remove work repetitions for 'the'
This commit is contained in:
@ -2830,7 +2830,7 @@ temp/drude"_compute_temp_drude.html. This requires also to use the
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command {comm_modify vel yes}.
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command {comm_modify vel yes}.
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Short-range damping of the induced dipole interactions can be achieved
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Short-range damping of the induced dipole interactions can be achieved
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using Thole functions through the the "pair style
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using Thole functions through the "pair style
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thole"_pair_thole.html in "pair_style hybrid/overlay"_pair_hybrid.html
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thole"_pair_thole.html in "pair_style hybrid/overlay"_pair_hybrid.html
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with a Coulomb pair style. It may be useful to use {coul/long/cs} or
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with a Coulomb pair style. It may be useful to use {coul/long/cs} or
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similar from the CORESHELL package if the core and Drude particle come
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similar from the CORESHELL package if the core and Drude particle come
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@ -536,7 +536,7 @@ For the {bin/cylinder} style the details are as follows. If {discard}
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is set to {yes}, an out-of-domain atom will have its chunk ID set to
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is set to {yes}, an out-of-domain atom will have its chunk ID set to
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0. If {discard} is set to {no}, the atom will have its chunk ID set
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0. If {discard} is set to {no}, the atom will have its chunk ID set
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to the first or last bin in both the radial and axis dimensions. If
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to the first or last bin in both the radial and axis dimensions. If
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{discard} is set to {mixed}, which is the default, the the radial
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{discard} is set to {mixed}, which is the default, the radial
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dimension is treated the same as for {discard} = no. But for the axis
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dimension is treated the same as for {discard} = no. But for the axis
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dimensinon, it will only have its chunk ID set to the first or last
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dimensinon, it will only have its chunk ID set to the first or last
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bin if bins extend to the simulation box boundary in the axis
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bin if bins extend to the simulation box boundary in the axis
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@ -154,7 +154,7 @@ radians instead of degrees. (Note: This changes the way the forces
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are scaled in the 4th column of the data file.)
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are scaled in the 4th column of the data file.)
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The optional "CHECKU" keyword is followed by a filename. This allows
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The optional "CHECKU" keyword is followed by a filename. This allows
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the user to save all of the the {Ntable} different entries in the
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the user to save all of the {Ntable} different entries in the
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interpolated energy table to a file to make sure that the interpolated
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interpolated energy table to a file to make sure that the interpolated
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function agrees with the user's expectations. (Note: You can
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function agrees with the user's expectations. (Note: You can
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temporarily increase the {Ntable} parameter to a high value for this
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temporarily increase the {Ntable} parameter to a high value for this
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@ -165,7 +165,7 @@ extra buffering.
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:line
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:line
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The {element} keyword applies only to the the dump {cfg}, {xyz}, and
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The {element} keyword applies only to the dump {cfg}, {xyz}, and
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{image} styles. It associates element names (e.g. H, C, Fe) with
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{image} styles. It associates element names (e.g. H, C, Fe) with
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LAMMPS atom types. See the list of element names at the bottom of
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LAMMPS atom types. See the list of element names at the bottom of
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this page.
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this page.
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@ -150,7 +150,7 @@ initial box length is 100 Angstroms, and V is 10 Angstroms/psec, then
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after 10 psec, the box length will have doubled. After 20 psec, it
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after 10 psec, the box length will have doubled. After 20 psec, it
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will have tripled.
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will have tripled.
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The {erate} style changes a dimension of the the box at a "constant
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The {erate} style changes a dimension of the box at a "constant
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engineering strain rate". The units of the specified strain rate are
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engineering strain rate". The units of the specified strain rate are
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1/time. See the "units"_units.html command for the time units
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1/time. See the "units"_units.html command for the time units
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associated with different choices of simulation units,
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associated with different choices of simulation units,
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@ -237,7 +237,7 @@ described in the papers cited below, the purpose of this method is to
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enable longer timesteps to be used (up to the numerical stability
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enable longer timesteps to be used (up to the numerical stability
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limit of the integrator), while still producing the correct Boltzmann
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limit of the integrator), while still producing the correct Boltzmann
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distribution of atom positions. It is implemented within LAMMPS, by
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distribution of atom positions. It is implemented within LAMMPS, by
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changing how the the random force is applied so that it is composed of
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changing how the random force is applied so that it is composed of
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the average of two random forces representing half-contributions from
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the average of two random forces representing half-contributions from
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the previous and current time intervals.
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the previous and current time intervals.
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@ -87,7 +87,7 @@ end of each run. A positive value N means that the diagnostics are reported once
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per N time-steps.
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per N time-steps.
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The diagnostics report the average # of integrator steps and RHS function evaluations
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The diagnostics report the average # of integrator steps and RHS function evaluations
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and run-time per ODE as well as the the average/RMS/min/max per process. If the
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and run-time per ODE as well as the average/RMS/min/max per process. If the
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reporting frequency is 1, the RMS/min/max per ODE are also reported. The per ODE
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reporting frequency is 1, the RMS/min/max per ODE are also reported. The per ODE
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statistics can be used to adjust the tolerance and min/max step parameters. The
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statistics can be used to adjust the tolerance and min/max step parameters. The
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statistics per MPI process can be useful to examine any load imbalance caused by the
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statistics per MPI process can be useful to examine any load imbalance caused by the
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@ -28,7 +28,7 @@ fix 1 all smd/adjust_dt 0.1 :pre
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The fix calculates a new stable time increment for use with the SMD time integrators.
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The fix calculates a new stable time increment for use with the SMD time integrators.
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The stable time increment is based on multiple conditions. For the SPH pair styles, a
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The stable time increment is based on multiple conditions. For the SPH pair styles, a
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CFL criterion (Courant, Friedrichs & Lewy, 1928) is evaluated, which determines the the speed of
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CFL criterion (Courant, Friedrichs & Lewy, 1928) is evaluated, which determines the speed of
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sound cannot propagate further than a typical spacing between particles within a single time step to ensure
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sound cannot propagate further than a typical spacing between particles within a single time step to ensure
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no information is lost. For the contact pair styles, a linear analysis of the pair potential determines a
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no information is lost. For the contact pair styles, a linear analysis of the pair potential determines a
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stable maximum time step.
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stable maximum time step.
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@ -101,7 +101,7 @@ particles move in the normal way via a time integration "fix"_fix.html
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with a short timestep dt. SRD particles advect with a large timestep
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with a short timestep dt. SRD particles advect with a large timestep
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dt_SRD >= dt.
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dt_SRD >= dt.
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If the {lamda} keyword is not specified, the the SRD temperature
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If the {lamda} keyword is not specified, the SRD temperature
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{Tsrd} is used in the above formula to compute lamda. If the {lamda}
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{Tsrd} is used in the above formula to compute lamda. If the {lamda}
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keyword is specified, then the {Tsrd} setting is ignored and the above
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keyword is specified, then the {Tsrd} setting is ignored and the above
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equation is used to compute the SRD temperature.
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equation is used to compute the SRD temperature.
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@ -107,7 +107,7 @@ specified as parameters to the fix. The other quantities are derived.
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The form of the heat diffusion equation used here is almost the same
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The form of the heat diffusion equation used here is almost the same
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as that in equation 6 of "(Duffy)"_#Duffy, with the exception that the
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as that in equation 6 of "(Duffy)"_#Duffy, with the exception that the
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electronic density is explicitly reprensented, rather than being part
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electronic density is explicitly reprensented, rather than being part
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of the the specific heat parameter.
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of the specific heat parameter.
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Currently, fix ttm assumes that none of the user-supplied parameters
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Currently, fix ttm assumes that none of the user-supplied parameters
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will vary with temperature. Note that "(Duffy)"_#Duffy used a tanh()
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will vary with temperature. Note that "(Duffy)"_#Duffy used a tanh()
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@ -27,7 +27,7 @@ between quadruplets of atoms, which remain in force for the duration
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of the simulation. The list of improper quadruplets is read in by a
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of the simulation. The list of improper quadruplets is read in by a
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"read_data"_read_data.html or "read_restart"_read_restart.html command
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"read_data"_read_data.html or "read_restart"_read_restart.html command
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from a data or restart file. Note that the ordering of the 4 atoms in
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from a data or restart file. Note that the ordering of the 4 atoms in
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an improper quadruplet determines the the definition of the improper
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an improper quadruplet determines the definition of the improper
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angle used in the formula for each style. See the doc pages of
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angle used in the formula for each style. See the doc pages of
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individual styles for details.
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individual styles for details.
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@ -284,7 +284,7 @@ ID2 x2 y2 z2
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...
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...
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IDN xN yN zN :pre
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IDN xN yN zN :pre
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The fields are the the atom ID, followed by the x,y,z coordinates.
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The fields are the atom ID, followed by the x,y,z coordinates.
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The lines can be listed in any order. Additional trailing information
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The lines can be listed in any order. Additional trailing information
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on the line is OK, such as a comment.
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on the line is OK, such as a comment.
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@ -44,7 +44,7 @@ one value from their respective list of values. A {file}-style
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variable reads the next line from its associated file. An
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variable reads the next line from its associated file. An
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{atomfile}-style variable reads the next set of lines (one per atom)
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{atomfile}-style variable reads the next set of lines (one per atom)
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from its associated file. {String-} or {atom}- or {equal}- or
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from its associated file. {String-} or {atom}- or {equal}- or
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{world}-style variables cannot be used with the the next command,
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{world}-style variables cannot be used with the next command,
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since they only store a single value.
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since they only store a single value.
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When any of the variables in the next command has no more values, a
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When any of the variables in the next command has no more values, a
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@ -99,7 +99,7 @@ The optional {exclude} keyword determines if forces are computed
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between first neighbor (directly connected) bonds. For a setting of
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between first neighbor (directly connected) bonds. For a setting of
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{no}, first neighbor forces are computed; for {yes} they are not
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{no}, first neighbor forces are computed; for {yes} they are not
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computed. A setting of {no} cannot be used with the {min} option for
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computed. A setting of {no} cannot be used with the {min} option for
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distance calculation because the the minimum distance between directly
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distance calculation because the minimum distance between directly
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connected bonds is zero.
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connected bonds is zero.
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Pair style {srp} turns off normalization of thermodynamic properties
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Pair style {srp} turns off normalization of thermodynamic properties
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@ -214,7 +214,7 @@ when a correlated event occurs during the third stage of the loop
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listed above, i.e. when only one replica is running dynamics.
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listed above, i.e. when only one replica is running dynamics.
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When more than one replica detects an event at the end of the same
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When more than one replica detects an event at the end of the same
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event check (every {t_event} steps) during the the second stage, then
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event check (every {t_event} steps) during the second stage, then
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one of them is chosen at random. The number of coincident events is
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one of them is chosen at random. The number of coincident events is
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the number of replicas that detected an event. Normally, this value
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the number of replicas that detected an event. Normally, this value
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should be 1. If it is often greater than 1, then either the number of
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should be 1. If it is often greater than 1, then either the number of
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@ -241,7 +241,7 @@ time was spent in each stage (dephasing, dynamics, quenching, etc).
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Any "dump files"_dump.html defined in the input script, will be
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Any "dump files"_dump.html defined in the input script, will be
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written to during a PRD run at timesteps corresponding to both
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written to during a PRD run at timesteps corresponding to both
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uncorrelated and correlated events. This means the the requested dump
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uncorrelated and correlated events. This means the requested dump
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frequency in the "dump"_dump.html command is ignored. There will be
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frequency in the "dump"_dump.html command is ignored. There will be
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one dump file (per dump command) created for all partitions.
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one dump file (per dump command) created for all partitions.
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@ -188,7 +188,7 @@ is assumed to have been previously loaded by another python command.
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Note that the Python code that is loaded and run must contain a
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Note that the Python code that is loaded and run must contain a
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function with the specified {func} name. To operate properly when
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function with the specified {func} name. To operate properly when
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later invoked, the the function code must match the {input} and
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later invoked, the function code must match the {input} and
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{return} and {format} keywords specified by the python command.
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{return} and {format} keywords specified by the python command.
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Otherwise Python will generate an error.
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Otherwise Python will generate an error.
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@ -185,7 +185,7 @@ For dump files in {xyz} format, only the {x}, {y}, and {z} fields are
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supported. The dump file does not store atom IDs, so these are
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supported. The dump file does not store atom IDs, so these are
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assigned consecutively to the atoms as they appear in the dump file,
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assigned consecutively to the atoms as they appear in the dump file,
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starting from 1. Thus you should insure that order of atoms is
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starting from 1. Thus you should insure that order of atoms is
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consistent from snapshot to snapshot in the the XYZ dump file. See
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consistent from snapshot to snapshot in the XYZ dump file. See
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the "dump_modify sort"_dump_modify.html command if the XYZ dump file
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the "dump_modify sort"_dump_modify.html command if the XYZ dump file
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was written by LAMMPS.
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was written by LAMMPS.
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@ -195,7 +195,7 @@ velocities, or their respective plugins may not support reading of
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velocities. The molfile dump files do not store atom IDs, so these
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velocities. The molfile dump files do not store atom IDs, so these
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are assigned consecutively to the atoms as they appear in the dump
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are assigned consecutively to the atoms as they appear in the dump
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file, starting from 1. Thus you should insure that order of atoms are
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file, starting from 1. Thus you should insure that order of atoms are
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consistent from snapshot to snapshot in the the molfile dump file.
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consistent from snapshot to snapshot in the molfile dump file.
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See the "dump_modify sort"_dump_modify.html command if the dump file
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See the "dump_modify sort"_dump_modify.html command if the dump file
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was written by LAMMPS.
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was written by LAMMPS.
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@ -231,7 +231,7 @@ time was spent in each stage (NEB, dynamics, quenching, etc).
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Any "dump files"_dump.html defined in the input script will be written
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Any "dump files"_dump.html defined in the input script will be written
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to during a TAD run at timesteps when an event is executed. This
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to during a TAD run at timesteps when an event is executed. This
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means the the requested dump frequency in the "dump"_dump.html command
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means the requested dump frequency in the "dump"_dump.html command
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is ignored. There will be one dump file (per dump command) created
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is ignored. There will be one dump file (per dump command) created
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for all partitions. The atom coordinates of the dump snapshot are
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for all partitions. The atom coordinates of the dump snapshot are
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those of the minimum energy configuration resulting from quenching
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those of the minimum energy configuration resulting from quenching
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@ -33,7 +33,7 @@ created by the surrounding particles. Drude oscillators represent
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these dipoles by two fixed charges: the core (DC) and the Drude
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these dipoles by two fixed charges: the core (DC) and the Drude
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particle (DP) bound by a harmonic potential. The Drude particle can be
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particle (DP) bound by a harmonic potential. The Drude particle can be
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thought of as the electron cloud whose center can be displaced from
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thought of as the electron cloud whose center can be displaced from
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the position of the the corresponding nucleus.
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the position of the corresponding nucleus.
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The sum of the masses of a core-Drude pair should be the mass of the
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The sum of the masses of a core-Drude pair should be the mass of the
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initial (unsplit) atom, \(m_C + m_D = m\). The sum of their charges
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initial (unsplit) atom, \(m_C + m_D = m\). The sum of their charges
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Reference in New Issue
Block a user