See (MacKerell) for a description of the CHARMM force -field. See (Cornell) for a description of the AMBER force +
See (MacKerell) for a description of the CHARMM force +field. See (Cornell) for a description of the AMBER force field.
These style choices compute force field formulas that are consistent with common options in CHARMM or AMBER. See each command’s @@ -389,7 +389,7 @@ atoms involved in the bond, angle, or torsion terms. DREIDING has an explicit hydrogen bond term to describe interactions involving a hydrogen atom on very electronegative atoms (N, O, F).
-See (Mayo) for a description of the DREIDING force field
+See (Mayo) for a description of the DREIDING force field
These style choices compute force field formulas that are consistent with the DREIDING force field. See each command’s documentation for the formula it computes.
@@ -587,7 +587,7 @@ computations between frozen atoms by using this command:6.7. TIP3P water model
The TIP3P water model as implemented in CHARMM -(MacKerell) specifies a 3-site rigid water molecule with +(MacKerell) specifies a 3-site rigid water molecule with charges and Lennard-Jones parameters assigned to each of the 3 atoms. In LAMMPS the fix shake command can be used to hold the two O-H bonds and the H-O-H angle rigid. A bond style of @@ -766,7 +766,7 @@ the partial charge assignemnts change:
See the (Berendsen) reference for more details on both +
See the (Berendsen) reference for more details on both the SPC and SPC/E models.
Wikipedia also has a nice article on water models.
@@ -1749,7 +1749,7 @@ do NOT perform time integration updates. Thus they should be used in conjunction with a constant NVE integration fix such as these:
-
-
- fix nve +
- fix nve
- fix nve/sphere
- fix nve/asphere
-
@@ -2731,7 +2731,7 @@ pairs as chunks.
model, representes induced dipoles by a pair of charges (the core atom
and the Drude particle) connected by a harmonic spring. The Drude
model has a number of features aimed at its use in molecular systems
-(Lamoureux and Roux):
+(Lamoureux and Roux):
- Thermostating of the additional degrees of freedom associated with the
induced dipoles at very low temperature, in terms of the reduced
diff --git a/doc/html/Section_packages.html b/doc/html/Section_packages.html
index e35f269dac..537efd4d5e 100644
--- a/doc/html/Section_packages.html
+++ b/doc/html/Section_packages.html
@@ -2329,7 +2329,7 @@ classical limits in the simulation.
See these two doc pages to get started:
fix qtb provides quantum nulcear correction through a colored thermostat and can be used with other time integration schemes -like fix nve or fix nph.
+like fix nve or fix nph.fix qbmsst enables quantum nuclear correction of a multi-scale shock technique simulation by coupling the quantum thermal bath with the shocked system.
diff --git a/doc/html/angle_charmm.html b/doc/html/angle_charmm.html index 01aff21dc3..17487df462 100644 --- a/doc/html/angle_charmm.html +++ b/doc/html/angle_charmm.html @@ -155,7 +155,7 @@with an additional Urey_Bradley term based on the distance r between the 1st and 3rd atoms in the angle. K, theta0, Kub, and Rub are coefficients defined for each angle type.
-See (MacKerell) for a description of the CHARMM force +
See (MacKerell) for a description of the CHARMM force field.
The following coefficients must be defined for each angle type via the angle_coeff command as in the example above, or in diff --git a/doc/html/angle_class2.html b/doc/html/angle_class2.html index 7ecdcae37a..9c5073c4b5 100644 --- a/doc/html/angle_class2.html +++ b/doc/html/angle_class2.html @@ -151,7 +151,7 @@
where Ea is the angle term, Ebb is a bond-bond term, and Eba is a bond-angle term. Theta0 is the equilibrium angle and r1 and r2 are the equilibrium bond lengths.
-See (Sun) for a description of the COMPASS class2 force field.
+See (Sun) for a description of the COMPASS class2 force field.
Coefficients for the Ea, Ebb, and Eba formulas must be defined for each angle type via the angle_coeff command as in the example above, or in the data file or restart files read by the diff --git a/doc/html/angle_cosine_periodic.html b/doc/html/angle_cosine_periodic.html index d733a4a9e7..8fb86c916a 100644 --- a/doc/html/angle_cosine_periodic.html +++ b/doc/html/angle_cosine_periodic.html @@ -151,7 +151,7 @@ used for an octahedral complex and n = 3 might be used for a trigonal center:
where C, B and n are coefficients defined for each angle type.
-See (Mayo) for a description of the DREIDING force field
+See (Mayo) for a description of the DREIDING force field
The following coefficients must be defined for each angle type via the angle_coeff command as in the example above, or in the data file or restart files read by the read_data diff --git a/doc/html/atom_modify.html b/doc/html/atom_modify.html index b2e3f8585d..365aaee0e8 100644 --- a/doc/html/atom_modify.html +++ b/doc/html/atom_modify.html @@ -210,7 +210,7 @@ over the smaller set of atoms. Otherwise the reordering required by this option will be a net slow-down. The neigh_modify include and comm_modify group commands are two examples of commands that require this setting to work efficiently. Several fixes, most notably time -integration fixes like fix nve, also take advantage of +integration fixes like fix nve, also take advantage of this setting if the group they operate on is the group specified by this command. Note that specifying “all” as the group-ID effectively turns off the first option.
diff --git a/doc/html/bond_class2.html b/doc/html/bond_class2.html index dce4a2b06d..696c3d1c22 100644 --- a/doc/html/bond_class2.html +++ b/doc/html/bond_class2.html @@ -147,7 +147,7 @@The class2 bond style uses the potential
where r0 is the equilibrium bond distance.
-See (Sun) for a description of the COMPASS class2 force field.
+See (Sun) for a description of the COMPASS class2 force field.
The following coefficients must be defined for each bond type via the bond_coeff command as in the example above, or in the data file or restart files read by the read_data diff --git a/doc/html/bond_fene.html b/doc/html/bond_fene.html index 5a18de630d..f136e86c5f 100644 --- a/doc/html/bond_fene.html +++ b/doc/html/bond_fene.html @@ -150,7 +150,7 @@
The fene bond style uses the potential
to define a finite extensible nonlinear elastic (FENE) potential -(Kremer), used for bead-spring polymer models. The first +(Kremer), used for bead-spring polymer models. The first term is attractive, the 2nd Lennard-Jones term is repulsive. The first term extends to R0, the maximum extent of the bond. The 2nd term is cutoff at 2^(1/6) sigma, the minimum of the LJ potential.
diff --git a/doc/html/bond_fene_expand.html b/doc/html/bond_fene_expand.html index 9a0d3c81c5..d0d7bdcfd5 100644 --- a/doc/html/bond_fene_expand.html +++ b/doc/html/bond_fene_expand.html @@ -147,7 +147,7 @@The fene/expand bond style uses the potential
to define a finite extensible nonlinear elastic (FENE) potential -(Kremer), used for bead-spring polymer models. The first +(Kremer), used for bead-spring polymer models. The first term is attractive, the 2nd Lennard-Jones term is repulsive.
The fene/expand bond style is similar to fene except that an extra shift factor of delta (positive or negative) is added to r to diff --git a/doc/html/compute_saed.html b/doc/html/compute_saed.html index a42da1c77b..2f88ae8f11 100644 --- a/doc/html/compute_saed.html +++ b/doc/html/compute_saed.html @@ -169,7 +169,7 @@
diff --git a/doc/html/fix_ipi.html b/doc/html/fix_ipi.html index 615515d668..c9df463700 100644 --- a/doc/html/fix_ipi.html +++ b/doc/html/fix_ipi.html @@ -193,7 +193,7 @@ environment.Description
Define a computation that calculates electron diffraction intensity as -described in (Coleman) on a mesh of reciprocal lattice nodes +described in (Coleman) on a mesh of reciprocal lattice nodes defined by the entire simulation domain (or manually) using simulated radiation of wavelength lambda.
The electron diffraction intensity I at each reciprocal lattice point diff --git a/doc/html/compute_xrd.html b/doc/html/compute_xrd.html index 278301034a..d594e6ce55 100644 --- a/doc/html/compute_xrd.html +++ b/doc/html/compute_xrd.html @@ -167,7 +167,7 @@
Description
Define a computation that calculates x-ray diffraction intensity as described -in (Coleman) on a mesh of reciprocal lattice nodes defined +in (Coleman) on a mesh of reciprocal lattice nodes defined by the entire simulation domain (or manually) using a simulated radiation of wavelength lambda.
The x-ray diffraction intensity, I, at each reciprocal lattice point, k, diff --git a/doc/html/dihedral_charmm.html b/doc/html/dihedral_charmm.html index 7e484d1e67..629d2161b3 100644 --- a/doc/html/dihedral_charmm.html +++ b/doc/html/dihedral_charmm.html @@ -152,9 +152,9 @@
Description
The charmm dihedral style uses the potential
-See (MacKerell) for a description of the CHARMM force +
See (MacKerell) for a description of the CHARMM force field. This dihedral style can also be used for the AMBER force field -(see comment on weighting factors below). See (Cornell) +(see comment on weighting factors below). See (Cornell) for a description of the AMBER force field.
The following coefficients must be defined for each dihedral type via the dihedral_coeff command as in the example above, or in diff --git a/doc/html/dihedral_class2.html b/doc/html/dihedral_class2.html index a796fdfb4e..931013ddec 100644 --- a/doc/html/dihedral_class2.html +++ b/doc/html/dihedral_class2.html @@ -156,7 +156,7 @@ Eebt is an end-bond-torsion term, Eat is an angle-torsion term, Eaat is an angle-angle-torsion term, and Ebb13 is a bond-bond-13 term.
Theta1 and theta2 are equilibrium angles and r1 r2 r3 are equilibrium bond lengths.
-See (Sun) for a description of the COMPASS class2 force field.
+See (Sun) for a description of the COMPASS class2 force field.
Coefficients for the Ed, Embt, Eebt, Eat, Eaat, and Ebb13 formulas must be defined for each dihedral type via the dihedral_coeff command as in the example above, diff --git a/doc/html/fix.html b/doc/html/fix.html index c0cb063015..c80e1397a2 100644 --- a/doc/html/fix.html +++ b/doc/html/fix.html @@ -166,7 +166,7 @@ underscores.
The unfix command is the only way to turn off a fix; simply specifying a new fix with a similar style will not turn off the first one. This is especially important to realize for -integration fixes. For example, using a fix nve +integration fixes. For example, using a fix nve command for a second run after using a fix nvt command for the first run, will not cancel out the NVT time integration invoked by the “fix nvt” command. Thus two time integrators would be @@ -318,7 +318,7 @@ of npt/asphere - NPT for aspherical particles
- npt/body - NPT for body particles
- npt/sphere - NPT for spherical particles
-- nve - constant NVE time integration
+- nve - constant NVE time integration
- nve/asphere - NVE for aspherical particles
- nve/asphere/noforce - NVE for aspherical particles without forces”
- nve/body - NVE for body particles
diff --git a/doc/html/fix_drude_transform.html b/doc/html/fix_drude_transform.html index 7134e2dbf5..50c9c75471 100644 --- a/doc/html/fix_drude_transform.html +++ b/doc/html/fix_drude_transform.html @@ -208,7 +208,7 @@ atoms will simply not be transformed.
This fix does NOT perform time integration. It only transform masses, coordinates, velocities and forces. Thus you must use separate time -integration fixes, like fix nve or fix npt to actually update the velocities and positions of +integration fixes, like fix nve or fix npt to actually update the velocities and positions of atoms. In order to thermalize the reduced degrees of freedom at different temperatures, two Nose-Hoover thermostats must be defined, acting on two distinct groups.
diff --git a/doc/html/fix_gld.html b/doc/html/fix_gld.html index aba80b6a9d..83d5871554 100644 --- a/doc/html/fix_gld.html +++ b/doc/html/fix_gld.html @@ -173,7 +173,7 @@ to be a Prony series.While this fix bears many similarities to fix langevin, it has one significant difference. Namely, fix gld performs time integration, whereas fix langevin does NOT. To this end, the -specification of another fix to perform time integration, such as fix nve, is NOT necessary.
+specification of another fix to perform time integration, such as fix nve, is NOT necessary.With this fix active, the force on the jth atom is given as
diff --git a/doc/html/fix_gle.html b/doc/html/fix_gle.html
index 9f9296aea3..624bef06d3 100644
--- a/doc/html/fix_gle.html
+++ b/doc/html/fix_gle.html
@@ -164,7 +164,7 @@ vibrational modes in the system to inexpensive (approximate)
modelling of nuclear quantum effects. Contrary to
fix langevin, this fix performs both
thermostatting and evolution of the Hamiltonian equations of motion, so it
-should not be used together with fix nve – at least not
+should not be used together with fix nve – at least not
on the same atom groups.
Each degree of freedom in the thermostatted group is supplemented with Ns additional degrees of freedom s, and the equations of motion diff --git a/doc/html/fix_heat.html b/doc/html/fix_heat.html index 701cdc1be4..b3c9f19161 100644 --- a/doc/html/fix_heat.html +++ b/doc/html/fix_heat.html @@ -209,7 +209,7 @@ energy change is 0.0 or use fix nve) on the affected atoms. This fix should +(e.g. fix nve) on the affected atoms. This fix should not normally be used on atoms that have their temperature controlled by another fix - e.g. fix nvt or fix langevin fix.
Related commands
- +fix nve
(IPI-CPC) Ceriotti, More and Manolopoulos, Comp Phys Comm, 185, 1019-1026 (2014).
diff --git a/doc/html/fix_langevin.html b/doc/html/fix_langevin.html index edf3efa19a..ec87ca12c6 100644 --- a/doc/html/fix_langevin.html +++ b/doc/html/fix_langevin.html @@ -177,7 +177,7 @@Description
Apply a Langevin thermostat as described in (Schneider) to a group of atoms which models an interaction with a background -implicit solvent. Used with fix nve, this command +implicit solvent. Used with fix nve, this command performs Brownian dynamics (BD), since the total force on each atom will have the form:
diff --git a/doc/html/fix_nh.html b/doc/html/fix_nh.html index bdf5b051b7..27d0fa579a 100644 --- a/doc/html/fix_nh.html +++ b/doc/html/fix_nh.html @@ -240,11 +240,11 @@ particles will match the target values specified by Tstart/Tstop and Pstart/Pstop.F = Fc + Ff + Fr @@ -218,7 +218,7 @@ thermostatting takes place; see the description below. Nose/Hoover thermostatting AND time integration, this fix does NOT perform time integration. It only modifies forces to effect thermostatting. Thus you must use a separate time integration fix, -like fix nve to actually update the velocities and +like fix nve to actually update the velocities and positions of atoms using the modified forces. Likewise, this fix should not normally be used on atoms that also have their temperature controlled by another fix - e.g. by fix nvt or fix temp/rescale commands. diff --git a/doc/html/fix_langevin_drude.html b/doc/html/fix_langevin_drude.html index f01d0bd451..f86b0d1bb1 100644 --- a/doc/html/fix_langevin_drude.html +++ b/doc/html/fix_langevin_drude.html @@ -209,7 +209,7 @@ from them before thermostating takes place; see the description below.
Like the fix langevin command, this fix does NOT perform time integration. It only modifies forces to effect thermostating. Thus you must use a separate time integration fix, like -fix nve or fix nph to actually update the +fix nve or fix nph to actually update the velocities and positions of atoms using the modified forces. Likewise, this fix should not normally be used on atoms that also have their temperature controlled by another fix - e.g. by fix nvt or fix temp/rescale commands.
diff --git a/doc/html/fix_lb_fluid.html b/doc/html/fix_lb_fluid.html index 201785ea67..5f779c9a19 100644 --- a/doc/html/fix_lb_fluid.html +++ b/doc/html/fix_lb_fluid.html @@ -210,7 +210,7 @@ finite difference LB integrator is used. If LBtype is set equal to functions,
Full details of the lattice-Boltzmann algorithm used can be found in -Mackay et al..
+Mackay et al..The fluid is coupled to the MD particles described by group-ID through a velocity dependent force. The contribution to the fluid force on a given lattice mesh site j due to MD particle alpha is @@ -242,7 +242,7 @@ using the setArea keyword.
The user also has the option of specifying their own value for the force coupling constant, for all the MD particles associated with the fix, through the use of the setGamma keyword. This may be useful -when modelling porous particles. See Mackay et al. for a +when modelling porous particles. See Mackay et al. for a detailed description of the method by which the user can choose an appropriate gamma value.
@@ -256,7 +256,7 @@ This fix adds the hydrodynamic force to the total force acting on the particles, after which any of the built-in LAMMPS integrators can be used to integrate the particle motion. However, if the user specifies their own value for the force coupling constant, as mentioned in -Mackay et al., the built-in LAMMPS integrators may prove to +Mackay et al., the built-in LAMMPS integrators may prove to be unstable. Therefore, we have included our own integrators fix lb/rigid/pc/sphere, and fix lb/pc, to solve for the particle motion in these cases. These integrators should not be used with the lb/viscous fix, as they add hydrodynamic forces @@ -341,7 +341,7 @@ N timesteps.diff --git a/doc/html/fix_move.html b/doc/html/fix_move.html index 66cf61d80e..42af823a51 100644 --- a/doc/html/fix_move.html +++ b/doc/html/fix_move.html @@ -175,14 +175,14 @@ whose movement can influence nearby atoms.If the keyword trilinear is used, the trilinear stencil is used to interpolate the particle nodes onto the fluid mesh. By default, the immersed boundary method, Peskin stencil is used. Both of these -interpolation methods are described in Mackay et al..
+interpolation methods are described in Mackay et al..If the keyword D3Q19 is used, the 19 velocity (D3Q19) lattice is used by the lattice-Boltzmann algorithm. By default, the 15 velocity (D3Q15) lattice is used.
@@ -371,7 +371,7 @@ the fluid densities and velocities at each lattice site are printed to the screen every N timesteps.
For further details, as well as descriptions and results of several -test runs, see Mackay et al.. Please include a citation to +test runs, see Mackay et al.. Please include a citation to this paper if the lb_fluid fix is used in work contributing to published research.
Note
The atoms affected by this fix should not normally be time -integrated by other fixes (e.g. fix nve, fix nvt), since that will change their positions and +integrated by other fixes (e.g. fix nve, fix nvt), since that will change their positions and velocities twice.
@@ -211,7 +211,7 @@ specified, V is the specified velocity vector with components specified. This style also sets the velocity of each atom to V = (Vx,Vy,Vz). If any of the velocity components is specified as NULL, then the position and velocity of that component is time integrated -the same as the fix nve command would perform, using +the same as the fix nve command would perform, using the corresponding force component on the atom.Note
As atoms move due to this fix, they will pass thru periodic boundaries and be remapped to the other side of the simulation box, -just as they would during normal time integration (e.g. via the fix nve command). It is up to you to decide whether +just as they would during normal time integration (e.g. via the fix nve command). It is up to you to decide whether periodic boundaries are appropriate with the kind of atom motion you are prescribing with this fix.
Note that the linear style is identical to using the variable style with an equal-style variable that uses the @@ -234,7 +234,7 @@ elapsed since the fix was specified. This style also sets the velocity of each atom to the time derivative of this expression. If any of the amplitude components is specified as NULL, then the position and velocity of that component is time integrated the same as -the fix nve command would perform, using the +the fix nve command would perform, using the corresponding force component on the atom.
Note that the wiggle style is identical to using the variable style with equal-style variables that use the @@ -282,7 +282,7 @@ atom.
Any of the 6 variables can be specified as NULL. If both the displacement and velocity variables for a particular x,y,z component are specified as NULL, then the position and velocity of that -component is time integrated the same as the fix nve +component is time integrated the same as the fix nve command would perform, using the corresponding force component on the atom. If only the velocity variable for a component is specified as NULL, then the displacement variable will be used to set the position @@ -337,7 +337,7 @@ position and velocity of atoms on the outermost rRESPA level.
The equations of motion used are those of Shinoda et al in (Shinoda), which combine the hydrostatic equations of -Martyna, Tobias and Klein in (Martyna) with the strain +Martyna, Tobias and Klein in (Martyna) with the strain energy proposed by Parrinello and Rahman in -(Parrinello). The time integration schemes closely +(Parrinello). The time integration schemes closely follow the time-reversible measure-preserving Verlet and rRESPA -integrators derived by Tuckerman et al in (Tuckerman).
+integrators derived by Tuckerman et al in (Tuckerman).
The thermostat parameters for fix styles nvt and npt is specified using the temp keyword. Other thermostat-related keywords are @@ -325,7 +325,7 @@ be used with care, since it can be unphysical to dilate some atoms and not others, because it can introduce large, instantaneous displacements between a pair of atoms (one dilated, one not) that are far from the dilation origin. Also note that for atoms not in the fix -group, a separate time integration fix like fix nve or +group, a separate time integration fix like fix nve or fix nvt can be used on them, independent of whether they are dilated or not.
@@ -402,7 +402,7 @@ freedom. A value of 0 corresponds to no thermostatting of the barostat variables.The mtk keyword controls whether or not the correction terms due to Martyna, Tuckerman, and Klein are included in the equations of motion -(Martyna). Specifying no reproduces the original +(Martyna). Specifying no reproduces the original Hoover barostat, whose volume probability distribution function differs from the true NPT and NPH ensembles by a factor of 1/V. Hence using yes is more correct, but in many cases the difference is @@ -411,7 +411,7 @@ negligible.
scheme at little extra cost. The initial and final updates of the thermostat variables are broken up into tloop substeps, each of length dt/tloop. This corresponds to using a first-order -Suzuki-Yoshida scheme (Tuckerman). The keyword ploop +Suzuki-Yoshida scheme (Tuckerman). The keyword ploop does the same thing for the barostat thermostat.The keyword nreset controls how often the reference dimensions used to define the strain energy are reset. If this keyword is not used, @@ -494,7 +494,7 @@ become inefficient due to the highly skewed simulation box.
Unlike the fix temp/berendsen command which performs thermostatting but NO time integration, these fixes perform thermostatting/barostatting AND time integration. Thus you -should not use any other time integration fix, such as fix nve on atoms to which this fix is applied. Likewise, +should not use any other time integration fix, such as fix nve on atoms to which this fix is applied. Likewise, fix nvt and fix npt should not normally be used on atoms that also have their temperature controlled by another fix - e.g. by fix langevin or fix temp/rescale commands.
@@ -706,7 +706,7 @@ over time or the atom count becomes very small.diff --git a/doc/html/fix_nphug.html b/doc/html/fix_nphug.html index 3cfe716619..1af5563180 100644 --- a/doc/html/fix_nphug.html +++ b/doc/html/fix_nphug.html @@ -221,7 +221,7 @@ the simulation. These can be overridden using the fix_modify keywords e0Unlike the fix temp/berendsen command which performs thermostatting but NO time integration, this fix performs thermostatting/barostatting AND time integration. Thus you -should not use any other time integration fix, such as fix nve on atoms to which this fix is applied. Likewise, +should not use any other time integration fix, such as fix nve on atoms to which this fix is applied. Likewise, this fix should not be used on atoms that have their temperature controlled by another fix - e.g. by fix langevin or fix temp/rescale commands.diff --git a/doc/html/fix_nve_asphere.html b/doc/html/fix_nve_asphere.html index 02455768c3..5df47100de 100644 --- a/doc/html/fix_nve_asphere.html +++ b/doc/html/fix_nve_asphere.html @@ -151,7 +151,7 @@ orientation, and angular velocity for aspherical particles in the group each timestep. V is volume; E is energy. This creates a system trajectory consistent with the microcanonical ensemble. -This fix differs from the fix nve command, which +
This fix differs from the fix nve command, which assumes point particles and only updates their position and velocity.
@@ -192,7 +192,7 @@ shape attribute.diff --git a/doc/html/fix_nve_body.html b/doc/html/fix_nve_body.html index cd459a4379..e6e8a9af75 100644 --- a/doc/html/fix_nve_body.html +++ b/doc/html/fix_nve_body.html @@ -149,7 +149,7 @@ orientation, and angular velocity for body particles in the group each timestep. V is volume; E is energy. This creates a system trajectory consistent with the microcanonical ensemble. See Section_howto 14 of the manual and the body doc page for more details on using body particles. -This fix differs from the fix nve command, which +
This fix differs from the fix nve command, which assumes point particles and only updates their position and velocity.
@@ -172,7 +172,7 @@ point particles.diff --git a/doc/html/fix_nve_eff.html b/doc/html/fix_nve_eff.html index d7e486fe39..378ded5f30 100644 --- a/doc/html/fix_nve_eff.html +++ b/doc/html/fix_nve_eff.html @@ -147,7 +147,7 @@Perform constant NVE integration to update position and velocity for nuclei and electrons in the group for the electron force field model. V is volume; E is energy. This creates a system trajectory consistent with the microcanonical ensemble.
-The operation of this fix is exactly like that described by the fix nve command, except that the radius and radial velocity +
The operation of this fix is exactly like that described by the fix nve command, except that the radius and radial velocity of electrons are also updated.
diff --git a/doc/html/fix_nve_limit.html b/doc/html/fix_nve_limit.html index ede833982c..edd03ec70f 100644 --- a/doc/html/fix_nve_limit.html +++ b/doc/html/fix_nve_limit.html @@ -164,7 +164,7 @@ missed on successive timesteps as atoms move. See the for details.Note that if a velocity reset occurs the integrator will not conserve energy. On steps where no velocity resets occur, this integrator is -exactly like the fix nve command. Since forces are +exactly like the fix nve command. Since forces are unaltered, pressures computed by thermodynamic output will still be very large for overlapped configurations.
@@ -202,7 +202,7 @@ the run diff --git a/doc/html/fix_nve_line.html b/doc/html/fix_nve_line.html index 5168b08db0..2e8e1916d4 100644 --- a/doc/html/fix_nve_line.html +++ b/doc/html/fix_nve_line.html @@ -150,7 +150,7 @@ group each timestep. V is volume; E is energy. This creates a system trajectory consistent with the microcanonical ensemble. See Section_howto 14 of the manual for an overview of using line segment particles. -This fix differs from the fix nve command, which +
This fix differs from the fix nve command, which assumes point particles and only updates their position and velocity.
@@ -170,7 +170,7 @@ was built with that package. See thediff --git a/doc/html/fix_nve_noforce.html b/doc/html/fix_nve_noforce.html index 495a804493..8174af5a24 100644 --- a/doc/html/fix_nve_noforce.html +++ b/doc/html/fix_nve_noforce.html @@ -171,7 +171,7 @@ This fix is not invoked duringRelated commands
- +fix nve, fix nve/asphere
Default: none
Related commands
- +fix nve
Default: none
diff --git a/doc/html/fix_nve_sphere.html b/doc/html/fix_nve_sphere.html index addd994810..75c7106258 100644 --- a/doc/html/fix_nve_sphere.html +++ b/doc/html/fix_nve_sphere.html @@ -158,7 +158,7 @@ angular velocity for finite-size spherical particles in the group each timestep. V is volume; E is energy. This creates a system trajectory consistent with the microcanonical ensemble. -This fix differs from the fix nve command, which +
This fix differs from the fix nve command, which assumes point particles and only updates their position and velocity.
If the update keyword is used with the dipole value, then the orientation of the dipole moment of each particle is also updated @@ -203,7 +203,7 @@ be point particles.
diff --git a/doc/html/fix_nve_tri.html b/doc/html/fix_nve_tri.html index e707401c30..51e228e884 100644 --- a/doc/html/fix_nve_tri.html +++ b/doc/html/fix_nve_tri.html @@ -150,7 +150,7 @@ group each timestep. V is volume; E is energy. This creates a system trajectory consistent with the microcanonical ensemble. See Section_howto 14 of the manual for an overview of using triangular particles. -This fix differs from the fix nve command, which +
This fix differs from the fix nve command, which assumes point particles and only updates their position and velocity.
@@ -170,7 +170,7 @@ was built with that package. See thediff --git a/doc/html/fix_nvt_sllod.html b/doc/html/fix_nvt_sllod.html index 76ee24d9f6..c60c9e9d64 100644 --- a/doc/html/fix_nvt_sllod.html +++ b/doc/html/fix_nvt_sllod.html @@ -267,7 +267,7 @@ equilibration.Related commands
- +fix nve, fix nve/asphere
Default: none
diff --git a/doc/html/fix_pimd.html b/doc/html/fix_pimd.html index 6d835d4fc4..9fd1a77fa6 100644 --- a/doc/html/fix_pimd.html +++ b/doc/html/fix_pimd.html @@ -171,7 +171,7 @@ index (the second term in the effective potential above). The quasi-beads also interact with the two neighboring quasi-beads through the spring potential in imaginary-time space (first term in effective potential). To sample the canonical ensemble, a Nose-Hoover massive -chain thermostat is applied (Tuckerman). With the +chain thermostat is applied (Tuckerman). With the massive chain algorithm, a chain of NH thermostats is coupled to each degree of freedom for each quasi-bead. The keyword temp sets the target temperature for the system and the keyword nhc sets the diff --git a/doc/html/fix_press_berendsen.html b/doc/html/fix_press_berendsen.html index ffd58394b6..7569f7b850 100644 --- a/doc/html/fix_press_berendsen.html +++ b/doc/html/fix_press_berendsen.html @@ -175,7 +175,7 @@ unchanged and controlling the pressure of a surrounding fluid. commands which perform Nose/Hoover barostatting AND time integration, this fix does NOT perform time integration. It only modifies the box size and atom coordinates to effect barostatting. Thus you must use a -separate time integration fix, like fix nve or fix nvt to actually update the positions and velocities of +separate time integration fix, like fix nve or fix nvt to actually update the positions and velocities of atoms. This fix can be used in conjunction with thermostatting fixes to control the temperature, such as fix nvt or fix langevin or fix temp/berendsen.@@ -316,7 +316,7 @@ variousdiff --git a/doc/html/fix_qtb.html b/doc/html/fix_qtb.html index 2f8934ddd0..188cb22fc6 100644 --- a/doc/html/fix_qtb.html +++ b/doc/html/fix_qtb.html @@ -158,7 +158,7 @@Description
This command performs the quantum thermal bath scheme proposed by (Dammak) to include self-consistent quantum nuclear effects, -when used in conjunction with the fix nve or fix nph commands.
+when used in conjunction with the fix nve or fix nph commands.Classical molecular dynamics simulation does not include any quantum nuclear effect. Quantum treatment of the vibrational modes will introduce zero point energy into the system, alter the energy power @@ -241,7 +241,7 @@ Mbytes.
Nose/Hoover thermostatting AND time integration, this fix does NOT perform time integration. It only modifies forces to a colored thermostat. Thus you must use a separate time integration fix, like -fix nve or fix nph to actually update the +fix nve or fix nph to actually update the velocities and positions of atoms (as shown in the examples). Likewise, this fix should not normally be used with other fixes or commands that also specify system temperatures , e.g. fix nvt and fix temp/rescale. @@ -263,7 +263,7 @@ LAMMPS was built with that package. See the
diff --git a/doc/html/fix_recenter.html b/doc/html/fix_recenter.html index 4f1bdc2285..0263f3b12b 100644 --- a/doc/html/fix_recenter.html +++ b/doc/html/fix_recenter.html @@ -187,7 +187,7 @@ velocities with zero aggregate linear and/or angular momentum.Note
This fix performs its operations at the same point in the -timestep as other time integration fixes, such as fix nve, fix nvt, or fix npt. +timestep as other time integration fixes, such as fix nve, fix nvt, or fix npt. Thus fix recenter should normally be the last such fix specified in the input script, since the adjustments it makes to atom coordinates should come after the changes made by time integration. LAMMPS will diff --git a/doc/html/fix_rigid.html b/doc/html/fix_rigid.html index d543973b84..80620f544c 100644 --- a/doc/html/fix_rigid.html +++ b/doc/html/fix_rigid.html @@ -288,10 +288,10 @@ differences may accumulate to produce divergent trajectories.
Note
You should not update the atoms in rigid bodies via other -time-integration fixes (e.g. fix nve, fix nvt, fix npt), or you will be integrating +time-integration fixes (e.g. fix nve, fix nvt, fix npt), or you will be integrating their motion more than once each timestep. When performing a hybrid simulation with some atoms in rigid bodies, and some not, a separate -time integration fix like fix nve or fix nvt should be used for the non-rigid particles.
+time integration fix like fix nve or fix nvt should be used for the non-rigid particles.Note
@@ -303,7 +303,7 @@ your time integration fix. E.g. use “fix 1 mobile nve” instead of move. You can move atoms with a constant velocity by assigning them an initial velocity (via the velocity command), setting the force on them to 0.0 (via the fix setforce command), and integrating them as usual -(e.g. via the fix nve command). +(e.g. via the fix nve command).Note
@@ -685,10 +685,10 @@ also accounted for by this fix.
If your simlulation is a hybrid model with a mixture of rigid bodies and non-rigid particles (e.g. solvent) there are several ways these -rigid fixes can be used in tandem with fix nve, fix nvt, fix npt, and fix nph.
+rigid fixes can be used in tandem with fix nve, fix nvt, fix npt, and fix nph.If you wish to perform NVE dynamics (no thermostatting or barostatting), use fix rigid or fix rigid/nve to integrate the rigid -bodies, and fix nve to integrate the non-rigid +bodies, and fix nve to integrate the non-rigid particles.
If you wish to perform NVT dynamics (thermostatting, but no barostatting), you can use fix rigid/nvt for the rigid bodies, and any diff --git a/doc/html/fix_shardlow.html b/doc/html/fix_shardlow.html index 44f54e89ce..de4d97580f 100644 --- a/doc/html/fix_shardlow.html +++ b/doc/html/fix_shardlow.html @@ -148,7 +148,7 @@ integrate the DPD equations of motion. The SSA splits the integration into a stochastic and deterministic integration step. The fix shardlow performs the stochastic integration step and must be used -in conjunction with a deterministic integrator (e.g. fix nve or fix nph). The stochastic +in conjunction with a deterministic integrator (e.g. fix nve or fix nph). The stochastic integration of the dissipative and random forces is performed prior to the deterministic integration of the conservative force. Further details regarding the method are provided in (Lisal) and @@ -176,7 +176,7 @@ for more info.
This fix is currently limited to orthogonal simulation cell geometries.
This fix must be used with an additional fix that specifies time -integration, e.g. fix nve or fix nph.
+integration, e.g. fix nve or fix nph.The Shardlow splitting algorithm requires the sizes of the sub-domain lengths to be larger than twice the cutoff+skin. Generally, the domain decomposition is dependant on the number of processors diff --git a/doc/html/fix_temp_berendsen.html b/doc/html/fix_temp_berendsen.html index ebbb13626c..1b7b3f80b8 100644 --- a/doc/html/fix_temp_berendsen.html +++ b/doc/html/fix_temp_berendsen.html @@ -184,7 +184,7 @@ time. Thus it is easy to specify a time-dependent temperature.
Nose/Hoover thermostatting AND time integration, this fix does NOT perform time integration. It only modifies velocities to effect thermostatting. Thus you must use a separate time integration fix, -like fix nve to actually update the positions of atoms +like fix nve to actually update the positions of atoms using the modified velocities. Likewise, this fix should not normally be used on atoms that also have their temperature controlled by another fix - e.g. by fix nvt or fix langevin commands. @@ -270,7 +270,7 @@ over time or the atom count becomes very small.Related commands
-fix nve, fix nvt, fix temp/rescale, fix langevin, +
fix nve, fix nvt, fix temp/rescale, fix langevin, fix_modify, compute temp, fix temp/berendsen
Default: none
diff --git a/doc/html/fix_temp_rescale.html b/doc/html/fix_temp_rescale.html index a7f6d52287..1f54e85e42 100644 --- a/doc/html/fix_temp_rescale.html +++ b/doc/html/fix_temp_rescale.html @@ -193,7 +193,7 @@ value. Nose/Hoover thermostatting AND time integration, this fix does NOT perform time integration. It only modifies velocities to effect thermostatting. Thus you must use a separate time integration fix, -like fix nve to actually update the positions of atoms +like fix nve to actually update the positions of atoms using the modified velocities. Likewise, this fix should not normally be used on atoms that also have their temperature controlled by another fix - e.g. by fix nvt or fix langevin commands. diff --git a/doc/html/fix_tfmc.html b/doc/html/fix_tfmc.html index 1fa84393e7..abfcb7131b 100644 --- a/doc/html/fix_tfmc.html +++ b/doc/html/fix_tfmc.html @@ -192,7 +192,7 @@ Carlo algorithm and thus strictly speaking does not perform time integration, it is similar in the sense that it uses the forces on all atoms in order to update their positions. Therefore, it is implemented as a time integration fix, and no other fixes of this type (such as -fix nve) should be used at the same time. Because +fix nve) should be used at the same time. Because velocities do not play a role in this kind of Monte Carlo simulations, instantaneous temperatures as calculated by temperature computes or thermodynamic output have no meaning: the only relevant temperature is the sampling temperature Temp. Similarly, performing diff --git a/doc/html/fix_ttm.html b/doc/html/fix_ttm.html index af630d2964..8762bbb3b6 100644 --- a/doc/html/fix_ttm.html +++ b/doc/html/fix_ttm.html @@ -273,7 +273,7 @@ the electronic subsystem. The ordering of the Nx*Ny*Nz columns is with the z index varing fastest, y the next fastest, and x the slowest.These fixes do not change the coordinates of their atoms; they only -scales their velocities. Thus a time integration fix (e.g. fix nve) should still be used to time integrate the affected +scales their velocities. Thus a time integration fix (e.g. fix nve) should still be used to time integrate the affected atoms. The fixes should not normally be used on atoms that have their temperature controlled by another fix - e.g. fix nvt or fix langevin.
diff --git a/doc/html/fix_wall_piston.html b/doc/html/fix_wall_piston.html index 8ebde444af..b4b27f85e1 100644 --- a/doc/html/fix_wall_piston.html +++ b/doc/html/fix_wall_piston.html @@ -169,7 +169,7 @@ specified group and drive the system with an effective infinite-mass piston capable of driving shock waves.A momentum mirror technique is used, which means that if an atom (or the wall) moves such that an atom is outside the wall on a timestep by -a distance delta (e.g. due to fix nve), then it is put +a distance delta (e.g. due to fix nve), then it is put back inside the face by the same delta, and the velocity relative to the moving wall is flipped in z. For instance, a stationary particle hit with a piston wall with velocity vz, will end the timestep with a diff --git a/doc/html/fix_wall_reflect.html b/doc/html/fix_wall_reflect.html index c103099fae..48c56aa178 100644 --- a/doc/html/fix_wall_reflect.html +++ b/doc/html/fix_wall_reflect.html @@ -173,10 +173,10 @@
Bound the simulation with one or more walls which reflect particles in the specified group when they attempt to move thru them.
Reflection means that if an atom moves outside the wall on a timestep -by a distance delta (e.g. due to fix nve), then it is +by a distance delta (e.g. due to fix nve), then it is put back inside the face by the same delta, and the sign of the corresponding component of its velocity is flipped.
-When used in conjunction with fix nve and run_style verlet, the resultant time-integration algorithm is +
When used in conjunction with fix nve and run_style verlet, the resultant time-integration algorithm is equivalent to the primitive splitting algorithm (PSA) described by Bond. Because each reflection event divides the corresponding timestep asymmetrically, energy conservation is only diff --git a/doc/html/genindex.html b/doc/html/genindex.html index cda2a3aa6c..8bf2786796 100644 --- a/doc/html/genindex.html +++ b/doc/html/genindex.html @@ -1206,10 +1206,6 @@ -
- fix nve -
- -- fix nve/asphere
diff --git a/doc/html/improper_class2.html b/doc/html/improper_class2.html index 495228c950..0d190caf4c 100644 --- a/doc/html/improper_class2.html +++ b/doc/html/improper_class2.html @@ -165,7 +165,7 @@ theta angles, since it is always the center atom.Since atom J is the atom of symmetry, normally the bonds J-I, J-K, J-L would exist for an improper to be defined between the 4 atoms, but this is not required.
-See (Sun) for a description of the COMPASS class2 force field.
+See (Sun) for a description of the COMPASS class2 force field.
Coefficients for the Ei and Eaa formulas must be defined for each improper type via the improper_coeff command as in the example above, or in the data file or restart files read by the diff --git a/doc/html/improper_umbrella.html b/doc/html/improper_umbrella.html index 278f2db6d2..716c7c95c2 100644 --- a/doc/html/improper_umbrella.html +++ b/doc/html/improper_umbrella.html @@ -154,7 +154,7 @@ axis and the IJK plane:
If omega0 = 0 the potential term has a minimum for the planar structure. Otherwise it has two minima at +/- omega0, with a barrier in between.
-See (Mayo) for a description of the DREIDING force field.
+See (Mayo) for a description of the DREIDING force field.
The following coefficients must be defined for each improper type via the improper_coeff command as in the example above, or in the data file or restart files read by the diff --git a/doc/html/pair_charmm.html b/doc/html/pair_charmm.html index aa95dafcfd..61434f9e63 100644 --- a/doc/html/pair_charmm.html +++ b/doc/html/pair_charmm.html @@ -222,7 +222,7 @@ additional switching function S(r) that ramps the energy and force smoothly to zero between an inner and outer cutoff. It is a widely used potential in the CHARMM MD code. -See (MacKerell) for a description of the CHARMM force +See (MacKerell) for a description of the CHARMM force field.
Both the LJ and Coulombic terms require an inner and outer cutoff. diff --git a/doc/html/pair_class2.html b/doc/html/pair_class2.html index 0d814a4666..811c54043a 100644 --- a/doc/html/pair_class2.html +++ b/doc/html/pair_class2.html @@ -213,7 +213,7 @@
Rc is the cutoff.
The lj/class2/coul/cut and lj/class2/coul/long styles add a Coulombic term as described for the lj/cut pair styles.
-See (Sun) for a description of the COMPASS class2 force field.
+See (Sun) for a description of the COMPASS class2 force field.
The following coefficients must be defined for each pair of atoms types via the pair_coeff command as in the examples above, or in the data file or restart files read by the diff --git a/doc/html/pair_hbond_dreiding.html b/doc/html/pair_hbond_dreiding.html index 3ccb65b0d9..d8a9bd8c31 100644 --- a/doc/html/pair_hbond_dreiding.html +++ b/doc/html/pair_hbond_dreiding.html @@ -181,7 +181,7 @@ the donor atom, e.g. in a bond list read in from a data file via the hydrogen atoms for each donor/acceptor type pair are specified by the pair_coeff command (see below).
Style hbond/dreiding/lj is the original DREIDING potential of -(Mayo). It uses a LJ 12/10 functional for the Donor-Acceptor +(Mayo). It uses a LJ 12/10 functional for the Donor-Acceptor interactions. To match the results in the original paper, use n = 4.
Style hbond/dreiding/morse is an improved version using a Morse potential for the Donor-Acceptor interactions. (Liu) showed diff --git a/doc/html/rerun.html b/doc/html/rerun.html index 520ea38241..d6512a6c5e 100644 --- a/doc/html/rerun.html +++ b/doc/html/rerun.html @@ -250,7 +250,7 @@ simulation.
include and perform all the usual operations of an input script that uses the run command. There are a few exceptions and points to consider, as discussed here. -Fixes that perform time integration, such as fix nve or +
Fixes that perform time integration, such as fix nve or fix npt are not invoked, since no time integration is performed. Fixes that perturb or constrain the forces on atoms will be invoked, just as they would during a normal run. Examples are fix indent and fix langevin. So you diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js index 25c3902bf4..9900fe7741 100644 --- a/doc/html/searchindex.js +++ b/doc/html/searchindex.js @@ -1 +1 @@ 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adust:172,advanc:[3,250,392,482,493],advantag:[1,6,8,11,14,18,40,41,42,226,386,411,496,501],advect:[3,6,329],advertis:8,advis:[381,448],afer:3,affect:[1,6,10,14,15,16,17,41,63,64,76,97,129,153,162,176,182,205,206,211,218,219,221,222,223,224,227,228,229,230,232,233,243,249,251,253,259,266,270,271,272,273,275,276,277,283,288,289,290,292,313,314,327,341,351,364,371,377,378,379,381,382,383,386,412,433,434,441,484,485,487,489,490,492,495,497],affin:[16,17,18,232,386,401],afil:247,aforement:18,afresh:[301,495,514],afshar:406,after:[],afterrun:495,afterward:3,afterword:42,ag1:177,ag2:177,again:[6,11,12,16,17,65,152,158,164,172,202,206,232,249,299,355,370,381,433,434,482,484,485,487,489,494,501,503,514,517],against:[11,12,13,67,233,381,449,450],aggreg:[6,12,69,72,74,85,103,120,127,249,265,311,313,327,482,515],aggress:[249,501],agilio:[9,13],agre:[3,8,198,379,388,421,450],agreement:[5,7],ahd:418,ahead:348,aidan:[0,5,7,9,13,374],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:205,akohlmei:[7,9,13,207,250],aktulga:[7,9,306,450],al2o3:457,al2o3_001:[130,314],al3:177,ala:[256,457],alain:9,alat:[294,436],alb:[447,470,472],albeit:312,albert:9,alchem:[96,172],alcohol:344,alcu:[387,392],alcu_eam:447,alderton:405,alejandr:[269,270],alessandro:13,algebra:439,algorithm:[0,1,6,7,8,9,42,64,206,215,226,229,232,256,258,259,283,296,304,313,316,317,336,337,341,344,349,377,378,379,383,386,408,412,434,439,454,456,482,484,501],alia:[9,16],alias:[1,372],aliceblu:206,align:[6,9,12,29,42,76,180,198,222,226,251,374,487,490,508],alkali:412,all:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,43,45,51,55,56,58,59,60,62,63,64,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,166,171,172,173,174,175,176,177,178,179,180,181,182,184,186,191,197,198,199,202,203,204,205,206,207,209,210,211,212,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,262,264,265,267,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,298,299,300,301,302,303,304,305,306,308,309,310,311,312,313,314,315,316,317,318,319,320,321,325,326,328,329,330,331,332,333,336,337,338,339,340,341,342,343,344,346,347,348,349,350,351,352,353,354,355,356,360,365,367,369,370,371,372,373,374,376,379,380,381,382,383,385,386,387,388,389,391,392,393,395,396,397,398,399,401,402,405,406,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,428,432,433,434,435,436,437,438,439,440,441,442,443,444,446,447,448,449,450,451,452,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,478,479,480,481,482,484,485,486,487,488,489,490,491,492,494,495,496,497,498,499,500,501,502,504,505,506,508,509,513,514,515,517,518,519],allen:[29,96,405,415],allentildeslei:96,allign:3,allindex:353,alloc:[3,5,6,8,9,11,12,63,243,343,380,382,386,445,450,487,495],allocat:3,alloi:[],allosw:76,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,42,56,58,59,60,61,62,64,65,66,82,101,118,120,154,156,157,158,171,176,177,178,180,186,197,198,199,202,203,205,206,207,209,210,212,214,215,216,218,219,220,221,222,223,224,226,228,229,230,231,232,233,237,238,243,245,246,247,248,250,253,256,259,260,264,266,269,270,294,298,299,300,301,302,303,307,313,314,316,318,320,321,325,329,336,337,338,339,341,342,343,344,345,346,352,354,356,365,367,371,372,374,379,380,381,382,385,386,388,389,392,393,394,395,396,397,402,410,412,416,417,418,419,424,428,433,434,439,441,447,450,451,454,456,457,466,473,476,478,480,482,485,487,489,490,491,492,493,494,497,499,500,501,504,505,509,514,515],almost:[2,3,12,63,251,303,341,372,383,386,466],alo:402,alon:[6,7,229,309,449,450,485],alond:13,along:[6,8,12,29,41,76,96,130,176,177,178,201,202,205,218,229,251,256,257,261,266,268,303,313,316,318,322,326,327,336,340,341,347,350,352,374,377,378,379,381,402,405,416,419,422,424,428,436,449,450,469,487,490,497,498,514],alonso:[437,438],alpha:[6,12,52,210,256,303,304,308,379,387,390,393,402,406,408,410,411,413,418,423,424,436,442,446,471,473,505,508],alpha_c:432,alpha_i:458,alpha_lj:432,alphabet:[2,3,22,37,45,56,66,186,197,209,356,365,380,399,467,487],alphanumer:[3,66,209,302,310,354,380,514],alreadi:[3,7,8,9,12,16,17,18,43,58,178,179,181,204,214,218,222,223,226,228,232,260,301,303,329,352,353,380,381,406,417,419,426,434,466,476,479,483,487,488,492,497,513,514],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,40,41,42,43,45,55,56,57,61,62,64,66,70,76,77,78,80,82,87,88,96,98,99,101,104,114,115,116,117,118,119,124,126,128,129,131,152,153,154,155,156,157,158,159,160,161,162,164,165,166,167,168,170,171,172,173,174,175,178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2,449,450],chen:341,cheng:401,chenoweth:[449,450],chenoweth_2008:[449,450],chi:[103,167,201,294,304,306,367,413,415,515],chiefli:448,child:8,chip:[7,9,17,18,386,500],chipot:231,chiral:364,chmod:[11,12],cho:436,chocol:[7,206],choic:[3,6,9,12,15,16,18,41,42,55,96,153,156,157,171,182,198,218,222,223,226,229,232,233,247,253,256,267,269,296,300,304,313,336,365,372,377,378,381,383,386,419,432,441,445,487,496,497,500,501,507,508,513],choos:[1,3,6,7,8,9,12,16,17,18,29,40,55,96,129,168,169,205,227,228,229,230,233,242,253,256,267,269,271,272,273,274,275,276,277,299,300,317,329,333,347,371,372,378,476,482,484,496,502],chose:[470,472],chosen:[2,3,6,12,17,152,178,181,190,198,205,211,216,230,233,242,245,246,254,256,267,269,274,296,299,310,329,333,336,337,342,344,345,351,372,373,378,386,407,408,412,416,423,426,452,470,482,496,501,502,508],chri:176,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[70,80,87,99,104,115,117,126,158,173,175,218],chute:[4,9,10,248],ciccotti:316,cieplak:[6,184,499],cii:219,cij:219,ciko:2,circl:[43,76,325],circular:[3,6,156,200],circumst:18,circumv:[101,118,308],citat:[],cite:[3,7,8,12,253,457],civ:9,ckio:2,cko:2,cl1:177,clarendon:[29,405],clarifi:[7,470,472],clariti:354,clark:444,class2:[],classic:[0,3,5,6,7,8,9,243,296,303,308,341,366,412],classifi:[467,475],claus:485,clean:[6,12,14,15,17,495],cleanli:[486,518],clear:[],clearli:7,clebsch:152,clermont:[9,13],clever:491,click:[2,11,22,37,45,56,178,186,197,205,250,356,365,381,399,467,509],client:[250,252],climb:[268,381,501],clinic:[7,13],clo:[167,201,515],clock:[12,482,501],clockwis:347,clone:509,close:[3,6,11,12,13,40,42,71,76,153,181,202,228,229,230,247,254,256,269,290,313,316,347,350,370,372,375,377,378,381,386,388,392,402,403,422,436,441,449,453,455,469,472,491,497,508,509,511],closer:[3,10,42,128,176,201,202,226,230,234,338,381],closest:[228,294,313,344,415,451,466,476],cloud:[457,508],clovertown:18,clsuter:77,clump1:[298,313],clump2:[298,313],clump3:[298,313],clump:313,cluster:[],clutter:3,cmap:487,cmatrix:247,cmax:436,cmd:[11,12,296,498],cmdarg:11,cmin:436,cmm:[],cmoput:145,cn1:219,cn2:219,cna:[],cnn:219,cnr:[9,13],cnt:[419,491],co2:[41,177,316,380],coars:[7,9,10,29,36,41,55,190,298,313,329,417,452,496,499],coarser:[372,514],coarsest:152,code:[],coeff:[3,7,8,12,21,22,33,45,51,184,185,186,191,355,356,362,399,419,423,441,454,456,459,487,516],coeffcient:487,coeffici:[],coefficienct:406,coefficient0:410,coefficient1:410,coeffieci:[6,390,422],coeffincientn:410,coexist:[245,412],cohes:[6,413,436],coincid:[134,350,397,433,434,482],colberg:204,cold:[6,163,245,249,382,508],coldest:337,coleman8:9,coleman:[9,130,177,314],colin:9,collabor:[7,8,15],collect:[3,6,7,8,9,13,41,43,70,80,87,92,99,104,109,115,117,126,158,166,173,175,178,202,203,206,218,231,259,265,298,308,311,313,352,371,380,382,400,487,494,500,506,519],collid:[237,329,351],colliex:177,collinear:[3,298],collis:[3,256,329,347,351,409,416,479],colllis:329,colloid:[],colombo:40,colon:[207,352,488],color1:206,color2:206,color:[3,9,42,202,205,206,226,246,303,308],column:[3,6,9,12,13,43,66,69,70,71,72,74,76,80,82,85,87,88,90,99,101,103,104,115,117,118,120,122,125,126,127,128,129,131,152,153,158,166,173,175,176,177,198,202,203,206,209,217,218,219,221,222,223,224,259,266,267,303,313,330,331,341,351,414,418,449,450,488,502,504,514],columnar:176,colvar:[],colvarmodul:12,com:[],comamnd:232,comand:229,comannd:386,comb3:[],comb:[],comb_1:305,comb_2:305,combiant:403,combin:[3,6,7,9,11,13,36,41,66,69,74,85,96,103,114,120,127,156,157,171,202,205,215,221,250,259,269,296,302,317,333,342,350,353,355,371,372,374,378,386,400,402,403,408,412,413,419,431,432,458,468,470,472,473,475,478,490,495,500,508,514,516],come:[],comfort:[12,13],comit:509,comm:[0,3,11,12,64,78,204,250,252,253,372,381,386,406,441,446,469,489],comm_modifi:[],comm_modift:64,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,38,57,184,198,202,241,254,313,341,380,381,387,410,411,413,423,436,443,450,457,458,468,469,470,471,472,475,484,485,487,508,509,514],commerci:7,commit:[9,509],commmand:[3,6,12,62,119,291,422,481,482,484,501,518],common:[],commonli:[3,6,9,12,17,25,60,62,116,118,180,202,205,207,366,417,426,458,470,472,487,490,499],commun:[1,3,6,7,8,9,10,11,12,14,15,16,18,41,42,61,64,65,76,176,181,182,205,206,226,227,228,230,231,232,250,252,256,258,259,260,269,295,302,304,305,306,313,317,329,341,352,369,371,382,383,384,386,408,409,445,480,484,485,496,497,514,517,519],communc:371,comp:[7,204,252,253,316,372,381,412,441,446,451,465,469,471],compact:[66,209,399,467],compani:[5,7],compar:[1,3,4,6,8,12,17,40,95,122,130,161,177,186,197,206,236,304,352,354,371,372,379,381,436,457,482,501,502,508,513],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,9,21,22,37,44,45,56,185,186,197,355,356,365,398,467],compat:[3,5,7,8,9,11,12,13,17,18,42,76,129,131,189,202,207,211,217,218,219,221,222,223,224,226,295,307,333,336,343,346,349,371,386,420,439,441,469,484,485,514],compens:[6,227,228,311,382,412],compet:340,competit:372,compil:[3,7,8,9,12,13,14,15,16,17,18,19,176,202,204,205,207,250,340,372,386,439,487,488,492,514],compl:17,complain:[11,12,17],complement:436,complementari:[7,402,424],complet:[3,6,9,11,12,15,42,62,76,206,222,226,231,259,296,299,302,329,340,342,353,354,370,381,386,413,454,456,474,482,487,492,495,499,501,504,508,514],complex:[4,6,8,11,12,13,25,41,43,65,101,118,152,154,166,178,179,256,325,350,369,381,412,439,469,485,487,490,514],compli:[336,340],complic:[6,7,9,12,13,216,245,485],complier:12,compon:[3,6,8,12,64,66,70,71,78,87,88,97,98,99,100,101,104,105,108,113,115,116,117,118,119,120,121,122,124,125,129,139,142,143,144,145,148,149,150,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,174,175,201,202,203,205,206,212,213,217,218,219,220,221,222,223,224,225,229,230,232,233,238,243,248,252,253,256,259,261,265,266,268,269,270,274,275,276,277,288,289,290,292,293,295,296,297,300,311,313,315,316,318,322,323,326,329,332,333,334,336,343,344,349,350,351,371,374,378,379,380,381,386,406,412,416,433,434,454,456,457,458,487,488,497,505,514,515],componenet:6,composit:[6,216,256,410],compound:[401,412,413,475],compres:[76,126,218],compress:[],compris:[41,350,451,474],compton:[130,177],comptu:3,compuat:372,comput:[],computation:[3,6,227,228,341,392],computational:508,compute_arrai:8,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[130,314],compute_scalar:8,compute_temp:8,compute_vector:8,compute_xrd:177,concaten:[2,3,518],concav:350,concentr:[76,410],concept:[6,158,168,218,496],conceptu:[3,6,76,166,230,232,381,402,419,436,492],concern:[6,78,96,204,246],concetr:76,concis:[11,340],conclud:12,concret:8,concurr:[16,372,514],conden:[341,470,472],condens:[6,160,341,388,404,410,424,475],condit:[],conducit:6,conduct:[],cone:490,confer:439,confid:[3,501],config:[12,202,484],configfil:231,configur:[1,2,6,12,15,17,38,62,134,180,198,201,202,205,209,230,231,232,233,237,245,252,253,283,296,304,340,369,379,381,388,392,411,436,439,468,470,472,475,482,487,489,490,501,509],confin:[487,501],conflict:[3,12,41,203,441,485,509],conform:[3,6,13,62,229,230,268,312,318,340,364,381,412,499],confus:[3,475],conjuct:[9,406],conjug:[7,8,253,378,412,449,450],conjunct:[6,7,76,95,96,126,161,166,172,178,182,206,210,211,253,256,260,283,299,300,304,305,306,308,313,317,329,337,344,349,371,372,381,393,395,399,402,406,412,418,424,441,444,452,473,487,490,494,508,519],connect:[3,6,9,96,163,181,229,250,298,313,316,326,381,403,416,449,450,466,472,484,485,487,491,508],conner:388,connor:388,conput:3,consecut:[3,11,12,40,76,178,206,210,211,233,250,251,402,424,428,482,488,490],consequ:[1,6,216,341,423,501],conserv:[],consid:[6,75,76,83,96,127,160,163,164,181,202,203,206,210,211,217,219,222,226,228,229,233,257,270,295,313,336,337,340,341,344,372,399,412,419,450,451,457,466,482,483,485,488,489,490,492,495,497,505,508,514],consider:[6,8,253,254,332,333,334,386,496],consist:[3,6,8,9,11,12,41,43,69,74,85,103,115,120,123,124,127,158,161,163,178,190,201,207,212,213,218,232,233,236,238,243,246,253,254,255,266,269,271,272,273,274,275,276,277,278,279,281,282,283,284,286,287,288,289,290,291,292,300,303,308,310,312,313,332,333,334,335,345,371,372,374,380,381,386,388,392,394,400,402,412,415,419,422,433,434,436,439,441,451,454,456,457,469,476,485,487,488,489,490,491,492,499,508,514],consistent_fe_initi:215,consit:313,constant:[],constitu:[3,6,259,313,346,350,400,451],constitut:[454,456],constrain:[3,6,8,155,156,157,158,159,161,164,165,166,167,168,170,171,209,218,233,245,246,251,259,263,298,299,311,313,316,327,337,344,379,380,412,492,499,508],constraint:[],construct:[6,8,12,14,38,55,57,64,67,71,75,77,78,82,101,118,130,152,177,230,269,295,312,350,382,386,405,439,441,466,468,469,490,491,506,514],constructor:[8,11],consult:450,consum:[1,308,445,514],consumpt:369,contact:[],contact_stiff:[453,455],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,66,96,100,128,130,152,154,158,166,176,177,178,180,184,186,197,198,202,203,205,206,207,209,210,211,215,217,218,219,221,222,223,224,226,231,233,238,241,247,251,252,253,256,267,283,294,295,298,299,301,302,303,306,310,313,314,319,329,336,340,341,350,351,354,370,372,380,381,384,385,387,388,389,392,401,402,405,410,411,412,419,420,436,439,443,447,448,449,450,458,468,469,470,471,472,473,475,482,483,484,485,487,488,489,490,492,494,496,499,501,502,504,505,508,509,514,517,519],content:[4,8,9,12,18,450,503,505],context:[3,6,8,12,17,128,129,206,227,228,233,298,310,345,378,478,487,494,503,513,514,515],contibut:75,contigu:484,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,76,88,114,115,174,206,209,210,211,216,218,219,220,221,222,223,224,226,229,230,231,232,233,245,246,247,249,250,251,253,254,255,261,266,267,269,271,272,273,274,275,276,277,288,289,290,291,292,297,299,302,303,313,314,318,328,329,331,338,339,341,347,350,354,370,385,386,392,406,409,426,429,449,450,451,454,456,471,482,485,487,489,490,495,501,502,504,505,514,517],continuum:[6,7,9,215,341,454,456],contour_integr:215,contract:[62,230,232,269,300,313],contradictori:3,contrain:316,contraint:283,contrari:[247,254],contrast:[1,6,43,56,67,160,163,203,232,352,454,456,478,518],contrib:341,contribut:[3,4,5,6,7,8,9,12,13,17,66,68,70,72,73,75,76,79,80,82,84,86,87,93,96,97,98,99,100,102,104,113,115,117,119,120,121,122,124,126,129,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,211,216,217,218,219,221,222,223,224,230,245,253,256,259,260,264,270,290,291,298,299,307,310,313,314,316,343,371,379,381,389,406,409,410,412,419,433,434,439,441,449,450,457,499,505,508,509],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,96,100,134,152,187,202,203,205,209,215,216,226,230,231,232,249,250,253,254,269,271,272,273,274,275,276,277,300,305,313,320,321,332,333,334,341,345,369,371,383,412,415,439,449,450,453,455,468,472,482,484,496,502,503],control_typ:215,controlfil:450,convect:100,conveni:[6,12,29,202,207,224,314,374,458,473,509,514],convent:[3,8,29,189,196,197,203,206,312,326,353,410,412,514],converg:[3,6,42,97,202,203,205,207,212,226,229,230,238,243,274,303,305,308,312,316,377,378,379,381,401,402,424,457,482,494,501],convers:[3,8,152,205,206,216,219,300,371,402,403,404,412,424,428,432,444,485,501,513],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,62,66,76,100,178,185,202,205,206,219,224,267,299,302,352,355,357,361,364,374,381,387,410,439,470,472,479,485,487,488,489,494,504,508,513,514,517,519],convex:[43,350],convinc:[7,12],cook:9,cooki:7,cool:[7,168,249,311],cooordin:[202,203],cooper:[5,7],coord123:126,coord1:[3,126,218,222,223],coord2:[3,126,218,222,223],coord3:[3,126,218,222,223],coord:[],coordb:457,coordbb:457,coordiat:379,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,62,64,65,66,70,72,76,79,80,82,87,88,96,98,99,104,114,115,117,125,126,128,146,152,161,167,173,175,176,178,182,201,202,203,204,205,206,207,209,212,217,218,221,222,223,226,227,228,229,230,231,232,233,236,238,239,243,245,248,249,250,251,252,253,254,266,268,269,271,272,273,275,276,277,290,293,294,295,298,299,300,310,311,313,315,316,318,323,326,327,328,329,331,339,340,341,348,349,351,352,374,379,380,381,386,387,388,391,411,457,482,487,488,489,490,492,495,497,501,508,514,515],coordn:[126,218],copi:[0,3,4,8,9,11,12,15,17,41,131,205,341,381,399,449,485,509],copper:479,coproccesor:16,coprocessor:[1,7,9,16,17,386,500],coproprocessor:17,copy_arrai:8,copyright:[7,8,298],coral:206,core:[],core_shel:160,coreshel:[],cornel:[6,184,499],corner123i:125,corner123x:125,corner123z:125,corner1i:125,corner1x:125,corner1z:125,corner2i:125,corner2x:125,corner2z:125,corner3i:125,corner3x:125,corner3z:125,corner:[3,6,41,125,205,350,351,374,474,487,509],cornflowerblu:206,cornsilk:206,corp:9,corpor:16,corr:401,correct:[3,6,9,11,12,16,17,62,87,96,97,113,114,119,122,128,160,165,172,203,205,232,245,247,253,269,270,290,298,300,303,340,346,350,371,381,387,388,389,390,391,392,393,394,395,396,397,398,400,401,402,403,404,405,406,409,410,411,412,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,474,475,477,478,479,480,487,502,505,508,509],correction_max_iter:215,correctli:[3,8,11,17,76,88,113,114,115,155,156,157,159,161,163,164,165,166,167,170,171,174,202,206,212,233,238,243,254,263,269,270,306,313,316,326,328,347,350,381,382,386,404,434,439,484,485,487,497,509,513,515],correl:[],correpond:241,correspond:[1,2,4,6,8,9,10,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,75,76,96,107,108,121,124,125,126,127,130,131,139,142,143,144,145,146,148,149,150,152,155,156,165,172,176,177,184,185,186,187,188,189,190,192,193,195,196,198,201,202,203,205,206,210,211,212,218,220,221,222,223,225,228,230,232,239,243,244,248,253,256,257,265,266,267,269,271,272,273,274,275,276,277,278,279,283,286,288,289,290,292,295,296,300,305,313,315,316,332,334,336,345,346,347,349,350,351,353,355,356,357,358,360,361,364,366,372,376,378,380,381,387,388,390,393,394,395,396,397,398,399,400,401,402,405,406,410,411,412,413,414,415,416,417,418,419,422,424,425,426,427,428,429,430,431,432,433,436,437,439,441,442,443,444,446,447,449,450,451,452,457,458,459,468,469,470,471,472,473,475,477,478,479,482,484,485,487,488,490,500,501,502,504,505,508,514],correspondingli:[433,434,496],corrupt:3,cosin:[],cosineshift:27,cosmo:[247,252],cossq:[],cost:[1,6,10,11,12,17,40,42,76,121,130,153,177,205,206,218,222,223,226,227,228,242,269,305,341,371,372,384,402,424,428,439,441,468,484,496],costheta0:[468,470,472,475],costheta:447,costli:[11,97,247,382],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,62,70,76,80,87,96,99,104,115,117,121,124,126,158,168,173,175,191,202,203,205,206,210,211,218,219,222,226,232,243,252,302,303,304,308,311,313,315,329,330,336,340,341,342,346,350,352,354,362,368,370,377,379,382,386,389,414,418,419,422,449,450,483,484,485,487,489,491,494,495,502,503,508,514,515],coulomb:[3,5,6,7,8,9,10,12,14,15,18,77,97,119,120,128,153,179,183,304,306,342,371,372,379,386,393,395,396,397,398,401,402,403,404,405,412,416,417,419,424,428,432,435,441,444,449,450,452,457,467,472,473,475,478,492,499,505,508,513],coulommb:6,cound:3,count:[1,3,6,8,11,12,16,42,66,72,82,100,126,128,129,166,176,182,212,213,216,218,221,222,223,225,226,233,238,242,245,251,269,283,299,316,332,333,350,372,379,380,381,383,386,414,418,441,505,514],counter:[3,347,482,493,495,501],counteract:245,counterbal:249,counterbalanc:29,counterpart:[202,313,482],counterproduct:18,coupl:[],courant:319,cours:[3,8,138,140,172,202,210,211,246,312,326,340,346,348,349,351,352,372,433,459,484,487,500,508,514,517],courtesi:374,cov:457,coval:[6,9,29,412,436,457,508],covari:247,cover:[6,12,76,198,206,215,256,412,474],coverag:[76,222],cpc:252,cpp:[1,3,6,8,9,11,12,13,96,202,210,211,243,316],cpu:[1,3,9,10,12,14,15,16,17,18,66,76,206,220,236,254,342,369,372,386,399,467,482,500,501,504,505,506,514],cpuremain:505,cr2:177,cr3:177,crack:[4,382],crada:[5,7],crai:[5,7,13,18,202],crash:[3,12,382,508],craympi:386,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:215,create_faceset:215,create_group:204,create_nodeset:215,createatom:[],creation:[],crimson:206,critchlei:298,criteria:[3,128,179,205,206,227,228,229,264,379,446,474,489,492,514],criterion:[12,42,133,178,181,216,226,229,245,283,305,319,347,352,379,381,401,412,416,457,492,501,502],criterioni:501,critic:[6,49,50,267,336,341,379],crmax:76,crmin:76,cross:[3,12,22,76,98,156,176,186,202,203,205,217,222,228,232,266,268,290,313,322,326,328,337,344,356,374,381,397,406,409,410,417,418,419,424,426,428,447,452,454,456,470,472,479,487,491,497,517],crossov:1,crossterm:487,crozier:[0,7,13],crucial:303,crystal:[3,4,6,13,78,118,294,295,339,374,382,487,491,505,508],crystallin:[6,114,295,374,471,508],crystallis:336,crystallogr:[130,177],crystallograph:[374,505],crystallographi:[130,177,374],cs1:177,cs_chunk:6,cs_im:[41,487],cs_re:[41,487],csanyi:[152,448,458],cscl:436,csequ:6,csh:[11,12,399],cshrc:[11,12],csic:[411,468,470,472,475],csinfo:6,csisi:[411,468,470,472,475],csld:[],cst:410,cstherm:6,cstyle:484,csvr:[],ctcm:[387,410],ctemp_cor:236,cterm:318,ctr:9,ctype:11,cu1:177,cu2:177,cu3au:436,cube:[6,42,176,181,226,236,350,374,508],cubic:[],cuda:[],cuda_arch:[9,15],cuda_get:15,cuda_hom:[9,15],cuda_prec:[9,15],cufft:14,cuh:392,cummul:[3,6,224,227,228,229,231,242,247,253,255,329,332,333,334,335,337,344,418,505],cumul:[6,216,218,221,222,223,237,245,253,267,269,274,283,313,314,381],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,15,16,17,18,41,42,43,58,62,64,66,76,78,88,96,113,114,120,128,129,142,153,158,166,168,174,176,179,182,201,202,203,204,205,206,207,210,211,215,218,222,223,224,226,227,228,229,230,231,232,233,237,238,243,245,247,250,251,253,259,266,269,270,275,276,277,283,288,289,290,292,298,299,304,305,307,310,311,312,313,316,317,318,319,320,321,322,323,325,327,328,329,332,333,334,340,341,344,345,346,347,348,349,351,352,354,369,370,371,372,375,376,378,379,380,381,386,392,399,401,405,410,412,413,416,419,420,423,433,434,436,437,438,441,447,449,450,453,454,455,456,459,470,472,473,476,482,483,484,485,487,488,489,490,491,493,494,495,497,499,501,502,504,505,509,514,515,516,517,518,519],curv:[6,178,245,295],curvatur:[415,451,479],custom:[],cut0:485,cut1:496,cut2:496,cut:[],cuthi:[294,306],cutinn:[394,433,434],cutlo:[294,306],cutmax:447,cutoff1:[398,405,424,428,432,435,444,452],cutoff2:[393,395,396,398,404,405,424,428,432,435,444,452,473],cutoff:[3,6,8,10,16,18,40,46,47,55,56,64,75,77,78,82,96,101,118,120,127,128,152,176,179,181,182,228,229,234,241,294,303,304,306,308,310,313,317,329,342,346,350,352,369,371,372,379,382,383,384,386,387,388,389,390,391,392,393,394,395,396,397,398,400,402,403,404,405,406,407,408,409,410,411,412,413,414,415,417,418,419,420,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,449,450,451,452,457,458,459,460,461,462,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,485,489,492,496,508,514],cutoffa:411,cutoffc:411,cuu3:410,cval:177,cvd:336,cvel:318,cvff:[],cwiggl:[3,266,346,349,351,514],cyan:[2,205,206],cycl:[3,245,267,269,270,274],cyclic:[3,198],cygwin:12,cylind:[3,4,76,205,218,251,299,347,350,490],cylindr:[6,251,326,347],cypress:386,cyrot:392,cyrstal:295,d3q15:256,d3q19:256,d_double_doubl:15,d_e:341,d_flag2:302,d_flag:302,d_name:[125,202,302,331,497],d_single_doubl:15,d_single_singl:15,d_sx:302,d_sy:302,d_sz:302,daan:339,dai:12,daili:12,daivi:290,damag:[],dammak:308,damp:[3,6,209,214,253,254,255,260,269,270,274,300,303,304,308,313,332,333,345,347,348,378,379,381,393,395,397,402,405,412,416,424,432,444,452,467,473,501,508],damp_com:254,damp_drud:254,dampen:[313,508],dampflag:[347,416],dan:17,danger:[3,12,245,352,406,505],dangl:181,daniel:9,darden:[372,405],darkblu:206,darkcyan:206,darken:205,darkgoldenrod:206,darkgrai:206,darkgreen:206,darkkhaki:206,darkmagenta:206,darkolivegreen:206,darkorang:206,darkorchid:206,darkr:206,darksalmon:206,darkseagreen:206,darkslateblu:206,darkslategrai:206,darkturquois:206,darkviolet:206,dasgupta:304,dash:[416,504],dat:[6,100,198,215,483],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,314],dataset:314,datatyp:3,date:[0,4,6,12,13,201,449,450,514],datom1:127,datom2:127,datom3:127,datom4:127,datum:[3,6,43,69,72,74,85,103,120,127,202,219],davenport:435,davi:346,david:[9,19,371,372,470,472],daw:[410,447],dbg:14,dcd:[3,6,7,202,204,205,206,207,296,488,492],ddim:201,deactiv:432,dealt:252,debug:[6,7,11,12,13,14,17,58,130,134,177,178,296,301,369,371,386,420,441,476,485,486,494,497,504,514],deby:[],decai:[101,402,479],decid:[3,6,12,16,76,266,302,313,342,502,509],decipher:374,deck:302,declar:204,declin:329,decod:205,decompos:[96,458],decomposit:[3,5,7,18,65,215,296,317],decoupl:[6,508],decreas:[3,202,203,212,213,220,229,232,238,243,245,253,340,371],decrement:318,deepli:368,deeppink:206,deepskyblu:206,def:[12,13,485],defaul:64,defect:[6,75,176,439],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,62,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,184,185,186,187,188,189,190,192,193,195,196,197,198,199,200,201,202,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,221,222,223,224,225,226,227,228,229,230,232,233,236,237,238,240,243,244,245,248,251,252,253,254,255,256,264,266,268,269,270,271,272,273,274,275,276,277,279,280,281,284,286,287,288,289,290,291,292,294,295,296,298,299,300,302,304,306,311,313,314,315,316,319,323,327,329,331,332,333,334,335,337,338,339,341,343,344,346,347,348,349,350,351,352,354,355,356,357,358,359,360,361,364,365,366,367,369,371,372,374,376,378,379,380,381,382,383,384,385,386,388,389,390,391,393,394,395,396,397,398,399,400,402,403,405,406,407,408,409,411,412,414,415,416,417,418,419,420,422,424,425,426,427,428,429,430,431,432,433,434,435,439,440,441,442,443,444,446,447,449,450,451,452,453,454,455,456,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,484,485,487,488,490,491,492,493,496,497,498,499,501,502,504,505,508,510,511,512,513,514,515,516],definit:[2,3,6,8,12,13,83,86,128,152,206,218,219,220,221,222,223,224,232,240,251,274,314,331,343,346,349,351,353,365,369,380,389,392,400,407,408,412,422,447,454,456,458,474,485,487,489,496,498,513,514],defint:505,deform:[],deg2theta:177,deg:508,degener:[3,298],degrad:[8,18,295,372,496],degre:[3,6,8,20,21,24,28,29,32,35,36,38,69,85,101,103,105,107,108,110,112,113,118,124,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,177,178,184,185,188,189,196,198,201,205,218,229,236,245,247,248,253,254,259,269,270,274,275,276,277,288,289,290,292,296,298,312,313,316,332,333,334,339,355,357,361,364,366,379,405,410,418,497,505,508,515],degress:[158,218],del:501,delai:[3,6,12,382,409,505],deleg:419,delet:[2,3,7,8,12,55,60,63,66,176,181,182,209,218,219,221,222,223,224,227,229,242,245,269,314,332,333,352,354,370,380,382,385,441,466,487,488,489,490,498,499,504,509,510,512,514,515],delete_atom:[],delete_bond:[],delete_el:215,deli:201,delimit:[485,514],deloc:[270,412,457],delr:436,delt_lo:501,delta:[],delta_1:392,delta_3:392,delta_7:392,delta_conf:3,delta_ij:[436,447],delta_pi:392,delta_r:447,delta_sigma:392,delx:201,delz:201,demand:308,demo:11,demon:293,demonstr:[303,436],den:299,dendrim:418,denniston:[9,256,258,259,260,295],denomin:[7,183],denot:[130,236,254,295,306,308,402,417,419,450,454,456],dens:[76,229,412],densiti:[3,6,7,9,18,41,42,62,111,128,138,152,164,176,178,210,211,215,218,222,223,226,232,243,256,259,262,263,295,299,300,302,304,341,346,374,376,380,387,388,392,410,436,437,438,447,451,457,461,463,464,465,487,496,497,505,513],density_continu:456,density_summ:456,depart:[0,7],departur:[267,303],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,64,66,69,72,74,75,76,85,101,103,114,120,121,124,125,126,127,131,152,154,155,161,165,166,172,178,179,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,205,206,209,210,211,212,213,216,218,220,221,222,224,225,226,228,230,232,238,239,244,247,248,249,251,253,254,256,258,259,266,269,271,272,273,274,275,276,277,278,279,286,288,289,290,292,294,305,308,310,313,315,316,317,323,329,332,333,334,336,338,340,341,343,345,346,349,350,351,352,354,355,356,357,358,360,361,364,366,372,374,379,380,382,383,384,386,387,388,390,391,392,393,394,395,396,397,398,399,400,401,402,403,405,406,410,411,412,413,414,415,416,417,418,419,424,425,426,427,428,429,430,431,432,433,436,437,439,440,442,443,444,446,447,449,450,451,452,457,458,459,467,468,469,470,471,472,473,475,477,478,479,482,484,487,489,490,493,497,499,501,504,505,507,514,515],dependend:6,depflag:12,dephas:[482,501],depos:233,deposit:[],deprec:[3,304,449],depth:[52,156,205,341,415,451],dequidt:9,der:[96,119,400,401,432,449,450,478,508],deriv:[6,7,8,9,38,57,66,96,152,172,198,219,230,232,245,253,266,269,271,272,273,274,275,276,277,294,300,304,308,338,339,341,346,347,350,378,380,388,392,400,405,412,413,417,426,430,431,436,439,449,450,467,469,478,508],derjagin:478,derlet:294,descend:206,descent:[7,378],descib:[41,205,304],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,65,66,72,75,76,78,97,122,125,128,130,142,152,153,156,157,158,162,163,166,169,171,172,176,177,178,180,181,190,195,198,202,203,204,209,210,211,218,219,220,221,222,223,224,226,229,230,231,232,233,235,236,241,246,247,250,251,252,253,254,255,256,258,259,260,264,268,269,270,274,282,291,294,296,301,302,303,304,305,306,313,318,326,329,330,331,332,333,334,335,336,337,338,339,344,346,347,349,354,371,372,374,377,378,379,380,381,385,388,389,391,393,394,395,397,398,399,400,401,402,405,410,412,413,415,416,417,419,422,424,425,426,427,428,429,430,431,432,433,434,435,436,439,440,446,447,448,449,450,451,452,457,458,459,466,467,468,469,470,471,472,473,475,477,478,479,480,482,484,485,487,488,489,490,491,497,500,501,504,509,514,515,517],descript:[],descriptor:[152,202,420],deserno:372,design:[0,3,6,7,8,11,13,14,15,17,130,160,163,177,215,229,235,236,269,270,294,295,314,336,341,389,390,391,394,397,402,404,412,432,433,434,437,438,447,450,469],desir:[2,3,6,7,9,11,12,14,15,16,33,41,51,62,76,97,100,124,129,153,160,178,191,201,218,224,230,232,243,245,246,253,254,255,259,269,290,298,299,300,301,304,308,313,316,329,332,333,334,335,340,347,362,368,371,372,374,377,379,380,381,406,410,418,433,434,468,470,472,483,484,485,487,491,496,501,502,504,505,514,515,517],desk:7,desktop:[4,6,7,10,12,205],despit:508,destabil:392,destre:364,destroi:[9,11,40,227,228],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,66,70,71,72,76,80,83,87,99,100,104,113,115,117,119,121,123,124,126,129,131,152,153,155,156,157,158,161,171,172,173,175,178,179,182,183,186,197,201,202,203,205,206,209,210,211,215,218,219,220,221,222,224,226,228,229,230,231,232,233,243,245,246,247,248,250,251,253,255,256,260,266,267,268,269,270,271,272,273,274,275,276,277,281,283,288,289,290,291,292,295,298,299,300,302,303,305,306,307,313,316,317,329,332,333,334,335,336,337,339,340,341,342,343,344,345,352,354,356,365,371,372,375,379,380,382,383,386,387,388,389,391,392,394,396,397,398,399,400,401,402,405,406,412,413,415,416,417,418,419,424,425,426,427,428,429,430,431,432,433,434,435,436,440,441,446,449,450,451,457,458,459,467,474,477,478,480,485,487,488,489,490,492,493,496,497,499,502,505,506,509,514,515,519],detect:[2,3,12,43,64,66,95,101,244,299,340,381,401,418,423,482,484,487,498,501,514],determ:386,determin:[1,3,6,8,9,12,15,40,41,43,52,60,61,62,64,65,72,76,96,113,119,121,124,130,131,139,153,166,167,176,177,178,201,202,203,205,206,207,208,212,213,214,217,218,219,220,221,222,223,224,225,226,230,232,233,236,238,245,248,249,251,253,254,259,264,266,267,269,275,276,277,288,289,290,292,294,296,299,300,303,310,311,312,313,314,315,319,321,323,329,332,333,334,336,342,343,346,347,348,349,350,351,352,365,371,372,374,380,382,383,386,388,389,396,401,405,409,410,414,416,419,420,428,436,439,441,450,451,457,466,469,473,478,484,487,488,490,492,494,497,501,503,504,506,513,514,515],determinist:317,detil:120,devan:[9,452],devanathan:472,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,250,274,298,303,304,307,388,392,412,438,439,457,475,489],devemi:9,deviat:[267,274,294,414],deviator:9,devic:[1,3,12,15,17,250,386],device_typ:386,devin:[305,401],devis:438,dfactor:205,dff:508,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,372],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,307,439],dhi:[62,201,232,299],dhug:[267,303],dhugoniot:[267,303],dia:436,diagnost:[],diagon:[3,6,92,152,153,154,230,269,300,313,344,454,456],diagonalstyl:458,diagram:[42,130,177,197,226,296],diallo:418,diam:[205,206,299,380],diamet:[3,6,41,43,125,178,202,203,205,206,210,211,253,299,302,313,329,331,345,347,380,400,415,416,426,451,474,478,487,488,497],diamond:[374,412,436],diamter:[41,299],dick:6,dicsuss:266,dictat:[216,267],did:[3,12,379,406,409,410,416,441,470,472,495],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,174,343,371],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,64,67,72,75,76,96,101,105,107,108,132,152,154,155,156,157,158,159,161,164,165,166,167,168,170,171,172,178,179,181,186,197,198,201,202,205,206,209,211,214,216,218,221,226,227,228,229,230,231,232,236,241,244,245,246,247,248,249,250,253,254,256,266,269,270,271,272,273,275,276,277,279,281,284,286,287,288,289,292,294,296,298,300,303,304,305,308,311,313,316,318,326,327,329,332,333,334,337,338,339,341,344,345,346,347,350,354,355,365,368,370,371,372,374,375,377,378,380,381,383,384,385,386,387,388,392,396,397,399,400,401,406,407,408,410,412,415,416,417,419,422,424,425,427,428,435,436,437,438,440,441,443,447,449,450,451,452,453,454,456,457,458,459,467,468,469,470,472,474,475,478,481,482,484,485,487,489,490,491,492,495,496,497,499,501,502,504,505,506,508,513,514,515,517],differenti:[1,3,6,29,198,371,402,447,471],difficult:[230,296,386,418,496],difficulti:[101,118,316,449],diffract:[],diffus:[],digit:[2,3,206,354,439,514],dih_table1:198,dih_table2:198,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:[3,199],dihedraltyp:228,dihydrid:412,dij:316,dilat:[],dim1:3,dim2:3,dim:[3,62,76,155,159,160,161,164,165,166,167,168,170,178,201,222,232,251,347,374,436,490,513,514,515],dimdim:514,dimems:295,dimens:[],dimensinon:76,dimension:[3,40,101,124,130,152,155,158,159,160,161,164,165,166,167,168,170,177,200,218,222,268,295,341,374,377,381,447,487,497],dimensionless:[116,133,134,136,139,141,143,148,152,341,372,458,478],diment:3,dimentionless:147,dimer:[6,313,436],dimgrai:206,dimstr:[42,226],dinola:[300,332],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,41,202,203,331,508],dir1:498,dir2:498,dir:[1,3,4,8,10,11,12,267,294,303,328,447,449,450,485,498,514],dirac:152,direc:447,direct:[],directli:[3,6,8,9,11,12,96,125,152,154,202,203,204,205,212,238,247,251,256,295,314,333,345,347,348,349,350,374,378,386,387,388,393,395,396,402,405,410,412,424,428,441,444,452,466,485,497,498,499,505,514],directoi:14,directori:[],disabl:[3,12,16,341,423,485,500,514],disadvantag:[6,226],disallow:[202,232,269],disappear:489,discard:[2,3,42,76,220,222,226,342,350,484,489,490],discontinu:[198,379,430],discourag:436,discov:[13,342],discret:[6,8,41,43,205,206,253,256],discuss:[],disk:[6,93,94,101,171,200,233,245,299,485],disloc:[75,439],disord:[40,75,439],disp:[],dispar:451,disperion:[405,428],dispers:[3,6,7,9,176,295,371,372,396,405,428,433,441,450,469,475],displac:[],displace_atom:[],displace_box:62,displacemet:490,displai:[11,13,22,37,45,56,186,197,202,205,356,365,399,467],dispters:3,disregard:439,dissip:[6,9,41,89,90,240,246,253,295,317,338,339,394,406,407,408,416,433,434,467],dissolut:227,dist:[6,74,100,120,129,202,296,312,409,466,482,515],distanc:[],distinct:[6,236,310,371,451],distinguish:[6,95,152,259,412,486,514],distort:[176,387],distrbut:387,distribut:[],distro:[123,399,446,447],ditto:[8,12,14,15,16,17,18,43,127,228,479,485],div:8,divd:129,diverg:[3,12,40,313,339,388,489,508,517],divid:[3,6,16,42,100,124,129,138,140,153,175,176,186,197,206,218,219,221,226,232,294,337,344,349,371,379,381,413,450,457,475,496,504,514],divis:[6,256,392,422,432,484,505,514],dl_poli:[6,7],dlambda:172,dlammps_async_imd:250,dlammps_bigbig:[12,40],dlammps_ffmpeg:[3,12,205],dlammps_gzip:[3,12,202,205,340,487,488,492],dlammps_jpeg:[3,12,205],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,16],dlammps_png:[3,12,205],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,202],dlen:497,dlmp_intel_offload:[9,16],dlo:[62,201,232,299],dlopen:6,dlvo:[7,400,478],dm_lb:256,dmax:[329,377],dmpvtk:203,dmpvtp:203,dna:7,doc:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,22,37,41,43,56,60,62,66,70,72,80,87,96,99,104,113,115,116,117,119,121,123,124,126,129,131,153,156,157,158,171,173,175,178,179,180,186,197,201,202,203,204,205,206,207,209,210,211,216,217,218,219,220,221,222,223,224,233,245,253,254,264,269,270,275,276,277,281,288,289,290,291,292,299,302,313,326,329,332,333,334,343,347,350,352,354,356,365,370,379,380,381,386,387,388,391,399,401,402,410,411,413,418,419,421,422,436,437,438,441,443,446,447,448,458,467,468,470,472,474,475,485,487,488,489,490,492,495,496,497,504,505,509,514,515,517,518],docuement:451,dodd:43,dodgerblu:206,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,33,38,40,42,43,51,55,57,62,65,66,71,75,76,77,96,97,100,115,119,122,128,129,130,154,156,158,160,161,166,168,172,177,178,179,180,182,184,186,191,197,198,201,202,203,204,205,206,209,215,216,218,222,225,226,228,229,230,232,236,238,241,242,245,246,249,251,253,254,256,259,265,269,270,271,272,273,275,276,277,288,289,290,291,292,300,301,302,306,308,311,313,329,332,334,336,337,341,344,345,346,349,350,351,352,357,358,359,361,362,364,370,371,372,373,374,380,381,382,387,388,389,390,391,392,394,396,397,398,400,401,402,403,405,406,409,410,411,412,414,415,416,417,419,420,421,422,423,426,427,429,430,431,433,434,436,437,438,439,441,447,448,449,450,451,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,470,471,472,473,474,475,477,478,479,480,482,483,484,485,487,488,489,490,491,494,495,497,498,499,500,501,504,505,508,509,514,519],doegenomestolif:7,doesn:[3,7,8,12,178,202,203,216,222,223,326,380,382,386,388,401,411,421,449,450,468,470,471,472,475,487,489],dof:[3,8,124,156,157,158,171,218,313,515],dof_per_atom:[158,218],dof_per_chunk:[158,218],doff:[380,487],dog:[],doi:[6,231],domain:[3,6,7,12,13,18,40,42,43,61,64,65,76,130,167,177,180,201,204,205,206,209,216,226,230,232,233,249,252,256,269,270,296,3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505,514],elt:436,emac:[],email:[0,3,5,7,8,9,11,413],emb:[3,9,350],emb_lin_neg:436,embed:[3,4,5,7,9,11,12,13,29,97,154,176,341,387,410,413,432,436,437,438,447,467,476,485],embt:185,emi:[7,9],emil:9,emol:[449,450,505],emphas:416,empir:[9,215,333,388,412],emploi:[295,304,308,471],empti:[3,60,76,176,180,313,371,382,423,487,498,499,514],enabl:[3,6,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,37,38,40,41,44,46,47,48,49,50,51,52,54,55,56,57,63,64,65,67,71,83,86,92,96,97,107,108,109,110,111,112,116,119,121,123,124,130,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,154,155,156,157,160,162,164,165,169,170,172,176,177,184,185,187,188,189,190,191,192,193,195,196,197,198,202,203,204,206,207,209,210,211,212,213,214,216,220,223,225,227,228,229,231,232,233,238,239,242,243,244,245,246,247,248,250,251,252,253,254,255,256,257,258,259,260,262,263,265,267,269,270,271,272,273,274,275,276,277,278,279,280,281,282,284,286,287,288,289,290,291,292,294,295,296,298,299,303,304,305,306,307,308,309,310,312,313,315,316,318,319,320,321,322,323,325,326,328,329,332,334,335,336,337,338,339,341,342,344,345,346,347,348,349,350,353,355,357,358,360,361,362,364,365,366,372,379,381,385,386,387,388,390,391,392,393,394,395,396,397,398,400,401,402,403,404,405,406,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,436,437,438,439,441,442,443,444,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,479,485,488,489,490,494,496,506,514,519],enclos:[2,6,12,180,202,301,354,436,457,483,485,495,514],encod:[13,40,43,202,205,206,302,419],encompass:[3,6,41,43,60,62,128,179,325,343,467,490],encount:[3,8,12,62,118,221,385,492,514],encourag:[7,8,307,327],end12i:125,end12x:125,end12z:125,end1i:125,end1x:125,end1z:125,end2i:125,end2x:125,end2z:125,end:[1,2,3,5,6,8,11,12,15,16,17,18,19,38,41,42,43,58,60,62,76,125,181,182,185,201,202,203,205,206,207,210,211,219,221,223,224,229,232,246,251,253,255,268,269,270,283,300,312,313,318,329,332,333,334,335,337,340,341,344,348,351,352,370,371,380,381,385,386,406,410,415,422,435,439,451,454,456,458,459,476,482,485,487,488,489,490,492,494,495,499,503,505,508,514,519],end_of_step:8,endbondtors:[3,185,191,487],endif:8,energet:[229,388,450],energi:[],energy_compon:457,energy_update_freq:450,enforc:[6,9,60,61,115,201,202,203,204,205,207,209,216,229,232,269,293,295,305,313,316,354,371,424,484,514,515],enforce2d:[],eng:[11,69,74,120,202,243,352,354,401,438],eng_previ:354,engil:9,engilitycorp:9,engin:[215,232,298,318,338,410,437],enhanc:[211,215,482],enlarg:[62,205],enough:[3,41,64,95,178,179,181,182,226,254,299,303,308,313,342,346,347,350,382,386,402,445,487,491,492],enpub:410,ensembl:[],ensight:6,ensur:[3,6,152,202,203,216,220,230,245,246,269,319,340,372,392,409,432,468,475],enter:[60,168,413,439,475,501],enthalpi:[135,271,272,273,410,504,505,514],entir:[0,2,3,6,11,14,15,42,43,66,89,90,97,121,122,124,128,130,153,158,177,178,206,209,210,211,218,222,223,226,229,231,242,245,246,249,253,254,265,269,271,272,273,274,275,276,277,294,296,298,311,313,327,341,343,354,386,405,428,441,469,487,495,496],entireti:474,entiti:[6,8,41,43,202,313],entri:[3,8,12,38,43,57,69,74,85,103,120,127,130,139,142,143,144,145,146,148,149,150,176,198,203,206,210,221,222,223,231,241,303,352,380,392,411,436,443,450,458,468,469,470,471,472,475,514],entropi:501,entry1:[38,57,206,399,469],entry2:206,entryn:206,enumer:[179,202,480],enumuer:6,env:386,environ:[1,3,6,11,12,16,17,18,205,247,252,294,386,387,392,399,401,411,412,447,470,484,498,514],epair:[119,206,414,418,449,450,505],epen:[449,450],epfl:[247,252],epp:405,epq:405,eps0:478,eps14:432,epsilon0:472,epsilon:[3,6,36,46,47,51,54,55,96,184,210,211,245,313,329,346,350,377,379,391,397,398,400,402,403,404,405,415,417,418,419,422,423,424,425,426,427,428,429,430,431,432,435,440,444,451,452,462,468,473,474,477,478,496,508,513],epsilon_0:479,epsilon_14:397,epsilon_:451,epsilon_d:403,epsilon_i:[415,441,451],epsilon_i_:451,epsilon_i_a:[415,451],epsilon_i_b:[415,451],epsilon_i_c:[415,451],epsilon_ij:441,epsilon_j:[415,441,451],epsilon_j_:451,epsilon_j_a:[415,451],epsilon_j_b:[415,451],epsilon_j_c:[415,451],epsilon_lj:451,epton:446,eqch:173,eqeq:[449,450],eqp:405,eqq:405,equal:[2,3,6,8,11,12,17,40,42,55,66,69,72,74,76,81,85,95,96,100,103,120,122,127,129,131,153,156,172,174,176,178,201,205,206,209,210,211,212,213,216,219,220,221,224,225,226,230,232,233,238,245,246,248,249,251,253,254,256,259,260,266,267,274,285,294,296,299,301,303,304,305,308,310,312,313,315,318,323,325,332,333,334,337,338,339,341,343,344,346,349,351,352,354,370,374,379,381,382,383,385,386,401,406,408,414,415,418,422,433,439,440,447,449,450,451,453,454,455,457,458,459,469,474,475,479,483,484,485,487,489,490,494,495,498,501,503,505,514,515],equat:[3,6,7,8,9,100,118,124,130,177,186,197,209,230,236,237,240,241,247,253,254,256,259,267,268,269,270,274,290,294,296,303,304,308,316,317,329,337,341,344,346,347,349,351,364,371,372,400,405,406,408,412,413,416,421,433,434,436,441,451,454,456,461,462,464,465,479,508],equi:270,equidist:268,equil:[3,304,375,494,519],equilater:497,equilibr:[3,4,5,6,7,9,62,100,178,209,216,219,229,230,245,267,269,270,290,291,300,303,304,305,306,337,338,339,344,401,402,449,450,483,497],equilibria:344,equilibribum:[227,228],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,39,44,48,49,50,52,54,57,59,62,161,162,185,187,230,232,245,246,247,254,256,269,274,290,303,304,308,312,316,318,326,329,336,337,339,344,355,357,361,364,401,436,443,457,508],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:215,equival:[6,12,13,29,62,64,136,137,145,150,176,180,206,221,224,230,232,245,253,269,290,300,312,313,349,388,406,412,457,470,472,473,487,490,495,496,505,508],equlibrium:6,equliibr:[304,306],er3:177,eradiu:[41,125,203,412,487],eras:[315,338],erat:[232,434],erc:402,erfc:[402,424,441],erforc:[125,203],erg:513,erhart:[216,410,470,472],ermscal:389,ernst:9,eror:3,eros:436,erose_form:436,erot:[],errata:[470,472],erratum:346,erron:3,error:[],erta:416,ervel:[125,203,487],escap:[233,508],especi:[8,16,166,178,209,216,226,245,303,308,311,312,386,484],espresso:[9,307],essenti:[8,11,12,27,97,140,159,160,161,164,165,166,167,168,170,187,219,274,295,345,372,388,402,424,472,492,505],essex:29,establish:[96,249],estim:[1,3,6,10,12,38,42,57,100,153,215,226,237,267,329,336,371,372,377,441,450,469,501,505],esu:513,esub:436,eta:[6,256,269,303,304,306,345,411,413,415,447,471,475,513],eta_dot:269,eta_ij:447,eta_ji:413,etag:[41,487],etail:505,etap:269,etap_dot:269,etc:[1,2,3,4,6,7,8,9,10,11,12,13,15,16,40,41,43,55,64,72,98,99,100,105,121,122,125,127,153,155,158,159,160,161,162,164,165,166,167,168,170,172,178,180,181,182,191,202,203,205,206,209,210,215,216,217,218,221,222,223,224,227,228,232,233,243,245,246,253,269,299,310,314,341,342,350,354,370,371,379,380,381,382,384,410,411,419,432,434,439,445,449,450,468,470,472,475,482,485,487,488,489,494,496,497,501,502,503,504,505,506,508,513,514,517,519],ethernet:18,etol:[379,381,482,501],etot0:303,etot:[6,105,107,108,122,153,164,206,236,254,267,303,504,505],eu2:177,eu3:177,euler:[379,381],eulerian:215,euqat:460,europhi:256,ev_tal:8,evalu:[2,3,9,11,12,38,57,76,96,97,100,119,129,131,152,154,158,168,176,178,201,202,203,205,206,210,211,212,213,215,217,218,219,220,221,222,223,224,225,232,238,246,248,249,251,252,253,254,295,301,304,315,319,323,332,333,334,343,346,349,351,352,354,371,372,377,379,386,439,441,447,453,455,457,469,482,483,485,489,490,492,494,495,496,497,501,503,505,514,515],evalut:[354,485],evan:[166,290],evanseck:[6,20,184,397,499],evapor:[],evaul:[8,379],evdwl:[119,154,449,450,505],even:[3,6,8,12,15,17,18,34,40,42,53,58,60,62,64,66,75,76,97,119,131,176,179,180,194,198,202,203,206,209,210,211,216,217,218,221,222,223,224,226,227,228,230,232,233,236,251,254,267,269,270,295,299,308,310,313,314,325,329,337,341,344,346,350,352,363,371,377,379,381,386,391,412,413,416,419,422,441,451,475,476,480,487,488,490,492,493,494,496,497,499,502,504,505,506,508,519],evenli:[3,42,58,153,198,226,256,422,476],event:[],eventu:[3,6,12,15,180,304,501],ever:[9,55,57,252,329],evera:[400,415,451,467],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,76,77,100,125,131,140,166,181,202,203,204,205,206,207,209,210,211,212,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,232,233,237,242,243,245,247,249,250,251,256,257,265,269,270,274,293,294,295,299,300,301,302,303,304,305,306,308,310,311,313,314,316,318,329,331,332,333,334,335,336,337,340,341,342,343,344,352,354,370,372,381,382,383,386,406,409,419,432,449,450,457,463,481,482,483,487,489,491,492,494,495,496,501,502,503,505,509,514,519],everyth:[8,119,509],everywher:[128,426],eviri:412,evolut:[247,256,296,482],evolv:[256,296,342],ewald:[2,3,5,6,7,8,9,12,97,122,130,153,342,371,372,379,393,395,396,402,405,412,424,428,444,452,467,469,473],ewald_disp:405,ewalddisp:3,exact:[22,42,45,76,134,172,181,186,226,229,246,247,253,254,255,299,308,309,329,341,356,371,399,489,494,501,514,517,519],exactli:[3,6,12,14,17,38,42,43,57,62,76,77,100,128,156,162,169,178,198,210,211,221,226,232,237,241,246,253,254,255,270,282,283,291,295,302,303,329,334,335,348,386,399,406,410,416,419,433,441,469,489,490,497,501,514],exager:508,examin:[6,8,17,229,295],examp:[485,514],exampl:[],exce:[3,6,16,17,18,42,61,76,180,217,218,221,222,223,224,226,230,232,237,242,269,295,310,314,320,321,329,379,386,487,514],exceed:[3,42,62,226,232,269,329,495],excel:412,except:[1,2,5,6,8,10,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,62,63,66,76,98,99,120,121,124,129,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,178,182,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,206,209,212,218,219,221,225,226,230,232,239,244,245,248,251,253,255,269,270,271,272,273,274,275,276,277,278,279,282,283,286,288,289,290,291,292,296,305,306,313,315,316,326,329,332,334,335,341,345,349,352,353,354,355,356,357,358,360,361,364,365,366,371,372,374,376,380,381,382,384,385,386,387,388,390,393,394,395,396,397,398,399,400,401,402,404,405,406,410,411,412,413,414,415,416,417,418,419,424,425,426,427,428,429,430,431,432,433,434,437,442,443,444,446,449,450,451,452,459,467,468,469,470,471,472,473,475,477,478,479,482,484,485,487,489,490,492,495,496,497,498,499,501,505,508,513,514,515,518],excess:[220,412],exchang:[2,3,6,8,64,65,209,215,216,245,253,305,313,337,341,344,371,386,412,502],exchange:371,excit:412,exclud:[3,6,9,12,16,17,66,76,113,124,152,158,165,166,182,202,218,222,227,228,257,265,298,311,313,336,347,352,379,380,382,394,416,419,422,433,434,441,466,499],exclus:[1,3,12,16,96,386,401,439,441,496,506],excurs:[269,482],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,17,63,179,205,250,307,354,370,373,385,483,485,495,498,501,514],exempl:457,exemplari:246,exemplifi:412,exert:[6,251,254,308,348,349,350,372],exhaust:[215,385,514],exhibit:[101,269,378,412,496],exist:[3,6,7,8,11,12,13,16,37,56,58,62,72,75,134,178,179,197,204,205,206,209,214,225,228,230,233,245,298,299,301,302,352,353,355,357,358,359,361,365,375,380,386,407,408,419,449,466,476,483,485,487,488,489,498,499,500,509,514,515,517],exit:[2,3,11,12,42,60,202,226,241,370,385,485,486,495,504,514],exlanatori:3,exp:[],expand:[],expans:[12,152,202,498,514],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,76,113,159,170,176,198,226,238,245,247,266,294,300,302,303,308,313,352,372,382,399,436,439,441,482,485,487,489,492,496,501,514],expens:[6,76,206,294,298,313,341,352,371,372,382,386,485],experi:[6,13,15,17,225,233,250,259,268,300,312,313,377,381,406,441,496,501],experienc:[6,12,258,259],experiment:[245,371,386,501],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,42,62,66,69,72,74,76,77,78,81,82,85,95,103,158,166,198,202,203,205,206,209,218,219,224,226,228,230,232,269,294,302,313,326,352,354,370,371,374,380,381,385,391,410,422,457,459,474,485,488,489,492,494,497,508,509,514,519],explan:[3,6,62,125,152,202,203,218,268,294,419,481,484,485,487,496],explanatori:[3,8,129,202,203,217,218,221,222,223,313,380,484,514],explantori:[3,309],explic:440,explicit:[6,9,11,22,45,82,96,125,128,172,186,210,211,232,320,321,356,376,388,389,392,397,399,410,412,423,433,473,481,484,488,491,509],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,76,121,124,155,165,168,176,178,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,222,225,232,239,244,246,248,253,269,271,272,273,274,275,276,277,278,279,286,288,289,290,292,302,303,305,313,315,316,332,334,335,341,345,349,355,357,358,360,361,364,366,380,386,387,388,390,393,394,395,396,397,398,399,400,401,402,403,405,406,409,410,411,413,414,415,416,417,418,419,423,424,425,426,427,428,429,430,431,432,433,437,439,441,442,443,444,446,451,452,459,460,461,462,463,464,465,467,468,469,470,471,472,473,475,477,478,479,487,489,490,496,497,499,500,506,508,509],explictli:[16,500],exploit:[15,17,296],explor:[130,177],expon:[3,304,306,410,415,418,432,440,452],exponenti:[96,447,468,475,479,501,514],expos:11,exposit:[215,406,409],express:[6,152,164,178,210,211,230,266,294,304,341,347,354,392,410,412,426,436,457,458,467,514],expressiont:392,extend:[],extens:[3,6,9,17,45,46,47,54,56,66,68,73,84,91,92,93,96,97,100,102,105,108,109,119,121,129,131,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,203,209,212,213,216,224,225,231,234,238,243,244,245,247,248,249,251,253,255,267,269,274,283,294,295,311,312,313,315,318,323,326,328,332,333,334,335,336,338,339,341,343,346,350,351,415,436,439,450,451,458,504,505,513],extent:[1,3,42,43,46,60,76,176,180,202,214,222,226,251,348,351,371,374,388,453,455,469,484,487,490],exterior:[3,6,176,350],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,64,76,113,121,122,124,130,153,155,156,157,159,161,164,165,166,167,168,170,171,177,178,179,180,184,206,221,226,228,269,301,302,303,313,329,379,380,383,384,405,416,419,422,436,441,484,485,487,490,499,508,514],extract:[3,6,11,13,36,66,68,73,84,96,102,119,127,129,131,210,211,306,381,402,413,436,458,485,492,504],extract_atom:11,extract_comput:[11,485],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,61,205,220,230,232,269,339,412,471,508],extrema:432,extrins:215,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[174,343],f_a:[470,471,472],f_ave:129,f_c:471,f_f:472,f_fix_id:303,f_foo:514,f_harm:339,f_i:[29,447],f_id:[6,76,129,131,202,203,209,217,218,219,220,221,222,223,224,264,331,343,505,514],f_ij:447,f_indent:224,f_int:338,f_j:29,f_jj:100,f_k:447,f_langevin:341,f_max:[303,308],f_msst:267,f_r:[254,470,471,472],f_sigma:392,f_solid:339,f_ss:6,face:[3,6,60,62,76,166,176,180,214,222,223,346,348,349,350,351,374,415,436,451,487,490],face_threshold:176,facet:176,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,247,299,329,339,416,449,457,499],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,60,61,62,77,96,100,113,120,127,128,130,152,172,177,180,184,195,201,202,205,206,210,211,219,226,230,232,233,245,250,253,255,256,267,269,270,274,296,300,304,312,316,319,321,329,333,337,344,345,346,350,361,372,374,380,386,388,389,392,393,395,397,402,403,404,406,407,408,412,416,419,423,424,436,439,441,443,444,450,452,459,468,473,484,487,490,491,496,499,501,502,505,508,513,514],factori:[3,485],factoriz:371,fail:[3,9,11,12,62,182,230,233,371,379,381,404,450,485],failur:[133,454,486,514],fairli:[11,441,496,501,509],faken:78,falcon:250,fall:[3,6,206,221,299,485,514],fals:[95,352,354,457,514],fame:8,famili:[475,484],familiar:[0,11,509],fan:447,far:[3,6,12,17,60,62,64,95,202,203,206,207,226,227,228,230,233,269,294,312,313,329,346,357,361,377,381,382,474,485,487,492,505],farago:253,farrel:[470,472],farther:202,fashion:[6,8,42,76,178,206,209,210,211,216,222,226,228,233,245,247,251,266,267,269,271,272,273,274,275,276,277,285,288,289,290,291,292,302,303,305,313,318,322,328,331,339,341,345,346,347,349,351,381,419,433,490,499,514,518],fasolino:421,fast:[6,7,9,12,13,17,40,202,203,280,303,342,371,372,394,433,434,439,467,469,489,494,496,505,515,519],faster:[1,6,9,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,64,66,116,121,124,155,165,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,225,226,232,239,244,248,252,253,269,271,272,273,274,275,276,277,278,279,286,288,289,290,292,300,304,305,313,315,316,329,332,334,336,338,341,345,349,355,357,358,360,361,364,366,371,372,383,384,386,387,388,390,392,393,394,395,396,397,398,399,400,401,402,405,406,410,411,413,414,415,416,417,418,419,424,425,426,427,428,429,430,431,432,433,437,442,443,444,446,451,452,459,467,468,469,470,471,472,473,475,477,478,479,482,490,496,500,508],fastest:[1,6,14,17,166,222,341,342,386,484],fatal:[3,504],fault:[75,450],faulti:12,fava:415,favor:229,favorit:7,fbmc:336,fcc:[],fcm:[285,514],fdirect:236,fdotr:420,fdt:[],fdti:96,fe2:177,fe3:177,fe_md_boundari:215,featu:8,featur:[],fecr:410,feedback:[7,250],feel:[7,250,251,259,294,350,352,381,441],felling:438,felt:350,femtosecond:513,fene:[],fennel:[402,424],fep:[],ferguson:[6,184,499],fermi:[1,9,10,12,15,164,386,472],fermion:412,fernando:435,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,40,66,207,217,218,219,221,222,223,224,254,269,299,302,304,316,343,371,379,380,381,388,457,484,487,492,496,498,506,517],fewer:[1,3,11,15,16,64,259,496],fewest:3,fextern:243,feynman:296,fff:485,ffield:[401,413,449,450,457],ffmpeg:[3,12,205],ffplai:205,fft:[1,3,7,9,11,12,14,15,97,121,122,153,295,371,372,496],fft_inc:[12,372],fft_lib:12,fft_path:12,fftbench:[371,506],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],ficiti:466,fictiti:[6,212,213,238,243,247,296,312,402,424,428,466],field1:[488,492],field2:488,field:[],fifth:[6,326,443],figur:[1,3,8,12,303,484,485,509],fij:405,file0:294,file1:[11,13,294,340,354,380,492,494,498],file2:[11,13,340,354,380,492,494,498],file:[],file_from:204,filen:380,filenam:[3,12,13,38,42,57,198,202,203,205,206,207,215,218,219,220,221,222,223,224,226,231,241,294,298,301,304,305,306,309,310,313,314,340,341,368,369,370,380,381,387,388,392,402,410,411,413,421,436,437,438,443,447,448,449,450,457,458,468,469,470,471,472,475,483,484,485,488,489,494,498,505,514,517,518,519],filennam:494,filep:[3,202,203,206,489,494,519],filepo:310,fill:[7,9,178,205,299,341,374,382,392,439,450,490,509],filter:[206,215],final_integr:8,final_integrate_respa:8,finchham:[6,160,404],find:[0,3,4,6,7,8,9,11,12,13,14,16,38,40,57,64,76,78,96,129,181,198,207,216,229,230,241,242,245,268,294,299,300,308,312,377,379,381,382,402,419,424,428,436,457,467,469,508,509,514],find_custom:8,fine:[16,17,182,212,238,339,382,386,509,514],finer:[152,178,514],finest:371,finger:[178,201,266,490],finish:[6,11,42,226,354,368,370,371,383,385,386,474,492,514,515],finit:[],finni:[7,410,467],finvers:236,fiorin:[9,231],fire:[],firebrick:206,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,60,62,64,65,76,88,97,100,114,115,116,118,124,128,129,139,142,145,146,150,153,163,166,172,174,176,177,179,180,181,185,198,202,203,204,205,206,207,209,210,218,219,221,222,223,224,226,229,232,241,245,246,251,256,266,267,268,269,294,296,301,302,303,305,310,313,316,318,326,327,329,330,331,338,339,340,341,343,347,352,354,355,362,374,379,380,381,382,385,386,387,388,391,392,393,395,397,399,401,402,410,412,413,416,417,419,420,421,422,423,424,428,433,434,436,438,439,441,443,447,449,450,457,458,466,468,469,470,471,472,475,479,482,483,484,485,487,488,489,492,494,496,499,500,501,504,505,508,509,514,515,516,517,519],fischer:[6,9,19,20,184,397,499],fit:[3,6,9,12,38,57,198,241,312,329,388,392,421,436,441,462,469,471,495,509,514],five:[78,164,303,380,392,437,487,501],fix:[],fix_deposit:3,fix_flux:215,fix_id:[3,230,267,269,271,272,273,274,275,276,277,300,303],fix_manifoldforc:509,fix_modifi:[],fix_nh:8,fix_nv:509,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:316,fix_reax_bond:449,fix_saed_vtk:314,fix_setforc:8,fix_shak:316,fix_srd:3,fixedpoint:[230,269],fixextern:243,fixid:215,fji:405,flag1:[235,384],flag2:[235,384],flag:[3,8,9,11,12,14,15,16,17,39,41,59,70,79,80,87,88,95,98,99,104,114,115,117,130,173,177,181,199,202,203,205,206,207,224,229,231,235,250,253,257,259,265,266,295,302,313,326,328,329,336,340,349,352,367,369,372,380,384,385,386,388,418,423,436,439,466,480,482,484,485,487,488,489,491,492,493,497,509,514],flag_buck:396,flag_coul:[396,405,428],flag_lj:[405,428],flagfld:[394,433,434],flaghi:[3,394,433,434],flaglog:[394,433,434],flagn:235,flagvf:[394,433,434],flat:[6,341,346,347,351],flavor:[2,7,12],fld:[346,433,434],flen:389,flex_press:389,flexibl:[3,6,8,179,205,218,222,231,247,270,337,344,412,471,505],flip:[3,6,232,269,348,349],floor:514,flop:12,floralwhit:206,flow:[],fluctuat:[6,67,96,230,245,246,253,256,269,274,294,295,300,317,339,341,364,408],fluid:[],fluid_veloc:260,flush:[3,206,504],flux:[],flv:205,fly:[7,9,12,42,205,209,215,220,233,236,313,316,342,392,439,505,508],fmackai:9,fmag:234,fmass:296,fmax:[379,505],fmomentum:236,fmsec:[2,206,253,254,266,269,300,313,332,333,496,507,513,515],fname:370,fno:[9,16],fnorm:[379,505],fnpt:236,fnvt:236,foce:419,fock:389,focu:316,fogarti:[9,306,450],foil:[152,294,458],fold:[327,496],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,62,66,67,75,76,78,89,100,101,107,108,118,125,128,129,131,152,153,156,157,158,164,166,171,174,176,178,179,184,187,188,189,190,192,193,195,196,198,202,204,205,206,209,215,216,217,218,219,220,221,222,223,224,226,231,232,233,236,237,240,241,243,245,246,247,250,252,253,254,256,259,267,269,274,275,276,277,288,289,290,292,295,296,298,301,302,303,304,306,308,310,312,313,314,316,331,332,333,334,337,338,339,340,341,343,344,352,353,357,358,359,360,361,364,366,369,374,376,379,380,381,386,387,388,389,390,391,392,393,394,395,396,397,398,400,401,402,403,404,405,406,407,408,409,410,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,442,443,444,446,447,448,449,450,451,452,454,456,457,458,459,460,461,462,463,464,465,466,468,469,470,471,472,473,474,475,477,478,479,480,482,484,485,487,488,490,492,494,495,496,499,501,502,503,508,509,514,515,518],foo:[4,8,11,12,202,205,243,485,498,514],foot:6,footprint:[12,386],fopenmp:[9,16,18],forc:[],force_uvm:17,forceatom:259,forcefield:[312,418],forcegroup:256,forcezero:377,ford:405,forestgreen:206,forev:76,forget:[254,508],forgiv:269,fork:[],form:[2,3,6,8,12,19,22,45,55,58,66,70,79,80,82,87,88,96,98,99,101,104,114,115,117,128,152,153,172,173,182,186,206,209,210,211,228,246,247,253,255,259,266,290,295,306,308,312,313,341,346,350,355,356,359,364,376,378,380,381,388,389,392,399,407,408,410,412,414,418,419,423,435,436,438,439,443,444,447,449,450,451,457,458,459,467,469,470,471,472,478,481,484,485,487,492,497,504,508,514],formal:[6,83,86,100,246,247,253,269,296,329,337,457],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,58,72,82,186,198,202,203,204,205,206,207,218,221,222,223,224,226,228,241,295,298,302,304,306,309,313,314,325,340,341,352,353,356,376,380,381,387,388,392,399,410,413,423,436,438,448,449,450,452,458,469,475,476,484,485,487,488,489,492,503,504,505,514,516,517],former:[6,12,16,40,42,206,226,341,345,392,394,493,499,514],formerli:[7,13],formul:[1,6,9,41,67,153,212,238,253,269,290,304,306,312,316,340,371,388,392,410,412,415,436,446],formula:[2,3,6,7,13,21,22,37,45,55,56,75,78,96,98,99,100,105,107,108,117,124,130,131,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,177,178,183,185,186,197,201,202,210,211,212,213,218,219,220,221,224,225,232,238,248,249,251,253,254,266,294,295,301,310,315,323,327,329,332,333,334,343,346,349,351,352,354,355,356,358,365,374,380,388,389,391,392,397,398,399,400,405,406,410,411,415,416,417,418,420,423,424,426,427,428,430,431,433,434,436,440,441,442,451,452,459,467,468,469,470,471,472,475,477,478,483,487,490,497,504,505,513,514,515],forth:[1,6,11,12,13,14,15,385,485,490,494],fortran:[3,6,9,11,12,13,243,410,419,436,449,450],fortun:8,forward:[3,8,96,370,381,386],foster:[392,446,447],foul:181,found:[3,6,9,12,78,172,202,229,231,245,250,256,295,336,342,354,370,382,399,402,405,482,488,489,504],four:[6,11,55,88,114,115,152,174,267,341,364,380,381,439,482],fourier:[],fourth:[6,116,312,326,336,397,443,457],fox:[6,130,184,465,499],fphi:[38,57,469],fpic:12,fplo:[38,57,469],fprime:469,fqdn:252,fqq:405,fraction:[1,3,6,8,12,16,40,42,86,121,153,181,201,205,206,216,227,228,229,230,267,299,303,310,311,329,334,335,374,381,386,392,394,416,433,434,492,497],fragment:[43,250,310],fraig:43,frame:[92,152,206,215,267,303,348,415],framer:[205,206],framework:[5,247,387,458],franc:9,fraunhof:9,free:[5,6,7,9,13,29,63,66,75,96,172,210,211,294,329,338,339,340,341,378,381,389,412,432,439,447,478,484],freedom:[3,6,8,105,107,108,110,112,113,124,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,218,229,236,245,247,253,254,259,269,270,274,275,276,277,288,289,290,292,296,298,313,316,332,333,334,339,379,405,505,508,515],freeli:[0,6,7,12,156,157,171,176,205],freez:[],frenkel:[245,339],freq:214,frequenc:[3,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ermophys:441,thermost:[6,160,214,231,236,254,348,508],thermostat:[],thermostatequ:6,thesi:[371,372,433,448],thess:393,theta0:[20,21,24,26,27,28,32,33,35,36,152,187,312,364],theta0max:152,theta10:392,theta1:[185,355,392],theta2:[185,355,392],theta3:[355,392],theta4:392,theta5:392,theta6:392,theta7:392,theta8:392,theta9:392,theta:[3,6,26,27,37,38,39,66,69,86,101,118,152,177,178,187,199,201,205,248,308,312,341,355,364,418,447,471,487,490,497],theta_0:443,theta_:[364,392],theta_c:418,theta_ijk:392,theta_ijl:355,theta_jik:[437,438],theta_pi:392,theta_sigma:392,thex:304,thi:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,436,437,438,439,440,441,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,508,509,510,511,512,513,514,515,516,517,518,519],thick:[76,130,205,222,490],thie:122,thijss:336,thin:[128,205],thing:[3,6,11,12,55,72,76,230,269,300,313,329,484,485,489,509,514],think:[3,6,7,8,11,13,206,313,352,357,361,374,379,419,449,450,469,485,489,492,514],third:[6,9,12,29,100,146,152,153,176,218,219,221,222,223,224,246,310,326,327,341,401,413,436,443,473,475,482,483,485,487,490],thirumalai:190,thistl:206,tho:411,thole:[],thompson:[0,5,7,9,13,124,152,153,304,374,458],those:[1,2,3,5,6,7,8,9,10,12,13,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,38,40,41,43,44,46,47,48,49,50,51,52,54,55,57,64,76,77,82,96,100,101,118,120,121,122,124,128,152,153,155,158,165,168,176,178,182,184,185,187,188,189,190,191,192,193,195,196,198,201,202,203,205,206,216,217,218,219,222,223,224,230,232,233,242,248,250,251,252,253,259,266,268,269,271,272,273,274,275,276,277,278,279,286,288,289,290,292,299,302,305,313,331,338,339,343,347,348,349,352,353,355,357,358,360,361,362,364,366,371,372,379,381,382,386,387,388,390,393,394,395,396,397,398,399,400,401,402,405,406,410,411,413,414,415,416,417,418,419,424,425,426,427,428,429,430,431,432,433,436,437,441,442,443,444,446,449,450,451,452,458,459,467,468,469,470,471,472,473,475,477,478,479,482,484,485,487,489,490,491,492,494,496,497,499,501,504,505,506,508,509,514,518,519],though:[6,8,12,40,41,66,76,100,115,178,199,202,206,216,222,227,228,230,232,237,270,311,313,315,325,337,344,354,367,371,374,381,406,409,410,412,413,415,416,432,433,441,475,482,487,489,490,495,499,506,514],thought:[161,253,290,313,345,346,378,416,423,508],thread:[1,3,9,12,16,17,18,250,342,369,386,500,506],threads_per_atom:3,three:[1,3,6,55,66,79,96,100,101,116,129,130,142,152,156,177,178,190,209,229,230,235,257,269,274,295,300,304,313,329,336,338,341,359,360,364,371,372,380,386,387,388,392,410,411,413,415,416,420,423,436,437,438,439,443,447,450,451,457,458,468,470,471,472,475,485,487,490,514],threebodi:468,thresh:[42,202,203,205,206,226,485],threshhold:[3,42,205,226,352,485],threshold:[3,42,95,176,206,226,294,382,450,482,501],thrid:485,through:[3,6,7,9,11,12,66,178,182,202,203,207,230,243,245,250,251,256,258,259,260,269,270,296,304,322,336,341,346,350,370,377,388,408,411,412,416,422,424,439,452,457,459,466,473,482,485,488,498,504,508],throughout:[6,16,128,130,342,386,439,487],thru:[3,6,7,11,12,70,79,80,87,88,98,99,104,114,115,116,117,173,201,202,206,221,266,329,349,354,370,379,385,490],thrust:1,thu:[1,2,3,6,8,11,12,18,33,38,40,42,43,51,62,64,66,67,70,71,75,76,77,78,80,82,87,88,97,99,100,101,104,114,115,117,118,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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","angle_style zero 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","bond_write command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond 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 command","compute dihedral/local command","compute dilatation/atom command","compute dipole/chunk command","compute displace/atom command","compute dpd command","compute dpd/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 hexorder/atom command","compute improper 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 orientorder/atom 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 force/tally command","compute temp command","compute temp/asphere command","compute temp/body 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","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md 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/correlate/long 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 eos/cv command","fix eos/table 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/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body 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/body 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 shardlow 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 distance 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","improper_style zero 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 dpd/conservative command","pair_style dpd/fdt 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 lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_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 smtbq 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_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero 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","timer command","timestep command","<no title>","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_coeff command","write_data command","write_dump command","write_restart command"],titleterms:{"break":227,"default":[37,40,41,56,60,61,62,64,65,76,96,97,101,113,114,116,118,119,130,134,135,152,158,166,167,171,177,178,181,183,197,200,201,202,203,205,206,207,208,210,211,212,214,215,216,218,222,223,224,227,228,230,231,232,233,237,242,245,246,251,253,254,255,256,257,259,264,267,269,270,274,290,291,295,296,299,300,301,302,303,305,308,310,311,313,314,329,331,336,337,338,339,342,344,346,348,352,365,369,371,372,374,375,377,378,380,382,383,384,386,389,392,394,412,433,434,439,441,449,450,466,467,482,483,484,487,488,490,492,494,495,496,499,501,503,504,505,506,507,513,515,517,518],"function":514,"long":[220,393,395,396,397,398,402,404,405,424,428,432,444,452,473],"new":8,"static":12,acceler:1,account:509,ackland:67,acknowledg:7,adapt:[210,211],addforc:212,addit:[12,13,509],addtorqu:213,adiabat:6,adjust_dt:319,adp:387,after:509,airebo:388,alloi:410,amber2lmp:13,amber:6,angl:[8,68,69],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],angmom:70,append:214,arrai:6,aspher:[6,9,91,156,271,275,279,280,288],atc:[9,215],atom:[6,7,8,67,71,75,76,77,78,81,82,83,86,88,90,94,101,106,107,110,111,112,118,122,123,125,152,153,176,214,216,217,302,514],atom_modifi:40,atom_styl:41,attract:5,aveforc:225,awpmd:[9,389],balanc:[42,226],barostat:6,basal:71,beck:390,berendsen:[300,332],between:6,binary2txt:13,bodi:[6,8,9,43,72,157,272,276,281,289,391],bond:[8,13,73,74,227,228,229,309],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,59],bond_writ:58,bop:392,born:[393,404],boundari:[7,60],box:[6,61,230],branch:509,brownian:394,buck:[395,396,404,435],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:75,ch2lmp:13,chain:13,chang:509,change_box:62,charmm:[6,20,184,397,432],chunk:[6,70,76,80,87,99,104,115,117,126,158,173,175,218],citat:7,class2:[9,21,44,185,355,398],clear:63,cluster:77,cmm:9,cna:78,code:6,coeffici:6,colloid:[9,346,400,478],colvar:[9,13,231],com:[79,80,159],comb3:401,comb:[305,401],come:5,comm_modifi:64,comm_styl:65,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,510,511,512,513,514,515,516,517,518,519],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,514],compute_modifi:113,condit:7,conduct:[6,337],conserv:407,constant:[6,514],constraint:7,contact:[81,132],coord:82,core:6,coreshel:9,correl:[219,220],cosin:[23,24,25,26,27,28,187],cossq:357,coul:[393,395,396,397,398,402,403,404,417,424,428,432,444,452],coupl:6,creat:228,create_atom:178,create_bond:179,create_box:180,createatom:13,creation:7,csld:333,csvr:333,cubic:426,cuda:[9,14,121,124,155,165,212,225,239,244,248,269,278,315,316,332,334,345,393,395,397,398,410,416,417,424,425,427,430,442,468,470],custom:[8,202,203],cut:[50,389,395,398,402,405,412,414,424,425,432,440,444,473],cvff:358,damag: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chenoweth_2008:[448,449],chi:[103,167,201,293,303,305,366,412,414,514],chiefli:447,child:8,chip:[7,9,17,18,385,499],chipot:231,chiral:363,chmod:[11,12],cho:435,chocol:[7,206],choic:[3,6,9,12,15,16,18,41,42,55,96,153,156,157,171,182,198,218,222,223,226,229,232,233,247,253,256,267,269,295,299,303,312,335,364,371,376,377,380,382,385,418,431,440,444,486,495,496,499,500,506,507,512],choos:[1,3,6,7,8,9,12,16,17,18,29,40,55,96,129,168,169,205,227,228,229,230,233,242,253,256,267,269,271,272,273,274,275,276,277,298,299,316,328,332,346,370,371,377,475,481,483,495,501],chose:[469,471],chosen:[2,3,6,12,17,152,178,181,190,198,205,211,216,230,233,242,245,246,254,256,267,269,274,295,298,309,328,332,335,336,341,343,344,350,371,372,377,385,406,407,411,415,422,425,451,469,481,495,500,501,507],chri:176,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[70,80,87,99,104,115,117,126,158,173,175,218],chute:[4,9,10,248],ciccotti:315,cieplak:[6,184,498],cii:219,cij:219,ciko:2,circl:[43,76,324],circular:[3,6,156,200],circumst:18,circumv:[101,118,307],citat:[],cite:[3,7,8,12,253,456],civ:9,ckio:2,cko:2,cl1:177,clarendon:[29,404],clarifi:[7,469,471],clariti:353,clark:443,class2:[],classic:[0,3,5,6,7,8,9,243,295,302,307,340,365,411],classifi:[466,474],claus:484,clean:[6,12,14,15,17,494],cleanli:[485,517],clear:[],clearli:7,clebsch:152,clermont:[9,13],clever:490,click:[2,11,22,37,45,56,178,186,197,205,250,355,364,380,398,466,508],client:[250,252],climb:[268,380,500],clinic:[7,13],clo:[167,201,514],clock:[12,481,500],clockwis:346,clone:508,close:[3,6,11,12,13,40,42,71,76,153,181,202,228,229,230,247,254,256,269,289,312,315,346,349,369,371,374,376,377,380,385,387,391,401,402,421,435,440,448,452,454,468,471,490,496,507,508,510],closer:[3,10,42,128,176,201,202,226,230,234,337,380],closest:[228,293,312,343,414,450,465,475],cloud:[456,507],clovertown:18,clsuter:77,clump1:[297,312],clump2:[297,312],clump3:[297,312],clump:312,cluster:[],clutter:3,cmap:486,cmatrix:247,cmax:435,cmd:[11,12,295,497],cmdarg:11,cmin:435,cmm:[],cmoput:145,cn1:219,cn2:219,cna:[],cnn:219,cnr:[9,13],cnt:[418,490],co2:[41,177,315,379],coars:[7,9,10,29,36,41,55,190,297,312,328,416,451,495,498],coarser:[371,513],coarsest:152,code:[],coeff:[3,7,8,12,21,22,33,45,51,184,185,186,191,354,355,361,398,418,422,440,453,455,458,486,515],coeffcient:486,coeffici:[],coefficienct:405,coefficient0:409,coefficient1:409,coeffieci:[6,389,421],coeffincientn:409,coexist:[245,411],cohes:[6,412,435],coincid:[134,349,396,432,433,481],colberg:204,cold:[6,163,245,249,381,507],coldest:336,coleman8:9,coleman:[9,130,177,313],colin:9,collabor:[7,8,15],collect:[3,6,7,8,9,13,41,43,70,80,87,92,99,104,109,115,117,126,158,166,173,175,178,202,203,206,218,231,259,265,297,307,310,312,351,370,379,381,399,486,493,499,505,518],collid:[237,328,350],colliex:177,collinear:[3,297],collis:[3,256,328,346,350,408,415,478],colllis:328,colloid:[],colombo:40,colon:[207,351,487],color1:206,color2:206,color:[3,9,42,202,205,206,226,246,302,307],column:[3,6,9,12,13,43,66,69,70,71,72,74,76,80,82,85,87,88,90,99,101,103,104,115,117,118,120,122,125,126,127,128,129,131,152,153,158,166,173,175,176,177,198,202,203,206,209,217,218,219,221,222,223,224,259,266,267,302,312,329,330,340,350,413,417,448,449,487,501,503,513],columnar:176,colvar:[],colvarmodul:12,com:[],comamnd:232,comand:229,comannd:385,comb3:[],comb:[],comb_1:304,comb_2:304,combiant:402,combin:[3,6,7,9,11,13,36,41,66,69,74,85,96,103,114,120,127,156,157,171,202,205,215,221,250,259,269,295,301,316,332,341,349,352,354,370,371,373,377,385,399,401,402,407,411,412,418,430,431,457,467,469,471,472,474,477,489,494,499,507,513,515],come:[],comfort:[12,13],comit:508,comm:[0,3,11,12,64,78,204,250,252,253,371,380,385,405,440,445,468,488],comm_modifi:[],comm_modift:64,comm_styl:[],comm_world:11,command:[],comment:[2,4,7,11,12,38,57,184,198,202,241,254,312,340,379,380,386,409,410,412,422,435,442,449,456,457,467,468,469,470,471,474,483,484,486,507,508,513],commerci:7,commit:[9,508],commmand:[3,6,12,62,119,290,421,480,481,483,500,517],common:[],commonli:[3,6,9,12,17,25,60,62,116,118,180,202,205,207,365,416,425,457,469,471,486,489,498],commun:[1,3,6,7,8,9,10,11,12,14,15,16,18,41,42,61,64,65,76,176,181,182,205,206,226,227,228,230,231,232,250,252,256,258,259,260,269,294,301,303,304,305,312,316,328,340,351,368,370,381,382,383,385,407,408,444,479,483,484,495,496,513,516,518],communc:370,comp:[7,204,252,253,315,371,380,411,440,445,450,464,468,470],compact:[66,209,398,466],compani:[5,7],compar:[1,3,4,6,8,12,17,40,95,122,130,161,177,186,197,206,236,303,351,353,370,371,378,380,435,456,481,500,501,507,512],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,9,21,22,37,44,45,56,185,186,197,354,355,364,397,466],compat:[3,5,7,8,9,11,12,13,17,18,42,76,129,131,189,202,207,211,217,218,219,221,222,223,224,226,294,306,332,335,342,345,348,370,385,419,438,440,468,483,484,513],compens:[6,227,228,310,381,411],compet:339,competit:371,compil:[3,7,8,9,12,13,14,15,16,17,18,19,176,202,204,205,207,250,339,371,385,438,486,487,491,513],compl:17,complain:[11,12,17],complement:435,complementari:[7,401,423],complet:[3,6,9,11,12,15,42,62,76,206,222,226,231,259,295,298,301,328,339,341,352,353,369,380,385,412,453,455,473,481,486,491,494,498,500,503,507,513],complex:[4,6,8,11,12,13,25,41,43,65,101,118,152,154,166,178,179,256,324,349,368,380,411,438,468,484,486,489,513],compli:[335,339],complic:[6,7,9,12,13,216,245,484],complier:12,compon:[3,6,8,12,64,66,70,71,78,87,88,97,98,99,100,101,104,105,108,113,115,116,117,118,119,120,121,122,124,125,129,139,142,143,144,145,148,149,150,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,174,175,201,202,203,205,206,212,213,217,218,219,220,221,222,223,224,225,229,230,232,233,238,243,248,252,253,256,259,261,265,266,268,269,270,274,275,276,277,287,288,289,291,292,294,295,296,299,310,312,314,315,317,321,322,325,328,331,332,333,335,342,343,348,349,350,370,373,377,378,379,380,385,405,411,415,432,433,453,455,456,457,486,487,496,504,513,514],componenet:6,composit:[6,216,256,409],compound:[400,411,412,474],compres:[76,126,218],compress:[],compris:[41,349,450,473],compton:[130,177],comptu:3,compuat:371,comput:[],computation:[3,6,227,228,340,391],computational:507,compute_arrai:8,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[130,313],compute_scalar:8,compute_temp:8,compute_vector:8,compute_xrd:177,concaten:[2,3,517],concav:349,concentr:[76,409],concept:[6,158,168,218,495],conceptu:[3,6,76,166,230,232,380,401,418,435,491],concern:[6,78,96,204,246],concetr:76,concis:[11,339],conclud:12,concret:8,concurr:[16,371,513],conden:[340,469,471],condens:[6,160,340,387,403,409,423,474],condit:[],conducit:6,conduct:[],cone:489,confer:438,confid:[3,500],config:[12,202,483],configfil:231,configur:[1,2,6,12,15,17,38,62,134,180,198,201,202,205,209,230,231,232,233,237,245,252,253,282,295,303,339,368,378,380,387,391,410,435,438,467,469,471,474,481,486,488,489,500,508],confin:[486,500],conflict:[3,12,41,203,440,484,508],conform:[3,6,13,62,229,230,268,311,317,339,363,380,411,498],confus:[3,474],conjuct:[9,405],conjug:[7,8,253,377,411,448,449],conjunct:[6,7,76,95,96,126,161,166,172,178,182,206,210,211,253,256,260,282,298,299,303,304,305,307,312,316,328,336,343,348,370,371,380,392,394,398,401,405,411,417,423,440,443,451,472,486,489,493,507,518],connect:[3,6,9,96,163,181,229,250,297,312,315,325,380,402,415,448,449,465,471,483,484,486,490,507],conner:387,connor:387,conput:3,consecut:[3,11,12,40,76,178,206,210,211,233,250,251,401,423,427,481,487,489],consequ:[1,6,216,340,422,500],conserv:[],consid:[6,75,76,83,96,127,160,163,164,181,202,203,206,210,211,217,219,222,226,228,229,233,257,270,294,312,335,336,339,340,343,371,398,411,418,449,450,456,465,481,482,484,487,488,489,491,494,496,504,507,513],consider:[6,8,253,254,331,332,333,385,495],consist:[3,6,8,9,11,12,41,43,69,74,85,103,115,120,123,124,127,158,161,163,178,190,201,207,212,213,218,232,233,236,238,243,246,253,254,255,266,269,271,272,273,274,275,276,277,278,280,281,282,283,285,286,287,288,289,290,291,299,302,307,309,311,312,331,332,333,334,344,370,371,373,379,380,385,387,391,393,399,401,411,414,418,421,432,433,435,438,440,450,453,455,456,468,475,484,486,487,488,489,490,491,498,507,513],consistent_fe_initi:215,consit:312,constant:[],constitu:[3,6,259,312,345,349,399,450],constitut:[453,455],constrain:[3,6,8,155,156,157,158,159,161,164,165,166,167,168,170,171,209,218,233,245,246,251,259,263,297,298,310,312,315,326,336,343,378,379,411,491,498,507],constraint:[],construct:[6,8,12,14,38,55,57,64,67,71,75,77,78,82,101,118,130,152,177,230,269,294,311,349,381,385,404,438,440,465,467,468,489,490,505,513],constructor:[8,11],consult:449,consum:[1,307,444,513],consumpt:368,contact:[],contact_stiff:[452,454],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,66,96,100,128,130,152,154,158,166,176,177,178,180,184,186,197,198,202,203,205,206,207,209,210,211,215,217,218,219,221,222,223,224,226,231,233,238,241,247,251,252,253,256,267,282,293,294,297,298,300,301,302,305,309,312,313,318,328,335,339,340,349,350,353,369,371,379,380,383,384,386,387,388,391,400,401,404,409,410,411,418,419,435,438,442,446,447,448,449,457,467,468,469,470,471,472,474,481,482,483,484,486,487,488,489,491,493,495,498,500,501,503,504,507,508,513,516,518],content:[4,8,9,12,18,449,502,504],context:[3,6,8,12,17,128,129,206,227,228,233,297,309,344,377,477,486,493,502,512,513,514],contibut:75,contigu:483,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,76,88,114,115,174,206,209,210,211,216,218,219,220,221,222,223,224,226,229,230,231,232,233,245,246,247,249,250,251,253,254,255,261,266,267,269,271,272,273,274,275,276,277,287,288,289,290,291,296,298,301,302,312,313,317,327,328,330,337,338,340,346,349,353,369,384,385,391,405,408,425,428,448,449,450,453,455,470,481,484,486,488,489,494,500,501,503,504,513,516],continuum:[6,7,9,215,340,453,455],contour_integr:215,contract:[62,230,232,269,299,312],contradictori:3,contrain:315,contraint:282,contrari:[247,254],contrast:[1,6,43,56,67,160,163,203,232,351,453,455,477,517],contrib:340,contribut:[3,4,5,6,7,8,9,12,13,17,66,68,70,72,73,75,76,79,80,82,84,86,87,93,96,97,98,99,100,102,104,113,115,117,119,120,121,122,124,126,129,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,211,216,217,218,219,221,222,223,224,230,245,253,256,259,260,264,270,289,290,297,298,306,309,312,313,315,342,370,378,380,388,405,408,409,411,418,432,433,438,440,448,449,456,498,504,507,508],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,42,96,100,134,152,187,202,203,205,209,215,216,226,230,231,232,249,250,253,254,269,271,272,273,274,275,276,277,299,304,312,319,320,331,332,333,340,344,368,370,382,411,414,438,448,449,452,454,467,471,481,483,495,501,502],control_typ:215,controlfil:449,convect:100,conveni:[6,12,29,202,207,224,313,373,457,472,508,513],convent:[3,8,29,189,196,197,203,206,311,325,352,409,411,513],converg:[3,6,42,97,202,203,205,207,212,226,229,230,238,243,274,302,304,307,311,315,376,377,378,380,400,401,423,456,481,493,500],convers:[3,8,152,205,206,216,219,299,370,401,402,403,411,423,427,431,443,484,500,512],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,62,66,76,100,178,185,202,205,206,219,224,267,298,301,351,354,356,360,363,373,380,386,409,438,469,471,478,484,486,487,488,493,503,507,512,513,516,518],convex:[43,349],convinc:[7,12],cook:9,cooki:7,cool:[7,168,249,310],cooordin:[202,203],cooper:[5,7],coord123:126,coord1:[3,126,218,222,223],coord2:[3,126,218,222,223],coord3:[3,126,218,222,223],coord:[],coordb:456,coordbb:456,coordiat:378,coordin:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,62,64,65,66,70,72,76,79,80,82,87,88,96,98,99,104,114,115,117,125,126,128,146,152,161,167,173,175,176,178,182,201,202,203,204,205,206,207,209,212,217,218,221,222,223,226,227,228,229,230,231,232,233,236,238,239,243,245,248,249,250,251,252,253,254,266,268,269,271,272,273,275,276,277,289,292,293,294,297,298,299,309,310,312,314,315,317,322,325,326,327,328,330,338,339,340,347,348,350,351,373,378,379,380,385,386,387,390,410,456,481,486,487,488,489,491,494,496,500,507,513,514],coordn:[126,218],copi:[0,3,4,8,9,11,12,15,17,41,131,205,340,380,398,448,484,508],copper:478,coproccesor:16,coprocessor:[1,7,9,16,17,385,499],coproprocessor:17,copy_arrai:8,copyright:[7,8,297],coral:206,core:[],core_shel:160,coreshel:[],cornel:[6,184,498],corner123i:125,corner123x:125,corner123z:125,corner1i:125,corner1x:125,corner1z:125,corner2i:125,corner2x:125,corner2z:125,corner3i:125,corner3x:125,corner3z:125,corner:[3,6,41,125,205,349,350,373,473,486,508],cornflowerblu:206,cornsilk:206,corp:9,corpor:16,corr:400,correct:[3,6,9,11,12,16,17,62,87,96,97,113,114,119,122,128,160,165,172,203,205,232,245,247,253,269,270,289,297,299,302,339,345,349,370,380,386,387,388,389,390,391,392,393,394,395,396,397,399,400,401,402,403,404,405,408,409,410,411,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,443,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,473,474,476,477,478,479,486,501,504,507,508],correction_max_iter:215,correctli:[3,8,11,17,76,88,113,114,115,155,156,157,159,161,163,164,165,166,167,170,171,174,202,206,212,233,238,243,254,263,269,270,305,312,315,325,327,346,349,380,381,385,403,433,438,483,484,486,496,508,512,514],correl:[],correpond:241,correspond:[1,2,4,6,8,9,10,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,75,76,96,107,108,121,124,125,126,127,130,131,139,142,143,144,145,146,148,149,150,152,155,156,165,172,176,177,184,185,186,187,188,189,190,192,193,195,196,198,201,202,203,205,206,210,211,212,218,220,221,222,223,225,228,230,232,239,243,244,248,253,256,257,265,266,267,269,271,272,273,274,275,276,277,278,282,285,287,288,289,291,294,295,299,304,312,314,315,331,333,335,344,345,346,348,349,350,352,354,355,356,357,359,360,363,365,371,375,377,379,380,386,387,389,392,393,394,395,396,397,398,399,400,401,404,405,409,410,411,412,413,414,415,416,417,418,421,423,424,425,426,427,428,429,430,431,432,435,436,438,440,441,442,443,445,446,448,449,450,451,456,457,458,467,468,469,470,471,472,474,476,477,478,481,483,484,486,487,489,499,500,501,503,504,507,513],correspondingli:[432,433,495],corrupt:3,cosin:[],cosineshift:27,cosmo:[247,252],cossq:[],cost:[1,6,10,11,12,17,40,42,76,121,130,153,177,205,206,218,222,223,226,227,228,242,269,304,340,370,371,383,401,423,427,438,440,467,483,495],costheta0:[467,469,471,474],costheta:446,costli:[11,97,247,381],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,42,51,62,70,76,80,87,96,99,104,115,117,121,124,126,158,168,173,175,191,202,203,205,206,210,211,218,219,222,226,232,243,252,301,302,303,307,310,312,314,328,329,335,339,340,341,345,349,351,353,361,367,369,376,378,381,385,388,413,417,418,421,448,449,482,483,484,486,488,490,493,494,501,502,507,513,514],coulomb:[3,5,6,7,8,9,10,12,14,15,18,77,97,119,120,128,153,179,183,303,305,341,370,371,378,385,392,394,395,396,397,400,401,402,403,404,411,415,416,418,423,427,431,434,440,443,448,449,451,456,466,471,472,474,477,491,498,504,507,512],coulommb:6,cound:3,count:[1,3,6,8,11,12,16,42,66,72,82,100,126,128,129,166,176,182,212,213,216,218,221,222,223,225,226,233,238,242,245,251,269,282,298,315,331,332,349,371,378,379,380,382,385,413,417,440,504,513],counter:[3,346,481,492,494,500],counteract:245,counterbal:249,counterbalanc:29,counterpart:[202,312,481],counterproduct:18,coupl:[],courant:318,cours:[3,8,138,140,172,202,210,211,246,311,325,339,345,347,348,350,351,371,432,458,483,486,499,507,513,516],courtesi:373,cov:456,coval:[6,9,29,411,435,456,507],covari:247,cover:[6,12,76,198,206,215,256,411,473],coverag:[76,222],cpc:252,cpp:[1,3,6,8,9,11,12,13,96,202,210,211,243,315],cpu:[1,3,9,10,12,14,15,16,17,18,66,76,206,220,236,254,341,368,371,385,398,466,481,499,500,503,504,505,513],cpuremain:504,cr2:177,cr3:177,crack:[4,381],crada:[5,7],crai:[5,7,13,18,202],crash:[3,12,381,507],craympi:385,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:215,create_faceset:215,create_group:204,create_nodeset:215,createatom:[],creation:[],crimson:206,critchlei:297,criteria:[3,128,179,205,206,227,228,229,264,378,445,473,488,491,513],criterion:[12,42,133,178,181,216,226,229,245,282,304,318,346,351,378,380,400,411,415,456,491,500,501],criterioni:500,critic:[6,49,50,267,335,340,378],crmax:76,crmin:76,cross:[3,12,22,76,98,156,176,186,202,203,205,217,222,228,232,266,268,289,312,321,325,327,336,343,355,373,380,396,405,408,409,416,417,418,423,425,427,446,451,453,455,469,471,478,486,490,496,516],crossov:1,crossterm:486,crozier:[0,7,13],crucial:302,crystal:[3,4,6,13,78,118,293,294,338,373,381,486,490,504,507],crystallin:[6,114,294,373,470,507],crystallis:335,crystallogr:[130,177],crystallograph:[373,504],crystallographi:[130,177,373],cs1:177,cs_chunk:6,cs_im:[41,486],cs_re:[41,486],csanyi:[152,447,457],cscl:435,csequ:6,csh:[11,12,398],cshrc:[11,12],csic:[410,467,469,471,474],csinfo:6,csisi:[410,467,469,471,474],csld:[],cst:409,cstherm:6,cstyle:483,csvr:[],ctcm:[386,409],ctemp_cor:236,cterm:317,ctr:9,ctype:11,cu1:177,cu2:177,cu3au:435,cube:[6,42,176,181,226,236,349,373,507],cubic:[],cuda:[],cuda_arch:[9,15],cuda_get:15,cuda_hom:[9,15],cuda_prec:[9,15],cufft:14,cuh:391,cummul:[3,6,224,227,228,229,231,242,247,253,255,328,331,332,333,334,336,343,417,504],cumul:[6,216,218,221,222,223,237,245,253,267,269,274,282,312,313,380],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,15,16,17,18,41,42,43,58,62,64,66,76,78,88,96,113,114,120,128,129,142,153,158,166,168,174,176,179,182,201,202,203,204,205,206,207,210,211,215,218,222,223,224,226,227,228,229,230,231,232,233,237,238,243,245,247,250,251,253,259,266,269,270,275,276,277,282,287,288,289,291,297,298,303,304,306,309,310,311,312,315,316,317,318,319,320,321,322,324,326,327,328,331,332,333,339,340,343,344,345,346,347,348,350,351,353,368,369,370,371,374,375,377,378,379,380,385,391,398,400,404,409,411,412,415,418,419,422,432,433,435,436,437,440,446,448,449,452,453,454,455,458,469,471,472,475,481,482,483,484,486,487,488,489,490,492,493,494,496,498,500,501,503,504,508,513,514,515,516,517,518],curv:[6,178,245,294],curvatur:[414,450,478],custom:[],cut0:484,cut1:495,cut2:495,cut:[],cuthi:[293,305],cutinn:[393,432,433],cutlo:[293,305],cutmax:446,cutoff1:[397,404,423,427,431,434,443,451],cutoff2:[392,394,395,397,403,404,423,427,431,434,443,451,472],cutoff:[3,6,8,10,16,18,40,46,47,55,56,64,75,77,78,82,96,101,118,120,127,128,152,176,179,181,182,228,229,234,241,293,302,303,305,307,309,312,316,328,341,345,349,351,368,370,371,378,381,382,383,385,386,387,388,389,390,391,392,393,394,395,396,397,399,401,402,403,404,405,406,407,408,409,410,411,412,413,414,416,417,418,419,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,448,449,450,451,456,457,458,459,460,461,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,484,488,491,495,507,513],cutoffa:410,cutoffc:410,cuu3:409,cval:177,cvd:335,cvel:317,cvff:[],cwiggl:[3,266,345,348,350,513],cyan:[2,205,206],cycl:[3,245,267,269,270,274],cyclic:[3,198],cygwin:12,cylind:[3,4,76,205,218,251,298,346,349,489],cylindr:[6,251,325,346],cypress:385,cyrot:391,cyrstal:294,d3q15:256,d3q19:256,d_double_doubl:15,d_e:340,d_flag2:301,d_flag:301,d_name:[125,202,301,330,496],d_single_doubl:15,d_single_singl:15,d_sx:301,d_sy:301,d_sz:301,daan:338,dai:12,daili:12,daivi:289,damag:[],dammak:307,damp:[3,6,209,214,253,254,255,260,269,270,274,299,302,303,307,312,331,332,344,346,347,377,378,380,392,394,396,401,404,411,415,423,431,443,451,466,472,500,507],damp_com:254,damp_drud:254,dampen:[312,507],dampflag:[346,415],dan:17,danger:[3,12,245,351,405,504],dangl:181,daniel:9,darden:[371,404],darkblu:206,darkcyan:206,darken:205,darkgoldenrod:206,darkgrai:206,darkgreen:206,darkkhaki:206,darkmagenta:206,darkolivegreen:206,darkorang:206,darkorchid:206,darkr:206,darksalmon:206,darkseagreen:206,darkslateblu:206,darkslategrai:206,darkturquois:206,darkviolet:206,dasgupta:303,dash:[415,503],dat:[6,100,198,215,482],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,313],dataset:313,datatyp:3,date:[0,4,6,12,13,201,448,449,513],datom1:127,datom2:127,datom3:127,datom4:127,datum:[3,6,43,69,72,74,85,103,120,127,202,219],davenport:434,davi:345,david:[9,19,370,371,469,471],daw:[409,446],dbg:14,dcd:[3,6,7,202,204,205,206,207,295,487,491],ddim:201,deactiv:431,dealt:252,debug:[6,7,11,12,13,14,17,58,130,134,177,178,295,300,368,370,385,419,440,475,484,485,493,496,503,513],deby:[],decai:[101,401,478],decid:[3,6,12,16,76,266,301,312,341,501,508],decipher:373,deck:301,declar:204,declin:328,decod:205,decompos:[96,457],decomposit:[3,5,7,18,65,215,295,316],decoupl:[6,507],decreas:[3,202,203,212,213,220,229,232,238,243,245,253,339,370],decrement:317,deepli:367,deeppink:206,deepskyblu:206,def:[12,13,484],defaul:64,defect:[6,75,176,438],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,52,54,55,56,57,58,59,60,61,62,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,184,185,186,187,188,189,190,192,193,195,196,197,198,199,200,201,202,203,204,205,206,209,210,211,212,213,214,215,216,217,218,219,221,222,223,224,225,226,227,228,229,230,232,233,236,237,238,240,243,244,245,248,251,252,253,254,255,256,264,266,268,269,270,271,272,273,274,275,276,277,278,279,280,283,285,286,287,288,289,290,291,293,294,295,297,298,299,301,303,305,310,312,313,314,315,318,322,326,328,330,331,332,333,334,336,337,338,340,342,343,345,346,347,348,349,350,351,353,354,355,356,357,358,359,360,363,364,365,366,368,370,371,373,375,377,378,379,380,381,382,383,384,385,387,388,389,390,392,393,394,395,396,397,398,399,401,402,404,405,406,407,408,410,411,413,414,415,416,417,418,419,421,423,424,425,426,427,428,429,430,431,432,433,434,438,439,440,441,442,443,445,446,448,449,450,451,452,453,454,455,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,483,484,486,487,489,490,491,492,495,496,497,498,500,501,503,504,507,509,510,511,512,513,514,515],definit:[2,3,6,8,12,13,83,86,128,152,206,218,219,220,221,222,223,224,232,240,251,274,313,330,342,345,348,350,352,364,368,379,388,391,399,406,407,411,421,446,453,455,457,473,484,486,488,495,497,512,513],defint:504,deform:[],deg2theta:177,deg:507,degener:[3,297],degrad:[8,18,294,371,495],degre:[3,6,8,20,21,24,28,29,32,35,36,38,69,85,101,103,105,107,108,110,112,113,118,124,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,177,178,184,185,188,189,196,198,201,205,218,229,236,245,247,248,253,254,259,269,270,274,275,276,277,287,288,289,291,295,297,311,312,315,331,332,333,338,354,356,360,363,365,378,404,409,417,496,504,507,514],degress:[158,218],del:500,delai:[3,6,12,381,408,504],deleg:418,delet:[2,3,7,8,12,55,60,63,66,176,181,182,209,218,219,221,222,223,224,227,229,242,245,269,313,331,332,351,353,369,379,381,384,440,465,486,487,488,489,497,498,503,508,509,511,513,514],delete_atom:[],delete_bond:[],delete_el:215,deli:201,delimit:[484,513],deloc:[270,411,456],delr:435,delt_lo:500,delta:[],delta_1:391,delta_3:391,delta_7:391,delta_conf:3,delta_ij:[435,446],delta_pi:391,delta_r:446,delta_sigma:391,delx:201,delz:201,demand:307,demo:11,demon:292,demonstr:[302,435],den:298,dendrim:417,denniston:[9,256,258,259,260,294],denomin:[7,183],denot:[130,236,254,294,305,307,401,416,418,449,453,455],dens:[76,229,411],densiti:[3,6,7,9,18,41,42,62,111,128,138,152,164,176,178,210,211,215,218,222,223,226,232,243,256,259,262,263,294,298,299,301,303,340,345,373,375,379,386,387,391,409,435,436,437,446,450,456,460,462,463,464,486,495,496,504,512],density_continu:455,density_summ:455,depart:[0,7],departur:[267,302],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,64,66,69,72,74,75,76,85,101,103,114,120,121,124,125,126,127,131,152,154,155,161,165,166,172,178,179,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,205,206,209,210,211,212,213,216,218,220,221,222,224,225,226,228,230,232,238,239,244,247,248,249,251,253,254,256,258,259,266,269,271,272,273,274,275,276,277,278,285,287,288,289,291,293,304,307,309,312,314,315,316,322,328,331,332,333,335,337,339,340,342,344,345,348,349,350,351,353,354,355,356,357,359,360,363,365,371,373,378,379,381,382,383,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,404,405,409,410,411,412,413,414,415,416,417,418,423,424,425,426,427,428,429,430,431,432,435,436,438,439,441,442,443,445,446,448,449,450,451,456,457,458,466,467,468,469,470,471,472,474,476,477,478,481,483,486,488,489,492,496,498,500,503,504,506,513,514],dependend:6,depflag:12,dephas:[481,500],depos:233,deposit:[],deprec:[3,303,448],depth:[52,156,205,340,414,450],dequidt:9,der:[96,119,399,400,431,448,449,477,507],deriv:[6,7,8,9,38,57,66,96,152,172,198,219,230,232,245,253,266,269,271,272,273,274,275,276,277,293,299,303,307,337,338,340,345,346,349,377,379,387,391,399,404,411,412,416,425,429,430,435,438,448,449,466,468,477,507],derjagin:477,derlet:293,descend:206,descent:[7,377],descib:[41,205,303],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,65,66,72,75,76,78,97,122,125,128,130,142,152,153,156,157,158,162,163,166,169,171,172,176,177,178,180,181,190,195,198,202,203,204,209,210,211,218,219,220,221,222,223,224,226,229,230,231,232,233,235,236,241,246,247,250,251,252,253,254,255,256,258,259,260,264,268,269,270,274,281,290,293,295,300,301,302,303,304,305,312,317,325,328,329,330,331,332,333,334,335,336,337,338,343,345,346,348,353,370,371,373,376,377,378,379,380,384,387,388,390,392,393,394,396,397,398,399,400,401,404,409,411,412,414,415,416,418,421,423,424,425,426,427,428,429,430,431,432,433,434,435,438,439,445,446,447,448,449,450,451,456,457,458,465,466,467,468,469,470,471,472,474,476,477,478,479,481,483,484,486,487,488,489,490,496,499,500,503,508,513,514,516],descript:[],descriptor:[152,202,419],deserno:371,design:[0,3,6,7,8,11,13,14,15,17,130,160,163,177,215,229,235,236,269,270,293,294,313,335,340,388,389,390,393,396,401,403,411,431,432,433,436,437,446,449,468],desir:[2,3,6,7,9,11,12,14,15,16,33,41,51,62,76,97,100,124,129,153,160,178,191,201,218,224,230,232,243,245,246,253,254,255,259,269,289,297,298,299,300,303,307,312,315,328,331,332,333,334,339,346,361,367,370,371,373,376,378,379,380,405,409,417,432,433,467,469,471,482,483,484,486,490,495,500,501,503,504,513,514,516],desk:7,desktop:[4,6,7,10,12,205],despit:507,destabil:391,destre:363,destroi:[9,11,40,227,228],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,66,70,71,72,76,80,83,87,99,100,104,113,115,117,119,121,123,124,126,129,131,152,153,155,156,157,158,161,171,172,173,175,178,179,182,183,186,197,201,202,203,205,206,209,210,211,215,218,219,220,221,222,224,226,228,229,230,231,232,233,243,245,246,247,248,250,251,253,255,256,260,266,267,268,269,270,271,272,273,274,275,276,277,280,282,287,288,289,290,291,294,297,298,299,301,302,304,305,306,312,315,316,328,331,332,333,334,335,336,338,339,340,341,342,343,344,351,353,355,364,370,371,374,378,379,381,382,385,386,387,388,390,391,393,395,396,397,398,399,400,401,404,405,411,412,414,415,416,417,418,423,424,425,426,427,428,429,430,431,432,433,434,435,439,440,445,448,449,450,456,457,458,466,473,476,477,479,484,486,487,488,489,491,492,495,496,498,501,504,505,508,513,514,518],detect:[2,3,12,43,64,66,95,101,244,298,339,380,400,417,422,481,483,486,497,500,513],determ:385,determin:[1,3,6,8,9,12,15,40,41,43,52,60,61,62,64,65,72,76,96,113,119,121,124,130,131,139,153,166,167,176,177,178,201,202,203,205,206,207,208,212,213,214,217,218,219,220,221,222,223,224,225,226,230,232,233,236,238,245,248,249,251,253,254,259,264,266,267,269,275,276,277,287,288,289,291,293,295,298,299,302,309,310,311,312,313,314,318,320,322,328,331,332,333,335,341,342,345,346,347,348,349,350,351,364,370,371,373,379,381,382,385,387,388,395,400,404,408,409,413,415,418,419,427,435,438,440,449,450,456,465,468,472,477,483,486,487,489,491,493,496,500,502,503,505,512,513,514],determinist:316,detil:120,devan:[9,451],devanathan:471,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,43,250,274,297,302,303,306,387,391,411,437,438,456,474,488],devemi:9,deviat:[267,274,293,413],deviator:9,devic:[1,3,12,15,17,250,385],device_typ:385,devin:[304,400],devis:437,dfactor:205,dff:507,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,371],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,306,438],dhi:[62,201,232,298],dhug:[267,302],dhugoniot:[267,302],dia:435,diagnost:[],diagon:[3,6,92,152,153,154,230,269,299,312,343,453,455],diagonalstyl:457,diagram:[42,130,177,197,226,295],diallo:417,diam:[205,206,298,379],diamet:[3,6,41,43,125,178,202,203,205,206,210,211,253,298,301,312,328,330,344,346,379,399,414,415,425,450,473,477,486,487,496],diamond:[373,411,435],diamter:[41,298],dick:6,dicsuss:266,dictat:[216,267],did:[3,12,378,405,408,409,415,440,469,471,494],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,174,342,370],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,64,67,72,75,76,96,101,105,107,108,132,152,154,155,156,157,158,159,161,164,165,166,167,168,170,171,172,178,179,181,186,197,198,201,202,205,206,209,211,214,216,218,221,226,227,228,229,230,231,232,236,241,244,245,246,247,248,249,250,253,254,256,266,269,270,271,272,273,275,276,277,278,280,283,285,286,287,288,291,293,295,297,299,302,303,304,307,310,312,315,317,325,326,328,331,332,333,336,337,338,340,343,344,345,346,349,353,354,364,367,369,370,371,373,374,376,377,379,380,382,383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,433,435,440,450,453,455,460,461,463,464,478,507],equi:270,equidist:268,equil:[3,303,374,493,518],equilater:496,equilibr:[3,4,5,6,7,9,62,100,178,209,216,219,229,230,245,267,269,270,289,290,299,302,303,304,305,336,337,338,343,400,401,448,449,482,496],equilibria:343,equilibribum:[227,228],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,39,44,48,49,50,52,54,57,59,62,161,162,185,187,230,232,245,246,247,254,256,269,274,289,302,303,307,311,315,317,325,328,335,336,338,343,354,356,360,363,400,435,442,456,507],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:215,equival:[6,12,13,29,62,64,136,137,145,150,176,180,206,221,224,230,232,245,253,269,289,299,311,312,348,387,405,411,456,469,471,472,486,489,494,495,504,507],equlibrium:6,equliibr:[303,305],er3:177,eradiu:[41,125,203,411,486],eras:[314,337],erat:[232,433],erc:401,erfc:[401,423,440],erforc:[125,203],erg:512,erhart:[216,409,469,471],ermscal:388,ernst:9,eror:3,eros:435,erose_form:435,erot:[],errata:[469,471],erratum:345,erron:3,error:[],erta:415,ervel:[125,203,486],escap:[233,507],especi:[8,16,166,178,209,216,226,245,302,307,310,311,385,483],espresso:[9,306],essenti:[8,11,12,27,97,140,159,160,161,164,165,166,167,168,170,187,219,274,294,344,371,387,401,423,471,491,504],essex:29,establish:[96,249],estim:[1,3,6,10,12,38,42,57,100,153,215,226,237,267,328,335,370,371,376,440,449,468,500,504],esu:512,esub:435,eta:[6,256,269,302,303,305,344,410,412,414,446,470,474,512],eta_dot:269,eta_ij:446,eta_ji:412,etag:[41,486],etail:504,etap:269,etap_dot:269,etc:[1,2,3,4,6,7,8,9,10,11,12,13,15,16,40,41,43,55,64,72,98,99,100,105,121,122,125,127,153,155,158,159,160,161,162,164,165,166,167,168,170,172,178,180,181,182,191,202,203,205,206,209,210,215,216,217,218,221,222,223,224,227,228,232,233,243,245,246,253,269,298,309,313,340,341,349,353,369,370,378,379,380,381,383,409,410,418,431,433,438,444,448,449,467,469,471,474,481,484,486,487,488,493,495,496,500,501,502,503,504,505,507,512,513,516,518],ethernet:18,etol:[378,380,481,500],etot0:302,etot:[6,105,107,108,122,153,164,206,236,254,267,302,503,504],eu2:177,eu3:177,euler:[378,380],eulerian:215,euqat:459,europhi:256,ev_tal:8,evalu:[2,3,9,11,12,38,57,76,96,97,100,119,129,131,152,154,158,168,176,178,201,202,203,205,206,210,211,212,213,215,217,218,219,220,221,222,223,224,225,232,238,246,248,249,251,252,253,254,294,300,303,314,318,322,331,332,333,342,345,348,350,351,353,370,371,376,378,385,438,440,446,452,454,456,468,481,482,484,488,489,491,493,494,495,496,500,502,504,513,514],evalut:[353,484],evan:[166,289],evanseck:[6,20,184,396,498],evapor:[],evaul:[8,378],evdwl:[119,154,448,449,504],even:[3,6,8,12,15,17,18,34,40,42,53,58,60,62,64,66,75,76,97,119,131,176,179,180,194,198,202,203,206,209,210,211,216,217,218,221,222,223,224,226,227,228,230,232,233,236,251,254,267,269,270,294,298,307,309,312,313,324,328,336,340,343,345,349,351,362,370,376,378,380,385,390,411,412,415,418,421,440,450,474,475,479,486,487,489,491,492,493,495,496,498,501,503,504,505,507,518],evenli:[3,42,58,153,198,226,256,421,475],event:[],eventu:[3,6,12,15,180,303,500],ever:[9,55,57,252,328],evera:[399,414,450,466],everi:[0,1,2,3,6,8,9,11,12,15,16,40,42,76,77,100,125,131,140,166,181,202,203,204,205,206,207,209,210,211,212,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,232,233,237,242,243,245,247,249,250,251,256,257,265,269,270,274,292,293,294,298,299,300,301,302,303,304,305,307,309,310,312,313,315,317,328,330,331,332,333,334,335,336,339,340,341,342,343,351,353,369,371,380,381,382,385,405,408,418,431,448,449,456,462,480,481,482,486,488,490,491,493,494,495,500,501,502,504,508,513,518],everyth:[8,119,508],everywher:[128,425],eviri:411,evolut:[247,256,295,481],evolv:[256,295,341],ewald:[2,3,5,6,7,8,9,12,97,122,130,153,341,370,371,378,392,394,395,401,404,411,423,427,443,451,466,468,472],ewald_disp:404,ewalddisp:3,exact:[22,42,45,76,134,172,181,186,226,229,246,247,253,254,255,298,307,308,328,340,355,370,398,488,493,500,513,516,518],exactli:[3,6,12,14,17,38,42,43,57,62,76,77,100,128,156,162,169,178,198,210,211,221,226,232,237,241,246,253,254,255,270,281,282,290,294,301,302,328,333,334,347,385,398,405,409,415,418,432,440,468,488,489,496,500,513],exager:507,examin:[6,8,17,229,294],examp:[484,513],exampl:[],exce:[3,6,16,17,18,42,61,76,180,217,218,221,222,223,224,226,230,232,237,242,269,294,309,313,319,320,328,378,385,486,513],exceed:[3,42,62,226,232,269,328,494],excel:411,except:[1,2,5,6,8,10,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,62,63,66,76,98,99,120,121,124,129,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,178,182,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,206,209,212,218,219,221,225,226,230,232,239,244,245,248,251,253,255,269,270,271,272,273,274,275,276,277,278,281,282,285,287,288,289,290,291,295,304,305,312,314,315,325,328,331,333,334,340,344,348,351,352,353,354,355,356,357,359,360,363,364,365,370,371,373,375,379,380,381,383,384,385,386,387,389,392,393,394,395,396,397,398,399,400,401,403,404,405,409,410,411,412,413,414,415,416,417,418,423,424,425,426,427,428,429,430,431,432,433,436,441,442,443,445,448,449,450,451,458,466,467,468,469,470,471,472,474,476,477,478,481,483,484,486,488,489,491,494,495,496,497,498,500,504,507,512,513,514,517],excess:[220,411],exchang:[2,3,6,8,64,65,209,215,216,245,253,304,312,336,340,343,370,385,411,501],exchange:370,excit:411,exclud:[3,6,9,12,16,17,66,76,113,124,152,158,165,166,182,202,218,222,227,228,257,265,297,310,312,335,346,351,378,379,381,393,415,418,421,432,433,440,465,498],exclus:[1,3,12,16,96,385,400,438,440,495,505],excurs:[269,481],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,17,63,179,205,250,306,353,369,372,384,482,484,494,497,500,513],exempl:456,exemplari:246,exemplifi:411,exert:[6,251,254,307,347,348,349,371],exhaust:[215,384,513],exhibit:[101,269,377,411,495],exist:[3,6,7,8,11,12,13,16,37,56,58,62,72,75,134,178,179,197,204,205,206,209,214,225,228,230,233,245,297,298,300,301,351,352,354,356,357,358,360,364,374,379,385,406,407,418,448,465,475,482,484,486,487,488,497,498,499,508,513,514,516],exit:[2,3,11,12,42,60,202,226,241,369,384,484,485,494,503,513],exlanatori:3,exp:[],expand:[],expans:[12,152,202,497,513],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,76,113,159,170,176,198,226,238,245,247,266,293,299,301,302,307,312,351,371,381,398,435,438,440,481,484,486,488,491,495,500,513],expens:[6,76,206,293,297,312,340,351,370,371,381,385,484],experi:[6,13,15,17,225,233,250,259,268,299,311,312,376,380,405,440,495,500],experienc:[6,12,258,259],experiment:[245,370,385,500],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,42,62,66,69,72,74,76,77,78,81,82,85,95,103,158,166,198,202,203,205,206,209,218,219,224,226,228,230,232,269,293,301,312,325,351,353,369,370,373,379,380,384,390,409,421,456,458,473,484,487,488,491,493,496,507,508,513,518],explan:[3,6,62,125,152,202,203,218,268,293,418,480,483,484,486,495],explanatori:[3,8,129,202,203,217,218,221,222,223,312,379,483,513],explantori:[3,308],explic:439,explicit:[6,9,11,22,45,82,96,125,128,172,186,210,211,232,319,320,355,375,387,388,391,396,398,409,411,422,432,472,480,483,487,490,508],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,76,121,124,155,165,168,176,178,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,222,225,232,239,244,246,248,253,269,271,272,273,274,275,276,277,278,285,287,288,289,291,301,302,304,312,314,315,331,333,334,340,344,348,354,356,357,359,360,363,365,379,385,386,387,389,392,393,394,395,396,397,398,399,400,401,402,404,405,408,409,410,412,413,414,415,416,417,418,422,423,424,425,426,427,428,429,430,431,432,436,438,440,441,442,443,445,450,451,458,459,460,461,462,463,464,466,467,468,469,470,471,472,474,476,477,478,486,488,489,495,496,498,499,505,507,508],explictli:[16,499],exploit:[15,17,295],explor:[130,177],expon:[3,303,305,409,414,417,431,439,451],exponenti:[96,446,467,474,478,500,513],expos:11,exposit:[215,405,408],express:[6,152,164,178,210,211,230,266,293,303,340,346,353,391,409,411,425,435,456,457,466,513],expressiont:391,extend:[],extens:[3,6,9,17,45,46,47,54,56,66,68,73,84,91,92,93,96,97,100,102,105,108,109,119,121,129,131,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,203,209,212,213,216,224,225,231,234,238,243,244,245,247,248,249,251,253,255,267,269,274,282,293,294,310,311,312,314,317,322,325,327,331,332,333,334,335,337,338,340,342,345,349,350,414,435,438,449,450,457,503,504,512],extent:[1,3,42,43,46,60,76,176,180,202,214,222,226,251,347,350,370,373,387,452,454,468,483,486,489],exterior:[3,6,176,349],extern:[],extra:[3,6,8,11,12,16,17,41,42,47,64,76,113,121,122,124,130,153,155,156,157,159,161,164,165,166,167,168,170,171,177,178,179,180,184,206,221,226,228,269,300,301,302,312,328,378,379,382,383,404,415,418,421,435,440,483,484,486,489,498,507,513],extract:[3,6,11,13,36,66,68,73,84,96,102,119,127,129,131,210,211,305,380,401,412,435,457,484,491,503],extract_atom:11,extract_comput:[11,484],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,61,205,220,230,232,269,338,411,470,507],extrema:431,extrins:215,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[174,342],f_a:[469,470,471],f_ave:129,f_c:470,f_f:471,f_fix_id:302,f_foo:513,f_harm:338,f_i:[29,446],f_id:[6,76,129,131,202,203,209,217,218,219,220,221,222,223,224,264,330,342,504,513],f_ij:446,f_indent:224,f_int:337,f_j:29,f_jj:100,f_k:446,f_langevin:340,f_max:[302,307],f_msst:267,f_r:[254,469,470,471],f_sigma:391,f_solid:338,f_ss:6,face:[3,6,60,62,76,166,176,180,214,222,223,345,347,348,349,350,373,414,435,450,486,489],face_threshold:176,facet:176,facil:[0,12],facilit:[6,13,43],fact:[6,8,16,247,298,328,338,415,448,456,498],factor:[1,3,6,12,18,24,28,32,35,36,40,42,47,48,60,61,62,77,96,100,113,120,127,128,130,152,172,177,180,184,195,201,202,205,206,210,211,219,226,230,232,233,245,250,253,255,256,267,269,270,274,295,299,303,311,315,318,320,328,332,336,343,344,345,349,360,371,373,379,385,387,388,391,392,394,396,401,402,403,405,406,407,411,415,418,422,423,435,438,440,442,443,449,451,458,467,472,483,486,489,490,495,498,500,501,504,507,512,513],factori:[3,484],factoriz:370,fail:[3,9,11,12,62,182,230,233,370,378,380,403,449,484],failur:[133,453,485,513],fairli:[11,440,495,500,508],faken:78,falcon:250,fall:[3,6,206,221,298,484,513],fals:[95,351,353,456,513],fame:8,famili:[474,483],familiar:[0,11,508],fan:446,far:[3,6,12,17,60,62,64,95,202,203,206,207,226,227,228,230,233,269,293,311,312,328,345,356,360,376,380,381,473,484,486,491,504],farago:253,farrel:[469,471],farther:202,fashion:[6,8,42,76,178,206,209,210,211,216,222,226,228,233,245,247,251,266,267,269,271,272,273,274,275,276,277,284,287,288,289,290,291,301,302,304,312,317,321,327,330,338,340,344,345,346,348,350,380,418,432,489,498,513,517],fasolino:420,fast:[6,7,9,12,13,17,40,202,203,279,302,341,370,371,393,432,433,438,466,468,488,493,495,504,514,518],faster:[1,6,9,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,64,66,116,121,124,155,165,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,225,226,232,239,244,248,252,253,269,271,272,273,274,275,276,277,278,285,287,288,289,291,299,303,304,312,314,315,328,331,333,335,337,340,344,348,354,356,357,359,360,363,365,370,371,382,383,385,386,387,389,391,392,393,394,395,396,397,398,399,400,401,404,405,409,410,412,413,414,415,416,417,418,423,424,425,426,427,428,429,430,431,432,436,441,442,443,445,450,451,458,466,467,468,469,470,471,472,474,476,477,478,481,489,495,499,507],fastest:[1,6,14,17,166,222,340,341,385,483],fatal:[3,503],fault:[75,449],faulti:12,fava:414,favor:229,favorit:7,fbmc:335,fcc:[],fcm:[284,513],fdirect:236,fdotr:419,fdt:[],fdti:96,fe2:177,fe3:177,fe_md_boundari:215,featu:8,featur:[],fecr:409,feedback:[7,250],feel:[7,250,251,259,293,349,351,380,440],felling:437,felt:349,femtosecond:512,fene:[],fennel:[401,423],fep:[],ferguson:[6,184,498],fermi:[1,9,10,12,15,164,385,471],fermion:411,fernando:434,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,40,66,207,217,218,219,221,222,223,224,254,269,298,301,303,315,342,370,378,379,380,387,456,483,486,491,495,497,505,516],fewer:[1,3,11,15,16,64,259,495],fewest:3,fextern:243,feynman:295,fff:484,ffield:[400,412,448,449,456],ffmpeg:[3,12,205],ffplai:205,fft:[1,3,7,9,11,12,14,15,97,121,122,153,294,370,371,495],fft_inc:[12,371],fft_lib:12,fft_path:12,fftbench:[370,505],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],ficiti:465,fictiti:[6,212,213,238,243,247,295,311,401,423,427,465],field1:[487,491],field2:487,field:[],fifth:[6,325,442],figur:[1,3,8,12,302,483,484,508],fij:404,file0:293,file1:[11,13,293,339,353,379,491,493,497],file2:[11,13,339,353,379,491,493,497],file:[],file_from:204,filen:379,filenam:[3,12,13,38,42,57,198,202,203,205,206,207,215,218,219,220,221,222,223,224,226,231,241,293,297,300,303,304,305,308,309,312,313,339,340,367,368,369,379,380,386,387,391,401,409,410,412,420,435,436,437,442,446,447,448,449,456,457,467,468,469,470,471,474,482,483,484,487,488,493,497,504,513,516,517,518],filennam:493,filep:[3,202,203,206,488,493,518],filepo:309,fill:[7,9,178,205,298,340,373,381,391,438,449,489,508],filter:[206,215],final_integr:8,final_integrate_respa:8,finchham:[6,160,403],find:[0,3,4,6,7,8,9,11,12,13,14,16,38,40,57,64,76,78,96,129,181,198,207,216,229,230,241,242,245,268,293,298,299,307,311,376,378,380,381,401,418,423,427,435,456,466,468,507,508,513],find_custom:8,fine:[16,17,182,212,238,338,381,385,508,513],finer:[152,178,513],finest:370,finger:[178,201,266,489],finish:[6,11,42,226,353,367,369,370,382,384,385,473,491,513,514],finit:[],finni:[7,409,466],finvers:236,fiorin:[9,231],fire:[],firebrick:206,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,60,62,64,65,76,88,97,100,114,115,116,118,124,128,129,139,142,145,146,150,153,163,166,172,174,176,177,179,180,181,185,198,202,203,204,205,206,207,209,210,218,219,221,222,223,224,226,229,232,241,245,246,251,256,266,267,268,269,293,295,300,301,302,304,309,312,315,317,325,326,328,329,330,337,338,339,340,342,346,351,353,354,361,373,378,379,380,381,384,385,386,387,390,391,392,394,396,398,400,401,409,411,412,415,416,418,419,420,421,422,423,427,432,433,435,437,438,440,442,446,448,449,456,457,465,467,468,469,470,471,474,478,481,482,483,484,486,487,488,491,493,495,498,499,500,503,504,507,508,513,514,515,516,518],fischer:[6,9,19,20,184,396,498],fit:[3,6,9,12,38,57,198,241,311,328,387,391,420,435,440,461,468,470,494,508,513],five:[78,164,302,379,391,436,486,500],fix:[],fix_deposit:3,fix_flux:215,fix_id:[3,230,267,269,271,272,273,274,275,276,277,299,302],fix_manifoldforc:508,fix_modifi:[],fix_nh:8,fix_nv:508,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:315,fix_reax_bond:448,fix_saed_vtk:313,fix_setforc:8,fix_shak:315,fix_srd:3,fixedpoint:[230,269],fixextern:243,fixid:215,fji:404,flag1:[235,383],flag2:[235,383],flag:[3,8,9,11,12,14,15,16,17,39,41,59,70,79,80,87,88,95,98,99,104,114,115,117,130,173,177,181,199,202,203,205,206,207,224,229,231,235,250,253,257,259,265,266,294,301,312,325,327,328,335,339,348,351,366,368,371,379,383,384,385,387,417,422,435,438,465,479,481,483,484,486,487,488,490,491,492,496,508,513],flag_buck:395,flag_coul:[395,404,427],flag_lj:[404,427],flagfld:[393,432,433],flaghi:[3,393,432,433],flaglog:[393,432,433],flagn:235,flagvf:[393,432,433],flat:[6,340,345,346,350],flavor:[2,7,12],fld:[345,432,433],flen:388,flex_press:388,flexibl:[3,6,8,179,205,218,222,231,247,270,336,343,411,470,504],flip:[3,6,232,269,347,348],floor:513,flop:12,floralwhit:206,flow:[],fluctuat:[6,67,96,230,245,246,253,256,269,274,293,294,299,316,338,340,363,407],fluid:[],fluid_veloc:260,flush:[3,206,503],flux:[],flv:205,fly:[7,9,12,42,205,209,215,220,233,236,312,315,341,391,438,504,507],fmackai:9,fmag:234,fmass:295,fmax:[378,504],fmomentum:236,fmsec:[2,206,253,254,266,269,299,312,331,332,495,506,512,514],fname:369,fno:[9,16],fnorm:[378,504],fnpt:236,fnvt:236,foce:418,fock:388,focu:315,fogarti:[9,305,449],foil:[152,293,457],fold:[326,495],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,62,66,67,75,76,78,89,100,101,107,108,118,125,128,129,131,152,153,156,157,158,164,166,171,174,176,178,179,184,187,188,189,190,192,193,195,196,198,202,204,205,206,209,215,216,217,218,219,220,221,222,223,224,226,231,232,233,236,237,240,241,243,245,246,247,250,252,253,254,256,259,267,269,274,275,276,277,287,288,289,291,294,295,297,300,301,302,303,305,307,309,311,312,313,315,330,331,332,333,336,337,338,339,340,342,343,351,352,356,357,358,359,360,363,365,368,373,375,378,379,380,385,386,387,388,389,390,391,392,393,394,395,396,397,399,400,401,402,403,404,405,406,407,408,409,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,439,440,441,442,443,445,446,447,448,449,450,451,453,455,456,457,458,459,460,461,462,463,464,465,467,468,469,470,471,472,473,474,476,477,478,479,481,483,484,486,487,489,491,493,494,495,498,500,501,502,507,508,513,514,517],foo:[4,8,11,12,202,205,243,484,497,513],foot:6,footprint:[12,385],fopenmp:[9,16,18],forc:[],force_uvm:17,forceatom:259,forcefield:[311,417],forcegroup:256,forcezero:376,ford:404,forestgreen:206,forev:76,forget:[254,507],forgiv:269,fork:[],form:[2,3,6,8,12,19,22,45,55,58,66,70,79,80,82,87,88,96,98,99,101,104,114,115,117,128,152,153,172,173,182,186,206,209,210,211,228,246,247,253,255,259,266,289,294,305,307,311,312,340,345,349,354,355,358,363,375,377,379,380,387,388,391,398,406,407,409,411,413,417,418,422,434,435,437,438,442,443,446,448,449,450,456,457,458,466,468,469,470,471,477,480,483,484,486,491,496,503,507,513],formal:[6,83,86,100,246,247,253,269,295,328,336,456],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,58,72,82,186,198,202,203,204,205,206,207,218,221,222,223,224,226,228,241,294,297,301,303,305,308,312,313,324,339,340,351,352,355,375,379,380,386,387,391,398,409,412,422,435,437,447,448,449,451,457,468,474,475,483,484,486,487,488,491,502,503,504,513,515,516],former:[6,12,16,40,42,206,226,340,344,391,393,492,498,513],formerli:[7,13],formul:[1,6,9,41,67,153,212,238,253,269,289,303,305,311,315,339,370,387,391,409,411,414,435,445],formula:[2,3,6,7,13,21,22,37,45,55,56,75,78,96,98,99,100,105,107,108,117,124,130,131,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,177,178,183,185,186,197,201,202,210,211,212,213,218,219,220,221,224,225,232,238,248,249,251,253,254,266,293,294,300,309,314,322,326,328,331,332,333,342,345,348,350,351,353,354,355,357,364,373,379,387,388,390,391,396,397,398,399,404,405,409,410,414,415,416,417,419,422,423,425,426,427,429,430,432,433,435,439,440,441,450,451,458,466,467,468,469,470,471,474,476,477,482,486,489,496,503,504,512,513,514],forth:[1,6,11,12,13,14,15,384,484,489,493],fortran:[3,6,9,11,12,13,243,409,418,435,448,449],fortun:8,forward:[3,8,96,369,380,385],foster:[391,445,446],foul:181,found:[3,6,9,12,78,172,202,229,231,245,250,256,294,335,341,353,369,381,398,401,404,481,487,488,503],four:[6,11,55,88,114,115,152,174,267,340,363,379,380,438,481],fourier:[],fourth:[6,116,311,325,335,396,442,456],fox:[6,130,184,464,498],fphi:[38,57,468],fpic:12,fplo:[38,57,468],fprime:468,fqdn:252,fqq:404,fraction:[1,3,6,8,12,16,40,42,86,121,153,181,201,205,206,216,227,228,229,230,267,298,302,309,310,328,333,334,373,380,385,391,393,415,432,433,491,496],fragment:[43,250,309],fraig:43,frame:[92,152,206,215,267,302,347,414],framer:[205,206],framework:[5,247,386,457],franc:9,fraunhof:9,free:[5,6,7,9,13,29,63,66,75,96,172,210,211,293,328,337,338,339,340,377,380,388,411,431,438,446,477,483],freedom:[3,6,8,105,107,108,110,112,113,124,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,218,229,236,245,247,253,254,259,269,270,274,275,276,277,287,288,289,291,295,297,312,315,331,332,333,338,378,404,504,507,514],freeli:[0,6,7,12,156,157,171,176,205],freez:[],frenkel:[245,338],freq:214,frequenc:[3,6,16,40,114,206,220,282,294,295,302,307,368,405,411,449,456,481,495,500,513,517],frequent: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:315,invers:[],invert:[1,6,182,294],invis:349,invoc:[176,229,385,453,455,484],invok:[1,3,6,7,8,9,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,58,62,66,70,76,79,80,87,88,96,97,98,99,104,114,115,117,121,122,123,124,129,131,155,165,172,173,176,178,179,181,182,184,185,187,188,189,190,192,193,195,196,198,202,203,205,206,207,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,232,233,234,235,237,238,239,242,243,244,245,246,248,249,250,251,253,254,255,256,257,258,259,260,261,262,263,265,266,268,269,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,296,297,298,299,300,301,303,304,305,306,307,308,309,310,312,313,314,315,317,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,354,356,357,359,360,363,365,369,370,371,372,373,378,380,385,386,387,389,392,393,394,395,396,397,399,400,401,404,405,409,410,412,413,414,415,416,417,418,419,423,424,425,426,427,428,429,430,431,432,433,436,440,441,442,443,445,450,451,453,455,457,458,467,468,469,470,471,472,474,475,476,477,478,480,483,484,485,487,489,491,494,495,497,498,500,503,504,507,513,514],invokd:3,involv:[3,6,7,8,12,66,120,127,128,129,158,182,209,216,227,245,256,297,300,305,328,370,377,378,380,390,408,414,421,467,469,471,482,483,489,491,495,500,501],ioff:[379,486],ion:[6,7,9,160,292,325,340,371,391,402,412,413,435,438,456,466,471,478,486,507],ionic:[6,9,392,394,402,411,412,443,456,507],ioniz:[400,411],ionocoval:9,iparam:[3,228],ipi:[],ipp:[],ir3:177,ir4:177,irregular:[6,42,61,226,230,232,269,312],irrelev:442,irrespect:[432,433],irrevers:236,is_act:[3,513],is_avail:[3,513],is_defin:[3,513],isbn:477,isel:[370,371],isenthalp:[9,269,270,271,272,273],ismail:[370,371,395,427],isn:[3,8,11,12,249],iso:[3,230,236,254,269,270,271,272,273,274,275,276,277,299,307,312,507],isobar:[9,269,270,275,276,277,316,407],isodem:411,isoenerget:[9,316,407],isoenthalp:[316,407],isol:[3,181,351],isomorph:295,isotherm:[9,245,269,270,275,276,277,299,316,407],isotop:301,isotrop:[6,101,253,299,370,371,393,414,432,433],isovolum:313,isralewitz:317,issu:[1,3,6,9,11,12,13,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,44,46,47,48,49,50,52,54,55,57,62,76,78,88,114,121,124,155,165,184,185,187,188,189,190,192,193,195,196,198,205,212,215,225,229,230,232,233,238,239,244,245,248,253,267,269,271,272,273,274,275,276,277,278,285,287,288,289,291,295,299,301,304,312,314,315,327,331,332,333,338,344,348,350,353,354,356,357,359,360,363,365,371,379,380,383,386,387,389,392,393,394,395,396,397,399,400,401,404,405,409,410,412,413,414,415,416,417,423,424,425,426,427,428,429,430,431,432,436,441,442,443,445,450,451,458,465,467,468,469,470,471,472,474,476,477,478,486,488,489,495,498,503,504,513,514],ital:[448,449],itali:13,item:[6,7,8,42,202,206,226],iter:[3,6,12,40,42,66,204,212,213,225,226,230,236,238,243,251,294,303,304,312,315,335,351,353,369,376,377,378,380,384,456,481,491,495,500,504,513],ith:[76,129,131,217,218,219,220,221,222,223,224,330,342,504,513],itself:[2,3,6,7,8,9,11,12,13,18,43,62,100,119,169,202,204,205,206,207,219,220,231,236,254,264,268,306,312,340,351,353,379,380,401,412,414,418,419,468,484,490,493,494,498,513,518],itset:496,ityp:[3,58,127,128,178,214,228,305,475],itype1:128,itype2:128,itypen:128,ivector:8,ivori:206,ixcm:312,ixi:[43,104,312,379,513],ixx:[43,104,312,379,513],ixz:[43,104,312,379,513],iycm:312,iyi:[43,104,312,379,513],iyz:[43,104,312,379,513],izcm:312,izrailev:317,izumi:470,izz:[43,104,312,379,513],j0jt:100,j20:219,j_m:152,jac:[6,184,498],jackson:439,jacobi:3,jacobsen:377,jagreat:13,jame:[9,19],janssen:293,januari:435,jaramillo:[7,9,13,411],jarzynski:317,jatempl:9,jcc:9,jcp:345,jec:13,jeff:13,jello:269,jensen:[253,370],jeremi:[9,437],jerom:9,jewett:13,jiang:[254,507],jiao:[9,13],jiht:[7,9],jik:391,jim:7,jku:[7,9],jmake:12,jmm:152,joannopoulo:267,job:[12,63,315,494],jochim:[269,270],john:[7,9,13,204],johnson:[9,13],join:[6,489],joint:[3,297,417],jon:[9,75],jonathan:9,jone:[1,3,6,7,9,10,12,13,46,47,67,96,119,122,209,215,299,328,345,349,371,373,378,387,390,394,395,396,397,399,404,414,416,417,418,421,422,423,424,425,427,428,430,431,434,439,440,446,450,451,461,466,473,498,507],jonsson:[78,268,377,380,456],jorgensen:[6,195,401,423,427],joul:512,journal:[172,190,215,305,371,409,438,448,449,460,461,463],jparam:[3,228],jpeg:[3,12,205],jpeglib:12,jpg:[4,8,12,202,205,206,517],jpg_inc:12,jpg_lib:12,jpg_path:12,jpl:[7,9],jth:513,jtype1:128,jtype2:128,jtype:[3,58,128,228,475],jtypen:128,judg:500,judici:6,julien:9,jump:[],june:207,just:[3,6,8,11,12,13,17,19,22,29,43,45,62,64,100,119,122,128,153,156,157,171,182,186,202,205,218,222,223,232,236,242,259,266,299,301,312,335,340,351,353,355,379,380,385,387,390,398,418,446,473,484,488,490,491,493,494,505,507,508,513,517,518],justo:410,jusufi:[402,413],jut:349,jzimmer:9,k11:100,k22:100,k33:100,k_2:358,k_4:358,k_d:507,k_sigma:391,k_ub:20,kadiri:71,kalia:474,kamberaj:312,kapf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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","angle_style zero 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","bond_write command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond 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 command","compute dihedral/local command","compute dilatation/atom command","compute dipole/chunk command","compute displace/atom command","compute dpd command","compute dpd/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 hexorder/atom command","compute improper 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 orientorder/atom 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 force/tally command","compute temp command","compute temp/asphere command","compute temp/body 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","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md 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/correlate/long 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 eos/cv command","fix eos/table 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/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere 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/body 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 shardlow 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 distance 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","improper_style zero 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 dpd/conservative command","pair_style dpd/fdt 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 lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_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 smtbq 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_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero 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","timer command","timestep command","<no title>","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_coeff command","write_data command","write_dump command","write_restart command"],titleterms:{"break":227,"default":[37,40,41,56,60,61,62,64,65,76,96,97,101,113,114,116,118,119,130,134,135,152,158,166,167,171,177,178,181,183,197,200,201,202,203,205,206,207,208,210,211,212,214,215,216,218,222,223,224,227,228,230,231,232,233,237,242,245,246,251,253,254,255,256,257,259,264,267,269,270,274,289,290,294,295,298,299,300,301,302,304,307,309,310,312,313,328,330,335,336,337,338,341,343,345,347,351,364,368,370,371,373,374,376,377,379,381,382,383,385,388,391,393,411,432,433,438,440,448,449,465,466,481,482,483,486,487,489,491,493,494,495,498,500,502,503,504,505,506,512,514,516,517],"function":513,"long":[220,392,394,395,396,397,401,403,404,423,427,431,443,451,472],"new":8,"static":12,acceler:1,account:508,ackland:67,acknowledg:7,adapt:[210,211],addforc:212,addit:[12,13,508],addtorqu:213,adiabat:6,adjust_dt:318,adp:386,after:508,airebo:387,alloi:409,amber2lmp:13,amber:6,angl:[8,68,69],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39],angmom:70,append:214,arrai:6,aspher:[6,9,91,156,271,275,278,279,287],atc:[9,215],atom:[6,7,8,67,71,75,76,77,78,81,82,83,86,88,90,94,101,106,107,110,111,112,118,122,123,125,152,153,176,214,216,217,301,513],atom_modifi:40,atom_styl:41,attract:5,aveforc:225,awpmd:[9,388],balanc:[42,226],barostat:6,basal:71,beck:389,berendsen:[299,331],between:6,binary2txt:13,bodi:[6,8,9,43,72,157,272,276,280,288,390],bond:[8,13,73,74,227,228,229,308],bond_coeff:45,bond_styl:[2,44,46,47,48,49,50,51,52,53,54,55,56,57,59],bond_writ:58,bop:391,born:[392,403],boundari:[7,60],box:[6,61,230],branch:508,brownian:393,buck:[394,395,403,434],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:75,ch2lmp:13,chain:13,chang:508,change_box:62,charmm:[6,20,184,396,431],chunk:[6,70,76,80,87,99,104,115,117,126,158,173,175,218],citat:7,class2:[9,21,44,185,354,397],clear:63,cluster:77,cmm:9,cna:78,code:6,coeffici:6,colloid:[9,345,399,477],colvar:[9,13,231],com:[79,80,159],comb3:400,comb:[304,400],come:5,comm_modifi:64,comm_styl:65,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,509,510,511,512,513,514,515,516,517,518],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,513],compute_modifi:113,condit:7,conduct:[6,336],conserv:406,constant:[6,513],constraint:7,contact:[81,132],coord:82,core:6,coreshel:9,correl:[219,220],cosin:[23,24,25,26,27,28,187],cossq:356,coul:[392,394,395,396,397,401,402,403,416,423,427,431,443,451],coupl:6,creat:228,create_atom:178,create_bond:179,create_box:180,createatom:13,creation:7,csld:332,csvr:332,cubic:425,cuda:[9,14,121,124,155,165,212,225,239,244,248,269,314,315,331,333,344,392,394,396,397,409,415,416,423,424,426,429,441,467,469],custom:[8,202,203],cut:[50,388,394,397,401,404,411,413,423,424,431,439,443,472],cvff:357,damag:[83,133],data2xmovi:13,data:6,databas:13,deby:[401,423],defgrad:139,deform:[161,162,232],delete_atom:181,delete_bond:182,delta:24,deposit:233,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,509,510,511,512,513,514,515,516,517,518],diagnost:7,diel:402,dielectr:183,diffract:9,diffus:6,dihedr:[8,84,85],dihedral_coeff:186,dihedral_styl:[2,184,185,187,188,189,190,191,192,193,194,195,196,197,198,199],dilat:86,dimens:200,dipol:[6,9,29,87,404],direct:236,directori:4,discuss:6,disp:6,displac:[88,95],displace_atom:201,distanc:358,distribut:[7,12],document:0,dpd:[9,89,90,405,406,407],drag:234,dreid:[6,417],drude:[6,9,163,235,236,254],dsf:[401,423],dsmc:408,dump:[6,8,202,203,204,205,207],dump_modifi:206,dynam:303,eam:[13,409],echo:208,edip:410,eff:[9,13,107,108,162,164,169,255,270,281,290,334,411],efield:238,eim:412,elast:6,emac:13,energi:[135,407],enforce2d:239,ensembl:7,erot:[91,92,93,94],error:[3,134],evapor:242,event:95,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,324,325,326,327,328,329,330,331,332,333,334,335,336,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,499,500,501,502,503,504,505,506,509,510,511,512,513,514,515,516,517,518],exp:[27,187],expand:[47,426],extend:[8,11],extern:243,fcc:293,fdt:407,featur:[7,8,508,513],fene:[46,47],fep:[9,13,96,211],field:[6,7],file:6,finit:6,fire:303,fix:[2,6,8,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256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