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:
H charge = 0.4238
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.
@@ -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_modify.html b/doc/html/Section_modify.html index 2af9707e6d..88ab26a836 100644 --- a/doc/html/Section_modify.html +++ b/doc/html/Section_modify.html @@ -254,7 +254,7 @@ parallel. E.g. don’t accumulate a bunch of data on a single processor and analyze it. You run the risk of seriously degrading the parallel efficiency.
- If your new feature reads arguments or writes output, make sure you -follow the unit conventions discussed by the units +follow the unit conventions discussed by the units command.
- If you add something you think is truly useful and doesn’t impact
LAMMPS performance when it isn’t used, send an email to the
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/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/change_box.html b/doc/html/change_box.html index 67d959720c..d7aa07bbc1 100644 --- a/doc/html/change_box.html +++ b/doc/html/change_box.html @@ -409,7 +409,7 @@ including this one, have been processed.
The units keyword determines the meaning of the distance units used to define various arguments. A box value selects standard distance -units as defined by the units command, e.g. Angstroms for +units as defined by the units command, e.g. Angstroms for units = real or metal. A lattice value means the distance units are in lattice spacings. The lattice command must have been previously used to define the lattice spacing.
diff --git a/doc/html/compute_angle.html b/doc/html/compute_angle.html index 998f44a241..b29151ede2 100644 --- a/doc/html/compute_angle.html +++ b/doc/html/compute_angle.html @@ -158,7 +158,7 @@ number of sub_styles defined by the this section for an overview of LAMMPS output options.The vector values are “extensive” and will be in energy -units.
+units.Restrictions
diff --git a/doc/html/compute_angle_local.html b/doc/html/compute_angle_local.html index 80d36a8df2..3cb8c9f1e7 100644 --- a/doc/html/compute_angle_local.html +++ b/doc/html/compute_angle_local.html @@ -181,7 +181,7 @@ keywords. The vector or array can be accessed by any command that uses local values from a compute as input. See this section for an overview of LAMMPS output options.The output for theta will be in degrees. The output for eng will -be in energy units.
+be in energy units.Restrictions
diff --git a/doc/html/compute_angmom_chunk.html b/doc/html/compute_angmom_chunk.html index 5e2921771e..a8722b532a 100644 --- a/doc/html/compute_angmom_chunk.html +++ b/doc/html/compute_angmom_chunk.html @@ -191,7 +191,7 @@ These values can be accessed by any command that uses global array values from a compute as input. See Section_howto 15 for an overview of LAMMPS output options.The array values are “intensive”. The array values will be in -mass-velocity-distance units.
+mass-velocity-distance units.Restrictions
diff --git a/doc/html/compute_body_local.html b/doc/html/compute_body_local.html index af9e525674..33119b8b46 100644 --- a/doc/html/compute_body_local.html +++ b/doc/html/compute_body_local.html @@ -196,7 +196,7 @@ specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that uses local values from a compute as input. See this section for an overview of LAMMPS output options. -The units for output values depend on the body style.
+The units for output values depend on the body style.
Restrictions
diff --git a/doc/html/compute_bond.html b/doc/html/compute_bond.html index 05dbb6b21a..615004f913 100644 --- a/doc/html/compute_bond.html +++ b/doc/html/compute_bond.html @@ -158,7 +158,7 @@ These values can be used by any command that uses global scalar or vector values from a compute as input. See this section for an overview of LAMMPS output options.The vector values are “extensive” and will be in energy -units.
+units.Restrictions
diff --git a/doc/html/compute_bond_local.html b/doc/html/compute_bond_local.html index 1ece04f5b0..d1def02d18 100644 --- a/doc/html/compute_bond_local.html +++ b/doc/html/compute_bond_local.html @@ -187,9 +187,9 @@ local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that uses local values from a compute as input. See this section for an overview of LAMMPS output options. -The output for dist will be in distance units. The -output for eng will be in energy units. The output for -force will be in force units.
+The output for dist will be in distance units. The +output for eng will be in energy units. The output for +force will be in force units.
Restrictions
diff --git a/doc/html/compute_chunk_atom.html b/doc/html/compute_chunk_atom.html index c40f622fef..8319769579 100644 --- a/doc/html/compute_chunk_atom.html +++ b/doc/html/compute_chunk_atom.html @@ -644,7 +644,7 @@ and crmax. be used. For non-orthogonal (triclinic) simulation boxes, only the reduced option may be used.A box value selects standard distance units as defined by the -units command, e.g. Angstroms for units = real or metal. +units command, e.g. Angstroms for units = real or metal. A lattice value means the distance units are in lattice spacings. The lattice command must have been previously used to define the lattice spacing. A reduced value means normalized diff --git a/doc/html/compute_com.html b/doc/html/compute_com.html index c50edf375b..e7754ad7c7 100644 --- a/doc/html/compute_com.html +++ b/doc/html/compute_com.html @@ -165,7 +165,7 @@ accessed by indices 1-3 by any command that uses global vector values from a compute as input. See this section for an overview of LAMMPS output options.
The vector values are “intensive”. The vector values will be in -distance units.
+distance units.Restrictions
diff --git a/doc/html/compute_com_chunk.html b/doc/html/compute_com_chunk.html index 12dd5d56ad..f18084b1b9 100644 --- a/doc/html/compute_com_chunk.html +++ b/doc/html/compute_com_chunk.html @@ -189,7 +189,7 @@ values can be accessed by any command that uses global array values from a compute as input. See Section_howto 15 for an overview of LAMMPS output options.The array values are “intensive”. The array values will be in -distance units.
+distance units.Restrictions
diff --git a/doc/html/compute_dihedral.html b/doc/html/compute_dihedral.html index 55916e86eb..ba623d5684 100644 --- a/doc/html/compute_dihedral.html +++ b/doc/html/compute_dihedral.html @@ -157,7 +157,7 @@ number of sub_styles defined by the this section for an overview of LAMMPS output options.The vector values are “extensive” and will be in energy -units.
+units.Restrictions
diff --git a/doc/html/compute_dipole_chunk.html b/doc/html/compute_dipole_chunk.html index de0651b194..82317cf95d 100644 --- a/doc/html/compute_dipole_chunk.html +++ b/doc/html/compute_dipole_chunk.html @@ -194,7 +194,7 @@ chunk. These values can be accessed by any command that uses global array values from a compute as input. See Section_howto 15 for an overview of LAMMPS output options.The array values are “intensive”. The array values will be in -dipole units, i.e. charge units times distance units.
+dipole units, i.e. charge units times distance units.Restrictions
diff --git a/doc/html/compute_displace_atom.html b/doc/html/compute_displace_atom.html index f24a84160a..14b3b05284 100644 --- a/doc/html/compute_displace_atom.html +++ b/doc/html/compute_displace_atom.html @@ -177,7 +177,7 @@ correctly with time=0 atom coordinates from the restart file. accessed by indices 1-4 by any command that uses per-atom values from a compute as input. See Section_howto 15 for an overview of LAMMPS output options. -The per-atom array values will be in distance units.
+The per-atom array values will be in distance units.
Restrictions
diff --git a/doc/html/compute_dpd_atom.html b/doc/html/compute_dpd_atom.html index b37d01442f..195981a949 100644 --- a/doc/html/compute_dpd_atom.html +++ b/doc/html/compute_dpd_atom.html @@ -156,7 +156,7 @@ that uses per-particle values from a compute as input. See Section_howto15 for an overview of LAMMPS output options.The per-particle array values will be in energy (u_cond, u_mech) and -temperature (dpdTheta) units.
+temperature (dpdTheta) units.Restrictions
diff --git a/doc/html/compute_erotate_asphere.html b/doc/html/compute_erotate_asphere.html index c9e784b28a..4af35ae60a 100644 --- a/doc/html/compute_erotate_asphere.html +++ b/doc/html/compute_erotate_asphere.html @@ -165,7 +165,7 @@ used by any command that uses a global scalar value from a compute as input. See Section_howto 15 for an overview of LAMMPS output options.The scalar value calculated by this compute is “extensive”. The -scalar value will be in energy units.
+scalar value will be in energy units.Restrictions
diff --git a/doc/html/compute_erotate_rigid.html b/doc/html/compute_erotate_rigid.html index cc5c52525a..0e46c9e7fe 100644 --- a/doc/html/compute_erotate_rigid.html +++ b/doc/html/compute_erotate_rigid.html @@ -163,7 +163,7 @@ uses a global scalar value from a compute as input. See Section_howto 15 for an overview of LAMMPS output options.The scalar value calculated by this compute is “extensive”. The -scalar value will be in energy units.
+scalar value will be in energy units.Restrictions
diff --git a/doc/html/compute_erotate_sphere.html b/doc/html/compute_erotate_sphere.html index 1a0559fdb7..4785bf0a12 100644 --- a/doc/html/compute_erotate_sphere.html +++ b/doc/html/compute_erotate_sphere.html @@ -160,7 +160,7 @@ used by any command that uses a global scalar value from a compute as input. See Section_howto 15 for an overview of LAMMPS output options.The scalar value calculated by this compute is “extensive”. The -scalar value will be in energy units.
+scalar value will be in energy units.Restrictions
diff --git a/doc/html/compute_erotate_sphere_atom.html b/doc/html/compute_erotate_sphere_atom.html index d33818079d..0ab254c224 100644 --- a/doc/html/compute_erotate_sphere_atom.html +++ b/doc/html/compute_erotate_sphere_atom.html @@ -162,7 +162,7 @@ in the specified compute group or for point particles with a radius = any command that uses per-atom values from a compute as input. See Section_howto 15 for an overview of LAMMPS output options. -The per-atom vector values will be in energy units.
+The per-atom vector values will be in energy units.
Restrictions
diff --git a/doc/html/compute_group_group.html b/doc/html/compute_group_group.html index bab284060f..a7a46a6236 100644 --- a/doc/html/compute_group_group.html +++ b/doc/html/compute_group_group.html @@ -213,8 +213,8 @@ These values can be used by any command that uses global scalar or vector values from a compute as input. See this section for an overview of LAMMPS output options.Both the scalar and vector values calculated by this compute are -“extensive”. The scalar value will be in energy units. -The vector values will be in force units.
+“extensive”. The scalar value will be in energy units. +The vector values will be in force units.Restrictions
diff --git a/doc/html/compute_improper.html b/doc/html/compute_improper.html index b8a180f76e..5b1e51e336 100644 --- a/doc/html/compute_improper.html +++ b/doc/html/compute_improper.html @@ -157,7 +157,7 @@ number of sub_styles defined by the this section for an overview of LAMMPS output options.The vector values are “extensive” and will be in energy -units.
+units.Restrictions
diff --git a/doc/html/compute_inertia_chunk.html b/doc/html/compute_inertia_chunk.html index 6472b84eed..ac29221054 100644 --- a/doc/html/compute_inertia_chunk.html +++ b/doc/html/compute_inertia_chunk.html @@ -190,7 +190,7 @@ as listed above. These values can be accessed by any command that uses global array values from a compute as input. See Section_howto 15 for an overview of LAMMPS output options.The array values are “intensive”. The array values will be in -mass*distance^2 units.
+mass*distance^2 units.Restrictions
diff --git a/doc/html/compute_ke.html b/doc/html/compute_ke.html index b3d25227a3..a3000f0f0d 100644 --- a/doc/html/compute_ke.html +++ b/doc/html/compute_ke.html @@ -166,7 +166,7 @@ can be used by any command that uses a global scalar value from a compute as input. See Section_howto 15 for an overview of LAMMPS output options.The scalar value calculated by this compute is “extensive”. The -scalar value will be in energy units.
+scalar value will be in energy units.Restrictions
diff --git a/doc/html/compute_ke_atom.html b/doc/html/compute_ke_atom.html index 60e2752d10..ea8c40a8bb 100644 --- a/doc/html/compute_ke_atom.html +++ b/doc/html/compute_ke_atom.html @@ -155,7 +155,7 @@ specified compute group. any command that uses per-atom values from a compute as input. See Section_howto 15 for an overview of LAMMPS output options. -The per-atom vector values will be in energy units.
+The per-atom vector values will be in energy units.
Restrictions
diff --git a/doc/html/compute_ke_atom_eff.html b/doc/html/compute_ke_atom_eff.html index 0c5ec701d7..00b22b9256 100644 --- a/doc/html/compute_ke_atom_eff.html +++ b/doc/html/compute_ke_atom_eff.html @@ -180,7 +180,7 @@ electrons) not in the specified compute group. accessed by any command that uses per-atom computes as input. See Section_howto 15 for an overview of LAMMPS output options. -The per-atom vector values will be in energy units.
+The per-atom vector values will be in energy units.
Restrictions
diff --git a/doc/html/compute_ke_eff.html b/doc/html/compute_ke_eff.html index 3f0d224ac6..b614a9d25b 100644 --- a/doc/html/compute_ke_eff.html +++ b/doc/html/compute_ke_eff.html @@ -181,7 +181,7 @@ used by any command that uses a global scalar value from a compute as input. See Section_howto 15 for an overview of LAMMPS output options.The scalar value calculated by this compute is “extensive”. The -scalar value will be in energy units.
+scalar value will be in energy units.Restrictions
diff --git a/doc/html/compute_ke_rigid.html b/doc/html/compute_ke_rigid.html index d8d1905549..27c5451b25 100644 --- a/doc/html/compute_ke_rigid.html +++ b/doc/html/compute_ke_rigid.html @@ -161,7 +161,7 @@ rigid bodies). This value can be used by any command that uses a global scalar value from a compute as input. See Section_howto 15 for an overview of LAMMPS output options.The scalar value calculated by this compute is “extensive”. The -scalar value will be in energy units.
+scalar value will be in energy units.Restrictions
diff --git a/doc/html/compute_meso_e_atom.html b/doc/html/compute_meso_e_atom.html index a88d739406..21b1e95553 100644 --- a/doc/html/compute_meso_e_atom.html +++ b/doc/html/compute_meso_e_atom.html @@ -158,7 +158,7 @@ specified compute group. any command that uses per-atom values from a compute as input. See Section_howto 15 for an overview of LAMMPS output options. -The per-atom vector values will be in energy units.
+The per-atom vector values will be in energy units.
Restrictions
diff --git a/doc/html/compute_meso_rho_atom.html b/doc/html/compute_meso_rho_atom.html index c4da0bc379..dd832b844d 100644 --- a/doc/html/compute_meso_rho_atom.html +++ b/doc/html/compute_meso_rho_atom.html @@ -158,7 +158,7 @@ specified compute group. any command that uses per-atom values from a compute as input. See Section_howto 15 for an overview of LAMMPS output options. -The per-atom vector values will be in mass/volume units.
+The per-atom vector values will be in mass/volume units.
Restrictions
diff --git a/doc/html/compute_meso_t_atom.html b/doc/html/compute_meso_t_atom.html index ae8859ba9a..c6111acd65 100644 --- a/doc/html/compute_meso_t_atom.html +++ b/doc/html/compute_meso_t_atom.html @@ -159,7 +159,7 @@ specified compute group. any command that uses per-atom values from a compute as input. See Section_howto 15 for an overview of LAMMPS output options. -The per-atom vector values will be in temperature units.
+The per-atom vector values will be in temperature units.
Restrictions
diff --git a/doc/html/compute_msd.html b/doc/html/compute_msd.html index ff4d0ca8cf..71b3e59085 100644 --- a/doc/html/compute_msd.html +++ b/doc/html/compute_msd.html @@ -215,7 +215,7 @@ accessed by indices 1-4 by any command that uses global vector values from a compute as input. See this section for an overview of LAMMPS output options.The vector values are “intensive”. The vector values will be in -distance^2 units.
+distance^2 units.Restrictions
diff --git a/doc/html/compute_msd_chunk.html b/doc/html/compute_msd_chunk.html index 9db300a8a1..0aba6d8d95 100644 --- a/doc/html/compute_msd_chunk.html +++ b/doc/html/compute_msd_chunk.html @@ -226,7 +226,7 @@ accessed by any command that uses global array values from a compute as input. See this section for an overview of LAMMPS output options.The array values are “intensive”. The array values will be in -distance^2 units.
+distance^2 units.Restrictions
diff --git a/doc/html/compute_omega_chunk.html b/doc/html/compute_omega_chunk.html index e2873b3b56..80f35b0737 100644 --- a/doc/html/compute_omega_chunk.html +++ b/doc/html/compute_omega_chunk.html @@ -191,7 +191,7 @@ These values can be accessed by any command that uses global array values from a compute as input. See Section_howto 15 for an overview of LAMMPS output options.The array values are “intensive”. The array values will be in -velocity/distance units.
+velocity/distance units.Restrictions
diff --git a/doc/html/compute_pair.html b/doc/html/compute_pair.html index a90747a5bb..a38d482dcb 100644 --- a/doc/html/compute_pair.html +++ b/doc/html/compute_pair.html @@ -185,8 +185,8 @@ from a compute as input. See units. The vector -values will typically also be in energy units, but see +The scalar value will be in energy units. The vector +values will typically also be in energy units, but see the doc page for the pair style for details.
diff --git a/doc/html/compute_pair_local.html b/doc/html/compute_pair_local.html index 531e15cada..922b25d56a 100644 --- a/doc/html/compute_pair_local.html +++ b/doc/html/compute_pair_local.html @@ -179,9 +179,9 @@ example of ones that do are the units. The output -eng will be in energy units. The outputs force, -fx, fy, and fz will be in force units. The output +The output dist will be in distance units. The output +eng will be in energy units. The outputs force, +fx, fy, and fz will be in force units. The output pN will be in whatever units the pair style defines.
Note that as atoms migrate from processor to processor, there will be no consistent ordering of the entries within the local vector or array @@ -217,9 +217,9 @@ local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that uses local values from a compute as input. See this section for an overview of LAMMPS output options.
-The output for dist will be in distance units. The -output for eng will be in energy units. The output for -force will be in force units.
+The output for dist will be in distance units. The +output for eng will be in energy units. The output for +force will be in force units.
Restrictions
diff --git a/doc/html/compute_pe.html b/doc/html/compute_pe.html index aaaa9370ff..9c71a10b65 100644 --- a/doc/html/compute_pe.html +++ b/doc/html/compute_pe.html @@ -200,7 +200,7 @@ value can be used by any command that uses a global scalar value from a compute as input. See Section_howto 15 for an overview of LAMMPS output options.The scalar value calculated by this compute is “extensive”. The -scalar value will be in energy units.
+scalar value will be in energy units.Restrictions
diff --git a/doc/html/compute_pe_atom.html b/doc/html/compute_pe_atom.html index b5a74ff29b..2b95c153cf 100644 --- a/doc/html/compute_pe_atom.html +++ b/doc/html/compute_pe_atom.html @@ -191,7 +191,7 @@ those are global contributions to the system energy. any command that uses per-atom values from a compute as input. See Section_howto 15 for an overview of LAMMPS output options. -The per-atom vector values will be in energy units.
+The per-atom vector values will be in energy units.
diff --git a/doc/html/compute_property_chunk.html b/doc/html/compute_property_chunk.html index d2cb052319..73abeb96ac 100644 --- a/doc/html/compute_property_chunk.html +++ b/doc/html/compute_property_chunk.html @@ -186,7 +186,7 @@ is the center point of the bin in the corresponding dimension. Style bin/1d only defines a coord1 attribute. Style bin/2d adds a coord2 attribute. Style bin/3d adds a coord3 attribute.Restrictions
diff --git a/doc/html/compute_property_atom.html b/doc/html/compute_property_atom.html index 66c8df0d2e..417c581ce8 100644 --- a/doc/html/compute_property_atom.html +++ b/doc/html/compute_property_atom.html @@ -262,7 +262,7 @@ per-atom array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any command that uses per-atom values from a compute as input. See this section for an overview of LAMMPS output options. -The vector or array values will be in whatever units the +
The vector or array values will be in whatever units the corresponding attribute is in, e.g. velocity units for vx, charge units for q, etc.
Note that if the value of the units keyword used in the compute chunk/atom command is box or lattice, the -coordN attributes will be in distance units. If the +coordN attributes will be in distance units. If the value of the units keyword is reduced, the coordN attributes will be in unitless reduced units (0-1).
The simplest way to output the results of the compute property/chunk diff --git a/doc/html/compute_rdf.html b/doc/html/compute_rdf.html index 90808a40ed..c8d486553f 100644 --- a/doc/html/compute_rdf.html +++ b/doc/html/compute_rdf.html @@ -242,7 +242,7 @@ by any command that uses a global values from a compute as input. See LAMMPS output options.
The array values calculated by this compute are all “intensive”.
The first column of array values will be in distance -units. The g(r) columns of array values are normalized +units. The g(r) columns of array values are normalized numbers >= 0.0. The coordination number columns of array values are also numbers >= 0.0.
diff --git a/doc/html/compute_reduce.html b/doc/html/compute_reduce.html index 001fd9b0ce..217f3fd4bf 100644 --- a/doc/html/compute_reduce.html +++ b/doc/html/compute_reduce.html @@ -281,7 +281,7 @@ for an overview of LAMMPS output options. “intensive”, except when the sum or sumsq modes are used on per-atom or local vectors, in which case the calculated values are “extensive”. -The scalar or vector values will be in whatever units the +
The scalar or vector values will be in whatever units the quantities being reduced are in.
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/compute_smd_tlsph_stress.html b/doc/html/compute_smd_tlsph_stress.html index e8b2465097..d14538fad5 100644 --- a/doc/html/compute_smd_tlsph_stress.html +++ b/doc/html/compute_smd_tlsph_stress.html @@ -154,7 +154,7 @@ accessed by any command that uses per-particle values from a compute as input. See How-to discussions, section 6.15 for an overview of LAMMPS output options. -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_slice.html b/doc/html/compute_slice.html index ffe52d1230..427f49ee77 100644 --- a/doc/html/compute_slice.html +++ b/doc/html/compute_slice.html @@ -220,7 +220,7 @@ array values calculated by this compute are “intensive”. If there a multiple input vectors, and any value in them is extensive, then the array values calculated by this compute are “extensive”. Values produced by a variable are treated as intensive.
-The vector or array values will be in whatever units the +
The vector or array values will be in whatever units the input quantities are in.
diff --git a/doc/html/compute_smd_contact_radius.html b/doc/html/compute_smd_contact_radius.html index 72a940008a..0e19b35fa0 100644 --- a/doc/html/compute_smd_contact_radius.html +++ b/doc/html/compute_smd_contact_radius.html @@ -158,7 +158,7 @@ specified compute group. any command that uses per-particle values from a compute as input. See Section_howto 15 for an overview of LAMMPS output options. -The per-particle vector values will be in distance units.
+The per-particle vector values will be in distance units.
Restrictions
diff --git a/doc/html/compute_smd_hourglass_error.html b/doc/html/compute_smd_hourglass_error.html index 9c92105981..595c8b3498 100644 --- a/doc/html/compute_smd_hourglass_error.html +++ b/doc/html/compute_smd_hourglass_error.html @@ -162,7 +162,7 @@ any command that uses per-particle values from a compute as input. See How-to discussions, section 6.15 for an overview of LAMMPS output options.The per-particle vector values will are dimensionless. See -units.
+units.Restrictions
diff --git a/doc/html/compute_smd_internal_energy.html b/doc/html/compute_smd_internal_energy.html index 5b084754cc..14290c8b0a 100644 --- a/doc/html/compute_smd_internal_energy.html +++ b/doc/html/compute_smd_internal_energy.html @@ -153,7 +153,7 @@ Mach Dynamics in LAMMPS. by any command that uses per-particle values from a compute as input. See How-to discussions, section 6.15 for an overview of LAMMPS output options. -The per-particle vector values will be given in units of energy.
+The per-particle vector values will be given in units of energy.
Restrictions
diff --git a/doc/html/compute_smd_plastic_strain.html b/doc/html/compute_smd_plastic_strain.html index aab190912e..90dd34a979 100644 --- a/doc/html/compute_smd_plastic_strain.html +++ b/doc/html/compute_smd_plastic_strain.html @@ -154,7 +154,7 @@ Mach Dynamics in LAMMPS. by any command that uses per-particle values from a compute as input. See How-to discussions, section 6.15 for an overview of LAMMPS output options. -The per-particle values will be given dimensionless. See units.
+The per-particle values will be given dimensionless. See units.
Restrictions
diff --git a/doc/html/compute_smd_plastic_strain_rate.html b/doc/html/compute_smd_plastic_strain_rate.html index d97551d270..e0848e3f41 100644 --- a/doc/html/compute_smd_plastic_strain_rate.html +++ b/doc/html/compute_smd_plastic_strain_rate.html @@ -154,7 +154,7 @@ Mach Dynamics in LAMMPS. by any command that uses per-particle values from a compute as input. See How-to discussions, section 6.15 for an overview of LAMMPS output options. -The per-particle values will be given in units of one over time.
+The per-particle values will be given in units of one over time.
Restrictions
diff --git a/doc/html/compute_smd_rho.html b/doc/html/compute_smd_rho.html index 3872b047f9..2d199a90cd 100644 --- a/doc/html/compute_smd_rho.html +++ b/doc/html/compute_smd_rho.html @@ -155,7 +155,7 @@ Mach Dynamics in LAMMPS. by any command that uses per-particle values from a compute as input. See How-to discussions, section 6.15 for an overview of LAMMPS output options. -The per-particle values will be in units of mass over volume.
+The per-particle values will be in units of mass over volume.
Restrictions
diff --git a/doc/html/compute_smd_tlsph_defgrad.html b/doc/html/compute_smd_tlsph_defgrad.html index dc3d4ba56a..8e23bd77f5 100644 --- a/doc/html/compute_smd_tlsph_defgrad.html +++ b/doc/html/compute_smd_tlsph_defgrad.html @@ -155,7 +155,7 @@ which can be accessed by any command that uses per-particle values from a compute as input. See How-to discussions, section 6.15 for an overview of LAMMPS output options.The per-particle vector values will be given dimensionless. See -units. The per-particle vector has 10 entries. The first +units. The per-particle vector has 10 entries. The first nine entries correspond to the xx, xy, xz, yx, yy, yz, zx, zy, zz components of the asymmetric deformation gradient tensor. The tenth entry is the determinant of the deformation gradient.
diff --git a/doc/html/compute_smd_tlsph_dt.html b/doc/html/compute_smd_tlsph_dt.html index 78f5e83e4f..9bc9c23e81 100644 --- a/doc/html/compute_smd_tlsph_dt.html +++ b/doc/html/compute_smd_tlsph_dt.html @@ -159,7 +159,7 @@ Mach Dynamics in LAMMPS. by any command that uses per-particle values from a compute as input. See How-to discussions, section 6.15 for an overview of LAMMPS output options. -The per-particle values will be given in units of time.
+The per-particle values will be given in units of time.
Restrictions
diff --git a/doc/html/compute_smd_tlsph_num_neighs.html b/doc/html/compute_smd_tlsph_num_neighs.html index 9b005a819c..926a1661c8 100644 --- a/doc/html/compute_smd_tlsph_num_neighs.html +++ b/doc/html/compute_smd_tlsph_num_neighs.html @@ -154,7 +154,7 @@ Mach Dynamics in LAMMPS. by any command that uses per-particle values from a compute as input. See How-to discussions, section 6.15 for an overview of LAMMPS output options. -The per-particle values are dimensionless. See units.
+The per-particle values are dimensionless. See units.
diff --git a/doc/html/compute_smd_tlsph_strain_rate.html b/doc/html/compute_smd_tlsph_strain_rate.html index 06b2ca6984..e1b430b23f 100644 --- a/doc/html/compute_smd_tlsph_strain_rate.html +++ b/doc/html/compute_smd_tlsph_strain_rate.html @@ -153,7 +153,7 @@ Mach Dynamics in LAMMPS. which can be accessed by any command that uses per-particle values from a compute as input. See How-to discussions, section 6.15 for an overview of LAMMPS output options. -Restrictions
diff --git a/doc/html/compute_smd_tlsph_strain.html b/doc/html/compute_smd_tlsph_strain.html index 3dfc7b01b4..6b58d8c318 100644 --- a/doc/html/compute_smd_tlsph_strain.html +++ b/doc/html/compute_smd_tlsph_strain.html @@ -154,7 +154,7 @@ which can be accessed by any command that uses per-particle values from a compute as input. See How-to discussions, section 6.15 for an overview of LAMMPS output options.The per-particle tensor values will be given dimensionless. See -units.
+units.The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components of the symmetric strain tensor.
The values will be given in units of one over time.
+The values will be given in units of one over time.
The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components of the symmetric strain rate tensor.
The values will be given in units of pressure.
+The values will be given in units of pressure.
The per-particle vector has 7 entries. The first six entries correspond to the xx, yy, zz, xy, xz and yz components of the symmetric Cauchy stress tensor. The seventh entry is the second diff --git a/doc/html/compute_smd_triangle_mesh_vertices.html b/doc/html/compute_smd_triangle_mesh_vertices.html index b4b047eadd..2b4077d564 100644 --- a/doc/html/compute_smd_triangle_mesh_vertices.html +++ b/doc/html/compute_smd_triangle_mesh_vertices.html @@ -161,7 +161,7 @@ which is created via the `fix
which can be accessed by any command that uses per-particle values from a compute as input. See Section_howto 15 for an overview of LAMMPS output options. -The output of this compute can be used with the dump2vtk_tris tool to generate a VTK representation of the smd/wall_surace mesh for visualization purposes.
-The values will be given in units of distance.
+The values will be given in units of distance.
Restrictions
diff --git a/doc/html/compute_smd_ulsph_num_neighs.html b/doc/html/compute_smd_ulsph_num_neighs.html index 865324dc9a..425c4b81e5 100644 --- a/doc/html/compute_smd_ulsph_num_neighs.html +++ b/doc/html/compute_smd_ulsph_num_neighs.html @@ -154,7 +154,7 @@ Mach Dynamics in LAMMPS. any command that uses per-particle values from a compute as input. See Section_howto 15 for an overview of LAMMPS output options. -The per-particle values will be given dimentionless, see units.
+The per-particle values will be given dimentionless, see units.
Restrictions
diff --git a/doc/html/compute_smd_ulsph_strain.html b/doc/html/compute_smd_ulsph_strain.html index 65c590ba28..86f90ceb6a 100644 --- a/doc/html/compute_smd_ulsph_strain.html +++ b/doc/html/compute_smd_ulsph_strain.html @@ -156,7 +156,7 @@ LAMMPS output options.The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components of the symmetric strain rate tensor.
The per-particle tensor values will be given dimensionless, see -units.
+units.diff --git a/doc/html/compute_smd_ulsph_stress.html b/doc/html/compute_smd_ulsph_stress.html index dad5e3e8e2..51654a43e0 100644 --- a/doc/html/compute_smd_ulsph_stress.html +++ b/doc/html/compute_smd_ulsph_stress.html @@ -152,7 +152,7 @@ Mach Dynamics in LAMMPS.Restrictions
diff --git a/doc/html/compute_smd_ulsph_strain_rate.html b/doc/html/compute_smd_ulsph_strain_rate.html index f899e66f21..0f60ae8efd 100644 --- a/doc/html/compute_smd_ulsph_strain_rate.html +++ b/doc/html/compute_smd_ulsph_strain_rate.html @@ -154,7 +154,7 @@ Mach Dynamics in LAMMPS. which can be accessed by any command that uses per-particle values from a compute as input. See Section_howto 15 for an overview of LAMMPS output options. -The values will be given in units of one over time.
+The values will be given in units of one over time.
The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components of the symmetric strain rate tensor.
The values will be given in units of pressure.
+The values will be given in units of pressure.
The per-particle vector has 7 entries. The first six entries correspond to the xx, yy, zz, xy, xz, yz components of the symmetric Cauchy stress tensor. The seventh entry is the second invariant of the diff --git a/doc/html/compute_smd_vol.html b/doc/html/compute_smd_vol.html index 462bdec670..4029e0eb2f 100644 --- a/doc/html/compute_smd_vol.html +++ b/doc/html/compute_smd_vol.html @@ -153,7 +153,7 @@ Mach Dynamics in LAMMPS.
by any command that uses per-particle values from a compute as input. See How-to discussions, section 6.15 for an overview of LAMMPS output options. -The per-particle vector values will be given in units of +
The per-particle vector values will be given in units of volume.
Additionally, the compute returns a scalar, which is the sum of the per-particle volumes of the group for which the fix is defined.
diff --git a/doc/html/compute_temp.html b/doc/html/compute_temp.html index 865d29ee59..b11eee9e07 100644 --- a/doc/html/compute_temp.html +++ b/doc/html/compute_temp.html @@ -207,8 +207,8 @@ vector values from a compute as input. See units. The -vector values will be in energy units. +The scalar value will be in temperature units. The +vector values will be in energy units.
Restrictions
diff --git a/doc/html/compute_temp_asphere.html b/doc/html/compute_temp_asphere.html index 164ab2a234..06c17edaa9 100644 --- a/doc/html/compute_temp_asphere.html +++ b/doc/html/compute_temp_asphere.html @@ -238,8 +238,8 @@ vector values from a compute as input. See units. The -vector values will be in energy units. +The scalar value will be in temperature units. The +vector values will be in energy units.
Restrictions
diff --git a/doc/html/compute_temp_body.html b/doc/html/compute_temp_body.html index 6115c821b9..807216d419 100644 --- a/doc/html/compute_temp_body.html +++ b/doc/html/compute_temp_body.html @@ -219,8 +219,8 @@ vector values from a compute as input. See units. The -vector values will be in energy units. +The scalar value will be in temperature units. The +vector values will be in energy units.
Restrictions
diff --git a/doc/html/compute_temp_chunk.html b/doc/html/compute_temp_chunk.html index 7c593e7a80..3d0d3eeb6d 100644 --- a/doc/html/compute_temp_chunk.html +++ b/doc/html/compute_temp_chunk.html @@ -312,10 +312,10 @@ compute as input. Again, see units. The -vector values will be in energy units. The array values -will be in temperature units for the temp value, and in -energy units for the kecom and internal values. +The scalar value will be in temperature units. The +vector values will be in energy units. The array values +will be in temperature units for the temp value, and in +energy units for the kecom and internal values.
Restrictions
diff --git a/doc/html/compute_temp_com.html b/doc/html/compute_temp_com.html index 96cf303b8d..cd57a0da57 100644 --- a/doc/html/compute_temp_com.html +++ b/doc/html/compute_temp_com.html @@ -189,8 +189,8 @@ vector values from a compute as input. See units. The -vector values will be in energy units. +The scalar value will be in temperature units. The +vector values will be in energy units.
Restrictions
diff --git a/doc/html/compute_temp_cs.html b/doc/html/compute_temp_cs.html index 8daa29344c..4751726a56 100644 --- a/doc/html/compute_temp_cs.html +++ b/doc/html/compute_temp_cs.html @@ -204,8 +204,8 @@ These values can be used by any command that uses global scalar or vector values from a compute as input.The scalar value calculated by this compute is “intensive”. The vector values are “extensive”.
-The scalar value will be in temperature units. The -vector values will be in energy units.
+The scalar value will be in temperature units. The +vector values will be in energy units.
Restrictions
diff --git a/doc/html/compute_temp_deform.html b/doc/html/compute_temp_deform.html index c29816af3c..2922d5ce4a 100644 --- a/doc/html/compute_temp_deform.html +++ b/doc/html/compute_temp_deform.html @@ -229,8 +229,8 @@ vector values from a compute as input. See units. The -vector values will be in energy units. +The scalar value will be in temperature units. The +vector values will be in energy units.
Restrictions
diff --git a/doc/html/compute_temp_deform_eff.html b/doc/html/compute_temp_deform_eff.html index fbe48b1ac5..748ee79b41 100644 --- a/doc/html/compute_temp_deform_eff.html +++ b/doc/html/compute_temp_deform_eff.html @@ -170,8 +170,8 @@ vector values from a compute as input. See units. The -vector values will be in energy units. +The scalar value will be in temperature units. The +vector values will be in energy units.
Restrictions
diff --git a/doc/html/compute_temp_partial.html b/doc/html/compute_temp_partial.html index 09178601b7..e20787b288 100644 --- a/doc/html/compute_temp_partial.html +++ b/doc/html/compute_temp_partial.html @@ -209,8 +209,8 @@ vector values from a compute as input. See units. The -vector values will be in energy units. +The scalar value will be in temperature units. The +vector values will be in energy units.
Restrictions
diff --git a/doc/html/compute_temp_profile.html b/doc/html/compute_temp_profile.html index fcff076551..849b471064 100644 --- a/doc/html/compute_temp_profile.html +++ b/doc/html/compute_temp_profile.html @@ -262,10 +262,10 @@ vector or array values from a compute as input. See units. The -vector values will be in energy units. The first column +The scalar value will be in temperature units. The +vector values will be in energy units. The first column of array values are counts; the values in the second column will be in -temperature units.
+temperature units.Restrictions
diff --git a/doc/html/compute_temp_ramp.html b/doc/html/compute_temp_ramp.html index 46ecafd332..bb551f9957 100644 --- a/doc/html/compute_temp_ramp.html +++ b/doc/html/compute_temp_ramp.html @@ -169,7 +169,7 @@ simulation, N = number of atoms in the group, k = Boltzmann constant, and T = temperature.The units keyword determines the meaning of the distance units used for coordinates (c1,c2) and velocities (vlo,vhi). A box value -selects standard distance units as defined by the units +selects standard distance units as defined by the units command, e.g. Angstroms for units = real or metal. A lattice value means the distance units are in lattice spacings; e.g. velocity = lattice spacings / tau. The lattice command must have @@ -207,8 +207,8 @@ vector values from a compute as input. See units. The -vector values will be in energy units.
+The scalar value will be in temperature units. The +vector values will be in energy units.
Restrictions
diff --git a/doc/html/compute_temp_region.html b/doc/html/compute_temp_region.html index 8c82ba5c23..028fae2b9a 100644 --- a/doc/html/compute_temp_region.html +++ b/doc/html/compute_temp_region.html @@ -202,8 +202,8 @@ vector values from a compute as input. See units. The -vector values will be in energy units. +The scalar value will be in temperature units. The +vector values will be in energy units.
Restrictions
diff --git a/doc/html/compute_temp_region_eff.html b/doc/html/compute_temp_region_eff.html index e58cfd8664..25c158a78c 100644 --- a/doc/html/compute_temp_region_eff.html +++ b/doc/html/compute_temp_region_eff.html @@ -162,8 +162,8 @@ vector values from a compute as input. See units. The -vector values will be in energy units. +The scalar value will be in temperature units. The +vector values will be in energy units.
Restrictions
diff --git a/doc/html/compute_temp_rotate.html b/doc/html/compute_temp_rotate.html index a3d6dccafb..dd664c2735 100644 --- a/doc/html/compute_temp_rotate.html +++ b/doc/html/compute_temp_rotate.html @@ -188,8 +188,8 @@ vector values from a compute as input. See units. The -vector values will be in energy units. +The scalar value will be in temperature units. The +vector values will be in energy units.
Restrictions
diff --git a/doc/html/compute_temp_sphere.html b/doc/html/compute_temp_sphere.html index 7ab79fd53d..0dec80de72 100644 --- a/doc/html/compute_temp_sphere.html +++ b/doc/html/compute_temp_sphere.html @@ -226,8 +226,8 @@ vector values from a compute as input. See units. The -vector values will be in energy units. +The scalar value will be in temperature units. The +vector values will be in energy units.
Restrictions
diff --git a/doc/html/compute_ti.html b/doc/html/compute_ti.html index efb269d33a..5701aeee75 100644 --- a/doc/html/compute_ti.html +++ b/doc/html/compute_ti.html @@ -226,7 +226,7 @@ value can be used by any command that uses a global scalar value from a compute as input. See Section_howto 15 for an overview of LAMMPS output options.The scalar value calculated by this compute is “extensive”.
-The scalar value will be in energy units.
+The scalar value will be in energy units.
Restrictions
diff --git a/doc/html/compute_torque_chunk.html b/doc/html/compute_torque_chunk.html index bb1e4de5c4..fb17297e21 100644 --- a/doc/html/compute_torque_chunk.html +++ b/doc/html/compute_torque_chunk.html @@ -190,7 +190,7 @@ can be accessed by any command that uses global array values from a compute as input. See Section_howto 15 for an overview of LAMMPS output options.The array values are “intensive”. The array values will be in -force-distance units.
+force-distance units.Restrictions
diff --git a/doc/html/compute_vacf.html b/doc/html/compute_vacf.html index 019154cb07..713789bce4 100644 --- a/doc/html/compute_vacf.html +++ b/doc/html/compute_vacf.html @@ -180,7 +180,7 @@ accessed by indices 1-4 by any command that uses global vector values from a compute as input. See this section for an overview of LAMMPS output options.The vector values are “intensive”. The vector values will be in -velocity^2 units.
+velocity^2 units.Restrictions
diff --git a/doc/html/compute_vcm_chunk.html b/doc/html/compute_vcm_chunk.html index 689e4d3d34..9672e1f90d 100644 --- a/doc/html/compute_vcm_chunk.html +++ b/doc/html/compute_vcm_chunk.html @@ -180,7 +180,7 @@ These values can be accessed by any command that uses global array values from a compute as input. See Section_howto 15 for an overview of LAMMPS output options.The array values are “intensive”. The array values will be in -velocity units.
+velocity units.-Restrictions
diff --git a/doc/html/compute_voronoi_atom.html b/doc/html/compute_voronoi_atom.html index c4ede1f7ec..5b05cb77a6 100644 --- a/doc/html/compute_voronoi_atom.html +++ b/doc/html/compute_voronoi_atom.html @@ -317,8 +317,8 @@ keyword to turn off the production of the per-atom quantities. For the default value yes both quantities are produced. For the value no, only the local array is produced.The Voronoi cell volume will be in distance units cubed. -The Voronoi face area will be in distance units squared.
+The Voronoi cell volume will be in distance units cubed. +The Voronoi face area will be in distance units squared.
diff --git a/doc/html/fix_gravity.html b/doc/html/fix_gravity.html index 6d6aac1460..006dcb0889 100644 --- a/doc/html/fix_gravity.html +++ b/doc/html/fix_gravity.html @@ -179,7 +179,7 @@ adds the same force to each atom, independent of its mass. This command imparts the same acceleration to each atom (force/mass).Restrictions
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/displace_atoms.html b/doc/html/displace_atoms.html index 21efabec21..241ed70662 100644 --- a/doc/html/displace_atoms.html +++ b/doc/html/displace_atoms.html @@ -217,7 +217,7 @@ atom’s rotation.
Distance units for displacements and the origin point of the rotate style are determined by the setting of box or lattice for the units keyword. Box means distance units as defined by the -units command - e.g. Angstroms for real units. +units command - e.g. Angstroms for real units. Lattice means distance units are in lattice spacings. The lattice command must have been previously used to define the lattice spacing.
diff --git a/doc/html/dump.html b/doc/html/dump.html index 16ab8c594f..9a927a1fa5 100644 --- a/doc/html/dump.html +++ b/doc/html/dump.html @@ -587,7 +587,7 @@ mass. Vx, vy, vz, fx, fy, fzThere are several options for outputting atom coordinates. The x, y, z attributes write atom coordinates “unscaled”, in the -appropriate distance units (Angstroms, sigma, etc). Use +appropriate distance units (Angstroms, sigma, etc). Use xs, ys, zs if you want the coordinates “scaled” to the box size, so that each value is 0.0 to 1.0. If the simulation box is triclinic (tilted), then all atom coords will still be between 0.0 and 1.0. Use diff --git a/doc/html/dump_custom_vtk.html b/doc/html/dump_custom_vtk.html index 425fc7dec2..d23a7c09f7 100644 --- a/doc/html/dump_custom_vtk.html +++ b/doc/html/dump_custom_vtk.html @@ -312,7 +312,7 @@ atom type. mass is the atom mass. vx, vy, vz
each chunk, i.e. number/volume. The density/mass value means the mass density is computed for each chunk, i.e. total-mass/volume. The output values are in units of 1/volume or density (mass/volume). See -the units command doc page for the definition of density +the units command doc page for the definition of density for each choice of units, e.g. gram/cm^3. If the chunks defined by the compute chunk/atom command are spatial bins, the volume is the bin volume. Otherwise it is the volume of the @@ -475,11 +475,11 @@ coordinate. For bin/cylinder, Coord1 and Coord2 are used. Coord1 is the radial coordinate (away from the cylinder axis), and coord2 is the coordinate along the cylinder axis.There are several options for outputting atom coordinates. The x, y, z attributes are used to write atom coordinates “unscaled”, in -the appropriate distance units (Angstroms, sigma, etc). +the appropriate distance units (Angstroms, sigma, etc). Additionaly, you can use xs, ys, zs if you want to also save the coordinates “scaled” to the box size, so that each value is 0.0 to 1.0. If the simulation box is triclinic (tilted), then all atom diff --git a/doc/html/dump_modify.html b/doc/html/dump_modify.html index 40e325766e..455724908b 100644 --- a/doc/html/dump_modify.html +++ b/doc/html/dump_modify.html @@ -444,7 +444,7 @@ nanometer accuracy, e.g. for N = 1000, the coordinates are written to
The sfactor and tfactor keywords only apply to the dump xtc style. They allow customization of the unit conversion factors used when writing to XTC files. By default they are initialized for -whatever units style is being used, to write out +whatever units style is being used, to write out coordinates in nanometers and time in picoseconds. I.e. for real units, LAMMPS defines sfactor = 0.1 and tfactor = 0.001, since the Angstroms and fmsec used by real units are 0.1 nm and 0.001 psec @@ -542,7 +542,7 @@ that atoms of each type will be drawn in the image. The specified type should be an integer from 1 to Ntypes. As with the acolor keyword, a wildcard asterisk can be used as part of the type argument to specify a range of atomt types. The specified diam is -the size in whatever distance units the input script is +the size in whatever distance units the input script is using, e.g. Angstroms.
The amap keyword can be used with the dump image @@ -687,7 +687,7 @@ set the diameter that bonds of each type will be drawn in the image. The specified type should be an integer from 1 to Nbondtypes. As with the bcolor keyword, a wildcard asterisk can be used as part of the type argument to specify a range of bond types. The specified -diam is the size in whatever distance units you are +diam is the size in whatever distance units you are using, e.g. Angstroms.
The bitrate keyword can be used with the dump movie command to define the size of the resulting diff --git a/doc/html/fix_append_atoms.html b/doc/html/fix_append_atoms.html index 8f394db17e..d53243c00f 100644 --- a/doc/html/fix_append_atoms.html +++ b/doc/html/fix_append_atoms.html @@ -193,7 +193,7 @@ measured from zhi and is set with the extent argument.
The units keyword determines the meaning of the distance units used to define a wall position, but only when a numeric constant is used. A box value selects standard distance units as defined by the -units command, e.g. Angstroms for units = real or metal. +units command, e.g. Angstroms for units = real or metal. A lattice value means the distance units are in lattice spacings. The lattice command must have been previously used to define the lattice spacings.
diff --git a/doc/html/fix_ave_chunk.html b/doc/html/fix_ave_chunk.html index c5895fe148..b636808101 100644 --- a/doc/html/fix_ave_chunk.html +++ b/doc/html/fix_ave_chunk.html @@ -293,7 +293,7 @@ an input value from that compute.Note that if the value of the units keyword used in the compute chunk/atom command is box or lattice, the -coordinate values will be in distance units. If the +coordinate values will be in distance units. If the value of the units keyword is reduced, the coordinate values will be in unitless reduced units (0-1). This is not true for the Coord1 value of style bin/sphere or bin/cylinder which both represent radial -dimensions. Those values are always in distance units.
+dimensions. Those values are always in distance units.
diff --git a/doc/html/fix_ave_spatial.html b/doc/html/fix_ave_spatial.html index e8eb9f1a64..a435667770 100644 --- a/doc/html/fix_ave_spatial.html +++ b/doc/html/fix_ave_spatial.html @@ -345,7 +345,7 @@ each bin, i.e. a weighting of 1 for each atom. The density/mass value means the mass density is computed in each bind, i.e. each atom is weighted by its mass. The resulting density is normalized by the volume of the bin so that units of number/volume or density are -output. See the units command doc page for the +output. See the units command doc page for the definition of density for each choice of units, e.g. gram/cm^3.If a value begins with “c_”, a compute ID must follow which has been previously defined in the input script. If no bracketed integer is @@ -409,7 +409,7 @@ are coordinate value. For orthogonal simulation boxes, any of the 3 options may be used. For non-orthogonal (triclinic) simulation boxes, only the reduced option may be used.
A box value selects standard distance units as defined by the -units command, e.g. Angstroms for units = real or metal. +units command, e.g. Angstroms for units = real or metal. A lattice value means the distance units are in lattice spacings. The lattice command must have been previously used to define the lattice spacing. A reduced value means normalized diff --git a/doc/html/fix_ave_spatial_sphere.html b/doc/html/fix_ave_spatial_sphere.html index 07c8229dac..109f9aa98d 100644 --- a/doc/html/fix_ave_spatial_sphere.html +++ b/doc/html/fix_ave_spatial_sphere.html @@ -257,7 +257,7 @@ each bin, i.e. a weighting of 1 for each atom. The density/mass value means the mass density is computed in each bin, i.e. each atom is weighted by its mass. The resulting density is normalized by the volume of the bin so that units of number/volume or density are -output. See the units command doc page for the +output. See the units command doc page for the definition of density for each choice of units, e.g. gram/cm^3. The bin volume will always be calculated in box units, independent of the use of the units keyword in this command.
@@ -323,7 +323,7 @@ simulation boxes, any of the 3 options may be used. For non-orthogonal (triclinic) simulation boxes, only the reduced option may be used.A box value selects standard distance units as defined by the -units command, e.g. Angstroms for units = real or metal. +units command, e.g. Angstroms for units = real or metal. A lattice value means the distance units are in lattice spacings. The lattice command must have been previously used to define the lattice spacing.
diff --git a/doc/html/fix_deform.html b/doc/html/fix_deform.html index 8192f41e59..82306671d2 100644 --- a/doc/html/fix_deform.html +++ b/doc/html/fix_deform.html @@ -266,7 +266,7 @@ after 10 psec, the box length will have doubled. After 20 psec, it will have tripled.The erate style changes a dimension of the the box at a “constant engineering strain rate”. The units of the specified strain rate are -1/time. See the units command for the time units +1/time. See the units command for the time units associated with different choices of simulation units, e.g. picoseconds for “metal” units). Tensile strain is unitless and is defined as delta/L0, where L0 is the original box length and delta @@ -289,7 +289,7 @@ strain rate”. Note that this is not an “engineering strain rateR the other styles are. Rather, for a “true” rate, the rate of change is constant, which means the box dimension changes non-linearly with time from its initial to final value. The units of the specified -strain rate are 1/time. See the units command for the +strain rate are 1/time. See the units command for the time units associated with different choices of simulation units, e.g. picoseconds for “metal” units). Tensile strain is unitless and is defined as delta/L0, where L0 is the original box length and delta @@ -405,7 +405,7 @@ tilt factor will be 15 Angstroms. After 2 psec, it will be 25 Angstroms.
The erate style changes a tilt factor at a “constant engineering shear strain rate”. The units of the specified shear strain rate are -1/time. See the units command for the time units +1/time. See the units command for the time units associated with different choices of simulation units, e.g. picoseconds for “metal” units). Shear strain is unitless and is defined as offset/length, where length is the box length perpendicular @@ -433,7 +433,7 @@ rate”, as the other styles are. Rather, for a “true” rate, th of change is constant, which means the tilt factor changes non-linearly with time from its initial to final value. The units of the specified shear strain rate are 1/time. See the -units command for the time units associated with +units command for the time units associated with different choices of simulation units, e.g. picoseconds for “metal” units). Shear strain is unitless and is defined as offset/length, where length is the box length perpendicular to the shear direction @@ -608,7 +608,7 @@ irregular-shaped sub-domain. For extreme values of tilt, LAMMPS may also lose atoms and generate an error.
The units keyword determines the meaning of the distance units used to define various arguments. A box value selects standard distance -units as defined by the units command, e.g. Angstroms for +units as defined by the units command, e.g. Angstroms for units = real or metal. A lattice value means the distance units are in lattice spacings. The lattice command must have been previously used to define the lattice spacing. Note that the diff --git a/doc/html/fix_deposit.html b/doc/html/fix_deposit.html index d74fda40ee..278f20266c 100644 --- a/doc/html/fix_deposit.html +++ b/doc/html/fix_deposit.html @@ -334,7 +334,7 @@ particles will be consecutive even if particles leave the system over time.
The units keyword determines the meaning of the distance units used for the other deposition parameters. A box value selects standard -distance units as defined by the units command, +distance units as defined by the units command, e.g. Angstroms for units = real or metal. A lattice value means the distance units are in lattice spacings. The lattice command must have been previously used to define the lattice spacing. diff --git a/doc/html/fix_external.html b/doc/html/fix_external.html index 1005484ea5..d2a176da50 100644 --- a/doc/html/fix_external.html +++ b/doc/html/fix_external.html @@ -217,7 +217,7 @@ method of the FixExternal class:
where eng is the potential energy. Eng is an extensive quantity, meaning it should be the sum over per-atom energies of all affected -atoms. It should also be provided in energy units +atoms. It should also be provided in energy units consistent with the simulation. See the details below for how to insure this energy setting is used appropriately in a minimization.
The magnitude of the acceleration is specified in force/mass units. For granular systems (LJ units) this is typically 1.0. See the -units command for details.
+units command for details.Style chute is typically used for simulations of chute flow where the specified angle is the chute angle, with flow occurring in the +x direction. For 3d systems, the tilt is away from the z axis; for 2d diff --git a/doc/html/fix_heat.html b/doc/html/fix_heat.html index ecf031e9cf..701cdc1be4 100644 --- a/doc/html/fix_heat.html +++ b/doc/html/fix_heat.html @@ -170,7 +170,7 @@ parameter can be specified as a numeric constant or as a variable (see below). If it is a numeric constant or equal-style variable which evaluates to a scalar value, then the eflux determines the change in aggregate energy of the entire group of atoms per unit time, e.g. in -eV/psec for metal units. In this case it is an +eV/psec for metal units. In this case it is an “extensive” quantity, meaning its magnitude should be scaled with the number of atoms in the group. Note that since eflux has per-time units (i.e. it is a flux), this means that a larger value of N will diff --git a/doc/html/fix_indent.html b/doc/html/fix_indent.html index 7fc26b7806..c8a8ce8bb9 100644 --- a/doc/html/fix_indent.html +++ b/doc/html/fix_indent.html @@ -253,7 +253,7 @@ is now a containing wall that traps the particles inside it. If the radius shrinks over time, it will squeeze the particles.
The units keyword determines the meaning of the distance units used to define the indenter geometry. A box value selects standard -distance units as defined by the units command, +distance units as defined by the units command, e.g. Angstroms for units = real or metal. A lattice value means the distance units are in lattice spacings. The lattice command must have been previously used to define the lattice spacing. @@ -267,7 +267,7 @@ the the lattice spacings in a variable formula.
The force constant K is not affected by the units keyword. It is always in force/distance^2 units where force and distance are defined -by the units command. If you wish K to be scaled by the +by the units command. If you wish K to be scaled by the lattice spacing, you can define K with a variable whose formula contains xlat, ylat, zlat keywords of the thermo_style command, e.g.
diff --git a/doc/html/fix_langevin.html b/doc/html/fix_langevin.html index 1df0b59dbb..edf3efa19a 100644 --- a/doc/html/fix_langevin.html +++ b/doc/html/fix_langevin.html @@ -257,7 +257,7 @@ in.The damp parameter is specified in time units and determines how rapidly the temperature is relaxed. For example, a value of 100.0 means to relax the temperature in a timespan of (roughly) 100 time -units (tau or fmsec or psec - see the units command). +units (tau or fmsec or psec - see the units command). The damp factor can be thought of as inversely related to the viscosity of the solvent. I.e. a small relaxation time implies a hi-viscosity solvent and vice versa. See the discussion about gamma diff --git a/doc/html/fix_langevin_drude.html b/doc/html/fix_langevin_drude.html index 188354f331..f01d0bd451 100644 --- a/doc/html/fix_langevin_drude.html +++ b/doc/html/fix_langevin_drude.html @@ -273,7 +273,7 @@ particles.
damp_com is the characteristic time for reaching thermal equilibrium of the centers of mass. For example, a value of 100.0 means to relax the temperature of the centers of mass in a timespan of (roughly) 100 -time units (tau or fmsec or psec - see the units +time units (tau or fmsec or psec - see the units command). damp_drude is the characteristic time for reaching thermal equilibrium of the dipoles. It is typically a few timesteps.
The number seed_com and seed_drude are positive integers. They set 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 d1f6c72c2f..66cf61d80e 100644 --- a/doc/html/fix_move.html +++ b/doc/html/fix_move.html @@ -294,7 +294,7 @@ velocity.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.
The units keyword determines the meaning of the distance units used to define the linear velocity and wiggle amplitude and rotate origin. This setting is ignored for the variable style. A box -value selects standard units as defined by the units +value selects standard units as defined by the units command, e.g. velocity in Angstroms/fmsec and amplitude and position in Angstroms for units = real. A lattice value means the velocity units are in lattice spacings per time and the amplitude and position diff --git a/doc/html/fix_nh.html b/doc/html/fix_nh.html index bdf5b051b7..f542b04a18 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.
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 @@ -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, diff --git a/doc/html/fix_nve_limit.html b/doc/html/fix_nve_limit.html index 0167dbee46..ede833982c 100644 --- a/doc/html/fix_nve_limit.html +++ b/doc/html/fix_nve_limit.html @@ -156,7 +156,7 @@ be computable (which typically means 2 atoms must have a separation distance > 0.0). But large velocities generated by large forces are reset to a value that corresponds to a displacement of length xmax in a single timestep. Xmax is specified in distance units; see the -units command for details. The value of xmax should be +units command for details. The value of xmax should be consistent with the neighbor skin distance and the frequency of neighbor list re-building, so that pairwise interactions are not missed on successive timesteps as atoms move. See the diff --git a/doc/html/fix_phonon.html b/doc/html/fix_phonon.html index 74398f2dd0..0eed3acb9e 100644 --- a/doc/html/fix_phonon.html +++ b/doc/html/fix_phonon.html @@ -236,7 +236,7 @@ dynamical matrix at only the gamma-point will/can be evaluated. Please keep in mind that fix-phonon is designed for cyrstals, it will be inefficient and even degrade the performance of lammps in case the unit cell is too large.
The calculated dynamical matrix elements are written out in -energy/distance^2/mass units. The coordinates for q +energy/distance^2/mass units. The coordinates for q points in the log file is in the units of the basis vectors of the corresponding reciprocal lattice.
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 5480fb3db8..ffd58394b6 100644 --- a/doc/html/fix_press_berendsen.html +++ b/doc/html/fix_press_berendsen.html @@ -205,7 +205,7 @@ although you have the option to change that dimension via the units command). +(tau or fmsec or psec - see the units command).Note
A Berendsen barostat will not work well for arbitrary values of @@ -214,7 +214,7 @@ fluctuate wildly; if it is too large, the pressure will take a very long time to equilibrate. A good choice for many models is a Pdamp of around 1000 timesteps. However, note that Pdamp is specified in time units, and that timesteps are NOT the same as time units for most -units settings.
+units settings.Note
@@ -322,7 +322,7 @@ variousDefault
The keyword defaults are dilate = all, modulus = 10.0 in units of -pressure for whatever units are defined.
+pressure for whatever units are defined.
(Berendsen) Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem Phys, 81, 3684 (1984).
diff --git a/doc/html/fix_recenter.html b/doc/html/fix_recenter.html index ae3ced35a4..4f1bdc2285 100644 --- a/doc/html/fix_recenter.html +++ b/doc/html/fix_recenter.html @@ -176,7 +176,7 @@ example, the COM could be computed on a protein to keep it in the center of the simulation box. But the entire system (protein + water) could be shifted.If the units keyword is set to box, then the distance units of -x,y,z are defined by the units command - e.g. Angstroms +x,y,z are defined by the units command - e.g. Angstroms for real units. A lattice value means the distance units are in lattice spacings. The lattice command must have been previously used to define the lattice spacing. A fraction value diff --git a/doc/html/fix_rigid.html b/doc/html/fix_rigid.html index 357919f88a..d543973b84 100644 --- a/doc/html/fix_rigid.html +++ b/doc/html/fix_rigid.html @@ -467,7 +467,7 @@ that dimension via the
+the units command).Tdamp parameter, determining the time scale on which pressure is relaxed. For example, a value of 10.0 means to relax the pressure in a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see -the units command). Regardless of what atoms are in the fix group (the only atoms which are time integrated), a global pressure or stress tensor is computed for all atoms. Similarly, when the size of the simulation box is @@ -532,7 +532,7 @@ run from Tstart to Tstop. The Tdamp parameter is spe time units and determines how rapidly the temperature is relaxed. For example, a value of 100.0 means to relax the temperature in a timespan of (roughly) 100 time units (tau or fmsec or psec - see the -units command). The random # seed must be a positive +units command). The random # seed must be a positive integer.
The way that Langevin thermostatting operates is explained on the fix langevin doc page. If you wish to simply viscously damp the rotational motion without thermostatting, you can set @@ -555,7 +555,7 @@ from Tstart to Tstop. The Tdamp parameter is specifi units and determines how rapidly the temperature is relaxed. For example, a value of 100.0 means to relax the temperature in a timespan of (roughly) 100 time units (tau or fmsec or psec - see the -units command).
+units command).Nose/Hoover chains are used in conjunction with this thermostat. The tparam keyword can optionally be used to change the chain settings used. Tchain is the number of thermostats in the Nose Hoover chain. diff --git a/doc/html/fix_temp_berendsen.html b/doc/html/fix_temp_berendsen.html index 3f4a5f9a88..ebbb13626c 100644 --- a/doc/html/fix_temp_berendsen.html +++ b/doc/html/fix_temp_berendsen.html @@ -168,7 +168,7 @@ run from Tstart to Tstop. The Tdamp parameter is spe time units and determines how rapidly the temperature is relaxed. For example, a value of 100.0 means to relax the temperature in a timespan of (roughly) 100 time units (tau or fmsec or psec - see the -units command).
+units command).Tstart can be specified as an equal-style variable. In this case, the Tstop setting is ignored. If the value is a variable, it should be specified as v_name, where name is the variable diff --git a/doc/html/fix_temp_csvr.html b/doc/html/fix_temp_csvr.html index f157f77c32..0d3874ecdd 100644 --- a/doc/html/fix_temp_csvr.html +++ b/doc/html/fix_temp_csvr.html @@ -183,7 +183,7 @@ run from Tstart to Tstop. The Tdamp parameter is spe time units and determines how rapidly the temperature is relaxed. For example, a value of 100.0 means to relax the temperature in a timespan of (roughly) 100 time units (tau or fmsec or psec - see the -units command).
+units command).Tstart can be specified as an equal-style variable. In this case, the Tstop setting is ignored. If the value is a variable, it should be specified as v_name, where name is the variable diff --git a/doc/html/fix_thermal_conductivity.html b/doc/html/fix_thermal_conductivity.html index 071608653d..2d0426f6fe 100644 --- a/doc/html/fix_thermal_conductivity.html +++ b/doc/html/fix_thermal_conductivity.html @@ -232,7 +232,7 @@ cummulative kinetic energy transferred between the bottom and middle of the simulation box (in the edim direction) is stored as a scalar quantity by this fix. This quantity is zeroed when the fix is defined and accumlates thereafter, once every N steps. The units of the -quantity are energy; see the units command for details. +quantity are energy; see the units command for details. The scalar value calculated by this fix is “intensive”.
No parameter of this fix can be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization.
diff --git a/doc/html/fix_viscous.html b/doc/html/fix_viscous.html index 00e6da04ee..af89e65c1d 100644 --- a/doc/html/fix_viscous.html +++ b/doc/html/fix_viscous.html @@ -174,7 +174,7 @@ times to adjust gamma for several atom types.Note
You should specify gamma in force/velocity units. This is not the same as mass/time units, at least for some of the LAMMPS -units options like “real” or “metal” that are not +units options like “real” or “metal” that are not self-consistent.
In a Brownian dynamics context, gamma = Kb T / D, where Kb = diff --git a/doc/html/fix_wall_piston.html b/doc/html/fix_wall_piston.html index 7146d85180..8ebde444af 100644 --- a/doc/html/fix_wall_piston.html +++ b/doc/html/fix_wall_piston.html @@ -195,7 +195,7 @@ wall/piston.
The units keyword determines the meaning of the distance units used to define a wall position, but only when a numeric constant is used.
A box value selects standard distance units as defined by the -units command, e.g. Angstroms for units = real or metal. +units command, e.g. Angstroms for units = real or metal. A lattice value means the distance units are in lattice spacings. The lattice command must have been previously used to define the lattice spacings.
diff --git a/doc/html/fix_wall_reflect.html b/doc/html/fix_wall_reflect.html index b74be31273..c103099fae 100644 --- a/doc/html/fix_wall_reflect.html +++ b/doc/html/fix_wall_reflect.html @@ -207,7 +207,7 @@ variable is used. It is not relevant when EDGE is used to specify a face position. In the variable case, the variable is assumed to produce a value compatible with the units setting you specify.A box value selects standard distance units as defined by the -units command, e.g. Angstroms for units = real or metal. +units command, e.g. Angstroms for units = real or metal. A lattice value means the distance units are in lattice spacings. The lattice command must have been previously used to define the lattice spacings.
diff --git a/doc/html/fix_wall_srd.html b/doc/html/fix_wall_srd.html index db9ceab4fa..c72f90b6bb 100644 --- a/doc/html/fix_wall_srd.html +++ b/doc/html/fix_wall_srd.html @@ -241,7 +241,7 @@ to define a wall position, but only when a numeric constant is used. It is not relevant when EDGE or a variable is used to specify a face position.A box value selects standard distance units as defined by the -units command, e.g. Angstroms for units = real or metal. +units command, e.g. Angstroms for units = real or metal. A lattice value means the distance units are in lattice spacings. The lattice command must have been previously used to define the lattice spacings.
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/lattice.html b/doc/html/lattice.html index c86217a804..636cba7437 100644 --- a/doc/html/lattice.html +++ b/doc/html/lattice.html @@ -214,7 +214,7 @@ be used by other commands as distance units. No additional keyword/value pairs can be specified for the none style. By default, a “lattice none 1.0” is defined, which means the lattice spacing is the same as one distance unit, as defined by the -units command.
+units command.Lattices of style sc, fcc, bcc, and diamond are 3d lattices that define a cubic unit cell with edge length = 1.0. This means a1 = 1 0 0, a2 = 0 1 0, and a3 = 0 0 1. Style hcp has a1 = 1 0 0, a2 = 0 @@ -252,7 +252,7 @@ simulation box.
scaled when mapping it into the simulation box. I.e. it determines a multiplicative factor to apply to the unit cell, to convert it to a lattice of the desired size and distance units in the simulation box. -The meaning of the scale argument depends on the units +The meaning of the scale argument depends on the units being used in your simulation.For all unit styles except lj, the scale argument is specified in the distance units defined by the unit style. For example, in real @@ -303,7 +303,7 @@ E.g. the regi
+units of mass/volume.Note
Though they are called lattice spacings, all the commands that have a “units lattice” option, simply use the 3 values as scale -factors on the distance units defined by the units +factors on the distance units defined by the units command. Thus if you do not like the lattice spacings computed by LAMMPS (e.g. for a non-orthogonal or rotated unit cell), you can define the 3 values to be whatever you wish, via the spacing option.
diff --git a/doc/html/mass.html b/doc/html/mass.html index 4a114e414e..b52482445a 100644 --- a/doc/html/mass.html +++ b/doc/html/mass.html @@ -148,7 +148,7 @@Description
Set the mass for all atoms of one or more atom types. Per-type mass values can also be set in the read_data data file -using the “Masses” keyword. See the units command for +using the “Masses” keyword. See the units command for what mass units to use.
The I index can be specified in one of two ways. An explicit numeric value can be used, as in the 1st example above. Or a wild-card diff --git a/doc/html/min_modify.html b/doc/html/min_modify.html index b611c15acb..5434586014 100644 --- a/doc/html/min_modify.html +++ b/doc/html/min_modify.html @@ -161,7 +161,7 @@ a particular search direction. The dmax parameter is how far any atom can move in a single line search in any dimension (x, y, or z). For the quickmin and fire minimization styles, the dmax setting is how far any atom can move in a single iteration (timestep). Thus a -value of 0.1 in real units means no atom will move +value of 0.1 in real units means no atom will move further than 0.1 Angstroms in a single outer iteration. This prevents highly overlapped atoms from being moved long distances (e.g. through another atom) due to large forces.
diff --git a/doc/html/molecule.html b/doc/html/molecule.html index ad70071851..5c395f38e7 100644 --- a/doc/html/molecule.html +++ b/doc/html/molecule.html @@ -359,7 +359,7 @@ support per-atom mass, as opposed to per-type mass. See the mass command for details. If this section is not included, the default mass for each atom is derived from its volume (see Diameters section) and a default density of 1.0, in -units of mass/volume.
Bonds section:
-
diff --git a/doc/html/neighbor.html b/doc/html/neighbor.html
index bd83c40781..d1c2630e8b 100644
--- a/doc/html/neighbor.html
+++ b/doc/html/neighbor.html
@@ -191,7 +191,7 @@ are printed to the screen and log file. See
- x,y,z = coordinates of atom (distance units)
- units +
- units
- atom style and atom_modify settings id, map, sort
- comm style and comm_modify settings mode, cutoff, vel
- timestep diff --git a/doc/html/region.html b/doc/html/region.html index 1429773e67..de04067047 100644 --- a/doc/html/region.html +++ b/doc/html/region.html @@ -330,7 +330,7 @@ with the vel keyword, the amplitude vector specified with the wiggle keyword, and the rotation point specified with the rotate keyword, since they each involve a distance metric.
diff --git a/doc/html/package.html b/doc/html/package.html index c736f2a56e..5f676a479c 100644 --- a/doc/html/package.html +++ b/doc/html/package.html @@ -366,7 +366,7 @@ cutoff, e.g. to allow for a smaller fraction of KSpace work with a long-range Coulombic solver because the GPU is faster at performing pairwise interactions, then it may be optimal to make the binsize smaller than the default. For example, with a -cutoff of 20*sigma in LJ units and a neighbor skin +cutoff of 20*sigma in LJ units and a neighbor skin distance of sigma, a binsize = 5.25*sigma can be more efficient than the default.The split keyword can be used for load balancing force calculations 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/pair_lcbop.html b/doc/html/pair_lcbop.html index fdfff24b22..7e2e82ff4a 100644 --- a/doc/html/pair_lcbop.html +++ b/doc/html/pair_lcbop.html @@ -189,7 +189,7 @@ the This pair potential requires the newton setting to be “on” for pair interactions.
The C.lcbop potential file provided with LAMMPS (see the potentials -directory) is parameterized for metal units. You can use +directory) is parameterized for metal units. You can use the LCBOP potential with any LAMMPS units, but you would need to create your own LCBOP potential file with coefficients listed in the appropriate units if your simulation doesn’t use “metal” units.
diff --git a/doc/html/pair_quip.html b/doc/html/pair_quip.html index 809b7af472..e2bae6d90b 100644 --- a/doc/html/pair_quip.html +++ b/doc/html/pair_quip.html @@ -188,7 +188,7 @@ script that reads a restart file.This pair style is part of the USER-QUIP package. It is only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info.
QUIP potentials are parametrized in electron-volts and Angstroms and -therefore should be used with LAMMPS metal units.
+therefore should be used with LAMMPS metal units.Related commands
diff --git a/doc/html/pair_reax.html b/doc/html/pair_reax.html index 441498d8bc..3093a0b62b 100644 --- a/doc/html/pair_reax.html +++ b/doc/html/pair_reax.html @@ -303,7 +303,7 @@ script that reads a restart file.Restrictions
The ReaxFF potential files provided with LAMMPS in the potentials -directory are parameterized for real units. You can use +directory are parameterized for real units. You can use the ReaxFF potential with any LAMMPS units, but you would need to create your own potential file with coefficients listed in the appropriate units if your simulation doesn’t use “real” units.
diff --git a/doc/html/pair_reax_c.html b/doc/html/pair_reax_c.html index 28ec735904..2019b8ecd1 100644 --- a/doc/html/pair_reax_c.html +++ b/doc/html/pair_reax_c.html @@ -367,7 +367,7 @@ script that reads a restart file.This pair style is part of the USER-REAXC package. It is only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info.
The ReaxFF potential files provided with LAMMPS in the potentials -directory are parameterized for real units. You can use +directory are parameterized for real units. You can use the ReaxFF potential with any LAMMPS units, but you would need to create your own potential file with coefficients listed in the appropriate units if your simulation doesn’t use “real” units.
diff --git a/doc/html/read_data.html b/doc/html/read_data.html index 0df3ff5d6b..6a15a6f1a2 100644 --- a/doc/html/read_data.html +++ b/doc/html/read_data.html @@ -711,7 +711,7 @@ of analysis.The units for these quantities depend on the unit style; see the -units command for details.
+units command for details.For 2d simulations specify z as 0.0, or a value within the zlo zhi setting in the data file header.
The atom-ID is used to identify the atom throughout the simulation and @@ -1249,7 +1249,7 @@ ervel = electron radial velocity (0 for fixed-core):ul
used after an Atoms section. This is because the Atoms section must have assigned a unique atom ID to each atom so that velocities can be assigned to them. -Vx, vy, vz, and ervel are in units of velocity. Lx, ly, +
Vx, vy, vz, and ervel are in units of velocity. Lx, ly, lz are in units of angular momentum (distance-velocity-mass). Wx, Wy, Wz are in units of angular velocity (radians/time).
For atom_style hybrid, following the 4 initial values (ID,vx,vy,vz), diff --git a/doc/html/read_restart.html b/doc/html/read_restart.html index c69218b4a7..c42c14766e 100644 --- a/doc/html/read_restart.html +++ b/doc/html/read_restart.html @@ -248,7 +248,7 @@ means these quantities do not need to be re-specified in the input script that reads the restart file, though you can redefine many of these settings after the restart file is read.
-
-
A box value selects standard distance units as defined by the -units command, e.g. Angstroms for units = real or metal. +units command, e.g. Angstroms for units = real or metal. A lattice value means the distance units are in lattice spacings. The lattice command must have been previously used to define the lattice spacings which are used as follows:
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,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:[301,495,513],afshar:406,after:[],afterrun:495,afterward:3,afterword:42,ag1:177,ag2:177,again:[6,11,12,16,17,65,152,158,164,172,202,206,232,249,299,355,370,381,433,434,482,484,485,487,489,494,501,503,513,516],against:[11,12,13,67,233,381,449,450],aggreg:[6,12,69,72,74,85,103,120,127,249,265,311,313,327,482,514],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:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,43,45,51,55,56,58,59,60,62,63,64,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,166,171,172,173,174,175,176,177,178,179,180,181,182,184,186,191,197,198,199,202,203,204,205,206,207,209,210,211,212,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,262,264,265,267,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,298,299,300,301,302,303,304,305,306,308,309,310,311,312,313,314,315,316,317,318,319,320,321,325,326,328,329,330,331,332,333,336,337,338,339,340,341,342,343,344,346,347,348,349,350,351,352,353,354,355,356,360,365,367,369,370,371,372,373,374,376,379,380,381,382,383,385,386,387,388,389,391,392,393,395,396,397,398,399,401,402,405,406,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,428,432,433,434,435,436,437,438,439,440,441,442,443,444,446,447,448,449,450,451,452,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,478,479,480,481,482,484,485,486,487,488,489,490,491,492,494,495,496,497,498,499,500,501,502,504,505,506,508,509,513,514,516,517,518],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:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,42,56,58,59,60,61,62,64,65,66,82,101,118,120,154,156,157,158,171,176,177,178,180,186,197,198,199,202,203,205,206,207,209,210,212,214,215,216,218,219,220,221,222,223,224,226,228,229,230,231,232,233,237,238,243,245,246,247,248,250,253,256,259,260,264,266,269,270,294,298,299,300,301,302,303,307,313,314,316,318,320,321,325,329,336,337,338,339,341,342,343,344,345,346,352,354,356,365,367,371,372,374,379,380,381,382,385,386,388,389,392,393,394,395,396,397,402,410,412,416,417,418,419,424,428,433,434,439,441,447,450,451,454,456,457,466,473,476,478,480,482,485,487,489,490,491,492,493,494,497,499,500,501,504,505,509,513,514],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:[6,8,12,29,41,76,96,130,176,177,178,201,202,205,218,229,251,256,257,261,266,268,303,313,316,318,322,326,327,336,340,341,347,350,352,374,377,378,379,381,402,405,416,419,422,424,428,436,449,450,469,487,490,497,498,513],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:[3,66,209,302,310,354,380,513],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],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,40,41,42,43,45,55,56,57,61,62,64,66,70,76,77,78,80,82,87,88,96,98,99,101,104,114,115,116,117,118,119,124,126,128,129,131,152,153,154,155,156,157,158,159,160,161,162,164,165,166,167,168,170,171,172,173,174,175,178,179,180,181,182,184,186,19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201,294,304,306,367,413,415,514],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],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:[486,517],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:[167,201,514],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:[372,513],coarsest:152,code:[],coeff:[3,7,8,12,21,22,33,45,51,184,185,186,191,355,356,362,399,419,423,441,454,456,459,487,515],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:[3,6,7,8,9,13,41,43,70,80,87,92,99,104,109,115,117,126,158,166,173,175,178,202,203,206,218,231,259,265,298,308,311,313,352,371,380,382,400,487,494,500,506,518],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:[3,6,9,12,13,43,66,69,70,71,72,74,76,80,82,85,87,88,90,99,101,103,104,115,117,118,120,122,125,126,127,128,129,131,152,153,158,166,173,175,176,177,198,202,203,206,209,217,218,219,221,222,223,224,259,266,267,303,313,330,331,341,351,414,418,449,450,488,502,504,513],columnar:176,colvar:[],colvarmodul:12,com:[],comamnd:232,comand:229,comannd:386,comb3:[],comb:[],comb_1:305,comb_2:305,combiant:403,combin:[3,6,7,9,11,13,36,41,66,69,74,85,96,103,114,120,127,156,157,171,202,205,215,221,250,259,269,296,302,317,333,342,350,353,355,371,372,374,378,386,400,402,403,408,412,413,419,431,432,458,468,470,472,473,475,478,490,495,500,508,513,515],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:[2,4,7,11,12,38,57,184,198,202,241,254,313,341,380,381,387,410,411,413,423,436,443,450,457,458,468,469,470,471,472,475,484,485,487,508,509,513],commerci:7,commit:[9,509],commmand:[3,6,12,62,119,291,422,481,482,484,501,517],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:[1,3,6,7,8,9,10,11,12,14,15,16,18,41,42,61,64,65,76,176,181,182,205,206,226,227,228,230,231,232,250,252,256,258,259,260,269,295,302,304,305,306,313,317,329,341,352,369,371,382,383,384,386,408,409,445,480,484,485,496,497,513,516,518],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],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:[3,5,7,8,9,11,12,13,17,18,42,76,129,131,189,202,207,211,217,218,219,221,222,223,224,226,295,307,333,336,343,346,349,371,386,420,439,441,469,484,485,513],compens:[6,227,228,311,382,412],compet:340,competit:372,compil:[3,7,8,9,12,13,14,15,16,17,18,19,176,202,204,205,207,250,340,372,386,439,487,488,492,513],compl:17,complain:[11,12,17],complement:436,complementari:[7,402,424],complet:[3,6,9,11,12,15,42,62,76,206,222,226,231,259,296,299,302,329,340,342,353,354,370,381,386,413,454,456,474,482,487,492,495,499,501,504,508,513],complex:[4,6,8,11,12,13,25,41,43,65,101,118,152,154,166,178,179,256,325,350,369,381,412,439,469,485,487,490,513],compli:[336,340],complic:[6,7,9,12,13,216,245,485],complier:12,compon:[3,6,8,12,64,66,70,71,78,87,88,97,98,99,100,101,104,105,108,113,115,116,117,118,119,120,121,122,124,125,129,139,142,143,144,145,148,149,150,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,174,175,201,202,203,205,206,212,213,217,218,219,220,221,222,223,224,225,229,230,232,233,238,243,248,252,253,256,259,261,265,266,268,269,270,274,275,276,277,288,289,290,292,293,295,296,297,300,311,313,315,316,318,322,323,326,329,332,333,334,336,343,344,349,350,351,371,374,378,379,380,381,386,406,412,416,433,434,454,456,457,458,487,488,497,505,513,514],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:[2,3,517],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:[16,372,513],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:[6,7,76,95,96,126,161,166,172,178,182,206,210,211,253,256,260,283,299,300,304,305,306,308,313,317,329,337,344,349,371,372,381,393,395,399,402,406,412,418,424,441,444,452,473,487,490,494,508,518],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:[6,75,76,83,96,127,160,163,164,181,202,203,206,210,211,217,219,222,226,228,229,233,257,270,295,313,336,337,340,341,344,372,399,412,419,450,451,457,466,482,483,485,488,489,490,492,495,497,505,508,513],consider:[6,8,253,254,332,333,334,386,496],consist:[3,6,8,9,11,12,41,43,69,74,85,103,115,120,123,124,127,158,161,163,178,190,201,207,212,213,218,232,233,236,238,243,246,253,254,255,266,269,271,272,273,274,275,276,277,278,279,281,282,283,284,286,287,288,289,290,291,292,300,303,308,310,312,313,332,333,334,335,345,371,372,374,380,381,386,388,392,394,400,402,412,415,419,422,433,434,436,439,441,451,454,456,457,469,476,485,487,488,489,490,491,492,499,508,513],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:[6,8,12,14,38,55,57,64,67,71,75,77,78,82,101,118,130,152,177,230,269,295,312,350,382,386,405,439,441,466,468,469,490,491,506,513],constructor:[8,11],consult:450,consum:[1,308,445,513],consumpt:369,contact:[],contact_stiff:[453,455],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,41,42,57,66,96,100,128,130,152,154,158,166,176,177,178,180,184,186,197,198,202,203,205,206,207,209,210,211,215,217,218,219,221,222,223,224,226,231,233,238,241,247,251,252,253,256,267,283,294,295,298,299,301,302,303,306,310,313,314,319,329,336,340,341,350,351,354,370,372,380,381,384,385,387,388,389,392,401,402,405,410,411,412,419,420,436,439,443,447,448,449,450,458,468,469,470,471,472,473,475,482,483,484,485,487,488,489,490,492,494,496,499,501,502,504,505,508,509,513,516,518],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],contibut:75,contigu:484,contin:16,continu:[0,2,3,5,6,9,12,13,14,42,76,88,114,115,174,206,209,210,211,216,218,219,220,221,222,223,224,226,229,230,231,232,233,245,246,247,249,250,251,253,254,255,261,266,267,269,271,272,273,274,275,276,277,288,289,290,291,292,297,299,302,303,313,314,318,328,329,331,338,339,341,347,350,354,370,385,386,392,406,409,426,429,449,450,451,454,456,471,482,485,487,489,490,495,501,502,504,505,513,516],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:[1,6,43,56,67,160,163,203,232,352,454,456,478,517],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:[6,12,29,202,207,224,314,374,458,473,509,513],convent:[3,8,29,189,196,197,203,206,312,326,353,410,412,513],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],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,62,66,76,100,178,185,202,205,206,219,224,267,299,302,352,355,357,361,364,374,381,387,410,439,470,472,479,485,487,488,489,494,504,508,513,516,518],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:[1,3,4,6,7,8,11,13,14,15,17,41,42,43,62,64,65,66,70,72,76,79,80,82,87,88,96,98,99,104,114,115,117,125,126,128,146,152,161,167,173,175,176,178,182,201,202,203,204,205,206,207,209,212,217,218,221,222,223,226,227,228,229,230,231,232,233,236,238,239,243,245,248,249,250,251,252,253,254,266,268,269,271,272,273,275,276,277,290,293,294,295,298,299,300,310,311,313,315,316,318,323,326,327,328,329,331,339,340,341,348,349,351,352,374,379,380,381,386,387,388,391,411,457,482,487,488,489,490,492,495,497,501,508,513,514],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:[3,8,11,17,76,88,113,114,115,155,156,157,159,161,163,164,165,166,167,170,171,174,202,206,212,233,238,243,254,263,269,270,306,313,316,326,328,347,350,381,382,386,404,434,439,484,485,487,497,509,514],correl:[],correpond:241,correspond:[1,2,4,6,8,9,10,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,41,43,44,45,46,47,48,49,50,52,54,55,57,75,76,96,107,108,121,124,125,126,127,130,131,139,142,143,144,145,146,148,149,150,152,155,156,165,172,176,177,184,185,186,187,188,189,190,192,193,195,196,198,201,202,203,205,206,210,211,212,218,220,221,222,223,225,228,230,232,239,243,244,248,253,256,257,265,266,267,269,271,272,273,274,275,276,277,278,279,283,286,288,289,290,292,295,296,300,305,313,315,316,332,334,336,345,346,347,349,350,351,353,355,356,357,358,360,361,364,366,372,376,378,380,381,387,388,390,393,394,395,396,397,398,399,400,401,402,405,406,410,411,412,413,414,415,416,417,418,419,422,424,425,426,427,428,429,430,431,432,433,436,437,439,441,442,443,444,446,447,449,450,451,452,457,458,459,468,469,470,471,472,473,475,477,478,479,482,484,485,487,488,490,500,501,502,504,505,508,513],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:[2,3,6,9,11,12,17,33,42,51,62,70,76,80,87,96,99,104,115,117,121,124,126,158,168,173,175,191,202,203,205,206,210,211,218,219,222,226,232,243,252,302,303,304,308,311,313,315,329,330,336,340,341,342,346,350,352,354,362,368,370,377,379,382,386,389,414,418,419,422,449,450,483,484,485,487,489,491,494,495,502,503,508,513,514],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],coulommb:6,cound:3,count:[1,3,6,8,11,12,16,42,66,72,82,100,126,128,129,166,176,182,212,213,216,218,221,222,223,225,226,233,238,242,245,251,269,283,299,316,332,333,350,372,379,380,381,383,386,414,418,441,505,513],counter:[3,347,482,493,495,501],counteract:245,counterbal:249,counterbalanc:29,counterpart:[202,313,482],counterproduct:18,coupl:[],courant:319,cours:[3,8,138,140,172,202,210,211,246,312,326,340,346,348,349,351,352,372,433,459,484,487,500,508,513,516],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:[1,3,9,10,12,14,15,16,17,18,66,76,206,220,236,254,342,369,372,386,399,467,482,500,501,504,505,506,513],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:[3,128,179,205,206,227,228,229,264,379,446,474,489,492,513],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:[3,12,22,76,98,156,176,186,202,203,205,217,222,228,232,266,268,290,313,322,326,328,337,344,356,374,381,397,406,409,410,417,418,419,424,426,428,447,452,454,456,470,472,479,487,491,497,516],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:[0,1,3,5,6,7,8,9,10,11,12,13,15,16,17,18,41,42,43,58,62,64,66,76,78,88,96,113,114,120,128,129,142,153,158,166,168,174,176,179,182,201,202,203,204,205,206,207,210,211,215,218,222,223,224,226,227,228,229,230,231,232,233,237,238,243,245,247,250,251,253,259,266,269,270,275,276,277,283,288,289,290,292,298,299,304,305,307,310,311,312,313,316,317,318,319,320,321,322,323,325,327,328,329,332,333,334,340,341,344,345,346,347,348,349,351,352,354,369,370,371,372,375,376,378,379,380,381,386,392,399,401,405,410,412,413,416,419,420,423,433,434,436,437,438,441,447,449,450,453,454,455,456,459,470,472,473,476,482,483,484,485,487,488,489,490,491,493,494,495,497,499,501,502,504,505,509,513,514,515,516,517,518],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:[3,6,8,10,16,18,40,46,47,55,56,64,75,77,78,82,96,101,118,120,127,128,152,176,179,181,182,228,229,234,241,294,303,304,306,308,310,313,317,329,342,346,350,352,369,371,372,379,382,383,384,386,387,388,389,390,391,392,393,394,395,396,397,398,400,402,403,404,405,406,407,408,409,410,411,412,413,414,415,417,418,419,420,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,449,450,451,452,457,458,459,460,461,462,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,485,489,492,496,508,513],cutoffa:411,cutoffc:411,cuu3:410,cval:177,cvd:336,cvel:318,cvff:[],cwiggl:[3,266,346,349,351,513],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:[0,4,6,12,13,201,449,450,513],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:[6,7,11,12,13,14,17,58,130,134,177,178,296,301,369,371,386,420,441,476,485,486,494,497,504,513],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],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],defint:505,deform:[],deg2theta:177,deg:508,degener:[3,298],degrad:[8,18,295,372,496],degre:[3,6,8,20,21,24,28,29,32,35,36,38,69,85,101,103,105,107,108,110,112,113,118,124,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,177,178,184,185,188,189,196,198,201,205,218,229,236,245,247,248,253,254,259,269,270,274,275,276,277,288,289,290,292,296,298,312,313,316,332,333,334,339,355,357,361,364,366,379,405,410,418,497,505,508,514],degress:[158,218],del:501,delai:[3,6,12,382,409,505],deleg:419,delet:[2,3,7,8,12,55,60,63,66,176,181,182,209,218,219,221,222,223,224,227,229,242,245,269,314,332,333,352,354,370,380,382,385,441,466,487,488,489,490,498,499,504,509,510,512,513,514],delete_atom:[],delete_bond:[],delete_el:215,deli:201,delimit:[485,513],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],density_continu:456,density_summ:456,depart:[0,7],departur:[267,303],deped:8,depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,44,45,46,47,48,49,50,52,54,55,57,64,66,69,72,74,75,76,85,101,103,114,120,121,124,125,126,127,131,152,154,155,161,165,166,172,178,179,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,205,206,209,210,211,212,213,216,218,220,221,222,224,225,226,228,230,232,238,239,244,247,248,249,251,253,254,256,258,259,266,269,271,272,273,274,275,276,277,278,279,286,288,289,290,292,294,305,308,310,313,315,316,317,323,329,332,333,334,336,338,340,341,343,345,346,349,350,351,352,354,355,356,357,358,360,361,364,366,372,374,379,380,382,383,384,386,387,388,390,391,392,393,394,395,396,397,398,399,400,401,402,403,405,406,410,411,412,413,414,415,416,417,418,419,424,425,426,427,428,429,430,431,432,433,436,437,439,440,442,443,444,446,447,449,450,451,452,457,458,459,467,468,469,470,471,472,473,475,477,478,479,482,484,487,489,490,493,497,499,501,504,505,507,513,514],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:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,40,41,42,43,57,65,66,72,75,76,78,97,122,125,128,130,142,152,153,156,157,158,162,163,166,169,171,172,176,177,178,180,181,190,195,198,202,203,204,209,210,211,218,219,220,221,222,223,224,226,229,230,231,232,233,235,236,241,246,247,250,251,252,253,254,255,256,258,259,260,264,268,269,270,274,282,291,294,296,301,302,303,304,305,306,313,318,326,329,330,331,332,333,334,335,336,337,338,339,344,346,347,349,354,371,372,374,377,378,379,380,381,385,388,389,391,393,394,395,397,398,399,400,401,402,405,410,412,413,415,416,417,419,422,424,425,426,427,428,429,430,431,432,433,434,435,436,439,440,446,447,448,449,450,451,452,457,458,459,466,467,468,469,470,471,472,473,475,477,478,479,480,482,484,485,487,488,489,490,491,497,500,501,504,509,513,514,516],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:[2,3,6,7,9,11,12,14,15,16,33,41,51,62,76,97,100,124,129,153,160,178,191,201,218,224,230,232,243,245,246,253,254,255,259,269,290,298,299,300,301,304,308,313,316,329,332,333,334,335,340,347,362,368,371,372,374,377,379,380,381,406,410,418,433,434,468,470,472,483,484,485,487,491,496,501,502,504,505,513,514,516],desk:7,desktop:[4,6,7,10,12,205],despit:508,destabil:392,destre:364,destroi:[9,11,40,227,228],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,41,42,43,56,66,70,71,72,76,80,83,87,99,100,104,113,115,117,119,121,123,124,126,129,131,152,153,155,156,157,158,161,171,172,173,175,178,179,182,183,186,197,201,202,203,205,206,209,210,211,215,218,219,220,221,222,224,226,228,229,230,231,232,233,243,245,246,247,248,250,251,253,255,256,260,266,267,268,269,270,271,272,273,274,275,276,277,281,283,288,289,290,291,292,295,298,299,300,302,303,305,306,307,313,316,317,329,332,333,334,335,336,337,339,340,341,342,343,344,345,352,354,356,365,371,372,375,379,380,382,383,386,387,388,389,391,392,394,396,397,398,399,400,401,402,405,406,412,413,415,416,417,418,419,424,425,426,427,428,429,430,431,432,433,434,435,436,440,441,446,449,450,451,457,458,459,467,474,477,478,480,485,487,488,489,490,492,493,496,497,499,502,505,506,509,513,514,518],detect:[2,3,12,43,64,66,95,101,244,299,340,381,401,418,423,482,484,487,498,501,513],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],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:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,18,22,37,38,40,42,43,55,56,57,64,67,72,75,76,96,101,105,107,108,132,152,154,155,156,157,158,159,161,164,165,166,167,168,170,171,172,178,179,181,186,197,198,201,202,205,206,209,211,214,216,218,221,226,227,228,229,230,231,232,236,241,244,245,246,247,248,249,250,253,254,256,266,269,270,271,272,273,275,276,277,279,281,284,286,287,288,289,292,294,296,298,300,303,304,305,308,311,313,316,318,326,327,329,332,333,334,337,338,339,341,344,345,346,347,350,354,355,365,368,370,371,372,374,375,377,378,380,381,383,384,385,386,387,388,392,396,397,399,400,401,406,407,408,410,412,415,416,4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87,509],donadio:333,done:[1,3,6,7,8,12,14,15,16,17,18,38,40,42,57,62,65,76,172,175,178,181,198,202,205,206,215,216,218,220,221,222,223,224,226,227,228,229,230,232,233,241,243,245,250,251,253,254,261,269,275,276,277,288,289,290,292,293,295,296,297,299,302,310,313,314,316,329,332,333,334,336,338,339,352,354,370,371,372,379,381,382,385,386,388,396,410,419,420,421,428,434,435,436,441,449,466,469,474,482,483,484,485,488,491,492,495,505,506,508,509,513,514],donor:418,dot:[153,174,212,238,248,268],doti:[392,447],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,40,96,232,243,301,350,354,370,372,385,386,392,413,417,439,449,450,483,487,491,495,500,513,514],dover:215,down:[3,6,7,8,11,40,76,230,245,253,329,345,386,412,441,457,486,506],downhil:[377,378],download:[5,7,8,9,11,12,13,17,250,420,448],downsid:6,downward:310,dozen:[8,9,12,119,209,449,450],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:262,dpdtheta:[41,89,90,408],dpdtheta_i:[240,241],dproduct:389,dr_ewald:[130,314],drag:[],dragforc:256,drai:[267,303],drain:[249,345,379],dramat:[9,62,201,227,228,229,230,232,269,329,332,333,372,386,441,457,484],drautz:392,draw:205,drawback:302,drawn:[43,202,205,206,246,482],drayleigh:[267,303],dreid:[],drfourth:116,drho:[125,387,410],drift:[6,114,116,246,247,253,254,265,311,329,496,504,508],drive:[11,12,213,230,232,248,269,294,300,313,348,381],driven:[6,190],driver:[6,12,14,15,209,243,250],drop:[3,206,406],droplet:419,drsquar:116,drude:[],dry:242,dsecriptor:420,dsf:[],dsmc:[],dstyle:299,dt_collis:256,dt_lb:256,dt_md:256,dt_srd:329,dtilt:[62,232],dtneb:501,dtqm:303,dtype:[127,228],dual:[16,17,329,386],dudarev:177,due:[1,3,6,9,12,16,17,19,41,55,58,60,61,64,70,75,76,79,80,87,88,95,97,98,99,104,113,114,115,116,117,122,128,130,138,152,153,155,156,157,159,161,164,165,166,167,168,170,171,173,177,178,181,182,202,203,205,209,212,213,221,225,227,228,229,230,231,232,233,238,239,242,243,246,247,250,251,253,254,255,256,259,260,261,265,266,267,268,269,274,283,294,297,299,311,312,313,315,326,328,329,330,332,333,334,335,336,338,339,341,345,346,348,349,350,352,372,377,379,381,382,383,403,406,407,408,410,414,415,419,433,434,441,447,449,451,452,466,469,470,472,476,478,479,482,484,487,488,489,496,501,504,505,506,508,513,514],duffi:341,duin:[9,304,309,449,450],duke:372,dummi:[12,29,471],dump0:203,dump10000:203,dump1:492,dump20000:203,dump2:492,dump2vtk_tri:146,dump:[],dump_0:203,dump_1:203,dump_atom:8,dump_custom:8,dump_h5md:204,dump_modifi:[],dump_p:203,dumpcustom:8,dumptimestep:492,dunbrack:[6,20,184,397,499],dunweg:[253,255],duplic:[2,3,14,15,17,42,43,179,203,226,247,294,487],dupont:[5,7,13],durat:[37,56,155,156,157,159,160,161,163,164,165,166,167,170,171,197,206,218,245,308,341,365,416,467],dure:[2,3,6,8,9,12,16,17,38,40,42,57,76,96,138,140,154,160,179,182,198,202,203,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,232,233,234,237,238,239,241,242,243,244,245,246,247,248,249,250,251,253,254,255,256,257,258,259,260,261,262,263,265,266,268,269,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,318,322,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,372,379,381,385,386,406,432,439,441,450,469,482,483,485,487,490,492,494,495,497,499,501,502,505,506,513,517,518],dvector:8,dvlo:478,dvx:6,dx_lb:256,dy3:177,dyamic:12,dyanam:6,dyanmic:501,dynam:[],dynamo:[5,387,410,436],dyne:[],dyre:429,dysam:490,e28637:29,e_1:392,e_2:392,e_b:413,e_data:203,e_e:412,e_hbond:418,e_i:[6,392,413],e_j:[6,392],e_k:[392,412],e_kl:6,e_lj:[388,405],e_n:[392,412],e_nn:412,e_pr:412,e_rebo:388,e_tors:388,e_tot:439,e_vol:439,eaa:355,eaat:185,each:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,42,43,44,46,47,48,49,50,51,52,54,55,56,57,58,60,62,64,65,66,67,68,70,71,72,73,75,76,77,78,79,80,81,82,83,84,86,87,88,90,92,94,96,98,99,101,102,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,121,122,123,124,125,126,127,128,129,130,131,132,146,152,153,154,156,157,158,159,160,161,162,165,166,167,168,170,171,172,173,174,175,176,177,178,181,182,184,185,186,187,188,189,190,191,192,193,195,196,197,198,201,202,203,204,205,206,207,208,209,210,211,212,213,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,265,266,267,268,269,271,272,273,274,275,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,294,295,296,297,298,299,300,301,302,304,305,306,308,310,313,314,315,316,317,318,322,323,325,326,327,328,329,330,331,332,333,334,336,339,340,341,342,343,344,345,346,347,349,350,351,352,354,355,357,358,359,360,361,362,364,365,366,370,371,372,374,378,379,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,413,4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5,494,518],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:[],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:[],esub:436,eta:[6,256,269,303,304,306,345,411,413,415,447,471,475],eta_dot:269,eta_ij:447,eta_ji:413,etag:[41,487],etail:505,etap:269,etap_dot:269,etc:[1,2,3,4,6,7,8,9,10,11,12,13,15,16,40,41,43,55,64,72,98,99,100,105,121,122,125,127,153,155,158,159,160,161,162,164,165,166,167,168,170,172,178,180,181,182,191,202,203,205,206,209,210,215,216,217,218,221,222,223,224,227,228,232,233,243,245,246,253,269,299,310,314,341,342,350,354,370,371,379,380,381,382,384,410,411,419,432,434,439,445,449,450,468,470,472,475,482,485,487,488,489,494,496,497,501,502,503,504,505,506,508,513,516,518],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:[2,3,9,11,12,38,57,76,96,97,100,119,129,131,152,154,158,168,176,178,201,202,203,205,206,210,211,212,213,215,217,218,219,220,221,222,223,224,225,232,238,246,248,249,251,252,253,254,295,301,304,315,319,323,332,333,334,343,346,349,351,352,354,371,372,377,379,386,439,441,447,453,455,457,469,482,483,485,489,490,492,494,495,496,497,501,503,505,513,514],evalut:[354,485],evan:[166,290],evanseck:[6,20,184,397,499],evapor:[],evaul:[8,379],evdwl:[119,154,449,450,505],even:[3,6,8,12,15,17,18,34,40,42,53,58,60,62,64,66,75,76,97,119,131,176,179,180,194,198,202,203,206,209,210,211,216,217,218,221,222,223,224,226,227,228,230,232,233,236,251,254,267,269,270,295,299,308,310,313,314,325,329,337,341,344,346,350,352,363,371,377,379,381,386,391,412,413,416,419,422,441,451,475,476,480,487,488,490,492,493,494,496,497,499,502,504,505,506,508,518],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:[0,1,2,3,6,8,9,11,12,15,16,40,42,76,77,100,125,131,140,166,181,202,203,204,205,206,207,209,210,211,212,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,232,233,237,242,243,245,247,249,250,251,256,257,265,269,270,274,293,294,295,299,300,301,302,303,304,305,306,308,310,311,313,314,316,318,329,331,332,333,334,335,336,337,340,341,342,343,344,352,354,370,372,381,382,383,386,406,409,419,432,449,450,457,463,481,482,483,487,489,491,492,494,495,496,501,502,503,505,509,513,518],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:[22,42,45,76,134,172,181,186,226,229,246,247,253,254,255,299,308,309,329,341,356,371,399,489,494,501,513,516,518],exactli:[3,6,12,14,17,38,42,43,57,62,76,77,100,128,156,162,169,178,198,210,211,221,226,232,237,241,246,253,254,255,270,282,283,291,295,302,303,329,334,335,348,386,399,406,410,416,419,433,441,469,489,490,497,501,513],exager:508,examin:[6,8,17,229,295],examp:[485,513],exampl:[],exce:[3,6,16,17,18,42,61,76,180,217,218,221,222,223,224,226,230,232,237,242,269,295,310,314,320,321,329,379,386,487,513],exceed:[3,42,62,226,232,269,329,495],excel:412,except:[1,2,5,6,8,10,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,41,42,44,45,46,47,48,49,50,52,54,55,56,57,62,63,66,76,98,99,120,121,124,129,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,178,182,184,185,186,187,188,189,190,192,193,195,196,197,198,201,202,203,206,209,212,218,219,221,225,226,230,232,239,244,245,248,251,253,255,269,270,271,272,273,274,275,276,277,278,279,282,283,286,288,289,290,291,292,296,305,306,313,315,316,326,329,332,334,335,341,345,349,352,353,354,355,356,357,358,360,361,364,365,366,371,372,374,376,380,381,382,384,385,386,387,388,390,393,394,395,396,397,398,399,400,401,402,404,405,406,410,411,412,413,414,415,416,417,418,419,424,425,426,427,428,429,430,431,432,433,434,437,442,443,444,446,449,450,451,452,459,467,468,469,470,471,472,473,475,477,478,479,482,484,485,487,489,490,492,495,496,497,498,499,501,505,508,513,514,517],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:[1,2,3,4,6,8,9,11,12,17,63,179,205,250,307,354,370,373,385,483,485,495,498,501,513],exempl:457,exemplari:246,exemplifi:412,exert:[6,251,254,308,348,349,350,372],exhaust:[215,385,513],exhibit:[101,269,378,412,496],exist:[3,6,7,8,11,12,13,16,37,56,58,62,72,75,134,178,179,197,204,205,206,209,214,225,228,230,233,245,298,299,301,302,352,353,355,357,358,359,361,365,375,380,386,407,408,419,449,466,476,483,485,487,488,489,498,499,500,509,513,514,516],exit:[2,3,11,12,42,60,202,226,241,370,385,485,486,495,504,513],exlanatori:3,exp:[],expand:[],expans:[12,152,202,498,513],expect:[1,3,8,12,13,14,15,16,17,18,19,42,43,76,113,159,170,176,198,226,238,245,247,266,294,300,302,303,308,313,352,372,382,399,436,439,441,482,485,487,489,492,496,501,513],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:[1,3,6,8,9,11,12,16,18,42,62,66,69,72,74,76,77,78,81,82,85,95,103,158,166,198,202,203,205,206,209,218,219,224,226,228,230,232,269,294,302,313,326,352,354,370,371,374,380,381,385,391,410,422,457,459,474,485,488,489,492,494,497,508,509,513,518],explan:[3,6,62,125,152,202,203,218,268,294,419,481,484,485,487,496],explanatori:[3,8,129,202,203,217,218,221,222,223,313,380,484,513],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:[96,447,468,475,479,501,513],expos:11,exposit:[215,406,409],express:[6,152,164,178,210,211,230,266,294,304,341,347,354,392,410,412,426,436,457,458,467,513],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],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:[3,6,8,11,12,16,17,41,42,47,64,76,113,121,122,124,130,153,155,156,157,159,161,164,165,166,167,168,170,171,177,178,179,180,184,206,221,226,228,269,301,302,303,313,329,379,380,383,384,405,416,419,422,436,441,484,485,487,490,499,508,513],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:513,f_harm:339,f_i:[29,447],f_id:[6,76,129,131,202,203,209,217,218,219,220,221,222,223,224,264,331,343,505,513],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],factori:[3,485],factoriz:371,fail:[3,9,11,12,62,182,230,233,371,379,381,404,450,485],failur:[133,454,486,513],fairli:[11,441,496,501,509],faken:78,falcon:250,fall:[3,6,206,221,299,485,513],fals:[95,352,354,457,513],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:[6,8,42,76,178,206,209,210,211,216,222,226,228,233,245,247,251,266,267,269,271,272,273,274,275,276,277,285,288,289,290,291,292,302,303,305,313,318,322,328,331,339,341,345,346,347,349,351,381,419,433,490,499,513,517],fasolino:421,fast:[6,7,9,12,13,17,40,202,203,280,303,342,371,372,394,433,434,439,467,469,489,494,496,505,514,518],faster:[1,6,9,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,41,42,44,46,47,48,49,50,52,54,55,57,64,66,116,121,124,155,165,184,185,187,188,189,190,192,193,195,196,198,202,203,206,212,225,226,232,239,244,248,252,253,269,271,272,273,274,275,276,277,278,279,286,288,289,290,292,300,304,305,313,315,316,329,332,334,336,338,341,345,349,355,357,358,360,361,364,366,371,372,383,384,386,387,388,390,392,393,394,395,396,397,398,399,400,401,402,405,406,410,411,413,414,415,416,417,418,419,424,425,426,427,428,429,430,431,432,433,437,442,443,444,446,451,452,459,467,468,469,470,471,472,473,475,477,478,479,482,490,496,500,508],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:[285,513],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:[],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:[1,3,4,5,6,7,9,10,11,12,13,14,18,40,66,207,217,218,219,221,222,223,224,254,269,299,302,304,316,343,371,379,380,381,388,457,484,487,492,496,498,506,516],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:[3,12,13,38,42,57,198,202,203,205,206,207,215,218,219,220,221,222,223,224,226,231,241,294,298,301,304,305,306,309,310,313,314,340,341,368,369,370,380,381,387,388,392,402,410,411,413,421,436,437,438,443,447,448,449,450,457,458,468,469,470,471,472,475,483,484,485,488,489,494,498,505,513,516,517,518],filennam:494,filep:[3,202,203,206,489,494,518],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:[0,3,4,6,7,8,9,11,12,13,14,16,38,40,57,64,76,78,96,129,181,198,207,216,229,230,241,242,245,268,294,299,300,308,312,377,379,381,382,402,419,424,428,436,457,467,469,508,509,513],find_custom:8,fine:[16,17,182,212,238,339,382,386,509,513],finer:[152,178,513],finest:371,finger:[178,201,266,490],finish:[6,11,42,226,354,368,370,371,383,385,386,474,492,513,514],finit:[],finni:[7,410,467],finvers:236,fiorin:[9,231],fire:[],firebrick:206,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,17,21,38,40,42,43,46,47,55,57,60,62,64,65,76,88,97,100,114,115,116,118,124,128,129,139,142,145,146,150,153,163,166,172,174,176,177,179,180,181,185,198,202,203,204,205,206,207,209,210,218,219,221,222,223,224,226,229,232,241,245,246,251,256,266,267,268,269,294,296,301,302,303,305,310,313,316,318,326,327,329,330,331,338,339,340,341,343,347,352,354,355,362,374,379,380,381,382,385,386,387,388,391,392,393,395,397,399,401,402,410,412,413,416,417,419,420,421,422,423,424,428,433,434,436,438,439,441,443,447,449,450,457,458,466,468,469,470,471,472,475,479,482,483,484,485,487,488,489,492,494,496,499,500,501,504,505,508,509,513,514,515,516,518],fischer:[6,9,19,20,184,397,499],fit:[3,6,9,12,38,57,198,241,312,329,388,392,421,436,441,462,469,471,495,509,513],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:[3,8,9,11,12,14,15,16,17,39,41,59,70,79,80,87,88,95,98,99,104,114,115,117,130,173,177,181,199,202,203,205,206,207,224,229,231,235,250,253,257,259,265,266,295,302,313,326,328,329,336,340,349,352,367,369,372,380,384,385,386,388,418,423,436,439,466,480,482,484,485,487,488,489,491,492,493,497,509,513],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:513,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:[2,206,253,254,266,269,300,313,332,333,496,507,514],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:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,44,46,47,48,49,50,52,54,55,57,62,66,67,75,76,78,89,100,101,107,108,118,125,128,129,131,152,153,156,157,158,164,166,171,174,176,178,179,184,187,188,189,190,192,193,195,196,198,202,204,205,206,209,215,216,217,218,219,220,221,222,223,224,226,231,232,233,236,237,240,241,243,245,246,247,250,252,253,254,256,259,267,269,274,275,276,277,288,289,290,292,295,296,298,301,302,303,304,306,308,310,312,313,314,316,331,332,333,334,337,338,339,340,341,343,344,352,353,357,358,359,360,361,364,366,369,374,376,379,380,381,386,387,388,389,390,391,392,393,394,395,396,397,398,400,401,402,403,404,405,406,407,408,409,410,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,442,443,444,446,447,448,449,450,451,452,454,456,457,458,459,460,461,462,463,464,465,466,468,469,470,471,472,473,474,475,477,478,479,480,482,484,485,487,488,490,492,494,495,496,499,501,502,503,508,509,513,514,517],foo:[4,8,11,12,202,205,243,485,498,513],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:[2,3,6,8,12,19,22,45,55,58,66,70,79,80,82,87,88,96,98,99,101,104,114,115,117,128,152,153,172,173,182,186,206,209,210,211,228,246,247,253,255,259,266,290,295,306,308,312,313,341,346,350,355,356,359,364,376,378,380,381,388,389,392,399,407,408,410,412,414,418,419,423,435,436,438,439,443,444,447,449,450,451,457,458,459,467,469,470,471,472,478,481,484,485,487,492,497,504,508,513],formal:[6,83,86,100,246,247,253,269,296,329,337,457],format:[2,3,6,7,8,9,12,13,22,38,42,45,57,58,72,82,186,198,202,203,204,205,206,207,218,221,222,223,224,226,228,241,295,298,302,304,306,309,313,314,325,340,341,352,353,356,376,380,381,387,388,392,399,410,413,423,436,438,448,449,450,452,458,469,475,476,484,485,487,488,489,492,503,504,505,513,515,516],former:[6,12,16,40,42,206,226,341,345,392,394,493,499,513],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],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:[3,6,8,105,107,108,110,112,113,124,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,218,229,236,245,247,253,254,259,269,270,274,275,276,277,288,289,290,292,296,298,313,316,332,333,334,339,379,405,505,508,514],freeli:[0,6,7,12,156,157,171,176,205],freez:[],frenkel:[245,339],freq:214,frequenc:[3,6,16,40,114,206,220,283,295,296,303,308,369,406,412,450,457,482,496,501,513,517],frequent:[3,67,71,75,77,78,82,97,101,118,152,206,227,228,242,337,344,441,473,494],fri:[267,303],friction:[4,5,6,9,1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],yate:439,yb2:177,yb3:177,ybox:232,ycm:313,year:[5,7],yeh:371,yellow:[205,206],yellowgreen:206,yet:[3,7,17,40,43,205,210,310,346,372,378,379,386,398,400,401,412,478,485,487,488,509,513,515,516,517],yflag:[165,166,257,259,265,313,336],yhi:[6,62,180,202,232,340,346,349,351,487,490,505],yhi_bound:[6,202],yield:[6,100,122,129,153,161,166,206,219,230,236,269,290,304,337,343,344,347,352,371,391,406,416,441,446,505,513],yip:338,ylat:[178,232,251,505],ylo:[6,62,180,202,232,340,346,349,351,487,490,505],ylo_bound:[6,202],ymax:[214,513],ymin:513,yorig:76,york:[296,372],yoshida:[269,313],you:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,33,35,38,40,41,42,43,44,46,47,48,49,50,51,52,54,55,57,60,61,62,64,66,68,70,72,73,76,77,78,79,80,82,84,87,88,89,90,96,97,98,99,100,101,102,104,113,114,115,117,118,119,121,122,124,126,128,129,152,153,155,156,157,158,161,165,166,171,172,173,174,175,176,178,179,180,181,182,184,185,186,187,188,189,190,191,192,193,195,196,197,198,201,202,203,205,206,207,209,210,211,212,213,216,217,218,219,221,222,223,224,225,226,227,228,229,230,232,233,236,238,239,241,242,243,244,245,246,247,248,249,250,251,253,254,255,264,266,269,271,272,273,274,275,276,277,278,279,283,285,286,288,289,290,291,292,295,296,298,299,300,302,304,305,308,311,312,313,315,316,318,326,328,329,330,332,333,334,335,337,338,339,340,341,343,344,345,346,347,349,350,351,352,354,355,357,358,360,361,362,364,366,370,371,372,374,376,378,379,380,381,382,385,386,387,388,390,392,393,394,395,396,397,398,399,400,401,402,405,406,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,436,437,438,439,441,442,443,444,445,446,447,448,449,450,451,452,457,458,459,460,461,462,463,464,465,466,468,469,470,471,472,473,475,477,478,479,481,482,483,484,485,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,504,505,506,508,509,513,514,515,516,518],young:[416,453,455],your:[],yourself:[6,8,12,13,230,380,509],yplane:347,ypo:178,ysu:[3,202,203,331,488],yuan:9,yukawa:[],yukawa_1_1:476,yxz:484,yzx:484,z_i:[412,472,479],z_j:[472,479],z_meam:436,zachari:13,zannoni:415,zbl:[],zblcut:472,zblcutinn:458,zblcutout:458,zblexpscal:472,zblz:458,zcm:313,zcylind:347,zepeda:216,zero:[],zeta:[3,256,304,413],zfactor:205,zflag:[165,166,257,259,265,313,336],zhang:[313,337,416],zhi:[3,6,180,202,214,340,346,349,351,487,490,505],zhi_bound:[6,202],zhou:[13,392,413,447,470,472],zhu:465,ziegenhain:13,ziegler:[298,436,467,472,479],zimmerman2004:215,zimmerman2010:215,zimmerman:[9,75,215,392],zlat:[232,251,505],zlib:[9,202],zlim:457,zlo:[3,6,180,202,214,340,346,348,349,351,487,490,505],zlo_bound:[6,202],zmax:[214,256,513],zmin:[256,513],zn2:177,zone:[130,314],zoom:[3,202,205,206],zorig:76,zplane:347,zr4:177,zrest:328,zsu:[3,202,203,331,488],zwall:346,zwall_veloc:256,zxy:484,zybin:450,zyx:484},titles:["LAMMPS 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","variable command","velocity command","write_coeff command","write_data command","write_dump command","write_restart command"],titleterms:{"break":227,"default":[37,40,41,56,60,61,62,64,65,76,96,97,101,113,114,116,118,119,130,134,135,152,158,166,167,171,177,178,181,183,197,200,201,202,203,205,206,207,208,210,211,212,214,215,216,218,222,223,224,227,228,230,231,232,233,237,242,245,246,251,253,254,255,256,257,259,264,267,269,270,274,290,291,295,296,299,300,301,302,303,305,308,310,311,313,314,329,331,336,337,338,339,342,344,346,348,352,365,369,371,372,374,375,377,378,380,382,383,384,386,389,392,394,412,433,434,439,441,449,450,466,467,482,483,484,487,488,490,492,494,495,496,499,501,503,504,505,506,507,514,516,517],"function":513,"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:[6,7,8,67,71,75,76,77,78,81,82,83,86,88,90,94,101,106,107,110,111,112,118,122,123,125,152,153,176,214,216,217,302,513],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],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:[6,337],conserv:407,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: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:[83,133],data2xmovi:13,data:6,databas:13,deby:[402,424],defgrad:139,deform:[161,162,232],delete_atom:181,delete_bond:182,delta:24,deposit:233,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,510,511,512,513,514,515,516,517,518],diagnost:7,diel:403,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:[6,9,29,87,405],direct:236,directori:4,discuss:6,disp:6,displac:[88,95],displace_atom:201,distanc:359,distribut:[7,12],document:0,dpd:[9,89,90,406,407,408],drag:234,dreid:[6,418],drude:[6,9,163,235,236,254],dsf:[402,424],dsmc:409,dump:[6,8,202,203,204,205,207],dump_modifi:206,dynam:304,eam:[13,410],echo:208,edip:411,eff:[9,13,107,108,162,164,169,255,270,282,291,335,412],efield:238,eim:413,elast:6,emac:13,energi:[135,408],enforce2d:239,ensembl:7,erot:[91,92,93,94],error:[3,134],evapor:242,event:95,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,325,326,327,328,329,330,331,332,333,334,335,336,337,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,500,501,502,503,504,505,506,507,510,511,512,513,514,515,516,517,518],exp:[27,187],expand:[47,427],extend:[8,11],extern:243,fcc:294,fdt:408,featur:[7,8,509,513],fene:[46,47],fep:[9,13,96,211],field:[6,7],file:6,finit:6,fire:304,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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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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\ No newline at end of file diff --git a/doc/html/thermo_style.html b/doc/html/thermo_style.html index 6b7762882e..f3c15b1f9d 100644 --- a/doc/html/thermo_style.html +++ b/doc/html/thermo_style.html @@ -325,8 +325,8 @@ keywords for the elapsed and elaplong are the same value.The dt keyword is the current timestep size in time -units. The time keyword is the current elapsed -simulation time, also in time units, which is simply +units. The time keyword is the current elapsed +simulation time, also in time units, which is simply (step*dt) if the timestep size has not changed and the timestep has not been reset. If the timestep has changed (e.g. via fix dt/reset) or the timestep has been reset (e.g. via the “reset_timestep” command), then the simulation time is effectively @@ -335,7 +335,7 @@ a cummulative value up to the current point.
run. The tpcpu and spcpu keywords are measures of how fast your simulation is currently running. The tpcpu keyword is simulation time per CPU second, where simulation time is in time -units. E.g. for metal units, the tpcpu value would be +units. E.g. for metal units, the tpcpu value would be picoseconds per CPU second. The spcpu keyword is the number of timesteps per CPU second. Both quantities are on-the-fly metrics, measured relative to the last time they were invoked. Thus if you are diff --git a/doc/html/timestep.html b/doc/html/timestep.html index fdd732fda4..259788b107 100644 --- a/doc/html/timestep.html +++ b/doc/html/timestep.html @@ -145,7 +145,7 @@Description
Set the timestep size for subsequent molecular dynamics simulations. -See the units command for the time units associated with +See the units command for the time units associated with each choice of units that LAMMPS supports.
The default value for the timestep size also depends on the choice of units for the simulation; see the default values below.
@@ -160,7 +160,7 @@ the outer loop (largest) timestep.Default
@@ -171,7 +171,7 @@ the outer loop (largest) timestep.- choice of units +choice of units time units default timestep size All temperatures specified in the velocity command are in temperature -units; see the units command. The units of velocities and +units; see the units command. The units of velocities and coordinates depend on whether the units keyword is set to box or lattice, as discussed below.
For all styles, no atoms are assigned z-component velocities if the @@ -316,7 +316,7 @@ zeroing of linear or angular momentum is then performed for each rigid body defined by the fix, as described above.
The units keyword is used by set and ramp. If units = box, the velocities and coordinates specified in the velocity command are -in the standard units described by the units command +in the standard units described by the units command (e.g. Angstroms/fmsec for real units). If units = lattice, velocities are in units of lattice spacings per time (e.g. spacings/fmsec) and coordinates are in lattice spacings. The lattice