diff --git a/doc/_sources/fix.txt b/doc/_sources/fix.txt index a96411f8c3..abcf0208ea 100644 --- a/doc/_sources/fix.txt +++ b/doc/_sources/fix.txt @@ -170,8 +170,10 @@ of :ref:`this page `. * :doc:`adapt ` - change a simulation parameter over time * :doc:`addforce ` - add a force to each atom * :doc:`append/atoms ` - append atoms to a running simulation +* :doc:`atom/swap ` - Monte Carlo atom type swapping * :doc:`aveforce ` - add an averaged force to each atom * :doc:`ave/atom ` - compute per-atom time-averaged quantities +* :doc:`ave/chunk ` - compute per-chunk time-averaged quantities * :doc:`ave/correlate ` - compute/output time correlations * :doc:`ave/histo ` - compute/output time-averaged histograms * :doc:`ave/spatial ` - compute/output time-averaged per-atom quantities by layer @@ -221,6 +223,7 @@ of :ref:`this page `. * :doc:`nvt/asphere ` - NVT for aspherical particles * :doc:`nvt/sllod ` - NVT for NEMD with SLLOD equations * :doc:`nvt/sphere ` - NVT for spherical particles +* :doc:`oneway ` - constrain particles on move in one direction * :doc:`orient/fcc ` - add grain boundary migration force * :doc:`planeforce ` - constrain atoms to move in a plane * :doc:`poems ` - constrain clusters of atoms to move as coupled rigid bodies @@ -228,7 +231,7 @@ of :ref:`this page `. * :doc:`press/berendsen ` - pressure control by Berendsen barostat * :doc:`print ` - print text and variables during a simulation * :doc:`property/atom ` - add customized per-atom values -* :doc:`qeq/comb ` - charge equilibration for COMB potential :doc:`qeq/dynamic ` - charge equilibration via dynamic method :doc:`qeq/point ` - charge equilibration via point method :doc:`qeq/shielded ` - charge equilibration via shielded method :doc:`qeq/slater ` - charge equilibration via Slater method :doc:`reax/bonds ` - write out ReaxFF bond information :doc:`recenter ` - constrain the center-of-mass position of a group of atoms +* :doc:`qeq/comb ` - charge equilibration for COMB potential :doc:`qeq/dynamic ` - charge equilibration via dynamic method :doc:`qeq/fire ` - charge equilibration via FIRE minimizer :doc:`qeq/point ` - charge equilibration via point method :doc:`qeq/shielded ` - charge equilibration via shielded method :doc:`qeq/slater ` - charge equilibration via Slater method :doc:`reax/bonds ` - write out ReaxFF bond information :doc:`recenter ` - constrain the center-of-mass position of a group of atoms * :doc:`restrain ` - constrain a bond, angle, dihedral * :doc:`rigid ` - constrain one or more clusters of atoms to move as a rigid body with NVE integration * :doc:`rigid/nph ` - constrain one or more clusters of atoms to move as a rigid body with NPH integration @@ -236,6 +239,10 @@ of :ref:`this page `. * :doc:`rigid/nve ` - constrain one or more clusters of atoms to move as a rigid body with alternate NVE integration * :doc:`rigid/nvt ` - constrain one or more clusters of atoms to move as a rigid body with NVT integration * :doc:`rigid/small ` - constrain many small clusters of atoms to move as a rigid body with NVE integration +* :doc:`rigid/small/nph ` - constrain many small clusters of atoms to move as a rigid body with NPH integration +* :doc:`rigid/small/npt ` - constrain many small clusters of atoms to move as a rigid body with NPT integration +* :doc:`rigid/small/nve ` - constrain many small clusters of atoms to move as a rigid body with alternate NVE integration +* :doc:`rigid/small/nvt ` - constrain many small clusters of atoms to move as a rigid body with NVT integration * :doc:`setforce ` - set the force on each atom * :doc:`shake ` - SHAKE constraints on bonds and/or angles * :doc:`spring ` - apply harmonic spring force to group of atoms @@ -245,7 +252,10 @@ of :ref:`this page `. * :doc:`store/force ` - store force on each atom * :doc:`store/state ` - store attributes for each atom * :doc:`temp/berendsen ` - temperature control by Berendsen thermostat +* :doc:`temp/csld ` - canonical sampling thermostat with Langevin dynamics +* :doc:`temp/csvr ` - canonical sampling thermostat with Hamiltonian dynamics * :doc:`temp/rescale ` - temperature control by velocity rescaling +* :doc:`tfmc ` - perform force-bias Monte Carlo with time-stamped method * :doc:`thermal/conductivity ` - Muller-Plathe kinetic energy exchange for thermal conductivity calculation * :doc:`tmd ` - guide a group of atoms to a new configuration * :doc:`ttm ` - two-temperature model for electronic/atomic coupling diff --git a/doc/_sources/pair_style.txt b/doc/_sources/pair_style.txt index e8f73e0b3f..0e2a1feb8c 100644 --- a/doc/_sources/pair_style.txt +++ b/doc/_sources/pair_style.txt @@ -155,11 +155,13 @@ in the pair section of :ref:`this page `. * :doc:`pair_style lj/class2 ` - COMPASS (class 2) force field with no Coulomb * :doc:`pair_style lj/class2/coul/cut ` - COMPASS with cutoff Coulomb * :doc:`pair_style lj/class2/coul/long ` - COMPASS with long-range Coulomb +* :doc:`pair_style lj/cubic ` - LJ with cubic after inflection point * :doc:`pair_style lj/cut ` - cutoff Lennard-Jones potential with no Coulomb * :doc:`pair_style lj/cut/coul/cut ` - LJ with cutoff Coulomb * :doc:`pair_style lj/cut/coul/debye ` - LJ with Debye screening added to Coulomb * :doc:`pair_style lj/cut/coul/dsf ` - LJ with Coulombics via damped shifted forces * :doc:`pair_style lj/cut/coul/long ` - LJ with long-range Coulombics +* :doc:`pair_style lj/cut/coul/long/cs ` - LJ with long-range Coulombics and core/shell * :doc:`pair_style lj/cut/coul/msm ` - LJ with long-range MSM Coulombics * :doc:`pair_style lj/cut/dipole/cut ` - point dipoles with cutoff * :doc:`pair_style lj/cut/dipole/long ` - point dipoles with long-range Ewald diff --git a/doc/_sources/run_style.txt b/doc/_sources/run_style.txt index f9a7dd5b36..c98db07afe 100644 --- a/doc/_sources/run_style.txt +++ b/doc/_sources/run_style.txt @@ -43,10 +43,10 @@ Syntax cut2 = outer cutoff between pair middle and pair outer (distance units) *outer* value = M M = which level (1-N) to compute pair outer forces in - *hybrid* values = M1 [M2 ...] (as many values as there are hybrid sub-styles + *hybrid* values = M1 M2 ... (as many values as there are hybrid sub-styles M1 = which level (1-N) to compute the first pair_style hybrid sub-style in M2 = which level (1-N) to compute the second pair_style hybrid sub-style in - ... + M3,etc *kspace* value = M M = which level (1-N) to compute kspace forces in @@ -185,15 +185,16 @@ with that pair style, meaning all pairwise forces are computed at the same rRESPA level. See the doc pages for individual pair styles for details.i -Another variant to use pair potentials in rRESPA is with the *hybrid* -keyword, which requires the use of a :doc:`hybrid pair_style ` -In this scenario, different sub-styles of the hybrid pair style are -evaluated at different rRESPA levels. Thus the hybrid keyword requires -as many level assignments as there are hybrid substyles which designate -the respective sub-styles to the rRESPA level according to their order -of definition in the pair_style command. Since the *hybrid* designates -pair force computations, it is mututally exclusive with either the *pair* -or the *inner*/*middle*/*outer* keywords. +Another option for using pair potentials with rRESPA is with the +*hybrid* keyword, which requires the use of the :doc:`pair_style hybrid or hybrid/overlay ` command. In this scenario, different +sub-styles of the hybrid pair style are evaluated at different rRESPA +levels. This can be useful, for example, to set different timesteps +for hybrid coarse-grained/all-atom models. The *hybrid* keyword +requires as many level assignments as there are hybrid substyles, +which assigns each sub-style to a rRESPA level, following their order +of definition in the pair_style command. Since the *hybrid* keyword +operates on pair style computations, it is mututally exclusive with +either the *pair* or the *inner*/*middle*/*outer* keywords. When using rRESPA (or for any MD simulation) care must be taken to choose a timestep size(s) that insures the Hamiltonian for the chosen diff --git a/doc/fix.html b/doc/fix.html index e27b486085..ebddae8661 100644 --- a/doc/fix.html +++ b/doc/fix.html @@ -276,8 +276,10 @@ of this p
  • adapt - change a simulation parameter over time
  • addforce - add a force to each atom
  • append/atoms - append atoms to a running simulation
    • +
  • atom/swap - Monte Carlo atom type swapping
  • aveforce - add an averaged force to each atom
  • ave/atom - compute per-atom time-averaged quantities
    • +
  • ave/chunk - compute per-chunk time-averaged quantities
  • ave/correlate - compute/output time correlations
  • ave/histo - compute/output time-averaged histograms
  • ave/spatial - compute/output time-averaged per-atom quantities by layer
    • @@ -327,6 +329,7 @@ of this p
  • nvt/asphere - NVT for aspherical particles
  • nvt/sllod - NVT for NEMD with SLLOD equations
  • nvt/sphere - NVT for spherical particles
    • +
  • oneway - constrain particles on move in one direction
  • orient/fcc - add grain boundary migration force
  • planeforce - constrain atoms to move in a plane
  • poems - constrain clusters of atoms to move as coupled rigid bodies
    • @@ -334,7 +337,7 @@ of this p
  • press/berendsen - pressure control by Berendsen barostat
  • print - print text and variables during a simulation
  • property/atom - add customized per-atom values
    • -
  • qeq/comb - charge equilibration for COMB potential qeq/dynamic - charge equilibration via dynamic method qeq/point - charge equilibration via point method qeq/shielded - charge equilibration via shielded method qeq/slater - charge equilibration via Slater method reax/bonds - write out ReaxFF bond information recenter - constrain the center-of-mass position of a group of atoms
    • +
  • qeq/comb - charge equilibration for COMB potential qeq/dynamic - charge equilibration via dynamic method qeq/fire - charge equilibration via FIRE minimizer qeq/point - charge equilibration via point method qeq/shielded - charge equilibration via shielded method qeq/slater - charge equilibration via Slater method reax/bonds - write out ReaxFF bond information recenter - constrain the center-of-mass position of a group of atoms
  • restrain - constrain a bond, angle, dihedral
  • rigid - constrain one or more clusters of atoms to move as a rigid body with NVE integration
  • rigid/nph - constrain one or more clusters of atoms to move as a rigid body with NPH integration
    • @@ -342,6 +345,10 @@ of this p
  • rigid/nve - constrain one or more clusters of atoms to move as a rigid body with alternate NVE integration
  • rigid/nvt - constrain one or more clusters of atoms to move as a rigid body with NVT integration
  • rigid/small - constrain many small clusters of atoms to move as a rigid body with NVE integration
    • +
  • rigid/small/nph - constrain many small clusters of atoms to move as a rigid body with NPH integration
    • +
  • rigid/small/npt - constrain many small clusters of atoms to move as a rigid body with NPT integration
    • +
  • rigid/small/nve - constrain many small clusters of atoms to move as a rigid body with alternate NVE integration
    • +
  • rigid/small/nvt - constrain many small clusters of atoms to move as a rigid body with NVT integration
  • setforce - set the force on each atom
  • shake - SHAKE constraints on bonds and/or angles
  • spring - apply harmonic spring force to group of atoms
    • @@ -351,7 +358,10 @@ of this p
  • store/force - store force on each atom
  • store/state - store attributes for each atom
  • temp/berendsen - temperature control by Berendsen thermostat
    • +
  • temp/csld - canonical sampling thermostat with Langevin dynamics
    • +
  • temp/csvr - canonical sampling thermostat with Hamiltonian dynamics
  • temp/rescale - temperature control by velocity rescaling
    • +
  • tfmc - perform force-bias Monte Carlo with time-stamped method
  • thermal/conductivity - Muller-Plathe kinetic energy exchange for thermal conductivity calculation
  • tmd - guide a group of atoms to a new configuration
  • ttm - two-temperature model for electronic/atomic coupling
    • diff --git a/doc/fix.txt b/doc/fix.txt index 8d7e55924f..d4018751f9 100644 --- a/doc/fix.txt +++ b/doc/fix.txt @@ -165,8 +165,10 @@ of "this page"_Section_commands.html#cmd_5. "adapt"_fix_adapt.html - change a simulation parameter over time "addforce"_fix_addforce.html - add a force to each atom "append/atoms"_fix_append_atoms.html - append atoms to a running simulation +"atom/swap"_fix_atom_swap.html - Monte Carlo atom type swapping "aveforce"_fix_aveforce.html - add an averaged force to each atom "ave/atom"_fix_ave_atom.html - compute per-atom time-averaged quantities +"ave/chunk"_fix_ave_chunk.html - compute per-chunk time-averaged quantities "ave/correlate"_fix_ave_correlate.html - compute/output time correlations "ave/histo"_fix_ave_histo.html - compute/output time-averaged histograms "ave/spatial"_fix_ave_spatial.html - compute/output time-averaged per-atom quantities by layer @@ -216,6 +218,7 @@ of "this page"_Section_commands.html#cmd_5. "nvt/asphere"_fix_nvt_asphere.html - NVT for aspherical particles "nvt/sllod"_fix_nvt_sllod.html - NVT for NEMD with SLLOD equations "nvt/sphere"_fix_nvt_sphere.html - NVT for spherical particles +"oneway"_fix_oneway.html - constrain particles on move in one direction "orient/fcc"_fix_orient_fcc.html - add grain boundary migration force "planeforce"_fix_planeforce.html - constrain atoms to move in a plane "poems"_fix_poems.html - constrain clusters of atoms to move \ @@ -227,6 +230,7 @@ of "this page"_Section_commands.html#cmd_5. "property/atom"_fix_property_atom.html - add customized per-atom values "qeq/comb"_fix_qeq_comb.html - charge equilibration for COMB potential \ "qeq/dynamic"_fix_qeq.html - charge equilibration via dynamic method \ +"qeq/fire"_fix_qeq.html - charge equilibration via FIRE minimizer \ "qeq/point"_fix_qeq.html - charge equilibration via point method \ "qeq/shielded"_fix_qeq.html - charge equilibration via shielded method \ "qeq/slater"_fix_qeq.html - charge equilibration via Slater method \ @@ -246,6 +250,14 @@ of "this page"_Section_commands.html#cmd_5. move as a rigid body with NVT integration "rigid/small"_fix_rigid.html - constrain many small clusters of atoms to \ move as a rigid body with NVE integration +"rigid/small/nph"_fix_rigid.html - constrain many small clusters of atoms to \ + move as a rigid body with NPH integration +"rigid/small/npt"_fix_rigid.html - constrain many small clusters of atoms to \ + move as a rigid body with NPT integration +"rigid/small/nve"_fix_rigid.html - constrain many small clusters of atoms to \ + move as a rigid body with alternate NVE integration +"rigid/small/nvt"_fix_rigid.html - constrain many small clusters of atoms to \ + move as a rigid body with NVT integration "setforce"_fix_setforce.html - set the force on each atom "shake"_fix_shake.html - SHAKE constraints on bonds and/or angles "spring"_fix_spring.html - apply harmonic spring force to group of atoms @@ -257,8 +269,11 @@ of "this page"_Section_commands.html#cmd_5. "store/state"_fix_store_state.html - store attributes for each atom "temp/berendsen"_fix_temp_berendsen.html - temperature control by \ Berendsen thermostat +"temp/csld"_fix_temp_csvr.html - canonical sampling thermostat with Langevin dynamics +"temp/csvr"_fix_temp_csvr.html - canonical sampling thermostat with Hamiltonian dynamics "temp/rescale"_fix_temp_rescale.html - temperature control by \ velocity rescaling +"tfmc"_fix_tfmc.html - perform force-bias Monte Carlo with time-stamped method "thermal/conductivity"_fix_thermal_conductivity.html - Muller-Plathe kinetic energy exchange for \ thermal conductivity calculation "tmd"_fix_tmd.html - guide a group of atoms to a new configuration diff --git a/doc/pair_style.html b/doc/pair_style.html index 150131edd0..6ac498a6e1 100644 --- a/doc/pair_style.html +++ b/doc/pair_style.html @@ -261,11 +261,13 @@ in the pair section of pair_style lj/class2 - COMPASS (class 2) force field with no Coulomb
  • pair_style lj/class2/coul/cut - COMPASS with cutoff Coulomb
  • pair_style lj/class2/coul/long - COMPASS with long-range Coulomb
    • +
  • pair_style lj/cubic - LJ with cubic after inflection point
  • pair_style lj/cut - cutoff Lennard-Jones potential with no Coulomb
  • pair_style lj/cut/coul/cut - LJ with cutoff Coulomb
  • pair_style lj/cut/coul/debye - LJ with Debye screening added to Coulomb
  • pair_style lj/cut/coul/dsf - LJ with Coulombics via damped shifted forces
  • pair_style lj/cut/coul/long - LJ with long-range Coulombics
    • +
  • pair_style lj/cut/coul/long/cs - LJ with long-range Coulombics and core/shell
  • pair_style lj/cut/coul/msm - LJ with long-range MSM Coulombics
  • pair_style lj/cut/dipole/cut - point dipoles with cutoff
  • pair_style lj/cut/dipole/long - point dipoles with long-range Ewald
    • diff --git a/doc/pair_style.txt b/doc/pair_style.txt index 1f26b4d522..622a71e8ae 100644 --- a/doc/pair_style.txt +++ b/doc/pair_style.txt @@ -152,11 +152,13 @@ in the pair section of "this page"_Section_commands.html#cmd_5. "pair_style lj/class2"_pair_class2.html - COMPASS (class 2) force field with no Coulomb "pair_style lj/class2/coul/cut"_pair_class2.html - COMPASS with cutoff Coulomb "pair_style lj/class2/coul/long"_pair_class2.html - COMPASS with long-range Coulomb +"pair_style lj/cubic"_pair_lj_cubic.html - LJ with cubic after inflection point "pair_style lj/cut"_pair_lj.html - cutoff Lennard-Jones potential with no Coulomb "pair_style lj/cut/coul/cut"_pair_lj.html - LJ with cutoff Coulomb "pair_style lj/cut/coul/debye"_pair_lj.html - LJ with Debye screening added to Coulomb "pair_style lj/cut/coul/dsf"_pair_lj.html - LJ with Coulombics via damped shifted forces "pair_style lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulombics +"pair_style lj/cut/coul/long/cs"_pair_lj.html - LJ with long-range Coulombics and core/shell "pair_style lj/cut/coul/msm"_pair_lj.html - LJ with long-range MSM Coulombics "pair_style lj/cut/dipole/cut"_pair_dipole.html - point dipoles with cutoff "pair_style lj/cut/dipole/long"_pair_dipole.html - point dipoles with long-range Ewald diff --git a/doc/run_style.html b/doc/run_style.html index a52c24009b..53bb4b1ce3 100644 --- a/doc/run_style.html +++ b/doc/run_style.html @@ -165,10 +165,10 @@ cut2 = outer cutoff between pair middle and pair outer (distance units) outer value = M M = which level (1-N) to compute pair outer forces in - hybrid values = M1 [M2 ...] (as many values as there are hybrid sub-styles + hybrid values = M1 M2 ... (as many values as there are hybrid sub-styles M1 = which level (1-N) to compute the first pair_style hybrid sub-style in M2 = which level (1-N) to compute the second pair_style hybrid sub-style in - ... + M3,etc kspace value = M M = which level (1-N) to compute kspace forces in @@ -280,15 +280,16 @@ and outer keywords. If not, only the pair keyword can be used with that pair style, meaning all pairwise forces are computed at the same rRESPA level. See the doc pages for individual pair styles for details.i

    -

    Another variant to use pair potentials in rRESPA is with the hybrid -keyword, which requires the use of a hybrid pair_style -In this scenario, different sub-styles of the hybrid pair style are -evaluated at different rRESPA levels. Thus the hybrid keyword requires -as many level assignments as there are hybrid substyles which designate -the respective sub-styles to the rRESPA level according to their order -of definition in the pair_style command. Since the hybrid designates -pair force computations, it is mututally exclusive with either the pair -or the inner/middle/outer keywords.

    +

    Another option for using pair potentials with rRESPA is with the +hybrid keyword, which requires the use of the pair_style hybrid or hybrid/overlay command. In this scenario, different +sub-styles of the hybrid pair style are evaluated at different rRESPA +levels. This can be useful, for example, to set different timesteps +for hybrid coarse-grained/all-atom models. The hybrid keyword +requires as many level assignments as there are hybrid substyles, +which assigns each sub-style to a rRESPA level, following their order +of definition in the pair_style command. Since the hybrid keyword +operates on pair style computations, it is mututally exclusive with +either the pair or the inner/middle/outer keywords.

    When using rRESPA (or for any MD simulation) care must be taken to choose a timestep size(s) that insures the Hamiltonian for the chosen ensemble is conserved. For the constant NVE ensemble, total energy diff --git a/doc/run_style.txt b/doc/run_style.txt index 36bd6e3c50..9fc2465203 100644 --- a/doc/run_style.txt +++ b/doc/run_style.txt @@ -43,10 +43,10 @@ style = {verlet} or {verlet/split} or {respa} or {respa/omp} :ulb,l cut2 = outer cutoff between pair middle and pair outer (distance units) {outer} value = M M = which level (1-N) to compute pair outer forces in - {hybrid} values = M1 \[M2 ...\] (as many values as there are hybrid sub-styles + {hybrid} values = M1 M2 ... (as many values as there are hybrid sub-styles M1 = which level (1-N) to compute the first pair_style hybrid sub-style in M2 = which level (1-N) to compute the second pair_style hybrid sub-style in - ... + M3,etc {kspace} value = M M = which level (1-N) to compute kspace forces in :pre :ule @@ -170,15 +170,17 @@ with that pair style, meaning all pairwise forces are computed at the same rRESPA level. See the doc pages for individual pair styles for details.i -Another variant to use pair potentials in rRESPA is with the {hybrid} -keyword, which requires the use of a "hybrid pair_style"_pair_hybrid.html -In this scenario, different sub-styles of the hybrid pair style are -evaluated at different rRESPA levels. Thus the hybrid keyword requires -as many level assignments as there are hybrid substyles which designate -the respective sub-styles to the rRESPA level according to their order -of definition in the pair_style command. Since the {hybrid} designates -pair force computations, it is mututally exclusive with either the {pair} -or the {inner}/{middle}/{outer} keywords. +Another option for using pair potentials with rRESPA is with the +{hybrid} keyword, which requires the use of the "pair_style hybrid or +hybrid/overlay"_pair_hybrid.html command. In this scenario, different +sub-styles of the hybrid pair style are evaluated at different rRESPA +levels. This can be useful, for example, to set different timesteps +for hybrid coarse-grained/all-atom models. The {hybrid} keyword +requires as many level assignments as there are hybrid substyles, +which assigns each sub-style to a rRESPA level, following their order +of definition in the pair_style command. Since the {hybrid} keyword +operates on pair style computations, it is mututally exclusive with +either the {pair} or the {inner}/{middle}/{outer} keywords. When using rRESPA (or for any MD simulation) care must be taken to choose a timestep size(s) that insures the Hamiltonian for the chosen diff --git a/doc/searchindex.js b/doc/searchindex.js index bc676e11ff..86b36d7b53 100644 --- a/doc/searchindex.js +++ b/doc/searchindex.js @@ -1 +1 @@ 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hics_processing_unit:14,compass:[7,21,22,37,43,44,55,177,178,189,345,346,355,388,457],compat:[3,5,7,8,9,11,12,13,17,18,41,71,121,123,181,193,197,201,207,208,209,211,212,213,214,216,285,297,323,326,333,336,339,360,375,410,429,431,459,473,474,502],compens:[6,217,218,301,371,402],compet:330,competit:361,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,168,193,194,195,197,240,330,361,375,429,476,477,481,502],compl:17,complain:[12,17],complement:426,complementari:[7,392,414],complet:[3,6,9,11,12,15,41,59,71,196,212,216,221,249,286,289,292,319,330,332,344,359,370,375,403,444,446,464,471,476,481,484,488,490,493,497,502],complex:[6,8,11,12,13,25,40,42,62,94,110,144,146,158,170,171,246,315,340,358,370,402,429,459,474,476,479,502],compli:[326,330],complic:[6,7,9,12,13,206,235,474],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,90,91,92,93,94,96,97,100,107,108,109,110,111,112,113,114,116,117,121,131,134,135,136,137,140,141,142,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,165,166,167,192,193,195,196,202,203,207,208,209,210,211,212,213,214,215,219,220,222,223,228,233,238,242,243,246,249,251,255,256,258,259,260,264,265,266,267,278,279,280,282,283,285,286,287,290,301,303,305,306,308,312,313,316,319,322,323,324,326,333,334,339,340,341,360,363,367,368,369,370,375,381,396,402,406,423,424,444,446,447,448,476,477,486,494,502,503],componenet:6,composit:[6,206,246,400],compound:[391,402,403,465],compres:[71,118,208],compress:[],compris:[40,340,441,464],compton:[122,169],comptu:3,compuat:361,comput:[],computation:[3,6,217,218,331,382],computational:497,compute_arrai:8,compute_fep:[201,422],compute_group_group:235,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[122,304],compute_scalar:8,compute_temp:8,compute_ti:201,compute_vector:8,compute_xrd:169,concaten:[2,3,505],concav:340,concentr:[71,400],concept:[6,150,160,208,485],conceptu:[3,6,71,158,220,222,370,392,409,426,481],concern:[6,73,89,194,236],concetr:71,concis:[11,330],conclud:12,concret:8,concurr:[9,16,361,502],conden:[331,460,462],condens:[6,152,331,377,394,400,414,465],condit:[],conducit:6,conduct:[],cone:479,confer:429,confid:[3,490],config:[12,193,473],configfil:221,configur:[1,2,6,12,15,17,38,59,126,172,190,192,193,195,199,220,221,222,223,227,235,242,243,273,286,294,330,358,368,370,377,382,401,426,429,458,460,462,465,471,476,478,479,490],confin:[476,490],conflict:[3,12,40,431,474],conform:[3,6,13,59,219,220,258,302,308,330,354,370,402,488],confus:[3,465],conjuct:396,conjug:[7,8,243,367,402,439,440],conjunct:[6,7,71,88,89,118,153,158,164,170,174,196,200,201,243,246,250,273,289,290,294,295,296,298,303,307,319,327,334,339,360,361,370,383,385,389,392,396,402,408,414,431,434,442,463,476,479,483,497,506],connect:[3,6,89,155,173,219,240,288,303,306,316,370,393,406,456,462,473,474,480,497],conput:3,consecut:[3,11,12,39,71,170,196,200,201,223,240,241,392,414,418,471,477,479],consequ:[1,6,206,331,413,490],conserv:[],consid:[6,9,70,71,78,89,119,152,155,156,173,193,196,200,201,207,209,212,216,218,219,223,247,260,285,303,326,327,330,331,334,361,389,402,409,440,441,447,456,471,472,474,477,478,479,481,484,486,494,497,502],consider:[6,8,243,244,322,323,324,375,485],consist:[3,6,8,9,11,12,40,42,65,69,79,95,107,112,115,116,119,150,153,155,170,182,192,197,202,203,208,222,223,226,228,233,236,243,244,245,256,259,261,262,263,264,265,266,267,268,269,271,272,273,274,276,277,278,279,280,281,282,290,293,298,300,302,303,322,323,324,325,335,360,361,363,369,370,375,377,382,384,390,392,402,405,409,412,423,424,426,429,431,441,444,446,447,459,466,474,476,477,478,479,480,481,488,497,502],consistent_fe_initi:205,consit:303,constant:[],constitu:[3,6,249,303,336,340,390,441],constitut:[444,446],constrain:[3,6,8,147,148,149,150,151,153,156,157,158,159,160,162,163,199,208,223,235,236,241,249,253,288,289,301,303,306,317,327,334,368,369,402,481,488,497],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,94,110,122,144,169,220,259,285,302,340,371,375,395,429,431,456,458,459,479,480,495,502],constructor:[8,11],consult:440,consum:[1,298,435,502],consumpt:358,contact:[],contact_stiff:[443,445],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,89,93,120,122,144,150,158,168,169,170,172,176,178,189,190,193,195,196,197,199,200,201,205,207,208,209,211,212,213,214,216,221,223,228,231,237,241,242,243,246,257,273,284,285,288,289,291,293,296,300,303,304,309,319,326,330,331,340,341,344,359,361,369,370,373,374,376,377,378,382,391,392,395,400,401,402,409,410,426,429,433,437,438,439,440,448,458,459,460,461,462,463,465,471,472,473,474,476,477,478,479,481,483,485,488,490,491,493,494,497,502,504,506],content:[12,18,440,492,494],context:[3,6,8,12,17,120,121,196,217,218,223,288,300,335,367,468,476,483,492,501,502,503],contibut:70,contigu:473,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,106,107,166,196,199,200,201,206,208,209,210,211,212,213,214,216,219,220,221,222,223,235,236,237,239,240,241,243,244,245,251,256,257,259,261,262,263,264,265,266,267,278,279,280,281,282,287,289,292,293,303,304,308,318,319,321,328,329,331,337,340,344,359,374,375,382,396,399,416,419,439,440,441,444,446,461,471,474,476,478,479,484,490,491,493,494,502,504],continuum:[6,7,9,205,331,444,446],contour_integr:205,contract:[59,220,222,259,290,303],contradictori:3,contrain:306,contraint:273,contrari:[237,244],contrast:[1,6,42,55,64,152,155,222,342,444,446,468,505],contrib:331,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,86,89,90,91,92,93,96,105,107,109,111,112,113,114,116,118,121,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,201,206,207,208,209,211,212,213,214,220,235,243,246,249,250,254,260,280,281,288,289,297,300,303,304,306,333,360,368,370,378,396,399,400,402,409,423,424,429,431,439,440,447,488,494,497],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,89,93,126,144,179,193,195,199,205,206,216,220,221,222,239,240,243,244,259,261,262,263,264,265,266,267,290,295,303,310,311,322,323,324,331,335,358,360,372,402,405,429,439,440,443,445,458,462,471,473,485,491,492],control_typ:205,controlfil:440,convect:93,conveni:[6,12,29,193,197,214,304,363,448,502],convent:[3,8,9,29,181,188,189,196,302,316,343,400,402,502],converg:[3,6,41,90,193,195,197,202,216,219,220,228,233,264,293,295,298,302,306,366,367,368,370,391,392,414,447,471,483,490],convers:[3,8,144,195,196,206,209,290,360,392,393,394,402,414,418,422,434,474,490,501],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,93,170,177,193,195,196,214,257,289,342,345,347,351,354,363,370,376,400,429,460,462,469,474,476,477,478,483,493,497,501,502,504,506],convex:[42,340,381],convinc:[7,12],cook:9,cooki:7,cool:[7,160,239,301],cooordin:193,cooper:[5,7],coord123:118,coord1:[3,118,208,212,213],coord2:[3,118,208,212,213],coord3:[3,118,208,212,213],coord:[],coordb:447,coordbb:447,coordiat:368,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,89,91,92,96,106,107,109,117,118,120,138,144,153,159,165,167,168,170,174,192,193,194,195,196,197,199,202,207,208,211,212,213,216,217,218,219,220,221,222,223,226,228,229,233,235,238,239,240,241,242,243,244,256,258,259,261,262,263,265,266,267,280,283,284,285,288,289,290,300,301,303,305,306,308,313,316,317,318,319,321,329,330,331,338,339,341,342,363,368,369,370,375,376,377,380,381,401,447,471,476,477,478,479,481,484,486,490,497,502,503],coordn:[118,208],coorind:[],copi:[0,3,4,8,11,12,15,17,40,123,195,331,370,389,439,474],copper:469,coproccesor:16,coprocessor:[1,4,7,9,16,17,375,489],coproprocessor:17,copy_arrai:8,copyright:[7,8,288],coral:196,core:[],core_shel:152,coreshel:[6,9,385,392,394],cornel:[6,176,488],corner123i:117,corner123x:117,corner123z:117,corner1i:117,corner1x:117,corner1z:117,corner2i:117,corner2x:117,corner2z:117,corner3i:117,corner3x:117,corner3z:117,corner:[3,6,40,117,195,340,341,363,464,476],cornflowerblu:196,cornsilk:196,corp:9,corpor:16,corr:391,correct:[3,6,9,11,12,16,17,59,89,90,105,106,114,120,152,157,164,195,222,235,237,243,259,260,280,288,290,293,330,336,340,360,370,376,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,395,396,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,464,465,467,468,469,476,491,494,497],correction_max_iter:205,correctli:[3,8,9,11,17,71,81,105,106,107,147,148,149,151,153,155,156,157,158,159,162,163,166,193,196,202,223,228,233,244,253,259,260,296,303,306,316,318,337,340,370,371,375,394,424,429,473,474,476,486,501,503],correl:[],correpond:231,correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,44,45,46,47,48,49,51,53,54,56,70,71,89,99,100,113,116,117,118,119,122,123,131,134,135,136,137,138,140,141,142,144,147,148,157,164,168,169,176,177,178,179,180,181,182,184,185,187,188,190,192,193,195,196,200,201,202,208,210,211,212,213,215,218,220,222,229,233,234,238,243,246,247,255,256,257,259,261,262,263,264,265,266,267,268,269,273,276,278,279,280,282,285,286,290,295,303,305,306,322,324,326,335,336,337,339,340,341,343,345,346,347,348,350,351,354,356,361,365,367,369,370,376,377,379,383,384,385,386,387,388,389,390,391,392,395,396,400,401,402,403,404,405,406,407,408,409,412,414,415,416,417,418,419,420,421,422,423,426,427,429,431,432,433,434,436,437,439,440,441,442,447,448,449,458,459,460,461,462,465,467,468,469,471,473,474,476,477,479,489,490,491,493,494,497,502],correspondingli:[423,424,485],cosin:[],cosineshift:27,cosmo:[237,242],cossq:[],cost:[1,6,10,11,12,17,39,41,71,113,122,145,169,195,196,208,212,213,216,217,218,232,259,295,331,360,361,373,392,414,418,429,431,458,473,485],costheta0:[458,460,462,465],costheta:437,costli:[11,90,237,371],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,89,92,96,107,109,113,116,118,150,160,165,167,183,193,195,196,200,201,208,209,212,216,222,233,242,292,293,294,298,301,303,305,319,320,326,330,331,332,336,340,342,344,352,357,359,366,368,371,375,378,404,408,409,412,439,440,472,473,474,476,478,480,483,484,491,492,497,502,503],coulomb:[3,5,6,7,8,9,10,12,14,15,18,72,90,111,112,120,145,171,175,294,296,332,360,361,368,375,383,385,386,387,388,391,392,393,394,395,402,406,407,409,414,418,422,425,431,434,439,440,442,447,457,462,463,465,468,481,488,494,497,501],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,93,118,120,121,158,168,174,202,203,206,208,211,212,213,215,216,223,228,232,235,241,259,273,289,306,322,323,340,361,368,369,370,372,375,404,408,431,494,502],counter:[337,471,482,484,490],counteract:235,counterbal:239,counterbalanc:29,counterpart:[193,303,471],counterproduct:18,coupl:[],courant:309,cours:[3,8,130,132,164,193,200,201,236,302,316,330,336,338,339,341,342,361,423,449,473,476,489,497,502,504],courtesi:363,cov:447,coval:[6,29,402,426,447,497],covari:237,cover:[6,71,190,196,205,246,402,464],coverag:[71,212],cpc:242,cpp:[1,3,6,8,9,11,12,13,89,193,200,201,233,306],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,196,210,226,244,332,358,361,375,389,457,471,489,490,493,494,495,502],cpuremain:494,cr2:169,cr3:169,crack:[4,371],crada:[5,7],crai:[5,7,13,18,193],crash:[3,12,371,497],craympi:375,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:205,create_faceset:205,create_group:194,create_nodeset:205,createatom:[],creation:[],crimson:196,critchlei:288,criteria:[3,120,171,195,196,217,218,219,254,368,436,464,478,481,502],criterion:[12,41,125,170,173,206,216,219,235,273,295,309,337,342,368,370,391,402,406,447,481,490,491],criterioni:490,critic:[6,48,49,257,326,331,368],crmax:71,crmin:71,cross:[3,12,22,71,91,148,168,178,193,195,207,212,218,222,256,258,280,303,312,316,318,327,334,346,363,370,387,396,399,400,407,408,409,414,416,418,437,442,444,446,460,462,469,476,480,486,504],crossov:1,crossterm:476,crozier:[0,7,13],crucial:293,crystal:[4,6,13,73,110,284,285,329,363,371,480,494,497],crystallin:[6,106,285,363,461,497],crystallis:326,crystallogr:[122,169],crystallograph:[363,494],crystallographi:[122,169,363],cs1:169,cs_chunk:6,cs_im:[40,476],cs_re:[40,476],csanyi:[144,438,448],cscl:426,csequ:6,csh:[11,12,389],cshrc:[11,12],csic:[401,458,460,462,465],csinfo:6,csisi:[401,458,460,462,465],csld:[],cst:400,cstherm:6,cstyle:473,csvr:[],ctcm:[376,400],ctemp_cor:226,cterm:308,ctr:9,ctype:11,cu1:169,cu2:169,cu3au:426,cube:[6,41,168,173,216,226,340,363,497],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:382,cummul:[3,6,214,217,218,219,221,232,237,243,245,319,322,323,324,325,327,334,408,494],cumul:[6,206,208,211,212,213,227,235,243,257,259,264,273,303,304,370],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,89,105,106,112,120,121,134,145,150,158,160,166,168,171,174,192,193,194,195,196,197,200,201,205,208,212,213,214,216,217,218,219,220,221,222,223,227,228,233,235,237,240,241,243,249,256,259,260,265,266,267,273,278,279,280,282,288,289,294,295,297,300,301,302,303,306,307,308,309,310,311,312,313,315,317,318,319,322,323,324,330,331,334,335,336,337,338,339,341,342,344,358,359,360,361,364,365,367,368,369,370,375,381,382,389,391,395,400,402,403,406,409,410,413,423,424,426,427,428,431,437,439,440,443,444,445,446,449,460,462,463,466,471,472,473,474,476,477,478,479,480,482,483,484,486,488,490,491,493,494,502,503,504,505,506],curv:[6,170,235,285],curvatur:[405,441,469],custom:[],cut0:474,cut1:485,cut2:485,cut:[],cuthi:[284,296],cutinn:[384,423,424],cutlo:[284,296],cutmax:437,cutoff1:[388,395,414,418,422,425,434,442],cutoff2:[383,385,386,388,394,395,414,418,422,425,434,442],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,89,94,110,112,119,120,144,168,171,173,174,218,219,224,231,284,293,294,296,298,300,303,307,319,332,336,340,342,358,360,361,368,371,372,373,375,376,377,378,379,380,381,382,383,384,385,386,387,388,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,439,440,441,442,447,448,449,450,451,452,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,474,478,481,485,497,502],cutoff_glob:381,cutoff_inn:381,cutoffa:401,cutoffc:401,cuu3:400,cval:169,cvd:326,cvel:308,cvff:[],cwiggl:[3,256,336,339,341,502],cyan:[2,195,196],cycl:[3,235,257,259,260,264],cyclic:[3,190],cygwin:12,cylind:[3,4,71,195,208,241,289,337,340,479],cylindr:[6,241,316,337],cypress:375,cyrot:382,cyrstal:285,d3q15:246,d3q19:246,d_double_doubl:15,d_e:331,d_flag2:292,d_flag:292,d_name:[117,193,292,321,486],d_single_doubl:15,d_single_singl:15,d_sx:292,d_sy:292,d_sz:292,daan:329,dai:12,daili:12,daivi:280,damag:[],dammak:298,damp:[3,6,199,204,243,244,245,250,259,260,264,290,293,294,298,303,322,323,335,337,338,367,368,370,383,385,387,392,395,402,406,414,422,434,442,457,463,490,497],damp_com:244,damp_drud:244,dampen:[303,497],dampflag:[337,406],dan:17,danger:[3,12,235,342,396,494],dangl:173,daniel:9,darden:[361,395],darkblu:196,darkcyan:196,darken:195,darkgoldenrod:196,darkgrai:196,darkgreen:196,darkkhaki:196,darkmagenta:196,darkolivegreen:196,darkorang:196,darkorchid:196,darkr:196,darksalmon:196,darkseagreen:196,darkslateblu:196,darkslategrai:196,darkturquois:196,darkviolet:196,dasgupta:294,dash:[406,493],dat:[6,93,190,205,472],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,304],dataset:304,datatyp:3,date:[0,6,12,13,192,439,440,502],datom1:119,datom2:119,datom3:119,datom4:119,datum:[3,6,42,65,68,69,79,95,112,119,193,209],davenport:425,davi:336,david:[9,19,360,361,460,462],daw:[400,437],dbg:14,dcd:[3,6,7,193,194,195,196,197,286,477,481],ddim:192,deactiv:422,dealt:242,debug:[6,7,11,12,13,14,17,122,126,169,170,286,291,358,360,375,410,431,466,474,475,483,486,493,502],deby:[],decai:[94,392,469],decid:[3,6,12,16,71,256,292,303,332,491],decipher:363,declar:194,declin:319,decod:195,decompos:[89,448],decomposit:[3,5,7,18,62,205,286,307],decoupl:[6,497],decreas:[3,193,202,203,210,219,222,228,233,235,243,330,360],decrement:308,deepli:357,deeppink:196,deepskyblu:196,def:[12,13,474],defaul:61,defect:[6,70,168,429],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,176,177,178,179,180,181,182,184,185,187,188,189,190,191,192,193,194,195,196,199,200,201,202,203,204,205,206,207,208,209,211,212,213,214,215,216,217,218,219,220,222,223,226,227,228,230,233,234,235,238,241,242,243,244,245,246,254,256,258,259,260,261,262,263,264,265,266,267,269,270,271,274,276,277,278,279,280,281,282,284,285,286,288,289,290,292,294,296,301,303,304,305,306,309,313,317,319,321,322,323,324,325,327,328,329,331,333,334,336,337,338,339,340,341,342,344,345,346,347,348,349,350,351,354,355,356,358,360,361,363,365,367,368,369,370,371,372,373,374,375,377,378,379,380,381,383,384,385,386,387,388,389,390,392,393,395,396,397,398,399,401,402,404,405,406,407,408,409,410,412,414,415,416,417,418,419,420,421,422,423,424,425,429,430,431,432,433,434,436,437,439,440,441,442,443,444,445,446,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,473,474,476,477,479,480,481,482,485,486,487,488,490,491,493,494,497,498,499,500,501,502,503],definit:[2,3,6,8,12,13,78,80,120,144,196,208,209,210,211,212,213,214,222,230,241,264,304,321,333,336,339,341,343,355,358,369,378,382,390,397,398,402,412,437,444,446,448,464,474,476,478,485,487,501,502],defint:494,deform:[],deg2theta:169,deg:497,degener:[3,288],degrad:[8,18,285,361,485],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,94,95,97,99,100,102,104,105,110,116,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,169,170,176,177,180,181,188,190,192,195,208,219,226,235,237,238,243,244,249,259,260,264,265,266,267,278,279,280,282,286,288,302,303,306,322,323,324,329,345,347,351,354,356,368,395,400,408,486,494,497,503],degress:[150,208],del:490,delai:[3,6,12,371,399,494],deleg:409,delet:[2,3,7,8,12,54,57,60,63,168,173,174,199,208,209,211,212,213,214,217,219,232,235,259,304,322,323,342,344,359,369,371,374,431,456,476,477,478,479,487,488,493,498,500,502,503],delete_atom:[],delete_bond:[],delete_el:205,deli:192,delimit:[474,502],deloc:[260,402,447],delr:426,delt_lo:490,delta:[],delta_1:382,delta_3:382,delta_7:382,delta_conf:3,delta_ij:[426,437],delta_mu:3,delta_pi:382,delta_r:437,delta_sigma:382,delta_ua:381,delx:192,delz:192,dem:381,demand:298,demo:11,demon:283,demonstr:[293,426],den:289,dendrim:408,denniston:[9,246,248,249,250,285],denomin:[7,175],denot:[122,226,244,285,296,298,392,407,409,440,444,446],dens:[71,219,402],densiti:[3,6,7,9,18,40,41,59,103,120,130,144,156,168,170,200,201,205,208,212,213,216,222,233,246,249,252,253,285,289,290,294,331,336,363,365,369,376,382,400,426,427,428,437,441,447,451,453,454,455,476,485,486,494,501],density_continu:446,density_summ:446,depart:[0,7],departur:[257,293],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,94,95,106,112,113,116,117,118,119,123,144,147,153,157,158,164,170,171,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,195,196,199,200,201,202,203,206,208,210,211,212,214,215,216,218,220,222,228,229,234,237,238,239,241,243,244,246,248,249,256,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,284,295,298,300,303,305,306,307,313,319,322,323,324,326,328,330,331,333,335,336,339,340,341,342,344,345,346,347,348,350,351,354,356,361,363,368,369,371,372,373,375,376,377,379,380,382,383,384,385,386,387,388,389,390,391,392,393,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,426,427,429,430,432,433,434,436,437,439,440,441,442,447,448,449,457,458,459,460,461,462,463,465,467,468,469,471,473,476,478,479,482,486,488,490,493,494,496,502,503],dependend:6,depflag:12,dephas:[471,490],depos:223,deposit:[],deprec:[294,439],depth:[51,148,195,331,405,441],dequidt:9,der:[89,111,390,391,422,439,440,468,497],deriv:[6,7,8,9,38,56,63,89,144,164,190,209,220,222,235,243,256,259,261,262,263,264,265,266,267,284,290,294,298,328,329,331,336,337,340,367,369,377,382,390,395,402,403,407,416,420,421,426,429,439,440,457,459,468,497],derjagin:468,derlet:284,descend:196,descent:[7,367],descib:[40,195,294],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,90,114,117,120,122,134,144,145,148,149,150,154,155,158,161,163,164,168,169,170,172,173,182,187,190,193,194,199,200,201,208,209,210,211,212,213,214,216,219,220,221,222,223,225,226,231,236,237,240,241,242,243,244,245,246,248,249,250,254,258,259,260,264,272,281,284,286,291,292,293,294,295,296,303,308,316,319,320,321,322,323,324,325,326,327,328,329,334,336,337,339,344,360,361,363,366,367,368,369,370,374,377,378,380,381,383,384,385,387,388,389,390,391,392,395,400,402,403,405,406,407,409,412,414,415,416,417,418,419,420,421,422,423,424,425,426,429,430,436,437,438,439,440,441,442,447,448,449,456,457,458,459,460,461,462,463,465,467,468,469,471,473,474,476,477,478,479,480,486,489,490,493,502,503,504],descript:[],descriptor:[144,193,410],deserno:361,design:[0,3,6,7,8,9,11,13,14,15,17,122,152,155,169,205,219,225,226,259,260,284,285,304,326,331,378,379,380,381,384,387,392,394,402,422,423,424,427,428,437,440,459,485],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,90,93,116,121,145,152,170,183,192,208,214,220,222,233,235,236,243,244,245,249,259,280,288,289,290,291,294,298,303,306,319,322,323,324,325,330,337,352,357,360,361,363,366,368,369,370,396,400,408,423,424,458,460,462,472,473,474,476,480,485,490,491,493,494,502,503,504],desk:7,desktop:[4,6,7,10,12,195],despit:497,destabil:382,destre:354,destroi:[11,39,217,218],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,92,93,96,105,107,109,111,113,115,116,118,121,123,144,145,147,148,149,150,153,163,164,165,167,170,171,174,175,178,189,192,193,195,196,199,200,201,205,208,209,210,211,212,214,216,218,219,220,221,222,223,233,235,236,237,238,240,241,243,245,246,250,256,257,258,259,260,261,262,263,264,265,266,267,271,273,278,279,280,281,282,285,288,289,290,292,293,295,296,297,303,306,307,319,322,323,324,325,326,327,329,330,331,332,333,334,335,342,344,346,355,360,361,364,368,369,371,372,375,376,377,378,380,381,382,384,386,387,388,389,390,391,392,395,396,402,403,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,425,426,430,431,436,439,440,441,447,448,449,457,464,467,468,474,476,477,478,479,481,482,485,486,488,491,494,495,502,503,506],detect:[2,3,12,42,61,63,88,94,234,289,330,370,391,408,413,471,473,476,487,490,502],determ:375,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,89,105,111,113,116,122,123,131,145,158,159,168,169,170,192,193,195,196,197,198,202,203,204,207,208,209,210,211,212,213,214,215,216,220,222,223,226,228,235,238,239,241,243,244,249,254,256,257,259,265,266,267,278,279,280,282,284,286,289,290,293,300,301,302,303,304,305,309,311,313,319,322,323,324,326,332,333,336,337,338,339,340,341,342,355,360,361,363,369,371,372,375,377,378,386,391,395,399,400,404,406,409,410,418,426,429,431,440,441,447,456,459,463,468,473,476,477,479,481,483,486,490,492,493,495,501,502,503],determinist:307,detil:112,devan:[9,442],devanathan:462,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,240,264,288,293,294,297,377,382,402,428,429,447,465,478],devemi:9,deviat:[257,264,284,404],deviator:9,devic:[1,3,12,15,17,240,375],device_typ:375,devin:[295,391],devis:428,dfactor:195,dff:497,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,361],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,297,429],dhi:[59,192,222,289],dhug:[257,293],dhugoniot:[257,293],dia:426,diagnost:[],diagon:[3,6,85,144,145,146,220,259,290,303,334,444,446],diagonalstyl:448,diagram:[41,122,169,189,216,286],diallo:408,diam:[195,196,289,369],diamet:[3,6,40,42,117,170,193,195,196,200,201,243,289,303,319,321,335,337,369,381,390,405,406,416,441,464,468,476,477,486],diamond:[363,402,426],diamter:[40,289],dick:6,dicsuss:256,dictat:[206,257],did:[3,12,368,396,399,400,406,431,460,462,484],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,166,333,360],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,89,94,97,99,100,124,144,147,148,149,150,151,153,156,157,158,159,160,162,163,164,170,171,173,178,189,190,192,193,195,196,199,201,204,206,208,211,216,217,218,219,220,221,222,226,231,234,235,236,237,238,239,240,243,244,246,256,259,260,261,262,263,265,266,267,269,271,274,276,277,278,279,282,284,286,288,290,293,294,295,298,301,303,306,30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1,354,360,361,390,395,396,398,402,403,406,411,423,424,426,431,441,444,446,451,452,454,455,469,497],equi:260,equidist:258,equil:[3,294,364,483,506],equilater:486,equilibr:[3,4,5,6,7,9,59,93,170,199,206,209,219,220,235,257,259,260,280,281,293,294,295,296,327,328,329,334,391,392,439,440,472,486],equilibria:334,equilibribum:[217,218],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,153,154,177,179,220,222,235,236,237,244,246,259,264,280,293,294,298,302,306,308,316,319,326,327,329,334,345,347,351,354,391,426,433,447,497],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:205,equival:[6,12,13,29,59,61,128,129,137,142,168,172,196,211,214,220,222,235,243,259,280,290,302,303,339,396,402,447,460,462,476,479,484,485,494,497],equlibrium:6,equliibr:[294,296],er3:169,eradiu:[40,117,402,476],eras:[305,328],erat:[222,424],erc:392,erfc:[392,414,431],erforc:117,erg:501,erhart:[206,400,460,462],ermscal:378,ernst:9,eror:3,eros:426,erose_form:426,erot:[],errata:[460,462],erratum:336,erron:3,error:[],erta:406,ervel:[117,476],escap:[223,497],especi:[8,11,16,158,170,199,206,216,235,293,298,301,302,375,473],espresso:[9,297],essenti:[8,11,12,27,90,132,151,152,153,156,157,158,159,160,162,179,209,264,285,335,361,377,392,414,462,481,494],essex:29,establish:[89,239],estim:[1,3,6,10,12,38,41,56,93,145,205,216,227,257,319,326,360,361,366,431,440,459,490,494],esu:501,esub:426,eta:[6,246,259,293,294,296,335,401,403,405,437,461,465,501],eta_dot:259,eta_ij:437,eta_ji:403,etag:[40,476],etail:494,etap:259,etap_dot:259,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,91,92,93,97,113,114,117,119,145,147,150,151,152,153,154,156,157,158,159,160,162,164,170,172,173,174,183,193,195,196,199,200,205,206,207,208,211,212,213,214,217,218,222,223,233,235,236,243,259,289,300,304,331,332,340,344,359,360,368,369,370,371,373,400,401,409,422,424,429,435,439,440,458,460,462,465,471,474,476,477,478,483,485,486,490,491,492,493,494,495,497,501,502,504,506],ethernet:18,etol:[368,370,471,490],etot0:293,etot:[6,97,99,100,114,145,156,196,226,244,257,293,493,494],eu2:169,eu3:169,euler:[368,370],eulerian:205,euqat:450,europhi:246,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,89,90,93,111,121,144,146,150,160,168,170,192,193,195,196,200,201,202,203,205,207,208,209,210,211,212,213,214,215,222,228,236,238,239,241,242,243,244,285,291,294,305,309,313,322,323,324,333,336,339,341,342,344,360,361,366,368,375,429,431,437,443,445,447,459,471,472,474,478,479,481,483,484,485,486,490,492,494,502,503],evalut:[344,474],evan:[158,280],evanseck:[6,20,176,387,488],evapor:[],evaul:[8,368],evdwl:[111,439,440,494],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,123,168,171,172,186,190,193,196,199,200,201,206,207,208,211,212,213,214,216,217,218,220,222,223,226,241,244,257,259,260,285,289,298,300,303,304,315,319,327,331,334,336,340,342,353,360,366,368,370,375,380,402,403,406,409,412,431,441,465,466,476,477,479,481,482,483,485,486,488,491,493,494,495,497,506],evenli:[3,41,145,190,216,246,412,466],event:[],eventu:[3,6,12,15,172,294,490],ever:[54,56,242,319],evera:[390,405,441,457],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,93,117,123,132,158,173,193,194,195,196,197,199,200,201,202,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,222,223,227,232,233,235,237,239,240,241,246,247,255,259,260,264,283,284,285,289,290,291,292,293,294,295,296,298,300,301,303,304,306,308,319,321,322,323,324,325,326,327,330,331,332,333,334,342,344,359,361,370,371,372,375,396,399,409,422,439,440,447,453,470,471,472,476,478,480,481,483,484,485,490,491,492,494,502,506],everyth:[8,111],everywher:[120,416],eviri:402,evolut:[237,246,286,471],evolv:[246,286,332],ewald:[2,3,5,6,7,8,12,90,114,122,145,332,360,361,368,383,385,386,392,395,402,414,418,434,442,457,459],ewald_disp:395,ewalddisp:3,exact:[22,41,44,71,126,164,173,178,216,219,236,237,243,244,245,289,298,299,319,331,346,360,389,478,483,490,502,504,506],exactli:[3,6,12,14,17,38,41,42,56,59,71,72,93,120,148,154,161,170,190,200,201,211,216,222,227,231,236,243,244,245,260,272,273,281,285,293,319,324,325,338,375,389,396,400,406,409,423,431,459,478,479,486,490,502],exager:497,examin:[6,8,9,17,219,285],examp:[474,502],exampl:[],exce:[3,6,16,17,18,41,58,71,172,207,208,211,212,213,214,216,220,222,227,232,259,285,300,304,310,311,319,368,375,476,502],exceed:[3,41,59,216,222,259,319,484],excel:402,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,63,71,91,92,112,113,116,121,145,147,148,149,150,151,152,153,154,156,157,158,159,160,161,162,163,170,174,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,196,199,202,208,209,211,215,216,220,222,229,234,235,238,241,243,245,259,260,261,262,263,264,265,266,267,268,269,272,273,276,278,279,280,281,282,286,295,296,303,305,306,316,319,322,324,325,331,335,339,342,344,345,346,347,348,350,351,354,355,356,360,361,363,365,369,370,371,373,374,375,376,377,379,383,384,385,386,387,388,389,390,391,392,394,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,427,432,433,434,436,439,440,441,442,449,457,458,459,460,461,462,465,467,468,469,471,473,474,476,478,479,481,484,485,486,487,488,490,494,497,501,502,503,505],excess:[210,402],exchang:[2,3,6,8,9,61,62,199,205,206,235,243,295,303,327,331,334,360,375,402,491],exchange:360,excit:[9,402],exclud:[3,6,9,12,16,17,63,71,116,144,150,157,158,174,193,208,212,217,218,247,255,288,301,303,326,337,342,368,369,371,384,406,409,412,423,424,431,456,488],exclus:[1,3,9,12,16,89,375,391,429,431,485,495],excurs:[259,471],exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,171,195,240,297,344,359,362,374,472,474,484,487,490,502],exempl:447,exemplari:236,exemplifi:402,exert:[6,241,244,298,338,339,340,361],exhaust:[205,374,502],exhibit:[94,259,367,402,485],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,126,170,171,189,194,195,196,199,204,215,218,220,223,235,288,289,291,342,345,347,348,349,351,355,364,369,375,397,398,409,439,456,466,472,474,476,477,478,487,488,489,502,503,504],exit:[2,3,11,12,41,57,193,216,231,359,374,474,475,484,493,502],exlanatori:3,exp:[],expand:[],expans:[12,144,193,487,502],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,105,151,162,168,190,216,228,235,237,256,284,290,292,293,298,303,342,361,371,389,426,429,431,471,474,476,478,481,485,490,502],expens:[6,10,71,196,284,288,303,331,342,360,361,371,375,474],experi:[6,13,15,17,215,223,240,249,258,290,302,303,366,370,396,431,485,490],experienc:[6,12,248,249],experiment:[235,360,375,490],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,88,95,150,158,190,193,195,196,199,208,209,214,216,218,220,222,259,284,292,303,316,342,344,359,360,363,369,370,374,380,400,412,447,449,464,474,477,478,481,483,486,497,502,506],explan:[3,6,59,117,144,193,208,258,284,409,470,473,474,476,485],explanatori:[3,8,121,193,207,208,211,212,213,303,369,473,502],explantori:[3,299],explic:430,explicit:[6,9,11,22,44,77,89,117,120,164,178,200,201,222,310,311,346,365,377,378,382,387,389,400,402,413,423,463,470,473,477,480],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,113,116,147,157,160,168,170,176,177,179,180,181,182,184,185,187,188,190,193,196,202,212,215,222,229,234,236,238,243,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,292,293,295,303,305,306,322,324,325,331,335,339,345,347,348,350,351,354,356,369,375,376,377,379,383,384,385,386,387,388,389,390,391,392,393,395,396,399,400,401,403,404,405,406,407,408,409,413,414,415,416,417,418,419,420,421,422,423,427,429,431,432,433,434,436,441,442,449,450,451,452,453,454,455,457,458,459,460,461,462,463,465,467,468,469,476,478,479,485,486,488,489,495,497],explictli:[16,489],exploit:[9,15,17,286],explor:[122,169],expon:[3,294,296,400,405,408,422,430,442],exponenti:[89,437,458,465,469,490,502],expos:11,exposit:[205,396,399],express:[6,144,156,170,200,201,220,256,284,294,331,337,344,382,400,402,416,426,447,448,457,502],expressiont:382,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,84,85,86,89,90,93,97,100,101,111,113,121,123,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,199,202,203,206,214,215,221,224,228,233,234,235,237,238,239,241,243,245,257,259,264,273,284,285,301,302,303,305,308,313,316,318,322,323,324,325,326,328,329,331,333,336,340,341,405,426,429,440,441,448,493,494],extent:[1,3,41,42,45,57,71,168,172,193,204,212,216,241,338,341,360,363,377,443,445,459,473,476,479],exterior:[3,6,168,340],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,105,113,114,116,122,145,147,148,149,151,153,156,157,158,159,160,162,163,169,170,171,172,176,196,211,216,218,259,291,292,293,303,319,368,369,372,373,395,406,409,412,426,431,473,474,476,479,488,497,502],extract:[3,6,11,13,36,63,89,111,119,121,123,200,201,296,370,392,403,426,448,474,481,493],extract_atom:11,extract_comput:[11,474],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,195,210,220,222,259,329,402,461,497],extrema:422,extrins:205,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[166,333],f_a:[460,461,462],f_ave:121,f_c:461,f_f:462,f_fix_id:293,f_harm:329,f_i:[29,437],f_id:[6,71,121,123,193,199,207,208,209,210,211,212,213,214,254,321,333,494,502],f_ij:437,f_indent:214,f_int:328,f_j:29,f_jj:93,f_k:437,f_langevin:331,f_max:[293,298],f_msst:257,f_r:[244,460,461,462],f_sigma:382,f_solid:329,f_ss:6,f_temp:[],face:[3,6,57,59,71,158,168,172,204,212,213,336,338,339,340,341,363,405,426,441,476,479],face_threshold:168,facet:168,facil:[0,12],facilit:[6,13,42],fact:[6,8,16,237,289,319,329,406,447,488],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,72,89,93,105,112,119,120,122,144,164,169,172,176,187,192,193,195,196,200,201,209,216,220,222,223,235,240,243,245,246,257,259,260,264,286,290,294,302,306,309,311,319,323,327,334,335,336,340,351,361,363,369,375,377,378,382,383,385,387,392,393,394,396,397,398,402,406,409,413,414,426,429,431,433,434,440,442,449,458,463,473,476,479,480,485,488,490,491,494,497,501,502],factori:[3,474],factoriz:360,fail:[3,11,12,59,174,220,223,360,368,370,394,440,474],failur:[125,444,475,502],fairli:[11,431,485,490],faken:73,falcon:240,fall:[3,6,196,211,289,474,502],fals:[88,342,344,447,502],fame:8,famili:[465,473],familiar:[0,11],fan:437,far:[3,6,12,17,57,59,61,88,193,196,197,216,217,218,220,223,259,284,302,303,319,336,347,351,366,370,371,464,474,476,481,494],farago:243,farrel:[460,462],farther:193,fashion:[6,8,41,71,170,196,199,200,201,206,212,216,218,223,235,237,241,256,257,259,261,262,263,264,265,266,267,275,278,279,280,281,282,292,293,295,303,308,312,318,321,329,331,335,336,337,339,341,370,409,423,479,488,502,505],fasolino:411,fast:[6,7,9,12,13,17,39,193,270,293,332,360,361,384,423,424,429,457,459,478,483,485,494,503,506],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,108,113,116,147,157,176,177,179,180,181,182,184,185,187,188,190,193,196,202,215,216,222,229,234,238,242,243,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,290,294,295,303,305,306,319,322,324,326,328,331,335,339,345,347,348,350,351,354,356,360,361,372,373,375,376,377,379,382,383,384,385,386,387,388,389,390,391,392,395,396,400,401,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,427,432,433,434,436,441,442,449,457,458,459,460,461,462,465,467,468,469,471,479,485,489,497],fastest:[1,6,14,17,158,212,331,332,375,473],fatal:[3,493],fault:[70,440],faulti:12,fava:405,favor:219,favorit:7,fbmc:326,fcc:[],fcm:[275,502],fdirect:226,fdotr:410,fdt:[],fdti:89,fe2:169,fe3:169,fe_md_boundari:205,featu:8,featur:[],fecr:400,feedback:[7,240],feel:[7,240,241,249,284,340,342,370,431],felling:428,felt:340,femtosecond:501,fene:[],fennel:[392,414],fep:[],ferguson:[6,176,488],fermi:[1,12,15,156,375,462],fermion:[9,402],fernando:425,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,63,197,207,208,209,211,212,213,214,244,259,289,292,294,306,333,360,368,369,370,377,447,473,476,481,485,487,495,502,504],fewer:[1,3,11,15,16,61,249,485],fewest:3,fextern:233,feynman:286,fff:474,ffield:[391,403,439,440,447],ffmpeg:[3,12,195],ffplai:195,fft:[1,3,7,12,14,15,90,113,114,145,285,360,361,485],fft_inc:[12,361],fft_lib:12,fft_path:12,fftbench:[360,495],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],ficiti:456,fictiti:[6,202,203,228,233,237,286,302,392,414,418,456],field1:[477,481],field2:477,field:[],fifth:[316,433],figur:[1,3,8,11,12,293,473,474],fij:395,file0:284,file1:[11,13,284,330,344,369,481,483,487],file2:[11,13,330,344,369,481,483,487],file:[],file_from:194,filen:369,filenam:[3,12,13,38,41,56,190,193,195,196,197,205,208,209,210,211,212,213,214,216,221,231,284,288,291,294,295,296,299,300,303,304,330,331,357,358,359,369,370,376,377,382,392,400,401,403,411,426,427,428,433,437,438,439,440,447,448,458,459,460,461,462,465,472,473,474,477,478,483,487,494,502,504,505,506],filennam:483,filep:[3,193,196,478,483,506],filepo:300,fill:[7,9,170,195,289,331,363,371,382,429,440,479],filter:[196,205],final_integr:8,final_integrate_respa:8,finchham:[6,152,394],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,89,121,173,190,197,206,219,220,231,232,235,258,284,289,290,298,302,366,368,370,371,392,409,414,418,426,447,457,459,497,502],find_custom:8,fine:[16,17,174,202,228,329,371,375,502],finer:[144,170,502],finest:360,finger:[170,192,256,479],finish:[6,11,41,216,344,357,359,360,372,374,375,464,481,502,503],finit:[],finni:[7,400,457],finvers:226,fiorin:[9,221],fire:[],firebrick:196,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,90,93,106,107,108,110,116,120,121,131,134,137,138,142,145,155,158,164,166,168,169,171,172,173,177,190,193,194,195,196,197,199,200,208,209,211,212,213,214,216,219,222,231,235,236,241,246,256,257,258,259,284,286,291,292,293,295,300,303,306,308,316,317,319,320,321,328,329,330,331,333,337,342,344,345,352,363,368,369,370,371,374,375,376,377,380,382,383,385,387,389,391,392,400,402,403,406,407,409,410,411,412,413,414,418,423,424,426,428,429,431,433,437,439,440,447,448,456,458,459,460,461,462,465,469,471,472,473,474,476,477,478,481,483,485,488,489,490,493,494,497,502,503,504,506],fischer:[6,9,19,20,176,387,488],fit:[3,6,9,12,38,56,190,231,302,319,377,382,411,426,431,452,459,461,484,502],five:[73,156,293,369,382,427,476,490],fix:[],fix_adapt:[164,201,422],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,206,289],fix_eo:9,fix_evapor:206,fix_flux:205,fix_gcmc:[206,369],fix_gl:237,fix_gld:237,fix_grav:289,fix_id:[3,220,257,259,261,262,263,264,265,266,267,290,293],fix_modifi:[],fix_mov:[192,337],fix_nh:8,fix_npt:237,fix_nvt:[206,235],fix_poem:[3,6],fix_pour:[3,223],fix_qbmsst:9,fix_qeq:[3,391],fix_rattl:306,fix_reax_bond:439,fix_rigid:[249,380],fix_saed_vtk:304,fix_setforc:8,fix_shak:306,fix_shardlow:9,fix_srd:3,fix_styl:264,fix_temp_rescal:325,fixedpoint:[220,259],fixextern:233,fixid:205,fji:395,flag1:[225,373],flag2:[225,373],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,88,91,92,96,106,107,109,122,165,169,173,193,195,19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123,321],input:[],input_doubl:3,inquir:309,insensit:12,insert:[3,5,7,8,12,59,170,199,223,235,241,289,360,448,456,474,480,497],insid:[2,3,6,8,11,71,133,139,170,193,196,207,212,213,223,224,232,235,241,246,249,289,303,319,336,338,339,340,341,342,358,363,416,474,475,476,478,479,486,490,502],insight:[6,13],instabl:[246,395,446],instal:[],instanc:[6,11,200,221,237,338,404,409,431,437,474,497],instantan:[6,63,219,220,236,237,259,264,285,290,293,298,300,303,326,482,494],instanti:[6,11,12,205,409,473],instead:[1,3,6,8,9,11,12,13,17,18,40,41,59,61,63,70,71,92,106,121,148,152,174,190,193,201,208,211,212,213,214,216,220,221,235,243,246,249,250,285,291,301,303,321,339,358,360,361,364,371,375,385,386,400,413,415,422,426,429,471,479,483,490,492,497,502],institut:[9,240,288],instruct:[],insuffici:[3,6,12],insult:259,insur:[3,6,11,12,17,39,40,61,73,105,107,170,171,190,193,195,196,202,217,218,223,228,229,232,233,235,238,243,255,291,292,301,303,319,331,336,340,341,342,344,359,369,371,375,390,405,409,435,441,459,473,474,476,477,481,484,485,493,494,502,503],int_max:3,integ:[3,6,8,11,12,39,40,42,64,68,70,71,110,117,119,121,123,144,168,170,173,174,176,180,181,185,190,192,193,195,196,206,208,212,213,217,218,219,223,225,233,235,236,237,240,243,244,245,246,285,288,289,292,293,298,303,319,321,323,326,330,331,350,360,363,384,396,398,399,412,426,439,440,444,446,448,471,473,474,475,476,484,485,486,490,493,502,503],integr:[],integrate_ulsph:[],intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,210,236,438,476],intens:[1,3,6,9,63,66,74,75,88,91,92,93,96,106,107,108,109,116,118,120,121,122,123,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,165,166,167,169,199,208,209,211,212,213,214,216,217,218,219,227,232,239,249,257,259,264,300,303,304,319,327,331,333,334,493,494],intepol:502,inter:[14,18,42,61,62,150,173,174,193,219,243,245,258,295,303,360,370,382,486,497,502,504,506],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,37,39,40,42,44,50,54,55,57,61,63,65,69,72,77,79,89,90,94,95,110,111,112,114,116,119,120,126,127,128,129,131,132,133,134,135,136,137,139,140,141,142,144,145,146,148,149,163,164,168,171,172,173,174,175,176,178,182,183,189,193,199,200,201,217,218,219,234,235,240,241,243,245,249,273,284,286,288,289,294,296,302,303,310,311,319,320,326,331,335,336,337,340,341,346,347,348,349,351,355,360,361,368,369,370,371,372,373,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,436,437,440,441,442,444,446,447,448,449,456,457,458,460,461,462,463,464,465,466,467,468,469,471,474,476,478,480,481,485,486,488,493,494,497,504],interatom:[3,4,7,170,193,258,328,329,376,382,400,402,410,426,429,447,461,502],intercept:122,interchang:6,interconnect:18,interconvert:402,intereract:39,interesect:340,interest:[1,5,7,8,9,11,13,71,169,286,326,329,361,401,424,439,440,474,502],interf:375,interfac:[],interfer:[12,259,377],interg:[6,497],intergr:[485,489],interi:424,interior:[3,6,41,340,479],interlac:426,interleav:[6,170,484],intermedi:[6,12,59,195,258,284,354,370,474,475,484,488],intermix:471,intermolecular:377,intern:[],internal_element_set:205,internal_quadratur:205,internet:242,interpenetr:426,interpentr:[451,452,454],interpol:[6,15,38,56,103,190,195,196,205,231,246,284,360,361,370,382,431,440,453,459,460],interpret:[2,6,11,195,211,406,449,471,474,490,502],interrupt:293,intersect:[3,6,122,196,340,342,479],intersert:340,interspers:368,interstiti:[168,429],intertia:[3,96],interv:[3,6,93,194,209,243,259,293,298,299,311,447,453,471,490,502],intestieti:122,intial:[6,375,377],intiial:[41,481],intiti:[3,318],intra:303,intra_energi:235,intramolecular:[29,235],introduc:[6,9,94,110,195,259,293,298,303,354,360,376,392,402,414,418,422,458,490,502],introduct:[],intsal:[],intuit:363,inv:[122,169,304],invalid:[3,12,71,91,173,273,370,423,424,478],invari:[110,137,142,144],invent:306,invers:[],invert:[1,6,174,285],invis:340,invoc:[168,219,375,444,446,474],invok:[1,3,6,7,8,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,59,63,66,71,74,75,81,89,90,91,92,96,106,107,109,113,114,115,116,121,147,157,164,165,168,170,171,173,174,176,177,179,180,181,182,184,185,187,188,190,193,195,196,197,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,222,223,224,225,227,228,229,232,233,234,235,236,238,239,240,241,243,244,245,246,247,248,249,250,251,252,253,255,256,258,259,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,287,288,289,290,291,292,294,295,296,297,298,299,300,301,303,304,305,306,308,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,345,347,348,350,351,354,356,359,360,361,362,363,368,370,375,376,377,379,383,384,385,386,387,388,390,391,392,395,396,400,401,403,404,405,406,407,408,4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9,320,322,323,324,325,327,328,329,330,331,333,334,335,336,337,339,340,341,342,344,345,347,348,350,351,352,354,356,359,360,361,363,365,367,368,369,370,371,374,375,376,377,379,382,383,384,385,386,387,388,389,390,391,392,395,396,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,426,427,428,429,431,432,433,434,435,436,437,438,439,440,441,442,447,448,449,450,451,452,453,454,455,456,458,459,460,461,462,465,467,468,469,470,471,472,473,474,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,493,494,495,497,501,502,503,504,506],young:[406,443,445],your:[0,1,2,3,4,5,6,7,8,11,12,13,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,43,45,46,47,48,49,51,53,54,56,59,61,111,113,116,120,147,148,149,153,157,163,168,170,171,172,173,174,176,177,179,180,181,182,184,185,187,188,190,192,193,194,195,202,205,209,211,214,215,217,218,219,220,222,223,229,234,235,238,240,243,256,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,289,292,295,301,303,305,306,308,321,322,324,327,331,333,334,335,336,337,339,340,341,342,345,347,348,350,351,354,356,361,363,369,370,371,374,375,376,377,379,382,383,384,385,386,387,388,389,390,391,392,395,396,399,400,401,403,404,405,406,407,408,409,410,411,414,415,416,417,418,419,420,421,422,423,426,427,428,429,431,432,433,434,436,437,439,440,441,442,449,456,458,459,460,461,462,465,467,468,469,470,473,474,476,478,479,480,483,484,485,486,487,488,489,493,494,501,502,504,506],yourself:[6,8,12,13,220,369],yplane:337,ypo:170,ysu:[3,193,321,477],yuan:9,yukawa:[],yukawa_1_1:466,yxz:473,yzx:473,z_i:[402,462,469],z_j:[462,469],z_meam:426,zachari:13,zannoni:405,zbl:[],zblcut:462,zblcutinn:448,zblcutout:448,zblexpscal:462,zblz:448,zcm:303,zcylind:337,zepeda:206,zero:[3,4,6,9,11,12,26,27,39,41,48,49,59,61,63,66,71,72,75,89,90,92,94,96,105,106,107,108,109,110,112,113,114,116,117,118,119,120,121,122,125,144,145,148,149,150,151,158,159,162,163,165,167,168,169,170,172,173,174,176,179,188,190,192,193,195,196,199,200,201,202,204,206,207,208,209,210,211,212,213,214,215,216,217,218,220,222,227,228,229,232,234,235,236,237,239,243,244,245,246,247,249,255,256,257,259,264,273,276,286,291,292,293,294,295,298,300,301,303,304,305,306,310,311,313,319,321,326,327,329,331,334,335,336,337,338,339,341,342,343,344,350,363,366,368,369,370,371,375,378,382,383,385,386,387,390,392,395,396,397,398,402,405,407,408,409,410,414,416,418,419,422,424,425,426,429,431,436,440,441,442,447,456,459,463,465,469,471,472,473,476,477,479,481,483,484,485,486,490,491,494,497,502,503,504,506],zeta:[3,246,294,403],zfactor:195,zflag:[157,158,247,249,255,303,326],zhang:[303,327,406],zhi:[3,6,172,193,204,330,336,339,341,476,479,494],zhi_bound:[6,193],zhou:[13,382,403,437,460,462],zhu:455,ziegenhain:13,ziegler:[288,426,457,462,469],zimmerman2004:205,zimmerman2010:205,zimmerman:[9,70,205,382],zlat:[222,241,494],zlib:193,zlim:447,zlo:[3,6,172,193,204,330,336,338,339,341,476,479,494],zlo_bound:[6,193],zmax:[204,246,502],zmin:[246,502],zn2:169,zone:[122,304],zoom:[3,193,195,196],zorig:71,zplane:337,zr4:169,zrest:318,zsu:[3,193,321,477],zwall:336,zwall_veloc:246,zxy:473,zybin:440,zyx:473},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","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute 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/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","dimension command","displace_atoms command","dump 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","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 body/rounded/polygon 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","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>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":217,"default":[37,39,40,55,57,58,59,61,62,71,89,90,94,105,106,108,110,111,122,126,127,144,150,158,159,163,169,170,173,175,189,191,192,193,195,196,197,198,200,201,202,204,205,206,208,212,213,214,217,218,220,221,222,223,227,232,235,236,241,243,244,245,246,247,249,254,257,259,260,264,280,281,285,286,289,290,291,292,293,295,298,300,301,303,304,319,321,326,327,328,329,332,334,336,338,342,355,358,360,361,363,364,366,367,369,371,372,373,375,378,382,384,402,423,424,429,431,439,440,456,457,471,472,473,476,477,479,481,483,484,485,488,490,492,493,494,495,496,501,503,504,505],"function":502,"long":[210,383,385,386,387,388,392,394,395,414,418,422,434,442],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[200,201],addforc:202,addit:[12,13],addtorqu:203,adiabat:6,adjust_dt:309,adp:376,airebo:377,alloi:400,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:204,arrai:6,aspher:[6,84,148,261,265,269,270,278],atc:[9,205],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,83,87,94,98,99,102,103,104,110,114,115,117,144,145,168,204,206,207,292,502],atom_modifi:39,atom_styl:40,attract:5,aug:[],aveforc:215,awpmd:[9,378],balanc:[41,216],barostat:6,basal:67,beck:379,berendsen:[290,322],between:6,binary2txt:13,bodi:[6,8,42,68,149,262,266,271,279,380,381],bond:[8,13,69,217,218,219,299],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:382,born:[383,394],boundari:[7,57],box:[6,58,220],brownian:384,buck:[385,386,394,425],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,176,387,422],chunk:[6,66,71,75,92,96,107,109,118,150,165,167,208],citat:7,class2:[21,43,177,345,388],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[336,390,468],colvar:[9,13,221],com:[74,75,151],comb3:391,comb:[295,391],come:5,comm_modifi:61,comm_styl:62,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,502],compute_modifi:105,condit:7,conduct:[6,327],conserv:397,constant:6,constraint:7,contact:[76,124],contact_radiu:[],coord:77,core:6,correl:[209,210],cosin:[23,24,25,26,27,28,179],cossq:347,coul:[383,385,386,387,388,392,393,394,407,414,418,422,434,442],coupl:6,creat:218,create_atom:170,create_bond:171,create_box:172,createatom:13,creation:7,csld:323,csvr:323,cubic:416,cuda:[9,14,113,116,147,157,202,215,229,234,238,259,268,305,306,322,324,335,383,385,387,388,400,406,407,414,415,417,420,432,458,460],custom:8,cut:[49,378,385,388,392,395,402,404,414,415,422,430,434],cvff:348,damag:[78,125],data2xmovi:13,data:6,databas:13,deby:[392,414],dec:[],defgrad:131,deform:[153,154,222],delete_atom:173,delete_bond:174,delta:24,deposit:223,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],diagnost:7,diel:393,dielectr:175,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:178,dihedral_styl:[2,176,177,179,180,181,182,183,184,185,186,187,188,189,190],dilat:80,dimens:191,dipol:[6,29,395],direct:226,discuss:6,disp:6,displac:[81,88],displace_atom:192,distanc:349,distribut:[7,12],document:0,dpd:[9,82,83,396,397,398],drag:224,dreid:[6,408],drude:[6,9,155,225,226,244],dsf:[392,414],dsmc:399,dump:[6,8,193,194,195,197],dump_modifi:196,dynam:294,eam:[13,400],echo:198,edip:401,eff:[9,13,99,100,154,156,161,245,260,272,281,325,402],efield:228,eim:403,elast:6,emac:13,energi:[127,398],enforce2d:229,ensembl:7,erot:[84,85,86,87],error:[3,126],evapor:232,event:88,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],exp:[27,179],expand:[46,417],extend:[8,11],extern:233,fcc:284,fdt:398,featur:[7,8,502],feb:0,fene:[45,46],fep:[9,13,89,201],field:[6,7],file:6,finit:6,fire:294,fix:[2,6,8,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,3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er:3,affect:[1,6,10,14,15,16,17,40,60,61,71,90,121,145,154,168,174,195,196,201,208,209,211,212,213,214,217,218,219,220,222,223,233,239,241,243,249,256,260,261,262,263,265,266,267,273,278,279,280,282,303,304,317,331,341,354,360,366,367,368,370,371,372,375,402,423,424,431,473,474,476,478,479,481,484,486],affin:[16,17,18,222,375,391],afil:237,aforement:18,afresh:[291,484,502],afshar:396,after:[2,3,5,6,8,9,11,12,15,21,22,33,39,40,41,44,50,57,58,59,61,63,71,148,149,150,151,152,153,154,157,158,159,160,162,163,170,171,173,174,177,178,183,192,193,194,195,196,197,199,200,201,205,206,208,209,216,217,218,219,220,222,226,235,246,247,248,249,250,255,256,257,259,265,266,267,273,278,279,280,282,285,289,293,301,303,306,315,320,322,323,324,326,327,328,329,330,334,336,338,342,345,346,352,359,365,366,368,369,371,373,374,375,376,377,382,389,391,400,401,402,403,409,410,411,422,423,424,426,427,428,429,433,437,439,440,447,448,457,458,460,461,462,465,471,473,475,476,477,478,479,481,482,484,486,488,490,493,494,497,501,502,503,504,505,506],afterrun:484,afterward:3,afterword:41,ag1:169,ag2:169,again:[6,11,12,16,17,62,144,150,156,164,193,196,222,239,289,345,359,370,423,424,471,473,474,476,478,483,490,492,502,504],against:[11,12,13,64,223,370,439,440],aggreg:[6,12,65,68,69,79,95,112,119,239,255,301,303,317,471,503],aggress:[239,490],agilio:[9,13],agre:[3,8,190,368,377,411,440],agreement:[5,7],ahd:408,ahead:338,aidan:[0,5,7,9,13,363],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:195,akohlmei:[7,9,13,197,240],aktulga:[7,9,296,440],al2o3:447,al2o3_001:[122,304],al3:169,ala:[246,447],alain:9,alat:[284,426],alb:[437,460,462],albeit:302,albert:9,alchem:[89,164],alcohol:334,alcu:[376,382],alcu_eam:437,alderton:395,alejandr:[259,260],alessandro:13,algebra:429,algorithm:[0,1,6,7,8,9,41,61,196,205,216,219,222,246,248,249,273,286,294,303,306,307,326,327,331,334,339,366,367,368,372,375,398,402,424,429,444,446,471,473,490],alia:[12,16],alias:[1,361],aliceblu:196,align:[6,12,29,41,71,172,190,212,216,241,363,476,479,497],alkali:402,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,158,163,164,165,166,167,168,169,170,171,172,173,174,176,178,183,189,190,193,194,195,196,197,199,200,201,202,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,252,254,255,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,298,299,300,301,302,303,304,305,306,307,308,309,310,311,315,316,318,319,320,321,322,323,326,327,328,329,330,331,332,333,334,336,337,338,339,340,341,342,343,344,345,346,350,355,358,359,360,361,362,363,365,368,369,370,371,372,374,375,376,377,378,380,381,382,383,385,386,387,388,389,391,392,395,396,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,422,423,424,425,426,427,428,429,430,431,432,433,434,436,437,438,439,440,441,442,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,470,471,473,474,475,476,477,478,479,480,481,483,484,485,486,487,488,489,490,491,493,494,495,497,501,502,503,504,505,506],allen:[29,89,395,405],allentildeslei:89,allign:3,allindex:343,alloc:[3,5,6,8,9,11,12,60,233,333,369,371,375,435,440,476,484],allocat:3,alloi:[],allosw:71,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,94,110,112,146,148,149,150,163,168,169,170,172,178,189,190,193,195,196,197,199,200,202,204,205,206,208,209,210,211,212,213,214,216,218,219,220,221,222,223,227,228,233,235,236,237,238,240,243,246,249,250,254,256,259,260,284,288,289,290,291,292,293,297,303,304,306,308,310,311,315,319,326,327,328,329,331,332,333,334,335,336,342,344,346,355,360,361,363,368,369,370,371,374,375,378,382,383,384,385,386,387,392,400,402,406,407,408,409,414,418,423,424,429,431,437,440,441,444,446,447,456,466,468,471,474,476,478,479,480,481,482,483,486,488,489,490,493,494,502,503],almost:[2,3,12,60,241,293,331,361,372,375,456],alo:392,alon:[6,7,219,299,439,440,474],alond:13,along:[6,8,9,12,29,40,71,89,122,168,169,170,192,193,195,208,219,241,246,247,251,256,258,293,303,306,308,312,316,317,326,330,331,337,340,342,363,366,367,368,370,392,395,406,409,412,414,418,426,439,440,459,476,479,486,487,502],alonso:[427,428],alpha:[6,12,51,200,246,285,293,294,298,368,376,379,383,392,396,398,400,401,403,408,413,414,426,432,436,461,463,494,497],alpha_:[],alpha_c:422,alpha_i:448,alpha_ialpha_j:[],alpha_lj:422,alphabet:[2,3,22,37,44,55,63,178,189,199,346,355,369,389,457,476],alphanumer:[3,63,199,292,300,344,369,502],alreadi:[3,7,8,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dia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,177,178,189,345,346,355,388,457],compat:[3,5,7,8,9,11,12,13,17,18,41,71,121,123,181,193,197,201,207,208,209,211,212,213,214,216,285,297,323,326,333,336,339,360,375,410,429,431,459,473,474,502],compens:[6,217,218,301,371,402],compet:330,competit:361,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,168,193,194,195,197,240,330,361,375,429,476,477,481,502],compl:17,complain:[12,17],complement:426,complementari:[7,392,414],complet:[3,6,9,11,12,15,41,59,71,196,212,216,221,249,286,289,292,319,330,332,344,359,370,375,403,444,446,464,471,476,481,484,488,490,493,497,502],complex:[6,8,11,12,13,25,40,42,62,94,110,144,146,158,170,171,246,315,340,358,370,402,429,459,474,476,479,502],compli:[326,330],complic:[6,7,9,12,13,206,235,474],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,90,91,92,93,94,96,97,100,107,108,109,110,111,112,113,114,116,117,121,131,134,135,136,137,140,141,142,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,165,166,167,192,193,195,196,202,203,207,208,209,210,211,212,213,214,215,219,220,222,223,228,233,238,242,243,246,249,251,255,256,258,259,260,264,265,266,267,278,279,280,282,283,285,286,287,290,301,303,305,306,308,312,313,316,319,322,323,324,326,333,334,339,340,341,360,363,367,368,369,370,375,381,396,402,406,423,424,444,446,447,448,476,477,486,494,502,503],componenet:6,composit:[6,206,246,400],compound:[391,402,403,465],compres:[71,118,208],compress:[],compris:[40,340,441,464],compton:[122,169],comptu:3,compuat:361,comput:[],computation:[3,6,217,218,331,382],computational:497,compute_arrai:8,compute_fep:[201,422],compute_group_group:235,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[122,304],compute_scalar:8,compute_temp:8,compute_ti:201,compute_vector:8,compute_xrd:169,concaten:[2,3,505],concav:340,concentr:[71,400],concept:[6,150,160,208,485],conceptu:[3,6,71,158,220,222,370,392,409,426,481],concern:[6,73,89,194,236],concetr:71,concis:[11,330],conclud:12,concret:8,concurr:[9,16,361,502],conden:[331,460,462],condens:[6,152,331,377,394,400,414,465],condit:[],conducit:6,conduct:[],cone:479,confer:429,confid:[3,490],config:[12,193,473],configfil:221,configur:[1,2,6,12,15,17,38,59,126,172,190,192,193,195,199,220,221,222,223,227,235,242,243,273,286,294,330,358,368,370,377,382,401,426,429,458,460,462,465,471,476,478,479,490],confin:[476,490],conflict:[3,12,40,431,474],conform:[3,6,13,59,219,220,258,302,308,330,354,370,402,488],confus:[3,465],conjuct:396,conjug:[7,8,243,367,402,439,440],conjunct:[6,7,71,88,89,118,153,158,164,170,174,196,200,201,243,246,250,273,289,290,294,295,296,298,303,307,319,327,334,339,360,361,370,383,385,389,392,396,402,408,414,431,434,442,463,476,479,483,497,506],connect:[3,6,89,155,173,219,240,288,303,306,316,370,393,406,456,462,473,474,480,497],conput:3,consecut:[3,11,12,39,71,170,196,200,201,223,240,241,392,414,418,471,477,479],consequ:[1,6,206,331,413,490],conserv:[],consid:[6,9,70,71,78,89,119,152,155,156,173,193,196,200,201,207,209,212,216,218,219,223,247,260,285,303,326,327,330,331,334,361,389,402,409,440,441,447,456,471,472,474,477,478,479,481,484,486,494,497,502],consider:[6,8,243,244,322,323,324,375,485],consist:[3,6,8,9,11,12,40,42,65,69,79,95,107,112,115,116,119,150,153,155,170,182,192,197,202,203,208,222,223,226,228,233,236,243,244,245,256,259,261,262,263,264,265,266,267,268,269,271,272,273,274,276,277,278,279,280,281,282,290,293,298,300,302,303,322,323,324,325,335,360,361,363,369,370,375,377,382,384,390,392,402,405,409,412,423,424,426,429,431,441,444,446,447,459,466,474,476,477,478,479,480,481,488,497,502],consistent_fe_initi:205,consit:303,constant:[],constitu:[3,6,249,303,336,340,390,441],constitut:[444,446],constrain:[3,6,8,147,148,149,150,151,153,156,157,158,159,160,162,163,199,208,223,235,236,241,249,253,288,289,301,303,306,317,327,334,368,369,402,481,488,497],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,94,110,122,144,169,220,259,285,302,340,371,375,395,429,431,456,458,459,479,480,495,502],constructor:[8,11],consult:440,consum:[1,298,435,502],consumpt:358,contact:[],contact_stiff:[443,445],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,89,93,120,122,144,150,158,168,169,170,172,176,178,189,190,193,195,196,197,199,200,201,205,207,208,209,211,212,213,214,216,221,223,228,231,237,241,242,243,246,257,273,284,285,288,289,291,293,296,300,303,304,309,319,326,330,331,340,341,344,359,361,369,370,373,374,376,377,378,382,391,392,395,400,401,402,409,410,426,429,433,437,438,439,440,448,458,459,460,461,462,463,465,471,472,473,474,476,477,478,479,481,483,485,488,490,491,493,494,497,502,504,506],content:[12,18,440,492,494],context:[3,6,8,12,17,120,121,196,217,218,223,288,300,335,367,468,476,483,492,501,502,503],contibut:70,contigu:473,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,106,107,166,196,199,200,201,206,208,209,210,211,212,213,214,216,219,220,221,222,223,235,236,237,239,240,241,243,244,245,251,256,257,259,261,262,263,264,265,266,267,278,279,280,281,282,287,289,292,293,303,304,308,318,319,321,328,329,331,337,340,344,359,374,375,382,396,399,416,419,439,440,441,444,446,461,471,474,476,478,479,484,490,491,493,494,502,504],continuum:[6,7,9,205,331,444,446],contour_integr:205,contract:[59,220,222,259,290,303],contradictori:3,contrain:306,contraint:273,contrari:[237,244],contrast:[1,6,42,55,64,152,155,222,342,444,446,468,505],contrib:331,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,86,89,90,91,92,93,96,105,107,109,111,112,113,114,116,118,121,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,201,206,207,208,209,211,212,213,214,220,235,243,246,249,250,254,260,280,281,288,289,297,300,303,304,306,333,360,368,370,378,396,399,400,402,409,423,424,429,431,439,440,447,488,494,497],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,89,93,126,144,179,193,195,199,205,206,216,220,221,222,239,240,243,244,259,261,262,263,264,265,266,267,290,295,303,310,311,322,323,324,331,335,358,360,372,402,405,429,439,440,443,445,458,462,471,473,485,491,492],control_typ:205,controlfil:440,convect:93,conveni:[6,12,29,193,197,214,304,363,448,502],convent:[3,8,9,29,181,188,189,196,302,316,343,400,402,502],converg:[3,6,41,90,193,195,197,202,216,219,220,228,233,264,293,295,298,302,306,366,367,368,370,391,392,414,447,471,483,490],convers:[3,8,144,195,196,206,209,290,360,392,393,394,402,414,418,422,434,474,490,501],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,93,170,177,193,195,196,214,257,289,342,345,347,351,354,363,370,376,400,429,460,462,469,474,476,477,478,483,493,497,501,502,504,506],convex:[42,340,381],convinc:[7,12],cook:9,cooki:7,cool:[7,160,239,301],cooordin:193,cooper:[5,7],coord123:118,coord1:[3,118,208,212,213],coord2:[3,118,208,212,213],coord3:[3,118,208,212,213],coord:[],coordb:447,coordbb:447,coordiat:368,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,89,91,92,96,106,107,109,117,118,120,138,144,153,159,165,167,168,170,174,192,193,194,195,196,197,199,202,207,208,211,212,213,216,217,218,219,220,221,222,223,226,228,229,233,235,238,239,240,241,242,243,244,256,258,259,261,262,263,265,266,267,280,283,284,285,288,289,290,300,301,303,305,306,308,313,316,317,318,319,321,329,330,331,338,339,341,342,363,368,369,370,375,376,377,380,381,401,447,471,476,477,478,479,481,484,486,490,497,502,503],coordn:[118,208],coorind:[],copi:[0,3,4,8,11,12,15,17,40,123,195,331,370,389,439,474],copper:469,coproccesor:16,coprocessor:[1,4,7,9,16,17,375,489],coproprocessor:17,copy_arrai:8,copyright:[7,8,288],coral:196,core:[],core_shel:152,coreshel:[6,9,385,392,394],cornel:[6,176,488],corner123i:117,corner123x:117,corner123z:117,corner1i:117,corner1x:117,corner1z:117,corner2i:117,corner2x:117,corner2z:117,corner3i:117,corner3x:117,corner3z:117,corner:[3,6,40,117,195,340,341,363,464,476],cornflowerblu:196,cornsilk:196,corp:9,corpor:16,corr:391,correct:[3,6,9,11,12,16,17,59,89,90,105,106,114,120,152,157,164,195,222,235,237,243,259,260,280,288,290,293,330,336,340,360,370,376,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,395,396,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,464,465,467,468,469,476,491,494,497],correction_max_iter:205,correctli:[3,8,9,11,17,71,81,105,106,107,147,148,149,151,153,155,156,157,158,159,162,163,166,193,196,202,223,228,233,244,253,259,260,296,303,306,316,318,337,340,370,371,375,394,424,429,473,474,476,486,501,503],correl:[],correpond:231,correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,44,45,46,47,48,49,51,53,54,56,70,71,89,99,100,113,116,117,118,119,122,123,131,134,135,136,137,138,140,141,142,144,147,148,157,164,168,169,176,177,178,179,180,181,182,184,185,187,188,190,192,193,195,196,200,201,202,208,210,211,212,213,215,218,220,222,229,233,234,238,243,246,247,255,256,257,259,261,262,263,264,265,266,267,268,269,273,276,278,279,280,282,285,286,290,295,303,305,306,322,324,326,335,336,337,339,340,341,343,345,346,347,348,350,351,354,356,361,365,367,369,370,376,377,379,383,384,385,386,387,388,389,390,391,392,395,396,400,401,402,403,404,405,406,407,408,409,412,414,415,416,417,418,419,420,421,422,423,426,427,429,431,432,433,434,436,437,439,440,441,442,447,448,449,458,459,460,461,462,465,467,468,469,471,473,474,476,477,479,489,490,491,493,494,497,502],correspondingli:[423,424,485],cosin:[],cosineshift:27,cosmo:[237,242],cossq:[],cost:[1,6,10,11,12,17,39,41,71,113,122,145,169,195,196,208,212,213,216,217,218,232,259,295,331,360,361,373,392,414,418,429,431,458,473,485],costheta0:[458,460,462,465],costheta:437,costli:[11,90,237,371],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,89,92,96,107,109,113,116,118,150,160,165,167,183,193,195,196,200,201,208,209,212,216,222,233,242,292,293,294,298,301,303,305,319,320,326,330,331,332,336,340,342,344,352,357,359,366,368,371,375,378,404,408,409,412,439,440,472,473,474,476,478,480,483,484,491,492,497,502,503],coulomb:[3,5,6,7,8,9,10,12,14,15,18,72,90,111,112,120,145,171,175,294,296,332,360,361,368,375,383,385,386,387,388,391,392,393,394,395,402,406,407,409,414,418,422,425,431,434,439,440,442,447,457,462,463,465,468,481,488,494,497,501],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,93,118,120,121,158,168,174,202,203,206,208,211,212,213,215,216,223,228,232,235,241,259,273,289,306,322,323,340,361,368,369,370,372,375,404,408,431,494,502],counter:[337,471,482,484,490],counteract:235,counterbal:239,counterbalanc:29,counterpart:[193,303,471],counterproduct:18,coupl:[],courant:309,cours:[3,8,130,132,164,193,200,201,236,302,316,330,336,338,339,341,342,361,423,449,473,476,489,497,502,504],courtesi:363,cov:447,coval:[6,29,402,426,447,497],covari:237,cover:[6,71,190,196,205,246,402,464],coverag:[71,212],cpc:242,cpp:[1,3,6,8,9,11,12,13,89,193,200,201,233,306],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,196,210,226,244,332,358,361,375,389,457,471,489,490,493,494,495,502],cpuremain:494,cr2:169,cr3:169,crack:[4,371],crada:[5,7],crai:[5,7,13,18,193],crash:[3,12,371,497],craympi:375,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:205,create_faceset:205,create_group:194,create_nodeset:205,createatom:[],creation:[],crimson:196,critchlei:288,criteria:[3,120,171,195,196,217,218,219,254,368,436,464,478,481,502],criterion:[12,41,125,170,173,206,216,219,235,273,295,309,337,342,368,370,391,402,406,447,481,490,491],criterioni:490,critic:[6,48,49,257,326,331,368],crmax:71,crmin:71,cross:[3,12,22,71,91,148,168,178,193,195,207,212,218,222,256,258,280,303,312,316,318,327,334,346,363,370,387,396,399,400,407,408,409,414,416,418,437,442,444,446,460,462,469,476,480,486,504],crossov:1,crossterm:476,crozier:[0,7,13],crucial:293,crystal:[4,6,13,73,110,284,285,329,363,371,480,494,497],crystallin:[6,106,285,363,461,497],crystallis:326,crystallogr:[122,169],crystallograph:[363,494],crystallographi:[122,169,363],cs1:169,cs_chunk:6,cs_im:[40,476],cs_re:[40,476],csanyi:[144,438,448],cscl:426,csequ:6,csh:[11,12,389],cshrc:[11,12],csic:[401,458,460,462,465],csinfo:6,csisi:[401,458,460,462,465],csld:[],cst:400,cstherm:6,cstyle:473,csvr:[],ctcm:[376,400],ctemp_cor:226,cterm:308,ctr:9,ctype:11,cu1:169,cu2:169,cu3au:426,cube:[6,41,168,173,216,226,340,363,497],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:382,cummul:[3,6,214,217,218,219,221,232,237,243,245,319,322,323,324,325,327,334,408,494],cumul:[6,206,208,211,212,213,227,235,243,257,259,264,273,303,304,370],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,89,105,106,112,120,121,134,145,150,158,160,166,168,171,174,192,193,194,195,196,197,200,201,205,208,212,213,214,216,217,218,219,220,221,222,223,227,228,233,235,237,240,241,243,249,256,259,260,265,266,267,273,278,279,280,282,288,289,294,295,297,300,301,302,303,306,307,308,309,310,311,312,313,315,317,318,319,322,323,324,330,331,334,335,336,337,338,339,341,342,344,358,359,360,361,364,365,367,368,369,370,375,381,382,389,391,395,400,402,403,406,409,410,413,423,424,426,427,428,431,437,439,440,443,444,445,446,449,460,462,463,466,471,472,473,474,476,477,478,479,480,482,483,484,486,488,490,491,493,494,502,503,504,505,506],curv:[6,170,235,285],curvatur:[405,441,469],custom:[],cut0:474,cut1:485,cut2:485,cut:[],cuthi:[284,296],cutinn:[384,423,424],cutlo:[284,296],cutmax:437,cutoff1:[388,395,414,418,422,425,434,442],cutoff2:[383,385,386,388,394,395,414,418,422,425,434,442],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,89,94,110,112,119,120,144,168,171,173,174,218,219,224,231,284,293,294,296,298,300,303,307,319,332,336,340,342,358,360,361,368,371,372,373,375,376,377,378,379,380,381,382,383,384,385,386,387,388,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,439,440,441,442,447,448,449,450,451,452,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,474,478,481,485,497,502],cutoff_glob:381,cutoff_inn:381,cutoffa:401,cutoffc:401,cuu3:400,cval:169,cvd:326,cvel:308,cvff:[],cwiggl:[3,256,336,339,341,502],cyan:[2,195,196],cycl:[3,235,257,259,260,264],cyclic:[3,190],cygwin:12,cylind:[3,4,71,195,208,241,289,337,340,479],cylindr:[6,241,316,337],cypress:375,cyrot:382,cyrstal:285,d3q15:246,d3q19:246,d_double_doubl:15,d_e:331,d_flag2:292,d_flag:292,d_name:[117,193,292,321,486],d_single_doubl:15,d_single_singl:15,d_sx:292,d_sy:292,d_sz:292,daan:329,dai:12,daili:12,daivi:280,damag:[],dammak:298,damp:[3,6,199,204,243,244,245,250,259,260,264,290,293,294,298,303,322,323,335,337,338,367,368,370,383,385,387,392,395,402,406,414,422,434,442,457,463,490,497],damp_com:244,damp_drud:244,dampen:[303,497],dampflag:[337,406],dan:17,danger:[3,12,235,342,396,494],dangl:173,daniel:9,darden:[361,395],darkblu:196,darkcyan:196,darken:195,darkgoldenrod:196,darkgrai:196,darkgreen:196,darkkhaki:196,darkmagenta:196,darkolivegreen:196,darkorang:196,darkorchid:196,darkr:196,darksalmon:196,darkseagreen:196,darkslateblu:196,darkslategrai:196,darkturquois:196,darkviolet:196,dasgupta:294,dash:[406,493],dat:[6,93,190,205,472],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,304],dataset:304,datatyp:3,date:[0,6,12,13,192,439,440,502],datom1:119,datom2:119,datom3:119,datom4:119,datum:[3,6,42,65,68,69,79,95,112,119,193,209],davenport:425,davi:336,david:[9,19,360,361,460,462],daw:[400,437],dbg:14,dcd:[3,6,7,193,194,195,196,197,286,477,481],ddim:192,deactiv:422,dealt:242,debug:[6,7,11,12,13,14,17,122,126,169,170,286,291,358,360,375,410,431,466,474,475,483,486,493,502],deby:[],decai:[94,392,469],decid:[3,6,12,16,71,256,292,303,332,491],decipher:363,declar:194,declin:319,decod:195,decompos:[89,448],decomposit:[3,5,7,18,62,205,286,307],decoupl:[6,497],decreas:[3,193,202,203,210,219,222,228,233,235,243,330,360],decrement:308,deepli:357,deeppink:196,deepskyblu:196,def:[12,13,474],defaul:61,defect:[6,70,168,429],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,176,177,178,179,180,181,182,184,185,187,188,189,190,191,192,193,194,195,196,199,200,201,202,203,204,205,206,207,208,209,211,212,213,214,215,216,217,218,219,220,222,223,226,227,228,230,233,234,235,238,241,242,243,244,245,246,254,256,258,259,260,261,262,263,264,265,266,267,269,270,271,274,276,277,278,279,280,281,282,284,285,286,288,289,290,292,294,296,301,303,304,305,306,309,313,317,319,321,322,323,324,325,327,328,329,331,333,334,336,337,338,339,340,341,342,344,345,346,347,348,349,350,351,354,355,356,358,360,361,363,365,367,368,369,370,371,372,373,374,375,377,378,379,380,381,383,384,385,386,387,388,389,390,392,393,395,396,397,398,399,401,402,404,405,406,407,408,409,410,412,414,415,416,417,418,419,420,421,422,423,424,425,429,430,431,432,433,434,436,437,439,440,441,442,443,444,445,446,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,473,474,476,477,479,480,481,482,485,486,487,488,490,491,493,494,497,498,499,500,501,502,503],definit:[2,3,6,8,12,13,78,80,120,144,196,208,209,210,211,212,213,214,222,230,241,264,304,321,333,336,339,341,343,355,358,369,378,382,390,397,398,402,412,437,444,446,448,464,474,476,478,485,487,501,502],defint:494,deform:[],deg2theta:169,deg:497,degener:[3,288],degrad:[8,18,285,361,485],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,94,95,97,99,100,102,104,105,110,116,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,169,170,176,177,180,181,188,190,192,195,208,219,226,235,237,238,243,244,249,259,260,264,265,266,267,278,279,280,282,286,288,302,303,306,322,323,324,329,345,347,351,354,356,368,395,400,408,486,494,497,503],degress:[150,208],del:490,delai:[3,6,12,371,399,494],deleg:409,delet:[2,3,7,8,12,54,57,60,63,168,173,174,199,208,209,211,212,213,214,217,219,232,235,259,304,322,323,342,344,359,369,371,374,431,456,476,477,478,479,487,488,493,498,500,502,503],delete_atom:[],delete_bond:[],delete_el:205,deli:192,delimit:[474,502],deloc:[260,402,447],delr:426,delt_lo:490,delta:[],delta_1:382,delta_3:382,delta_7:382,delta_conf:3,delta_ij:[426,437],delta_mu:3,delta_pi:382,delta_r:437,delta_sigma:382,delta_ua:381,delx:192,delz:192,dem:381,demand:298,demo:11,demon:283,demonstr:[293,426],den:289,dendrim:408,denniston:[9,246,248,249,250,285],denomin:[7,175],denot:[122,226,244,285,296,298,392,407,409,440,444,446],dens:[71,219,402],densiti:[3,6,7,9,18,40,41,59,103,120,130,144,156,168,170,200,201,205,208,212,213,216,222,233,246,249,252,253,285,289,290,294,331,336,363,365,369,376,382,400,426,427,428,437,441,447,451,453,454,455,476,485,486,494,501],density_continu:446,density_summ:446,depart:[0,7],departur:[257,293],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,94,95,106,112,113,116,117,118,119,123,144,147,153,157,158,164,170,171,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,195,196,199,200,201,202,203,206,208,210,211,212,214,215,216,218,220,222,228,229,234,237,238,239,241,243,244,246,248,249,256,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,284,295,298,300,303,305,306,307,313,319,322,323,324,326,328,330,331,333,335,336,339,340,341,342,344,345,346,347,348,350,351,354,356,361,363,368,369,371,372,373,375,376,377,379,380,382,383,384,385,386,387,388,389,390,391,392,393,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,426,427,429,430,432,433,434,436,437,439,440,441,442,447,448,449,457,458,459,460,461,462,463,465,467,468,469,471,473,476,478,479,482,486,488,490,493,494,496,502,503],dependend:6,depflag:12,dephas:[471,490],depos:223,deposit:[],deprec:[294,439],depth:[51,148,195,331,405,441],dequidt:9,der:[89,111,390,391,422,439,440,468,497],deriv:[6,7,8,9,38,56,63,89,144,164,190,209,220,222,235,243,256,259,261,262,263,264,265,266,267,284,290,294,298,328,329,331,336,337,340,367,369,377,382,390,395,402,403,407,416,420,421,426,429,439,440,457,459,468,497],derjagin:468,derlet:284,descend:196,descent:[7,367],descib:[40,195,294],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,90,114,117,120,122,134,144,145,148,149,150,154,155,158,161,163,164,168,169,170,172,173,182,187,190,193,194,199,200,201,208,209,210,211,212,213,214,216,219,220,221,222,223,225,226,231,236,237,240,241,242,243,244,245,246,248,249,250,254,258,259,260,264,272,281,284,286,291,292,293,294,295,296,303,308,316,319,320,321,322,323,324,325,326,327,328,329,334,336,337,339,344,360,361,363,366,367,368,369,370,374,377,378,380,381,383,384,385,387,388,389,390,391,392,395,400,402,403,405,406,407,409,412,414,415,416,417,418,419,420,421,422,423,424,425,426,429,430,436,437,438,439,440,441,442,447,448,449,456,457,458,459,460,461,462,463,465,467,468,469,471,473,474,476,477,478,479,480,486,489,490,493,502,503,504],descript:[],descriptor:[144,193,410],deserno:361,design:[0,3,6,7,8,9,11,13,14,15,17,122,152,155,169,205,219,225,226,259,260,284,285,304,326,331,378,379,380,381,384,387,392,394,402,422,423,424,427,428,437,440,459],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,90,93,116,121,145,152,170,183,192,208,214,220,222,233,235,236,243,244,245,249,259,280,288,289,290,291,294,298,303,306,319,322,323,324,325,330,337,352,357,360,361,363,366,368,369,370,396,400,408,423,424,458,460,462,472,473,474,476,480,485,490,491,493,494,502,503,504],desk:7,desktop:[4,6,7,10,12,195],despit:497,destabil:382,destre:354,destroi:[11,39,217,218],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,92,93,96,105,107,109,111,113,115,116,118,121,123,144,145,147,148,149,150,153,163,164,165,167,170,171,174,175,178,189,192,193,195,196,199,200,201,205,208,209,210,211,212,214,216,218,219,220,221,222,223,233,235,236,237,238,240,241,243,245,246,250,256,257,258,259,260,261,262,263,264,265,266,267,271,273,278,279,280,281,282,285,288,289,290,292,293,295,296,297,303,306,307,319,322,323,324,325,326,327,329,330,331,332,333,334,335,342,344,346,355,360,361,364,368,369,371,372,375,376,377,378,380,381,382,384,386,387,388,389,390,391,392,395,396,402,403,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,425,426,430,431,436,439,440,441,447,448,449,457,464,467,468,474,476,477,478,479,481,482,485,486,488,491,494,495,502,503,506],detect:[2,3,12,42,61,63,88,94,234,289,330,370,391,408,413,471,473,476,487,490,502],determ:375,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,89,105,111,113,116,122,123,131,145,158,159,168,169,170,192,193,195,196,197,198,202,203,204,207,208,209,210,211,212,213,214,215,216,220,222,223,226,228,235,238,239,241,243,244,249,254,256,257,259,265,266,267,278,279,280,282,284,286,289,290,293,300,301,302,303,304,305,309,311,313,319,322,323,324,326,332,333,336,337,338,339,340,341,342,355,360,361,363,369,371,372,375,377,378,386,391,395,399,400,404,406,409,410,418,426,429,431,440,441,447,456,459,463,468,473,476,477,479,481,483,486,490,492,493,495,501,502,503],determinist:307,detil:112,devan:[9,442],devanathan:462,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,240,264,288,293,294,297,377,382,402,428,429,447,465,478],devemi:9,deviat:[257,264,284,404],deviator:9,devic:[1,3,12,15,17,240,375],device_typ:375,devin:[295,391],devis:428,dfactor:195,dff:497,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,361],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,297,429],dhi:[59,192,222,289],dhug:[257,293],dhugoniot:[257,293],dia:426,diagnost:[],diagon:[3,6,85,144,145,146,220,259,290,303,334,444,446],diagonalstyl:448,diagram:[41,122,169,189,216,286],diallo:408,diam:[195,196,289,369],diamet:[3,6,40,42,117,170,193,195,196,200,201,243,289,303,319,321,335,337,369,381,390,405,406,416,441,464,468,476,477,486],diamond:[363,402,426],diamter:[40,289],dick:6,dicsuss:256,dictat:[206,257],did:[3,12,368,396,399,400,406,431,460,462,484],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,166,333,360],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,89,94,97,99,100,124,144,147,148,149,150,151,153,156,157,158,159,160,162,163,164,170,171,173,178,189,190,192,193,195,196,199,201,204,206,208,211,216,217,218,219,220,221,222,226,231,234,235,236,237,238,239,240,243,244,246,256,259,260,261,262,263,265,266,267,269,271,274,276,277,278,279,282,284,286,288,290,293,294,295,298,301,303,30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9,341,354,360,361,390,395,396,398,402,403,406,411,423,424,426,431,441,444,446,451,452,454,455,469,497],equi:260,equidist:258,equil:[3,294,364,483,506],equilater:486,equilibr:[3,4,5,6,7,9,59,93,170,199,206,209,219,220,235,257,259,260,280,281,293,294,295,296,327,328,329,334,391,392,439,440,472,486],equilibria:334,equilibribum:[217,218],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,153,154,177,179,220,222,235,236,237,244,246,259,264,280,293,294,298,302,306,308,316,319,326,327,329,334,345,347,351,354,391,426,433,447,497],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:205,equival:[6,12,13,29,59,61,128,129,137,142,168,172,196,211,214,220,222,235,243,259,280,290,302,303,339,396,402,447,460,462,476,479,484,485,494,497],equlibrium:6,equliibr:[294,296],er3:169,eradiu:[40,117,402,476],eras:[305,328],erat:[222,424],erc:392,erfc:[392,414,431],erforc:117,erg:501,erhart:[206,400,460,462],ermscal:378,ernst:9,eror:3,eros:426,erose_form:426,erot:[],errata:[460,462],erratum:336,erron:3,error:[],erta:406,ervel:[117,476],escap:[223,497],especi:[8,11,16,158,170,199,206,216,235,293,298,301,302,375,473],espresso:[9,297],essenti:[8,11,12,27,90,132,151,152,153,156,157,158,159,160,162,179,209,264,285,335,361,377,392,414,462,481,494],essex:29,establish:[89,239],estim:[1,3,6,10,12,38,41,56,93,145,205,216,227,257,319,326,360,361,366,431,440,459,490,494],esu:501,esub:426,eta:[6,246,259,293,294,296,335,401,403,405,437,461,465,501],eta_dot:259,eta_ij:437,eta_ji:403,etag:[40,476],etail:494,etap:259,etap_dot:259,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,91,92,93,97,113,114,117,119,145,147,150,151,152,153,154,156,157,158,159,160,162,164,170,172,173,174,183,193,195,196,199,200,205,206,207,208,211,212,213,214,217,218,222,223,233,235,236,243,259,289,300,304,331,332,340,344,359,360,368,369,370,371,373,400,401,409,422,424,429,435,439,440,458,460,462,465,471,474,476,477,478,483,485,486,490,491,492,493,494,495,497,501,502,504,506],ethernet:18,etol:[368,370,471,490],etot0:293,etot:[6,97,99,100,114,145,156,196,226,244,257,293,493,494],eu2:169,eu3:169,euler:[368,370],eulerian:205,euqat:450,europhi:246,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,89,90,93,111,121,144,146,150,160,168,170,192,193,195,196,200,201,202,203,205,207,208,209,210,211,212,213,214,215,222,228,236,238,239,241,242,243,244,285,291,294,305,309,313,322,323,324,333,336,339,341,342,344,360,361,366,368,375,429,431,437,443,445,447,459,471,472,474,478,479,481,483,484,485,486,490,492,494,502,503],evalut:[344,474],evan:[158,280],evanseck:[6,20,176,387,488],evapor:[],evaul:[8,368],evdwl:[111,439,440,494],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,123,168,171,172,186,190,193,196,199,200,201,206,207,208,211,212,213,214,216,217,218,220,222,223,226,241,244,257,259,260,285,289,298,300,303,304,315,319,327,331,334,336,340,342,353,360,366,368,370,375,380,402,403,406,409,412,431,441,465,466,476,477,479,481,482,483,485,486,488,491,493,494,495,497,506],evenli:[3,41,145,190,216,246,412,466],event:[],eventu:[3,6,12,15,172,294,490],ever:[54,56,242,319],evera:[390,405,441,457],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,93,117,123,132,158,173,193,194,195,196,197,199,200,201,202,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,222,223,227,232,233,235,237,239,240,241,246,247,255,259,260,264,283,284,285,289,290,291,292,293,294,295,296,298,300,301,303,304,306,308,319,321,322,323,324,325,326,327,330,331,332,333,334,342,344,359,361,370,371,372,375,396,399,409,422,439,440,447,453,470,471,472,476,478,480,481,483,484,485,490,491,492,494,502,506],everyth:[8,111],everywher:[120,416],eviri:402,evolut:[237,246,286,471],evolv:[246,286,332],ewald:[2,3,5,6,7,8,12,90,114,122,145,332,360,361,368,383,385,386,392,395,402,414,418,434,442,457,459],ewald_disp:395,ewalddisp:3,exact:[22,41,44,71,126,164,173,178,216,219,236,237,243,244,245,289,298,299,319,331,346,360,389,478,483,490,502,504,506],exactli:[3,6,12,14,17,38,41,42,56,59,71,72,93,120,148,154,161,170,190,200,201,211,216,222,227,231,236,243,244,245,260,272,273,281,285,293,319,324,325,338,375,389,396,400,406,409,423,431,459,478,479,486,490,502],exager:497,examin:[6,8,9,17,219,285],examp:[474,502],exampl:[],exce:[3,6,16,17,18,41,58,71,172,207,208,211,212,213,214,216,220,222,227,232,259,285,300,304,310,311,319,368,375,476,502],exceed:[3,41,59,216,222,259,319,484],excel:402,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,63,71,91,92,112,113,116,121,145,147,148,149,150,151,152,153,154,156,157,158,159,160,161,162,163,170,174,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,196,199,202,208,209,211,215,216,220,222,229,234,235,238,241,243,245,259,260,261,262,263,264,265,266,267,268,269,272,273,276,278,279,280,281,282,286,295,296,303,305,306,316,319,322,324,325,331,335,339,342,344,345,346,347,348,350,351,354,355,356,360,361,363,365,369,370,371,373,374,375,376,377,379,383,384,385,386,387,388,389,390,391,392,394,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,427,432,433,434,436,439,440,441,442,449,457,458,459,460,461,462,465,467,468,469,471,473,474,476,478,479,481,484,485,486,487,488,490,494,497,501,502,503,505],excess:[210,402],exchang:[2,3,6,8,9,61,62,199,205,206,235,243,295,303,327,331,334,360,375,402,491],exchange:360,excit:[9,402],exclud:[3,6,9,12,16,17,63,71,116,144,150,157,158,174,193,208,212,217,218,247,255,288,301,303,326,337,342,368,369,371,384,406,409,412,423,424,431,456,488],exclus:[1,3,9,12,16,89,375,391,429,431,485,495],excurs:[259,471],exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,171,195,240,297,344,359,362,374,472,474,484,487,490,502],exempl:447,exemplari:236,exemplifi:402,exert:[6,241,244,298,338,339,340,361],exhaust:[205,374,502],exhibit:[94,259,367,402,485],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,126,170,171,189,194,195,196,199,204,215,218,220,223,235,288,289,291,342,345,347,348,349,351,355,364,369,375,397,398,409,439,456,466,472,474,476,477,478,487,488,489,502,503,504],exit:[2,3,11,12,41,57,193,216,231,359,374,474,475,484,493,502],exlanatori:3,exp:[],expand:[],expans:[12,144,193,487,502],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,105,151,162,168,190,216,228,235,237,256,284,290,292,293,298,303,342,361,371,389,426,429,431,471,474,476,478,481,485,490,502],expens:[6,10,71,196,284,288,303,331,342,360,361,371,375,474],experi:[6,13,15,17,215,223,240,249,258,290,302,303,366,370,396,431,485,490],experienc:[6,12,248,249],experiment:[235,360,375,490],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,88,95,150,158,190,193,195,196,199,208,209,214,216,218,220,222,259,284,292,303,316,342,344,359,360,363,369,370,374,380,400,412,447,449,464,474,477,478,481,483,486,497,502,506],explan:[3,6,59,117,144,193,208,258,284,409,470,473,474,476,485],explanatori:[3,8,121,193,207,208,211,212,213,303,369,473,502],explantori:[3,299],explic:430,explicit:[6,9,11,22,44,77,89,117,120,164,178,200,201,222,310,311,346,365,377,378,382,387,389,400,402,413,423,463,470,473,477,480],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,113,116,147,157,160,168,170,176,177,179,180,181,182,184,185,187,188,190,193,196,202,212,215,222,229,234,236,238,243,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,292,293,295,303,305,306,322,324,325,331,335,339,345,347,348,350,351,354,356,369,375,376,377,379,383,384,385,386,387,388,389,390,391,392,393,395,396,399,400,401,403,404,405,406,407,408,409,413,414,415,416,417,418,419,420,421,422,423,427,429,431,432,433,434,436,441,442,449,450,451,452,453,454,455,457,458,459,460,461,462,463,465,467,468,469,476,478,479,485,486,488,489,495,497],explictli:[16,489],exploit:[9,15,17,286],explor:[122,169],expon:[3,294,296,400,405,408,422,430,442],exponenti:[89,437,458,465,469,490,502],expos:11,exposit:[205,396,399],express:[6,144,156,170,200,201,220,256,284,294,331,337,344,382,400,402,416,426,447,448,457,502],expressiont:382,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,84,85,86,89,90,93,97,100,101,111,113,121,123,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,199,202,203,206,214,215,221,224,228,233,234,235,237,238,239,241,243,245,257,259,264,273,284,285,301,302,303,305,308,313,316,318,322,323,324,325,326,328,329,331,333,336,340,341,405,426,429,440,441,448,493,494],extent:[1,3,41,42,45,57,71,168,172,193,204,212,216,241,338,341,360,363,377,443,445,459,473,476,479],exterior:[3,6,168,340],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,105,113,114,116,122,145,147,148,149,151,153,156,157,158,159,160,162,163,169,170,171,172,176,196,211,216,218,259,291,292,293,303,319,368,369,372,373,395,406,409,412,426,431,473,474,476,479,488,497,502],extract:[3,6,11,13,36,63,89,111,119,121,123,200,201,296,370,392,403,426,448,474,481,493],extract_atom:11,extract_comput:[11,474],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,195,210,220,222,259,329,402,461,497],extrema:422,extrins:205,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[166,333],f_a:[460,461,462],f_ave:121,f_c:461,f_f:462,f_fix_id:293,f_harm:329,f_i:[29,437],f_id:[6,71,121,123,193,199,207,208,209,210,211,212,213,214,254,321,333,494,502],f_ij:437,f_indent:214,f_int:328,f_j:29,f_jj:93,f_k:437,f_langevin:331,f_max:[293,298],f_msst:257,f_r:[244,460,461,462],f_sigma:382,f_solid:329,f_ss:6,f_temp:[],face:[3,6,57,59,71,158,168,172,204,212,213,336,338,339,340,341,363,405,426,441,476,479],face_threshold:168,facet:168,facil:[0,12],facilit:[6,13,42],fact:[6,8,16,237,289,319,329,406,447,488],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,72,89,93,105,112,119,120,122,144,164,169,172,176,187,192,193,195,196,200,201,209,216,220,222,223,235,240,243,245,246,257,259,260,264,286,290,294,302,306,309,311,319,323,327,334,335,336,340,351,361,363,369,375,377,378,382,383,385,387,392,393,394,396,397,398,402,406,409,413,414,426,429,431,433,434,440,442,449,458,463,473,476,479,480,485,488,490,491,494,497,501,502],factori:[3,474],factoriz:360,fail:[3,11,12,59,174,220,223,360,368,370,394,440,474],failur:[125,444,475,502],fairli:[11,431,485,490],faken:73,falcon:240,fall:[3,6,196,211,289,474,502],fals:[88,342,344,447,502],fame:8,famili:[465,473],familiar:[0,11],fan:437,far:[3,6,12,17,57,59,61,88,193,196,197,216,217,218,220,223,259,284,302,303,319,336,347,351,366,370,371,464,474,476,481,494],farago:243,farrel:[460,462],farther:193,fashion:[6,8,41,71,170,196,199,200,201,206,212,216,218,223,235,237,241,256,257,259,261,262,263,264,265,266,267,275,278,279,280,281,282,292,293,295,303,308,312,318,321,329,331,335,336,337,339,341,370,409,423,479,488,502,505],fasolino:411,fast:[6,7,9,12,13,17,39,193,270,293,332,360,361,384,423,424,429,457,459,478,483,485,494,503,506],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,108,113,116,147,157,176,177,179,180,181,182,184,185,187,188,190,193,196,202,215,216,222,229,234,238,242,243,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,290,294,295,303,305,306,319,322,324,326,328,331,335,339,345,347,348,350,351,354,356,360,361,372,373,375,376,377,379,382,383,384,385,386,387,388,389,390,391,392,395,396,400,401,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,427,432,433,434,436,441,442,449,457,458,459,460,461,462,465,467,468,469,471,479,485,489,497],fastest:[1,6,14,17,158,212,331,332,375,473],fatal:[3,493],fault:[70,440],faulti:12,fava:405,favor:219,favorit:7,fbmc:326,fcc:[],fcm:[275,502],fdirect:226,fdotr:410,fdt:[],fdti:89,fe2:169,fe3:169,fe_md_boundari:205,featu:8,featur:[],fecr:400,feedback:[7,240],feel:[7,240,241,249,284,340,342,370,431],felling:428,felt:340,femtosecond:501,fene:[],fennel:[392,414],fep:[],ferguson:[6,176,488],fermi:[1,12,15,156,375,462],fermion:[9,402],fernando:425,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,63,197,207,208,209,211,212,213,214,244,259,289,292,294,306,333,360,368,369,370,377,447,473,476,481,485,487,495,502,504],fewer:[1,3,11,15,16,61,249,485],fewest:3,fextern:233,feynman:286,fff:474,ffield:[391,403,439,440,447],ffmpeg:[3,12,195],ffplai:195,fft:[1,3,7,12,14,15,90,113,114,145,285,360,361,485],fft_inc:[12,361],fft_lib:12,fft_path:12,fftbench:[360,495],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],ficiti:456,fictiti:[6,202,203,228,233,237,286,302,392,414,418,456],field1:[477,481],field2:477,field:[],fifth:[316,433],figur:[1,3,8,11,12,293,473,474],fij:395,file0:284,file1:[11,13,284,330,344,369,481,483,487],file2:[11,13,330,344,369,481,483,487],file:[],file_from:194,filen:369,filenam:[3,12,13,38,41,56,190,193,195,196,197,205,208,209,210,211,212,213,214,216,221,231,284,288,291,294,295,296,299,300,303,304,330,331,357,358,359,369,370,376,377,382,392,400,401,403,411,426,427,428,433,437,438,439,440,447,448,458,459,460,461,462,465,472,473,474,477,478,483,487,494,502,504,505,506],filennam:483,filep:[3,193,196,478,483,506],filepo:300,fill:[7,9,170,195,289,331,363,371,382,429,440,479],filter:[196,205],final_integr:8,final_integrate_respa:8,finchham:[6,152,394],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,89,121,173,190,197,206,219,220,231,232,235,258,284,289,290,298,302,366,368,370,371,392,409,414,418,426,447,457,459,497,502],find_custom:8,fine:[16,17,174,202,228,329,371,375,502],finer:[144,170,502],finest:360,finger:[170,192,256,479],finish:[6,11,41,216,344,357,359,360,372,374,375,464,481,502,503],finit:[],finni:[7,400,457],finvers:226,fiorin:[9,221],fire:[],firebrick:196,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,90,93,106,107,108,110,116,120,121,131,134,137,138,142,145,155,158,164,166,168,169,171,172,173,177,190,193,194,195,196,197,199,200,208,209,211,212,213,214,216,219,222,231,235,236,241,246,256,257,258,259,284,286,291,292,293,295,300,303,306,308,316,317,319,320,321,328,329,330,331,333,337,342,344,345,352,363,368,369,370,371,374,375,376,377,380,382,383,385,387,389,391,392,400,402,403,406,407,409,410,411,412,413,414,418,423,424,426,428,429,431,433,437,439,440,447,448,456,458,459,460,461,462,465,469,471,472,473,474,476,477,478,481,483,485,488,489,490,493,494,497,502,503,504,506],fischer:[6,9,19,20,176,387,488],fit:[3,6,9,12,38,56,190,231,302,319,377,382,411,426,431,452,459,461,484,502],five:[73,156,293,369,382,427,476,490],fix:[],fix_adapt:[164,201,422],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,206,289],fix_eo:9,fix_evapor:206,fix_flux:205,fix_gcmc:[206,369],fix_gl:237,fix_gld:237,fix_grav:289,fix_id:[3,220,257,259,261,262,263,264,265,266,267,290,293],fix_modifi:[],fix_mov:[192,337],fix_nh:8,fix_npt:237,fix_nvt:[206,235],fix_poem:[3,6],fix_pour:[3,223],fix_qbmsst:9,fix_qeq:[3,391],fix_rattl:306,fix_reax_bond:439,fix_rigid:[249,380],fix_saed_vtk:304,fix_setforc:8,fix_shak:306,fix_shardlow:9,fix_srd:3,fix_styl:264,fix_temp_rescal:325,fixedpoint:[220,259],fixextern:233,fixid:205,fji:395,flag1:[225,373],flag2:[225,373],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,88,91,92,96,106,107,109,122,165,169,173,193,19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117,118,119,121,123,321],input:[],input_doubl:3,inquir:309,insensit:12,insert:[3,5,7,8,12,59,170,199,223,235,241,289,360,448,456,474,480,497],insid:[2,3,6,8,11,71,133,139,170,193,196,207,212,213,223,224,232,235,241,246,249,289,303,319,336,338,339,340,341,342,358,363,416,474,475,476,478,479,486,490,502],insight:[6,13],instabl:[246,395,446],instal:[],instanc:[6,11,200,221,237,338,404,409,431,437,474,497],instantan:[6,63,219,220,236,237,259,264,285,290,293,298,300,303,326,482,494],instanti:[6,11,12,205,409,473],instead:[1,3,6,8,9,11,12,13,17,18,40,41,59,61,63,70,71,92,106,121,148,152,174,190,193,201,208,211,212,213,214,216,220,221,235,243,246,249,250,285,291,301,303,321,339,358,360,361,364,371,375,385,386,400,413,415,422,426,429,471,479,483,490,492,497,502],institut:[9,240,288],instruct:[],insuffici:[3,6,12],insult:259,insur:[3,6,11,12,17,39,40,61,73,105,107,170,171,190,193,195,196,202,217,218,223,228,229,232,233,235,238,243,255,291,292,301,303,319,331,336,340,341,342,344,359,369,371,375,390,405,409,435,441,459,473,474,476,477,481,484,485,493,494,502,503],int_max:3,integ:[3,6,8,11,12,39,40,42,64,68,70,71,110,117,119,121,123,144,168,170,173,174,176,180,181,185,190,192,193,195,196,206,208,212,213,217,218,219,223,225,233,235,236,237,240,243,244,245,246,285,288,289,292,293,298,303,319,321,323,326,330,331,350,360,363,384,396,398,399,412,426,439,440,444,446,448,471,473,474,475,476,484,485,486,490,493,502,503],integr:[],integrate_ulsph:[],intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,210,236,438,476],intens:[1,3,6,9,63,66,74,75,88,91,92,93,96,106,107,108,109,116,118,120,121,122,123,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,165,166,167,169,199,208,209,211,212,213,214,216,217,218,219,227,232,239,249,257,259,264,300,303,304,319,327,331,333,334,493,494],intepol:502,inter:[14,18,42,61,62,150,173,174,193,219,243,245,258,295,303,360,370,382,486,497,502,504,506],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,37,39,40,42,44,50,54,55,57,61,63,65,69,72,77,79,89,90,94,95,110,111,112,114,116,119,120,126,127,128,129,131,132,133,134,135,136,137,139,140,141,142,144,145,146,148,149,163,164,168,171,172,173,174,175,176,178,182,183,189,193,199,200,201,217,218,219,234,235,240,241,243,245,249,273,284,286,288,289,294,296,302,303,310,311,319,320,326,331,335,336,337,340,341,346,347,348,349,351,355,360,361,368,369,370,371,372,373,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,436,437,440,441,442,444,446,447,448,449,456,457,458,460,461,462,463,464,465,466,467,468,469,471,474,476,478,480,481,485,486,488,493,494,497,504],interatom:[3,4,7,170,193,258,328,329,376,382,400,402,410,426,429,447,461,502],intercept:122,interchang:6,interconnect:18,interconvert:402,intereract:39,interesect:340,interest:[1,5,7,8,9,11,13,71,169,286,326,329,361,401,424,439,440,474,502],interf:375,interfac:[],interfer:[12,259,377],interg:[6,497],intergr:[485,489],interi:424,interior:[3,6,41,340,479],interlac:426,interleav:[6,170,484],intermedi:[6,12,59,195,258,284,354,370,474,475,484,488],intermix:471,intermolecular:377,intern:[],internal_element_set:205,internal_quadratur:205,internet:242,interpenetr:426,interpentr:[451,452,454],interpol:[6,15,38,56,103,190,195,196,205,231,246,284,360,361,370,382,431,440,453,459,460],interpret:[2,6,11,195,211,406,449,471,474,490,502],interrupt:293,intersect:[3,6,122,196,340,342,479],intersert:340,interspers:368,interstiti:[168,429],intertia:[3,96],interv:[3,6,93,194,209,243,259,293,298,299,311,447,453,471,490,502],intestieti:122,intial:[6,375,377],intiial:[41,481],intiti:[3,318],intra:303,intra_energi:235,intramolecular:[29,235],introduc:[6,9,94,110,195,259,293,298,303,354,360,376,392,402,414,418,422,458,490,502],introduct:[],intsal:[],intuit:363,inv:[122,169,304],invalid:[3,12,71,91,173,273,370,423,424,478],invari:[110,137,142,144],invent:306,invers:[],invert:[1,6,174,285],invis:340,invoc:[168,219,375,444,446,474],invok:[1,3,6,7,8,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,59,63,66,71,74,75,81,89,90,91,92,96,106,107,109,113,114,115,116,121,147,157,164,165,168,170,171,173,174,176,177,179,180,181,182,184,185,187,188,190,193,195,196,197,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,222,223,224,225,227,228,229,232,233,234,235,236,238,239,240,241,243,244,245,246,247,248,249,250,251,252,253,255,256,258,259,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,287,288,289,290,291,292,294,295,296,297,298,299,300,301,303,304,305,306,308,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,345,347,348,350,351,354,356,359,360,361,362,363,368,370,375,376,377,379,383,384,385,386,387,388,390,391,392,395,396,400,401,403,404,4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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute 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/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","dimension command","displace_atoms command","dump 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","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 body/rounded/polygon 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","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>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":217,"default":[37,39,40,55,57,58,59,61,62,71,89,90,94,105,106,108,110,111,122,126,127,144,150,158,159,163,169,170,173,175,189,191,192,193,195,196,197,198,200,201,202,204,205,206,208,212,213,214,217,218,220,221,222,223,227,232,235,236,241,243,244,245,246,247,249,254,257,259,260,264,280,281,285,286,289,290,291,292,293,295,298,300,301,303,304,319,321,326,327,328,329,332,334,336,338,342,355,358,360,361,363,364,366,367,369,371,372,373,375,378,382,384,402,423,424,429,431,439,440,456,457,471,472,473,476,477,479,481,483,484,485,488,490,492,493,494,495,496,501,503,504,505],"function":502,"long":[210,383,385,386,387,388,392,394,395,414,418,422,434,442],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[200,201],addforc:202,addit:[12,13],addtorqu:203,adiabat:6,adjust_dt:309,adp:376,airebo:377,alloi:400,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:204,arrai:6,aspher:[6,84,148,261,265,269,270,278],atc:[9,205],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,83,87,94,98,99,102,103,104,110,114,115,117,144,145,168,204,206,207,292,502],atom_modifi:39,atom_styl:40,attract:5,aug:[],aveforc:215,awpmd:[9,378],balanc:[41,216],barostat:6,basal:67,beck:379,berendsen:[290,322],between:6,binary2txt:13,bodi:[6,8,42,68,149,262,266,271,279,380,381],bond:[8,13,69,217,218,219,299],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:382,born:[383,394],boundari:[7,57],box:[6,58,220],brownian:384,buck:[385,386,394,425],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,176,387,422],chunk:[6,66,71,75,92,96,107,109,118,150,165,167,208],citat:7,class2:[21,43,177,345,388],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[336,390,468],colvar:[9,13,221],com:[74,75,151],comb3:391,comb:[295,391],come:5,comm_modifi:61,comm_styl:62,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,502],compute_modifi:105,condit:7,conduct:[6,327],conserv:397,constant:6,constraint:7,contact:[76,124],contact_radiu:[],coord:77,core:6,correl:[209,210],cosin:[23,24,25,26,27,28,179],cossq:347,coul:[383,385,386,387,388,392,393,394,407,414,418,422,434,442],coupl:6,creat:218,create_atom:170,create_bond:171,create_box:172,createatom:13,creation:7,csld:323,csvr:323,cubic:416,cuda:[9,14,113,116,147,157,202,215,229,234,238,259,268,305,306,322,324,335,383,385,387,388,400,406,407,414,415,417,420,432,458,460],custom:8,cut:[49,378,385,388,392,395,402,404,414,415,422,430,434],cvff:348,damag:[78,125],data2xmovi:13,data:6,databas:13,deby:[392,414],dec:[],defgrad:131,deform:[153,154,222],delete_atom:173,delete_bond:174,delta:24,deposit:223,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],diagnost:7,diel:393,dielectr:175,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:178,dihedral_styl:[2,176,177,179,180,181,182,183,184,185,186,187,188,189,190],dilat:80,dimens:191,dipol:[6,29,395],direct:226,discuss:6,disp:6,displac:[81,88],displace_atom:192,distanc:349,distribut:[7,12],document:0,dpd:[9,82,83,396,397,398],drag:224,dreid:[6,408],drude:[6,9,155,225,226,244],dsf:[392,414],dsmc:399,dump:[6,8,193,194,195,197],dump_modifi:196,dynam:294,eam:[13,400],echo:198,edip:401,eff:[9,13,99,100,154,156,161,245,260,272,281,325,402],efield:228,eim:403,elast:6,emac:13,energi:[127,398],enforce2d:229,ensembl:7,erot:[84,85,86,87],error:[3,126],evapor:232,event:88,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],exp:[27,179],expand:[46,417],extend:[8,11],extern:233,fcc:284,fdt:398,featur:[7,8,502],feb:0,fene:[45,46],fep:[9,13,89,201],field:[6,7],file:6,finit:6,fire:294,fix:[2,6,8,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,3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