everyth:[8,107],everywher:[116,371],eviri:357,evolut:[207,216,253,418],evolv:[216,253,291],ewald:[2,3,5,6,7,8,12,88,110,118,121,291,318,319,326,340,342,343,349,352,357,369,373,387,395,405,407,425],ewald_disp:352,ewalddisp:3,exact:[22,41,44,71,138,147,152,188,191,206,207,213,214,215,256,265,266,278,290,305,318,346,425,430,437,450,452],exactli:[3,6,12,14,17,38,41,56,59,71,91,123,128,135,144,164,173,174,183,188,194,199,206,213,214,215,230,240,241,248,252,260,278,283,284,297,333,346,353,355,361,364,367,378,384,407,425,426,433,437,448],exager:443,examin:[6,8,191,252],examp:[421,448],exampl:[],exce:[3,6,16,17,18,41,58,71,146,181,184,185,188,192,194,199,202,229,252,278,326,333,423,448],exceed:[3,41,59,188,194,229,278,431],excel:357,except:[1,2,5,6,8,11,14,16,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,108,109,112,117,121,122,123,124,125,126,127,128,130,131,132,133,134,135,136,137,144,148,150,151,152,153,154,155,156,158,159,161,162,163,164,166,167,169,172,175,181,182,183,187,188,192,194,201,204,205,208,211,213,215,229,230,231,232,233,234,235,236,240,241,244,246,247,248,249,253,262,263,270,272,273,275,278,281,283,284,290,294,301,303,304,305,306,307,308,309,312,313,314,318,319,321,323,327,328,329,331,332,333,334,335,337,340,341,342,343,344,345,346,347,348,349,351,352,353,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,379,381,385,386,387,389,392,393,394,395,397,405,406,407,408,409,410,412,414,415,416,418,420,421,423,425,426,428,431,432,433,434,435,437,441,443,447,448,449,451],excess:357,exchang:[2,3,6,8,9,61,62,172,178,179,205,213,262,270,286,290,293,318,333,357,438],exchange:318,excit:[9,357],exclud:[3,6,9,12,16,17,63,71,112,120,124,131,132,148,167,181,184,189,190,217,225,255,268,270,285,296,301,326,327,329,341,361,364,378,379,384,404,435],exclus:[1,3,9,12,16,87,333,348,384,432],excurs:418,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,145,168,210,264,303,317,320,332,419,421,431,434,437,448],exemplari:206,exemplifi:357,exert:[6,211,214,265,297,298,299,319],exhaust:[178,332,448],exhibit:[229,325,357,432],exist:[3,6,7,8,11,12,13,37,55,59,68,70,144,145,163,168,169,172,177,187,190,192,195,205,255,256,258,301,304,306,307,309,313,322,327,333,364,392,413,419,421,423,424,425,434,435,436,448,449,450],exit:[2,3,11,12,41,57,167,188,317,332,421,422,431,440,448],exlanatori:3,exp:[],expand:[],expans:[12,120,167,434],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,102,125,136,142,164,188,200,205,207,226,251,257,259,260,265,270,301,319,329,346,380,384,418,421,423,425,428,432,437,448],expens:[6,10,71,169,251,255,270,290,301,318,319,329,333,421],experi:[6,13,15,17,187,195,210,219,228,257,269,270,324,328,353,384,432,437],experienc:[6,12,218,219],experiment:[318,333,437],expert:12,expertis:7,explain:[1,3,6,8,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,92,124,132,164,167,168,169,172,181,182,186,188,190,192,194,229,251,259,270,275,301,303,317,318,321,327,328,332,338,355,367,397,412,416,421,424,425,428,430,433,443,448,452],explan:[3,6,59,113,120,167,181,228,251,364,417,420,421,423,432],explanatori:[3,8,117,167,180,181,183,184,185,270,327,420,448],explantori:[3,266],explic:383,explicit:[6,9,11,22,44,77,87,113,116,138,152,173,174,194,305,323,335,336,339,344,346,355,357,368,378,411,417,420,424,427],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,109,112,122,131,134,142,144,150,151,153,154,155,156,158,159,161,162,164,167,169,175,184,187,194,201,204,206,208,213,229,231,232,233,234,235,236,244,246,247,249,259,260,262,270,272,273,281,283,284,290,294,304,306,307,308,309,312,314,327,333,334,335,337,340,341,342,343,344,345,346,347,348,349,350,352,353,354,355,356,358,359,360,361,362,363,364,367,368,369,370,371,372,373,374,375,376,377,378,381,384,385,386,387,389,394,395,397,398,399,400,401,402,403,405,406,407,408,409,410,411,412,414,415,416,423,425,432,433,435,436,443],explictli:[16,436],exploit:[9,15,17,253],explor:[118,143],expon:[3,261,263,355,360,363,377,383,395],exponenti:[87,390,406,416,437,448],expos:11,exposit:[178,353,354],express:[6,120,130,144,173,174,192,226,251,261,290,296,303,339,355,357,371,380,396,405,448],expressiont:339,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,94,97,98,107,109,117,119,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,172,175,176,179,186,187,193,196,200,203,204,205,207,208,209,211,213,215,227,229,233,241,251,252,268,269,270,272,274,275,277,281,282,283,284,285,287,288,290,292,295,299,300,360,380,393,394,396,440,441],extent:[1,3,41,45,57,71,142,146,167,177,184,188,211,297,300,318,321,335,407,420,423,426],exterior:[3,6,299],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,102,109,110,112,118,121,122,123,125,127,130,131,132,133,134,136,137,143,144,145,146,150,169,183,188,190,229,258,259,260,270,278,326,327,330,331,352,361,364,367,380,384,420,421,423,426,435,443,448],extract:[3,6,11,13,36,63,87,107,115,117,119,173,174,263,328,349,358,380,396,421,428,440],extract_atom:11,extract_comput:[11,421],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,168,192,194,229,288,357,409,443],extrema:377,extrins:178,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[140,292],f_a:[408,409,410],f_ave:117,f_c:409,f_f:410,f_fix_id:260,f_harm:288,f_i:390,f_id:[6,71,117,119,167,172,180,181,182,183,184,185,186,224,280,292,441,448],f_ij:390,f_indent:186,f_int:287,f_jj:91,f_k:390,f_langevin:290,f_max:[260,265],f_msst:227,f_r:[214,408,409,410],f_sigma:339,f_solid:288,f_ss:6,f_temp:214,face:[3,6,57,59,71,132,142,146,177,184,185,295,297,298,299,300,321,360,380,394,423,426],face_threshold:142,facet:142,facil:[0,12],facilit:[6,13],fact:[6,8,16,207,278,288,361,435],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,118,120,138,143,146,150,161,167,168,169,173,174,182,188,192,194,195,205,210,213,215,216,227,229,230,233,253,257,269,273,278,282,286,293,294,295,299,309,319,321,333,335,336,339,340,342,344,349,350,351,353,357,361,364,368,369,380,384,386,387,393,395,397,406,411,420,423,426,427,432,435,437,438,441,443,447,448],factori:[3,421],factoriz:318,fail:[3,11,12,59,148,192,195,318,326,328,351,393,421],fairli:[11,384,432,437],faken:73,falcon:210,fall:[3,6,169,183,256,421],fals:[86,301,303,448],fame:8,famili:420,familiar:[0,11],fan:390,far:[3,6,12,17,57,59,61,86,167,169,170,188,189,190,192,195,205,229,251,269,270,278,295,306,309,324,328,329,412,421,423,428,441],farago:213,farrel:[408,410],farther:167,fashion:[6,8,41,71,144,169,172,173,174,179,184,188,190,195,205,207,211,226,227,229,231,232,233,234,235,243,246,247,248,249,259,260,262,270,274,277,280,288,290,294,295,296,298,300,328,364,378,426,435,448,451],fasolino:366,fast:[6,7,9,12,13,17,39,167,238,260,291,318,319,341,378,379,405,407,425,430,432,441,449,452],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,105,109,112,122,131,150,151,153,154,155,156,158,159,161,162,164,167,169,172,175,187,188,201,204,208,212,213,229,231,232,233,234,235,236,244,246,247,249,257,261,262,270,272,273,278,281,283,285,287,290,294,304,306,307,308,309,312,314,318,319,330,331,333,334,335,337,339,340,341,342,343,344,345,346,347,348,349,352,353,355,356,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,381,385,386,387,389,394,395,397,405,406,407,408,409,410,412,414,415,416,418,432,436,443],fastest:[6,14,17,132,184,290,291,333,420],fatal:[3,440],fault:[70,393],faulti:12,fava:360,favor:191,favorit:7,fbmc:285,fcc:[],fcm:[243,448],fdirect:198,fdotr:365,fdti:87,fe2:143,fe3:143,fe_md_boundari:178,featu:8,featur:[],fecr:355,feedback:[7,210],feel:[7,210,211,219,251,299,301,328,384],felling:382,felt:299,femtosecond:447,fene:[],fennel:[349,369],fep:[],ferguson:[6,150,435],fermi:[1,12,15,130,333,410],fermion:[9,357],ferrand:[9,13],few:[1,3,4,5,6,7,10,11,12,13,14,17,18,39,170,180,181,182,183,184,185,186,214,229,256,259,261,273,292,318,326,327,328,335,420,423,428,432,434,448,450],fewer:[1,3,11,15,16,61,219,432],fewest:3,fextern:203,feynman:253,fff:421,ffield:[348,358,392,393],ffmpeg:[3,12,168],ffplai:168,fft:[1,3,7,12,14,15,88,109,110,121,252,318,319,432],fft_inc:[12,319],fft_lib:12,fft_path:12,fftbench:318,fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],fictiti:[6,175,176,200,203,207,253,269,349,369,373,404],field1:[424,428],field2:424,field:[],fifth:[275,386],figur:[1,3,8,11,12,260,420,421],fij:352,file0:251,file1:[11,13,251,289,303,327,428,430,434],file2:[11,13,289,303,327,428,430,434],file:[],filenam:[3,12,13,38,41,56,164,167,168,169,170,178,181,182,183,184,185,186,188,193,251,255,258,261,262,263,266,267,270,271,289,290,315,316,317,328,334,335,339,349,355,356,358,366,380,381,382,386,390,391,392,393,396,406,407,408,409,410,419,420,421,424,425,430,434,441,448,450,451,452],filennam:430,filep:[3,167,169,425,430,452],filepo:267,fill:[7,144,168,256,290,321,329,339,393,426],filter:[169,178],final_integr:8,final_integrate_respa:8,finchham:[6,126,351],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,117,147,164,170,179,191,192,202,205,228,251,257,265,269,324,326,328,329,349,364,369,373,380,405,407,443,448],find_custom:8,fine:[16,17,148,175,200,288,329,333,448],finer:[120,144,448],finest:318,finger:[144,166,226,426],finish:[6,11,41,188,303,315,317,318,330,332,333,412,428,448,449],finit:[],finni:[7,355,405],finvers:198,fiorin:[9,193],fire:[324,325,326,328,437],firebrick:169,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,103,104,105,112,116,117,121,129,132,138,140,142,143,145,146,147,151,164,167,168,169,170,172,179,181,182,183,184,185,186,188,191,194,205,206,211,216,226,227,228,229,251,253,258,259,260,262,267,270,273,274,275,276,278,279,280,287,288,289,290,292,296,301,303,304,310,321,326,327,328,329,332,333,334,335,338,339,340,342,344,346,348,349,355,357,358,361,362,365,366,368,369,373,378,379,380,382,384,386,390,392,393,396,404,406,407,408,409,410,418,419,420,421,423,424,425,428,430,432,435,436,437,440,441,443,448,449,450,452],fischer:[6,9,19,20,150,344,435],fit:[3,6,9,12,38,56,164,269,278,335,339,366,380,384,400,407,409,431,448],five:[73,130,260,327,339,381,423,437],fix:[],fix_adapt:[138,174,377],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,179,256],fix_evapor:179,fix_flux:178,fix_gcmc:[179,327],fix_gl:207,fix_gld:207,fix_grav:256,fix_id:[3,192,227,229,231,232,233,234,235,257,260],fix_modifi:[],fix_mov:[166,296],fix_nh:8,fix_npt:207,fix_nvt:[179,205],fix_poem:[3,6],fix_pour:[3,195],fix_qbmsst:9,fix_qeq:[3,348],fix_rattl:273,fix_reax_bond:392,fix_rigid:[219,338],fix_saed_vtk:271,fix_setforc:8,fix_shak:273,fix_srd:3,fix_styl:233,fix_temp_rescal:284,fixedpoint:[192,229],fixextern:203,fixid:178,fji:352,flag1:[197,331],flag2:[197,331],flag:[3,8,11,12,14,15,16,17,18,40,66,74,75,81,86,89,90,93,103,104,106,118,139,143,147,167,168,169,170,186,191,193,197,210,213,217,219,225,226,252,259,270,275,277,278,285,289,298,301,316,319,327,331,332,333,335,363,368,380,404,418,420,421,423,424,425,427,428,429,433,448],flag_buck:343,flag_coul:[343,352,373],flag_lj:[352,373],flagfld:[341,378,379],flaghi:[3,341,378,379],flaglog:[341,378,379],flagn:197,flagvf:[341,378,379],flat:[6,290,295,296,300],flavor:[2,7,12],fld:[9,295,341,378,379],flen:336,flex_press:336,flexibl:[3,6,8,145,168,181,184,193,207,230,286,293,357,409,441],flip:[3,6,194,229,297,298],floor:448,flop:12,floralwhit:169,flow:[],fluctuat:[6,64,87,192,205,206,213,216,229,233,251,252,288,290,312],fluid:[],fluid_veloc:220,flush:[3,169,440],flux:[],flv:168,fly:[7,9,12,41,168,172,178,195,198,270,273,291,339,441,443],fmackai:9,fmag:196,fmass:253,fmax:[326,441],fmomentum:198,fmsec:[2,169,213,214,226,229,257,270,281,282,432,442,447,449],fname:317,fno:12,fnorm:[326,441],fnpt:198,fnvt:198,foce:364,fock:336,focu:273,fogarti:[9,263,393],foil:[120,251,396],fold:[276,432],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,120,121,123,124,130,132,137,140,142,144,145,150,153,154,155,156,158,159,161,162,164,167,168,169,172,178,179,180,181,182,183,184,185,186,188,193,194,195,198,199,203,205,206,207,210,212,213,214,216,219,227,229,233,234,235,246,247,249,252,253,255,258,259,260,261,263,265,267,269,270,271,273,280,281,282,283,286,287,288,289,290,292,293,301,302,306,307,308,309,312,314,316,321,323,326,327,328,333,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,351,352,353,354,355,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,3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3,71,143,253,285,288,319,356,379,392,393,421,448],interf:333,interfac:[],interfer:[229,335],interg:[6,443],intergr:[432,436],interi:379,interior:[3,6,41,299,426],interlac:380,interleav:[6,144,431],intermedi:[6,12,59,168,228,251,312,328,421,422,431,435],intermix:418,intermolecular:335,intern:[0,2,3,5,6,9,11,16,20,21,24,28,32,35,36,39,40,42,63,87,99,101,118,121,124,126,143,151,164,168,169,172,173,174,178,190,194,198,210,222,223,227,229,233,252,270,274,304,306,309,312,316,326,327,398,399,407,421,423,425,428,437,440,441,447,448,449,450],internal_element_set:178,internal_quadratur:178,internet:212,interpenetr:380,interpentr:[399,400,402],interpol:[6,15,38,56,100,164,168,169,178,216,251,318,319,328,339,384,393,401,407,408],interpret:[2,6,11,168,183,361,397,418,421,437,448],interrupt:260,intersect:[3,6,118,169,299,301,426],intersert:299,interspers:326,interstiti:142,intertia:[3,93],interv:[3,6,91,182,213,260,265,266,401,418,437,448],intestieti:118,intial:[6,333,335],intiial:[41,428],intiti:[3,277],intra:270,intra_energi:205,intramolecular:[29,205],introduc:[6,9,168,229,260,265,270,312,318,334,349,357,369,373,377,406,437],introduct:[],intsal:16,intuit:321,inv:[118,143,271],invalid:[3,12,71,89,147,241,328,378,379,425],invari:120,invent:273,invers:[],invert:[6,148,252],invis:299,invoc:[142,191,333,421],invok:[1,3,6,7,8,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,59,63,66,71,74,75,81,87,88,89,90,93,103,104,106,109,110,111,112,117,122,131,138,139,142,144,145,147,148,150,151,153,154,155,156,158,159,161,162,164,167,168,169,170,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,196,197,199,200,201,202,203,204,205,206,208,209,210,211,213,214,215,216,217,218,219,220,221,222,223,225,226,228,229,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,261,262,263,264,265,266,267,268,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,304,306,307,308,309,312,314,317,318,319,320,321,326,328,333,334,335,337,340,341,342,343,344,345,347,348,349,352,353,355,356,358,359,360,361,362,363,364,365,367,369,370,371,372,373,374,375,376,377,378,379,381,384,385,386,387,389,394,395,396,397,406,407,408,409,410,412,413,414,415,416,417,420,421,422,424,426,428,431,432,434,435,437,440,441,443,448,449],invokd:3,involv:[3,6,7,8,12,63,108,115,116,117,124,148,172,189,205,216,255,258,263,278,318,325,326,328,338,354,360,406,408,410,419,420,426,428,432,437],ioff:[327,423],ion:[6,7,250,275,290,319,339,350,358,359,380,405,410,416,423,443],ionic:[6,9,340,342,350,357,358,387,443],ioniz:[9,348,357],iparam:[3,190],ipi:[],ipp:[],ir3:143,ir4:143,irregular:[6,41,58,188,192,194,229,270],irrelev:386,irrespect:[378,379],irrevers:198,isbn:415,isel:[318,319],isenthalp:[229,230,231,232],ismail:[318,319,343,373],isn:[3,8,11,12,209],iso:[3,192,198,214,229,230,231,232,233,234,235,257,265,270,443],isobar:[229,230,234,235],isodem:357,isol:[3,147,301],isomorph:253,isotherm:[205,229,230,234,235,257],isotrop:[6,213,257,318,319,341,360,378,379],isovolum:271,isralewitz:274,issu:[1,3,6,9,11,12,13,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,59,71,73,81,103,109,112,122,131,150,151,153,154,155,156,158,159,161,162,164,168,175,178,187,191,192,195,200,201,204,205,208,213,227,229,231,232,233,234,235,236,244,246,247,249,253,257,259,262,270,272,273,277,281,282,283,288,294,300,303,304,306,307,308,309,312,314,319,327,328,331,334,335,337,340,341,342,343,344,345,347,348,349,352,353,355,356,358,359,360,361,362,363,367,369,370,371,372,373,374,375,376,377,378,381,385,386,387,389,394,395,397,404,406,407,408,409,410,412,414,415,416,423,425,432,435,440,441,448,449],ital:[392,393],itali:13,item:[6,7,8,41,167,169,188],iter:[3,6,12,39,41,63,175,176,187,188,192,198,200,203,211,252,261,262,270,273,285,301,303,317,324,325,326,328,332,418,428,432,437,441,448],ith:[71,117,119,180,181,182,183,184,185,186,280,292,441,448],itself:[2,3,4,6,7,8,9,11,12,13,18,42,59,91,107,135,167,168,169,170,182,193,198,214,224,228,264,270,290,301,303,327,328,349,358,360,364,365,407,421,427,430,431,435,448,452],ityp:[3,115,116,144,177,190,263,413],itype1:116,itype2:116,itypen:116,ivector:8,ivori:169,ixcm:270,ixi:[42,93,270,327,448],ixx:[42,93,270,327,448],ixz:[42,93,270,327,448],iycm:270,iyi:[42,93,270,327,448],iyz:[42,93,270,327,448],izcm:270,izrailev:274,izumi:409,izz:[42,93,270,327,448],j0jt:91,j20:182,j_m:120,jac:[6,150,435],jackson:383,jacobi:3,jacobsen:325,jagreat:13,jame:[9,19],janssen:251,januari:380,jaramillo:[7,9,13,357],jarzynski:274,jatempl:9,jcc:9,jcp:295,jec:13,jeff:13,jello:229,jensen:[213,318],jeremi:[9,382],jerom:9,jewett:13,jiang:[214,443],jiao:[9,13],jiht:[7,9],jik:339,jim:7,jku:7,jmake:12,jmm:120,joannopoulo:227,job:[12,60,273,431],jochim:[229,230],john:[7,13],johnson:13,join:[6,426],joint:[3,255,363],jon:[9,70],jonathan:9,jone:[1,3,6,7,9,10,12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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff 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 hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff 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 hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso_e/atom command","compute meso_rho/atom command","compute meso_t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute sna/atom command","compute stress/atom command","compute temp command","compute temp/asphere command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian 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_coeff 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 dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim 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 hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/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 meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":189,"default":[37,39,40,55,57,58,59,61,62,71,87,88,102,103,105,107,118,120,124,132,133,137,143,144,147,149,163,165,166,167,168,169,170,171,173,174,175,177,178,179,181,184,185,186,189,190,192,193,194,195,199,202,205,206,211,213,214,215,216,217,219,224,227,229,230,233,247,248,252,253,256,257,258,259,260,262,265,267,268,270,271,278,280,285,286,287,288,291,293,295,297,301,313,316,318,319,321,322,324,325,327,329,330,331,333,336,339,341,357,378,379,384,392,393,404,405,418,419,420,423,424,426,428,430,431,432,435,437,439,440,441,442,447,449,450,451],"function":448,"long":[340,342,343,344,345,349,351,352,369,373,377,387,395],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[173,174],addforc:175,addit:[12,13],addtorqu:176,adiabat:6,adp:334,airebo:335,alloi:355,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:177,arrai:6,aspher:[6,82,123,231,234,237,238,246],atc:[9,178],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,95,96,99,100,101,110,111,113,120,121,142,177,179,180,259,448],atom_modifi:39,atom_styl:40,attract:5,aveforc:187,awpmd:[9,336],balanc:[41,188],barostat:6,basal:67,beck:337,berendsen:[257,281],between:6,binary2txt:13,bodi:[6,8,42,68,239,338],bond:[8,13,69,189,190,191,266],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:339,born:[340,351],boundari:[7,57],box:[6,58,192],brownian:341,buck:[342,343,351],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,150,344,377],chunk:[6,66,71,75,90,93,104,106,114,124,139,141,181],citat:7,class2:[21,43,151,304,345],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[295,347,415],colvar:[9,13,193],com:[74,75,125],comb3:348,comb:[262,348],come:5,comm_modifi:61,comm_styl:62,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,445,446,447,448,449,450,451,452],common:3,comparison:1,compos:6,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,448],compute_modifi:102,condit:7,conduct:[6,286],constant:6,constraint:7,contact:76,coord:77,core:6,correl:182,cosin:[23,24,25,26,27,28,153],cossq:306,coul:[340,342,343,344,345,349,350,351,362,369,373,377,387,395],coupl:6,creat:190,create_atom:144,create_bond:145,create_box:146,createatom:13,creation:7,csld:282,csvr:282,cubic:371,cuda:[9,14,109,112,122,131,175,187,201,204,208,229,236,272,273,281,283,294,340,342,344,345,355,361,362,369,370,372,375,385,406,408],custom:8,cut:[49,336,342,345,349,352,357,359,369,370,377,383,387],cvff:307,damag:78,data2xmovi:13,data:6,databas:13,deby:[349,369],deform:[127,128,194],delete_atom:147,delete_bond:148,delta:24,deposit:195,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,16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\ No newline at end of file
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64,189,199,211,214,225,312,370,400,462,469],acceptor:390,access:[0,3,6,7,8,9,11,12,16,40,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,85,88,89,90,91,92,93,95,96,99,100,101,103,104,105,106,107,108,110,111,112,113,114,115,117,118,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,151,152,153,154,155,156,157,159,160,161,162,163,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,219,220,221,222,223,224,225,226,227,228,229,230,231,233,235,236,237,238,239,240,241,242,243,245,246,247,248,249,253,256,257,258,259,260,261,262,263,264,265,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,299,302,303,304,305,306,307,308,309,310,311,313,314,315,316,317,319,320,321,322,323,324,325,326,327,345,360,386,388,390,391,407,419,420,428,451,452,455,460,472,479],accidenti:339,accler:16,accommod:197,accomod:249,accompani:8,accomplish:[16,214,237,263],accord:[64,71,121,127,130,188,199,209,210,236,249,272,280,294,296,314,315,317,322,323,325,326,327,356,360,384,388,399,402,417,424,426,428,430,431,433,434,435,463,468,479],accordingli:[11,14,143,157,168,356,405,406],account:[3,6,9,87,118,162,163,172,183,202,203,219,230,231,233,249,254,255,266,267,269,271,275,281,290,291,293,302,303,304,305,308,309,310,313,317,320,335,354,376,388,396,400,405,406,407,451,468,480],accuml:[3,290,313,320],accumul:[1,6,8,15,71,192,202,233,290,294,319,343,360,460,478],accur:[1,3,6,15,17,38,41,56,147,208,247,285,290,293,305,313,320,326,328,346,366,384,387,388,411,421,436,438,439,441,468,479],accuraci:[1,3,6,12,41,187,189,208,227,249,282,293,318,328,345,346,352,384,411,419,420,438,444,463,468,474,479,482],ach:345,achiev:[1,3,6,16,17,18,41,208,227,249,250,272,273,280,345,391,463],achiv:18,acid:9,ackland1:382,ackland2:382,ackland:[],acknowledg:[],acml:12,aco:479,acolor:[188,189],acoust:272,acquir:[3,6,58,61,62,167,210,212,214,249,415,459,474],across:[1,2,3,6,9,12,13,15,41,57,61,65,68,69,71,79,92,107,108,115,117,152,166,168,201,203,204,205,208,219,229,290,291,295,313,317,320,326,330,355,360,449,454,457,458,462,471],act:[3,6,108,149,218,228,231,232,233,234,236,239,248,290,299,312,314,315,317,326,327,328,353,368,379,387,388,390,421,435],acta:[118,163,361],action:[2,6,11,12,71,226,231,315,474],activ:[5,8,11,12,13,14,55,59,87,162,199,213,226,230,233,239,248,270,290,297,316,343,404,436,448,476,479],actual:[1,3,6,8,12,56,62,122,147,187,189,193,194,207,209,210,218,233,234,267,271,277,285,294,305,307,308,309,310,312,318,327,328,345,356,387,389,399,405,406,451,452,463,464,472,479],adam:[345,346],adapt:[],add:[0,1,3,5,6,7,8,9,11,12,13,14,15,16,17,18,19,40,42,71,87,91,102,114,117,119,162,164,165,187,188,192,193,194,195,196,198,200,201,202,203,204,205,206,210,213,218,220,223,227,228,229,231,233,235,236,240,247,248,249,250,251,252,253,254,255,266,267,268,269,271,279,289,290,292,293,302,304,308,310,311,315,316,317,319,321,322,326,328,346,348,352,354,362,367,369,372,376,384,391,396,407,411,414,420,422,452,454,455,460,462,464,466,474],add_molecul:198,add_speci:198,add_to_nodeset:198,addforc:[],addit:[],addition:[6,8,16,139,305,327,387,421],address:[7,8,11,188,232],addtorqu:[],adequ:[305,318,345,355,463],adher:29,adhikari:236,adiabat:[],adiam:[188,189],adjac:[39,164,355,411,438,439,468,469],adjiman:410,adjust:[2,3,6,16,17,41,59,118,143,144,147,148,151,152,157,158,163,168,187,188,201,208,212,214,230,233,237,241,245,246,249,250,253,267,271,274,276,277,280,281,282,283,288,290,297,305,309,313,318,320,321,322,324,325,327,345,346,353,355,360,362,381,405,406,441,464,480],adjust_dt:128,adjust_radiu:297,adjust_radius_factor:297,admiss:253,adof:[144,201],adopt:[289,474],adp:[],adri:[9,286,419,420],adust:158,advanc:[3,230,366,449,460],advantag:[1,6,8,11,14,18,39,40,41,208,360,383,463,468],advect:[3,6,305],advertis:8,advis:[355,418],afer:3,affect:[1,6,10,14,15,16,17,40,60,61,71,88,117,141,148,162,168,189,194,201,202,203,204,205,206,209,210,211,212,214,215,223,229,231,233,239,246,250,251,252,254,255,261,266,267,269,290,291,303,317,327,339,345,351,352,353,355,356,357,360,384,405,406,411,451,452,454,457,459,462,464],affin:[16,17,18,214,360,375],afil:227,aforement:18,afresh:[278,462,479],afshar:380,after:[2,3,5,6,8,9,11,12,15,16,21,22,33,39,40,41,44,50,57,58,59,61,63,71,143,144,145,146,147,148,151,152,153,154,156,157,164,165,167,168,171,172,177,186,187,188,189,190,192,193,194,198,199,201,202,208,209,210,211,212,214,218,225,236,237,238,239,240,245,246,247,249,254,255,261,266,267,269,272,276,280,288,290,293,301,306,308,309,310,312,313,314,315,316,320,322,324,328,331,332,337,344,350,351,353,354,356,358,359,360,361,362,366,373,375,382,383,384,385,391,392,393,404,405,406,407,408,409,413,417,419,420,427,437,439,440,441,449,451,453,454,455,456,457,459,460,462,464,466,468,471,472,474,478,479,480,481,482,483],afterrun:462,afterward:3,afterword:41,ag1:163,ag2:163,again:[6,11,12,17,62,140,144,146,150,158,187,189,214,229,276,331,344,355,405,406,449,451,452,454,456,461,468,470,479,481],against:[11,12,13,64,215,355,419,420],aggreg:[6,12,65,68,69,79,92,108,115,229,245,288,290,303,449,480],aggress:[229,468],agilio:[9,13],agre:[3,8,184,353,362,393,420],agreement:[5,7],ahd:390,ahead:324,aidan:[0,5,7,9,13],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:188,akohlmei:[7,9,13,190,230],aktulga:[7,9,283,420],al2o3_001:[118,291],al3:163,ala:236,alain:9,alat:[271,407],alb:[417,439,441],albeit:289,albert:9,alchem:[87,158],alcohol:320,alcu:[361,366],alcu_eam:417,alderton:379,alejandr:[249,250],alessandro:13,algorithm:[0,1,6,7,8,9,41,61,189,198,208,211,214,236,238,239,261,273,290,293,312,313,317,320,325,351,352,353,357,360,384,406,424,426,449,451,468],alia:12,alias:[1,346],aliceblu:189,align:[6,12,29,41,71,166,184,204,208,231,348,454,457,474],alkali:384,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,152,157,158,159,160,161,162,163,164,165,166,167,168,170,172,177,183,184,187,188,189,190,192,193,194,195,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,242,244,245,247,249,250,251,252,253,254,255,256,257,258,259,260,261,262,264,265,266,267,268,269,270,271,272,273,275,276,277,278,279,280,281,282,283,285,286,287,288,289,290,291,292,293,294,295,296,297,301,302,304,305,306,307,308,309,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330,331,332,335,340,343,344,345,346,347,348,350,353,354,355,356,357,359,360,361,362,363,365,366,367,369,370,371,372,373,375,376,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,400,404,405,406,407,408,409,410,411,412,413,414,416,417,418,419,420,421,422,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,446,447,448,449,451,452,453,454,455,456,457,458,459,461,462,463,464,465,466,467,468,469,471,472,474,478,479,480,481,482,483],allen:[29,87,379,387],allentildeslei:87,allign:3,allindex:329,alloc:[3,5,6,8,9,11,12,60,223,319,354,356,360,415,420,454,462],allocat:3,alloi:[],allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,108,143,144,157,162,163,164,166,172,183,184,187,188,189,190,192,193,195,197,198,199,201,202,203,204,205,206,208,210,211,212,213,214,215,219,220,223,225,226,227,228,230,233,236,239,240,244,246,249,250,271,275,277,278,279,280,284,290,291,293,294,296,297,301,305,312,313,314,315,317,318,319,320,321,322,328,330,332,340,345,346,348,353,354,355,356,359,360,363,366,367,368,369,370,371,376,382,384,388,389,390,391,400,405,406,411,417,420,421,424,426,435,444,446,449,452,454,456,457,458,459,460,461,464,466,467,468,471,472,479,480],almost:[2,3,12,60,231,280,317,346,357,360,435],alo:376,alon:[6,7,211,286,419,420,452],alond:13,along:[6,8,9,12,29,40,87,118,163,164,186,187,188,211,231,236,237,241,246,248,280,290,293,294,298,302,303,312,316,317,323,326,328,348,351,352,353,355,376,379,388,391,394,396,400,407,419,420,438,454,457,464,465,479],alonso:[408,409],alpha:[6,51,193,236,272,280,285,353,361,364,367,376,380,382,383,385,390,395,396,407,412,416,440,442,472,474],alpha_:442,alpha_c:404,alpha_i:[427,442],alpha_ialpha_j:442,alpha_lj:404,alphabet:[2,3,22,37,44,55,63,172,183,192,332,340,354,373,436,454],alphanumer:[3,63,192,279,287,330,354,479],alreadi:[3,7,8,12,42,164,165,167,197,201,204,205,208,210,214,240,278,280,305,328,354,355,380,389,391,398,406,435,444,447,450,454,455,459,464,479],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,54,55,56,58,59,61,63,66,71,73,75,77,81,87,89,90,93,103,104,105,106,107,112,114,116,117,119,140,141,142,143,144,145,146,147,148,150,151,152,153,154,156,157,158,159,160,161,162,164,165,166,167,168,170,172,183,184,185,187,188,189,190,192,193,194,195,197,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,220,223,224,225,226,227,229,230,233,234,235,236,246,247,249,250,251,252,253,254,255,260,263,264,266,267,268,269,271,272,273,275,276,277,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,298,299,302,303,305,308,309,310,311,312,316,317,318,319,321,323,326,328,330,332,337,340,343,345,346,348,349,350,353,354,355,356,357,359,360,366,370,371,373,377,378,379,380,382,383,384,387,388,390,391,392,400,404,405,407,411,413,415,416,417,418,421,422,424,430,431,433,434,435,436,437,438,439,440,441,442,449,451,452,453,454,455,456,457,458,459,461,462,463,464,466,467,468,469,472,473,474,475,477,478,479,480,481,483],alter:[3,6,8,9,11,12,41,59,142,143,144,145,147,150,151,152,153,156,157,164,168,187,188,190,193,194,201,209,210,211,212,214,248,249,285,288,290,292,299,305,313,320,327,352,355,391,454,459,461,464,479,480,483],alter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,76,77,116,122,140,239,271,293,303,354,413,419,420,454],centro:[],centroid:[3,273,443,464],cerda:345,ceriotti2:227,ceriotti:[13,227,232],certain:[1,2,3,6,8,12,17,39,71,113,117,119,168,187,188,200,201,202,203,204,205,206,211,223,224,290,292,306,319,330,337,344,356,391,411,420,442,456,460,474,479],certainli:231,cerutti:346,cfg:[3,6,7,13,187,188,189,190],cfile:420,cfl:[128,295],cfor:294,cg_type:422,cgiko:2,cgikot:2,cgkio:2,cgko:2,cgkot:2,cgo:2,cgot:2,ch2:293,ch2lmp:[],ch3:293,chain3:356,chain:[],challeng:[6,294],chalopin:285,champaign:[230,345,346,405],chandler:[361,382],chandrasekhar:[6,396],chang:[1,2,3,6,8,9,11,12,14,15,16,17,39,40,41,46,55,57,59,62,71,80,87,116,126,128,146,147,148,164,165,166,168,184,186,187,188,189,190,192,193,194,195,196,198,199,204,205,207,208,209,210,211,212,213,214,215,219,220,222,224,227,229,230,231,233,235,236,237,239,245,246,247,249,250,251,252,253,254,255,261,266,267,268,269,271,272,276,277,279,280,284,287,288,289,290,292,293,294,305,308,309,310,311,313,314,315,316,317,318,320,323,326,328,346,351,353,355,358,360,380,384,388,391,405,406,407,411,419,420,436,449,450,451,452,454,455,456,457,458,459,460,462,463,464,465,466,469,472,475,477,478,479,480,481],change_box:[],changeabl:187,channel:[4,195],chapter:[273,346],charact:[2,3,6,12,38,41,56,63,184,187,188,189,190,192,208,279,287,330,354,359,384,395,417,419,420,438,451,452,456,461,462,479,481,482,483],character:[6,67,70,116,140,427,449,468],characterist:[234,305,314],charg:[1,3,4,5,6,7,9,11,15,40,87,88,113,118,163,164,187,190,192,193,194,199,215,220,225,279,281,282,283,287,307,320,345,346,354,367,369,375,376,378,379,382,384,385,391,396,400,404,414,419,420,436,441,442,444,446,447,454,455,459,464,466,474,478,479],charmm2lammp:13,charmm:[],chartreus:189,cheap:305,cheaper:[219,387,421],check:[3,6,8,11,12,15,17,39,41,71,91,184,199,204,208,209,210,215,222,225,231,232,289,293,305,313,315,320,328,330,344,353,354,355,356,357,360,381,392,395,411,420,435,449,451,452,454,462,468,471,472],checkf:184,checkqeq:420,checku:184,chem:[6,13,20,21,25,39,40,43,45,46,87,88,112,141,170,171,181,213,218,226,227,234,236,248,249,250,267,268,273,277,280,282,290,294,305,308,309,312,313,314,315,322,331,339,341,345,346,352,355,362,367,371,372,375,376,377,379,380,384,386,387,389,390,396,400,401,404,407,410,411,414,435,442,463,466,468,474],chemic:[9,118,158,163,187,198,199,225,281,286,287,312,346,419,420,431],chemistri:[9,280,281,283,366,384,419,420],chen:317,cheng:375,chenoweth:[419,420],chenoweth_2008:[419,420],chi:[92,153,186,271,281,283,385,387,480],chiefli:418,child:8,chip:[7,12,17,360,467],chipot:213,chiral:339,chmod:[11,12],cho:407,chocol:[7,189],choic:[3,6,12,15,16,18,40,41,54,87,141,143,157,168,184,201,204,205,208,211,214,215,227,233,236,247,249,273,281,290,312,340,346,351,352,355,357,360,391,404,411,415,454,463,464,467,468,473,474,478],choos:[1,3,6,7,8,12,16,17,18,29,39,54,87,117,154,155,188,209,210,211,212,215,222,233,236,247,249,251,252,253,254,255,277,305,309,323,345,346,352,444,449,451,463,469],chose:[439,441],chosen:[2,3,6,12,17,140,164,167,176,184,188,194,199,212,215,222,225,226,234,236,247,249,253,273,276,287,305,309,312,313,318,320,321,327,346,347,352,360,384,388,394,395,398,422,439,449,463,468,474],chri:162,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[66,75,90,93,104,106,114,144,159,161,201],chute:[4,10,228],ciccotti:293,cieplak:[6,170,466],cii:202,cij:202,circl:301,circular:[3,6,143,185],circumst:18,circumv:285,citat:[],cite:[3,7,8,12,233],cko:2,cl1:163,clarendon:[29,379],clarifi:[7,439,441],clariti:330,clark:414,class2:[],classic:[0,3,5,6,7,8,9,223,273,280,285,317,341,384],classifi:[9,436],claus:452,clean:[6,12,14,15,17,462],cleanli:[453,482],clear:[],clearli:7,clebsch:140,clermont:[9,13],clever:458,click:[2,11,22,37,44,55,164,172,183,188,230,332,340,355,373,436],client:[230,232],climb:[248,355,468],clinic:[7,13],clo:[153,186,480],clock:[12,449,468],clockwis:323,close:[3,6,11,12,13,39,41,67,141,167,187,210,211,212,227,234,236,249,267,290,293,323,326,344,346,349,351,352,355,360,362,366,376,377,407,411,423,425,441,458,464,474,476],closer:[3,41,116,162,186,187,208,212,216,314,355],closest:[210,271,290,320,387,421,435,444],cloud:474,clovertown:18,clsuter:72,clump1:[275,290],clump2:[275,290],clump3:[275,290],clump:290,cluster:[],clutter:[3,9],cmap:454,cmatrix:227,cmax:407,cmd:[11,12,273,465],cmin:407,cmm:[],cn1:202,cn2:202,cna:[],cnn:202,cnr:[9,13],cnt:[391,458],co2:[40,163,293,354],coars:[7,9,29,36,40,54,176,275,290,305,389,422,466],coarser:[346,479],coarsest:140,code:[],coeff:[3,7,8,12,21,22,33,44,50,170,171,172,177,331,332,337,373,391,395,411,424,426,428,454,456],coeffcient:454,coeffici:[],coefficienct:380,coefficient0:382,coefficient1:382,coeffieci:[6,364],coeffincientn:382,coexist:[9,225,384],cohes:[6,385,407],coincid:[122,326,371,405,406,449],cold:[6,149,229,356,474],coldest:313,coleman8:9,coleman:[9,118,163,291],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,93,98,104,106,114,144,152,159,161,164,187,189,201,213,239,245,275,285,288,290,328,345,354,356,374,394,454,461,467,483],collid:[219,305,327],colliex:163,collinear:[3,275],collis:[3,236,305,323,327,381,388,447],colllis:305,colloid:[],colombo:39,colon:[190,328,455],color1:189,color2:189,color:[3,9,41,187,188,189,208,226,280,285],column:[3,6,9,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,104,106,108,110,113,114,115,116,117,119,140,141,144,152,159,161,162,163,184,187,189,192,200,201,202,203,204,205,206,239,246,247,280,290,306,307,317,327,386,390,419,420,455,469,471,479],colvar:[],colvarmodul:12,com:[],comamnd:214,comand:[211,456],comannd:360,comb3:[],comb:[],comb_1:282,comb_2:282,combiant:377,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,92,108,115,143,157,187,188,198,203,230,239,249,273,279,309,318,326,329,331,345,346,348,352,360,374,376,377,384,385,391,403,404,427,437,439,441,446,457,462,474,479],come:[],comfort:[12,13],comm:[0,3,12,61,73,230,232,233,346,355,360,380,411,416,438],comm_modifi:[],comm_styl:[],command:[],comment:[2,7,11,12,38,56,170,184,187,234,290,317,354,355,361,382,383,385,395,407,413,420,427,437,438,439,440,441,451,452,454,474,479],commerci:7,commmand:[3,6,12,59,107,268,448,449,451,468,482],common:[],commonli:[3,6,12,17,25,57,59,105,166,187,188,190,341,389,398,427,439,441,454,457,466],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,167,168,188,189,208,209,210,212,213,214,230,232,236,238,239,240,249,272,279,281,282,283,290,305,317,328,345,356,357,358,360,381,415,451,452,456,463,464,481,483],communc:345,comp:[7,232,233,293,346,355,384,411,416,421,434,438,440],compact:[63,192,373,436],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,110,118,147,162,163,172,183,189,218,281,328,330,345,346,353,355,407,449,468,469,474,478],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,171,172,183,331,332,340,372,436],compat:[3,5,7,8,9,11,12,13,17,18,41,71,117,119,175,187,190,194,200,201,202,203,204,205,206,208,272,284,309,312,319,322,325,345,360,392,411,438,451,452,479],compens:[6,209,210,288,356,384],compet:316,competit:346,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,162,187,188,190,230,316,346,360,454,455,459],compl:17,complain:[12,17],complement:407,complementari:[7,376,396],complet:[3,6,9,12,15,41,59,71,189,204,208,213,239,273,276,279,305,316,318,330,344,355,360,385,424,426,443,449,454,459,462,466,468,471,474,479],complex:[6,8,11,12,13,25,40,42,62,140,152,164,165,236,301,326,343,355,384,438,452,454,457,479],compli:[312,316],complic:[6,7,9,12,13,199,225,452],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,93,94,97,104,105,106,107,108,109,110,112,113,117,127,130,131,132,133,136,137,138,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,156,157,159,160,161,187,188,189,195,196,200,201,202,203,204,205,206,207,211,212,214,215,220,223,228,232,233,236,239,241,245,246,248,249,250,253,254,255,266,267,269,270,272,273,274,277,288,290,292,293,294,298,299,302,305,308,309,310,312,319,320,325,326,327,345,348,352,353,354,355,360,380,384,388,405,406,424,426,427,454,455,464,472,479,480],componenet:6,composit:[6,199,236,382],compound:[375,384,385],compres:[71,114,201],compress:[3,6,59,71,114,167,187,188,189,201,214,247,253,277,280],compris:[40,326,394,421,443],compton:[118,163],comptu:[3,6],compuat:346,comput:[],computation:[3,6,209,210,317,366],computational:474,compute_arrai:8,compute_fep:[194,404],compute_group_group:225,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[118,291],compute_scalar:8,compute_temp:8,compute_ti:194,compute_vector:8,compute_xrd:163,concaten:[2,3,482],concav:326,concentr:382,concept:[6,144,154,201,463],conceptu:[3,6,71,152,212,214,355,376,391,407,459],concern:[6,73,87,226],concis:[11,316],conclud:12,concret:8,concurr:[9,16,346],conden:[317,439,441],condens:[6,146,317,362,378,382,396],condit:[],conducit:6,conduct:[],cone:457,confid:[3,468],config:[12,187,451],configfil:213,configur:[1,2,6,12,15,17,38,59,122,166,184,186,187,188,192,212,213,214,215,219,225,232,233,261,273,281,316,343,353,355,362,366,383,407,437,439,441,449,454,456,457,468],confin:[454,468],conflict:[3,40,411,452],conform:[3,6,13,59,211,212,248,289,294,316,339,355,384,466],confus:3,conjuct:380,conjug:[7,8,233,352,384,419,420],conjunct:[6,7,71,86,87,114,147,152,158,164,168,189,193,194,233,236,240,261,276,277,281,282,283,285,290,305,313,320,325,345,346,355,367,369,373,376,380,384,390,396,411,414,422,442,454,457,461,474,483],connect:[3,6,87,149,167,211,230,275,290,293,302,355,377,388,435,441,451,452,458,474],conput:3,consecut:[3,11,12,39,71,164,189,193,194,215,230,231,376,396,400,449,455,457],consequ:[1,6,317,395,468],conserv:[3,192,199,211,218,219,226,229,233,235,236,240,245,247,249,261,290,293,308,309,313,320,321,325,355,379,380,388,402,463,468],consid:[6,9,70,71,78,87,115,149,150,167,187,189,193,194,200,202,204,208,210,211,215,237,250,272,290,312,313,316,317,320,346,373,384,391,420,421,435,449,450,452,455,456,457,459,462,464,472,474,479],consider:[6,8,233,234,308,309,310,360,463],consist:[3,6,8,9,11,12,40,42,65,69,79,92,104,108,111,112,115,144,147,149,164,176,186,190,195,196,201,214,215,218,220,223,226,233,234,235,246,249,251,252,253,254,255,256,257,259,260,261,262,264,265,266,267,268,269,277,280,285,287,289,290,308,309,310,311,321,345,346,348,354,355,360,362,366,368,374,376,384,387,391,405,406,407,411,421,424,426,438,444,452,454,455,457,458,459,466,474,479],consistent_fe_initi:198,consit:290,constant:[],constitu:[3,6,239,290,322,326,374,421],constitut:[424,426],constrain:[3,6,8,142,143,144,145,147,150,151,152,153,154,156,157,192,201,215,225,226,231,239,243,275,276,288,290,293,303,313,320,353,354,384,459,466,474],constraint:[],construct:[6,8,14,38,54,56,61,64,67,70,72,73,77,118,140,163,212,249,272,289,326,356,360,379,411,435,437,438,457,458,479],constructor:8,consult:420,consum:[1,285,415,479],consumpt:343,contact:[],contact_stiff:[423,425],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,116,118,140,144,152,162,163,164,166,170,172,183,184,187,188,189,190,192,193,194,198,200,201,202,203,204,205,206,208,213,215,220,227,231,232,233,234,236,247,261,271,272,275,276,278,280,283,287,290,291,295,305,312,316,317,326,327,330,344,346,354,355,358,359,361,362,363,366,375,376,379,382,383,384,391,392,407,413,417,418,419,420,427,437,438,439,440,441,442,449,450,451,452,454,455,456,457,459,461,463,466,468,471,472,474,479,481,483],content:[12,18,420,470,472],context:[3,6,8,12,17,117,189,209,210,215,275,287,321,352,446,454,461,470,478,479,480],contibut:70,contigu:451,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,103,104,160,189,192,193,194,199,201,202,203,204,205,206,208,211,212,213,214,215,225,226,227,229,230,231,233,234,235,241,246,247,249,251,252,253,254,255,266,267,268,269,274,276,279,280,290,291,294,304,305,307,314,315,317,323,326,330,344,359,360,366,380,381,398,401,419,420,421,424,426,440,449,452,454,456,457,462,468,471,472,479,481],continuum:[6,7,9,198,317,424,426],contour_integr:198,contract:[59,212,214,249,277,290],contradictori:3,contrain:293,contraint:261,contrari:[227,234],contrast:[1,6,42,55,64,149,214,328,424,426,446,482],contrib:317,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,93,102,104,106,107,108,109,110,112,114,117,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,194,199,200,201,202,203,204,205,206,212,225,233,236,239,240,244,250,267,268,275,276,284,287,290,291,293,319,345,353,355,363,380,381,382,384,391,405,406,411,419,420,466,472,474],contributor:12,control:[3,5,6,7,8,11,13,16,27,29,41,87,91,122,140,173,187,188,192,198,199,208,212,213,214,229,230,233,234,249,251,252,253,254,255,277,282,290,296,297,308,309,310,317,321,343,345,357,384,387,419,420,423,425,437,441,449,451,463,469,470],control_typ:198,controlfil:420,convect:91,conveni:[6,12,29,187,190,206,291,348,427,479],convent:[3,8,9,29,175,182,183,189,289,302,329,382,384,479],converg:[3,6,41,88,187,188,190,195,208,211,212,220,223,253,280,282,285,289,293,351,352,353,355,375,376,396,449,461,468],convers:[3,8,140,188,189,199,202,277,345,376,377,378,384,396,400,404,414,452,468,478],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,164,171,187,188,189,206,247,328,331,333,336,339,348,355,361,382,439,441,447,452,454,455,456,461,471,474,478,479,481,483],convex:326,convinc:[7,12],cooki:7,cool:[7,154,229,288],cooordin:187,cooper:[5,7],coord123:114,coord1:[3,114,201,204,205],coord2:[3,114,201,204,205],coord3:[3,114,201,204,205],coord:[],coordiat:353,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,93,103,104,106,113,114,116,134,140,147,153,159,161,162,164,168,186,187,188,189,190,192,195,200,201,203,204,205,208,209,210,211,212,213,214,215,218,220,221,223,225,228,229,230,231,232,233,234,246,248,249,251,252,254,255,267,270,271,272,275,276,277,287,288,290,292,293,294,299,302,303,304,305,307,315,316,317,324,325,327,328,348,353,354,355,360,361,362,365,383,449,454,455,457,459,462,464,468,474,479,480],coordn:[114,201],coorind:104,copi:[0,3,4,8,11,12,15,17,40,119,188,317,355,373,419,452],copper:447,coproccesor:16,coprocessor:[1,4,7,9,16,17,360,467],coproprocessor:17,copy_arrai:8,copyright:[7,8,275],coral:189,core:[],core_shel:146,coreshel:[6,9,369,376,378],cornel:[6,170,466],corner123i:113,corner123x:113,corner123z:113,corner1i:113,corner1x:113,corner1z:113,corner2i:113,corner2x:113,corner2z:113,corner3i:113,corner3x:113,corner3z:113,corner:[3,6,40,113,188,326,327,348,443,454],cornflowerblu:189,cornsilk:189,corpor:16,corr:375,correct:[3,6,9,11,12,16,17,59,87,88,102,110,116,146,151,158,188,214,227,233,249,250,267,275,277,280,316,322,326,345,355,361,362,363,364,365,366,367,368,369,370,371,372,374,375,376,377,378,379,380,381,382,383,384,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,443,445,446,447,454,469,472,474],correction_max_iter:198,correctli:[3,8,9,11,17,71,81,102,103,142,143,145,147,149,150,151,152,153,156,157,160,187,189,195,215,220,223,234,243,249,250,283,290,293,302,304,323,326,355,356,360,378,406,451,452,454,464,478,480],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,96,97,109,112,113,114,115,118,119,127,130,131,132,133,134,136,137,138,140,142,143,151,158,163,170,171,172,173,174,175,176,178,179,181,182,184,187,188,189,193,194,195,201,203,204,205,207,210,212,214,221,223,224,228,233,236,237,245,246,247,249,251,252,253,254,255,256,261,264,266,267,269,272,273,277,282,290,292,293,308,310,312,321,322,323,325,326,327,329,331,332,333,334,335,336,339,341,346,350,352,354,355,361,362,364,367,368,369,370,371,372,373,374,375,376,379,380,382,383,384,385,386,387,388,389,390,391,394,396,397,398,399,400,401,402,403,404,405,407,408,411,412,413,414,416,417,419,420,421,422,427,428,437,438,439,440,441,443,445,446,447,449,451,452,454,455,457,467,468,469,471,472,474,479],correspondingli:[405,406,463],cosin:[],cosineshift:27,cosmo:[227,232],cossq:[],cost:[1,6,10,11,12,17,39,41,71,109,118,141,163,188,189,201,204,205,208,209,210,222,249,282,317,345,346,358,376,396,400,411,437,451,463],costheta0:[437,439,441],costheta:417,costli:[11,88,227,356],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,93,104,106,109,112,114,144,154,159,161,177,187,188,189,193,194,199,201,202,204,208,214,223,232,279,280,281,285,288,290,292,305,306,312,316,317,318,322,326,328,330,337,342,344,351,353,356,360,363,386,390,391,419,420,450,451,452,454,456,458,461,462,470,474,479,480],coulomb:[3,5,6,7,8,9,10,12,14,15,18,88,107,108,141,165,169,281,283,318,345,346,353,360,367,369,370,371,372,375,376,377,378,379,384,388,389,391,396,400,404,411,414,419,420,422,436,441,442,446,459,466,472,474,478],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,41,63,68,77,91,114,116,117,152,162,168,195,196,199,201,203,204,205,207,208,215,220,222,225,231,249,261,276,293,308,309,326,346,353,354,355,357,360,386,390,411,472,479],counter:[323,449,460,462,468],counterbal:229,counterpart:[187,290,449],counterproduct:18,coupl:[],courant:295,cours:[3,8,126,128,158,187,193,194,226,289,302,316,322,324,325,327,328,346,405,428,451,454,467,474,479,481],coval:[6,29,384,407,474],covari:227,cover:[6,71,184,189,198,236,384,394,443],coverag:[71,204],cpc:232,cpp:[1,3,6,8,9,11,12,13,87,187,193,194,223,293],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,189,192,218,234,318,343,346,360,373,436,449,467,468,471,472],cpuremain:472,cr2:163,cr3:163,crack:[4,356],crada:[5,7],crai:[5,7,13,18,187],crash:[3,356,474],craympi:360,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:198,create_faceset:198,create_nodeset:198,createatom:[],creation:[],crimson:189,critchlei:275,criteria:[3,116,165,188,189,209,210,211,244,353,416,443,456,459,479],criterion:[41,121,162,164,167,199,208,211,225,261,282,295,323,328,353,355,375,384,388,459,468,469],criterioni:468,critic:[48,49,247,312,317,353],cross:[3,12,22,71,89,143,172,187,188,200,204,210,214,246,248,267,290,298,302,304,313,320,332,348,355,371,380,381,382,389,390,391,396,398,400,417,422,424,426,439,441,454,458,464,481],crossov:1,crossterm:454,crozier:[0,7,13],crucial:280,crystal:[4,6,13,73,271,272,315,356,458,472,474],crystallin:[6,272,348,440,474],crystallis:312,crystallogr:[118,163],crystallograph:[348,472],crystallographi:[118,163,348],cs1:163,cs_chunk:6,cs_im:[40,454],cs_re:[40,454],csanyi:[140,418,427],cscl:407,csequ:6,csh:[11,12,373],cshrc:[11,12],csic:[383,437,439,441],csinfo:6,csisi:[383,437,439,441],csld:[],cst:382,cstherm:6,cstyle:451,csvr:[],ctcm:[361,382],ctemp_cor:218,cterm:294,ctr:9,ctype:11,cu1:163,cu2:163,cu3au:407,cube:[6,41,162,167,208,218,326,348,474],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:366,cummul:[3,6,206,209,210,211,213,222,227,233,235,305,308,309,310,311,313,320,390,472],cumul:[6,199,201,203,204,205,219,225,233,247,249,253,261,290,291,355],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,102,108,116,117,130,141,144,152,160,162,165,168,187,188,189,190,193,194,198,199,201,204,205,206,208,209,210,211,212,213,214,215,219,220,223,225,227,230,231,233,239,246,249,250,254,255,261,266,267,269,275,281,282,284,287,288,289,290,293,294,295,296,297,298,299,301,303,304,305,308,309,310,316,317,320,321,322,323,324,325,327,328,330,343,344,345,346,349,350,352,353,354,355,360,366,373,375,379,382,384,385,388,392,395,405,406,407,408,409,411,417,419,420,423,424,425,426,428,439,441,442,444,449,450,451,452,454,455,456,457,458,460,461,462,464,466,468,469,471,472,479,480,481,482,483],curv:[6,164,225,272],curvatur:[387,421,447],custom:[],cut0:452,cut1:463,cut2:463,cut:[],cuthi:[271,283],cutinn:[368,405,406],cutlo:[271,283],cutmax:417,cutoff1:[372,379,396,400,404,414,422],cutoff2:[367,369,370,372,378,379,396,400,404,414,422],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,108,115,116,140,162,165,167,210,211,216,271,280,281,283,285,287,290,305,318,322,326,328,345,346,353,356,357,358,360,361,362,363,364,365,366,367,368,369,370,371,372,374,376,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,419,420,421,422,427,428,429,430,431,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,452,456,459,463,474],cutoffa:383,cutoffc:383,cuu3:382,cval:163,cvd:312,cvel:294,cvff:[],cwiggl:[3,246,322,325,327,479],cyan:[2,188,189],cycl:[3,225,247,249,250,253],cyclic:[3,184],cygwin:12,cylind:[3,4,188,231,276,323,326,457],cylindr:[6,231,302,323],cypress:360,cyrot:366,cyrstal:272,d3q15:236,d3q19:236,d_double_doubl:15,d_e:317,d_flag2:279,d_flag:279,d_name:[113,187,279,307,464],d_single_doubl:15,d_single_singl:15,d_sx:279,d_sy:279,d_sz:279,daan:315,dai:12,daili:12,daivi:267,damag:[],dammak:285,damp:[3,6,192,197,233,234,235,240,249,250,253,277,280,285,290,308,309,321,323,324,352,353,355,367,369,371,376,379,384,388,396,404,414,422,436,442,468,474],damp_com:234,damp_drud:234,dampen:[290,474],dampflag:[323,388],dan:17,danger:[3,12,225,328,380,472],dangl:167,daniel:9,darden:[346,379],darkblu:189,darkcyan:189,darken:188,darkgoldenrod:189,darkgrai:189,darkgreen:189,darkkhaki:189,darkmagenta:189,darkolivegreen:189,darkorang:189,darkorchid:189,darkr:189,darksalmon:189,darkseagreen:189,darkslateblu:189,darkslategrai:189,darkturquois:189,darkviolet:189,dasgupta:281,dash:[388,471],dat:[6,91,184,198,450],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,291],dataset:291,datatyp:3,date:[0,6,12,13,419,420,479],datom1:115,datom2:115,datom3:115,datom4:115,datum:[3,6,42,65,68,69,79,92,108,115,187,202],davi:322,david:[9,19,345,346,439,441],daw:[382,417],dbg:14,dcd:[3,6,7,187,188,189,190,273,455,459],ddim:186,deactiv:404,dealt:232,debug:[6,7,11,12,13,14,17,118,122,163,164,273,278,343,345,360,392,411,444,452,453,456,461,464,471,479],deby:[],decai:[376,447],decid:[3,6,12,16,71,246,279,290,318,469],decipher:348,declin:305,decod:188,decompos:[87,427],decomposit:[3,5,7,18,62,198,273],decoupl:[6,474],decreas:[3,187,195,196,211,214,220,223,233,316,345],decrement:294,deepli:342,deeppink:189,deepskyblu:189,def:[12,13,452],defaul:61,defect:[6,70,162],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,170,171,172,173,174,175,176,178,179,181,182,183,184,185,186,187,188,189,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,218,219,220,223,224,225,228,231,232,233,234,235,236,244,246,248,249,250,251,252,253,254,255,257,258,259,262,264,265,266,267,268,269,271,272,273,275,276,277,279,281,283,288,290,291,292,293,295,299,303,305,307,308,309,310,311,313,314,315,317,319,320,322,323,324,325,326,327,328,330,331,332,333,334,335,336,339,340,341,343,345,346,348,350,352,353,354,355,356,357,358,359,360,362,363,364,365,367,368,369,370,371,372,373,374,376,377,379,380,381,383,384,386,387,388,389,390,391,392,394,396,397,398,399,400,401,402,403,404,405,406,410,411,412,413,414,416,417,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,451,452,454,455,457,458,459,460,463,464,465,466,468,469,471,472,474,475,476,477,478,479,480],definit:[2,3,6,8,12,13,78,80,116,140,189,201,202,203,204,205,206,214,231,253,291,307,319,322,325,327,329,340,343,354,363,366,374,384,394,417,424,426,427,443,452,454,456,463,465,478,479],defint:472,deform:[],deg2theta:163,deg:474,degener:[3,275],degrad:[8,18,272,346,463],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,94,96,97,99,101,102,112,142,143,144,145,146,147,148,149,150,151,152,153,154,156,157,163,164,170,171,174,175,182,184,186,188,201,211,218,225,227,228,233,234,239,249,250,253,254,255,266,267,269,273,275,289,290,293,308,309,310,315,331,333,336,339,341,353,379,382,390,464,472,474,480],degress:[144,201],del:468,delai:[3,6,12,356,381,472],deleg:391,delet:[2,3,7,8,12,54,57,60,63,162,167,168,192,201,202,203,204,205,206,209,211,222,225,249,291,308,309,328,330,344,354,356,359,411,454,455,457,465,466,471,475,477,479,480],delete_atom:[],delete_bond:[],delete_el:198,deli:186,delimit:[452,479],deloc:[250,384],delr:407,delt_lo:468,delta:[],delta_1:366,delta_3:366,delta_7:366,delta_conf:3,delta_ij:[407,417],delta_mu:[3,199],delta_pi:366,delta_r:417,delta_sigma:366,delx:186,delz:186,demand:285,demo:11,demon:270,demonstr:[280,407],den:276,dendrim:390,denniston:[9,236,238,239,240,272],denomin:[7,169],denot:[118,218,234,272,283,285,376,389,391,420,424,426],dens:[71,211,384],densiti:[3,6,7,9,18,40,41,59,100,116,126,140,150,162,164,193,194,198,201,204,205,208,214,223,236,239,242,243,272,276,277,281,317,322,348,350,354,361,366,382,407,408,409,417,421,430,432,433,434,454,463,464,472,478],density_continu:426,density_summ:426,depart:[0,7],departur:[247,280],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,108,109,112,113,114,115,119,140,142,147,151,152,158,164,165,170,171,172,173,174,175,176,178,179,181,182,183,184,186,187,188,189,192,193,194,195,196,199,201,203,204,206,207,208,210,212,220,221,224,227,228,229,231,233,234,236,238,239,246,249,251,252,253,254,255,256,264,266,267,269,271,282,285,287,290,292,293,299,305,308,309,310,312,314,316,317,319,321,322,325,326,327,328,330,331,332,333,334,335,336,339,341,346,348,353,354,356,357,358,360,361,362,364,365,366,367,368,369,370,371,372,373,374,375,376,377,379,380,382,383,384,385,386,387,388,389,390,391,394,396,397,398,399,400,401,402,403,404,405,407,408,410,412,413,414,416,417,419,420,421,422,427,428,436,437,438,439,440,441,442,443,445,446,447,449,451,454,456,457,460,464,466,468,471,472,473,479,480],dependend:6,depflag:12,dephas:[449,468],depos:215,deposit:[],deprec:281,depth:[51,143,188,317,387,421],dequidt:9,der:[87,107,374,375,404,419,420,446,474],deriv:[6,7,8,38,56,63,87,140,158,184,202,212,214,225,233,246,249,251,252,253,254,255,271,277,281,285,314,315,317,322,323,326,352,354,362,366,374,379,384,385,389,398,402,403,407,419,420,436,438,446,474],derjagin:446,derlet:271,descend:189,descent:[7,352],descib:[40,281],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,110,113,116,118,130,140,141,143,144,148,149,152,155,157,158,162,163,164,166,167,176,181,184,187,192,193,194,201,202,203,204,205,206,208,211,212,213,214,215,217,218,226,227,230,231,232,233,234,235,236,238,239,240,244,248,249,250,253,260,268,271,273,278,279,280,281,282,283,290,294,302,305,306,307,308,309,310,311,312,313,314,315,320,322,323,325,330,345,346,348,351,352,353,354,355,359,362,363,365,367,368,369,371,372,373,374,375,376,379,382,384,385,387,388,389,391,396,397,398,399,400,401,402,403,404,405,406,407,410,416,417,418,419,420,421,422,427,428,435,436,437,438,439,440,441,442,445,446,447,449,451,452,454,455,457,458,464,467,468,471,479,480,481],descript:[],descriptor:[140,187,392],deserno:346,design:[0,3,6,7,8,11,13,14,15,17,118,146,149,163,198,211,217,218,249,250,271,272,291,312,317,363,364,365,368,371,376,378,384,404,405,406,408,409,417,420,438,463],desir:[2,3,6,7,11,12,14,15,16,18,33,40,50,59,71,88,91,112,117,141,146,164,177,186,199,212,214,223,225,226,233,234,235,239,249,267,275,276,277,278,281,285,290,293,305,308,309,310,311,316,323,337,342,345,346,348,351,353,354,355,380,382,390,405,406,437,439,441,450,451,452,454,458,463,468,469,471,472,479,480,481],desk:7,desktop:[4,6,7,10,12,17,188],despit:474,destabil:366,destre:339,destroi:[11,39,209,210],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,93,102,104,106,107,109,111,112,114,117,119,140,141,142,143,144,147,157,158,159,161,164,165,168,169,172,183,187,188,189,192,193,194,198,201,202,203,204,206,208,210,211,212,213,214,215,223,225,226,227,228,230,231,233,235,236,240,246,247,248,249,250,251,252,253,254,255,259,261,266,267,268,269,272,275,276,277,279,280,282,283,284,290,293,305,308,309,310,311,312,313,315,316,317,318,319,320,321,328,330,332,340,345,346,349,353,354,356,357,360,361,362,363,365,366,368,370,371,372,373,374,375,376,379,380,384,385,387,388,389,390,391,394,396,397,398,399,400,401,402,403,404,405,406,407,410,411,416,419,420,421,427,428,436,443,445,446,452,454,455,456,457,459,460,463,464,466,469,472,479,480,483],detect:[2,3,12,61,63,86,224,276,316,355,375,390,395,449,451,454,465,468,479],determ:360,determin:[1,3,6,8,12,15,39,40,42,51,57,58,59,61,62,68,71,87,102,107,109,112,118,119,127,141,152,153,162,163,164,186,187,188,189,190,191,195,196,197,200,201,202,203,204,205,206,207,208,212,214,215,218,220,225,228,229,231,233,234,239,244,246,247,249,254,255,266,267,269,271,273,277,280,287,288,289,290,291,292,295,297,299,305,308,309,310,312,318,319,322,323,324,325,326,327,328,340,345,346,348,354,356,357,360,362,363,370,375,379,381,382,386,388,391,392,400,407,411,420,421,435,438,442,446,451,454,455,457,459,461,464,468,470,471,478,479,480],detil:108,devan:[9,422],devanathan:441,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,230,253,275,280,281,284,362,366,384,409,456],devemi:9,deviat:[247,253,271,386],devic:[1,3,12,15,17,230,360],device_typ:360,devin:[282,375],devis:409,dfactor:188,dff:474,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,346],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,284],dhi:[59,186,214,276],dhug:[247,280],dhugoniot:[247,280],dia:407,diagnost:[],diagon:[3,6,83,140,141,212,249,277,290,320,424,426],diagonalstyl:427,diagram:[41,118,163,183,208,273],diallo:390,diam:[188,189,276,354],diamet:[3,6,40,113,164,187,188,189,193,194,233,276,290,305,321,323,354,374,387,388,394,398,421,443,446,454,455,464],diamond:[348,384,407],diamter:[40,276],dick:6,dicsuss:246,dictat:[199,247],did:[3,12,353,380,381,382,388,411,439,441,462],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,160,319,345],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,94,96,97,120,140,142,143,144,145,147,150,151,152,153,154,156,157,158,164,165,167,172,183,184,186,187,188,189,192,194,197,199,201,203,208,209,210,211,212,213,214,218,224,225,226,227,228,229,230,233,234,236,246,249,250,251,252,254,255,257,259,262,264,265,266,269,271,273,275,277,280,281,282,285,288,290,293,294,302,303,305,308,309,310,313,314,315,317,320,321,322,323,326,330,331,340,342,344,345,346,348,349,351,352,354,355,357,358,359,360,361,362,366,370,371,373,374,375,380,382,384,387,388,389,391,394,396,397,399,400,407,408,409,410,411,413,417,419,420,421,422,423,424,426,427,428,436,437,438,439,441,443,446,447,448,449,451,452,454,456,457,458,459,462,463,464,466,468,469,471,472,474,478,479,480,481],differenti:[1,3,6,29,184,345,376,417,440],difficult:[212,273,360,390,463],difficulti:[293,419],diffract:[],diffus:[],digit:[2,3,189,330],dih_table1:184,dih_table2:184,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:210,dihydrid:384,dij:293,dilat:[],dim1:3,dim2:3,dim:[3,59,71,142,145,146,147,150,151,152,153,154,156,164,186,204,214,231,323,348,407,457,478,479,480],dimdim:479,dimems:272,dimens:[],dimension:[3,39,112,118,140,142,144,145,146,147,150,151,152,153,154,156,163,185,201,204,248,272,317,348,351,355,417,454,464],dimensionless:[105,121,122,124,127,129,131,136,140,317,346,427,446],dimentionless:135,dimer:[6,290,407],dimgrai:189,dimstr:[41,208],dinola:[277,308],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,187,307,474],dir1:465,dir2:465,dir:[1,3,4,8,11,12,247,271,280,304,417,419,420,452,465,479],dirac:140,direc:417,direct:[],directli:[3,6,8,9,11,12,87,113,140,187,188,195,220,227,231,236,272,291,309,321,323,324,325,326,348,352,360,361,362,367,369,370,376,379,382,384,396,400,411,414,422,435,452,464,465,466,472,479],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,60,190,213,232,275,281,284,301,305,314,315,355,359,361,362,366,373,375,376,382,383,385,392,393,404,407,408,409,413,417,418,419,420,427,437,439,440,441,452,454,455,456,465,479],disabl:[3,12,16,317,395,452,467],disadvantag:[6,208],disallow:[214,249],disappear:456,discard:[2,3,41,71,204,208,318,326,451,456,457],discontinu:[9,184,353,402],discourag:407,discov:[13,318],discret:[6,8,40,42,188,189,233,236],discuss:[],disk:[6,84,85,157,185,215,225,276,452],disloc:70,disord:[39,70],disp:[],dispar:421,disperion:[379,400],dispers:[3,6,7,9,162,272,345,346,370,379,400,405,411,420,438],displac:[],displace_atom:[],displace_box:59,displacemet:457,displai:[11,13,22,37,44,55,172,183,187,188,332,340,373,436],dispters:3,dissip:[6,226,233,272,314,315,368,380,388,405,406,436],dissolut:209,dist:[6,69,91,108,117,187,273,289,381,435,449,480],distanc:[3,6,7,9,12,20,21,29,39,43,45,46,47,48,49,51,53,54,55,56,58,59,61,63,64,66,69,71,72,73,74,75,76,77,81,86,89,90,93,103,104,105,106,108,114,115,116,117,118,120,134,140,153,159,162,164,165,166,167,171,186,187,188,189,197,201,204,205,209,210,211,212,214,215,216,219,225,231,236,246,247,248,249,253,261,271,272,276,280,281,288,289,290,293,294,298,302,303,304,305,312,313,315,316,317,320,322,323,324,325,326,327,331,345,346,348,351,353,355,356,357,360,363,364,365,366,367,368,369,370,371,372,374,376,377,378,379,380,381,382,383,384,386,387,388,389,390,394,395,396,397,398,399,400,401,402,403,404,405,406,407,410,411,412,413,414,415,416,417,419,420,421,422,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,449,452,454,457,463,464,468,472,474,478,480],distinct:[6,218,287,345,421],distinguish:[6,86,140,239,384],distort:361,distrbut:361,distribut:[],distro:[111,373,416,417],ditto:[8,11,12,14,15,16,17,18,115,210,452],div:8,divd:117,diverg:[3,12,39,290,315,456,474,481],divid:[3,6,16,41,91,112,117,126,128,141,161,162,172,183,189,201,202,203,208,214,271,313,320,325,345,353,355,385,420,463,471,479],divis:[6,236,366,394,404,451,454,472,479],dl_poli:7,dlambda:158,dlammps_async_imd:230,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,188],dlammps_gzip:[3,12,187,188,316,454,455,459],dlammps_jpeg:[3,12,188],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,188],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,187],dlen:464,dlmp_intel_offload:[12,16],dlo:[59,186,214,276],dlvo:[7,374,446],dm_lb:236,dmax:[305,351],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,93,102,104,105,106,107,109,111,112,114,117,119,141,143,144,157,159,161,164,165,166,172,183,187,188,189,190,192,193,194,199,200,201,202,203,204,205,206,215,225,233,234,244,249,250,254,255,259,266,267,268,269,276,279,290,302,305,308,309,310,319,32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,92,108,115,118,127,130,131,132,133,134,136,137,138,162,184,189,203,204,205,213,280,328,354,366,383,407,413,420,427,437,438,439,440,441],entropi:468,entry1:[38,56,189,373,438],entry2:189,entryn:189,enumer:[165,187],enumuer:6,env:360,environ:[1,3,6,11,12,16,17,18,188,227,232,271,360,361,366,373,375,383,384,417,439,451,465,479],epair:[107,189,386,390,419,420,472],epen:[419,420],epfl:[227,232],epp:379,epq:379,eps0:446,eps14:404,epsilon0:441,epsilon:[3,6,36,45,46,50,53,54,87,170,193,194,225,290,305,322,326,351,353,365,371,372,374,376,377,378,379,387,389,390,391,394,395,396,397,398,399,400,401,402,403,404,410,414,421,422,431,437,443,445,446,463,474,478],epsilon_0:447,epsilon_14:371,epsilon_:421,epsilon_d:377,epsilon_i:[387,411,421],epsilon_i_:421,epsilon_i_a:[387,421],epsilon_i_b:[387,421],epsilon_i_c:[387,421],epsilon_ij:411,epsilon_j:[387,411,421],epsilon_j_:421,epsilon_j_a:[387,421],epsilon_j_b:[387,421],epsilon_j_c:[387,421],epsilon_lj:421,epton:416,eqch:159,eqeq:[419,420],eqp:379,eqq:379,equal:[2,3,6,8,11,12,17,39,41,54,63,65,68,69,76,79,86,87,91,92,108,110,115,117,119,141,143,158,160,164,188,189,192,193,194,195,196,199,202,203,206,207,208,212,214,215,220,225,226,228,229,231,233,234,236,239,240,246,247,253,263,271,273,276,278,280,281,282,285,287,289,290,292,294,299,301,308,309,310,313,314,315,317,319,320,322,325,327,328,330,344,353,355,356,357,359,360,375,380,386,387,390,405,410,417,419,420,421,423,424,425,427,428,438,443,447,450,451,452,454,456,457,461,462,465,468,470,472,479,480],equat:[3,6,7,8,9,91,112,118,163,172,183,192,212,218,219,227,233,234,236,239,247,248,249,250,253,267,271,273,280,281,285,293,305,313,317,320,322,323,325,327,339,345,346,374,379,380,384,385,388,393,405,406,407,411,421,424,426,430,431,433,434,442,447,474],equi:250,equidist:248,equil:[3,281,349,461,483],equilater:464,equilibr:[3,4,5,6,7,9,59,91,164,192,199,202,211,212,225,247,249,250,267,268,280,281,282,283,313,314,315,320,375,376,419,420,450,464],equilibria:320,equilibribum:[209,210],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,147,148,171,173,212,214,225,226,227,234,236,249,253,267,280,285,289,293,294,302,305,312,313,315,320,331,333,336,339,375,407,413,474],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:198,equival:[6,12,13,59,124,125,133,138,162,166,189,203,206,212,214,225,233,249,267,277,289,290,325,380,384,439,441,454,457,462,463,472,474],equlibrium:6,equliibr:[281,283],er3:163,eradiu:[40,113,384,454],eras:[292,314],erat:[214,406],erc:376,erfc:[376,396,411],erforc:113,erg:478,erhart:[199,382,439,441],ermscal:363,ernst:9,eror:3,eros:407,erose_form:407,erot:[],errata:[439,441],erratum:322,erron:3,error:[],erta:388,ervel:[113,454],escap:[215,474],especi:[8,11,16,152,164,192,199,208,225,280,285,288,289,360,451],espresso:[9,284],essenti:[8,11,12,27,88,128,145,146,147,150,151,152,153,154,156,173,202,253,272,321,346,362,376,396,441,459,472],essex:29,establish:[87,229],estim:[1,3,6,10,12,38,41,56,91,141,198,208,219,247,305,312,345,346,351,411,420,438,468,472],esu:478,esub:407,eta:[6,236,249,280,281,283,321,383,385,387,417,440,478],eta_dot:249,eta_ij:417,eta_ji:385,etag:[40,454],etail:472,etap:249,etap_dot:249,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,17,39,40,42,54,61,68,89,90,91,94,109,110,113,115,141,142,144,145,146,147,148,150,151,152,153,154,156,158,164,166,167,168,177,187,188,189,192,198,199,200,201,203,204,205,206,209,210,214,215,223,225,226,233,249,276,287,291,317,318,326,330,344,345,353,354,355,356,358,382,383,391,404,406,415,419,420,437,439,441,449,452,454,455,456,461,463,464,468,470,471,472,474,478,479,481,483],ethernet:18,etol:[353,355,449,468],etot0:280,etot:[6,94,96,97,110,141,150,189,218,234,247,280,471,472],eu2:163,eu3:163,euler:[353,355],eulerian:198,euqat:429,europhi:236,evalu:[2,3,11,12,38,56,71,87,88,91,107,117,140,144,154,162,164,187,188,189,193,194,195,196,198,200,201,202,203,204,205,206,207,214,220,226,228,229,231,232,233,234,272,278,281,292,295,299,308,309,310,319,322,325,327,328,330,345,346,351,353,360,411,417,423,425,438,449,450,452,456,457,459,461,462,463,464,468,470,472,479,480],evalut:[330,452],evan:[152,267],evanseck:[6,20,170,371,466],evapor:[],evaul:[8,353],evdwl:[107,419,420,472],even:[3,6,8,12,15,16,17,18,34,39,41,52,57,59,61,63,70,71,119,165,166,180,184,187,189,192,193,194,199,200,201,203,204,205,206,208,209,210,212,214,215,218,231,234,247,249,250,272,285,287,290,291,301,305,313,317,320,322,326,328,338,345,351,353,355,360,365,384,385,388,391,411,421,444,454,455,457,459,460,461,463,464,466,469,471,472,474,483],evenli:[3,41,141,184,208,236,394,444,454],event:[],eventu:[3,6,12,15,166,281,468],ever:[54,56,232,305],evera:[374,387,421,436],everi:[0,1,2,3,6,8,11,12,15,16,39,41,71,72,91,113,119,128,152,167,187,188,189,190,192,193,194,195,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,219,222,223,225,227,229,230,231,236,237,245,249,250,253,270,271,272,276,277,278,279,280,281,282,283,285,287,288,290,291,293,294,305,307,308,309,310,311,312,313,316,317,318,319,320,328,330,344,346,355,356,357,360,380,381,391,404,419,420,432,448,449,450,454,456,458,459,461,462,463,468,469,470,472,479,483],everyth:[8,107],everywher:[116,398],eviri:384,evolut:[227,236,273,449],evolv:[236,273,318],ewald:[2,3,5,6,7,8,12,88,110,118,141,318,345,346,353,367,369,370,376,379,384,396,400,414,422,436,438,456],ewald_disp:379,ewalddisp:3,exact:[22,41,44,71,122,158,167,172,208,211,226,227,233,234,235,276,285,286,305,317,332,345,373,456,461,468,481,483],exactli:[3,6,12,14,17,38,41,56,59,71,91,143,148,155,164,184,193,194,203,208,214,219,226,233,234,235,250,260,261,268,272,280,305,310,311,324,360,373,380,382,388,391,394,405,411,438,456,457,464,468,479],exager:474,examin:[6,8,211,272],examp:[452,479],exampl:[],exce:[3,6,16,17,18,41,58,71,166,201,204,205,208,212,214,219,222,249,272,296,297,305,353,360,454,479],exceed:[3,41,59,208,214,249,305,462],excel:384,except:[1,2,5,6,8,11,14,16,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,108,109,112,117,141,142,143,144,145,146,147,148,150,151,152,153,154,155,156,157,164,168,170,171,172,173,174,175,176,178,179,181,182,183,184,186,187,189,192,195,201,202,203,207,208,212,214,221,224,225,228,231,233,235,249,250,251,252,253,254,255,256,260,261,264,266,267,268,269,273,282,283,290,292,293,302,305,308,310,311,317,321,328,330,331,332,333,334,335,336,339,340,341,345,346,348,350,354,355,356,358,359,360,361,362,364,367,368,369,370,371,372,373,374,375,376,378,379,380,382,383,384,385,386,387,388,389,390,391,394,396,397,398,399,400,401,402,403,404,405,406,408,412,413,414,416,419,420,421,422,428,436,437,438,439,440,441,443,445,446,447,449,451,452,454,456,457,459,462,463,464,465,466,468,472,474,478,479,480,482],excess:384,exchang:[2,3,6,8,9,61,62,192,198,199,225,233,282,290,313,317,320,345,360,384,469],exchange:345,excit:[9,384],exclud:[3,6,9,12,16,17,63,71,112,140,144,151,152,168,187,201,204,209,210,237,245,275,288,290,312,323,328,353,354,356,368,388,391,405,406,411,435,466],exclus:[1,3,9,12,16,87,360,375,411,463],excurs:449,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,165,188,230,284,330,344,347,359,450,452,462,465,468,479],exemplari:226,exemplifi:384,exert:[6,231,234,285,324,325,326,346],exhaust:[198,359,479],exhibit:[249,352,384,463],exist:[3,6,7,8,11,12,13,37,55,59,68,70,122,164,165,183,188,189,192,197,207,210,212,215,225,275,276,278,328,331,333,334,336,340,349,354,360,391,419,444,450,452,454,455,456,465,466,467,479,480,481],exit:[2,3,11,12,41,57,187,208,344,359,452,453,462,471,479],exlanatori:3,exp:[],expand:[],expans:[12,140,187,465],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,102,145,156,162,184,208,220,225,227,246,271,277,279,280,285,290,328,346,356,373,407,411,449,452,454,456,459,463,468,479],expens:[6,10,71,189,271,275,290,317,328,345,346,356,360,452],experi:[6,13,15,17,207,215,230,239,248,277,289,290,351,355,380,411,463,468],experienc:[6,12,238,239],experiment:[345,360,468],expert:12,expertis:7,explain:[1,3,6,8,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,92,144,152,184,187,188,189,192,201,202,206,208,210,212,214,249,271,279,290,302,328,330,344,345,348,354,355,359,365,382,394,428,443,447,452,455,456,459,461,464,474,479,483],explan:[3,6,59,113,140,187,201,248,271,391,448,451,452,454,463],explanatori:[3,8,117,187,200,201,203,204,205,290,354,451,479],explantori:[3,286],explic:410,explicit:[6,9,11,22,44,77,87,113,116,158,172,193,194,214,296,297,332,350,362,363,366,371,373,382,384,395,405,442,448,451,455,458],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,109,112,142,151,154,162,164,170,171,173,174,175,176,178,179,181,182,184,187,189,195,204,207,214,221,224,226,228,233,249,251,252,253,254,255,256,264,266,267,269,279,280,282,290,292,293,308,310,311,317,321,331,333,334,335,336,339,341,354,360,361,362,364,367,368,369,370,371,372,373,374,375,376,377,379,380,381,382,383,385,386,387,388,389,390,391,394,395,396,397,398,399,400,401,402,403,404,405,408,411,412,413,414,416,421,422,428,429,430,431,432,433,434,436,437,438,439,440,441,442,443,445,446,447,454,456,463,464,466,467,474],explictli:[16,467],exploit:[9,15,17,273],explor:[118,163],expon:[3,281,283,382,387,390,404,410,422],exponenti:[87,417,437,447,468,479],expos:11,exposit:[198,380,381],express:[6,140,150,164,193,194,212,246,271,281,317,323,330,366,382,384,398,407,427,436,479],expressiont:366,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,94,97,98,107,109,117,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,192,195,196,199,206,207,213,216,220,223,224,225,227,228,229,231,233,235,247,249,253,261,271,272,288,289,290,292,294,299,302,304,308,309,310,311,312,314,315,317,319,322,326,327,387,407,420,421,427,471,472],extent:[1,3,41,45,57,71,162,166,187,197,204,208,231,324,327,345,348,362,423,425,438,451,454,457],exterior:[3,6,326],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,102,109,110,112,118,141,142,143,145,147,150,151,152,153,154,156,157,163,164,165,166,170,189,203,208,210,249,278,279,280,290,305,353,354,357,358,379,388,391,394,407,411,451,452,454,457,466,474,479],extract:[3,6,11,13,36,63,87,107,115,117,119,193,194,283,355,376,385,407,427,452,459,471],extract_atom:11,extract_comput:[11,452],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,188,212,214,249,315,384,440,474],extrema:404,extrins:198,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[160,319],f_a:[439,440,441],f_ave:117,f_c:440,f_f:441,f_fix_id:280,f_harm:315,f_i:417,f_id:[6,71,117,119,187,192,200,201,202,203,204,205,206,244,307,319,472,479],f_ij:417,f_indent:206,f_int:314,f_jj:91,f_k:417,f_langevin:317,f_max:[280,285],f_msst:247,f_r:[234,439,440,441],f_sigma:366,f_solid:315,f_ss:6,f_temp:234,face:[3,6,57,59,71,152,162,166,197,204,205,322,324,325,326,327,348,387,407,421,454,457],face_threshold:162,facet:162,facil:[0,12],facilit:[6,13],fact:[6,8,16,227,305,315,388,466],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,118,140,158,163,166,170,181,187,188,189,193,194,202,208,212,214,215,225,230,233,235,236,247,249,250,253,273,277,289,293,295,297,305,309,313,320,321,322,326,336,346,348,360,362,363,366,367,369,371,376,377,378,380,384,388,391,395,396,407,411,413,414,420,422,428,437,442,451,454,457,458,463,466,468,469,472,474,478,479],factori:[3,452],factoriz:345,fail:[3,11,12,59,168,212,215,345,353,355,378,420,452],failur:[121,424],fairli:[11,411,463,468],faken:73,falcon:230,fall:[3,6,189,203,276,452],fals:[86,328,330,479],fame:8,famili:451,familiar:[0,11],fan:417,far:[3,6,12,17,57,59,61,86,187,189,190,208,209,210,212,215,249,271,289,290,305,322,333,336,351,355,356,443,452,454,459,472],farago:233,farrel:[439,441],farther:187,fashion:[6,8,41,71,164,189,192,193,194,199,204,208,210,215,225,227,231,246,247,249,251,252,253,254,255,263,266,267,268,269,279,280,282,290,294,298,304,307,315,317,321,322,323,325,327,355,391,405,457,466,479,482],fasolino:393,fast:[6,7,9,12,13,17,39,187,258,280,318,345,346,368,405,406,436,438,456,461,463,472,480,483],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,105,109,112,142,151,170,171,173,174,175,176,178,179,181,182,184,187,189,192,195,207,208,221,224,228,232,233,249,251,252,253,254,255,256,264,266,267,269,277,281,282,290,292,293,305,308,310,312,314,317,321,331,333,334,335,336,339,341,345,346,357,358,360,361,362,364,366,367,368,369,370,371,372,373,374,375,376,379,380,382,383,385,386,387,388,389,390,391,394,396,397,398,399,400,401,402,403,404,405,408,412,413,414,416,421,422,428,436,437,438,439,440,441,443,445,446,447,449,463,467,474],fastest:[6,14,17,152,204,317,318,360,451],fatal:[3,471],fault:[70,420],faulti:12,fava:387,favor:211,favorit:7,fbmc:312,fcc:[],fcm:[263,479],fdirect:218,fdotr:392,fdti:87,fe2:163,fe3:163,fe_md_boundari:198,featu:8,featur:[],fecr:382,feedback:[7,230],feel:[7,230,231,239,271,326,328,355,411],felling:409,felt:326,femtosecond:478,fene:[],fennel:[376,396],fep:[],ferguson:[6,170,466],fermi:[1,12,15,150,360,441],fermion:[9,384],ferrand:[9,13],few:[1,3,4,5,6,7,10,11,12,13,14,17,18,39,190,200,201,202,203,204,205,206,234,249,276,279,281,293,319,345,353,354,355,362,451,454,459,463,465,479,481],fewer:[1,3,11,15,16,61,239,463],fewest:3,fextern:223,feynman:273,fff:452,ffield:[375,385,419,420],ffmpeg:[3,12,188],ffplai:188,fft:[1,3,7,12,14,15,88,109,110,141,272,345,346,463],fft_inc:[12,346],fft_lib:12,fft_path:12,fftbench:345,fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],fictiti:[6,195,196,220,223,227,273,289,376,396,400,435],field1:[455,459],field2:455,field:[],fifth:[302,413],figur:[1,3,8,11,12,280,451,452],fij:379,file0:271,file1:[11,13,271,316,330,354,459,461,465],file2:[11,13,316,330,354,459,461,465],file:[],filenam:[3,12,13,38,41,56,184,187,188,189,190,198,201,202,203,204,205,206,208,213,271,275,278,281,282,283,286,287,290,291,316,317,342,343,344,355,361,362,366,376,382,383,385,393,407,408,409,413,417,418,419,420,427,437,438,439,440,441,450,451,452,455,456,461,465,472,479,481,482,483],filennam:461,filep:[3,187,189,456,461,483],filepo:287,fill:[7,164,188,276,317,348,356,366,420,457],filter:[189,198],final_integr:8,final_integrate_respa:8,finchham:[6,146,378],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,117,167,184,190,199,211,212,222,225,248,271,277,285,289,351,353,355,356,376,391,396,400,407,436,438,474,479],find_custom:8,fine:[16,17,168,195,220,315,356,360,479],finer:[140,164,479],finest:345,finger:[164,186,246,457],finish:[6,11,41,208,330,342,344,345,357,359,360,443,459,479,480],finit:[],finni:[7,382,436],finvers:218,fiorin:[9,213],fire:[351,352,353,355,468],firebrick:189,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,103,104,105,112,116,117,127,130,133,134,138,141,149,152,158,160,162,163,165,166,167,171,184,187,188,189,190,192,199,201,202,203,204,205,206,208,211,214,225,226,231,236,246,247,248,249,271,273,278,279,280,282,287,290,293,294,302,303,305,306,307,314,315,316,317,319,323,328,330,331,337,348,353,354,355,356,359,360,361,362,365,366,367,369,371,373,375,376,382,384,385,388,389,392,393,395,396,400,405,406,407,409,411,413,417,419,420,427,435,437,438,439,440,441,449,450,451,452,454,455,456,459,461,463,466,467,468,471,472,474,479,480,481,483],fischer:[6,9,19,20,170,371,466],fit:[3,6,9,12,38,56,184,289,305,362,366,393,407,411,431,438,440,462,479],five:[73,150,280,354,366,408,454,468],fix:[],fix_adapt:[158,194,404],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,199,276],fix_evapor:199,fix_flux:198,fix_gcmc:[199,354],fix_gl:227,fix_gld:227,fix_grav:276,fix_id:[3,212,247,249,251,252,253,254,255,277,280],fix_modifi:[],fix_mov:[186,323],fix_nh:8,fix_npt:227,fix_nvt:[199,225],fix_poem:[3,6],fix_pour:[3,215],fix_qbmsst:9,fix_qeq:[3,375],fix_rattl:293,fix_reax_bond:419,fix_rigid:[239,365],fix_saed_vtk:291,fix_setforc:8,fix_shak:293,fix_srd:3,fix_styl:253,fix_temp_rescal:311,fixedpoint:[212,249],fixextern:223,fixid:198,fji:379,flag1:[217,358],flag2:[217,358],flag:[3,8,11,12,14,15,16,17,18,40,66,74,75,81,86,89,90,93,103,104,106,118,159,163,167,187,188,189,190,206,211,213,217,230,233,237,239,245,246,272,279,290,302,304,305,312,316,325,328,343,346,354,358,359,360,362,390,395,407,435,449,451,452,454,455,456,458,459,460,464,479],flag_buck:370,flag_coul:[370,379,400],flag_lj:[379,400],flagfld:[368,405,406],flaghi:[3,368,405,406],flaglog:[368,405,406],flagn:217,flagvf:[368,405,406],flat:[6,317,322,323,327],flavor:[2,7,12],fld:[9,322,368,405,406],flen:363,flex_press:363,flexibl:[3,6,8,165,188,201,204,213,227,250,313,320,384,440,472],flip:[3,6,214,249,324,325],floor:479,flop:12,floralwhit:189,flow:[],fluctuat:[6,64,87,212,225,226,233,236,249,253,271,272,315,317,339],fluid:[],fluid_veloc:240,flush:[3,189,471],flux:[],flv:188,fly:[7,9,12,41,188,192,198,215,218,290,293,318,366,472,474],fmackai:9,fmag:216,fmass:273,fmax:[353,472],fmomentum:218,fmsec:[2,189,233,234,246,249,277,290,308,309,463,473,478,480],fname:344,fno:12,fnorm:[353,472],fnpt:218,fnvt:218,foce:391,fock:363,focu:293,fogarti:[9,283,420],foil:[140,271,427],fold:[303,463],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,140,141,143,144,150,152,157,160,162,164,165,170,173,174,175,176,178,179,181,182,184,187,188,189,192,198,199,200,201,202,203,204,205,206,208,213,214,215,218,219,223,225,226,227,230,232,233,234,236,239,247,249,253,254,255,266,267,269,272,273,275,278,279,280,281,283,285,287,289,290,291,293,307,308,309,310,313,314,315,316,317,319,320,328,329,333,334,335,336,339,341,343,348,350,353,354,355,360,361,362,363,364,365,366,367,368,369,370,371,372,374,375,376,377,378,379,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,416,417,418,419,420,421,422,424,426,427,428,429,430,431,432,433,434,435,437,438,439,440,441,442,443,445,446,447,449,451,452,454,455,456,457,459,461,462,463,466,468,469,470,474,479,480,482],foo:[4,8,11,12,187,188,223,452,465,479],foot:6,footprint:[12,360],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:239,forcefield:[289,390],forcegroup:236,forcezero:351,ford:379,forestgreen:189,forev:71,forget:[234,474],forgiv:249,form:[2,3,6,8,12,16,19,22,44,54,63,66,74,75,77,81,87,89,90,93,103,104,106,116,140,141,158,159,168,172,189,192,193,194,210,226,227,233,235,239,246,267,272,283,285,289,290,317,322,326,331,332,339,350,352,354,355,362,363,366,373,382,384,386,390,391,395,407,409,413,414,417,419,420,421,427,428,436,438,439,440,441,446,448,451,452,454,459,464,471,474,479],formal:[6,78,80,91,226,227,233,249,273,305,313],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,172,184,187,188,189,190,201,203,204,205,206,208,210,272,275,279,281,283,286,290,291,301,316,317,328,329,332,350,354,355,361,362,366,373,382,385,395,407,409,418,419,420,422,427,438,444,451,452,454,455,456,459,470,471,472,479,481],former:[6,12,16,39,41,189,208,317,321,366,368,460,466,479],formerli:[7,13],formul:[1,40,64,141,195,220,233,249,267,281,283,289,293,316,345,362,366,382,384,387,407,416],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,87,89,90,91,94,96,97,106,112,118,141,142,143,144,145,146,147,148,150,151,152,153,154,155,156,157,163,164,169,171,172,183,187,193,194,195,196,201,202,203,206,207,214,220,228,229,231,233,234,246,271,272,278,287,292,299,303,305,308,309,310,319,322,325,327,328,330,331,332,334,340,348,354,362,363,365,366,371,372,373,374,379,380,382,383,387,388,389,390,392,395,396,398,399,400,402,403,405,406,407,410,411,412,421,422,428,436,437,439,440,441,445,446,447,450,454,457,464,471,472,478,479,480],forth:[1,6,11,12,13,14,15,359,452,457,461],fortran:[3,6,9,11,12,13,223,382,391,407,419,420],fortun:8,forward:[3,8,87,344,355,360],foster:[366,416,417],foul:167,found:[3,6,9,12,73,158,187,211,213,225,230,236,272,312,318,330,344,356,373,376,379,449,455,456,471],four:[6,11,54,81,103,104,140,160,247,317,339,354,355,449],fourier:[],fourth:[6,105,289,302,312,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7,119,307],input:[],input_doubl:3,inquir:295,insensit:12,insert:[3,5,7,8,12,59,164,192,215,225,231,276,345,427,435,452,458,474],insid:[2,3,6,8,11,71,129,135,164,187,189,200,204,205,215,216,222,225,231,236,239,276,290,305,322,324,325,326,327,328,343,348,398,452,453,454,456,457,464,468,479],insight:[6,13],instabl:[236,379,426],instal:[],instanc:[6,11,213,227,324,386,391,411,417,452,474],instantan:[6,63,211,212,226,227,249,253,272,277,280,285,287,290,312,460,472],instanti:[6,11,12,198,391,451],instead:[1,3,6,8,9,11,12,13,17,18,40,41,59,63,70,71,90,117,143,146,168,184,187,194,201,203,204,205,206,208,212,213,233,236,239,240,272,278,288,290,307,325,343,345,346,349,356,360,369,370,382,395,397,404,407,449,457,461,468,470,474,479],institut:[9,230,275],instruct:[3,6,8,11,12,13,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,109,112,142,151,162,170,171,173,174,175,176,178,179,181,182,184,185,188,195,207,221,224,228,233,249,251,252,253,254,255,256,264,266,267,269,282,290,292,293,308,310,321,331,333,334,335,336,339,341,346,360,361,362,364,367,368,369,370,371,372,374,375,376,379,380,382,383,385,386,387,388,389,390,391,394,396,397,398,399,400,401,402,403,404,405,408,412,413,414,416,421,422,428,437,438,439,440,441,443,445,446,447,463,474],insuffici:[3,6,12],insult:249,insur:[3,6,11,12,17,39,40,61,73,102,104,164,165,184,187,188,189,195,209,210,215,220,221,222,223,225,228,233,245,278,279,288,290,305,317,322,326,327,328,330,344,354,356,360,374,387,391,415,421,438,451,452,454,455,459,462,463,471,472,479,480],int_max:3,integ:[3,6,8,11,12,39,40,42,64,68,70,71,113,115,117,119,140,162,164,167,168,170,174,175,179,184,186,187,188,189,199,201,204,205,209,210,211,215,217,223,225,226,227,230,233,234,235,236,272,275,276,279,280,285,290,305,307,309,312,316,317,335,345,348,368,380,381,394,407,419,420,424,426,427,449,451,452,454,462,463,464,468,471,479,480],integr:[],integrate_ulsph:296,intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,8,12,13,36,226,418,454],intens:[1,3,6,9,63,66,74,75,86,89,90,91,93,103,104,105,106,112,114,116,117,118,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,159,160,161,163,192,201,202,203,204,205,206,208,209,210,211,219,222,229,239,247,249,253,287,290,291,305,313,317,319,320,471,472],intepol:479,inter:[14,18,42,61,62,144,167,168,187,211,233,235,248,282,290,345,355,366,464,474,479,481,483],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,37,39,42,44,50,54,55,57,61,63,65,69,77,79,87,88,92,107,108,110,112,115,116,122,123,124,125,127,128,129,130,131,132,133,135,136,137,138,140,141,143,157,158,162,165,166,167,168,169,170,172,176,177,183,187,192,193,194,209,210,211,224,225,230,231,233,235,239,261,271,273,275,281,283,289,290,296,297,305,306,312,317,321,322,323,326,327,332,333,334,336,340,345,346,353,354,355,356,357,358,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,414,416,417,420,421,422,424,426,427,428,435,436,437,439,440,441,442,443,444,445,446,447,449,452,454,456,458,459,463,464,466,471,472,474,481],interatom:[3,4,7,164,187,248,314,315,361,366,382,384,392,407,440,479],intercept:118,interchang:6,interconnect:18,interconvert:384,intereract:39,interesect:326,interest:[1,5,7,8,9,11,13,71,163,273,312,315,346,383,406,419,420,452,479],interf:360,interfac:[],interfer:[249,362],interg:[6,474],intergr:[463,467],interi:406,interior:[3,6,41,326,457],interlac:407,interleav:[6,164,462],intermedi:[6,12,59,188,248,271,339,355,452,453,462,466],intermix:449,intermolecular:362,intern:[0,2,3,5,6,9,11,16,20,21,24,28,32,35,36,39,40,42,63,87,99,101,118,141,144,146,163,171,184,188,189,192,193,194,198,210,214,218,230,242,243,247,249,253,272,290,294,331,333,336,339,343,353,354,429,430,438,452,454,456,459,468,471,472,478,479,480,481],internal_element_set:198,internal_quadratur:198,internet:232,interpenetr:407,interpentr:[430,431,433],interpol:[6,15,38,56,100,184,188,189,198,236,271,345,346,355,366,411,420,432,438,439],interpret:[2,6,11,188,203,388,428,449,452,468,479],interrupt:280,intersect:[3,6,118,189,326,328,457],intersert:326,interspers:353,interstiti:162,intertia:[3,93],interv:[3,6,91,202,233,280,285,286,297,432,449,468,479],intestieti:118,intial:[6,360,362],intiial:[41,459],intiti:[3,304],intra:290,intra_energi:225,intramolecular:[29,225],introduc:[6,9,188,249,280,285,290,339,345,361,376,384,396,400,404,437,468],introduct:[],intsal:16,intuit:348,inv:[118,163,291],invalid:[3,12,71,89,167,261,355,405,406,456],invari:[133,138,140],invent:293,invers:[],invert:[6,168,272],invis:326,invoc:[162,211,360,424,426,452],invok:[1,3,6,7,8,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,59,63,66,71,74,75,81,87,88,89,90,93,103,104,106,109,110,111,112,117,142,151,158,159,162,164,165,167,168,170,171,173,174,175,176,178,179,181,182,184,187,188,189,190,192,193,194,195,196,197,198,199,200,201,2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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff 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 hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff 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 hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso_e/atom command","compute meso_rho/atom command","compute meso_t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact_radius command","compute smd/damage command","compute smd/hourglass_error command","compute smd/internal_energy command","compute smd/plastic_strain command","compute smd/plastic_strain_rate command","compute smd/rho command","compute smd/tlsph_defgrad command","compute smd/tlsph_dt command","compute smd/tlsph_num_neighs command","compute smd/tlsph_shape command","compute smd/tlsph_strain command","compute smd/tlsph_strain_rate command","compute smd/tlsph_stress command","compute smd/triangle_mesh_vertices","compute smd/ulsph_num_neighs command","compute smd/ulsph_strain command","compute smd/ulsph_strain_rate command","compute smd/ulsph_stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute temp command","compute temp/asphere command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian 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_coeff 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 dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim 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 hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/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 meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":209,"default":[37,39,40,55,57,58,59,61,62,71,87,88,102,103,105,107,118,122,123,140,144,152,153,157,163,164,167,169,183,185,186,187,188,189,190,191,193,194,195,197,198,199,201,204,205,206,209,210,212,213,214,215,219,222,225,226,231,233,234,235,236,237,239,244,247,249,250,253,267,268,272,273,276,277,278,279,280,282,285,287,288,290,291,305,307,312,313,314,315,318,320,322,324,328,340,343,345,346,348,349,351,352,354,356,357,358,360,363,366,368,384,405,406,411,419,420,435,436,449,450,451,454,455,457,459,461,462,463,466,468,470,471,472,473,478,480,481,482],"function":479,"long":[367,369,370,371,372,376,378,379,396,400,404,414,422],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[193,194],addforc:195,addit:[12,13],addtorqu:196,adiabat:6,adjust_dt:295,adp:361,airebo:362,alloi:382,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:197,arrai:6,aspher:[6,82,143,251,254,257,258,266],atc:[9,198],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,95,96,99,100,101,110,111,113,140,141,162,197,199,200,279,479],atom_modifi:39,atom_styl:40,attract:5,aveforc:207,awpmd:[9,363],balanc:[41,208],barostat:6,basal:67,beck:364,berendsen:[277,308],between:6,binary2txt:13,bodi:[6,8,42,68,259,365],bond:[8,13,69,209,210,211,286],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:366,born:[367,378],boundari:[7,57],box:[6,58,212],brownian:368,buck:[369,370,378],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,170,371,404],chunk:[6,66,71,75,90,93,104,106,114,144,159,161,201],citat:7,class2:[21,43,171,331,372],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[322,374,446],colvar:[9,13,213],com:[74,75,145],comb3:375,comb:[282,375],come:5,comm_modifi:61,comm_styl:62,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,475,476,477,478,479,480,481,482,483],common:3,comparison:1,compos:6,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,479],compute_modifi:102,condit:7,conduct:[6,313],constant:6,constraint:7,contact:76,contact_radiu:120,coord:77,core:6,correl:202,cosin:[23,24,25,26,27,28,173],cossq:333,coul:[367,369,370,371,372,376,377,378,389,396,400,404,414,422],coupl:6,creat:210,create_atom:164,create_bond:165,create_box:166,createatom:13,creation:7,csld:309,csvr:309,cubic:398,cuda:[9,14,109,112,142,151,195,207,221,224,228,249,256,292,293,308,310,321,367,369,371,372,382,388,389,396,397,399,402,412,437,439],custom:8,cut:[49,363,369,372,376,379,384,386,396,397,404,410,414],cvff:334,damag:[78,121],data2xmovi:13,data:6,databas:13,deby:[376,396],deform:[147,148,214],delete_atom:167,delete_bond:168,delta:24,deposit:215,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,475,476,477,478,479,480,481,482,483],diagnost:7,diel:377,dielectr:169,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:172,dihedral_styl:[2,170,171,173,174,175,176,177,178,179,180,181,182,183,184],dilat:80,dimens:185,dipol:[6,29,379],direct:218,discuss:6,disp:6,displac:[81,86],displace_atom:186,distribut:[7,12],document:0,dpd:380,drag:216,dreid:[6,390],drude:[6,9,149,217,218,234],dsf:[376,396],dsmc:381,dump:[6,8,187,188,190],dump_modifi:189,dynam:281,eam:[13,382],echo:191,edip:383,eff:[9,13,96,97,148,150,155,235,250,260,268,311,384],efield:220,eim:385,elast:6,emac:13,enforce2d:221,ensembl:7,erot:[82,83,84,85],error:3,evapor:222,event:86,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,467,468,469,470,471,472,473,475,476,477,478,479,480,481,482,483],exp:[27,173],expand:[46,399],extend:[8,11],extern:223,fcc:271,featur:[7,8],fene:[45,46],fep:[9,13,87,194],field:[6,7],file:6,finit:6,fix:[2,6,8,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,479],fix_modifi:[193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327],flow:6,fluid:236,flux:91,forc:[6,7,306],fourier:[30,31,174,335],freez:224,from:[6,11],futur:5,gauss:386,gaybern:387,gcmc:225,gener:[1,6,7,13],get:12,gld:226,gle:227,global:6,gpu:[15,364,367,369,371,372,374,376,379,380,382,386,387,389,396,397,399,410,412,421,422,428,437,438,445,446],gran:[323,388],granular:6,graviti:228,gromac:389,group2ndx:329,group:[88,328,479],gyrat:[89,90],harmon:[32,47,48,49,175,178,322,336,413],hbond:390,heat:[91,229],heatconduct:429,helix:176,hertz:[388,423],histo:203,histori:[5,388],hook:388,hourglass_error:122,how:6,hybrid:[33,50,177,337,391],idealga:430,imag:[187,188],imd:230,implicit:371,improp:[8,92],improper_coeff:332,improper_styl:[2,331,333,334,335,336,337,338,339,340,341],includ:342,inclus:8,indent:231,indic:0,individu:2,induc:6,inertia:93,info:[0,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,343],input:[2,6,8],instal:11,integr:[6,7],integrate_tlsph:296,integrate_ulsph:297,intel:[9,16,371,387,396,437],interfac:[6,11],internal_energi:123,introduct:7,invers:218,ipi:232,ipp:13,jul:0,jump:344,kate:13,keyword:411,kim:392,kokko:17,kspace:[2,8,318],kspace_modifi:345,kspace_styl:[6,346],label:347,lammp:[0,1,2,6,7,8,11,12],langevin:[233,234,235],lattic:348,lcbop:393,librari:[6,11,12],limit:[261,310],line:[12,262,394],linear:403,lineforc:241,list:[2,395],lj1043:322,lj126:322,lj93:322,lj96:397,lmp2arc:13,lmp2cfg:13,lmp2vmd:13,local:[6,65,68,69,79,92,108,115],log:349,lubric:405,lubricateu:406,make:12,mass:350,math:479,matlab:13,meam:[407,408,409],measur:1,meso:[242,243],meso_:99,meso_rho:100,meso_t:101,messag:3,micelle2d:13,mie:410,min_modifi:351,min_styl:352,minim:[8,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,353],misc:9,mod:[317,440],model:[6,7],modifi:8,molecul:354,molfil:[9,187,190],moltempl:13,momentum:[237,245],morri:434,mors:[51,390,412],move:246,move_tri_surf:298,movi:[187,188],mpi:11,msd:[103,104,105],msi2lmp:13,msm:[367,369,371,376,396],msst:247,multi:[6,7,178],multipl:6,nb3b:413,neb:[248,355],neigh_modifi:356,neighbor:357,nemd:6,newton:358,next:359,nharmon:179,noforc:[258,263],non:[6,7],none:[34,52,180,338,415],nongauss:105,nonlinear:53,nph:[249,250,251,252,290],nphug:253,npt:[249,250,254,255,290],nve:[256,257,258,259,260,261,262,263,264,265,290],nvt:[249,250,266,267,268,269,290],omega:106,omp:[9,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,43,45,46,47,48,49,51,53,54,56,170,171,173,174,175,176,178,179,181,182,184,228,249,251,252,253,254,255,256,264,266,267,269,282,331,333,334,335,336,339,341,361,362,364,367,368,369,370,371,372,374,375,376,377,379,380,382,385,386,387,388,389,390,391,394,396,397,398,399,400,401,402,403,404,405,408,409,412,413,414,416,421,422,428,437,438,439,440,441,443,445,446,447],onewai:270,open:7,oper:479,opl:181,opt:[19,371,382,396,400,412],optim:1,option:[6,8,12],orient:271,orthogon:6,other:6,output:[6,7,8,12,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327],overlai:391,overview:11,packag:[1,9,12,14,15,16,17,18,19,360],pair:[6,107,108],pair_coeff:373,pair_modifi:411,pair_styl:[2,361,362,363,364,365,366,367,368,369,370,371,372,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,445,446,447],pair_writ:444,pairwis:8,parallel:11,paramet:6,pars:2,partial:151,particl:[6,7,42],partit:448,past:5,per:6,perform:[1,10],peri:416,period:25,phonon:[9,13,272],pimd:273,piston:324,planeforc:274,plastic:111,plastic_strain:124,plastic_strain_r:125,pmb:416,poem:275,point:281,polariz:6,poli:[368,405,406],polym:13,polymorph:417,post:7,potenti:[2,6,8],pour:276,pppm:6,prd:449,pre:7,press:277,pressur:112,previou:12,print:[278,450],problem:[3,4],process:[6,7],processor:451,profil:152,properti:[6,113,114,115,279],pymol_aspher:13,python:[11,13,452],qbmsst:280,qeq:[281,282,283],qmmm:[9,284],qtb:[9,285],quadrat:182,quantiti:6,quartic:[35,54],quip:418,quit:453,ramp:153,rattl:293,rdf:116,read_data:454,read_dump:455,read_restart:456,reax:[13,283,286,287,419,420],reaxc:9,rebo:362,recent:288,reduc:117,refer:479,reflect:325,region:[8,117,154,155,326,457,479],relat:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,43,44,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,83,84,85,86,87,89,91,92,93,94,95,96,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,181,182,183,184,185,186,187,188,189,190,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,222,224,225,226,227,228,229,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,285,286,287,288,290,291,292,294,295,296,297,298,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,339,340,341,342,343,344,345,346,348,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,459,460,461,462,463,464,466,467,468,469,470,471,472,473,475,476,477,479,480,481,482,483],relax:212,replic:458,replica:[6,7],report:3,requir:12,rerun:459,rescal:[310,311],reset:219,reset_timestep:460,resquar:421,restart2data:13,restart:[6,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,461],restrain:289,restrict:[14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,475,476,477,478,479,480,481,482,483],rho:126,rhosum:432,rigid:[6,83,98,239,290],ring:339,rotat:156,rule:2,run:[6,11,12,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,462],run_styl:463,scalabl:10,scalar:6,screen:12,script:[2,6,8,11,12],sdk:[36,422],self:304,serial:11,set:[6,464],setforc:292,setvel:299,shake:293,share:[11,12],shell:[6,465],shield:281,shift:[26,27,48,49,173],simpl:31,simul:6,size:6,slater:281,slice:119,sllod:[267,268],small:290,smd:[9,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,294,295,296,297,298,299,301,423,424,425,426],smooth:[402,403],sna:140,snad:140,snap:427,snapshot:6,snav:140,soft:[404,428],solver:2,sourc:7,spatial:[204,205],spc:6,speci:287,special:[7,411,479],special_bond:466,sph:[9,429,430,431,432,433,434],sphere:[84,85,157,205,239,252,255,264,269],spheric:6,spline:[408,409],spring:[302,303,304,315],squar:28,srd:[305,327],srp:435,standard:9,start:[12,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327],state:307,stationari:243,stop:[193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327],store:[306,307],strategi:1,streitz:376,stress:141,structur:2,style:[1,2,6,8],submit:8,suffix:467,summari:6,swap:[199,211],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,272,273,274,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,475,476,477,478,479,480,481,482,483],system:6,tabl:[0,6,38,56,184,438,439],tad:468,taitwat:[433,434],temp:[142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,308,309,310,311],temper:469,temperatur:6,tersoff:[439,440,441],test:11,tfmc:312,thermal:[6,313],thermo:[6,470],thermo_modifi:471,thermo_styl:472,thermodynam:[6,8],thermostat:6,thole:442,time:[6,206],timestep:473,tip3p:6,tip4p:[6,376,396,400,404],tip:12,tlsph:424,tlsph_defgrad:127,tlsph_dt:128,tlsph_num_neigh:129,tlsph_shape:130,tlsph_strain:131,tlsph_strain_rat:132,tlsph_stress:133,tmd:316,tool:13,torqu:159,transform:218,tri:[265,443],tri_surfac:425,triangle_mesh_vertic:134,triclin:6,tstat:380,ttm:317,tune:318,type:7,ulsph:426,ulsph_num_neigh:135,ulsph_strain:136,ulsph_strain_r:137,ulsph_stress:138,umbrella:341,uncomput:475,undump:476,unfix:477,unit:478,user:[9,12,14,16,18],vacf:160,valu:[6,479],variabl:[6,8,479],variou:1,vcm:161,vector:[6,319,479],veloc:480,version:[0,5,12],via:12,vim:13,viscos:[6,320],viscou:[240,321],visual:6,vol:139,voronoi:162,vtk:291,wall:[6,322,323,324,325,326,327],wall_surfac:301,warn:3,water:6,weight:203,what:[7,12],wolf:[367,376],wrapper:11,write:6,write_data:481,write_dump:482,write_restart:483,xmgrace:13,xmovi:13,xrd:163,yukawa:[445,446],zbl:[441,447]}})
\ No newline at end of file
diff --git a/doc/set.html b/doc/set.html
index c90a9530f2..35f68d97c8 100644
--- a/doc/set.html
+++ b/doc/set.html
@@ -141,7 +141,7 @@
keyword = type or type/fraction or mol or x or y or z or charge or dipole or dipole/random or quat or quat/random or diameter or shape or length or tri or theta or angmom or mass or density or volume or image or
bond or angle or dihedral or improper or
-meso_e or meso_cv or meso_rho or i_name or d_name
+meso_e or meso_cv or meso_rho or smd_contact_radius or smd_mass_density or i_name or d_name
meso_rho value = density of SPH particles (need units)
value can be an atom-style variable (see below)
+smd_contact_radius = radius for short range interactions, i.e. contact and friction
+ value can be an atom-style variable (see below)
+smd_mass_density = set particle mass based on volume by providing a mass density
+ value can be an atom-style variable (see below)
i_name value = value for custom integer vector with name
- value can be an atom-style variable (see below)
d_name value = value for custom floating-point vector with name
- value can be an atom-style variable (see below)
@@ -405,6 +407,18 @@ mass is set from the density and triangle area (the input density is
assumed to be in mass/distance^2 units). If none of these cases are
valid, then the mass is set to the density value directly (the input
density is assumed to be in mass units).
+
Keyword smd_mass_density also sets the mass of all selected
+particles, but it is only applicable to the Smooth Mach Dynamics
+package USER-SMD. This command assumes that the particle volume has
+already been correctly set and calculates particle mass from the
+provided mass density value.
+
Keyword smd_contact_radius only applies to simulations with the
+Smooth Mach Dynamics package USER-SMD. This command sets an
+interaction radius for computing short-range interactions,
+e.g. repulsive forces to prevent different individual physical bodies
+from penetrating each other. Note that the SPH smoothing kernel
+diameter used for computing long range, nonlocal interactions, is set
+using the diameter keyword.
Keyword volume sets the volume of all selected particles.
Currently, only the atom_style peri dump
-
This command can be useful after a system has been equilibrated and
+specified. This keyword does not allow use of atom-style variables.
+This command can be useful after a system has been equilibrated and
atoms have diffused one or more box lengths in various directions.
This command can then reset the image values for atoms so that they
are effectively inside the simulation box, e.g if a diffusion
diff --git a/doc/set.txt b/doc/set.txt
index 6eb7b17a55..6a4e66dd95 100644
--- a/doc/set.txt
+++ b/doc/set.txt
@@ -21,7 +21,9 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
{length} or {tri} or {theta} or {angmom} or \
{mass} or {density} or {volume} or {image} or
{bond} or {angle} or {dihedral} or {improper} or
- {meso_e} or {meso_cv} or {meso_rho} or {i_name} or {d_name} :l
+ {meso_e} or {meso_cv} or {meso_rho} or \
+ {smd_contact_radius} or {smd_mass_density} or \
+ {i_name} or {d_name} :l
{type} value = atom type
value can be an atom-style variable (see below)
{type/fraction} values = type fraction seed
@@ -80,10 +82,12 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
value can be an atom-style variable (see below)
{meso_rho} value = density of SPH particles (need units)
value can be an atom-style variable (see below)
- {i_name} value = value for custom integer vector with name
+ {smd_contact_radius} = radius for short range interactions, i.e. contact and friction
+ value can be an atom-style variable (see below)
+ {smd_mass_density} = set particle mass based on volume by providing a mass density
value can be an atom-style variable (see below)
- {d_name} value = value for custom floating-point vector with name
- value can be an atom-style variable (see below) :pre
+ {i_name} value = value for custom integer vector with name
+ {d_name} value = value for custom floating-point vector with name :pre
:ule
[Examples:]
@@ -312,6 +316,20 @@ assumed to be in mass/distance^2 units). If none of these cases are
valid, then the mass is set to the density value directly (the input
density is assumed to be in mass units).
+Keyword {smd_mass_density} also sets the mass of all selected
+particles, but it is only applicable to the Smooth Mach Dynamics
+package USER-SMD. This command assumes that the particle volume has
+already been correctly set and calculates particle mass from the
+provided mass density value.
+
+Keyword {smd_contact_radius} only applies to simulations with the
+Smooth Mach Dynamics package USER-SMD. This command sets an
+interaction radius for computing short-range interactions,
+e.g. repulsive forces to prevent different individual physical bodies
+from penetrating each other. Note that the SPH smoothing kernel
+diameter used for computing long range, nonlocal interactions, is set
+using the {diameter} keyword.
+
Keyword {volume} sets the volume of all selected particles.
Currently, only the "atom_style peri"_atom_style.html command defines
particles with a volume attribute. Note that this command does not
@@ -327,7 +345,6 @@ the simulation. The flags can be output with atom snapshots via the
nx,ny,nz, then the current image value for that dimension is
unchanged. For non-periodic dimensions only a value of 0 can be
specified. This keyword does not allow use of atom-style variables.
-
This command can be useful after a system has been equilibrated and
atoms have diffused one or more box lengths in various directions.
This command can then reset the image values for atoms so that they