diff --git a/doc/Eqs/polymorphic1.jpg b/doc/Eqs/polymorphic1.jpg index dd609ea6b0..4757cb7ad8 100644 Binary files a/doc/Eqs/polymorphic1.jpg and b/doc/Eqs/polymorphic1.jpg differ diff --git a/doc/Eqs/polymorphic1.tex b/doc/Eqs/polymorphic1.tex new file mode 100644 index 0000000000..b4b925ccf8 --- /dev/null +++ b/doc/Eqs/polymorphic1.tex @@ -0,0 +1,9 @@ +\documentclass[12pt]{article} + +\begin{document} + +$$ +E=\frac{1}{2}\sum_{i=1}^{i=N}\sum_{j=1}^{j=N}\left[\left(1-\delta_{ij}\right)\cdot U_{IJ}\left(r_{ij}\right)-\left(1-\eta_{ij}\right)\cdot F_{IJ}\left(r_{ij}\right)\cdot V_{IJ}\left(r_{ij}\right)\right] +$$ + +\end{document} diff --git a/doc/Eqs/polymorphic2.jpg b/doc/Eqs/polymorphic2.jpg index 95ff19514f..05133f4849 100644 Binary files a/doc/Eqs/polymorphic2.jpg and b/doc/Eqs/polymorphic2.jpg differ diff --git a/doc/Eqs/polymorphic2.tex b/doc/Eqs/polymorphic2.tex new file mode 100644 index 0000000000..80b1c93821 --- /dev/null +++ b/doc/Eqs/polymorphic2.tex @@ -0,0 +1,10 @@ +\documentclass[12pt]{article} + +\begin{document} + +$$ +X_{ij}=\sum_{k=i_1,k\neq i,j}^{i_N}W_{IK}\left(r_{ik}\right)\cdot G_{JIK}\left(\theta_{jik}\right)\cdot P_{IK}\left(\Delta r_{jik}\right) +\label{X_eq2} +$$ + +\end{document} diff --git a/doc/Eqs/polymorphic3.jpg b/doc/Eqs/polymorphic3.jpg index d39f0c27fc..ba748e63c5 100644 Binary files a/doc/Eqs/polymorphic3.jpg and b/doc/Eqs/polymorphic3.jpg differ diff --git a/doc/Eqs/polymorphic3.tex b/doc/Eqs/polymorphic3.tex new file mode 100644 index 0000000000..71db8d81b0 --- /dev/null +++ b/doc/Eqs/polymorphic3.tex @@ -0,0 +1,10 @@ +\documentclass[12pt]{article} + +\begin{document} + +$$ +\Delta r_{jik}=r_{ij}-\xi_{IJ}\cdot r_{ik} +\label{Dr_eq3} +$$ + +\end{document} diff --git a/doc/Eqs/polymorphic4.jpg b/doc/Eqs/polymorphic4.jpg index c8805b7114..7a094d6a21 100644 Binary files a/doc/Eqs/polymorphic4.jpg and b/doc/Eqs/polymorphic4.jpg differ diff --git a/doc/Eqs/polymorphic4.tex b/doc/Eqs/polymorphic4.tex new file mode 100644 index 0000000000..b792df82a0 --- /dev/null +++ b/doc/Eqs/polymorphic4.tex @@ -0,0 +1,17 @@ +\documentclass[12pt]{article} + +\begin{document} + +\begin{eqnarray*} +\left\{\begin{array}{l} +\eta_{ij}=\delta_{ij},\xi_{IJ}=0 \\ +U_{IJ}\left(r\right)=A_{IJ}\cdot\epsilon_{IJ}\cdot \left(\frac{\sigma_{IJ}}{r}\right)^q\cdot \left[B_{IJ}\cdot \left(\frac{\sigma_{IJ}}{r}\right)^{p-q}-1\right]\cdot exp\left(\frac{\sigma_{IJ}}{r-a_{IJ}\cdot \sigma_{IJ}}\right) \\ +V_{IJ}\left(r\right)=\sqrt{\lambda_{IJ}\cdot \epsilon_{IJ}}\cdot exp\left(\frac{\gamma_{IJ}\cdot \sigma_{IJ}}{r-a_{IJ}\cdot \sigma_{IJ}}\right) \\ +F_{IJ}\left(X\right)=-X \\ +P_{IJ}\left(\Delta r\right)=1 \\ +W_{IJ}\left(r\right)=\sqrt{\lambda_{IJ}\cdot \epsilon_{IJ}}\cdot exp\left(\frac{\gamma_{IJ}\cdot \sigma_{IJ}}{r-a_{IJ}\cdot \sigma_{IJ}}\right) \\ +G_{JIK}\left(\theta\right)=\left(cos\theta+\frac{1}{3}\right)^2 +\end{array}\right. +\end{eqnarray*} + +\end{document} diff --git a/doc/Eqs/polymorphic5.jpg b/doc/Eqs/polymorphic5.jpg index 0f86a79e61..500238b2a9 100644 Binary files a/doc/Eqs/polymorphic5.jpg and b/doc/Eqs/polymorphic5.jpg differ diff --git a/doc/Eqs/polymorphic5.tex b/doc/Eqs/polymorphic5.tex new file mode 100644 index 0000000000..a5451b98d6 --- /dev/null +++ b/doc/Eqs/polymorphic5.tex @@ -0,0 +1,17 @@ +\documentclass[12pt]{article} + +\begin{document} + +\begin{eqnarray*} +\left\{\begin{array}{l} +\eta_{ij}=\delta_{ij},\xi_{IJ}=1 \\ +U_{IJ}\left(r\right)=\frac{D_{e,IJ}}{S_{IJ}-1}\cdot exp\left[-\beta_{IJ}\sqrt{2S_{IJ}\left(r-r_{e,IJ}\right)}\right]\cdot f_{c,IJ}\left(r\right) \\ +V_{IJ}\left(r\right)=\frac{S_{IJ}\cdot D_{e,IJ}}{S_{IJ}-1}\cdot exp\left[-\beta_{IJ}\sqrt{\frac{2}{S_{IJ}}\left(r-r_{e,IJ}\right)}\right]\cdot f_{c,IJ}\left(r\right) \\ +F_{IJ}\left(X\right)=\left(1+X\right)^{-\frac{1}{2}} \\ +P_{IJ}\left(\Delta r\right)=exp\left(2\mu_{IK}\cdot \Delta r\right) \\ +W_{IJ}\left(r\right)=f_{c,IK}\left(r\right) \\ +G_{JIK}\left(\theta\right)=\gamma_{IK}\left[1+\frac{c_{IK}^2}{d_{IK}^2}-\frac{c_{IK}^2}{d_{IK}^2+\left(h_{IK}+cos\theta\right)^2}\right] +\end{array}\right. +\end{eqnarray*} + +\end{document} diff --git a/doc/Eqs/polymorphic6.jpg b/doc/Eqs/polymorphic6.jpg index b94e3514f8..65ea78bf21 100644 Binary files a/doc/Eqs/polymorphic6.jpg and b/doc/Eqs/polymorphic6.jpg differ diff --git a/doc/Eqs/polymorphic6.tex b/doc/Eqs/polymorphic6.tex new file mode 100644 index 0000000000..c8f9f2f25b --- /dev/null +++ b/doc/Eqs/polymorphic6.tex @@ -0,0 +1,13 @@ +\documentclass[12pt]{article} + +\begin{document} + +\begin{eqnarray*} +f_{c,IJ}=\left\{\begin{array}{lr} +1, & r\leq r_{s,IJ} \\ +\frac{1}{2}+\frac{1}{2} cos \left[\frac{\pi \left(r-r_{s,IJ}\right)}{r_{c,IJ}-r_{s,IJ}}\right], & r_{s,IJ} source code for individual scripts for comments about what they do.

Here are screenshots of the vizplotgui_tool.py script in action for different visualization package options. Click to see larger images:

- width="25%" height="auto" alt=""/> - width="25%" height="auto" alt=""/> - width="25%" height="auto" alt=""/> - 
 id value = yes or no
-   map value = array or hash
-   first value = group-ID = group whose atoms will appear first in internal atom lists
-   sort values = Nfreq binsize
-     Nfreq = sort atoms spatially every this many time steps
-     binsize = bin size for spatial sorting (distance units)
+map value = array or hash
+first value = group-ID = group whose atoms will appear first in internal atom lists
+sort values = Nfreq binsize
+  Nfreq = sort atoms spatially every this many time steps
+  binsize = bin size for spatial sorting (distance units)
diff --git a/doc/atom_style.html b/doc/atom_style.html index a335d9a186..44c663f6b0 100644 --- a/doc/atom_style.html +++ b/doc/atom_style.html @@ -136,13 +136,13 @@ 
 args = none for any style except body and hybrid
-  body args = bstyle bstyle-args
-    bstyle = style of body particles
-    bstyle-args = additional arguments specific to the bstyle
-                  see the body doc page for details
-  template args = template-ID
-    template-ID = ID of molecule template specified in a separate molecule command
-  hybrid args = list of one or more sub-styles, each with their args
+body args = bstyle bstyle-args
+  bstyle = style of body particles
+  bstyle-args = additional arguments specific to the bstyle
+                see the body doc page for details
+template args = template-ID
+  template-ID = ID of molecule template specified in a separate molecule command
+hybrid args = list of one or more sub-styles, each with their args
 
 x args = uniform or Px-1 numbers between 0 and 1
-    uniform = evenly spaced cuts between processors in x dimension
-    numbers = Px-1 ascending values between 0 and 1, Px - # of processors in x dimension
-    x can be specified together with y or z
-  y args = uniform or Py-1 numbers between 0 and 1
-    uniform = evenly spaced cuts between processors in y dimension
-    numbers = Py-1 ascending values between 0 and 1, Py - # of processors in y dimension
-    y can be specified together with x or z
-  z args = uniform or Pz-1 numbers between 0 and 1
-    uniform = evenly spaced cuts between processors in z dimension
-    numbers = Pz-1 ascending values between 0 and 1, Pz - # of processors in z dimension
-    z can be specified together with x or y
-  shift args = dimstr Niter stopthresh
-    dimstr = sequence of letters containing "x" or "y" or "z", each not more than once
-    Niter = # of times to iterate within each dimension of dimstr sequence
-    stopthresh = stop balancing when this imbalance threshhold is reached
-  rcb args = none
+  uniform = evenly spaced cuts between processors in x dimension
+  numbers = Px-1 ascending values between 0 and 1, Px - # of processors in x dimension
+  x can be specified together with y or z
+y args = uniform or Py-1 numbers between 0 and 1
+  uniform = evenly spaced cuts between processors in y dimension
+  numbers = Py-1 ascending values between 0 and 1, Py - # of processors in y dimension
+  y can be specified together with x or z
+z args = uniform or Pz-1 numbers between 0 and 1
+  uniform = evenly spaced cuts between processors in z dimension
+  numbers = Pz-1 ascending values between 0 and 1, Pz - # of processors in z dimension
+  z can be specified together with x or y
+shift args = dimstr Niter stopthresh
+  dimstr = sequence of letters containing "x" or "y" or "z", each not more than once
+  Niter = # of times to iterate within each dimension of dimstr sequence
+  stopthresh = stop balancing when this imbalance threshhold is reached
+rcb args = none
 
 out value = filename
-    filename = write each processor's sub-domain to a file
+  filename = write each processor's sub-domain to a file
@@ -265,7 +265,7 @@ the processor that owns them. The leftmost diagram is the default partitioning of the simulation box across processors (one sub-box for each of 16 processors); the middle diagram is after a “grid” method has been applied.

- width="25%" height="auto" alt=""/> - width="25%" height="auto" alt=""/> - 
 args = none for any style except hybrid
-  hybrid args = list of one or more styles
+hybrid args = list of one or more styles
diff --git a/doc/boundary.html b/doc/boundary.html index ddb828d6d1..e88643e33a 100644 --- a/doc/boundary.html +++ b/doc/boundary.html @@ -136,9 +136,9 @@ 
 p is periodic
-  f is non-periodic and fixed
-  s is non-periodic and shrink-wrapped
-  m is non-periodic and shrink-wrapped with a minimum value
+f is non-periodic and fixed
+s is non-periodic and shrink-wrapped
+m is non-periodic and shrink-wrapped with a minimum value
diff --git a/doc/change_box.html b/doc/change_box.html index 965a0e2b13..035cb51631 100644 --- a/doc/change_box.html +++ b/doc/change_box.html @@ -169,8 +169,8 @@ parameter = x or y or z or xy or xz 
 units value = lattice or box
-    lattice = distances are defined in lattice units
-    box = distances are defined in simulation box units
+  lattice = distances are defined in lattice units
+  box = distances are defined in simulation box units
diff --git a/doc/comm_modify.html b/doc/comm_modify.html index afece0170d..0e6556cb96 100644 --- a/doc/comm_modify.html +++ b/doc/comm_modify.html @@ -137,9 +137,9 @@ 
 mode value = single or multi = communicate atoms within a single or multiple distances
-  cutoff value = Rcut (distance units) = communicate atoms from this far away
-  group value = group-ID = only communicate atoms in the group
-  vel value = yes or no = do or do not communicate velocity info with ghost atoms
+cutoff value = Rcut (distance units) = communicate atoms from this far away
+group value = group-ID = only communicate atoms in the group
+vel value = yes or no = do or do not communicate velocity info with ghost atoms
diff --git a/doc/compute_angle_local.html b/doc/compute_angle_local.html index 528a8cc3a4..3cb3b54153 100644 --- a/doc/compute_angle_local.html +++ b/doc/compute_angle_local.html @@ -139,7 +139,7 @@ 
 theta = tabulate angles
-  eng = tabulate angle energies
+eng = tabulate angle energies
diff --git a/doc/compute_body_local.html b/doc/compute_body_local.html index 7d49a8ae38..45627009ef 100644 --- a/doc/compute_body_local.html +++ b/doc/compute_body_local.html @@ -139,7 +139,7 @@ 
 type = atom type of the body particle
-  integer = 1,2,3,etc = index of fields defined by body style
+integer = 1,2,3,etc = index of fields defined by body style
diff --git a/doc/compute_bond_local.html b/doc/compute_bond_local.html index 16fc047c5f..e68b6c855e 100644 --- a/doc/compute_bond_local.html +++ b/doc/compute_bond_local.html @@ -139,8 +139,8 @@ 
 dist = bond distance
-  eng = bond energy
-  force = bond force
+eng = bond energy
+force = bond force
diff --git a/doc/compute_chunk_atom.html b/doc/compute_chunk_atom.html index 70a6675a0d..9436064703 100644 --- a/doc/compute_chunk_atom.html +++ b/doc/compute_chunk_atom.html @@ -164,30 +164,30 @@ style = bin/1d or bin/2d or bin/3d or type o 
 region value = region-ID
-    region-ID = ID of region atoms must be in to be part of a chunk
-  nchunk value = once or every
-    once = only compute the number of chunks once
-    every = re-compute the number of chunks whenever invoked
-  limit values = 0 or Nc max or Nc exact
-    0 = no limit on the number of chunks
-    Nc max = limit number of chunks to be <= Nc
-    Nc exact = set number of chunks to exactly Nc
-  ids value = once or nfreq or every
-    once = assign chunk IDs to atoms only once, they persist thereafter
-    nfreq = assign chunk IDs to atoms only once every Nfreq steps (if invoked by fix ave/chunk which sets Nfreq)
-    every = assign chunk IDs to atoms whenever invoked
-  compress value = yes or no
-    yes = compress chunk IDs to eliminate IDs with no atoms
-    no = do not compress chunk IDs even if some IDs have no atoms
-  discard value = yes or no or mixed
-    yes = discard atoms with out-of-range chunk IDs by assigning a chunk ID = 0
-    no = keep atoms with out-of-range chunk IDs by assigning a valid chunk ID
-    mixed = keep or discard such atoms according to spatial binning rule
-  bound values = x/y/z lo hi
-    x/y/z = x or y or z to bound sptial bins in this dimension
-    lo = lower or coordinate value (distance units)
-    hi = upper or coordinate value (distance units)
-  units value = box or lattice or reduced
+  region-ID = ID of region atoms must be in to be part of a chunk
+nchunk value = once or every
+  once = only compute the number of chunks once
+  every = re-compute the number of chunks whenever invoked
+limit values = 0 or Nc max or Nc exact
+  0 = no limit on the number of chunks
+  Nc max = limit number of chunks to be <= Nc
+  Nc exact = set number of chunks to exactly Nc
+ids value = once or nfreq or every
+  once = assign chunk IDs to atoms only once, they persist thereafter
+  nfreq = assign chunk IDs to atoms only once every Nfreq steps (if invoked by fix ave/chunk which sets Nfreq)
+  every = assign chunk IDs to atoms whenever invoked
+compress value = yes or no
+  yes = compress chunk IDs to eliminate IDs with no atoms
+  no = do not compress chunk IDs even if some IDs have no atoms
+discard value = yes or no or mixed
+  yes = discard atoms with out-of-range chunk IDs by assigning a chunk ID = 0
+  no = keep atoms with out-of-range chunk IDs by assigning a valid chunk ID
+  mixed = keep or discard such atoms according to spatial binning rule
+bound values = x/y/z lo hi
+  x/y/z = x or y or z to bound sptial bins in this dimension
+  lo = lower or coordinate value (distance units)
+  hi = upper or coordinate value (distance units)
+units value = box or lattice or reduced
diff --git a/doc/compute_fep.html b/doc/compute_fep.html index baa065c878..04b631a922 100644 --- a/doc/compute_fep.html +++ b/doc/compute_fep.html @@ -140,14 +140,14 @@ 
 pair args = pstyle pparam I J v_delta
-    pstyle = pair style name, e.g. lj/cut
-    pparam = parameter to perturb
-    I,J = type pair(s) to set parameter for
-    v_delta = variable with perturbation to apply (in the units of the parameter)
-  atom args = aparam I v_delta
-    aparam = parameter to perturb
-    I = type to set parameter for
-    v_delta = variable with perturbation to apply (in the units of the parameter)
+  pstyle = pair style name, e.g. lj/cut
+  pparam = parameter to perturb
+  I,J = type pair(s) to set parameter for
+  v_delta = variable with perturbation to apply (in the units of the parameter)
+atom args = aparam I v_delta
+  aparam = parameter to perturb
+  I = type to set parameter for
+  v_delta = variable with perturbation to apply (in the units of the parameter)
 
 tail value = no or yes
-    no = ignore tail correction to pair energies (usually small in fep)
-    yes = include tail correction to pair energies
-  volume value = no or yes
-    no = ignore volume changes (e.g. in NVE or NVT trajectories)
-    yes = include volume changes (e.g. in NpT trajectories)
+  no = ignore tail correction to pair energies (usually small in fep)
+  yes = include tail correction to pair energies
+volume value = no or yes
+  no = ignore volume changes (e.g. in NVE or NVT trajectories)
+  yes = include volume changes (e.g. in NpT trajectories)
diff --git a/doc/compute_group_group.html b/doc/compute_group_group.html index 8fb773e85d..12f39d64ca 100644 --- a/doc/compute_group_group.html +++ b/doc/compute_group_group.html @@ -140,8 +140,8 @@ 
 pair value = yes or no
-  kspace value = yes or no
-  boundary value = yes or no
+kspace value = yes or no
+boundary value = yes or no
diff --git a/doc/compute_modify.html b/doc/compute_modify.html index bae366645a..356a02d1ff 100644 --- a/doc/compute_modify.html +++ b/doc/compute_modify.html @@ -138,11 +138,11 @@ 
 extra value = N
-    N = # of extra degrees of freedom to subtract
-  dynamic value = yes or no
-    yes/no = do or do not recompute the number of atoms contributing to the temperature
-  thermo value = yes or no
-    yes/no = do or do not add contributions from fixes to the potential energy
+  N = # of extra degrees of freedom to subtract
+dynamic value = yes or no
+  yes/no = do or do not recompute the number of atoms contributing to the temperature
+thermo value = yes or no
+  yes/no = do or do not add contributions from fixes to the potential energy
diff --git a/doc/compute_pair_local.html b/doc/compute_pair_local.html index 5dfc14d934..575e145701 100644 --- a/doc/compute_pair_local.html +++ b/doc/compute_pair_local.html @@ -139,10 +139,10 @@ 
 dist = pairwise distance
-  eng = pairwise energy
-  force = pairwise force
-  fx,*fy*,*fz* = components of pairwise force
-  pN = pair style specific quantities for allowed N values
+eng = pairwise energy
+force = pairwise force
+fx,*fy*,*fz* = components of pairwise force
+pN = pair style specific quantities for allowed N values
diff --git a/doc/compute_property_atom.html b/doc/compute_property_atom.html index d89557b127..bbbd2b2a8d 100644 --- a/doc/compute_property_atom.html +++ b/doc/compute_property_atom.html @@ -137,73 +137,73 @@
  • input = one or more atom attributes
    • possible attributes = id, mol, proc, type, mass,
-                     x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
-                     vx, vy, vz, fx, fy, fz,
-                        q, mux, muy, muz, mu,
-                        radius, diameter, omegax, omegay, omegaz,
-                     angmomx, angmomy, angmomz,
-                     shapex,shapey, shapez,
-                     quatw, quati, quatj, quatk, tqx, tqy, tqz,
-                     end1x, end1y, end1z, end2x, end2y, end2z,
-                     corner1x, corner1y, corner1z,
-                     corner2x, corner2y, corner2z,
-                     corner3x, corner3y, corner3z,
-                     nbonds,
-                        vfrac, s0,
-                     spin, eradius, ervel, erforce,
-                        rho, drho, e, de, cv,
-                        i_name, d_name
+                   x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
+                   vx, vy, vz, fx, fy, fz,
+                      q, mux, muy, muz, mu,
+                      radius, diameter, omegax, omegay, omegaz,
+                   angmomx, angmomy, angmomz,
+                   shapex,shapey, shapez,
+                   quatw, quati, quatj, quatk, tqx, tqy, tqz,
+                   end1x, end1y, end1z, end2x, end2y, end2z,
+                   corner1x, corner1y, corner1z,
+                   corner2x, corner2y, corner2z,
+                   corner3x, corner3y, corner3z,
+                   nbonds,
+                      vfrac, s0,
+                   spin, eradius, ervel, erforce,
+                      rho, drho, e, de, cv,
+                      i_name, d_name
 
    id = atom ID
-      mol = molecule ID
-      proc = ID of processor that owns atom
-      type = atom type
-      mass = atom mass
-      x,y,z = unscaled atom coordinates
-      xs,ys,zs = scaled atom coordinates
-      xu,yu,zu = unwrapped atom coordinates
-      ix,iy,iz = box image that the atom is in
-      vx,vy,vz = atom velocities
-      fx,fy,fz = forces on atoms
-      q = atom charge
-      mux,muy,muz = orientation of dipole moment of atom
-      mu = magnitude of dipole moment of atom
-      radius,diameter = radius,diameter of spherical particle
-      omegax,omegay,omegaz = angular velocity of spherical particle
-      angmomx,angmomy,angmomz = angular momentum of aspherical particle
-      shapex,shapey,shapez = 3 diameters of aspherical particle
-      quatw,quati,quatj,quatk = quaternion components for aspherical or body particles
-      tqx,tqy,tqz = torque on finite-size particles
-      end12x, end12y, end12z = end points of line segment
-      corner123x, corner123y, corner123z = corner points of triangle
-      nbonds = number of bonds assigned to an atom
+mol = molecule ID
+proc = ID of processor that owns atom
+type = atom type
+mass = atom mass
+x,y,z = unscaled atom coordinates
+xs,ys,zs = scaled atom coordinates
+xu,yu,zu = unwrapped atom coordinates
+ix,iy,iz = box image that the atom is in
+vx,vy,vz = atom velocities
+fx,fy,fz = forces on atoms
+q = atom charge
+mux,muy,muz = orientation of dipole moment of atom
+mu = magnitude of dipole moment of atom
+radius,diameter = radius,diameter of spherical particle
+omegax,omegay,omegaz = angular velocity of spherical particle
+angmomx,angmomy,angmomz = angular momentum of aspherical particle
+shapex,shapey,shapez = 3 diameters of aspherical particle
+quatw,quati,quatj,quatk = quaternion components for aspherical or body particles
+tqx,tqy,tqz = torque on finite-size particles
+end12x, end12y, end12z = end points of line segment
+corner123x, corner123y, corner123z = corner points of triangle
+nbonds = number of bonds assigned to an atom
 
    PERI package per-atom properties:
-      vfrac = ???
-      s0 = ???
+vfrac = ???
+s0 = ???
 
    USER-EFF and USER-AWPMD package per-atom properties:
-      spin = electron spin
-      eradius = electron radius
-      ervel = electron radial velocity
-      erforce = electron radial force
+spin = electron spin
+eradius = electron radius
+ervel = electron radial velocity
+erforce = electron radial force
 
    USER-SPH package per-atom properties:
-      rho = ???
-      drho = ???
-      e = ???
-      de = ???
-      cv = ???
+rho = ???
+drho = ???
+e = ???
+de = ???
+cv = ???
 
     fix property/atom per-atom properties:
-      i_name = custom integer vector with name
-      d_name = custom integer vector with name
+i_name = custom integer vector with name
+d_name = custom integer vector with name
    diff --git a/doc/compute_property_chunk.html b/doc/compute_property_chunk.html index b1ed2e54f8..e64677384a 100644 --- a/doc/compute_property_chunk.html +++ b/doc/compute_property_chunk.html @@ -138,9 +138,9 @@ 
     attributes = count, id, coord1, coord2, coord3
-    count = # of atoms in chunk
-    id = original chunk IDs before compression by compute chunk/atom
-    coord123 = coordinates for spatial bins calculated by compute chunk/atom
+  count = # of atoms in chunk
+  id = original chunk IDs before compression by compute chunk/atom
+  coord123 = coordinates for spatial bins calculated by compute chunk/atom
    diff --git a/doc/compute_property_local.html b/doc/compute_property_local.html index 6880ac42ce..36d7d062c3 100644 --- a/doc/compute_property_local.html +++ b/doc/compute_property_local.html @@ -137,25 +137,25 @@
  • input = one or more attributes
    • possible attributes = natom1 natom2 ntype1 ntype2
-                     patom1 patom2 ptype1 ptype2
-                        batom1 batom2 btype
-                        aatom1 aatom2 aatom3 atype
-                        datom1 datom2 datom3 dtype
-                        iatom1 iatom2 iatom3 itype
+                   patom1 patom2 ptype1 ptype2
+                      batom1 batom2 btype
+                      aatom1 aatom2 aatom3 atype
+                      datom1 datom2 datom3 dtype
+                      iatom1 iatom2 iatom3 itype
 
    natom1, natom2 = IDs of 2 atoms in each pair (within neighbor cutoff)
-     ntype1, ntype2 = type of 2 atoms in each pair (within neighbor cutoff)
-     patom1, patom2 = IDs of 2 atoms in each pair (within force cutoff)
-     ptype1, ptype2 = type of 2 atoms in each pair (within force cutoff)
-     batom1, batom2 = IDs of 2 atoms in each bond
-     btype = bond type of each bond
-     aatom1, aatom2, aatom3 = IDs of 3 atoms in each angle
-     atype = angle type of each angle
-     datom1, datom2, datom3, datom4 = IDs of 4 atoms in each dihedral
-     dtype = dihedral type of each dihedral
-     iatom1, iatom2, iatom3, iatom4 = IDs of 4 atoms in each improper
-     itype = improper type of each improper
+ntype1, ntype2 = type of 2 atoms in each pair (within neighbor cutoff)
+patom1, patom2 = IDs of 2 atoms in each pair (within force cutoff)
+ptype1, ptype2 = type of 2 atoms in each pair (within force cutoff)
+batom1, batom2 = IDs of 2 atoms in each bond
+btype = bond type of each bond
+aatom1, aatom2, aatom3 = IDs of 3 atoms in each angle
+atype = angle type of each angle
+datom1, datom2, datom3, datom4 = IDs of 4 atoms in each dihedral
+dtype = dihedral type of each dihedral
+iatom1, iatom2, iatom3, iatom4 = IDs of 4 atoms in each improper
+itype = improper type of each improper
    diff --git a/doc/compute_reduce.html b/doc/compute_reduce.html index abe0a590e3..88ad4ce15d 100644 --- a/doc/compute_reduce.html +++ b/doc/compute_reduce.html @@ -140,8 +140,8 @@ 
     reduce arg = none
-  reduce/region arg = region-ID
-    region-ID = ID of region to use for choosing atoms
+reduce/region arg = region-ID
+  region-ID = ID of region to use for choosing atoms
 
    x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
-  c_ID = per-atom or local vector calculated by a compute with ID
-  c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID
-  f_ID = per-atom or local vector calculated by a fix with ID
-  f_ID[I] = Ith column of per-atom or local array calculated by a fix with ID
-  v_name = per-atom vector calculated by an atom-style variable with name
+c_ID = per-atom or local vector calculated by a compute with ID
+c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID
+f_ID = per-atom or local vector calculated by a fix with ID
+f_ID[I] = Ith column of per-atom or local array calculated by a fix with ID
+v_name = per-atom vector calculated by an atom-style variable with name
 
     replace args = vec1 vec2
-    vec1 = reduced value from this input vector will be replaced
-    vec2 = replace it with vec1[N] where N is index of max/min value from vec2
+  vec1 = reduced value from this input vector will be replaced
+  vec2 = replace it with vec1[N] where N is index of max/min value from vec2
    diff --git a/doc/compute_saed.html b/doc/compute_saed.html index 59e0cca8f4..82ac23e106 100644 --- a/doc/compute_saed.html +++ b/doc/compute_saed.html @@ -141,18 +141,18 @@ 
     Kmax value = Maximum distance explored from reciprocal space origin
-                 (inverse length units)
-  Zone values = z1 z2 z3
-    z1,z2,z3 = Zone axis of incident radiation. If z1=z2=z3=0 all
-               reciprocal space will be meshed up to Kmax
-  dR_Ewald value = Thickness of Ewald sphere slice intercepting
-                     reciprocal space (inverse length units)
-  c values = c1 c2 c3
-    c1,c2,c3 = parameters to adjust the spacing of the reciprocal
-               lattice nodes in the h, k, and l directions respectively
-  manual = flag to use manual spacing of reciprocal lattice points
-             based on the values of the c parameters
-  echo = flag to provide extra output for debugging purposes
+               (inverse length units)
+Zone values = z1 z2 z3
+  z1,z2,z3 = Zone axis of incident radiation. If z1=z2=z3=0 all
+             reciprocal space will be meshed up to Kmax
+dR_Ewald value = Thickness of Ewald sphere slice intercepting
+                   reciprocal space (inverse length units)
+c values = c1 c2 c3
+  c1,c2,c3 = parameters to adjust the spacing of the reciprocal
+             lattice nodes in the h, k, and l directions respectively
+manual = flag to use manual spacing of reciprocal lattice points
+           based on the values of the c parameters
+echo = flag to provide extra output for debugging purposes
    @@ -182,7 +182,7 @@ position of each atom, fj are atomic scattering factors.

    reciprocal lattice nodes. The mesh spacing is defined either (a) by the entire simulation domain or (b) manually using selected values as shown in the 2D diagram below.

    -dR_Ewald thick surface of the Ewald sphere. See the example 3D intestiety data and the intersection of a [010] zone axis in the below image.

    -    input = c_ID, c_ID[N], f_ID, f_ID[N] 
    c_ID = global vector calculated by a compute with ID
-  c_ID[I] = Ith column of global array calculated by a compute with ID
-  f_ID = global vector calculated by a fix with ID
-  f_ID[I] = Ith column of global array calculated by a fix with ID
+c_ID[I] = Ith column of global array calculated by a compute with ID
+f_ID = global vector calculated by a fix with ID
+f_ID[I] = Ith column of global array calculated by a fix with ID
    diff --git a/doc/compute_sna_atom.html b/doc/compute_sna_atom.html index ca1f38bb45..840a929347 100644 --- a/doc/compute_sna_atom.html +++ b/doc/compute_sna_atom.html @@ -152,14 +152,14 @@ compute ID group-ID snav/atom ntypes rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 . 
     diagonal value = 0 or 1 or 2 or 3
-     0 = all j1, j2, j <= twojmax, j2 <= j1
-     1 = subset satisfying j1 == j2
-     2 = subset satisfying j1 == j2 == j3
-     3 = subset satisfying j2 <= j1 <= j
-  rmin0 value = parameter in distance to angle conversion (distance units)
-  switchflag value = 0 or 1
-     0 = do not use switching function
-     1 = use switching function
+   0 = all j1, j2, j <= twojmax, j2 <= j1
+   1 = subset satisfying j1 == j2
+   2 = subset satisfying j1 == j2 == j3
+   3 = subset satisfying j2 <= j1 <= j
+rmin0 value = parameter in distance to angle conversion (distance units)
+switchflag value = 0 or 1
+   0 = do not use switching function
+   1 = use switching function
    diff --git a/doc/compute_temp_asphere.html b/doc/compute_temp_asphere.html index 46080aa81b..47e12a4149 100644 --- a/doc/compute_temp_asphere.html +++ b/doc/compute_temp_asphere.html @@ -139,10 +139,10 @@ 
     bias value = bias-ID
-    bias-ID = ID of a temperature compute that removes a velocity bias
-  dof value = all or rotate
-    all = compute temperature of translational and rotational degrees of freedom
-    rotate = compute temperature of just rotational degrees of freedom
+  bias-ID = ID of a temperature compute that removes a velocity bias
+dof value = all or rotate
+  all = compute temperature of translational and rotational degrees of freedom
+  rotate = compute temperature of just rotational degrees of freedom
    diff --git a/doc/compute_temp_chunk.html b/doc/compute_temp_chunk.html index 69baa0f1c7..e6705e267f 100644 --- a/doc/compute_temp_chunk.html +++ b/doc/compute_temp_chunk.html @@ -139,8 +139,8 @@
  • value = temp or kecom or internal
    • temp = temperature of each chunk
-  kecom = kinetic energy of each chunk based on velocity of center of mass
-  internal = internal kinetic energy of each chunk
+kecom = kinetic energy of each chunk based on velocity of center of mass
+internal = internal kinetic energy of each chunk
      @@ -149,14 +149,14 @@ 
     com value = yes or no
-    yes = subtract center-of-mass velocity from each chunk before calculating temperature
-    no = do not subtract center-of-mass velocity
-  bias value = bias-ID
-    bias-ID = ID of a temperature compute that removes a velocity bias
-  adof value = dof_per_atom
-    dof_per_atom = define this many degrees-of-freedom per atom
-  cdof value = dof_per_chunk
-    dof_per_chunk = define this many degrees-of-freedom per chunk
+  yes = subtract center-of-mass velocity from each chunk before calculating temperature
+  no = do not subtract center-of-mass velocity
+bias value = bias-ID
+  bias-ID = ID of a temperature compute that removes a velocity bias
+adof value = dof_per_atom
+  dof_per_atom = define this many degrees-of-freedom per atom
+cdof value = dof_per_chunk
+  dof_per_chunk = define this many degrees-of-freedom per chunk
    diff --git a/doc/compute_temp_cs.html b/doc/compute_temp_cs.html index cb41434594..fa304fa97e 100644 --- a/doc/compute_temp_cs.html +++ b/doc/compute_temp_cs.html @@ -167,7 +167,10 @@ dim = 2 or 3 = dimensionality of the simulation, N = number of atoms in the group, k = Boltzmann constant, and T = temperature. Note that the velocity of each core or shell atom used in the KE calculation is the velocity of the center-of-mass (COM) of the core/shell pair the -atom is part of.

    +atom is part of. Note that atoms that are not core or shell particles +are also included in the temperature calculation (if they are in the +specified group-ID); they contribute to the total kinetic energy in +the usual way.

    A kinetic energy tensor, stored as a 6-element vector, is also calculated by this compute for use in the computation of a pressure tensor. The formula for the components of the tensor is the same as diff --git a/doc/compute_temp_cs.txt b/doc/compute_temp_cs.txt index 4e880704a4..4171a09fd5 100644 --- a/doc/compute_temp_cs.txt +++ b/doc/compute_temp_cs.txt @@ -41,7 +41,7 @@ For this compute, core and shell particles are specified by two respective group IDs, which can be defined using the "group"_group.html command. The number of atoms in the two groups must be the same and there should be one bond defined between a pair -of atoms in the two groups. +of atoms in the two groups. The temperature is calculated by the formula KE = dim/2 N k T, where KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), @@ -49,7 +49,10 @@ dim = 2 or 3 = dimensionality of the simulation, N = number of atoms in the group, k = Boltzmann constant, and T = temperature. Note that the velocity of each core or shell atom used in the KE calculation is the velocity of the center-of-mass (COM) of the core/shell pair the -atom is part of. +atom is part of. Note that atoms that are not core or shell particles +are also included in the temperature calculation (if they are in the +specified group-ID); they contribute to the total kinetic energy in +the usual way. A kinetic energy tensor, stored as a 6-element vector, is also calculated by this compute for use in the computation of a pressure diff --git a/doc/compute_temp_profile.html b/doc/compute_temp_profile.html index e8ad060ae4..863bc1641c 100644 --- a/doc/compute_temp_profile.html +++ b/doc/compute_temp_profile.html @@ -139,13 +139,13 @@ 

     x arg = Nx
-  y arg = Ny
-  z arg = Nz
-  xy args = Nx Ny
-  yz args = Ny Nz
-  xz args = Nx Nz
-  xyz args = Nx Ny Nz
-    Nx,Ny,Nz = number of velocity bins in x,y,z dimensions
+y arg = Ny
+z arg = Nz
+xy args = Nx Ny
+yz args = Ny Nz
+xz args = Nx Nz
+xyz args = Nx Ny Nz
+  Nx,Ny,Nz = number of velocity bins in x,y,z dimensions
    • zero or more keyword/value pairs may be appended
      • diff --git a/doc/compute_temp_sphere.html b/doc/compute_temp_sphere.html index c08fa3f9a8..9ab8592083 100644 --- a/doc/compute_temp_sphere.html +++ b/doc/compute_temp_sphere.html @@ -139,10 +139,10 @@ 
     bias value = bias-ID
-    bias-ID = ID of a temperature compute that removes a velocity bias
-  dof value = all or rotate
-    all = compute temperature of translational and rotational degrees of freedom
-    rotate = compute temperature of just rotational degrees of freedom
+  bias-ID = ID of a temperature compute that removes a velocity bias
+dof value = all or rotate
+  all = compute temperature of translational and rotational degrees of freedom
+  rotate = compute temperature of just rotational degrees of freedom
    diff --git a/doc/compute_ti.html b/doc/compute_ti.html index 7cf0799669..d5dd5c072c 100644 --- a/doc/compute_ti.html +++ b/doc/compute_ti.html @@ -139,17 +139,17 @@ 
     pair style args = atype v_name1 v_name2
-    atype = atom type (see asterisk form below)
-    v_name1 = variable with name1 that is energy scale factor and function of lambda
-    v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda
-  tail args = atype v_name1 v_name2
-    atype = atom type (see asterisk form below)
-    v_name1 = variable with name1 that is energy tail correction scale factor and function of lambda
-    v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda
-  kspace args = atype v_name1 v_name2
-    atype = atom type (see asterisk form below)
-    v_name1 = variable with name1 that is K-Space scale factor and function of lambda
-    v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda
+  atype = atom type (see asterisk form below)
+  v_name1 = variable with name1 that is energy scale factor and function of lambda
+  v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda
+tail args = atype v_name1 v_name2
+  atype = atom type (see asterisk form below)
+  v_name1 = variable with name1 that is energy tail correction scale factor and function of lambda
+  v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda
+kspace args = atype v_name1 v_name2
+  atype = atom type (see asterisk form below)
+  v_name1 = variable with name1 that is K-Space scale factor and function of lambda
+  v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda
    diff --git a/doc/compute_voronoi_atom.html b/doc/compute_voronoi_atom.html index 5e8d8e2b5a..174502a1f4 100644 --- a/doc/compute_voronoi_atom.html +++ b/doc/compute_voronoi_atom.html @@ -139,18 +139,18 @@ 
     only_group = no arg
-  occupation = no arg
-  surface arg = sgroup-ID
-    sgroup-ID = compute the dividing surface between group-ID and sgroup-ID
-      this keyword adds a third column to the compute output
-  radius arg = v_r
-    v_r = radius atom style variable for a poly-disperse Voronoi tessellation
-  edge_histo arg = maxedge
-    maxedge = maximum number of Voronoi cell edges to be accounted in the histogram
-  edge_threshold arg = minlength
-    minlength = minimum length for an edge to be counted
-  face_threshold arg = minarea
-    minarea = minimum area for a face to be counted
+occupation = no arg
+surface arg = sgroup-ID
+  sgroup-ID = compute the dividing surface between group-ID and sgroup-ID
+    this keyword adds a third column to the compute output
+radius arg = v_r
+  v_r = radius atom style variable for a poly-disperse Voronoi tessellation
+edge_histo arg = maxedge
+  maxedge = maximum number of Voronoi cell edges to be accounted in the histogram
+edge_threshold arg = minlength
+  minlength = minimum length for an edge to be counted
+face_threshold arg = minarea
+  minarea = minimum area for a face to be counted
    diff --git a/doc/compute_xrd.html b/doc/compute_xrd.html index 09eef38a15..e12b3c68fa 100644 --- a/doc/compute_xrd.html +++ b/doc/compute_xrd.html @@ -141,16 +141,16 @@ 
     2Theta values = Min2Theta Max2Theta
-    Min2Theta,Max2Theta = minimum and maximum 2 theta range to explore
-    (radians or degrees)
-  c values = c1 c2 c3
-    c1,c2,c3 = parameters to adjust the spacing of the reciprocal
-               lattice nodes in the h, k, and l directions respectively
-  LP value = switch to apply Lorentz-polarization factor
-    0/1 = off/on
-  manual = flag to use manual spacing of reciprocal lattice points
-             based on the values of the c parameters
-  echo = flag to provide extra output for debugging purposes
+  Min2Theta,Max2Theta = minimum and maximum 2 theta range to explore
+  (radians or degrees)
+c values = c1 c2 c3
+  c1,c2,c3 = parameters to adjust the spacing of the reciprocal
+             lattice nodes in the h, k, and l directions respectively
+LP value = switch to apply Lorentz-polarization factor
+  0/1 = off/on
+manual = flag to use manual spacing of reciprocal lattice points
+           based on the values of the c parameters
+echo = flag to provide extra output for debugging purposes
    @@ -185,7 +185,7 @@ the optional LP keyword.

    reciprocal lattice nodes. The mesh spacing is defined either (a) by the entire simulation domain or (b) manually using selected values as shown in the 2D diagram below.

    -     
     box args = none
-  region args = region-ID
-    region-ID = particles will only be created if contained in the region
-  single args = x y z
-    x,y,z = coordinates of a single particle (distance units)
-  random args = N seed region-ID
-    N = number of particles to create
-    seed = random # seed (positive integer)
-    region-ID = create atoms within this region, use NULL for entire simulation box
+region args = region-ID
+  region-ID = particles will only be created if contained in the region
+single args = x y z
+  x,y,z = coordinates of a single particle (distance units)
+random args = N seed region-ID
+  N = number of particles to create
+  seed = random # seed (positive integer)
+  region-ID = create atoms within this region, use NULL for entire simulation box
    • zero or more keyword/value pairs may be appended
      • @@ -152,22 +152,22 @@ 
     mol value = template-ID seed
-    template-ID = ID of molecule template specified in a separate molecule command
-    seed = random # seed (positive integer)
-  basis values = M itype
-    M = which basis atom
-    itype = atom type (1-N) to assign to this basis atom
-  remap value = yes or no
-  var value = name = variable name to evaluate for test of atom creation
-  set values = dim vname
-    dim = x or y or z
-    name = name of variable to set with x,y,z atom position
-  rotate values = Rx Ry Rz theta
-    Rx,Ry,Rz = rotation vector for single molecule
-    theta = rotation angle for single molecule (degrees)
-  units value = lattice or box
-    lattice = the geometry is defined in lattice units
-    box = the geometry is defined in simulation box units
+  template-ID = ID of molecule template specified in a separate molecule command
+  seed = random # seed (positive integer)
+basis values = M itype
+  M = which basis atom
+  itype = atom type (1-N) to assign to this basis atom
+remap value = yes or no
+var value = name = variable name to evaluate for test of atom creation
+set values = dim vname
+  dim = x or y or z
+  name = name of variable to set with x,y,z atom position
+rotate values = Rx Ry Rz theta
+  Rx,Ry,Rz = rotation vector for single molecule
+  theta = rotation angle for single molecule (degrees)
+units value = lattice or box
+  lattice = the geometry is defined in lattice units
+  box = the geometry is defined in simulation box units
    @@ -341,7 +341,7 @@ variable v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + create_atoms 1 box var v set x xx set y yy
    - 
     bond/types value = # of bond types
-  angle/types value = # of angle types
-  dihedral/types value = # of dihedral types
-  improper/types value = # of improper types
-  extra/bond/per/atom value = # of bonds per atom
-  extra/angle/per/atom value = # of angles per atom
-  extra/dihedral/per/atom value = # of dihedrals per atom
-  extra/improper/per/atom value = # of impropers per atom
-  extra/special/per/atom value = # of special neighbors per atom
+angle/types value = # of angle types
+dihedral/types value = # of dihedral types
+improper/types value = # of improper types
+extra/bond/per/atom value = # of bonds per atom
+extra/angle/per/atom value = # of angles per atom
+extra/dihedral/per/atom value = # of dihedrals per atom
+extra/improper/per/atom value = # of impropers per atom
+extra/special/per/atom value = # of special neighbors per atom
    diff --git a/doc/delete_atoms.html b/doc/delete_atoms.html index 193b87af16..4d339a4514 100644 --- a/doc/delete_atoms.html +++ b/doc/delete_atoms.html @@ -136,15 +136,15 @@ 
     group args = group-ID
-  region args = region-ID
-  overlap args = cutoff group1-ID group2-ID
-    cutoff = delete one atom from pairs of atoms within the cutoff (distance units)
-    group1-ID = one atom in pair must be in this group
-    group2-ID = other atom in pair must be in this group
-  porosity args = region-ID fraction seed
-    region-ID = region within which to perform deletions
-    fraction = delete this fraction of atoms
-    seed = random number seed (positive integer)
+region args = region-ID
+overlap args = cutoff group1-ID group2-ID
+  cutoff = delete one atom from pairs of atoms within the cutoff (distance units)
+  group1-ID = one atom in pair must be in this group
+  group2-ID = other atom in pair must be in this group
+porosity args = region-ID fraction seed
+  region-ID = region within which to perform deletions
+  fraction = delete this fraction of atoms
+  seed = random number seed (positive integer)
    • zero or more keyword/value pairs may be appended
      • @@ -152,8 +152,8 @@ 
     compress value = no or yes
-  bond value = no or yes
-  mol value = no or yes
+bond value = no or yes
+mol value = no or yes
    diff --git a/doc/delete_bonds.html b/doc/delete_bonds.html index d302ba39d7..551efffd99 100644 --- a/doc/delete_bonds.html +++ b/doc/delete_bonds.html @@ -143,12 +143,12 @@ 
     multi arg = none
-  atom arg = an atom type or range of types (see below)
-  bond arg = a bond type or range of types (see below)
-  angle arg = an angle type or range of types (see below)
-  dihedral arg = a dihedral type or range of types (see below)
-  improper arg = an improper type or range of types (see below)
-  stats arg = none
+atom arg = an atom type or range of types (see below)
+bond arg = a bond type or range of types (see below)
+angle arg = an angle type or range of types (see below)
+dihedral arg = a dihedral type or range of types (see below)
+improper arg = an improper type or range of types (see below)
+stats arg = none
    • zero or more keywords may be appended
      • diff --git a/doc/displace_atoms.html b/doc/displace_atoms.html index d769595eda..5a36ff9779 100644 --- a/doc/displace_atoms.html +++ b/doc/displace_atoms.html @@ -137,26 +137,26 @@ 
     move args = delx dely delz
-    delx,dely,delz = distance to displace in each dimension (distance units)
-  ramp args = ddim dlo dhi dim clo chi
-    ddim = x or y or z
-    dlo,dhi = displacement distance between dlo and dhi (distance units)
-    dim = x or y or z
-    clo,chi = lower and upper bound of domain to displace (distance units)
-  random args = dx dy dz seed
-    dx,dy,dz = random displacement magnitude in each dimension (distance units)
-    seed = random # seed (positive integer)
-  rotate args = Px Py Pz Rx Ry Rz theta
-    Px,Py,Pz = origin point of axis of rotation (distance units)
-    Rx,Ry,Rz = axis of rotation vector
-    theta = angle of rotation (degrees)
+  delx,dely,delz = distance to displace in each dimension (distance units)
+ramp args = ddim dlo dhi dim clo chi
+  ddim = x or y or z
+  dlo,dhi = displacement distance between dlo and dhi (distance units)
+  dim = x or y or z
+  clo,chi = lower and upper bound of domain to displace (distance units)
+random args = dx dy dz seed
+  dx,dy,dz = random displacement magnitude in each dimension (distance units)
+  seed = random # seed (positive integer)
+rotate args = Px Py Pz Rx Ry Rz theta
+  Px,Py,Pz = origin point of axis of rotation (distance units)
+  Rx,Ry,Rz = axis of rotation vector
+  theta = angle of rotation (degrees)
    • zero or more keyword/value pairs may be appended
     keyword = units
-    value = box or lattice
+  value = box or lattice
    diff --git a/doc/doc2/Eqs/polymorphic1.jpg b/doc/doc2/Eqs/polymorphic1.jpg index dd609ea6b0..4757cb7ad8 100644 Binary files a/doc/doc2/Eqs/polymorphic1.jpg and b/doc/doc2/Eqs/polymorphic1.jpg differ diff --git a/doc/doc2/Eqs/polymorphic2.jpg b/doc/doc2/Eqs/polymorphic2.jpg index 95ff19514f..05133f4849 100644 Binary files a/doc/doc2/Eqs/polymorphic2.jpg and b/doc/doc2/Eqs/polymorphic2.jpg differ diff --git a/doc/doc2/Eqs/polymorphic3.jpg b/doc/doc2/Eqs/polymorphic3.jpg index d39f0c27fc..ba748e63c5 100644 Binary files a/doc/doc2/Eqs/polymorphic3.jpg and b/doc/doc2/Eqs/polymorphic3.jpg differ diff --git a/doc/doc2/Eqs/polymorphic4.jpg b/doc/doc2/Eqs/polymorphic4.jpg index c8805b7114..7a094d6a21 100644 Binary files a/doc/doc2/Eqs/polymorphic4.jpg and b/doc/doc2/Eqs/polymorphic4.jpg differ diff --git a/doc/doc2/Eqs/polymorphic5.jpg b/doc/doc2/Eqs/polymorphic5.jpg index 0f86a79e61..500238b2a9 100644 Binary files a/doc/doc2/Eqs/polymorphic5.jpg and b/doc/doc2/Eqs/polymorphic5.jpg differ diff --git a/doc/doc2/Eqs/polymorphic6.jpg b/doc/doc2/Eqs/polymorphic6.jpg index b94e3514f8..65ea78bf21 100644 Binary files a/doc/doc2/Eqs/polymorphic6.jpg and b/doc/doc2/Eqs/polymorphic6.jpg differ diff --git a/doc/doc2/Eqs/polymorphic7.jpg b/doc/doc2/Eqs/polymorphic7.jpg index dfd5d3172f..0749d537dd 100644 Binary files a/doc/doc2/Eqs/polymorphic7.jpg and b/doc/doc2/Eqs/polymorphic7.jpg differ diff --git a/doc/doc2/Eqs/polymorphic8.jpg b/doc/doc2/Eqs/polymorphic8.jpg index 94a3042793..f88d486a53 100644 Binary files a/doc/doc2/Eqs/polymorphic8.jpg and b/doc/doc2/Eqs/polymorphic8.jpg differ diff --git a/doc/doc2/Eqs/polymorphic9.jpg b/doc/doc2/Eqs/polymorphic9.jpg index b1e0a9a9bc..e538487c90 100644 Binary files a/doc/doc2/Eqs/polymorphic9.jpg and b/doc/doc2/Eqs/polymorphic9.jpg differ diff --git a/doc/doc2/compute_temp_cs.html b/doc/doc2/compute_temp_cs.html index 5d46f1374d..f548d3c652 100644 --- a/doc/doc2/compute_temp_cs.html +++ b/doc/doc2/compute_temp_cs.html @@ -44,7 +44,7 @@ temp/rescale, fix npt, etc. respective group IDs, which can be defined using the group command. The number of atoms in the two groups must be the same and there should be one bond defined between a pair -of atoms in the two groups. +of atoms in the two groups.

    The temperature is calculated by the formula KE = dim/2 N k T, where KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), @@ -52,7 +52,10 @@ dim = 2 or 3 = dimensionality of the simulation, N = number of atoms in the group, k = Boltzmann constant, and T = temperature. Note that the velocity of each core or shell atom used in the KE calculation is the velocity of the center-of-mass (COM) of the core/shell pair the -atom is part of. +atom is part of. Note that atoms that are not core or shell particles +are also included in the temperature calculation (if they are in the +specified group-ID); they contribute to the total kinetic energy in +the usual way.

    A kinetic energy tensor, stored as a 6-element vector, is also calculated by this compute for use in the computation of a pressure diff --git a/doc/doc2/fix_gcmc.html b/doc/doc2/fix_gcmc.html index 576e6d6b43..7a02e5b4b1 100644 --- a/doc/doc2/fix_gcmc.html +++ b/doc/doc2/fix_gcmc.html @@ -333,9 +333,9 @@ referenced by the user for each subsequent fix gcmc command.

    Related commands:

    -

    fix_atom_swap, -fix_nvt, neighbor, -fix_deposit, fix_evaporate, +

    fix atom/swap, +fix nvt, neighbor, +fix deposit, fix evaporate, delete_atoms

    Default: diff --git a/doc/doc2/pair_polymorphic.html b/doc/doc2/pair_polymorphic.html index 6cfd6bf3cf..44bee3163e 100644 --- a/doc/doc2/pair_polymorphic.html +++ b/doc/doc2/pair_polymorphic.html @@ -34,7 +34,7 @@ pair_coeff * * GaN_sw.polymorphic GaN

    -
    +

    where I, J, K represent species of atoms i, j, and k, i_1, ..., i_N represents a list of i's neighbors, delta_ij is a Direc constant diff --git a/doc/dump.html b/doc/dump.html index 2b8d87e770..1ab6b9b51b 100644 --- a/doc/dump.html +++ b/doc/dump.html @@ -150,12 +150,12 @@ 

     atom args = none
-  atom/mpiio args = none
-  cfg args = same as custom args, see below
-  cfg/mpiio args = same as custom args, see below
-  dcd args = none
-  xtc args = none
-  xyz args = none
+atom/mpiio args = none
+cfg args = same as custom args, see below
+cfg/mpiio args = same as custom args, see below
+dcd args = none
+xtc args = none
+xyz args = none
 
     xyz/mpiio args = none
@@ -171,53 +171,53 @@
 
     local args = list of local attributes
-    possible attributes = index, c_ID, c_ID[N], f_ID, f_ID[N]
-      index = enumeration of local values
-      c_ID = local vector calculated by a compute with ID
-      c_ID[N] = Nth column of local array calculated by a compute with ID
-      f_ID = local vector calculated by a fix with ID
-      f_ID[N] = Nth column of local array calculated by a fix with ID
+  possible attributes = index, c_ID, c_ID[N], f_ID, f_ID[N]
+    index = enumeration of local values
+    c_ID = local vector calculated by a compute with ID
+    c_ID[N] = Nth column of local array calculated by a compute with ID
+    f_ID = local vector calculated by a fix with ID
+    f_ID[N] = Nth column of local array calculated by a fix with ID
 
     custom or custom/mpiio args = list of atom attributes
-    possible attributes = id, mol, proc, procp1, type, element, mass,
-                       x, y, z, xs, ys, zs, xu, yu, zu,
-                       xsu, ysu, zsu, ix, iy, iz,
-                       vx, vy, vz, fx, fy, fz,
-                          q, mux, muy, muz, mu,
-                          radius, diameter, omegax, omegay, omegaz,
-                       angmomx, angmomy, angmomz, tqx, tqy, tqz,
-                       c_ID, c_ID[N], f_ID, f_ID[N], v_name
+  possible attributes = id, mol, proc, procp1, type, element, mass,
+                     x, y, z, xs, ys, zs, xu, yu, zu,
+                     xsu, ysu, zsu, ix, iy, iz,
+                     vx, vy, vz, fx, fy, fz,
+                        q, mux, muy, muz, mu,
+                        radius, diameter, omegax, omegay, omegaz,
+                     angmomx, angmomy, angmomz, tqx, tqy, tqz,
+                     c_ID, c_ID[N], f_ID, f_ID[N], v_name
 
     id = atom ID
-      mol = molecule ID
-      proc = ID of processor that owns atom
-      procp1 = ID+1 of processor that owns atom
-      type = atom type
-      element = name of atom element, as defined by dump_modify command
-      mass = atom mass
-      x,y,z = unscaled atom coordinates
-      xs,ys,zs = scaled atom coordinates
-      xu,yu,zu = unwrapped atom coordinates
-      xsu,ysu,zsu = scaled unwrapped atom coordinates
-      ix,iy,iz = box image that the atom is in
-      vx,vy,vz = atom velocities
-      fx,fy,fz = forces on atoms
-      q = atom charge
-      mux,muy,muz = orientation of dipole moment of atom
-      mu = magnitude of dipole moment of atom
-      radius,diameter = radius,diameter of spherical particle
-      omegax,omegay,omegaz = angular velocity of spherical particle
-      angmomx,angmomy,angmomz = angular momentum of aspherical particle
-      tqx,tqy,tqz = torque on finite-size particles
-      c_ID = per-atom vector calculated by a compute with ID
-      c_ID[N] = Nth column of per-atom array calculated by a compute with ID
-      f_ID = per-atom vector calculated by a fix with ID
-      f_ID[N] = Nth column of per-atom array calculated by a fix with ID
-      v_name = per-atom vector calculated by an atom-style variable with name
-      d_name = per-atom floating point vector with name, managed by fix property/atom
-      i_name = per-atom integer vector with name, managed by fix property/atom
+mol = molecule ID
+proc = ID of processor that owns atom
+procp1 = ID+1 of processor that owns atom
+type = atom type
+element = name of atom element, as defined by dump_modify command
+mass = atom mass
+x,y,z = unscaled atom coordinates
+xs,ys,zs = scaled atom coordinates
+xu,yu,zu = unwrapped atom coordinates
+xsu,ysu,zsu = scaled unwrapped atom coordinates
+ix,iy,iz = box image that the atom is in
+vx,vy,vz = atom velocities
+fx,fy,fz = forces on atoms
+q = atom charge
+mux,muy,muz = orientation of dipole moment of atom
+mu = magnitude of dipole moment of atom
+radius,diameter = radius,diameter of spherical particle
+omegax,omegay,omegaz = angular velocity of spherical particle
+angmomx,angmomy,angmomz = angular momentum of aspherical particle
+tqx,tqy,tqz = torque on finite-size particles
+c_ID = per-atom vector calculated by a compute with ID
+c_ID[N] = Nth column of per-atom array calculated by a compute with ID
+f_ID = per-atom vector calculated by a fix with ID
+f_ID[N] = Nth column of per-atom array calculated by a fix with ID
+v_name = per-atom vector calculated by an atom-style variable with name
+d_name = per-atom floating point vector with name, managed by fix property/atom
+i_name = per-atom integer vector with name, managed by fix property/atom
    diff --git a/doc/dump_image.html b/doc/dump_image.html index 98939d4dcb..04d02bffc7 100644 --- a/doc/dump_image.html +++ b/doc/dump_image.html @@ -147,47 +147,47 @@ 
     adiam value = number = numeric value for atom diameter (distance units)
-  atom = yes/no = do or do not draw atoms
-  bond values = color width = color and width of bonds
-    color = atom or type or none
-    width = number or atom or type or none
-      number = numeric value for bond width (distance units)
-  size values = width height = size of images
-    width = width of image in # of pixels
-    height = height of image in # of pixels
-  view values = theta phi = view of simulation box
-    theta = view angle from +z axis (degrees)
-    phi = azimuthal view angle (degrees)
-    theta or phi can be a variable (see below)
-  center values = flag Cx Cy Cz = center point of image
-    flag = "s" for static, "d" for dynamic
-    Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box)
-    Cx,Cy,Cz can be variables (see below)
-  up values = Ux Uy Uz = direction that is "up" in image
-    Ux,Uy,Uz = components of up vector
-    Ux,Uy,Uz can be variables (see below)
-  zoom value = zfactor = size that simulation box appears in image
-    zfactor = scale image size by factor > 1 to enlarge, factor < 1 to shrink
-    zfactor can be a variable (see below)
-  persp value = pfactor = amount of "perspective" in image
-    pfactor = amount of perspective (0 = none, < 1 = some, > 1 = highly skewed)
-    pfactor can be a variable (see below)
-  box values = yes/no diam = draw outline of simulation box
-    yes/no = do or do not draw simulation box lines
-    diam = diameter of box lines as fraction of shortest box length
-  axes values = yes/no length diam = draw xyz axes
-    yes/no = do or do not draw xyz axes lines next to simulation box
-    length = length of axes lines as fraction of respective box lengths
-    diam = diameter of axes lines as fraction of shortest box length
-  subbox values = yes/no diam = draw outline of processor sub-domains
-    yes/no = do or do not draw sub-domain lines
-    diam = diameter of sub-domain lines as fraction of shortest box length
-  shiny value = sfactor = shinyness of spheres and cylinders
-    sfactor = shinyness of spheres and cylinders from 0.0 to 1.0
-  ssao value = yes/no seed dfactor = SSAO depth shading
-    yes/no = turn depth shading on/off
-    seed = random # seed (positive integer)
-    dfactor = strength of shading from 0.0 to 1.0
+atom = yes/no = do or do not draw atoms
+bond values = color width = color and width of bonds
+  color = atom or type or none
+  width = number or atom or type or none
+    number = numeric value for bond width (distance units)
+size values = width height = size of images
+  width = width of image in # of pixels
+  height = height of image in # of pixels
+view values = theta phi = view of simulation box
+  theta = view angle from +z axis (degrees)
+  phi = azimuthal view angle (degrees)
+  theta or phi can be a variable (see below)
+center values = flag Cx Cy Cz = center point of image
+  flag = "s" for static, "d" for dynamic
+  Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box)
+  Cx,Cy,Cz can be variables (see below)
+up values = Ux Uy Uz = direction that is "up" in image
+  Ux,Uy,Uz = components of up vector
+  Ux,Uy,Uz can be variables (see below)
+zoom value = zfactor = size that simulation box appears in image
+  zfactor = scale image size by factor > 1 to enlarge, factor < 1 to shrink
+  zfactor can be a variable (see below)
+persp value = pfactor = amount of "perspective" in image
+  pfactor = amount of perspective (0 = none, < 1 = some, > 1 = highly skewed)
+  pfactor can be a variable (see below)
+box values = yes/no diam = draw outline of simulation box
+  yes/no = do or do not draw simulation box lines
+  diam = diameter of box lines as fraction of shortest box length
+axes values = yes/no length diam = draw xyz axes
+  yes/no = do or do not draw xyz axes lines next to simulation box
+  length = length of axes lines as fraction of respective box lengths
+  diam = diameter of axes lines as fraction of shortest box length
+subbox values = yes/no diam = draw outline of processor sub-domains
+  yes/no = do or do not draw sub-domain lines
+  diam = diameter of sub-domain lines as fraction of shortest box length
+shiny value = sfactor = shinyness of spheres and cylinders
+  sfactor = shinyness of spheres and cylinders from 0.0 to 1.0
+ssao value = yes/no seed dfactor = SSAO depth shading
+  yes/no = turn depth shading on/off
+  seed = random # seed (positive integer)
+  dfactor = strength of shading from 0.0 to 1.0
    @@ -220,7 +220,7 @@ from an existing dump file, and using these dump commands in the rerun script to generate the images/movie.

    Here are two sample images, rendered as 1024x1024 JPEG files. Click to see the full-size images:

    -
    width="25%" height="auto" alt=""/> - 
     append arg = yes or no
-  buffer arg = yes or no
-  element args = E1 E2 ... EN, where N = # of atom types
-    E1,...,EN = element name, e.g. C or Fe or Ga
-  every arg = N
-    N = dump every this many timesteps
-    N can be a variable (see below)
-  fileper arg = Np
-    Np = write one file for every this many processors
-  first arg = yes or no
-  format arg = C-style format string for one line of output
-  flush arg = yes or no
-  image arg = yes or no
-  label arg = string
-    string = character string (e.g. BONDS) to use in header of dump local file
-  nfile arg = Nf
-    Nf = write this many files, one from each of Nf processors
-  pad arg = Nchar = # of characters to convert timestep to
-  precision arg = power-of-10 value from 10 to 1000000
-  region arg = region-ID or "none"
-  scale arg = yes or no
-  sfactor arg = coordinate scaling factor (> 0.0)
-  tfactor arg = time scaling factor (> 0.0)
-  sort arg = off or id or N or -N
-     off = no sorting of per-atom lines within a snapshot
-     id = sort per-atom lines by atom ID
-     N = sort per-atom lines in ascending order by the Nth column
-     -N = sort per-atom lines in descending order by the Nth column
-  thresh args = attribute operation value
-    attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
-    operation = "<" or "<=" or ">" or ">=" or "==" or "!="
-    value = numeric value to compare to
-    these 3 args can be replaced by the word "none" to turn off thresholding
-  unwrap arg = yes or no
+buffer arg = yes or no
+element args = E1 E2 ... EN, where N = # of atom types
+  E1,...,EN = element name, e.g. C or Fe or Ga
+every arg = N
+  N = dump every this many timesteps
+  N can be a variable (see below)
+fileper arg = Np
+  Np = write one file for every this many processors
+first arg = yes or no
+format arg = C-style format string for one line of output
+flush arg = yes or no
+image arg = yes or no
+label arg = string
+  string = character string (e.g. BONDS) to use in header of dump local file
+nfile arg = Nf
+  Nf = write this many files, one from each of Nf processors
+pad arg = Nchar = # of characters to convert timestep to
+precision arg = power-of-10 value from 10 to 1000000
+region arg = region-ID or "none"
+scale arg = yes or no
+sfactor arg = coordinate scaling factor (> 0.0)
+tfactor arg = time scaling factor (> 0.0)
+sort arg = off or id or N or -N
+   off = no sorting of per-atom lines within a snapshot
+   id = sort per-atom lines by atom ID
+   N = sort per-atom lines in ascending order by the Nth column
+   -N = sort per-atom lines in descending order by the Nth column
+thresh args = attribute operation value
+  attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
+  operation = "<" or "<=" or ">" or ">=" or "==" or "!="
+  value = numeric value to compare to
+  these 3 args can be replaced by the word "none" to turn off thresholding
+unwrap arg = yes or no
 
     acolor args = type color
-    type = atom type or range of types (see below)
-    color = name of color or color1/color2/...
-  adiam args = type diam
-    type = atom type or range of types (see below)
-    diam = diameter of atoms of that type (distance units)
-  amap args = lo hi style delta N entry1 entry2 ... entryN
-    lo = number or min = lower bound of range of color map
-    hi = number or max = upper bound of range of color map
-    style = 2 letters = "c" or "d" or "s" plus "a" or "f"
-      "c" for continuous
-      "d" for discrete
-      "s" for sequential
-      "a" for absolute
-      "f" for fractional
-    delta = binsize (only used for style "s", otherwise ignored)
-      binsize = range is divided into bins of this width
-    N = # of subsequent entries
-    entry = value color (for continuous style)
-      value = number or min or max = single value within range
-      color = name of color used for that value
-    entry = lo hi color (for discrete style)
-      lo/hi = number or min or max = lower/upper bound of subset of range
-      color = name of color used for that subset of values
-    entry = color (for sequential style)
-      color = name of color used for a bin of values
-  backcolor arg = color
-    color = name of color for background
-  bcolor args = type color
-    type = bond type or range of types (see below)
-    color = name of color or color1/color2/...
-  bdiam args = type diam
-    type = bond type or range of types (see below)
-    diam = diameter of bonds of that type (distance units)
-  boxcolor arg = color
-    color = name of color for simulation box lines and processor sub-domain lines
-  color args = name R G B
-    name = name of color
-    R,G,B = red/green/blue numeric values from 0.0 to 1.0
-  bitrate arg = rate
-    rate = target bitrate for movie in kbps
-  framerate arg = fps
-    fps = frames per second for movie
+  type = atom type or range of types (see below)
+  color = name of color or color1/color2/...
+adiam args = type diam
+  type = atom type or range of types (see below)
+  diam = diameter of atoms of that type (distance units)
+amap args = lo hi style delta N entry1 entry2 ... entryN
+  lo = number or min = lower bound of range of color map
+  hi = number or max = upper bound of range of color map
+  style = 2 letters = "c" or "d" or "s" plus "a" or "f"
+    "c" for continuous
+    "d" for discrete
+    "s" for sequential
+    "a" for absolute
+    "f" for fractional
+  delta = binsize (only used for style "s", otherwise ignored)
+    binsize = range is divided into bins of this width
+  N = # of subsequent entries
+  entry = value color (for continuous style)
+    value = number or min or max = single value within range
+    color = name of color used for that value
+  entry = lo hi color (for discrete style)
+    lo/hi = number or min or max = lower/upper bound of subset of range
+    color = name of color used for that subset of values
+  entry = color (for sequential style)
+    color = name of color used for a bin of values
+backcolor arg = color
+  color = name of color for background
+bcolor args = type color
+  type = bond type or range of types (see below)
+  color = name of color or color1/color2/...
+bdiam args = type diam
+  type = bond type or range of types (see below)
+  diam = diameter of bonds of that type (distance units)
+boxcolor arg = color
+  color = name of color for simulation box lines and processor sub-domain lines
+color args = name R G B
+  name = name of color
+  R,G,B = red/green/blue numeric values from 0.0 to 1.0
+bitrate arg = rate
+  rate = target bitrate for movie in kbps
+framerate arg = fps
+  fps = frames per second for movie
    diff --git a/doc/fix_adapt.html b/doc/fix_adapt.html index b0556743b0..fe2d766375 100644 --- a/doc/fix_adapt.html +++ b/doc/fix_adapt.html @@ -140,15 +140,15 @@ 
     pair args = pstyle pparam I J v_name
-    pstyle = pair style name, e.g. lj/cut
-    pparam = parameter to adapt over time
-    I,J = type pair(s) to set parameter for
-    v_name = variable with name that calculates value of pparam
-  kspace arg = v_name
-    v_name = variable with name that calculates scale factor on K-space terms
-  atom args = aparam v_name
-    aparam = parameter to adapt over time
-    v_name = variable with name that calculates value of aparam
+  pstyle = pair style name, e.g. lj/cut
+  pparam = parameter to adapt over time
+  I,J = type pair(s) to set parameter for
+  v_name = variable with name that calculates value of pparam
+kspace arg = v_name
+  v_name = variable with name that calculates scale factor on K-space terms
+atom args = aparam v_name
+  aparam = parameter to adapt over time
+  v_name = variable with name that calculates value of aparam
    • zero or more keyword/value pairs may be appended
      • @@ -156,11 +156,11 @@ 
     scale value = no or yes
-    no = the variable value is the new setting
-    yes = the variable value multiplies the original setting
-  reset value = no or yes
-    no = values will remain altered at the end of a run
-    yes = reset altered values to their original values at the end of a run
+  no = the variable value is the new setting
+  yes = the variable value multiplies the original setting
+reset value = no or yes
+  no = values will remain altered at the end of a run
+  yes = reset altered values to their original values at the end of a run
    diff --git a/doc/fix_adapt_fep.html b/doc/fix_adapt_fep.html index 4e340b37f3..70a99ca6ad 100644 --- a/doc/fix_adapt_fep.html +++ b/doc/fix_adapt_fep.html @@ -140,16 +140,16 @@ 
     pair args = pstyle pparam I J v_name
-    pstyle = pair style name, e.g. lj/cut
-    pparam = parameter to adapt over time
-    I,J = type pair(s) to set parameter for
-    v_name = variable with name that calculates value of pparam
-  kspace arg = v_name
-    v_name = variable with name that calculates scale factor on K-space terms
-  atom args = aparam v_name
-    aparam = parameter to adapt over time
-    I = type(s) to set parameter for
-    v_name = variable with name that calculates value of aparam
+  pstyle = pair style name, e.g. lj/cut
+  pparam = parameter to adapt over time
+  I,J = type pair(s) to set parameter for
+  v_name = variable with name that calculates value of pparam
+kspace arg = v_name
+  v_name = variable with name that calculates scale factor on K-space terms
+atom args = aparam v_name
+  aparam = parameter to adapt over time
+  I = type(s) to set parameter for
+  v_name = variable with name that calculates value of aparam
    • zero or more keyword/value pairs may be appended
      • @@ -157,15 +157,15 @@ 
     scale value = no or yes
-    no = the variable value is the new setting
-    yes = the variable value multiplies the original setting
-  reset value = no or yes
-    no = values will remain altered at the end of a run
-    yes = reset altered values to their original values at the end
-    of a run
-  after value = no or yes
-    no = parameters are adapted at timestep N
-    yes = parameters are adapted one timestep after N
+  no = the variable value is the new setting
+  yes = the variable value multiplies the original setting
+reset value = no or yes
+  no = values will remain altered at the end of a run
+  yes = reset altered values to their original values at the end
+  of a run
+after value = no or yes
+  no = parameters are adapted at timestep N
+  yes = parameters are adapted one timestep after N
    diff --git a/doc/fix_addforce.html b/doc/fix_addforce.html index 752e019665..203531229b 100644 --- a/doc/fix_addforce.html +++ b/doc/fix_addforce.html @@ -148,11 +148,11 @@ 
     every value = Nevery
-    Nevery = add force every this many timesteps
-  region value = region-ID
-    region-ID = ID of region atoms must be in to have added force
-  energy value = v_name
-    v_name = variable with name that calculates the potential energy of each atom in the added force field
+  Nevery = add force every this many timesteps
+region value = region-ID
+  region-ID = ID of region atoms must be in to have added force
+energy value = v_name
+  v_name = variable with name that calculates the potential energy of each atom in the added force field
    diff --git a/doc/fix_append_atoms.html b/doc/fix_append_atoms.html index 009f8b510d..375d6dc713 100644 --- a/doc/fix_append_atoms.html +++ b/doc/fix_append_atoms.html @@ -140,23 +140,23 @@ 
     basis values = M itype
-    M = which basis atom
-    itype = atom type (1-N) to assign to this basis atom
-  size args = Lz
-    Lz = z size of lattice region appended in a single event(distance units)
-  freq args = freq
-    freq = the number of timesteps between append events
-  temp args = target damp seed extent
-    target = target temperature for the region between zhi-extent and zhi (temperature units)
-    damp = damping parameter (time units)
-    seed = random number seed for langevin kicks
-    extent = extent of thermostated region (distance units)
-  random args = xmax ymax zmax seed
-    xmax, ymax, zmax = maximum displacement in particular direction (distance units)
-    seed = random number seed for random displacement
-  units value = lattice or box
-    lattice = the wall position is defined in lattice units
-    box = the wall position is defined in simulation box units
+  M = which basis atom
+  itype = atom type (1-N) to assign to this basis atom
+size args = Lz
+  Lz = z size of lattice region appended in a single event(distance units)
+freq args = freq
+  freq = the number of timesteps between append events
+temp args = target damp seed extent
+  target = target temperature for the region between zhi-extent and zhi (temperature units)
+  damp = damping parameter (time units)
+  seed = random number seed for langevin kicks
+  extent = extent of thermostated region (distance units)
+random args = xmax ymax zmax seed
+  xmax, ymax, zmax = maximum displacement in particular direction (distance units)
+  seed = random number seed for random displacement
+units value = lattice or box
+  lattice = the wall position is defined in lattice units
+  box = the wall position is defined in simulation box units
    diff --git a/doc/fix_atc.html b/doc/fix_atc.html index fc3a49435f..eb014ea602 100644 --- a/doc/fix_atc.html +++ b/doc/fix_atc.html @@ -138,9 +138,9 @@ 
     thermal = thermal coupling with fields: temperature
- two_temperature = electron-phonon coupling with field: temperature and electron_temperature
- hardy = on-the-fly post-processing using kernel localization functions (see "related" section for possible fields)
- field = on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields)
+two_temperature = electron-phonon coupling with field: temperature and electron_temperature
+hardy = on-the-fly post-processing using kernel localization functions (see "related" section for possible fields)
+field = on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields)
    • parameter_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file
      • @@ -164,28 +164,28 @@ fix AtC internal atc field 
    # initial fix to designate coupling type and group to apply it to
- # tag group physics material_file
- fix AtC internal atc thermal Ar_thermal.mat
+# tag group physics material_file
+fix AtC internal atc thermal Ar_thermal.mat
 
    # create a uniform 12 x 2 x 2 mesh that covers region contain the group
- # nx ny nz region periodicity
- fix_modify AtC mesh create 12 2 2 mdRegion f p p
+# nx ny nz region periodicity
+fix_modify AtC mesh create 12 2 2 mdRegion f p p
 
    # specify the control method for the type of coupling
- # physics control_type
- fix_modify AtC thermal control flux
+# physics control_type
+fix_modify AtC thermal control flux
 
    # specify the initial values for the empirical field "temperature"
- # field node_group value
- fix_modify AtC initial temperature all 30
+# field node_group value
+fix_modify AtC initial temperature all 30
 
    # create an output stream for nodal fields
- # filename output_frequency
- fix_modify AtC output atc_fe_output 100
+# filename output_frequency
+fix_modify AtC output atc_fe_output 100
 
    run 1000
@@ -196,32 +196,32 @@ fix AtC internal atc field
 
    # initial fix to designate post-processing and the group to apply it to
- # no material file is allowed nor required
- fix AtC internal atc hardy
+# no material file is allowed nor required
+fix AtC internal atc hardy
 
    # for hardy fix, specific kernel function (function type and range) to # be used as a localization function
- fix AtC kernel quartic_sphere 10.0
+fix AtC kernel quartic_sphere 10.0
 
    # create a uniform 1 x 1 x 1 mesh that covers region contain the group
- # with periodicity this effectively creats a system average
- fix_modify AtC mesh create 1 1 1 box p p p
+# with periodicity this effectively creats a system average
+fix_modify AtC mesh create 1 1 1 box p p p
 
    # change from default lagrangian map to eulerian
- # refreshed every 100 steps
- fix_modify AtC atom_element_map eulerian 100
+# refreshed every 100 steps
+fix_modify AtC atom_element_map eulerian 100
 
    # start with no field defined
- # add mass density, potential energy density, stress and temperature
- fix_modify AtC fields add density energy stress temperature
+# add mass density, potential energy density, stress and temperature
+fix_modify AtC fields add density energy stress temperature
 
    # create an output stream for nodal fields
- # filename output_frequency
- fix_modify AtC output nvtFE 100 text
+# filename output_frequency
+fix_modify AtC output nvtFE 100 text
 
    run 1000
diff --git a/doc/fix_atom_swap.html b/doc/fix_atom_swap.html
index db6450a67d..b24f358e5a 100644
--- a/doc/fix_atom_swap.html
+++ b/doc/fix_atom_swap.html
@@ -143,15 +143,15 @@
 
 
     types values = two or more atom types
-  delta_mu values = number_of_types-1 relative chemical potentials (energy units)
-  ke value = no or yes
-    no = no conservation of kinetic energy after atom swaps
-    yes = kinetic energy is conserved after atom swaps
-  semi-grand value = no or yes
-    no = particle type counts and fractions conserved
-    yes = semi-grand canonical ensemble, particle fractions not conserved
-  region value = region-ID
-    region-ID = ID of region to use as an exchange/move volume
+delta_mu values = number_of_types-1 relative chemical potentials (energy units)
+ke value = no or yes
+  no = no conservation of kinetic energy after atom swaps
+  yes = kinetic energy is conserved after atom swaps
+semi-grand value = no or yes
+  no = particle type counts and fractions conserved
+  yes = semi-grand canonical ensemble, particle fractions not conserved
+region value = region-ID
+  region-ID = ID of region to use as an exchange/move volume
    diff --git a/doc/fix_ave_atom.html b/doc/fix_ave_atom.html index 5efc53bd23..925beefe1c 100644 --- a/doc/fix_ave_atom.html +++ b/doc/fix_ave_atom.html @@ -141,11 +141,11 @@ one or more input values can be listed
  • value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[i], f_ID, f_ID[i], v_name
    • x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
-  c_ID = per-atom vector calculated by a compute with ID
-  c_ID[I] = Ith column of per-atom array calculated by a compute with ID
-  f_ID = per-atom vector calculated by a fix with ID
-  f_ID[I] = Ith column of per-atom array calculated by a fix with ID
-  v_name = per-atom vector calculated by an atom-style variable with name
+c_ID = per-atom vector calculated by a compute with ID
+c_ID[I] = Ith column of per-atom array calculated by a compute with ID
+f_ID = per-atom vector calculated by a fix with ID
+f_ID[I] = Ith column of per-atom array calculated by a fix with ID
+v_name = per-atom vector calculated by an atom-style variable with name
    diff --git a/doc/fix_ave_chunk.html b/doc/fix_ave_chunk.html index 8cce0fdba3..bd87b28572 100644 --- a/doc/fix_ave_chunk.html +++ b/doc/fix_ave_chunk.html @@ -142,13 +142,13 @@
  • value = vx, vy, vz, fx, fy, fz, density/mass, density/number, temp, c_ID, c_ID[I], f_ID, f_ID[I], v_name
    • vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
-  density/number, density/mass = number or mass density
-  temp = temperature
-  c_ID = per-atom vector calculated by a compute with ID
-  c_ID[I] = Ith column of per-atom array calculated by a compute with ID
-  f_ID = per-atom vector calculated by a fix with ID
-  f_ID[I] = Ith column of per-atom array calculated by a fix with ID
-  v_name = per-atom vector calculated by an atom-style variable with name
+density/number, density/mass = number or mass density
+temp = temperature
+c_ID = per-atom vector calculated by a compute with ID
+c_ID[I] = Ith column of per-atom array calculated by a compute with ID
+f_ID = per-atom vector calculated by a fix with ID
+f_ID[I] = Ith column of per-atom array calculated by a fix with ID
+v_name = per-atom vector calculated by an atom-style variable with name
 
     norm arg = all or sample or none = how output on Nfreq steps is normalized
-    all = output is sum of atoms across all Nrepeat samples, divided by atom count
-    sample = output is sum of Nrepeat sample averages, divided by Nrepeat
-    none = output is sum of Nrepeat sums, divided by Nrepeat
-  ave args = one or running or window M
-    one = output new average value every Nfreq steps
-    running = output cumulative average of all previous Nfreq steps
-    window M = output average of M most recent Nfreq steps
-  bias arg = bias-ID
-    bias-ID = ID of a temperature compute that removes a velocity bias for temperature calculation
-  adof value = dof_per_atom
-    dof_per_atom = define this many degrees-of-freedom per atom for temperature calculation
-  cdof value = dof_per_chunk
-    dof_per_chunk = define this many degrees-of-freedom per chunk for temperature calculation
-  file arg = filename
-    filename = file to write results to
-  overwrite arg = none = overwrite output file with only latest output
-  title1 arg = string
-    string = text to print as 1st line of output file
-  title2 arg = string
-    string = text to print as 2nd line of output file
-  title3 arg = string
-    string = text to print as 3rd line of output file
+  all = output is sum of atoms across all Nrepeat samples, divided by atom count
+  sample = output is sum of Nrepeat sample averages, divided by Nrepeat
+  none = output is sum of Nrepeat sums, divided by Nrepeat
+ave args = one or running or window M
+  one = output new average value every Nfreq steps
+  running = output cumulative average of all previous Nfreq steps
+  window M = output average of M most recent Nfreq steps
+bias arg = bias-ID
+  bias-ID = ID of a temperature compute that removes a velocity bias for temperature calculation
+adof value = dof_per_atom
+  dof_per_atom = define this many degrees-of-freedom per atom for temperature calculation
+cdof value = dof_per_chunk
+  dof_per_chunk = define this many degrees-of-freedom per chunk for temperature calculation
+file arg = filename
+  filename = file to write results to
+overwrite arg = none = overwrite output file with only latest output
+title1 arg = string
+  string = text to print as 1st line of output file
+title2 arg = string
+  string = text to print as 2nd line of output file
+title3 arg = string
+  string = text to print as 3rd line of output file
    diff --git a/doc/fix_ave_correlate.html b/doc/fix_ave_correlate.html index f5bd22a971..d9a2b12340 100644 --- a/doc/fix_ave_correlate.html +++ b/doc/fix_ave_correlate.html @@ -141,10 +141,10 @@
  • value = c_ID, c_ID[N], f_ID, f_ID[N], v_name
    • c_ID = global scalar calculated by a compute with ID
-  c_ID[I] = Ith component of global vector calculated by a compute with ID
-  f_ID = global scalar calculated by a fix with ID
-  f_ID[I] = Ith component of global vector calculated by a fix with ID
-  v_name = global value calculated by an equal-style variable with name
+c_ID[I] = Ith component of global vector calculated by a compute with ID
+f_ID = global scalar calculated by a fix with ID
+f_ID[I] = Ith component of global vector calculated by a fix with ID
+v_name = global value calculated by an equal-style variable with name
 
     type arg = auto or upper or lower or auto/upper or auto/lower or full
-    auto = correlate each value with itself
-    upper = correlate each value with each succeeding value
-    lower = correlate each value with each preceding value
-    auto/upper = auto + upper
-    auto/lower = auto + lower
-    full = correlate each value with every other value, including itself = auto + upper + lower
-  ave args = one or running
-    one = zero the correlation accumulation every Nfreq steps
-    running = accumulate correlations continuously
-  start args = Nstart
-    Nstart = start accumulating correlations on this timestep
-  prefactor args = value
-    value = prefactor to scale all the correlation data by
-  file arg = filename
-    filename = name of file to output correlation data to
-  overwrite arg = none = overwrite output file with only latest output
-  title1 arg = string
-    string = text to print as 1st line of output file
-  title2 arg = string
-    string = text to print as 2nd line of output file
-  title3 arg = string
-    string = text to print as 3rd line of output file
+  auto = correlate each value with itself
+  upper = correlate each value with each succeeding value
+  lower = correlate each value with each preceding value
+  auto/upper = auto + upper
+  auto/lower = auto + lower
+  full = correlate each value with every other value, including itself = auto + upper + lower
+ave args = one or running
+  one = zero the correlation accumulation every Nfreq steps
+  running = accumulate correlations continuously
+start args = Nstart
+  Nstart = start accumulating correlations on this timestep
+prefactor args = value
+  value = prefactor to scale all the correlation data by
+file arg = filename
+  filename = name of file to output correlation data to
+overwrite arg = none = overwrite output file with only latest output
+title1 arg = string
+  string = text to print as 1st line of output file
+title2 arg = string
+  string = text to print as 2nd line of output file
+title3 arg = string
+  string = text to print as 3rd line of output file
    diff --git a/doc/fix_ave_histo.html b/doc/fix_ave_histo.html index 2d627f86fa..b3c9265854 100644 --- a/doc/fix_ave_histo.html +++ b/doc/fix_ave_histo.html @@ -146,11 +146,11 @@
  • value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name
    • x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
-  c_ID = scalar or vector calculated by a compute with ID
-  c_ID[I] = Ith component of vector or Ith column of array calculated by a compute with ID
-  f_ID = scalar or vector calculated by a fix with ID
-  f_ID[I] = Ith component of vector or Ith column of array calculated by a fix with ID
-  v_name = value(s) calculated by an equal-style or atom-style variable with name
+c_ID = scalar or vector calculated by a compute with ID
+c_ID[I] = Ith component of vector or Ith column of array calculated by a compute with ID
+f_ID = scalar or vector calculated by a fix with ID
+f_ID[I] = Ith component of vector or Ith column of array calculated by a fix with ID
+v_name = value(s) calculated by an equal-style or atom-style variable with name
 
     mode arg = scalar or vector
-    scalar = all input values are scalars
-    vector = all input values are vectors
-  file arg = filename
-    filename = name of file to output histogram(s) to
-  ave args = one or running or window
-    one = output a new average value every Nfreq steps
-    running = output cumulative average of all previous Nfreq steps
-    window M = output average of M most recent Nfreq steps
-  start args = Nstart
-    Nstart = start averaging on this timestep
-  beyond arg = ignore or end or extra
-    ignore = ignore values outside histogram lo/hi bounds
-    end = count values outside histogram lo/hi bounds in end bins
-    extra = create 2 extra bins for value outside histogram lo/hi bounds
-  overwrite arg = none = overwrite output file with only latest output
-  title1 arg = string
-    string = text to print as 1st line of output file
-  title2 arg = string
-    string = text to print as 2nd line of output file
-  title3 arg = string
-    string = text to print as 3rd line of output file, only for vector mode
+  scalar = all input values are scalars
+  vector = all input values are vectors
+file arg = filename
+  filename = name of file to output histogram(s) to
+ave args = one or running or window
+  one = output a new average value every Nfreq steps
+  running = output cumulative average of all previous Nfreq steps
+  window M = output average of M most recent Nfreq steps
+start args = Nstart
+  Nstart = start averaging on this timestep
+beyond arg = ignore or end or extra
+  ignore = ignore values outside histogram lo/hi bounds
+  end = count values outside histogram lo/hi bounds in end bins
+  extra = create 2 extra bins for value outside histogram lo/hi bounds
+overwrite arg = none = overwrite output file with only latest output
+title1 arg = string
+  string = text to print as 1st line of output file
+title2 arg = string
+  string = text to print as 2nd line of output file
+title3 arg = string
+  string = text to print as 3rd line of output file, only for vector mode
    diff --git a/doc/fix_ave_spatial.html b/doc/fix_ave_spatial.html index 4070005cfd..c52583da6d 100644 --- a/doc/fix_ave_spatial.html +++ b/doc/fix_ave_spatial.html @@ -141,20 +141,20 @@ 
     dim = x or y or z
-  origin = lower or center or upper or coordinate value (distance units)
-  delta = thickness of spatial bins in dim (distance units)
+origin = lower or center or upper or coordinate value (distance units)
+delta = thickness of spatial bins in dim (distance units)
 
    vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
-  density/number, density/mass = number or mass density
-  c_ID = per-atom vector calculated by a compute with ID
-  c_ID[I] = Ith column of per-atom array calculated by a compute with ID
-  f_ID = per-atom vector calculated by a fix with ID
-  f_ID[I] = Ith column of per-atom array calculated by a fix with ID
-  v_name = per-atom vector calculated by an atom-style variable with name
+density/number, density/mass = number or mass density
+c_ID = per-atom vector calculated by a compute with ID
+c_ID[I] = Ith column of per-atom array calculated by a compute with ID
+f_ID = per-atom vector calculated by a fix with ID
+f_ID[I] = Ith column of per-atom array calculated by a fix with ID
+v_name = per-atom vector calculated by an atom-style variable with name
 
     region arg = region-ID
-  bound args = x/y/z lo hi
-    x/y/z = x or y or z to bound bins in this dimension
-    lo = lower or coordinate value (distance units)
-    hi = upper or coordinate value (distance units)
-  discard arg = mixed or no or yes
-    mixed = discard atoms outside bins only if bin bounds are explicitly set
-    no = always keep out-of-bounds atoms
-    yes = always discard out-of-bounds atoms
-  norm arg = all or sample
-    region-ID = ID of region atoms must be in to contribute to spatial averaging
-  ave args = one or running or window M
-    one = output new average value every Nfreq steps
-    running = output cumulative average of all previous Nfreq steps
-    window M = output average of M most recent Nfreq steps
-  units arg = box or lattice or reduced
-  file arg = filename
-    filename = file to write results to
-  overwrite arg = none = overwrite output file with only latest output
-  title1 arg = string
-    string = text to print as 1st line of output file
-  title2 arg = string
-    string = text to print as 2nd line of output file
-  title3 arg = string
-    string = text to print as 3rd line of output file
+bound args = x/y/z lo hi
+  x/y/z = x or y or z to bound bins in this dimension
+  lo = lower or coordinate value (distance units)
+  hi = upper or coordinate value (distance units)
+discard arg = mixed or no or yes
+  mixed = discard atoms outside bins only if bin bounds are explicitly set
+  no = always keep out-of-bounds atoms
+  yes = always discard out-of-bounds atoms
+norm arg = all or sample
+  region-ID = ID of region atoms must be in to contribute to spatial averaging
+ave args = one or running or window M
+  one = output new average value every Nfreq steps
+  running = output cumulative average of all previous Nfreq steps
+  window M = output average of M most recent Nfreq steps
+units arg = box or lattice or reduced
+file arg = filename
+  filename = file to write results to
+overwrite arg = none = overwrite output file with only latest output
+title1 arg = string
+  string = text to print as 1st line of output file
+title2 arg = string
+  string = text to print as 2nd line of output file
+title3 arg = string
+  string = text to print as 3rd line of output file
    diff --git a/doc/fix_ave_spatial_sphere.html b/doc/fix_ave_spatial_sphere.html index bd31e9769f..9658925c96 100644 --- a/doc/fix_ave_spatial_sphere.html +++ b/doc/fix_ave_spatial_sphere.html @@ -145,12 +145,12 @@
  • value = vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID[I], f_ID, f_ID[I], v_name
    • vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
-  density/number, density/mass = number or mass density
-  c_ID = per-atom vector calculated by a compute with ID
-  c_ID[I] = Ith column of per-atom array calculated by a compute with ID
-  f_ID = per-atom vector calculated by a fix with ID
-  f_ID[I] = Ith column of per-atom array calculated by a fix with ID
-  v_name = per-atom vector calculated by an atom-style variable with name
+density/number, density/mass = number or mass density
+c_ID = per-atom vector calculated by a compute with ID
+c_ID[I] = Ith column of per-atom array calculated by a compute with ID
+f_ID = per-atom vector calculated by a fix with ID
+f_ID[I] = Ith column of per-atom array calculated by a fix with ID
+v_name = per-atom vector calculated by an atom-style variable with name
 
     region arg = region-ID
-    region-ID = ID of region atoms must be in to contribute to spatial averaging
-  norm arg = all or sample
-  units arg = box or lattice or reduced
-  ave args = one or running or window M
-    one = output new average value every Nfreq steps
-    running = output cumulative average of all previous Nfreq steps
-    window M = output average of M most recent Nfreq steps
-  file arg = filename
-    filename = file to write results to
-  overwrite arg = none = overwrite output file with only latest output
-  title1 arg = string
-    string = text to print as 1st line of output file
-  title2 arg = string
-    string = text to print as 2nd line of output file
-  title3 arg = string
-    string = text to print as 3rd line of output file
+  region-ID = ID of region atoms must be in to contribute to spatial averaging
+norm arg = all or sample
+units arg = box or lattice or reduced
+ave args = one or running or window M
+  one = output new average value every Nfreq steps
+  running = output cumulative average of all previous Nfreq steps
+  window M = output average of M most recent Nfreq steps
+file arg = filename
+  filename = file to write results to
+overwrite arg = none = overwrite output file with only latest output
+title1 arg = string
+  string = text to print as 1st line of output file
+title2 arg = string
+  string = text to print as 2nd line of output file
+title3 arg = string
+  string = text to print as 3rd line of output file
    diff --git a/doc/fix_ave_time.html b/doc/fix_ave_time.html index 55cb2b333b..8beb62f4da 100644 --- a/doc/fix_ave_time.html +++ b/doc/fix_ave_time.html @@ -141,10 +141,10 @@
  • value = c_ID, c_ID[N], f_ID, f_ID[N], v_name
    • c_ID = global scalar, vector, or array calculated by a compute with ID
-  c_ID[I] = Ith component of global vector or Ith column of global array calculated by a compute with ID
-  f_ID = global scalar, vector, or array calculated by a fix with ID
-  f_ID[I] = Ith component of global vector or Ith column of global array calculated by a fix with ID
-  v_name = global value calculated by an equal-style variable with name
+c_ID[I] = Ith component of global vector or Ith column of global array calculated by a compute with ID
+f_ID = global scalar, vector, or array calculated by a fix with ID
+f_ID[I] = Ith component of global vector or Ith column of global array calculated by a fix with ID
+v_name = global value calculated by an equal-style variable with name
 
     mode arg = scalar or vector
-    scalar = all input values are global scalars
-    vector = all input values are global vectors or global arrays
-  ave args = one or running or window M
-    one = output a new average value every Nfreq steps
-    running = output cummulative average of all previous Nfreq steps
-    window M = output average of M most recent Nfreq steps
-  start args = Nstart
-    Nstart = start averaging on this timestep
-  off arg = M = do not average this value
-    M = value # from 1 to Nvalues
-  file arg = filename
-    filename = name of file to output time averages to
-  overwrite arg = none = overwrite output file with only latest output
-  title1 arg = string
-    string = text to print as 1st line of output file
-  title2 arg = string
-    string = text to print as 2nd line of output file
-  title3 arg = string
-    string = text to print as 3rd line of output file, only for vector mode
+  scalar = all input values are global scalars
+  vector = all input values are global vectors or global arrays
+ave args = one or running or window M
+  one = output a new average value every Nfreq steps
+  running = output cummulative average of all previous Nfreq steps
+  window M = output average of M most recent Nfreq steps
+start args = Nstart
+  Nstart = start averaging on this timestep
+off arg = M = do not average this value
+  M = value # from 1 to Nvalues
+file arg = filename
+  filename = name of file to output time averages to
+overwrite arg = none = overwrite output file with only latest output
+title1 arg = string
+  string = text to print as 1st line of output file
+title2 arg = string
+  string = text to print as 2nd line of output file
+title3 arg = string
+  string = text to print as 3rd line of output file, only for vector mode
    diff --git a/doc/fix_aveforce.html b/doc/fix_aveforce.html index e053caefd0..f50b72d9a1 100644 --- a/doc/fix_aveforce.html +++ b/doc/fix_aveforce.html @@ -148,7 +148,7 @@ 
     region value = region-ID
-    region-ID = ID of region atoms must be in to have added force
+  region-ID = ID of region atoms must be in to have added force
    diff --git a/doc/fix_balance.html b/doc/fix_balance.html index 857339cd7f..5f316e608a 100644 --- a/doc/fix_balance.html +++ b/doc/fix_balance.html @@ -139,10 +139,10 @@
  • style = shift or rcb
    • shift args = dimstr Niter stopthresh
-    dimstr = sequence of letters containing "x" or "y" or "z", each not more than once
-    Niter = # of times to iterate within each dimension of dimstr sequence
-    stopthresh = stop balancing when this imbalance threshhold is reached
-  rcb args = none
+  dimstr = sequence of letters containing "x" or "y" or "z", each not more than once
+  Niter = # of times to iterate within each dimension of dimstr sequence
+  stopthresh = stop balancing when this imbalance threshhold is reached
+rcb args = none
 
     out value = filename
-    filename = write each processor's sub-domain to a file, at each re-balancing
+  filename = write each processor's sub-domain to a file, at each re-balancing
    @@ -237,7 +237,7 @@ that owns them. The leftmost diagram is the default partitioning of the simulation box across processors (one sub-box for each of 16 processors); the middle diagram is after a “grid” method has been applied.

    - width="25%" height="auto" alt=""/> - width="25%" height="auto" alt=""/> - 
     prob values = fraction seed
-    fraction = break a bond with this probability if otherwise eligible
-    seed = random number seed (positive integer)
+  fraction = break a bond with this probability if otherwise eligible
+  seed = random number seed (positive integer)
    diff --git a/doc/fix_bond_create.html b/doc/fix_bond_create.html index 07ff6811ee..74dbc9bc7c 100644 --- a/doc/fix_bond_create.html +++ b/doc/fix_bond_create.html @@ -143,20 +143,20 @@ 
     iparam values = maxbond, newtype
-    maxbond = max # of bonds of bondtype the itype atom can have
-    newtype = change the itype atom to this type when maxbonds exist
-  jparam values = maxbond, newtype
-    maxbond = max # of bonds of bondtype the jtype atom can have
-    newtype = change the jtype atom to this type when maxbonds exist
-  prob values = fraction seed
-    fraction = create a bond with this probability if otherwise eligible
-    seed = random number seed (positive integer)
-  atype value = angletype
-    angletype = type of created angles
-  dtype value = dihedraltype
-    dihedraltype = type of created dihedrals
-  itype value = impropertype
-    impropertype = type of created impropers
+  maxbond = max # of bonds of bondtype the itype atom can have
+  newtype = change the itype atom to this type when maxbonds exist
+jparam values = maxbond, newtype
+  maxbond = max # of bonds of bondtype the jtype atom can have
+  newtype = change the jtype atom to this type when maxbonds exist
+prob values = fraction seed
+  fraction = create a bond with this probability if otherwise eligible
+  seed = random number seed (positive integer)
+atype value = angletype
+  angletype = type of created angles
+dtype value = dihedraltype
+  dihedraltype = type of created dihedrals
+itype value = impropertype
+  impropertype = type of created impropers
    diff --git a/doc/fix_colvars.html b/doc/fix_colvars.html index b69823d441..66a350a050 100644 --- a/doc/fix_colvars.html +++ b/doc/fix_colvars.html @@ -139,11 +139,11 @@ 
     input arg = colvars.state file name or prefix or NULL (default: NULL)
-  output arg = output filename prefix (default: out)
-  seed arg = seed for random number generator (default: 1966)
-  unwrap arg = yes or no
-    use unwrapped coordinates in collective variables (default: yes)
-  tstat arg = fix id of a thermostat or NULL (default: NULL)
+output arg = output filename prefix (default: out)
+seed arg = seed for random number generator (default: 1966)
+unwrap arg = yes or no
+  use unwrapped coordinates in collective variables (default: yes)
+tstat arg = fix id of a thermostat or NULL (default: NULL)
    diff --git a/doc/fix_deform.html b/doc/fix_deform.html index b49b4b7aa4..7f7cf868b1 100644 --- a/doc/fix_deform.html +++ b/doc/fix_deform.html @@ -187,14 +187,14 @@ parameter = x or y or z or xy or xz 
     remap value = x or v or none
-    x = remap coords of atoms in group into deforming box
-    v = remap velocities of all atoms when they cross periodic boundaries
-    none = no remapping of x or v
-  flip value = yes or no
-    allow or disallow box flips when it becomes highly skewed
-  units value = lattice or box
-    lattice = distances are defined in lattice units
-    box = distances are defined in simulation box units
+  x = remap coords of atoms in group into deforming box
+  v = remap velocities of all atoms when they cross periodic boundaries
+  none = no remapping of x or v
+flip value = yes or no
+  allow or disallow box flips when it becomes highly skewed
+units value = lattice or box
+  lattice = distances are defined in lattice units
+  box = distances are defined in simulation box units
    diff --git a/doc/fix_deposit.html b/doc/fix_deposit.html index e586ff546d..1f38c377ea 100644 --- a/doc/fix_deposit.html +++ b/doc/fix_deposit.html @@ -143,40 +143,40 @@ 
     region value = region-ID
-    region-ID = ID of region to use as insertion volume
-  id value = max or next
-    max = atom ID for new atom(s) is max ID of all current atoms plus one
-    next = atom ID for new atom(s) increments by one for every deposition
-  global values = lo hi
-    lo,hi = put new atom/molecule a distance lo-hi above all other atoms (distance units)
-  local values = lo hi delta
-    lo,hi = put new atom/molecule a distance lo-hi above any nearby atom beneath it (distance units)
-    delta = lateral distance within which a neighbor is considered "nearby" (distance units)
-  near value = R
-    R = only insert atom/molecule if further than R from existing particles (distance units)
-  attempt value = Q
-    Q = attempt a single insertion up to Q times
-  rate value = V
-    V = z velocity (y in 2d) at which insertion volume moves (velocity units)
-  vx values = vxlo vxhi
-    vxlo,vxhi = range of x velocities for inserted atom/molecule (velocity units)
-  vy values = vylo vyhi
-    vylo,vyhi = range of y velocities for inserted atom/molecule (velocity units)
-  vz values = vzlo vzhi
-    vzlo,vzhi = range of z velocities for inserted atom/molecule (velocity units)
-  target values = tx ty tz
-    tx,ty,tz = location of target point (distance units)
-  mol value = template-ID
-    template-ID = ID of molecule template specified in a separate molecule command
-  molfrac values = f1 f2 ... fN
-    f1 to fN = relative probability of creating each of N molecules in template-ID
-  rigid value = fix-ID
-    fix-ID = ID of fix rigid/small command
-  shake value = fix-ID
-    fix-ID = ID of fix shake command
-  units value = lattice or box
-    lattice = the geometry is defined in lattice units
-    box = the geometry is defined in simulation box units
+  region-ID = ID of region to use as insertion volume
+id value = max or next
+  max = atom ID for new atom(s) is max ID of all current atoms plus one
+  next = atom ID for new atom(s) increments by one for every deposition
+global values = lo hi
+  lo,hi = put new atom/molecule a distance lo-hi above all other atoms (distance units)
+local values = lo hi delta
+  lo,hi = put new atom/molecule a distance lo-hi above any nearby atom beneath it (distance units)
+  delta = lateral distance within which a neighbor is considered "nearby" (distance units)
+near value = R
+  R = only insert atom/molecule if further than R from existing particles (distance units)
+attempt value = Q
+  Q = attempt a single insertion up to Q times
+rate value = V
+  V = z velocity (y in 2d) at which insertion volume moves (velocity units)
+vx values = vxlo vxhi
+  vxlo,vxhi = range of x velocities for inserted atom/molecule (velocity units)
+vy values = vylo vyhi
+  vylo,vyhi = range of y velocities for inserted atom/molecule (velocity units)
+vz values = vzlo vzhi
+  vzlo,vzhi = range of z velocities for inserted atom/molecule (velocity units)
+target values = tx ty tz
+  tx,ty,tz = location of target point (distance units)
+mol value = template-ID
+  template-ID = ID of molecule template specified in a separate molecule command
+molfrac values = f1 f2 ... fN
+  f1 to fN = relative probability of creating each of N molecules in template-ID
+rigid value = fix-ID
+  fix-ID = ID of fix rigid/small command
+shake value = fix-ID
+  fix-ID = ID of fix shake command
+units value = lattice or box
+  lattice = the geometry is defined in lattice units
+  box = the geometry is defined in simulation box units
    diff --git a/doc/fix_dt_reset.html b/doc/fix_dt_reset.html index c9b8194dfa..84bc14b7d2 100644 --- a/doc/fix_dt_reset.html +++ b/doc/fix_dt_reset.html @@ -143,8 +143,8 @@ 
     units value = lattice or box
-    lattice = Xmax is defined in lattice units
-    box = Xmax is defined in simulation box units
+  lattice = Xmax is defined in lattice units
+  box = Xmax is defined in simulation box units
    diff --git a/doc/fix_efield.html b/doc/fix_efield.html index c89f9c011c..78fbc2ddb1 100644 --- a/doc/fix_efield.html +++ b/doc/fix_efield.html @@ -141,9 +141,9 @@ 
     region value = region-ID
-    region-ID = ID of region atoms must be in to have added force
-  energy value = v_name
-    v_name = variable with name that calculates the potential energy of each atom in the added E-field
+  region-ID = ID of region atoms must be in to have added force
+energy value = v_name
+  v_name = variable with name that calculates the potential energy of each atom in the added E-field
    diff --git a/doc/fix_external.html b/doc/fix_external.html index afdcf9d3ea..447edfacb6 100644 --- a/doc/fix_external.html +++ b/doc/fix_external.html @@ -138,10 +138,10 @@ 
     pf/callback args = Ncall Napply
-    Ncall = make callback every Ncall steps
-    Napply = apply callback forces every Napply steps
-  pf/array args = Napply
-    Napply = apply array forces every Napply steps
+  Ncall = make callback every Ncall steps
+  Napply = apply callback forces every Napply steps
+pf/array args = Napply
+  Napply = apply array forces every Napply steps
    diff --git a/doc/fix_gcmc.html b/doc/fix_gcmc.html index dec2534783..cf26a12cc8 100644 --- a/doc/fix_gcmc.html +++ b/doc/fix_gcmc.html @@ -409,9 +409,9 @@ referenced by the user for each subsequent fix gcmc command.

    diff --git a/doc/fix_gcmc.txt b/doc/fix_gcmc.txt index 33e3691cee..ca3f424596 100644 --- a/doc/fix_gcmc.txt +++ b/doc/fix_gcmc.txt @@ -318,9 +318,9 @@ referenced by the user for each subsequent fix gcmc command. [Related commands:] -"fix_atom_swap"_fix_atom_swap.html, -"fix_nvt"_fix_nvt.html, "neighbor"_neighbor.html, -"fix_deposit"_fix_deposit.html, "fix_evaporate"_fix_evaporate.html, +"fix atom/swap"_fix_atom_swap.html, +"fix nvt"_fix_nvt.html, "neighbor"_neighbor.html, +"fix deposit"_fix_deposit.html, "fix evaporate"_fix_evaporate.html, "delete_atoms"_delete_atoms.html [Default:] diff --git a/doc/fix_gravity.html b/doc/fix_gravity.html index d9182988ae..bfd26b0dd5 100644 --- a/doc/fix_gravity.html +++ b/doc/fix_gravity.html @@ -146,15 +146,15 @@ 
     chute args = angle
-    angle = angle in +x away from -z or -y axis in 3d/2d (in degrees)
-    angle can be a variable (see below)
-  spherical args = phi theta
-    phi = azimuthal angle from +x axis (in degrees)
-    theta = angle from +z or +y axis in 3d/2d (in degrees)
-    phi or theta can be a variable (see below)
-  vector args = x y z
-    x y z = vector direction to apply the acceleration
-    x or y or z can be a variable (see below)
+  angle = angle in +x away from -z or -y axis in 3d/2d (in degrees)
+  angle can be a variable (see below)
+spherical args = phi theta
+  phi = azimuthal angle from +x axis (in degrees)
+  theta = angle from +z or +y axis in 3d/2d (in degrees)
+  phi or theta can be a variable (see below)
+vector args = x y z
+  x y z = vector direction to apply the acceleration
+  x or y or z can be a variable (see below)
    diff --git a/doc/fix_heat.html b/doc/fix_heat.html index 80536bf501..f33a3f45dc 100644 --- a/doc/fix_heat.html +++ b/doc/fix_heat.html @@ -142,7 +142,7 @@ 
     region value = region-ID
-    region-ID = ID of region atoms must be in to have added force
+  region-ID = ID of region atoms must be in to have added force
    diff --git a/doc/fix_imd.html b/doc/fix_imd.html index ae1654cdc4..02f93cb533 100644 --- a/doc/fix_imd.html +++ b/doc/fix_imd.html @@ -139,14 +139,14 @@ 
     unwrap arg = on or off
-    off = coordinates are wrapped back into the principal unit cell (default)
-    on = "unwrapped" coordinates using the image flags used
-  fscale arg = factor
-    factor = floating point number to scale IMD forces (default: 1.0)
-  trate arg = transmission rate of coordinate data sets (default: 1)
-  nowait arg = on or off
-    off = LAMMPS waits to be connected to an IMD client before continuing (default)
-    on = LAMMPS listens for an IMD client, but continues with the run
+  off = coordinates are wrapped back into the principal unit cell (default)
+  on = "unwrapped" coordinates using the image flags used
+fscale arg = factor
+  factor = floating point number to scale IMD forces (default: 1.0)
+trate arg = transmission rate of coordinate data sets (default: 1)
+nowait arg = on or off
+  off = LAMMPS waits to be connected to an IMD client before continuing (default)
+  on = LAMMPS listens for an IMD client, but continues with the run
    diff --git a/doc/fix_indent.html b/doc/fix_indent.html index 625ea18f16..3fdfac0f90 100644 --- a/doc/fix_indent.html +++ b/doc/fix_indent.html @@ -140,25 +140,25 @@ 
     sphere args = x y z R
-    x,y,z = initial position of center of indenter (distance units)
-    R = sphere radius of indenter (distance units)
-    any of x,y,z,R can be a variable (see below)
-  cylinder args = dim c1 c2 R
-    dim = x or y or z = axis of cylinder
-    c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
-    R = cylinder radius of indenter (distance units)
-    any of c1,c2,R can be a variable (see below)
-  plane args = dim pos side
-    dim = x or y or z = plane perpendicular to this dimension
-    pos = position of plane in dimension x, y, or z (distance units)
-    pos can be a variable (see below)
-    side = lo or hi
-  side value = in or out
-    in = the indenter acts on particles inside the sphere or cylinder
-    out = the indenter acts on particles outside the sphere or cylinder
-  units value = lattice or box
-    lattice = the geometry is defined in lattice units
-    box = the geometry is defined in simulation box units
+  x,y,z = initial position of center of indenter (distance units)
+  R = sphere radius of indenter (distance units)
+  any of x,y,z,R can be a variable (see below)
+cylinder args = dim c1 c2 R
+  dim = x or y or z = axis of cylinder
+  c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
+  R = cylinder radius of indenter (distance units)
+  any of c1,c2,R can be a variable (see below)
+plane args = dim pos side
+  dim = x or y or z = plane perpendicular to this dimension
+  pos = position of plane in dimension x, y, or z (distance units)
+  pos can be a variable (see below)
+  side = lo or hi
+side value = in or out
+  in = the indenter acts on particles inside the sphere or cylinder
+  out = the indenter acts on particles outside the sphere or cylinder
+units value = lattice or box
+  lattice = the geometry is defined in lattice units
+  box = the geometry is defined in simulation box units
    diff --git a/doc/fix_langevin.html b/doc/fix_langevin.html index 82b6ef3a03..f61783c1d2 100644 --- a/doc/fix_langevin.html +++ b/doc/fix_langevin.html @@ -146,23 +146,23 @@ 
     angmom value = no or scale
-    no = do not thermostat rotational degrees of freedom via the angular momentum
-    factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric factor as discussed below
-  gjf value = no or yes
-    no = use standard formulation
-    yes = use Gronbech-Jensen/Farago formulation
-  omega value = no or yes
-    no = do not thermostat rotational degrees of freedom via the angular velocity
-    yes = do thermostat rotational degrees of freedom via the angular velocity
-  scale values = type ratio
-    type = atom type (1-N)
-    ratio = factor by which to scale the damping coefficient
-  tally value = no or yes
-    no = do not tally the energy added/subtracted to atoms
-    yes = do tally the energy added/subtracted to atoms
-  zero value = no or yes
-    no = do not set total random force to zero
-    yes = set total random force to zero
+  no = do not thermostat rotational degrees of freedom via the angular momentum
+  factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric factor as discussed below
+gjf value = no or yes
+  no = use standard formulation
+  yes = use Gronbech-Jensen/Farago formulation
+omega value = no or yes
+  no = do not thermostat rotational degrees of freedom via the angular velocity
+  yes = do thermostat rotational degrees of freedom via the angular velocity
+scale values = type ratio
+  type = atom type (1-N)
+  ratio = factor by which to scale the damping coefficient
+tally value = no or yes
+  no = do not tally the energy added/subtracted to atoms
+  yes = do tally the energy added/subtracted to atoms
+zero value = no or yes
+  no = do not set total random force to zero
+  yes = set total random force to zero
    diff --git a/doc/fix_langevin_drude.html b/doc/fix_langevin_drude.html index b181e27176..9929070af1 100644 --- a/doc/fix_langevin_drude.html +++ b/doc/fix_langevin_drude.html @@ -145,8 +145,8 @@ 
     zero value = no or yes
-    no = do not set total random force on centers of mass to zero
-    yes = set total random force on centers of mass to zero
+  no = do not set total random force on centers of mass to zero
+  yes = set total random force on centers of mass to zero
    diff --git a/doc/fix_langevin_eff.html b/doc/fix_langevin_eff.html index 8b06af1be4..a46ea6eabb 100644 --- a/doc/fix_langevin_eff.html +++ b/doc/fix_langevin_eff.html @@ -150,8 +150,8 @@ keyword = scale or tally or zero 
     zero value = no or yes
-    no = do not set total random force to zero
-    yes = set total random force to zero
+  no = do not set total random force to zero
+  yes = set total random force to zero
    diff --git a/doc/fix_lb_fluid.html b/doc/fix_lb_fluid.html index 563c6d687f..c38a839610 100644 --- a/doc/fix_lb_fluid.html +++ b/doc/fix_lb_fluid.html @@ -144,29 +144,29 @@ 
     setArea values = type node_area
-      type = atom type (1-N)
-      node_area = portion of the surface area of the composite object associated with the particular atom type (used when the force coupling constant is set by default).
-  setGamma values = gamma
-      gamma = user set value for the force coupling constant.
-  scaleGamma values = type gammaFactor
-      type = atom type (1-N)
-      gammaFactor = factor to scale the setGamma gamma value by, for the specified atom type.
-  dx values = dx_LB = the lattice spacing.
-  dm values = dm_LB = the lattice-Boltzmann mass unit.
-  a0 values = a_0_real = the square of the speed of sound in the fluid.
-  noise values = Temperature seed
-      Temperature = fluid temperature.
-      seed = random number generator seed (positive integer)
-  calcforce values = N forcegroup-ID
-      N = output the force and torque every N timesteps
-      forcegroup-ID = ID of the particle group to calculate the force and torque of
-  trilinear values = none (used to switch from the default Peskin interpolation stencil to the trilinear stencil).
-  D3Q19 values = none (used to switch from the default D3Q15, 15 velocity lattice, to the D3Q19, 19 velocity lattice).
-  read_restart values = restart file = name of the restart file to use to restart a fluid run.
-  write_restart values = N = write a restart file every N MD timesteps.
-  zwall_velocity values = velocity_bottom velocity_top = velocities along the y-direction of the bottom and top walls (located at z=zmin and z=zmax).
-  bodyforce values = bodyforcex bodyforcey bodyforcez = the x,y and z components of a constant body force added to the fluid.
-  printfluid values = N = print the fluid density and velocity at each grid point every N timesteps.
+    type = atom type (1-N)
+    node_area = portion of the surface area of the composite object associated with the particular atom type (used when the force coupling constant is set by default).
+setGamma values = gamma
+    gamma = user set value for the force coupling constant.
+scaleGamma values = type gammaFactor
+    type = atom type (1-N)
+    gammaFactor = factor to scale the setGamma gamma value by, for the specified atom type.
+dx values = dx_LB = the lattice spacing.
+dm values = dm_LB = the lattice-Boltzmann mass unit.
+a0 values = a_0_real = the square of the speed of sound in the fluid.
+noise values = Temperature seed
+    Temperature = fluid temperature.
+    seed = random number generator seed (positive integer)
+calcforce values = N forcegroup-ID
+    N = output the force and torque every N timesteps
+    forcegroup-ID = ID of the particle group to calculate the force and torque of
+trilinear values = none (used to switch from the default Peskin interpolation stencil to the trilinear stencil).
+D3Q19 values = none (used to switch from the default D3Q15, 15 velocity lattice, to the D3Q19, 19 velocity lattice).
+read_restart values = restart file = name of the restart file to use to restart a fluid run.
+write_restart values = N = write a restart file every N MD timesteps.
+zwall_velocity values = velocity_bottom velocity_top = velocities along the y-direction of the bottom and top walls (located at z=zmin and z=zmax).
+bodyforce values = bodyforcex bodyforcey bodyforcez = the x,y and z components of a constant body force added to the fluid.
+printfluid values = N = print the fluid density and velocity at each grid point every N timesteps.
    diff --git a/doc/fix_lb_momentum.html b/doc/fix_lb_momentum.html index 59b26145f9..548f4c5213 100644 --- a/doc/fix_lb_momentum.html +++ b/doc/fix_lb_momentum.html @@ -140,7 +140,7 @@ 
     linear values = xflag yflag zflag
-    xflag,yflag,zflag = 0/1 to exclude/include each dimension.
+  xflag,yflag,zflag = 0/1 to exclude/include each dimension.
    diff --git a/doc/fix_lb_rigid_pc_sphere.html b/doc/fix_lb_rigid_pc_sphere.html index 711ec2554f..13848ce4df 100644 --- a/doc/fix_lb_rigid_pc_sphere.html +++ b/doc/fix_lb_rigid_pc_sphere.html @@ -154,13 +154,13 @@ 
     force values = M xflag yflag zflag
-    M = which rigid body from 1-Nbody (see asterisk form below)
-    xflag,yflag,zflag = off/on if component of center-of-mass force is active
-  torque values = M xflag yflag zflag
-    M = which rigid body from 1-Nbody (see asterisk form below)
-    xflag,yflag,zflag = off/on if component of center-of-mass torque is active
-  innerNodes values = innergroup-ID
-    innergroup-ID = ID of the atom group which does not experience a hydrodynamic force from the lattice-Boltzmann fluid
+  M = which rigid body from 1-Nbody (see asterisk form below)
+  xflag,yflag,zflag = off/on if component of center-of-mass force is active
+torque values = M xflag yflag zflag
+  M = which rigid body from 1-Nbody (see asterisk form below)
+  xflag,yflag,zflag = off/on if component of center-of-mass torque is active
+innerNodes values = innergroup-ID
+  innergroup-ID = ID of the atom group which does not experience a hydrodynamic force from the lattice-Boltzmann fluid
    diff --git a/doc/fix_modify.html b/doc/fix_modify.html index d1ea58b553..c312f598d2 100644 --- a/doc/fix_modify.html +++ b/doc/fix_modify.html @@ -138,8 +138,8 @@ 
     temp value = compute ID that calculates a temperature
-  press value = compute ID that calculates a pressure
-  energy value = yes or no
+press value = compute ID that calculates a pressure
+energy value = yes or no
    diff --git a/doc/fix_momentum.html b/doc/fix_momentum.html index 4f65a93965..570163e682 100644 --- a/doc/fix_momentum.html +++ b/doc/fix_momentum.html @@ -140,8 +140,8 @@ one or more keyword/value pairs may be appended 
     linear values = xflag yflag zflag
-    xflag,yflag,zflag = 0/1 to exclude/include each dimension
-  angular values = none
+  xflag,yflag,zflag = 0/1 to exclude/include each dimension
+angular values = none
 
     rescale values = none
diff --git a/doc/fix_move.html b/doc/fix_move.html
index 70ddaa89e9..980af0410d 100644
--- a/doc/fix_move.html
+++ b/doc/fix_move.html
@@ -138,17 +138,17 @@
 
 
     linear args = Vx Vy Vz
-    Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL
-  wiggle args = Ax Ay Az period
-    Ax,Ay,Az = components of amplitude vector (distance units), any component can be specified as NULL
-    period = period of oscillation (time units)
-  rotate args = Px Py Pz Rx Ry Rz period
-    Px,Py,Pz = origin point of axis of rotation (distance units)
-    Rx,Ry,Rz = axis of rotation vector
-    period = period of rotation (time units)
-  variable args = v_dx v_dy v_dz v_vx v_vy v_vz
-    v_dx,v_dy,v_dz = 3 variable names that calculate x,y,z displacement as function of time, any component can be specified as NULL
-    v_vx,v_vy,v_vz = 3 variable names that calculate x,y,z velocity as function of time, any component can be specified as NULL
+  Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL
+wiggle args = Ax Ay Az period
+  Ax,Ay,Az = components of amplitude vector (distance units), any component can be specified as NULL
+  period = period of oscillation (time units)
+rotate args = Px Py Pz Rx Ry Rz period
+  Px,Py,Pz = origin point of axis of rotation (distance units)
+  Rx,Ry,Rz = axis of rotation vector
+  period = period of rotation (time units)
+variable args = v_dx v_dy v_dz v_vx v_vy v_vz
+  v_dx,v_dy,v_dz = 3 variable names that calculate x,y,z displacement as function of time, any component can be specified as NULL
+  v_vx,v_vy,v_vz = 3 variable names that calculate x,y,z velocity as function of time, any component can be specified as NULL
 
    
 
      
 
    • zero or more keyword/value pairs may be appended
      • 
diff --git a/doc/fix_msst.html b/doc/fix_msst.html
index f79a088582..fcc8cc863c 100644
--- a/doc/fix_msst.html
+++ b/doc/fix_msst.html
@@ -141,11 +141,11 @@
 
    
 
     q value = cell mass-like parameter (mass^2/distance^4 units)
-  mu value = artificial viscosity (mass/length/time units)
-  p0 value = initial pressure in the shock equations (pressure units)
-  v0 value = initial simulation cell volume in the shock equations (distance^3 units)
-  e0 value = initial total energy (energy units)
-  tscale value = reduction in initial temperature (unitless fraction between 0.0 and 1.0)
+mu value = artificial viscosity (mass/length/time units)
+p0 value = initial pressure in the shock equations (pressure units)
+v0 value = initial simulation cell volume in the shock equations (distance^3 units)
+e0 value = initial total energy (energy units)
+tscale value = reduction in initial temperature (unitless fraction between 0.0 and 1.0)
    diff --git a/doc/fix_nve_sphere.html b/doc/fix_nve_sphere.html index 5af499e48a..ddb58d6d58 100644 --- a/doc/fix_nve_sphere.html +++ b/doc/fix_nve_sphere.html @@ -142,7 +142,7 @@ 
     update value = dipole
-    dipole = update orientation of dipole moment during integration
+  dipole = update orientation of dipole moment during integration
    diff --git a/doc/fix_orient_fcc.html b/doc/fix_orient_fcc.html index fa445260e3..02e899a6a8 100644 --- a/doc/fix_orient_fcc.html +++ b/doc/fix_orient_fcc.html @@ -260,21 +260,21 @@ Materials, 5, 124-127 (2006).

    Sigma=5 <100> tilt boundary. This is for a lattice constant of 3.5706 Angs.

    file0:

    -
    0.798410432046075    1.785300000000000    1.596820864092150
-    -0.798410432046075    1.785300000000000   -1.596820864092150
-     2.395231296138225    0.000000000000000    0.798410432046075
-     0.798410432046075    0.000000000000000   -2.395231296138225
-     1.596820864092150    1.785300000000000   -0.798410432046075
-     1.596820864092150   -1.785300000000000   -0.798410432046075
+
     0.798410432046075    1.785300000000000    1.596820864092150
+-0.798410432046075    1.785300000000000   -1.596820864092150
+ 2.395231296138225    0.000000000000000    0.798410432046075
+ 0.798410432046075    0.000000000000000   -2.395231296138225
+ 1.596820864092150    1.785300000000000   -0.798410432046075
+ 1.596820864092150   -1.785300000000000   -0.798410432046075
 
    
 
    
 
    file1:
    
 
    -0.798410432046075    1.785300000000000    1.596820864092150
-     0.798410432046075    1.785300000000000   -1.596820864092150
-     0.798410432046075    0.000000000000000    2.395231296138225
-     2.395231296138225    0.000000000000000   -0.798410432046075
-     1.596820864092150    1.785300000000000    0.798410432046075
-     1.596820864092150   -1.785300000000000    0.798410432046075
+ 0.798410432046075    1.785300000000000   -1.596820864092150
+ 0.798410432046075    0.000000000000000    2.395231296138225
+ 2.395231296138225    0.000000000000000   -0.798410432046075
+ 1.596820864092150    1.785300000000000    0.798410432046075
+ 1.596820864092150   -1.785300000000000    0.798410432046075
    diff --git a/doc/fix_phonon.html b/doc/fix_phonon.html index c68c69714b..241ade1457 100644 --- a/doc/fix_phonon.html +++ b/doc/fix_phonon.html @@ -144,8 +144,8 @@ 
     GAMMA flags to treate the whole simulation box as a unit cell, so that the mapping
-  info can be generated internally. In this case, dynamical matrix at only the gamma-point
-  will/can be evaluated.
+info can be generated internally. In this case, dynamical matrix at only the gamma-point
+will/can be evaluated.
    • prefix = prefix for output files
      • @@ -154,9 +154,9 @@ 
     sysdim value = d
-    d = dimension of the system, usually the same as the MD model dimension
-  nasr value = n
-    n = number of iterations to enforce the acoustic sum rule
+  d = dimension of the system, usually the same as the MD model dimension
+nasr value = n
+  n = number of iterations to enforce the acoustic sum rule
    diff --git a/doc/fix_pimd.html b/doc/fix_pimd.html index fb32b38d13..1abbf40098 100644 --- a/doc/fix_pimd.html +++ b/doc/fix_pimd.html @@ -139,10 +139,10 @@ 
     method value = pimd or nmpimd or cmd
-  fmass value = scaling factor on mass
-  sp value = scaling factor on Planck constant
-  temp value = temperature (temperarate units)
-  nhc value = Nc = number of chains in Nose-Hoover thermostat
+fmass value = scaling factor on mass
+sp value = scaling factor on Planck constant
+temp value = temperature (temperarate units)
+nhc value = Nc = number of chains in Nose-Hoover thermostat
    diff --git a/doc/fix_poems.html b/doc/fix_poems.html index ce79591184..86e21ba63d 100644 --- a/doc/fix_poems.html +++ b/doc/fix_poems.html @@ -137,8 +137,8 @@ 
     group values = list of group IDs
-  molecule values = none
-  file values = filename
+molecule values = none
+file values = filename

    Examples¶

    diff --git a/doc/fix_pour.html b/doc/fix_pour.html index 256b7043ea..bd45d82aa2 100644 --- a/doc/fix_pour.html +++ b/doc/fix_pour.html @@ -142,37 +142,37 @@ 
     region value = region-ID
-    region-ID = ID of region to use as insertion volume
-  diam values = dstyle args
-    dstyle = one or range or poly
-      one args = D
-        D = single diameter for inserted particles (distance units)
-      range args = Dlo Dhi
-        Dlo,Dhi = range of diameters for inserted particles (distance units)
-      poly args = Npoly D1 P1 D2 P2 ...
-        Npoly = # of (D,P) pairs
-        D1,D2,... = diameter for subset of inserted particles (distance units)
-        P1,P2,... = percentage of inserted particles with this diameter (0-1)
-  vol values = fraction Nattempt
-    fraction = desired volume fraction for filling insertion volume
-    Nattempt = max # of insertion attempts per atom
-  rate value = V
-    V = z velocity (3d) or y velocity (2d) at which
-        insertion volume moves (velocity units)
-  vel values (3d) = vxlo vxhi vylo vyhi vz
-  vel values (2d) = vxlo vxhi vy
-    vxlo,vxhi = range of x velocities for inserted particles (velocity units)
-    vylo,vyhi = range of y velocities for inserted particles (velocity units)
-    vz = z velocity (3d) assigned to inserted particles (velocity units)
-    vy = y velocity (2d) assigned to inserted particles (velocity units)
-  mol value = template-ID
-    template-ID = ID of molecule template specified in a separate molecule command
-  molfrac values = f1 f2 ... fN
-    f1 to fN = relative probability of creating each of N molecules in template-ID
-  rigid value = fix-ID
-    fix-ID = ID of fix rigid/small command
-  shake value = fix-ID
-    fix-ID = ID of fix shake command
+  region-ID = ID of region to use as insertion volume
+diam values = dstyle args
+  dstyle = one or range or poly
+    one args = D
+      D = single diameter for inserted particles (distance units)
+    range args = Dlo Dhi
+      Dlo,Dhi = range of diameters for inserted particles (distance units)
+    poly args = Npoly D1 P1 D2 P2 ...
+      Npoly = # of (D,P) pairs
+      D1,D2,... = diameter for subset of inserted particles (distance units)
+      P1,P2,... = percentage of inserted particles with this diameter (0-1)
+vol values = fraction Nattempt
+  fraction = desired volume fraction for filling insertion volume
+  Nattempt = max # of insertion attempts per atom
+rate value = V
+  V = z velocity (3d) or y velocity (2d) at which
+      insertion volume moves (velocity units)
+vel values (3d) = vxlo vxhi vylo vyhi vz
+vel values (2d) = vxlo vxhi vy
+  vxlo,vxhi = range of x velocities for inserted particles (velocity units)
+  vylo,vyhi = range of y velocities for inserted particles (velocity units)
+  vz = z velocity (3d) assigned to inserted particles (velocity units)
+  vy = y velocity (2d) assigned to inserted particles (velocity units)
+mol value = template-ID
+  template-ID = ID of molecule template specified in a separate molecule command
+molfrac values = f1 f2 ... fN
+  f1 to fN = relative probability of creating each of N molecules in template-ID
+rigid value = fix-ID
+  fix-ID = ID of fix rigid/small command
+shake value = fix-ID
+  fix-ID = ID of fix shake command
    diff --git a/doc/fix_print.html b/doc/fix_print.html index b29f5c1d37..cb5b4b539d 100644 --- a/doc/fix_print.html +++ b/doc/fix_print.html @@ -141,10 +141,10 @@ 
     file value = filename
-  append value = filename
-  screen value = yes or no
-  title value = string
-    string =  text to print as 1st line of output file
+append value = filename
+screen value = yes or no
+title value = string
+  string =  text to print as 1st line of output file
    diff --git a/doc/fix_property_atom.html b/doc/fix_property_atom.html index 7c5501c52d..4df5b09986 100644 --- a/doc/fix_property_atom.html +++ b/doc/fix_property_atom.html @@ -138,9 +138,9 @@ 
     mol = molecule IDs
-  q = charge
-  i_name = new integer vector referenced by name
-  d_name = new floating-point vector referenced by name
+q = charge
+i_name = new integer vector referenced by name
+d_name = new floating-point vector referenced by name
    • zero of more keyword/value pairs may be appended
      • diff --git a/doc/fix_qbmsst.html b/doc/fix_qbmsst.html index caf1b67ac4..2bdc71194e 100644 --- a/doc/fix_qbmsst.html +++ b/doc/fix_qbmsst.html @@ -141,18 +141,18 @@ 
     q value = cell mass-like parameter (mass^2/distance^4 units)
-  mu value = artificial viscosity (mass/distance/time units)
-  p0 value = initial pressure in the shock equations (pressure units)
-  v0 value = initial simulation cell volume in the shock equations (distance^3 units)
-  e0 value = initial total energy (energy units)
-  tscale value = reduction in initial temperature (unitless fraction between 0.0 and 1.0)
-  damp value = damping parameter (time units) inverse of friction <i>&gamma;</i>
-  seed value = random number seed (positive integer)
-  f_max value = upper cutoff frequency of the vibration spectrum (1/time units)
-  N_f value = number of frequency bins (positive integer)
-  eta value = coupling constant between the shock system and the quantum thermal bath (positive unitless)
-  beta value = the quantum temperature is updated every beta time steps (positive integer)
-  T_init value = quantum temperature for the initial state (temperature units)
+mu value = artificial viscosity (mass/distance/time units)
+p0 value = initial pressure in the shock equations (pressure units)
+v0 value = initial simulation cell volume in the shock equations (distance^3 units)
+e0 value = initial total energy (energy units)
+tscale value = reduction in initial temperature (unitless fraction between 0.0 and 1.0)
+damp value = damping parameter (time units) inverse of friction <i>&gamma;</i>
+seed value = random number seed (positive integer)
+f_max value = upper cutoff frequency of the vibration spectrum (1/time units)
+N_f value = number of frequency bins (positive integer)
+eta value = coupling constant between the shock system and the quantum thermal bath (positive unitless)
+beta value = the quantum temperature is updated every beta time steps (positive integer)
+T_init value = quantum temperature for the initial state (temperature units)
    diff --git a/doc/fix_qeq_comb.html b/doc/fix_qeq_comb.html index 61f509b833..5d9005dede 100644 --- a/doc/fix_qeq_comb.html +++ b/doc/fix_qeq_comb.html @@ -144,7 +144,7 @@ 
     file value = filename
-    filename = name of file to write QEQ equilibration info to
+  filename = name of file to write QEQ equilibration info to
    diff --git a/doc/fix_qtb.html b/doc/fix_qtb.html index f6fb026583..afa68726f9 100644 --- a/doc/fix_qtb.html +++ b/doc/fix_qtb.html @@ -139,10 +139,10 @@ 
     temp value = target quantum temperature (temperature units)
-  damp value = damping parameter (time units) inverse of friction <i>&gamma</i>;
-  seed value = random number seed (positive integer)
-  f_max value = upper cutoff frequency of the vibration spectrum (1/time units)
-  N_f value = number of frequency bins (positive integer)
+damp value = damping parameter (time units) inverse of friction <i>&gamma</i>;
+seed value = random number seed (positive integer)
+f_max value = upper cutoff frequency of the vibration spectrum (1/time units)
+N_f value = number of frequency bins (positive integer)
    diff --git a/doc/fix_reaxc_species.html b/doc/fix_reaxc_species.html index 77f008c2df..58fa7aa7ad 100644 --- a/doc/fix_reaxc_species.html +++ b/doc/fix_reaxc_species.html @@ -143,12 +143,12 @@ 
     cutoff value = I J Cutoff
-    I, J = atom types
-    Cutoff = Bond-order cutoff value for this pair of atom types
-  element value = Element1, Element2, ...
-  position value = posfreq filepos
-    posfreq = write position files every this many timestep
-    filepos = name of position output file
+  I, J = atom types
+  Cutoff = Bond-order cutoff value for this pair of atom types
+element value = Element1, Element2, ...
+position value = posfreq filepos
+  posfreq = write position files every this many timestep
+  filepos = name of position output file
    diff --git a/doc/fix_recenter.html b/doc/fix_recenter.html index 2ec206da59..6c8c298595 100644 --- a/doc/fix_recenter.html +++ b/doc/fix_recenter.html @@ -140,8 +140,8 @@ 
     shift value = group-ID
-    group-ID = group of atoms whose coords are shifted
-  units value = box or lattice or fraction
+  group-ID = group of atoms whose coords are shifted
+units value = box or lattice or fraction
    diff --git a/doc/fix_restrain.html b/doc/fix_restrain.html index 749d1bf08b..40069ef106 100644 --- a/doc/fix_restrain.html +++ b/doc/fix_restrain.html @@ -139,17 +139,17 @@ 
     bond args = atom1 atom2 Kstart Kstop r0
-    atom1,atom2 = IDs of 2 atoms in bond
-    Kstart,Kstop = restraint coefficients at start/end of run (energy units)
-    r0 = equilibrium bond distance (distance units)
-  angle args = atom1 atom2 atom3 Kstart Kstop theta0
-    atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom
-    Kstart,Kstop = restraint coefficients at start/end of run (energy units)
-    theta0 = equilibrium angle theta (degrees)
-  dihedral args = atom1 atom2 atom3 atom4 Kstart Kstop phi0
-    atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order
-    Kstart,Kstop = restraint coefficients at start/end of run (energy units)
-    phi0 = equilibrium dihedral angle phi (degrees)
+  atom1,atom2 = IDs of 2 atoms in bond
+  Kstart,Kstop = restraint coefficients at start/end of run (energy units)
+  r0 = equilibrium bond distance (distance units)
+angle args = atom1 atom2 atom3 Kstart Kstop theta0
+  atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom
+  Kstart,Kstop = restraint coefficients at start/end of run (energy units)
+  theta0 = equilibrium angle theta (degrees)
+dihedral args = atom1 atom2 atom3 atom4 Kstart Kstop phi0
+  atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order
+  Kstart,Kstop = restraint coefficients at start/end of run (energy units)
+  phi0 = equilibrium dihedral angle phi (degrees)
    diff --git a/doc/fix_rigid.html b/doc/fix_rigid.html index 1da87a532e..ddc7d170b5 100644 --- a/doc/fix_rigid.html +++ b/doc/fix_rigid.html @@ -165,10 +165,10 @@ 
     single args = none
-  molecule args = none
-  group args = N groupID1 groupID2 ...
-    N = # of groups
-    groupID1, groupID2, ... = list of N group IDs
+molecule args = none
+group args = N groupID1 groupID2 ...
+  N = # of groups
+  groupID1, groupID2, ... = list of N group IDs
    • zero or more keyword/value pairs may be appended
      • @@ -176,37 +176,37 @@ 
     langevin values = Tstart Tstop Tperiod seed
-    Tstart,Tstop = desired temperature at start/stop of run (temperature units)
-    Tdamp = temperature damping parameter (time units)
-    seed = random number seed to use for white noise (positive integer)
-  temp values = Tstart Tstop Tdamp
-    Tstart,Tstop = desired temperature at start/stop of run (temperature units)
-    Tdamp = temperature damping parameter (time units)
-  iso or aniso values = Pstart Pstop Pdamp
-    Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
-    Pdamp = pressure damping parameter (time units)
-  x or y or z values = Pstart Pstop Pdamp
-    Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
-    Pdamp = stress damping parameter (time units)
-  couple = none or xyz or xy or yz or xz
-  tparam values = Tchain Titer Torder
-    Tchain = length of Nose/Hoover thermostat chain
-    Titer = number of thermostat iterations performed
-    Torder = 3 or 5 = Yoshida-Suzuki integration parameters
-  pchain values = Pchain
-    Pchain = length of the Nose/Hoover thermostat chain coupled with the barostat
-  dilate value = dilate-group-ID
-    dilate-group-ID = only dilate atoms in this group due to barostat volume changes
-  force values = M xflag yflag zflag
-    M = which rigid body from 1-Nbody (see asterisk form below)
-    xflag,yflag,zflag = off/on if component of center-of-mass force is active
-  torque values = M xflag yflag zflag
-    M = which rigid body from 1-Nbody (see asterisk form below)
-    xflag,yflag,zflag = off/on if component of center-of-mass torque is active
-  infile filename
-    filename = file with per-body values of mass, center-of-mass, moments of inertia
-  mol value = template-ID
-    template-ID = ID of molecule template specified in a separate molecule command
+  Tstart,Tstop = desired temperature at start/stop of run (temperature units)
+  Tdamp = temperature damping parameter (time units)
+  seed = random number seed to use for white noise (positive integer)
+temp values = Tstart Tstop Tdamp
+  Tstart,Tstop = desired temperature at start/stop of run (temperature units)
+  Tdamp = temperature damping parameter (time units)
+iso or aniso values = Pstart Pstop Pdamp
+  Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
+  Pdamp = pressure damping parameter (time units)
+x or y or z values = Pstart Pstop Pdamp
+  Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
+  Pdamp = stress damping parameter (time units)
+couple = none or xyz or xy or yz or xz
+tparam values = Tchain Titer Torder
+  Tchain = length of Nose/Hoover thermostat chain
+  Titer = number of thermostat iterations performed
+  Torder = 3 or 5 = Yoshida-Suzuki integration parameters
+pchain values = Pchain
+  Pchain = length of the Nose/Hoover thermostat chain coupled with the barostat
+dilate value = dilate-group-ID
+  dilate-group-ID = only dilate atoms in this group due to barostat volume changes
+force values = M xflag yflag zflag
+  M = which rigid body from 1-Nbody (see asterisk form below)
+  xflag,yflag,zflag = off/on if component of center-of-mass force is active
+torque values = M xflag yflag zflag
+  M = which rigid body from 1-Nbody (see asterisk form below)
+  xflag,yflag,zflag = off/on if component of center-of-mass torque is active
+infile filename
+  filename = file with per-body values of mass, center-of-mass, moments of inertia
+mol value = template-ID
+  template-ID = ID of molecule template specified in a separate molecule command
    diff --git a/doc/fix_setforce.html b/doc/fix_setforce.html index 7a91130031..1179bde54c 100644 --- a/doc/fix_setforce.html +++ b/doc/fix_setforce.html @@ -144,7 +144,7 @@ 
     region value = region-ID
-    region-ID = ID of region atoms must be in to have added force
+  region-ID = ID of region atoms must be in to have added force
    diff --git a/doc/fix_shake.html b/doc/fix_shake.html index bdaea8ba19..8396a94ca4 100644 --- a/doc/fix_shake.html +++ b/doc/fix_shake.html @@ -148,9 +148,9 @@ 
     b values = one or more bond types
-  a values = one or more angle types
-  t values = one or more atom types
-  m value = one or more mass values
+a values = one or more angle types
+t values = one or more atom types
+m value = one or more mass values
    • zero or more keyword/value pairs may be appended
      • @@ -158,7 +158,7 @@ 
     mol value = template-ID
-    template-ID = ID of molecule template specified in a separate molecule command
+  template-ID = ID of molecule template specified in a separate molecule command
    diff --git a/doc/fix_smd.html b/doc/fix_smd.html index e6e0335784..3b7a04ed5d 100644 --- a/doc/fix_smd.html +++ b/doc/fix_smd.html @@ -138,22 +138,22 @@ 
     cvel values = K vel
-    K = spring constant (force/distance units)
-    vel = velocity of pulling (distance/time units)
-  cfor values = force
-    force = pulling force (force units)
+  K = spring constant (force/distance units)
+  vel = velocity of pulling (distance/time units)
+cfor values = force
+  force = pulling force (force units)
    • keyword = tether or couple
     tether values = x y z R0
-    x,y,z = point to which spring is tethered
-    R0 = distance of end of spring from tether point (distance units)
-  couple values = group-ID2 x y z R0
-    group-ID2 = 2nd group to couple to fix group with a spring
-    x,y,z = direction of spring, automatically computed with 'auto'
-    R0 = distance of end of spring (distance units)
+  x,y,z = point to which spring is tethered
+  R0 = distance of end of spring from tether point (distance units)
+couple values = group-ID2 x y z R0
+  group-ID2 = 2nd group to couple to fix group with a spring
+  x,y,z = direction of spring, automatically computed with 'auto'
+  R0 = distance of end of spring (distance units)
    diff --git a/doc/fix_spring.html b/doc/fix_spring.html index 329ec9650c..0f7fe361ee 100644 --- a/doc/fix_spring.html +++ b/doc/fix_spring.html @@ -138,14 +138,14 @@ 
     tether values = K x y z R0
-    K = spring constant (force/distance units)
-    x,y,z = point to which spring is tethered
-    R0 = equilibrium distance from tether point (distance units)
-  couple values = group-ID2 K x y z R0
-    group-ID2 = 2nd group to couple to fix group with a spring
-    K = spring constant (force/distance units)
-    x,y,z = direction of spring
-    R0 = equilibrium distance of spring (distance units)
+  K = spring constant (force/distance units)
+  x,y,z = point to which spring is tethered
+  R0 = equilibrium distance from tether point (distance units)
+couple values = group-ID2 K x y z R0
+  group-ID2 = 2nd group to couple to fix group with a spring
+  K = spring constant (force/distance units)
+  x,y,z = direction of spring
+  R0 = equilibrium distance of spring (distance units)
    diff --git a/doc/fix_srd.html b/doc/fix_srd.html index b2408e6ae1..04c126ed89 100644 --- a/doc/fix_srd.html +++ b/doc/fix_srd.html @@ -144,28 +144,28 @@ 
     lamda value = mean free path of SRD particles (distance units)
-  collision value = noslip or slip = collision model
-  overlap value = yes or no = whether big particles may overlap
-  inside value = error or warn or ignore = how SRD particles which end up inside a big particle are treated
-  exact value = yes or no
-  radius value = rfactor = scale collision radius by this factor
-  bounce value = Nbounce = max # of collisions an SRD particle can undergo in one timestep
-  search value = sgrid = grid spacing for collision partner searching (distance units)
-  cubic values = style tolerance
-    style = error or warn
-    tolerance = fractional difference allowed (0 <= tol <= 1)
-  shift values = flag shiftseed
-    flag = yes or no or possible = SRD bin shifting for better statistics
-      yes = perform bin shifting each time SRD velocities are rescaled
-      no = no shifting
-      possible = shift depending on mean free path and bin size
-    shiftseed = random # seed (positive integer)
-  tstat value = yes or no = thermostat SRD particles or not
-  rescale value = yes or no or rotate or collide = rescaling of SRD velocities
-    yes = rescale during velocity rotation and collisions
-    no = no rescaling
-    rotate = rescale during velocity rotation, but not collisions
-    collide = rescale during collisions, but not velocity rotation
+collision value = noslip or slip = collision model
+overlap value = yes or no = whether big particles may overlap
+inside value = error or warn or ignore = how SRD particles which end up inside a big particle are treated
+exact value = yes or no
+radius value = rfactor = scale collision radius by this factor
+bounce value = Nbounce = max # of collisions an SRD particle can undergo in one timestep
+search value = sgrid = grid spacing for collision partner searching (distance units)
+cubic values = style tolerance
+  style = error or warn
+  tolerance = fractional difference allowed (0 <= tol <= 1)
+shift values = flag shiftseed
+  flag = yes or no or possible = SRD bin shifting for better statistics
+    yes = perform bin shifting each time SRD velocities are rescaled
+    no = no shifting
+    possible = shift depending on mean free path and bin size
+  shiftseed = random # seed (positive integer)
+tstat value = yes or no = thermostat SRD particles or not
+rescale value = yes or no or rotate or collide = rescaling of SRD velocities
+  yes = rescale during velocity rotation and collisions
+  no = no rescaling
+  rotate = rescale during velocity rotation, but not collisions
+  collide = rescale during collisions, but not velocity rotation
    diff --git a/doc/fix_store_state.html b/doc/fix_store_state.html index 44defb1600..c0754d723f 100644 --- a/doc/fix_store_state.html +++ b/doc/fix_store_state.html @@ -138,38 +138,38 @@
  • input = one or more atom attributes
    • possible attributes = id, mol, type, mass,
-                     x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
-                     vx, vy, vz, fx, fy, fz,
-                        q, mux, muy, muz,
-                        radius, omegax, omegay, omegaz,
-                        angmomx, angmomy, angmomz, tqx, tqy, tqz,
-                        c_ID, c_ID[N], f_ID, f_ID[N], v_name,
-                        d_name, i_name
+                   x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
+                   vx, vy, vz, fx, fy, fz,
+                      q, mux, muy, muz,
+                      radius, omegax, omegay, omegaz,
+                      angmomx, angmomy, angmomz, tqx, tqy, tqz,
+                      c_ID, c_ID[N], f_ID, f_ID[N], v_name,
+                      d_name, i_name
 
    id = atom ID
-      mol = molecule ID
-      type = atom type
-      mass = atom mass
-      x,y,z = unscaled atom coordinates
-      xs,ys,zs = scaled atom coordinates
-      xu,yu,zu = unwrapped atom coordinates
-      ix,iy,iz = box image that the atom is in
-      vx,vy,vz = atom velocities
-      fx,fy,fz = forces on atoms
-      q = atom charge
-      mux,muy,muz = orientation of dipolar atom
-      radius = radius of spherical particle
-      omegax,omegay,omegaz = angular velocity of spherical particle
-      angmomx,angmomy,angmomz = angular momentum of aspherical particle
-      tqx,tqy,tqz = torque on finite-size particles
-      c_ID = per-atom vector calculated by a compute with ID
-      c_ID[I] = Ith column of per-atom array calculated by a compute with ID
-      f_ID = per-atom vector calculated by a fix with ID
-      f_ID[I] = Ith column of per-atom array calculated by a fix with ID
-      v_name = per-atom vector calculated by an atom-style variable with name
-      d_name = per-atom floating point vector name, managed by fix property/atom
-      i_name = per-atom integer vector name, managed by fix property/atom
+mol = molecule ID
+type = atom type
+mass = atom mass
+x,y,z = unscaled atom coordinates
+xs,ys,zs = scaled atom coordinates
+xu,yu,zu = unwrapped atom coordinates
+ix,iy,iz = box image that the atom is in
+vx,vy,vz = atom velocities
+fx,fy,fz = forces on atoms
+q = atom charge
+mux,muy,muz = orientation of dipolar atom
+radius = radius of spherical particle
+omegax,omegay,omegaz = angular velocity of spherical particle
+angmomx,angmomy,angmomz = angular momentum of aspherical particle
+tqx,tqy,tqz = torque on finite-size particles
+c_ID = per-atom vector calculated by a compute with ID
+c_ID[I] = Ith column of per-atom array calculated by a compute with ID
+f_ID = per-atom vector calculated by a fix with ID
+f_ID[I] = Ith column of per-atom array calculated by a fix with ID
+v_name = per-atom vector calculated by an atom-style variable with name
+d_name = per-atom floating point vector name, managed by fix property/atom
+i_name = per-atom integer vector name, managed by fix property/atom
      diff --git a/doc/fix_tfmc.html b/doc/fix_tfmc.html index 38ae722f70..38d84ba4da 100644 --- a/doc/fix_tfmc.html +++ b/doc/fix_tfmc.html @@ -142,8 +142,8 @@ 
     com args = xflag yflag zflag
-    xflag,yflag,zflag = 0/1 to exclude/include each dimension
-  rot args = none
+  xflag,yflag,zflag = 0/1 to exclude/include each dimension
+rot args = none
    diff --git a/doc/fix_ti_rs.html b/doc/fix_ti_rs.html index 64bbf0f477..f86d033987 100644 --- a/doc/fix_ti_rs.html +++ b/doc/fix_ti_rs.html @@ -140,7 +140,7 @@ 
     function value = function-ID
-    function-ID = ID of the switching function (1, 2 or 3)
+  function-ID = ID of the switching function (1, 2 or 3)

    Example:

    fix ref all ti/rs 50.0 2000 1000
diff --git a/doc/fix_ti_spring.html b/doc/fix_ti_spring.html
index 22a08955ea..327b4b8a74 100644
--- a/doc/fix_ti_spring.html
+++ b/doc/fix_ti_spring.html
@@ -141,7 +141,7 @@
 
 
     function value = function-ID
-    function-ID = ID of the switching function (1 or 2)
+  function-ID = ID of the switching function (1 or 2)
 
    
 
    Example:
    
 
    fix ref all ti/spring 50.0 2000 1000 function 2
diff --git a/doc/fix_ttm.html b/doc/fix_ttm.html
index fcb4b3b523..45971a1cef 100644
--- a/doc/fix_ttm.html
+++ b/doc/fix_ttm.html
@@ -142,29 +142,29 @@ fix ID group-ID ttm/mod seed init_file Nx Ny Nz T_infile N T_outfile
 
  • remaining arguments for fix ttm:
    • 
 
 
    C_e  = electronic specific heat (energy/(electron*temperature) units)
-  rho_e = electronic density (electrons/volume units)
-  kappa_e = electronic thermal conductivity (energy/(time*distance*temperature) units)
-  gamma_p = friction coefficient due to electron-ion interactions (mass/time units)
-  gamma_s = friction coefficient due to electronic stopping (mass/time units)
-  v_0 = electronic stopping critical velocity (velocity units)
-  Nx = number of thermal solve grid points in the x-direction (positive integer)
-  Ny = number of thermal solve grid points in the y-direction (positive integer)
-  Nz = number of thermal solve grid points in the z-direction (positive integer)
-  T_infile = filename to read initial electronic temperature from
-  N = dump TTM temperatures every this many timesteps, 0 = no dump
-  T_outfile = filename to write TTM temperatures to (only needed if N > 0)
+rho_e = electronic density (electrons/volume units)
+kappa_e = electronic thermal conductivity (energy/(time*distance*temperature) units)
+gamma_p = friction coefficient due to electron-ion interactions (mass/time units)
+gamma_s = friction coefficient due to electronic stopping (mass/time units)
+v_0 = electronic stopping critical velocity (velocity units)
+Nx = number of thermal solve grid points in the x-direction (positive integer)
+Ny = number of thermal solve grid points in the y-direction (positive integer)
+Nz = number of thermal solve grid points in the z-direction (positive integer)
+T_infile = filename to read initial electronic temperature from
+N = dump TTM temperatures every this many timesteps, 0 = no dump
+T_outfile = filename to write TTM temperatures to (only needed if N > 0)
 
    
 
    
 
      
 
    • remaining arguments for fix ttm/mod:
      • 
 
    
 
    init_file = file with the parameters to TTM
-  Nx = number of thermal solve grid points in the x-direction (positive integer)
-  Ny = number of thermal solve grid points in the y-direction (positive integer)
-  Nz = number of thermal solve grid points in the z-direction (positive integer)
-  T_infile = filename to read initial electronic temperature from
-  N = dump TTM temperatures every this many timesteps, 0 = no dump
-  T_outfile = filename to write TTM temperatures to (only needed if N > 0)
+Nx = number of thermal solve grid points in the x-direction (positive integer)
+Ny = number of thermal solve grid points in the y-direction (positive integer)
+Nz = number of thermal solve grid points in the z-direction (positive integer)
+T_infile = filename to read initial electronic temperature from
+N = dump TTM temperatures every this many timesteps, 0 = no dump
+T_outfile = filename to write TTM temperatures to (only needed if N > 0)
 
    
 
    
 
    
diff --git a/doc/fix_vector.html b/doc/fix_vector.html
index 62dd1805b4..e6be5371d5 100644
--- a/doc/fix_vector.html
+++ b/doc/fix_vector.html
@@ -139,10 +139,10 @@
 
  • value = c_ID, c_ID[N], f_ID, f_ID[N], v_name
    • 
 
 
    c_ID = global scalar calculated by a compute with ID
-  c_ID[I] = Ith component of global vector calculated by a compute with ID
-  f_ID = global scalar calculated by a fix with ID
-  f_ID[I] = Ith component of global vector calculated by a fix with ID
-  v_name = global value calculated by an equal-style variable with name
+c_ID[I] = Ith component of global vector calculated by a compute with ID
+f_ID = global scalar calculated by a fix with ID
+f_ID[I] = Ith component of global vector calculated by a fix with ID
+v_name = global value calculated by an equal-style variable with name
 
    
 
    
 
    
diff --git a/doc/fix_viscosity.html b/doc/fix_viscosity.html
index 12a706717f..8f0eab262f 100644
--- a/doc/fix_viscosity.html
+++ b/doc/fix_viscosity.html
@@ -143,7 +143,7 @@
 
 
     swap value = Nswap = number of swaps to perform every N steps
-  vtarget value = V or INF = target velocity of swap partners (velocity units)
+vtarget value = V or INF = target velocity of swap partners (velocity units)
    diff --git a/doc/fix_wall.html b/doc/fix_wall.html index 153b9590b7..8c04d166fc 100644 --- a/doc/fix_wall.html +++ b/doc/fix_wall.html @@ -151,15 +151,15 @@ 
     args = coord epsilon sigma cutoff
-    coord = position of wall = EDGE or constant or variable
-      EDGE = current lo or hi edge of simulation box
-      constant = number like 0.0 or -30.0 (distance units)
-      variable = equal-style variable like v_x or v_wiggle
-    epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units)
-      epsilon can be a variable (see below)
-    sigma = size factor for wall-particle interaction (distance units)
-      sigma can be a variable (see below)
-    cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
+  coord = position of wall = EDGE or constant or variable
+    EDGE = current lo or hi edge of simulation box
+    constant = number like 0.0 or -30.0 (distance units)
+    variable = equal-style variable like v_x or v_wiggle
+  epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units)
+    epsilon can be a variable (see below)
+  sigma = size factor for wall-particle interaction (distance units)
+    sigma can be a variable (see below)
+  cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
    • zero or more keyword/value pairs may be appended
      • @@ -167,14 +167,14 @@ args = coord epsilon sigma cutoff 
     units value = lattice or box
-    lattice = the wall position is defined in lattice units
-    box = the wall position is defined in simulation box units
-  fld value = yes or no
-    yes = invoke the wall constraint to be compatible with implicit FLD
-    no = invoke the wall constraint in the normal way
-  pbc value = yes or no
-    yes = allow periodic boundary in a wall dimension
-    no = require non-perioidic boundaries in any wall dimension
+  lattice = the wall position is defined in lattice units
+  box = the wall position is defined in simulation box units
+fld value = yes or no
+  yes = invoke the wall constraint to be compatible with implicit FLD
+  no = invoke the wall constraint in the normal way
+pbc value = yes or no
+  yes = allow periodic boundary in a wall dimension
+  no = require non-perioidic boundaries in any wall dimension
    diff --git a/doc/fix_wall_gran.html b/doc/fix_wall_gran.html index 3e30a61499..1216dd14af 100644 --- a/doc/fix_wall_gran.html +++ b/doc/fix_wall_gran.html @@ -145,9 +145,9 @@ 
     xplane or yplane or zplane args = lo hi
-    lo,hi = position of lower and upper plane (distance units), either can be NULL)
-  zcylinder args = radius
-    radius = cylinder radius (distance units)
+  lo,hi = position of lower and upper plane (distance units), either can be NULL)
+zcylinder args = radius
+  radius = cylinder radius (distance units)
    • zero or more keyword/value pairs may be appended to args
      • @@ -155,12 +155,12 @@ 
     wiggle values = dim amplitude period
-    dim = x or y or z
-    amplitude = size of oscillation (distance units)
-    period = time of oscillation (time units)
-  shear values = dim vshear
-    dim = x or y or z
-    vshear = magnitude of shear velocity (velocity units)
+  dim = x or y or z
+  amplitude = size of oscillation (distance units)
+  period = time of oscillation (time units)
+shear values = dim vshear
+  dim = x or y or z
+  vshear = magnitude of shear velocity (velocity units)
    diff --git a/doc/fix_wall_piston.html b/doc/fix_wall_piston.html index ba0204f5e6..463ced750f 100644 --- a/doc/fix_wall_piston.html +++ b/doc/fix_wall_piston.html @@ -140,18 +140,18 @@ 
     pos args = z
-    z = z coordinate at which the piston begins (distance units)
-  vel args = vz
-    vz = final velocity of the piston (velocity units)
-  ramp = use a linear velocity ramp from 0 to vz
-  temp args = target damp seed extent
-    target = target velocity for region immediately ahead of the piston
-    damp = damping paramter (time units)
-    seed = random number seed for langevin kicks
-    extent = extent of thermostated region (distance units)
-  units value = lattice or box
-    lattice = the wall position is defined in lattice units
-    box = the wall position is defined in simulation box units
+  z = z coordinate at which the piston begins (distance units)
+vel args = vz
+  vz = final velocity of the piston (velocity units)
+ramp = use a linear velocity ramp from 0 to vz
+temp args = target damp seed extent
+  target = target velocity for region immediately ahead of the piston
+  damp = damping paramter (time units)
+  seed = random number seed for langevin kicks
+  extent = extent of thermostated region (distance units)
+units value = lattice or box
+  lattice = the wall position is defined in lattice units
+  box = the wall position is defined in simulation box units
    diff --git a/doc/fix_wall_reflect.html b/doc/fix_wall_reflect.html index 6fecb8dc52..b8850e8645 100644 --- a/doc/fix_wall_reflect.html +++ b/doc/fix_wall_reflect.html @@ -139,13 +139,13 @@ 
     xlo,*ylo*,*zlo* arg = EDGE or constant or variable
-    EDGE = current lo edge of simulation box
-    constant = number like 0.0 or -30.0 (distance units)
-    variable = equal-style variable like v_x or v_wiggle
-  xhi,*yhi*,*zhi* arg = EDGE or constant or variable
-    EDGE = current hi edge of simulation box
-    constant = number like 50.0 or 100.3 (distance units)
-    variable = equal-style variable like v_x or v_wiggle
+  EDGE = current lo edge of simulation box
+  constant = number like 0.0 or -30.0 (distance units)
+  variable = equal-style variable like v_x or v_wiggle
+xhi,*yhi*,*zhi* arg = EDGE or constant or variable
+  EDGE = current hi edge of simulation box
+  constant = number like 50.0 or 100.3 (distance units)
+  variable = equal-style variable like v_x or v_wiggle
    • zero or more keyword/value pairs may be appended
      • @@ -153,8 +153,8 @@ 
     units value = lattice or box
-    lattice = the wall position is defined in lattice units
-    box = the wall position is defined in simulation box units
+  lattice = the wall position is defined in lattice units
+  box = the wall position is defined in simulation box units
    diff --git a/doc/fix_wall_srd.html b/doc/fix_wall_srd.html index a76c35a4b9..5e2e9d5092 100644 --- a/doc/fix_wall_srd.html +++ b/doc/fix_wall_srd.html @@ -139,13 +139,13 @@ 
     xlo,*ylo*,*zlo* arg = EDGE or constant or variable
-    EDGE = current lo edge of simulation box
-    constant = number like 0.0 or -30.0 (distance units)
-    variable = equal-style variable like v_x or v_wiggle
-  xhi,*yhi*,*zhi* arg = EDGE or constant or variable
-    EDGE = current hi edge of simulation box
-    constant = number like 50.0 or 100.3 (distance units)
-    variable = equal-style variable like v_x or v_wiggle
+  EDGE = current lo edge of simulation box
+  constant = number like 0.0 or -30.0 (distance units)
+  variable = equal-style variable like v_x or v_wiggle
+xhi,*yhi*,*zhi* arg = EDGE or constant or variable
+  EDGE = current hi edge of simulation box
+  constant = number like 50.0 or 100.3 (distance units)
+  variable = equal-style variable like v_x or v_wiggle
    • zero or more keyword/value pairs may be appended
      • @@ -153,8 +153,8 @@ 
     units value = lattice or box
-    lattice = the wall position is defined in lattice units
-    box = the wall position is defined in simulation box units
+  lattice = the wall position is defined in lattice units
+  box = the wall position is defined in simulation box units
    diff --git a/doc/group.html b/doc/group.html index 641c18c384..72c8d09872 100644 --- a/doc/group.html +++ b/doc/group.html @@ -137,32 +137,32 @@ 
     delete = no args
-  clear = no args
-  region args = region-ID
-  type or id or molecule
-    args = list of one or more atom types, atom IDs, or molecule IDs
-      any entry in list can be a sequence formatted as A:B or A:B:C where
-      A = starting index, B = ending index,
-      C = increment between indices, 1 if not specified
-    args = logical value
-      logical = "<" or "<=" or ">" or ">=" or "==" or "!="
-      value = an atom type or atom ID or molecule ID (depending on style)
-    args = logical value1 value2
-      logical = "<>"
-      value1,value2 = atom types or atom IDs or molecule IDs (depending on style)
-  variable args = variable-name
-  include args = molecule
-    molecule = add atoms to group with same molecule ID as atoms already in group
-  subtract args = two or more group IDs
-  union args = one or more group IDs
-  intersect args = two or more group IDs
-  dynamic args = parent-ID keyword value ...
-    one or more keyword/value pairs may be appended
-    keyword = region or var or every
-      region value = region-ID
-      var value = name of variable
-      every value = N = update group every this many timesteps
-  static = no args
+clear = no args
+region args = region-ID
+type or id or molecule
+  args = list of one or more atom types, atom IDs, or molecule IDs
+    any entry in list can be a sequence formatted as A:B or A:B:C where
+    A = starting index, B = ending index,
+    C = increment between indices, 1 if not specified
+  args = logical value
+    logical = "<" or "<=" or ">" or ">=" or "==" or "!="
+    value = an atom type or atom ID or molecule ID (depending on style)
+  args = logical value1 value2
+    logical = "<>"
+    value1,value2 = atom types or atom IDs or molecule IDs (depending on style)
+variable args = variable-name
+include args = molecule
+  molecule = add atoms to group with same molecule ID as atoms already in group
+subtract args = two or more group IDs
+union args = one or more group IDs
+intersect args = two or more group IDs
+dynamic args = parent-ID keyword value ...
+  one or more keyword/value pairs may be appended
+  keyword = region or var or every
+    region value = region-ID
+    var value = name of variable
+    every value = N = update group every this many timesteps
+static = no args
    diff --git a/doc/kspace_style.html b/doc/kspace_style.html index 0f0e1dbdef..ee953b3841 100644 --- a/doc/kspace_style.html +++ b/doc/kspace_style.html @@ -136,43 +136,43 @@ 
     none value = none
-  ewald value = accuracy
-    accuracy = desired relative error in forces
-  ewald/disp value = accuracy
-    accuracy = desired relative error in forces
-  ewald/omp value = accuracy
-    accuracy = desired relative error in forces
-  pppm value = accuracy
-    accuracy = desired relative error in forces
-  pppm/cg value = accuracy (smallq)
-    accuracy = desired relative error in forces
-    smallq = cutoff for charges to be considered (optional) (charge units)
-  pppm/disp value = accuracy
-    accuracy = desired relative error in forces
-  pppm/tip4p value = accuracy
-    accuracy = desired relative error in forces
-  pppm/disp/tip4p value = accuracy
-    accuracy = desired relative error in forces
-  pppm/gpu value = accuracy
-    accuracy = desired relative error in forces
-  pppm/omp value = accuracy
-    accuracy = desired relative error in forces
-  pppm/cg/omp value = accuracy
-    accuracy = desired relative error in forces
-  pppm/tip4p/omp value = accuracy
-    accuracy = desired relative error in forces
-  pppm/stagger value = accuracy
-    accuracy = desired relative error in forces
-  msm value = accuracy
-    accuracy = desired relative error in forces
-  msm/cg value = accuracy (smallq)
-    accuracy = desired relative error in forces
-    smallq = cutoff for charges to be considered (optional) (charge units)
-  msm/omp value = accuracy
-    accuracy = desired relative error in forces
-  msm/cg/omp value = accuracy (smallq)
-    accuracy = desired relative error in forces
-    smallq = cutoff for charges to be considered (optional) (charge units)
+ewald value = accuracy
+  accuracy = desired relative error in forces
+ewald/disp value = accuracy
+  accuracy = desired relative error in forces
+ewald/omp value = accuracy
+  accuracy = desired relative error in forces
+pppm value = accuracy
+  accuracy = desired relative error in forces
+pppm/cg value = accuracy (smallq)
+  accuracy = desired relative error in forces
+  smallq = cutoff for charges to be considered (optional) (charge units)
+pppm/disp value = accuracy
+  accuracy = desired relative error in forces
+pppm/tip4p value = accuracy
+  accuracy = desired relative error in forces
+pppm/disp/tip4p value = accuracy
+  accuracy = desired relative error in forces
+pppm/gpu value = accuracy
+  accuracy = desired relative error in forces
+pppm/omp value = accuracy
+  accuracy = desired relative error in forces
+pppm/cg/omp value = accuracy
+  accuracy = desired relative error in forces
+pppm/tip4p/omp value = accuracy
+  accuracy = desired relative error in forces
+pppm/stagger value = accuracy
+  accuracy = desired relative error in forces
+msm value = accuracy
+  accuracy = desired relative error in forces
+msm/cg value = accuracy (smallq)
+  accuracy = desired relative error in forces
+  smallq = cutoff for charges to be considered (optional) (charge units)
+msm/omp value = accuracy
+  accuracy = desired relative error in forces
+msm/cg/omp value = accuracy (smallq)
+  accuracy = desired relative error in forces
+  smallq = cutoff for charges to be considered (optional) (charge units)
    diff --git a/doc/lattice.html b/doc/lattice.html index 22bfda2176..9a7c8b7191 100644 --- a/doc/lattice.html +++ b/doc/lattice.html @@ -136,7 +136,7 @@
  • scale = scale factor between lattice and simulation box
    • scale = reduced density rho* (for LJ units)
-  scale = lattice constant in distance units (for all other units)
+scale = lattice constant in distance units (for all other units)
      @@ -145,16 +145,16 @@ 
     origin values = x y z
-    x,y,z = fractions of a unit cell (0 <= x,y,z < 1)
-  orient values = dim i j k
-    dim = x or y or z
-    i,j,k = integer lattice directions
-  spacing values = dx dy dz
-    dx,dy,dz = lattice spacings in the x,y,z box directions
-  a1,*a2*,*a3* values = x y z
-    x,y,z = primitive vector components that define unit cell
-  basis values = x y z
-    x,y,z = fractional coords of a basis atom (0 <= x,y,z < 1)
+  x,y,z = fractions of a unit cell (0 <= x,y,z < 1)
+orient values = dim i j k
+  dim = x or y or z
+  i,j,k = integer lattice directions
+spacing values = dx dy dz
+  dx,dy,dz = lattice spacings in the x,y,z box directions
+a1,*a2*,*a3* values = x y z
+  x,y,z = primitive vector components that define unit cell
+basis values = x y z
+  x,y,z = fractional coords of a basis atom (0 <= x,y,z < 1)
    diff --git a/doc/molecule.html b/doc/molecule.html index 76ffe8d40d..fc5b4506e9 100644 --- a/doc/molecule.html +++ b/doc/molecule.html @@ -139,11 +139,11 @@ 
     offset values = toff boff aoff doff ioff
-    toff = offset to add to atom types
-    boff = offset to add to bond types
-    aoff = offset to add to angle types
-    doff = offset to add to dihedral types
-    ioff = offset to add to improper types
+  toff = offset to add to atom types
+  boff = offset to add to bond types
+  aoff = offset to add to angle types
+  doff = offset to add to dihedral types
+  ioff = offset to add to improper types
    diff --git a/doc/neb.html b/doc/neb.html index c9f11cf447..45631fe49e 100644 --- a/doc/neb.html +++ b/doc/neb.html @@ -141,12 +141,12 @@ 
     final arg = filename
-    filename = file with initial coords for final replica
-      coords for intermediate replicas are linearly interpolated between first and last replica
-  each arg = filename
-    filename = unique filename for each replica (except first) with its initial coords
-  none arg = no argument
-    all replicas assumed to already have their initial coords
+  filename = file with initial coords for final replica
+    coords for intermediate replicas are linearly interpolated between first and last replica
+each arg = filename
+  filename = unique filename for each replica (except first) with its initial coords
+none arg = no argument
+  all replicas assumed to already have their initial coords
    @@ -479,7 +479,7 @@ barrier.

    neb_combine.py script run on the dump files produced by the two example input scripts in examples/neb. Click on them to see a larger image.

    - width="25%" height="auto" alt=""/> - 
     cuda args = Ngpu keyword value ...
-    Ngpu = # of GPUs per node
-    zero or more keyword/value pairs may be appended
-    keywords = newton or gpuID or timing or test or thread
-      newton = off or on
-        off = set Newton pairwise and bonded flags off (default)
-        on = set Newton pairwise and bonded flags on
-      gpuID values = gpu1 .. gpuN
-        gpu1 .. gpuN = IDs of the Ngpu GPUs to use
-      timing values = none
-      test values = id
-        id = atom-ID of a test particle
-      thread = auto or tpa or bpa
-        auto = test whether tpa or bpa is faster
-        tpa = one thread per atom
-        bpa = one block per atom
-  gpu args = Ngpu keyword value ...
-    Ngpu = # of GPUs per node
-    zero or more keyword/value pairs may be appended
-    keywords = neigh or newton or binsize or split or gpuID or tpa or device
-      neigh value = yes or no
-        yes = neighbor list build on GPU (default)
-        no = neighbor list build on CPU
-      newton = off or on
-        off = set Newton pairwise flag off (default and required)
-        on = set Newton pairwise flag on (currently not allowed)
-      binsize value = size
-        size = bin size for neighbor list construction (distance units)
-      split = fraction
-        fraction = fraction of atoms assigned to GPU (default = 1.0)
-      gpuID values = first last
-        first = ID of first GPU to be used on each node
-        last = ID of last GPU to be used on each node
-      tpa value = Nthreads
-        Nthreads = # of GPU threads used per atom
-      device value = device_type
-        device_type = kepler or fermi or cypress or generic
-  intel args = NPhi keyword value ...
-    Nphi = # of coprocessors per node
-    zero or more keyword/value pairs may be appended
-    keywords = omp or mode or balance or ghost or tpc or tptask or no_affinity
-      omp value = Nthreads
-        Nthreads = number of OpenMP threads to use on CPU (default = 0)
-      mode value = single or mixed or double
-        single = perform force calculations in single precision
-        mixed = perform force calculations in mixed precision
-        double = perform force calculations in double precision
-      balance value = split
-        split = fraction of work to offload to coprocessor, -1 for dynamic
-      ghost value = yes or no
-        yes = include ghost atoms for offload
-        no = do not include ghost atoms for offload
-      tpc value = Ntpc
-        Ntpc = max number of coprocessor threads per coprocessor core (default = 4)
-      tptask value = Ntptask
-        Ntptask = max number of coprocessor threads per MPI task (default = 240)
-      no_affinity values = none
-  kokkos args = keyword value ...
-    zero or more keyword/value pairs may be appended
-    keywords = neigh or newton or binsize or comm or comm/exchange or comm/forward
-      neigh value = full or half/thread or half or n2 or full/cluster
-        full = full neighbor list
-        half/thread = half neighbor list built in thread-safe manner
-        half = half neighbor list, not thread-safe, only use when 1 thread/MPI task
-        n2 = non-binning neighbor list build, O(N^2) algorithm
-        full/cluster = full neighbor list with clustered groups of atoms
-      newton = off or on
-        off = set Newton pairwise and bonded flags off (default)
-        on = set Newton pairwise and bonded flags on
-      binsize value = size
-        size = bin size for neighbor list construction (distance units)
-      comm value = no or host or device
-        use value for both comm/exchange and comm/forward
-      comm/exchange value = no or host or device
-      comm/forward value = no or host or device
-        no = perform communication pack/unpack in non-KOKKOS mode
-        host = perform pack/unpack on host (e.g. with OpenMP threading)
-        device = perform pack/unpack on device (e.g. on GPU)
-  omp args = Nthreads keyword value ...
-    Nthread = # of OpenMP threads to associate with each MPI process
-    zero or more keyword/value pairs may be appended
-    keywords = neigh
-      neigh value = yes or no
-        yes = threaded neighbor list build (default)
-        no = non-threaded neighbor list build
+  Ngpu = # of GPUs per node
+  zero or more keyword/value pairs may be appended
+  keywords = newton or gpuID or timing or test or thread
+    newton = off or on
+      off = set Newton pairwise and bonded flags off (default)
+      on = set Newton pairwise and bonded flags on
+    gpuID values = gpu1 .. gpuN
+      gpu1 .. gpuN = IDs of the Ngpu GPUs to use
+    timing values = none
+    test values = id
+      id = atom-ID of a test particle
+    thread = auto or tpa or bpa
+      auto = test whether tpa or bpa is faster
+      tpa = one thread per atom
+      bpa = one block per atom
+gpu args = Ngpu keyword value ...
+  Ngpu = # of GPUs per node
+  zero or more keyword/value pairs may be appended
+  keywords = neigh or newton or binsize or split or gpuID or tpa or device
+    neigh value = yes or no
+      yes = neighbor list build on GPU (default)
+      no = neighbor list build on CPU
+    newton = off or on
+      off = set Newton pairwise flag off (default and required)
+      on = set Newton pairwise flag on (currently not allowed)
+    binsize value = size
+      size = bin size for neighbor list construction (distance units)
+    split = fraction
+      fraction = fraction of atoms assigned to GPU (default = 1.0)
+    gpuID values = first last
+      first = ID of first GPU to be used on each node
+      last = ID of last GPU to be used on each node
+    tpa value = Nthreads
+      Nthreads = # of GPU threads used per atom
+    device value = device_type
+      device_type = kepler or fermi or cypress or generic
+intel args = NPhi keyword value ...
+  Nphi = # of coprocessors per node
+  zero or more keyword/value pairs may be appended
+  keywords = omp or mode or balance or ghost or tpc or tptask or no_affinity
+    omp value = Nthreads
+      Nthreads = number of OpenMP threads to use on CPU (default = 0)
+    mode value = single or mixed or double
+      single = perform force calculations in single precision
+      mixed = perform force calculations in mixed precision
+      double = perform force calculations in double precision
+    balance value = split
+      split = fraction of work to offload to coprocessor, -1 for dynamic
+    ghost value = yes or no
+      yes = include ghost atoms for offload
+      no = do not include ghost atoms for offload
+    tpc value = Ntpc
+      Ntpc = max number of coprocessor threads per coprocessor core (default = 4)
+    tptask value = Ntptask
+      Ntptask = max number of coprocessor threads per MPI task (default = 240)
+    no_affinity values = none
+kokkos args = keyword value ...
+  zero or more keyword/value pairs may be appended
+  keywords = neigh or newton or binsize or comm or comm/exchange or comm/forward
+    neigh value = full or half/thread or half or n2 or full/cluster
+      full = full neighbor list
+      half/thread = half neighbor list built in thread-safe manner
+      half = half neighbor list, not thread-safe, only use when 1 thread/MPI task
+      n2 = non-binning neighbor list build, O(N^2) algorithm
+      full/cluster = full neighbor list with clustered groups of atoms
+    newton = off or on
+      off = set Newton pairwise and bonded flags off (default)
+      on = set Newton pairwise and bonded flags on
+    binsize value = size
+      size = bin size for neighbor list construction (distance units)
+    comm value = no or host or device
+      use value for both comm/exchange and comm/forward
+    comm/exchange value = no or host or device
+    comm/forward value = no or host or device
+      no = perform communication pack/unpack in non-KOKKOS mode
+      host = perform pack/unpack on host (e.g. with OpenMP threading)
+      device = perform pack/unpack on device (e.g. on GPU)
+omp args = Nthreads keyword value ...
+  Nthread = # of OpenMP threads to associate with each MPI process
+  zero or more keyword/value pairs may be appended
+  keywords = neigh
+    neigh value = yes or no
+      yes = threaded neighbor list build (default)
+      no = non-threaded neighbor list build
    diff --git a/doc/pair_awpmd.html b/doc/pair_awpmd.html index 99fd54347c..84513ee995 100644 --- a/doc/pair_awpmd.html +++ b/doc/pair_awpmd.html @@ -138,18 +138,18 @@ 
     hartree value = none
-  dproduct value = none
-  uhf value = none
-  free value = none
-  pbc value = Plen
-    Plen = periodic width of electron = -1 or positive value (distance units)
-  fix value = Flen
-    Flen = fixed width of electron = -1 or positive value (distance units)
-  harm value = width
-    width = harmonic width constraint
-  ermscale value = factor
-    factor = scaling between electron mass and width variable mass
-  flex_press value = none
+dproduct value = none
+uhf value = none
+free value = none
+pbc value = Plen
+  Plen = periodic width of electron = -1 or positive value (distance units)
+fix value = Flen
+  Flen = fixed width of electron = -1 or positive value (distance units)
+harm value = width
+  width = harmonic width constraint
+ermscale value = factor
+  factor = scaling between electron mass and width variable mass
+flex_press value = none
    diff --git a/doc/pair_born.html b/doc/pair_born.html index 24cf823b69..8628ab51b1 100644 --- a/doc/pair_born.html +++ b/doc/pair_born.html @@ -173,17 +173,17 @@ 
     born args = cutoff
-    cutoff = global cutoff for non-Coulombic interactions (distance units)
-  born/coul/long or born/coul/long/cs args = cutoff (cutoff2)
-    cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  born/coul/msm args = cutoff (cutoff2)
-    cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  born/coul/wolf args = alpha cutoff (cutoff2)
-    alpha = damping parameter (inverse distance units)
-    cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
+  cutoff = global cutoff for non-Coulombic interactions (distance units)
+born/coul/long or born/coul/long/cs args = cutoff (cutoff2)
+  cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
+  cutoff2 = global cutoff for Coulombic (optional) (distance units)
+born/coul/msm args = cutoff (cutoff2)
+  cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
+  cutoff2 = global cutoff for Coulombic (optional) (distance units)
+born/coul/wolf args = alpha cutoff (cutoff2)
+  alpha = damping parameter (inverse distance units)
+  cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
+  cutoff2 = global cutoff for Coulombic (optional) (distance units)
    diff --git a/doc/pair_buck.html b/doc/pair_buck.html index 5804523f49..f93499e8bb 100644 --- a/doc/pair_buck.html +++ b/doc/pair_buck.html @@ -188,16 +188,16 @@ 
     buck args = cutoff
-    cutoff = global cutoff for Buckingham interactions (distance units)
-  buck/coul/cut args = cutoff (cutoff2)
-    cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  buck/coul/long or buck/coul/long/cs args = cutoff (cutoff2)
-    cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  buck/coul/msm args = cutoff (cutoff2)
-    cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
+  cutoff = global cutoff for Buckingham interactions (distance units)
+buck/coul/cut args = cutoff (cutoff2)
+  cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
+  cutoff2 = global cutoff for Coulombic (optional) (distance units)
+buck/coul/long or buck/coul/long/cs args = cutoff (cutoff2)
+  cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
+  cutoff2 = global cutoff for Coulombic (optional) (distance units)
+buck/coul/msm args = cutoff (cutoff2)
+  cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
+  cutoff2 = global cutoff for Coulombic (optional) (distance units)
    diff --git a/doc/pair_buck_long.html b/doc/pair_buck_long.html index 1b31e64a84..b3e9a9d1af 100644 --- a/doc/pair_buck_long.html +++ b/doc/pair_buck_long.html @@ -139,14 +139,14 @@ 
     long = use Kspace long-range summation for the dispersion term 1/r^6
-  cut = use a cutoff
+cut = use a cutoff
    • flag_coul = long or off
     long = use Kspace long-range summation for the Coulombic term 1/r
-  off = omit the Coulombic term
+off = omit the Coulombic term
    • cutoff = global cutoff for Buckingham (and Coulombic if only 1 cutoff) (distance units)
      • diff --git a/doc/pair_charmm.html b/doc/pair_charmm.html index b4689df222..637c3df5b0 100644 --- a/doc/pair_charmm.html +++ b/doc/pair_charmm.html @@ -176,17 +176,17 @@ 
     lj/charmm/coul/charmm args = inner outer (inner2) (outer2)
-    inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
-    inner2, outer2 = global switching cutoffs for Coulombic (optional)
-  lj/charmm/coul/charmm/implicit args = inner outer (inner2) (outer2)
-    inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
-    inner2, outer2 = global switching cutoffs for Coulombic (optional)
-  lj/charmm/coul/long args = inner outer (cutoff)
-    inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
-    cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
-  lj/charmm/coul/msm args = inner outer (cutoff)
-    inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
-    cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
+  inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
+  inner2, outer2 = global switching cutoffs for Coulombic (optional)
+lj/charmm/coul/charmm/implicit args = inner outer (inner2) (outer2)
+  inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
+  inner2, outer2 = global switching cutoffs for Coulombic (optional)
+lj/charmm/coul/long args = inner outer (cutoff)
+  inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
+  cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
+lj/charmm/coul/msm args = inner outer (cutoff)
+  inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
+  cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
    diff --git a/doc/pair_class2.html b/doc/pair_class2.html index 878fac51ca..2f8318c9aa 100644 --- a/doc/pair_class2.html +++ b/doc/pair_class2.html @@ -176,13 +176,13 @@ 
     lj/class2 args = cutoff
-    cutoff = global cutoff for class 2 interactions (distance units)
-  lj/class2/coul/cut args = cutoff (cutoff2)
-    cutoff = global cutoff for class 2 (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  lj/class2/coul/long args = cutoff (cutoff2)
-    cutoff = global cutoff for class 2 (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
+  cutoff = global cutoff for class 2 interactions (distance units)
+lj/class2/coul/cut args = cutoff (cutoff2)
+  cutoff = global cutoff for class 2 (and Coulombic if only 1 arg) (distance units)
+  cutoff2 = global cutoff for Coulombic (optional) (distance units)
+lj/class2/coul/long args = cutoff (cutoff2)
+  cutoff = global cutoff for class 2 (and Coulombic if only 1 arg) (distance units)
+  cutoff2 = global cutoff for Coulombic (optional) (distance units)
    diff --git a/doc/pair_cs.html b/doc/pair_cs.html index 247773cd8f..c0f8d88cd3 100644 --- a/doc/pair_cs.html +++ b/doc/pair_cs.html @@ -140,11 +140,11 @@ 
     born/coul/long/cs args = cutoff (cutoff2)
-    cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  buck/coul/long/cs args = cutoff (cutoff2)
-    cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
+  cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
+  cutoff2 = global cutoff for Coulombic (optional) (distance units)
+buck/coul/long/cs args = cutoff (cutoff2)
+  cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
+  cutoff2 = global cutoff for Coulombic (optional) (distance units)
    diff --git a/doc/pair_dipole.html b/doc/pair_dipole.html index 20e689001a..49c8efb8d3 100644 --- a/doc/pair_dipole.html +++ b/doc/pair_dipole.html @@ -162,15 +162,15 @@ pair_style lj/long/dipole/long flag_lj flag_coul cutoff (cutoff2) 
     long = use long-range damping on dispersion 1/r^6 term
-  cut = use a cutoff on dispersion 1/r^6 term
-  off = omit disperion 1/r^6 term entirely
+cut = use a cutoff on dispersion 1/r^6 term
+off = omit disperion 1/r^6 term entirely
    • flag_coul = long or off
     long = use long-range damping on Coulombic 1/r and point-dipole terms
-  off = omit Coulombic and point-dipole terms entirely
+off = omit Coulombic and point-dipole terms entirely
    diff --git a/doc/pair_gromacs.html b/doc/pair_gromacs.html index eb8f3d242d..fe0c2e9f90 100644 --- a/doc/pair_gromacs.html +++ b/doc/pair_gromacs.html @@ -155,10 +155,10 @@ 
     lj/gromacs args = inner outer
-    inner, outer = global switching cutoffs for Lennard Jones
-  lj/gromacs/coul/gromacs args = inner outer (inner2) (outer2)
-    inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
-    inner2, outer2 = global switching cutoffs for Coulombic (optional)
+  inner, outer = global switching cutoffs for Lennard Jones
+lj/gromacs/coul/gromacs args = inner outer (inner2) (outer2)
+  inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
+  inner2, outer2 = global switching cutoffs for Coulombic (optional)
    diff --git a/doc/pair_list.html b/doc/pair_list.html index 85a3edbf00..237fef4e54 100644 --- a/doc/pair_list.html +++ b/doc/pair_list.html @@ -170,10 +170,10 @@ Morse and a harmonic potential.

  • line syntax: ID1 ID2 style coeffs cutoff
    • ID1 = atom ID of first atom
-  ID2 = atom ID of second atom
-  style = style of interaction
-  coeffs = list of coeffs
-  cutoff = cutoff for interaction (optional)
+ID2 = atom ID of second atom
+style = style of interaction
+coeffs = list of coeffs
+cutoff = cutoff for interaction (optional)

    The cutoff parameter is optional. If not specified, the global cutoff diff --git a/doc/pair_lj.html b/doc/pair_lj.html index 7101fd7f99..977c5eb706 100644 --- a/doc/pair_lj.html +++ b/doc/pair_lj.html @@ -236,36 +236,36 @@ 

     lj/cut args = cutoff
-    cutoff = global cutoff for Lennard Jones interactions (distance units)
-  lj/cut/coul/cut args = cutoff (cutoff2)
-    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  lj/cut/coul/debye args = kappa cutoff (cutoff2)
-    kappa = inverse of the Debye length (inverse distance units)
-    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  lj/cut/coul/dsf args = alpha cutoff (cutoff2)
-    alpha = damping parameter (inverse distance units)
-    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (distance units)
-  lj/cut/coul/long args = cutoff (cutoff2)
-    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  lj/cut/coul/msm args = cutoff (cutoff2)
-    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  lj/cut/tip4p/cut args = otype htype btype atype qdist cutoff (cutoff2)
-    otype,htype = atom types for TIP4P O and H
-    btype,atype = bond and angle types for TIP4P waters
-    qdist = distance from O atom to massless charge (distance units)
-    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  lj/cut/tip4p/long args = otype htype btype atype qdist cutoff (cutoff2)
-    otype,htype = atom types for TIP4P O and H
-    btype,atype = bond and angle types for TIP4P waters
-    qdist = distance from O atom to massless charge (distance units)
-    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
+  cutoff = global cutoff for Lennard Jones interactions (distance units)
+lj/cut/coul/cut args = cutoff (cutoff2)
+  cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+  cutoff2 = global cutoff for Coulombic (optional) (distance units)
+lj/cut/coul/debye args = kappa cutoff (cutoff2)
+  kappa = inverse of the Debye length (inverse distance units)
+  cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+  cutoff2 = global cutoff for Coulombic (optional) (distance units)
+lj/cut/coul/dsf args = alpha cutoff (cutoff2)
+  alpha = damping parameter (inverse distance units)
+  cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+  cutoff2 = global cutoff for Coulombic (distance units)
+lj/cut/coul/long args = cutoff (cutoff2)
+  cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+  cutoff2 = global cutoff for Coulombic (optional) (distance units)
+lj/cut/coul/msm args = cutoff (cutoff2)
+  cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+  cutoff2 = global cutoff for Coulombic (optional) (distance units)
+lj/cut/tip4p/cut args = otype htype btype atype qdist cutoff (cutoff2)
+  otype,htype = atom types for TIP4P O and H
+  btype,atype = bond and angle types for TIP4P waters
+  qdist = distance from O atom to massless charge (distance units)
+  cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+  cutoff2 = global cutoff for Coulombic (optional) (distance units)
+lj/cut/tip4p/long args = otype htype btype atype qdist cutoff (cutoff2)
+  otype,htype = atom types for TIP4P O and H
+  btype,atype = bond and angle types for TIP4P waters
+  qdist = distance from O atom to massless charge (distance units)
+  cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+  cutoff2 = global cutoff for Coulombic (optional) (distance units)
    diff --git a/doc/pair_lj_long.html b/doc/pair_lj_long.html index 45faf1283b..827c1b8d9f 100644 --- a/doc/pair_lj_long.html +++ b/doc/pair_lj_long.html @@ -146,27 +146,27 @@ 
     lj/long/coul/long args = flag_lj flag_coul cutoff (cutoff2)
-    flag_lj = long or cut or off
-      long = use Kspace long-range summation for dispersion 1/r^6 term
-      cut = use a cutoff on dispersion 1/r^6 term
-      off = omit disperion 1/r^6 term entirely
-    flag_coul = long or off
-      long = use Kspace long-range summation for Coulombic 1/r term
-      off = omit Coulombic term
-    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  lj/long/tip4p/long args = flag_lj flag_coul otype htype btype atype qdist cutoff (cutoff2)
-    flag_lj = long or cut
-      long = use Kspace long-range summation for dispersion 1/r^6 term
-      cut = use a cutoff
-    flag_coul = long or off
-      long = use Kspace long-range summation for Coulombic 1/r term
-      off = omit Coulombic term
-    otype,htype = atom types for TIP4P O and H
-    btype,atype = bond and angle types for TIP4P waters
-    qdist = distance from O atom to massless charge (distance units)
-    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
+  flag_lj = long or cut or off
+    long = use Kspace long-range summation for dispersion 1/r^6 term
+    cut = use a cutoff on dispersion 1/r^6 term
+    off = omit disperion 1/r^6 term entirely
+  flag_coul = long or off
+    long = use Kspace long-range summation for Coulombic 1/r term
+    off = omit Coulombic term
+  cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+  cutoff2 = global cutoff for Coulombic (optional) (distance units)
+lj/long/tip4p/long args = flag_lj flag_coul otype htype btype atype qdist cutoff (cutoff2)
+  flag_lj = long or cut
+    long = use Kspace long-range summation for dispersion 1/r^6 term
+    cut = use a cutoff
+  flag_coul = long or off
+    long = use Kspace long-range summation for Coulombic 1/r term
+    off = omit Coulombic term
+  otype,htype = atom types for TIP4P O and H
+  btype,atype = bond and angle types for TIP4P waters
+  qdist = distance from O atom to massless charge (distance units)
+  cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+  cutoff2 = global cutoff for Coulombic (optional) (distance units)
    diff --git a/doc/pair_lj_soft.html b/doc/pair_lj_soft.html index 168b97ea82..4cfcce07d1 100644 --- a/doc/pair_lj_soft.html +++ b/doc/pair_lj_soft.html @@ -182,39 +182,39 @@ 
     lj/cut/soft args = n alpha_lj cutoff
-    n, alpha_LJ = parameters of soft-core potential
-    cutoff = global cutoff for Lennard-Jones interactions (distance units)
-  lj/cut/coul/cut/soft args = n alpha_LJ alpha_C cutoff (cutoff2)
-    n, alpha_LJ, alpha_C = parameters of soft-core potential
-    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  lj/cut/coul/long/soft args = n alpha_LJ alpha_C cutoff
-    n, alpha_LJ, alpha_C = parameters of the soft-core potential
-    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  lj/cut/tip4p/long/soft args = otype htype btype atype qdist n alpha_LJ alpha_C cutoff (cutoff2)
-    otype,htype = atom types for TIP4P O and H
-    btype,atype = bond and angle types for TIP4P waters
-    qdist = distance from O atom to massless charge (distance units)
-    n, alpha_LJ, alpha_C = parameters of the soft-core potential
-    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  lj/charmm/coul/long/soft args = n alpha_LJ alpha_C inner outer (cutoff)
-    n, alpha_LJ, alpha_C = parameters of the soft-core potential
-    inner, outer = global switching cutoffs for LJ (and Coulombic if only 5 args)
-    cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 5 args)
-  coul/cut/soft args = n alpha_C cutoff
-    n, alpha_C = parameters of the soft-core potential
-    cutoff = global cutoff for Coulomb interactions (distance units)
-  coul/long/soft args = n alpha_C cutoff
-    n, alpha_C = parameters of the soft-core potential
-    cutoff = global cutoff for Coulomb interactions (distance units)
-  tip4p/long/soft args = otype htype btype atype qdist n alpha_C cutoff
-    otype,htype = atom types for TIP4P O and H
-    btype,atype = bond and angle types for TIP4P waters
-    qdist = distance from O atom to massless charge (distance units)
-    n, alpha_C = parameters of the soft-core potential
-    cutoff = global cutoff for Coulomb interactions (distance units)
+  n, alpha_LJ = parameters of soft-core potential
+  cutoff = global cutoff for Lennard-Jones interactions (distance units)
+lj/cut/coul/cut/soft args = n alpha_LJ alpha_C cutoff (cutoff2)
+  n, alpha_LJ, alpha_C = parameters of soft-core potential
+  cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+  cutoff2 = global cutoff for Coulombic (optional) (distance units)
+lj/cut/coul/long/soft args = n alpha_LJ alpha_C cutoff
+  n, alpha_LJ, alpha_C = parameters of the soft-core potential
+  cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+  cutoff2 = global cutoff for Coulombic (optional) (distance units)
+lj/cut/tip4p/long/soft args = otype htype btype atype qdist n alpha_LJ alpha_C cutoff (cutoff2)
+  otype,htype = atom types for TIP4P O and H
+  btype,atype = bond and angle types for TIP4P waters
+  qdist = distance from O atom to massless charge (distance units)
+  n, alpha_LJ, alpha_C = parameters of the soft-core potential
+  cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+  cutoff2 = global cutoff for Coulombic (optional) (distance units)
+lj/charmm/coul/long/soft args = n alpha_LJ alpha_C inner outer (cutoff)
+  n, alpha_LJ, alpha_C = parameters of the soft-core potential
+  inner, outer = global switching cutoffs for LJ (and Coulombic if only 5 args)
+  cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 5 args)
+coul/cut/soft args = n alpha_C cutoff
+  n, alpha_C = parameters of the soft-core potential
+  cutoff = global cutoff for Coulomb interactions (distance units)
+coul/long/soft args = n alpha_C cutoff
+  n, alpha_C = parameters of the soft-core potential
+  cutoff = global cutoff for Coulomb interactions (distance units)
+tip4p/long/soft args = otype htype btype atype qdist n alpha_C cutoff
+  otype,htype = atom types for TIP4P O and H
+  btype,atype = bond and angle types for TIP4P waters
+  qdist = distance from O atom to massless charge (distance units)
+  n, alpha_C = parameters of the soft-core potential
+  cutoff = global cutoff for Coulomb interactions (distance units)
    diff --git a/doc/pair_meam.html b/doc/pair_meam.html index 6899a0e485..295fe5fbaf 100644 --- a/doc/pair_meam.html +++ b/doc/pair_meam.html @@ -250,12 +250,12 @@ background density (see e.g. equation 4.5 in -
    0 => G = sqrt(1+Gamma)
-   1 => G = exp(Gamma/2)
-   2 => not implemented
-   3 => G = 2/(1+exp(-Gamma))
-   4 => G = sqrt(1+Gamma)
-  -5 => G = +-sqrt(abs(1+Gamma))
+
     0 => G = sqrt(1+Gamma)
+ 1 => G = exp(Gamma/2)
+ 2 => not implemented
+ 3 => G = 2/(1+exp(-Gamma))
+ 4 => G = sqrt(1+Gamma)
+-5 => G = +-sqrt(abs(1+Gamma))
 
    
 
    
 
    If used, the MEAM parameter file contains settings that override or
diff --git a/doc/pair_modify.html b/doc/pair_modify.html
index 1bf713ad94..df61d1d294 100644
--- a/doc/pair_modify.html
+++ b/doc/pair_modify.html
@@ -137,23 +137,23 @@
 
 
     pair values = sub-style N special which w1 wt2 wt3
-    sub-style = sub-style of pair hybrid
-    N = which instance of sub-style (only if sub-style is used multiple times)
-  special values = flavor w1 w2 w3
-    flavor = lj/coul or lj or coul
-    w1,w2,w3 = weights from 0.0 to 1.0 inclusive
-  mix value = geometric or arithmetic or sixthpower
-  shift value = yes or no
-  table value = N
-    2^N = # of values in table
-  table/disp value = N
-    2^N = # of values in table
-  tabinner value = cutoff
-    cutoff = inner cutoff at which to begin table (distance units)
-  tabinner/disp value = cutoff
-    cutoff = inner cutoff at which to begin table (distance units)
-  tail value = yes or no
-  compute value = yes or no
+  sub-style = sub-style of pair hybrid
+  N = which instance of sub-style (only if sub-style is used multiple times)
+special values = flavor w1 w2 w3
+  flavor = lj/coul or lj or coul
+  w1,w2,w3 = weights from 0.0 to 1.0 inclusive
+mix value = geometric or arithmetic or sixthpower
+shift value = yes or no
+table value = N
+  2^N = # of values in table
+table/disp value = N
+  2^N = # of values in table
+tabinner value = cutoff
+  cutoff = inner cutoff at which to begin table (distance units)
+tabinner/disp value = cutoff
+  cutoff = inner cutoff at which to begin table (distance units)
+tail value = yes or no
+compute value = yes or no
    diff --git a/doc/pair_nm.html b/doc/pair_nm.html index a1c4668a7d..b64ce97f0b 100644 --- a/doc/pair_nm.html +++ b/doc/pair_nm.html @@ -152,13 +152,13 @@ 
     nm/cut args = cutoff
-    cutoff = global cutoff for Pair interactions (distance units)
-  nm/cut/coul/cut args = cutoff (cutoff2)
-    cutoff = global cutoff for Pair (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  nm/cut/coul/long args = cutoff (cutoff2)
-    cutoff = global cutoff for Pair (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
+  cutoff = global cutoff for Pair interactions (distance units)
+nm/cut/coul/cut args = cutoff (cutoff2)
+  cutoff = global cutoff for Pair (and Coulombic if only 1 arg) (distance units)
+  cutoff2 = global cutoff for Coulombic (optional) (distance units)
+nm/cut/coul/long args = cutoff (cutoff2)
+  cutoff = global cutoff for Pair (and Coulombic if only 1 arg) (distance units)
+  cutoff2 = global cutoff for Coulombic (optional) (distance units)
    diff --git a/doc/pair_polymorphic.html b/doc/pair_polymorphic.html index f3b220adae..c719f49552 100644 --- a/doc/pair_polymorphic.html +++ b/doc/pair_polymorphic.html @@ -149,7 +149,7 @@ pair_coeff * * GaN_sw.polymorphic GaN (Zhou) for the energy E of a system of atoms as

    _images/polymorphic1.jpg _images/polymorphic2.jpg -_images/polymorphic2.jpg +_images/polymorphic3.jpg

    where I, J, K represent species of atoms i, j, and k, i_1, ..., i_N represents a list of i’s neighbors, delta_ij is a Direc constant (i.e., delta_ij = 1 when i = j, and delta_ij = 0 otherwise), eta_ij is diff --git a/doc/pair_polymorphic.txt b/doc/pair_polymorphic.txt index f5355037dd..8d3b579511 100644 --- a/doc/pair_polymorphic.txt +++ b/doc/pair_polymorphic.txt @@ -29,7 +29,7 @@ The {polymorphic} pair style computes a 3-body free-form potential :c,image(Eqs/polymorphic1.jpg) :c,image(Eqs/polymorphic2.jpg) -:c,image(Eqs/polymorphic2.jpg) +:c,image(Eqs/polymorphic3.jpg) where I, J, K represent species of atoms i, j, and k, i_1, ..., i_N represents a list of i's neighbors, delta_ij is a Direc constant diff --git a/doc/pair_sdk.html b/doc/pair_sdk.html index f19f5f1878..0e6b4c6e2c 100644 --- a/doc/pair_sdk.html +++ b/doc/pair_sdk.html @@ -155,10 +155,10 @@ 

     lj/sdk args = cutoff
-    cutoff = global cutoff for Lennard Jones interactions (distance units)
-  lj/sdk/coul/long args = cutoff (cutoff2)
-    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
+  cutoff = global cutoff for Lennard Jones interactions (distance units)
+lj/sdk/coul/long args = cutoff (cutoff2)
+  cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+  cutoff2 = global cutoff for Coulombic (optional) (distance units)
    diff --git a/doc/pair_snap.html b/doc/pair_snap.html index 271b854457..5527c51e38 100644 --- a/doc/pair_snap.html +++ b/doc/pair_snap.html @@ -211,14 +211,14 @@ tantalum potential provided in the LAMMPS potentials directory combines the snap and zbl pair styles. It is invoked by the following commands:

    variable zblcutinner equal 4
-     variable zblcutouter equal 4.8
-     variable zblz equal 73
-     pair_style hybrid/overlay &
-     zbl ${zblcutinner} ${zblcutouter} snap
-     pair_coeff * * zbl 0.0
-     pair_coeff 1 1 zbl ${zblz}
-     pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta &
-     ../potentials/Ta06A.snapparam Ta
+variable zblcutouter equal 4.8
+variable zblz equal 73
+pair_style hybrid/overlay &
+zbl ${zblcutinner} ${zblcutouter} snap
+pair_coeff * * zbl 0.0
+pair_coeff 1 1 zbl ${zblz}
+pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta &
+../potentials/Ta06A.snapparam Ta

    It is convenient to keep these commands in a separate file that can diff --git a/doc/prd.html b/doc/prd.html index 65833d8c0c..07420fc597 100644 --- a/doc/prd.html +++ b/doc/prd.html @@ -144,18 +144,18 @@ 

     min values = etol ftol maxiter maxeval
-    etol = stopping tolerance for energy, used in quenching
-    ftol = stopping tolerance for force, used in quenching
-    maxiter = max iterations of minimize, used in quenching
-    maxeval = max number of force/energy evaluations, used in quenching
-  temp value = Tdephase
-    Tdephase = target temperature for velocity randomization, used in dephasing
-  vel values = loop dist
-    loop = all or local or geom, used in dephasing
-    dist = uniform or gaussian, used in dephasing
-  time value = step or clock
-    step = simulation runs for N timesteps on each replica (default)
-    clock = simulation runs for N timesteps across all replicas
+  etol = stopping tolerance for energy, used in quenching
+  ftol = stopping tolerance for force, used in quenching
+  maxiter = max iterations of minimize, used in quenching
+  maxeval = max number of force/energy evaluations, used in quenching
+temp value = Tdephase
+  Tdephase = target temperature for velocity randomization, used in dephasing
+vel values = loop dist
+  loop = all or local or geom, used in dephasing
+  dist = uniform or gaussian, used in dephasing
+time value = step or clock
+  step = simulation runs for N timesteps on each replica (default)
+  clock = simulation runs for N timesteps across all replicas
    diff --git a/doc/print.html b/doc/print.html index 12d4d825f5..6952113cf1 100644 --- a/doc/print.html +++ b/doc/print.html @@ -138,8 +138,8 @@ 
     file value = filename
-  append value = filename
-  screen value = yes or no
+append value = filename
+screen value = yes or no
    diff --git a/doc/processors.html b/doc/processors.html index e12d525612..29c6d2ba46 100644 --- a/doc/processors.html +++ b/doc/processors.html @@ -138,26 +138,26 @@ 
     grid arg = gstyle params ...
-    gstyle = onelevel or twolevel or numa or custom
-      onelevel params = none
-      twolevel params = Nc Cx Cy Cz
-        Nc = number of cores per node
-        Cx,Cy,Cz = # of cores in each dimension of 3d sub-grid assigned to each node
-      numa params = none
-      custom params = infile
-        infile = file containing grid layout
-  map arg = cart or cart/reorder or xyz or xzy or yxz or yzx or zxy or zyx
-     cart = use MPI_Cart() methods to map processors to 3d grid with reorder = 0
-     cart/reorder = use MPI_Cart() methods to map processors to 3d grid with reorder = 1
-     xyz,xzy,yxz,yzx,zxy,zyx = map procesors to 3d grid in IJK ordering
-  numa arg = none
-  part args = Psend Precv cstyle
-    Psend = partition # (1 to Np) which will send its processor layout
-    Precv = partition # (1 to Np) which will recv the processor layout
-    cstyle = multiple
-      multiple = Psend grid will be multiple of Precv grid in each dimension
-  file arg = outfile
-    outfile = name of file to write 3d grid of processors to
+  gstyle = onelevel or twolevel or numa or custom
+    onelevel params = none
+    twolevel params = Nc Cx Cy Cz
+      Nc = number of cores per node
+      Cx,Cy,Cz = # of cores in each dimension of 3d sub-grid assigned to each node
+    numa params = none
+    custom params = infile
+      infile = file containing grid layout
+map arg = cart or cart/reorder or xyz or xzy or yxz or yzx or zxy or zyx
+   cart = use MPI_Cart() methods to map processors to 3d grid with reorder = 0
+   cart/reorder = use MPI_Cart() methods to map processors to 3d grid with reorder = 1
+   xyz,xzy,yxz,yzx,zxy,zyx = map procesors to 3d grid in IJK ordering
+numa arg = none
+part args = Psend Precv cstyle
+  Psend = partition # (1 to Np) which will send its processor layout
+  Precv = partition # (1 to Np) which will recv the processor layout
+  cstyle = multiple
+    multiple = Psend grid will be multiple of Precv grid in each dimension
+file arg = outfile
+  outfile = name of file to write 3d grid of processors to
    diff --git a/doc/python.html b/doc/python.html index bc569c1749..7f76f45a34 100644 --- a/doc/python.html +++ b/doc/python.html @@ -181,13 +181,13 @@ def loop(lmpptr,N,cut0): 
    # loop N times, increasing cutoff each time
    -
    for i in range(N):
-    cut = cut0 + i*0.1
-    lmp.set_variable("cut",cut)               # set a variable in LAMMPS
-    lmp.command("pair_style lj/cut $*cut*")   # LAMMPS commands
-    lmp.command("pair_coeff * * 1.0 1.0")
-    lmp.command("run 100")
- """
+
     for i in range(N):
+   cut = cut0 + i*0.1
+   lmp.set_variable("cut",cut)               # set a variable in LAMMPS
+   lmp.command("pair_style lj/cut $*cut*")   # LAMMPS commands
+   lmp.command("pair_coeff * * 1.0 1.0")
+   lmp.command("run 100")
+"""
    @@ -425,19 +425,19 @@ which loads and runs the following function from examples/python/funcs.py:

    for i in range(N):
-    cut = cut0 + i*0.1
+  cut = cut0 + i*0.1
    -
    lmp.set_variable("cut",cut)                 # set a variable in LAMMPS
-    lmp.command("pair_style lj/cut $*cut*")     # LAMMPS command
-    #lmp.command("pair_style lj/cut %d" % cut)  # LAMMPS command option
+
    lmp.set_variable("cut",cut)                 # set a variable in LAMMPS
+lmp.command("pair_style lj/cut $*cut*")     # LAMMPS command
+#lmp.command("pair_style lj/cut %d" % cut)  # LAMMPS command option
 
    
 
    
 
    lmp.command("pair_coeff * * 1.0 1.0")       # ditto
-    lmp.command("run 10")                       # ditto
-    pe = lmp.extract_compute("thermo_pe",0,0)   # extract total PE from LAMMPS
-    print "PE",pe/natoms,thresh
-    if pe/natoms < thresh: return
+lmp.command("run 10")                       # ditto
+pe = lmp.extract_compute("thermo_pe",0,0)   # extract total PE from LAMMPS
+print "PE",pe/natoms,thresh
+if pe/natoms < thresh: return
 
    
 
    
 
    with these input script commands:
    
diff --git a/doc/read_data.html b/doc/read_data.html
index 42e8f24302..01d1b92d48 100644
--- a/doc/read_data.html
+++ b/doc/read_data.html
@@ -138,28 +138,28 @@
 
 
     add arg = append or Nstart or merge
-    append = add new atoms with IDs appended to current IDs
-    Nstart = add new atoms with IDs starting with Nstart
-    merge = add new atoms with their IDs unchanged
-  offset args = toff boff aoff doff ioff
-    toff = offset to add to atom types
-    boff = offset to add to bond types
-    aoff = offset to add to angle types
-    doff = offset to add to dihedral types
-    ioff = offset to add to improper types
-  shift args = Sx Sy Sz
-    Sx,Sy,Sz = distance to shift atoms when adding to system (distance units)
-  extra/atom/types arg = # of extra atom types
-  extra/bond/types arg = # of extra bond types
-  extra/angle/types arg = # of extra angle types
-  extra/dihedral/types arg = # of extra dihedral types
-  extra/improper/types arg = # of extra improper types
-  group args = groupID
-    groupID = add atoms in data file to this group
-  fix args = fix-ID header-string section-string
-    fix-ID = ID of fix to process header lines and sections of data file
-    header-string = header lines containing this string will be passed to fix
-    section-string = section names with this string will be passed to fix
+  append = add new atoms with IDs appended to current IDs
+  Nstart = add new atoms with IDs starting with Nstart
+  merge = add new atoms with their IDs unchanged
+offset args = toff boff aoff doff ioff
+  toff = offset to add to atom types
+  boff = offset to add to bond types
+  aoff = offset to add to angle types
+  doff = offset to add to dihedral types
+  ioff = offset to add to improper types
+shift args = Sx Sy Sz
+  Sx,Sy,Sz = distance to shift atoms when adding to system (distance units)
+extra/atom/types arg = # of extra atom types
+extra/bond/types arg = # of extra bond types
+extra/angle/types arg = # of extra angle types
+extra/dihedral/types arg = # of extra dihedral types
+extra/improper/types arg = # of extra improper types
+group args = groupID
+  groupID = add atoms in data file to this group
+fix args = fix-ID header-string section-string
+  fix-ID = ID of fix to process header lines and sections of data file
+  header-string = header lines containing this string will be passed to fix
+  section-string = section names with this string will be passed to fix
    @@ -530,7 +530,7 @@ Atoms section:

  • line syntax: ID coeffs
    • ID = angle type (1-N)
-  coeffs = list of coeffs
+coeffs = list of coeffs
      @@ -552,7 +552,7 @@ input script.

     ID = improper type (1-N)
-  coeffs = list of coeffs (see improper_coeff)
+coeffs = list of coeffs (see improper_coeff)

    AngleAngleTorsion Coeffs section:

    @@ -562,7 +562,7 @@ ID = improper type (1-N) 
     ID = dihedral type (1-N)
-  coeffs = list of coeffs (see dihedral_coeff)
+coeffs = list of coeffs (see dihedral_coeff)

    Angles section:

    @@ -571,8 +571,8 @@ ID = dihedral type (1-N)
  • line syntax: ID type atom1 atom2 atom3
    • ID = number of angle (1-Nangles)
-  type = angle type (1-Nangletype)
-  atom1,atom2,atom3 = IDs of 1st,2nd,3rd atoms in angle
+type = angle type (1-Nangletype)
+atom1,atom2,atom3 = IDs of 1st,2nd,3rd atoms in angle

    example: @@ -593,7 +593,7 @@ integers (1, not 1.0).

     ID = dihedral type (1-N)
-  coeffs = list of coeffs (see dihedral_coeff)
+coeffs = list of coeffs (see dihedral_coeff)

    Atoms section:

    @@ -815,7 +815,7 @@ script.

  • first line syntax: atom-ID ninteger ndouble
    • ninteger = # of integer quantities for this particle
-  ndouble = # of floating-point quantities for this particle
+ndouble = # of floating-point quantities for this particle
      @@ -824,16 +824,16 @@ script.

    • example:
    12 3 6
-  2 3 2
-  1.0 2.0 3.0 1.0 2.0 4.0
+2 3 2
+1.0 2.0 3.0 1.0 2.0 4.0
    • example:
    12 0 14
-  1.0 2.0 3.0 1.0 2.0 4.0 1.0 2.0 3.0 1.0
-  2.0 4.0 4.0 2.0
+1.0 2.0 3.0 1.0 2.0 4.0 1.0 2.0 3.0 1.0
+2.0 4.0 4.0 2.0

    The Bodies section must appear if atom_style body @@ -863,7 +863,7 @@ e.g. there are no integer lines in the last example above.

  • line syntax: ID coeffs
    • ID = bond type (1-N)
-  coeffs = list of coeffs
+coeffs = list of coeffs
      @@ -885,7 +885,7 @@ script.

     ID = angle type (1-N)
-  coeffs = list of coeffs (see class 2 section of angle_coeff)
+coeffs = list of coeffs (see class 2 section of angle_coeff)

    BondBond Coeffs section:

    @@ -895,7 +895,7 @@ ID = angle type (1-N) 
     ID = angle type (1-N)
-  coeffs = list of coeffs (see class 2 section of angle_coeff)
+coeffs = list of coeffs (see class 2 section of angle_coeff)

    BondBond13 Coeffs section:

    @@ -905,7 +905,7 @@ ID = angle type (1-N) 
     ID = dihedral type (1-N)
-  coeffs = list of coeffs (see class 2 section of dihedral_coeff)
+coeffs = list of coeffs (see class 2 section of dihedral_coeff)

    Bonds section:

    @@ -914,8 +914,8 @@ ID = dihedral type (1-N)
  • line syntax: ID type atom1 atom2
    • ID = bond number (1-Nbonds)
-  type = bond type (1-Nbondtype)
-  atom1,atom2 = IDs of 1st,2nd atoms in bond
+type = bond type (1-Nbondtype)
+atom1,atom2 = IDs of 1st,2nd atoms in bond
      @@ -933,7 +933,7 @@ in this section must be integers (1, not 1.0).

    • line syntax: ID coeffs
    ID = dihedral type (1-N)
-  coeffs = list of coeffs
+coeffs = list of coeffs
      @@ -954,8 +954,8 @@ Coefficients can also be set via the
    • line syntax: ID type atom1 atom2 atom3 atom4
    ID = number of dihedral (1-Ndihedrals)
-  type = dihedral type (1-Ndihedraltype)
-  atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in dihedral
+type = dihedral type (1-Ndihedraltype)
+atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in dihedral
      @@ -974,8 +974,8 @@ section must be integers (1, not 1.0).

    • line syntax: atom-ID shapex shapey shapez quatw quati quatj quatk
    atom-ID = ID of atom which is an ellipsoid
-  shapex,shapey,shapez = 3 diameters of ellipsoid (distance units)
-  quatw,quati,quatj,quatk = quaternion components for orientation of atom
+shapex,shapey,shapez = 3 diameters of ellipsoid (distance units)
+quatw,quati,quatj,quatk = quaternion components for orientation of atom
      @@ -1011,7 +1011,7 @@ specified as a unit vector.

     ID = dihedral type (1-N)
-  coeffs = list of coeffs (see class 2 section of dihedral_coeff)
+coeffs = list of coeffs (see class 2 section of dihedral_coeff)

    Improper Coeffs section:

    @@ -1020,7 +1020,7 @@ ID = dihedral type (1-N)
  • line syntax: ID coeffs
    • ID = improper type (1-N)
-  coeffs = list of coeffs
+coeffs = list of coeffs
      @@ -1041,8 +1041,8 @@ Coefficients can also be set via the
    • line syntax: ID type atom1 atom2 atom3 atom4
    ID = number of improper (1-Nimpropers)
-  type = improper type (1-Nimpropertype)
-  atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in improper
+type = improper type (1-Nimpropertype)
+atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in improper
      @@ -1063,8 +1063,8 @@ values in this section must be integers (1, not 1.0).

    • line syntax: atom-ID x1 y1 x2 y2
    atom-ID = ID of atom which is a line segment
-  x1,y1 = 1st end point
-  x2,y2 = 2nd end point
+x1,y1 = 1st end point
+x2,y2 = 2nd end point
      @@ -1091,7 +1091,7 @@ for defining some interactions.

    • line syntax: ID mass
    ID = atom type (1-N)
-  mass = mass value
+mass = mass value
 
     ID = dihedral type (1-N)
-  coeffs = list of coeffs (see class 2 section of dihedral_coeff)
+coeffs = list of coeffs (see class 2 section of dihedral_coeff)

    Pair Coeffs section:

    @@ -1121,7 +1121,7 @@ ID = dihedral type (1-N)
  • line syntax: ID coeffs
    • ID = atom type (1-N)
-  coeffs = list of coeffs
+coeffs = list of coeffs
      @@ -1145,15 +1145,15 @@ script.

    • line syntax: ID1 ID2 coeffs
    ID1 = atom type I = 1-N
-  ID2 = atom type J = I-N, with I <= J
-  coeffs = list of coeffs
+ID2 = atom type J = I-N, with I <= J
+coeffs = list of coeffs
    • examples:
    3 3 0.022 2.35197 0.022 2.35197
-  3 5 0.022 2.35197 0.022 2.35197
+3 5 0.022 2.35197 0.022 2.35197

    This section must have N*(N+1)/2 lines where N = # of atom types. The @@ -1172,9 +1172,9 @@ script.

  • line syntax: atom-ID x1 y1 x2 y2
    • atom-ID = ID of atom which is a line segment
-  x1,y1,z1 = 1st corner point
-  x2,y2,z2 = 2nd corner point
-  x3,y3,z3 = 3rd corner point
+x1,y1,z1 = 1st corner point
+x2,y2,z2 = 2nd corner point
+x3,y3,z3 = 3rd corner point
      diff --git a/doc/read_dump.html b/doc/read_dump.html index e986e9e9f9..98669011e1 100644 --- a/doc/read_dump.html +++ b/doc/read_dump.html @@ -149,21 +149,21 @@ field = x or y or z or vx or vy or 
     box value = yes or no = replace simulation box with dump box
-  replace value = yes or no = overwrite atoms with dump atoms
-  purge value = yes or no = delete all atoms before adding dump atoms
-  trim value = yes or no = trim atoms not in dump snapshot
-  add value = yes or no = add new dump atoms to system
-  label value = field column
-    field = one of the listed fields or id or type
-    column = label on corresponding column in dump file
-  scaled value = yes or no = coords in dump file are scaled/unscaled
-  wrapped value = yes or no = coords in dump file are wrapped/unwrapped
-  format values = format of dump file, must be last keyword if used
-    native = native LAMMPS dump file
-    xyz = XYZ file
-    molfile style path = VMD molfile plugin interface
-      style = dcd or xyz or others supported by molfile plugins
-      path = optional path for location of molfile plugins
+replace value = yes or no = overwrite atoms with dump atoms
+purge value = yes or no = delete all atoms before adding dump atoms
+trim value = yes or no = trim atoms not in dump snapshot
+add value = yes or no = add new dump atoms to system
+label value = field column
+  field = one of the listed fields or id or type
+  column = label on corresponding column in dump file
+scaled value = yes or no = coords in dump file are scaled/unscaled
+wrapped value = yes or no = coords in dump file are wrapped/unwrapped
+format values = format of dump file, must be last keyword if used
+  native = native LAMMPS dump file
+  xyz = XYZ file
+  molfile style path = VMD molfile plugin interface
+    style = dcd or xyz or others supported by molfile plugins
+    path = optional path for location of molfile plugins
    diff --git a/doc/region.html b/doc/region.html index e5a3e983cb..3ac0eae595 100644 --- a/doc/region.html +++ b/doc/region.html @@ -137,37 +137,37 @@ 
     delete = no args
-  block args = xlo xhi ylo yhi zlo zhi
-    xlo,xhi,ylo,yhi,zlo,zhi = bounds of block in all dimensions (distance units)
-  cone args = dim c1 c2 radlo radhi lo hi
-    dim = x or y or z = axis of cone
-    c1,c2 = coords of cone axis in other 2 dimensions (distance units)
-    radlo,radhi = cone radii at lo and hi end (distance units)
-    lo,hi = bounds of cone in dim (distance units)
-  cylinder args = dim c1 c2 radius lo hi
-    dim = x or y or z = axis of cylinder
-    c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
-    radius = cylinder radius (distance units)
-      radius can be a variable (see below)
-    lo,hi = bounds of cylinder in dim (distance units)
-  plane args = px py pz nx ny nz
-    px,py,pz = point on the plane (distance units)
-    nx,ny,nz = direction normal to plane (distance units)
-  prism args = xlo xhi ylo yhi zlo zhi xy xz yz
-    xlo,xhi,ylo,yhi,zlo,zhi = bounds of untilted prism (distance units)
-    xy = distance to tilt y in x direction (distance units)
-    xz = distance to tilt z in x direction (distance units)
-    yz = distance to tilt z in y direction (distance units)
-  sphere args = x y z radius
-    x,y,z = center of sphere (distance units)
-    radius = radius of sphere (distance units)
-      radius can be a variable (see below)
-  union args = N reg-ID1 reg-ID2 ...
-    N = # of regions to follow, must be 2 or greater
-    reg-ID1,reg-ID2, ... = IDs of regions to join together
-  intersect args = N reg-ID1 reg-ID2 ...
-    N = # of regions to follow, must be 2 or greater
-    reg-ID1,reg-ID2, ... = IDs of regions to intersect
+block args = xlo xhi ylo yhi zlo zhi
+  xlo,xhi,ylo,yhi,zlo,zhi = bounds of block in all dimensions (distance units)
+cone args = dim c1 c2 radlo radhi lo hi
+  dim = x or y or z = axis of cone
+  c1,c2 = coords of cone axis in other 2 dimensions (distance units)
+  radlo,radhi = cone radii at lo and hi end (distance units)
+  lo,hi = bounds of cone in dim (distance units)
+cylinder args = dim c1 c2 radius lo hi
+  dim = x or y or z = axis of cylinder
+  c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
+  radius = cylinder radius (distance units)
+    radius can be a variable (see below)
+  lo,hi = bounds of cylinder in dim (distance units)
+plane args = px py pz nx ny nz
+  px,py,pz = point on the plane (distance units)
+  nx,ny,nz = direction normal to plane (distance units)
+prism args = xlo xhi ylo yhi zlo zhi xy xz yz
+  xlo,xhi,ylo,yhi,zlo,zhi = bounds of untilted prism (distance units)
+  xy = distance to tilt y in x direction (distance units)
+  xz = distance to tilt z in x direction (distance units)
+  yz = distance to tilt z in y direction (distance units)
+sphere args = x y z radius
+  x,y,z = center of sphere (distance units)
+  radius = radius of sphere (distance units)
+    radius can be a variable (see below)
+union args = N reg-ID1 reg-ID2 ...
+  N = # of regions to follow, must be 2 or greater
+  reg-ID1,reg-ID2, ... = IDs of regions to join together
+intersect args = N reg-ID1 reg-ID2 ...
+  N = # of regions to follow, must be 2 or greater
+  reg-ID1,reg-ID2, ... = IDs of regions to intersect
    • zero or more keyword/arg pairs may be appended
      • @@ -175,17 +175,17 @@ 
     side value = in or out
-    in = the region is inside the specified geometry
-    out = the region is outside the specified geometry
-  units value = lattice or box
-    lattice = the geometry is defined in lattice units
-    box = the geometry is defined in simulation box units
-  move args = v_x v_y v_z
-    v_x,v_y,v_z = equal-style variables for x,y,z displacement of region over time
-  rotate args = v_theta Px Py Pz Rx Ry Rz
-    v_theta = equal-style variable for rotaton of region over time (in radians)
-    Px,Py,Pz = origin for axis of rotation (distance units)
-    Rx,Ry,Rz = axis of rotation vector
+  in = the region is inside the specified geometry
+  out = the region is outside the specified geometry
+units value = lattice or box
+  lattice = the geometry is defined in lattice units
+  box = the geometry is defined in simulation box units
+move args = v_x v_y v_z
+  v_x,v_y,v_z = equal-style variables for x,y,z displacement of region over time
+rotate args = v_theta Px Py Pz Rx Ry Rz
+  v_theta = equal-style variable for rotaton of region over time (in radians)
+  Px,Py,Pz = origin for axis of rotation (distance units)
+  Rx,Ry,Rz = axis of rotation vector
    diff --git a/doc/restart.html b/doc/restart.html index e1aedf7dbf..3bf2ce569e 100644 --- a/doc/restart.html +++ b/doc/restart.html @@ -143,9 +143,9 @@ restart N file1 file2 keyword value ... 
     fileper arg = Np
-    Np = write one file for every this many processors
-  nfile arg = Nf
-    Nf = write this many files, one from each of Nf processors
+  Np = write one file for every this many processors
+nfile arg = Nf
+  Nf = write this many files, one from each of Nf processors
    diff --git a/doc/run.html b/doc/run.html index b7ed152afd..b2b8ecd7fd 100644 --- a/doc/run.html +++ b/doc/run.html @@ -138,16 +138,16 @@ 
     upto value = none
-  start value = N1
-    N1 = timestep at which 1st run started
-  stop value = N2
-    N2 = timestep at which last run will end
-  pre value = no or yes
-  post value = no or yes
-  every values = M c1 c2 ...
-    M = break the run into M-timestep segments and invoke one or more commands between each segment
-    c1,c2,...,cN = one or more LAMMPS commands, each enclosed in quotes
-    c1 = NULL means no command will be invoked
+start value = N1
+  N1 = timestep at which 1st run started
+stop value = N2
+  N2 = timestep at which last run will end
+pre value = no or yes
+post value = no or yes
+every values = M c1 c2 ...
+  M = break the run into M-timestep segments and invoke one or more commands between each segment
+  c1,c2,...,cN = one or more LAMMPS commands, each enclosed in quotes
+  c1 = NULL means no command will be invoked
    diff --git a/doc/run_style.html b/doc/run_style.html index 0e9c499bdc..d9a467fc7d 100644 --- a/doc/run_style.html +++ b/doc/run_style.html @@ -136,41 +136,41 @@ 
     verlet args = none
-  verlet/split args = none
-  respa args = N n1 n2 ... keyword values ...
-    N = # of levels of rRESPA
-    n1, n2, ... = loop factor between rRESPA levels (N-1 values)
-    zero or more keyword/value pairings may be appended to the loop factors
-    keyword = bond or angle or dihedral or improper or
-           pair or inner or middle or outer or hybrid or kspace
-      bond value = M
-        M = which level (1-N) to compute bond forces in
-      angle value = M
-        M = which level (1-N) to compute angle forces in
-      dihedral value = M
-        M = which level (1-N) to compute dihedral forces in
-      improper value = M
-        M = which level (1-N) to compute improper forces in
-      pair value = M
-        M = which level (1-N) to compute pair forces in
-      inner values = M cut1 cut2
-        M = which level (1-N) to compute pair inner forces in
-     cut1 = inner cutoff between pair inner and
-            pair middle or outer  (distance units)
-     cut2 = outer cutoff between pair inner and
-            pair middle or outer  (distance units)
-      middle values = M cut1 cut2
-        M = which level (1-N) to compute pair middle forces in
-     cut1 = inner cutoff between pair middle and pair outer (distance units)
-     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
-        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
-        ...
-      kspace value = M
-        M = which level (1-N) to compute kspace forces in
+verlet/split args = none
+respa args = N n1 n2 ... keyword values ...
+  N = # of levels of rRESPA
+  n1, n2, ... = loop factor between rRESPA levels (N-1 values)
+  zero or more keyword/value pairings may be appended to the loop factors
+  keyword = bond or angle or dihedral or improper or
+         pair or inner or middle or outer or hybrid or kspace
+    bond value = M
+      M = which level (1-N) to compute bond forces in
+    angle value = M
+      M = which level (1-N) to compute angle forces in
+    dihedral value = M
+      M = which level (1-N) to compute dihedral forces in
+    improper value = M
+      M = which level (1-N) to compute improper forces in
+    pair value = M
+      M = which level (1-N) to compute pair forces in
+    inner values = M cut1 cut2
+      M = which level (1-N) to compute pair inner forces in
+   cut1 = inner cutoff between pair inner and
+          pair middle or outer  (distance units)
+   cut2 = outer cutoff between pair inner and
+          pair middle or outer  (distance units)
+    middle values = M cut1 cut2
+      M = which level (1-N) to compute pair middle forces in
+   cut1 = inner cutoff between pair middle and pair outer (distance units)
+   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
+      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
+      ...
+    kspace value = M
+      M = which level (1-N) to compute kspace forces in
    diff --git a/doc/searchindex.js b/doc/searchindex.js index 8f42177b6f..37653262c2 100644 --- a/doc/searchindex.js +++ b/doc/searchindex.js @@ -1 +1 @@ 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12,15,17,39,41,71,91,164,179,184,188,189,190,195,202,205,211,212,269,273,278,286,288,293,301,303,317,326,327,328,329,330,333,354,365,368,384,393,404,418,420,421,423,431,437,440,441],checkf:164,checkqeq:393,checku:164,chem:[6,13,20,21,25,39,40,43,45,46,87,88,112,121,150,151,161,193,198,206,207,214,216,228,229,230,247,248,253,257,260,262,270,274,278,281,282,285,286,287,288,295,304,312,314,318,319,325,328,335,340,344,345,348,349,350,352,353,357,359,360,362,363,369,373,374,377,380,383,384,387,404,411,432,435,437,443],chemic:[9,118,138,143,167,178,179,205,261,266,267,285,319,392,393,400],chemistri:[9,260,261,263,339,357,392,393],chen:290,cheng:348,chenoweth:[392,393],chenoweth_2008:[392,393],chi:[92,133,166,251,261,263,358,360,449],chiefli:391,child:8,chip:[7,12,17,333,436],chipot:193,chiral:312,chmod:[11,12],cho:380,chocol:[7,169],choic:[3,6,12,15,16,18,40,41,54,87,121,123,137,148,164,181,184,185,188,191,194,195,207,213,216,227,229,253,261,270,285,313,319,324,325,328,330,333,364,377,384,388,423,432,433,436,437,442,443,447],choos:[1,3,6,7,8,12,16,17,18,29,39,54,87,117,134,135,168,189,190,191,192,195,202,213,216,227,229,231,232,233,234,235,257,278,282,296,318,319,325,413,418,420,432,438],chose:[408,410],chosen:[2,3,6,12,17,120,144,147,156,164,168,174,179,192,195,202,205,206,214,216,227,229,233,253,256,267,278,282,285,286,291,293,294,300,319,320,325,333,357,361,367,368,371,395,408,418,432,437,443],chri:142,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[66,75,90,93,104,106,114,124,139,141,181],chute:[4,10,208],ciccotti:273,cieplak:[6,150,435],cii:182,cij:182,circular:[3,6,123,165],circumst:18,circumv:265,citat:[],cite:[3,7,8,12,213],cko:2,cl1:143,clarendon:[29,352],clarifi:[7,408,410],clariti:303,clark:387,class2:[],classic:[0,3,5,6,7,8,9,203,253,260,265,290,314,357],classifi:[9,405],claus:421,clean:[6,12,14,15,17,431],cleanli:[422,451],clear:[],clearli:7,clebsch:120,clermont:[9,13],clever:427,click:[2,11,22,37,44,55,144,152,163,168,210,305,313,328,346,405],client:[210,212],climb:[228,328,437],clinic:[7,13],clo:[133,166,449],clock:[12,418,437],clockwis:296,close:[3,6,11,12,13,39,41,67,121,147,167,190,191,192,207,214,216,229,247,270,273,296,299,317,319,322,324,325,328,333,335,339,349,350,380,384,410,427,433,443,445],closer:[3,41,116,142,166,167,188,192,196,287,328],closest:[190,251,270,293,360,394,404,413],cloud:443,clovertown:18,clsuter:72,clump1:[255,270],clump2:[255,270],clump3:[255,270],clump:270,cluster:[],clutter:[3,9],cmap:423,cmatrix:207,cmax:380,cmd:[11,12,253,434],cmin:380,cmm:[],cn1:182,cn2:182,cna:[],cnn:182,cnr:[9,13],cnt:[364,427],co2:[40,143,273,327],coars:[7,9,29,36,40,54,156,255,270,278,362,395,435],coarser:[319,448],coarsest:120,code:[],coeff:[3,7,8,12,21,22,33,44,50,150,151,152,157,304,305,310,346,364,368,384,397,423,425],coeffcient:423,coeffici:[],coefficienct:353,coefficient0:355,coefficient1:355,coeffieci:[6,337],coeffincientn:355,coexist:[9,205,357],cohes:[6,358,380],coincid:[205,299,344,378,379,418],cold:[6,129,209,329,443],coldest:286,coleman8:9,coleman:[9,118,143,271],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,93,98,104,106,114,124,132,139,141,144,167,169,181,193,219,225,255,265,268,270,301,318,327,329,347,367,423,430,436,452],collid:[199,278,300],colliex:143,collinear:[3,255],collis:[3,216,278,296,300,354,361,416],colllis:278,colloid:[],colombo:39,colon:[170,301,424],color1:169,color2:169,color:[3,9,41,167,168,169,188,206,260,265],column:[3,6,9,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,104,106,108,110,113,114,115,116,117,119,120,121,124,132,139,141,142,143,164,167,169,172,180,181,182,183,184,185,186,219,226,227,260,270,279,280,290,300,359,363,392,393,424,438,440,448],colvar:[],colvarmodul:12,com:[],comamnd:194,comand:[191,425],comannd:333,comb3:[],comb:[],comb_1:262,comb_2:262,combiant:350,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,92,108,115,123,137,167,168,178,183,210,219,229,253,259,282,291,299,302,304,318,319,321,325,333,347,349,350,357,358,364,376,377,396,406,408,410,415,426,431,443,448],come:[],comfort:[12,13],comm:[0,3,12,61,73,210,212,213,319,328,333,353,384,389,407],comm_modifi:[],comm_styl:[],command:[],comment:[2,7,11,12,38,56,150,164,167,214,270,290,327,328,334,355,356,358,368,380,386,393,396,406,407,408,409,410,420,421,423,443,448],commerci:7,commmand:[3,6,12,59,107,248,417,418,420,437,451],common:[],commonli:[3,6,12,17,25,57,59,105,146,167,168,170,314,362,371,396,408,410,423,426,435],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,147,148,168,169,188,189,190,192,193,194,210,212,216,218,219,220,229,252,259,261,262,263,270,278,290,301,318,329,330,331,333,354,388,420,421,425,432,433,450,452],communc:318,comp:[7,212,213,273,319,328,357,384,389,394,403,407,409],compact:[63,172,346,405],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,110,118,127,142,143,152,163,169,198,261,301,303,318,319,326,328,380,418,437,438,443,447],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,151,152,163,304,305,313,345,405],compat:[3,5,7,8,9,11,12,13,17,18,41,71,117,119,155,167,170,174,180,181,182,183,184,185,186,188,252,264,282,285,292,295,298,318,333,365,384,407,420,421,448],compens:[6,189,190,268,329,357],compet:289,competit:319,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,142,167,168,170,210,289,319,333,423,424,428],compl:17,complain:[12,17],complement:380,complementari:[7,349,369],complet:[3,6,9,12,15,41,59,71,169,184,188,193,219,253,256,259,278,289,291,303,317,328,333,358,412,418,423,428,431,435,437,440,443,448],complex:[6,8,11,12,13,25,40,42,62,120,132,144,145,216,299,316,328,357,407,421,423,426,448],compli:[285,289],complic:[6,7,9,12,13,179,205,421],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,93,94,97,104,105,106,107,108,109,110,112,113,117,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,136,137,139,140,141,167,168,169,175,176,180,181,182,183,184,185,186,187,191,192,194,195,200,203,208,212,213,216,219,221,225,226,228,229,230,233,234,235,246,247,249,250,252,253,254,257,268,270,272,273,274,275,278,281,282,283,285,292,293,298,299,300,318,321,325,326,327,328,333,353,357,361,378,379,396,423,424,433,441,448,449],componenet:6,composit:[6,179,216,355],compound:[348,357,358],compres:[71,114,181],compress:[3,6,59,71,114,147,167,168,169,181,194,227,233,257,260],compris:[40,299,367,394,412],compton:[118,143],comptu:[3,6],compuat:319,comput:[],computation:[3,6,189,190,290,339],computational:443,compute_arrai:8,compute_fep:[174,377],compute_group_group:205,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[118,271],compute_scalar:8,compute_temp:8,compute_ti:174,compute_vector:8,compute_xrd:143,concaten:[2,3,451],concav:299,concentr:355,concept:[6,124,134,181,432],conceptu:[3,6,71,132,192,194,328,349,364,380,428],concern:[6,73,87,206],concis:[11,289],conclud:12,concret:8,concurr:[9,16,319],conden:[290,408,410],condens:[6,126,290,335,351,355,369],condit:[],conducit:6,conduct:[],cone:426,confid:[3,437],config:[12,167,420],configfil:193,configur:[1,6,12,15,17,38,59,146,164,166,167,168,172,192,193,194,195,199,205,212,213,241,253,261,289,316,326,328,335,339,356,380,406,408,410,418,423,425,426,437],confin:[423,437],conflict:[3,40,384,421],conform:[3,6,13,59,191,192,228,269,274,289,312,328,357,435],confus:3,conjuct:353,conjug:[7,8,213,325,357,392,393],conjunct:[6,7,71,86,87,114,127,132,138,144,148,169,173,174,213,216,220,241,256,257,261,262,263,265,270,278,286,293,298,318,319,328,340,342,346,349,353,357,363,369,387,395,411,423,426,430,443,452],connect:[3,6,87,129,147,191,210,255,270,273,275,328,350,361,404,410,420,421,427,443],conput:3,consecut:[3,11,12,39,71,144,169,173,174,195,210,211,349,369,373,418,424,426],consequ:[1,6,290,368,437],conserv:[3,172,179,191,198,199,206,209,213,215,216,220,225,227,229,241,270,273,281,282,286,293,294,298,328,352,353,361,375,432,437],consid:[6,9,70,71,78,87,115,129,130,147,167,169,173,174,180,182,184,188,190,191,195,217,230,252,270,285,286,289,290,293,319,346,357,364,393,394,404,418,419,421,424,425,426,428,431,433,441,443,448],consider:[6,8,213,214,281,282,283,333,432],consist:[3,6,8,9,11,12,40,42,65,69,79,92,104,108,111,112,115,124,127,129,144,156,166,170,175,176,181,194,195,198,200,203,206,213,214,215,226,229,231,232,233,234,235,236,237,239,240,241,242,244,245,246,247,248,249,257,260,265,267,269,270,281,282,283,284,294,318,319,321,327,328,333,335,339,341,347,349,357,360,378,379,380,384,394,407,413,421,423,424,426,427,428,435,443,448],consistent_fe_initi:178,consit:270,constant:[],constitu:[3,6,219,270,295,299,347,394],constrain:[3,6,8,122,123,124,125,127,130,131,132,133,134,136,137,172,181,195,205,206,211,219,223,255,256,268,270,273,276,286,293,326,327,357,428,435,443],constraint:[],construct:[6,8,14,38,54,56,61,64,67,70,72,73,77,118,120,143,192,229,252,269,299,329,333,352,384,404,406,407,426,427,448],constructor:8,consult:393,consum:[1,265,388,448],consumpt:316,contact:[],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,116,118,120,124,132,142,143,144,146,150,152,163,164,167,168,169,170,172,173,174,178,180,181,182,183,184,185,186,188,193,195,200,207,211,212,213,214,216,227,241,251,252,255,256,258,260,263,267,270,271,278,285,289,290,299,300,303,317,319,327,328,331,332,334,335,336,339,348,349,352,355,356,357,364,365,380,386,390,391,392,393,396,406,407,408,409,410,411,418,419,420,421,423,424,425,426,428,430,432,435,437,440,441,443,448,450,452],content:[12,18,393,439,441],context:[3,6,8,12,17,117,169,189,190,195,255,267,294,325,415,423,430,439,447,448,449],contibut:70,contigu:420,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,103,104,140,169,172,173,174,179,181,182,183,184,185,186,188,191,192,193,194,195,205,206,207,209,210,211,213,214,215,221,226,227,229,231,232,233,234,235,246,247,248,249,254,256,259,260,270,271,274,277,278,280,287,288,290,296,299,303,317,332,333,339,353,354,371,374,392,393,394,409,418,421,423,425,426,431,437,440,441,448,450],continuum:[6,7,9,178,290],contour_integr:178,contract:[59,192,194,229,257,270],contradictori:3,contrain:273,contraint:241,contrari:[207,214],contrast:[1,6,42,55,64,129,194,301,415,451],contrib:290,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,93,102,104,106,107,108,109,110,112,114,117,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,174,179,180,181,182,183,184,185,186,192,205,213,216,219,220,224,230,247,248,255,256,264,267,270,271,273,292,318,326,328,336,353,354,355,357,364,378,379,384,392,393,435,441,443],contributor:12,control:[3,5,6,7,8,11,13,16,27,29,41,87,91,120,153,167,168,172,178,179,188,192,193,194,209,210,213,214,229,231,232,233,234,235,257,262,270,281,282,283,290,294,316,318,330,357,360,392,393,406,410,418,420,432,438,439],control_typ:178,controlfil:393,convect:91,conveni:[6,12,29,167,170,186,271,321,396,448],convent:[3,8,9,29,155,162,163,169,269,275,302,355,357,448],converg:[3,6,41,88,167,168,170,175,188,191,192,200,203,233,260,262,265,269,273,324,325,326,328,348,349,369,418,430,437],convers:[3,8,120,168,169,179,182,257,318,349,350,351,357,369,373,377,387,421,437,447],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,144,151,167,168,169,186,227,301,304,306,309,312,321,328,334,355,408,410,416,421,423,424,425,430,440,443,447,448,450,452],convex:299,convinc:[7,12],cooki:7,cool:[7,134,209,268],cooordin:167,cooper:[5,7],coord123:114,coord1:[3,114,181,184,185],coord2:[3,114,181,184,185],coord3:[3,114,181,184,185],coord:[],coordiat:326,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,93,103,104,106,113,114,116,120,127,133,139,141,142,144,148,166,167,168,169,170,172,175,180,181,183,184,185,188,189,190,191,192,193,194,195,198,200,201,203,205,208,209,210,211,212,213,214,226,228,229,231,232,234,235,247,250,251,252,255,256,257,267,268,270,272,273,274,275,276,277,278,280,288,289,290,297,298,300,301,321,326,327,328,333,334,335,338,356,418,423,424,426,428,431,433,437,443,448,449],coordn:[114,181],coorind:104,copi:[0,3,4,8,11,12,15,17,40,119,168,290,328,346,392,421],copper:416,coproccesor:16,coprocessor:[1,4,7,9,16,17,333,436],coproprocessor:17,copy_arrai:8,copyright:[7,8,255],coral:169,core:[],core_shel:126,coreshel:[6,9,342,349,351],cornel:[6,150,435],corner123i:113,corner123x:113,corner123z:113,corner1i:113,corner1x:113,corner1z:113,corner2i:113,corner2x:113,corner2z:113,corner3i:113,corner3x:113,corner3z:113,corner:[3,6,40,113,168,299,300,321,412,423],cornflowerblu:169,cornsilk:169,corpor:16,corr:348,correct:[3,6,9,11,12,16,17,59,87,88,102,110,116,126,131,138,168,194,207,213,229,230,247,255,257,260,289,295,299,318,328,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,351,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,414,415,416,423,438,441,443],correction_max_iter:178,correctli:[3,8,9,11,17,71,81,102,103,122,123,125,127,129,130,131,132,133,136,137,140,167,169,175,195,200,203,214,223,229,230,263,270,273,275,277,296,299,328,329,333,351,379,420,421,423,447,449],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,96,97,109,112,113,114,115,118,119,120,122,123,131,138,143,150,151,152,153,154,155,156,158,159,161,162,164,167,168,169,173,174,175,181,183,184,185,187,190,192,194,201,203,204,208,213,216,217,225,226,227,229,231,232,233,234,235,236,241,244,246,247,249,252,253,257,262,270,272,273,281,283,285,294,295,296,298,299,300,302,304,305,306,307,308,309,312,314,319,323,325,327,328,334,335,337,340,341,342,343,344,345,346,347,348,349,352,353,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,380,381,384,385,386,387,389,390,392,393,394,395,396,397,406,407,408,409,410,412,414,415,416,418,420,421,423,424,426,436,437,438,440,441,443,448],correspondingli:[378,379,432],cosin:[],cosineshift:27,cosmo:[207,212],cossq:[],cost:[1,6,10,11,12,17,39,41,71,109,118,121,143,168,169,181,184,185,188,189,190,202,229,262,290,318,319,331,349,369,373,384,406,420,432],costheta0:[406,408,410],costheta:390,costli:[11,88,207,329],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,93,104,106,109,112,114,124,134,139,141,157,167,168,169,173,174,179,181,182,184,188,194,203,212,259,260,261,265,268,270,272,278,279,285,289,290,291,295,299,301,303,310,315,317,324,326,329,333,336,359,363,364,392,393,419,420,421,423,425,427,430,431,439,443,448,449],coulomb:[3,5,6,7,8,9,10,12,14,15,18,88,107,108,121,145,149,261,263,291,318,319,326,333,340,342,343,344,345,348,349,350,351,352,357,361,362,364,369,373,377,384,387,392,393,395,405,410,411,415,428,435,441,443,447],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,41,63,68,77,91,114,116,117,132,142,148,175,176,179,181,183,184,185,187,188,195,200,202,205,211,229,241,256,273,281,282,299,319,326,327,328,330,333,359,363,384,441,448],counter:[296,418,429,431,437],counterbal:209,counterpart:[167,270,418],counterproduct:18,coupl:[],cours:[3,8,138,167,173,174,206,269,275,289,295,297,298,300,301,319,378,397,420,423,436,443,448,450],coval:[6,29,357,380,443],covari:207,cover:[6,71,164,169,178,216,357,367,412],coverag:[71,184],cpc:212,cpp:[1,3,6,8,9,11,12,13,87,167,173,174,203,273],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,169,172,198,214,291,316,319,333,346,405,418,436,437,440,441],cpuremain:441,cr2:143,cr3:143,crack:[4,329],crada:[5,7],crai:[5,7,13,18,167],crash:[3,329,443],craympi:333,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:178,create_faceset:178,create_nodeset:178,createatom:[],creation:[],crimson:169,critchlei:255,criteria:[3,116,145,168,169,189,190,191,224,326,389,412,425,428,448],criterion:[41,142,144,147,179,188,191,205,241,262,296,301,326,328,348,357,361,428,437,438],criterioni:437,critic:[48,49,227,285,290,326],cross:[3,12,22,71,89,123,152,167,168,180,184,190,194,226,228,247,270,275,277,286,293,305,321,328,344,353,354,355,362,363,364,369,371,373,390,395,408,410,423,427,433,450],crossov:1,crossterm:423,crozier:[0,7,13],crucial:260,crystal:[4,6,13,73,251,252,288,329,427,441,443],crystallin:[6,252,321,409,443],crystallis:285,crystallogr:[118,143],crystallograph:[321,441],crystallographi:[118,143,321],cs1:143,cs_chunk:6,cs_im:[40,423],cs_re:[40,423],csanyi:[120,391,396],cscl:380,csequ:6,csh:[11,12,346],cshrc:[11,12],csic:[356,406,408,410],csinfo:6,csisi:[356,406,408,410],csld:[],cst:355,cstherm:6,cstyle:420,csvr:[],ctcm:[334,355],ctemp_cor:198,cterm:274,ctr:9,ctype:11,cu1:143,cu2:143,cu3au:380,cube:[6,41,142,147,188,198,299,321,443],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:339,cummul:[3,6,186,189,190,191,193,202,207,213,215,278,281,282,283,284,286,293,363,441],cumul:[6,179,181,183,184,185,199,205,213,227,229,233,241,270,271,328],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,102,108,116,117,121,124,132,140,142,145,148,167,168,169,170,173,174,178,179,181,184,185,186,188,189,190,191,192,193,194,195,199,200,203,205,207,210,211,213,219,226,229,230,234,235,241,246,247,249,255,261,262,264,267,268,269,270,273,274,276,277,278,281,282,283,289,290,293,294,295,296,297,298,300,301,303,316,317,318,319,322,323,325,326,327,328,333,339,346,348,352,355,357,358,361,365,368,378,379,380,381,382,384,390,392,393,397,408,410,411,413,418,419,420,421,423,424,425,426,427,429,430,431,433,435,437,438,440,441,448,449,450,451,452],curv:[6,144,205,252],curvatur:[360,394,416],custom:[],cut0:421,cut1:432,cut2:432,cut:[],cuthi:[251,263],cutinn:[341,378,379],cutlo:[251,263],cutmax:390,cutoff1:[345,352,369,373,377,387,395],cutoff2:[340,342,343,345,351,352,369,373,377,387,395],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,108,115,116,120,142,145,147,190,191,196,251,260,261,263,265,267,270,278,291,295,299,301,318,319,326,329,330,331,333,334,335,336,337,338,339,340,341,342,343,344,345,347,349,350,351,352,353,354,355,356,357,358,359,360,362,363,364,365,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,392,393,394,395,396,397,398,399,400,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,421,425,428,432,443],cutoffa:356,cutoffc:356,cuu3:355,cval:143,cvd:285,cvel:274,cvff:[],cwiggl:[3,226,295,298,300,448],cyan:[2,168,169],cycl:[3,205,227,229,230,233],cyclic:[3,164],cygwin:12,cylind:[3,4,168,211,256,296,299,426],cylindr:[6,211,275,296],cypress:333,cyrot:339,cyrstal:252,d3q15:216,d3q19:216,d_double_doubl:15,d_e:290,d_flag2:259,d_flag:259,d_name:[113,167,259,280,433],d_single_doubl:15,d_single_singl:15,d_sx:259,d_sy:259,d_sz:259,daan:288,dai:12,daili:12,daivi:247,damag:[],dammak:265,damp:[3,6,172,177,213,214,215,220,229,230,233,257,260,265,270,281,282,294,296,297,325,326,328,340,342,344,349,352,357,361,369,377,387,395,405,411,437,443],damp_com:214,damp_drud:214,dampen:[270,443],dampflag:[296,361],dan:17,danger:[3,12,205,301,353,441],dangl:147,daniel:9,darden:[319,352],darkblu:169,darkcyan:169,darken:168,darkgoldenrod:169,darkgrai:169,darkgreen:169,darkkhaki:169,darkmagenta:169,darkolivegreen:169,darkorang:169,darkorchid:169,darkr:169,darksalmon:169,darkseagreen:169,darkslateblu:169,darkslategrai:169,darkturquois:169,darkviolet:169,dasgupta:261,dash:[361,440],dat:[6,91,164,178,419],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,271],dataset:271,datatyp:3,date:[0,6,12,13,392,393,448],datom1:115,datom2:115,datom3:115,datom4:115,datum:[3,6,42,65,68,69,79,92,108,115,167,182],davi:295,david:[9,19,318,319,408,410],daw:[355,390],dbg:14,dcd:[3,6,7,167,168,169,170,253,424,428],ddim:166,deactiv:377,dealt:212,debug:[6,7,11,12,13,14,17,118,143,144,253,258,316,318,333,365,384,413,421,422,425,430,433,440,448],deby:[],decai:[349,416],decid:[3,6,12,16,71,226,259,270,291,438],decipher:321,declin:278,decod:168,decompos:[87,396],decomposit:[3,5,7,18,62,178,253],decoupl:[6,443],decreas:[3,167,175,176,191,194,200,203,213,289,318],decrement:274,deepli:315,deeppink:169,deepskyblu:169,def:[12,13,421],defaul:61,defect:[6,70,142],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,150,151,152,153,154,155,156,158,159,161,162,163,164,165,166,167,168,169,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,198,199,200,203,204,205,208,211,212,213,214,215,216,224,226,228,229,230,231,232,233,234,235,237,238,239,242,244,245,246,247,248,249,251,252,253,255,256,257,259,261,263,268,270,271,272,273,276,278,280,281,282,283,284,286,287,288,290,292,293,295,296,297,298,299,300,301,303,304,305,306,307,308,309,312,313,314,316,318,319,321,323,325,326,327,328,329,330,331,332,333,335,336,337,338,340,341,342,343,344,345,346,347,349,350,352,353,354,356,357,359,360,361,362,363,364,365,367,369,370,371,372,373,374,375,376,377,378,379,383,384,385,386,387,389,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,420,421,423,424,426,427,428,429,432,433,434,435,437,438,440,441,443,444,445,446,447,448,449],definit:[2,3,6,8,12,13,78,80,116,120,169,181,182,183,184,185,186,194,211,233,271,280,292,295,298,300,302,313,316,327,336,339,347,357,367,390,396,412,421,423,425,432,434,447,448],defint:441,deform:[],deg2theta:143,deg:443,degener:[3,255],degrad:[8,18,252,319,432],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,94,96,97,99,101,102,112,122,123,124,125,126,127,128,129,130,131,132,133,134,136,137,143,144,150,151,154,155,162,164,166,168,181,191,198,205,207,208,213,214,219,229,230,233,234,235,246,247,249,253,255,269,270,273,281,282,283,288,304,306,309,312,314,326,352,355,363,433,441,443,449],degress:[124,181],del:437,delai:[3,6,12,329,354,441],deleg:364,delet:[2,3,7,8,12,54,57,60,63,142,147,148,172,181,182,183,184,185,186,189,191,202,205,229,271,281,282,301,303,317,327,329,332,384,423,424,426,434,435,440,444,446,448,449],delete_atom:[],delete_bond:[],delete_el:178,deli:166,delimit:[421,448],deloc:[230,357],delr:380,delt_lo:437,delta:[],delta_1:339,delta_3:339,delta_7:339,delta_conf:3,delta_ij:[380,390],delta_mu:[3,179],delta_pi:339,delta_r:390,delta_sigma:339,delx:166,delz:166,demand:265,demo:11,demon:250,demonstr:[260,380],den:256,dendrim:363,denniston:[9,216,218,219,220,252],denomin:[7,149],denot:[118,198,214,252,263,265,349,362,364,393],dens:[71,191,357],densiti:[3,6,7,9,18,40,41,59,100,116,120,130,142,144,173,174,178,181,184,185,188,194,203,216,219,222,223,252,256,257,261,290,295,321,323,327,334,339,355,380,381,382,390,394,399,401,402,403,423,432,433,441,447],depart:[0,7],departur:[227,260],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,108,109,112,113,114,115,119,120,122,127,131,132,138,144,145,150,151,152,153,154,155,156,158,159,161,162,163,164,166,167,168,169,172,173,174,175,176,179,181,183,184,186,187,188,190,192,200,201,204,207,208,209,211,213,214,216,218,219,226,229,231,232,233,234,235,236,244,246,247,249,251,262,265,267,270,272,273,278,281,282,283,285,287,289,290,292,294,295,298,299,300,301,303,304,305,306,307,308,309,312,314,319,321,326,327,329,330,331,333,334,335,337,338,339,340,341,342,343,344,345,346,347,348,349,350,352,353,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,380,381,383,385,386,387,389,390,392,393,394,395,396,397,405,406,407,408,409,410,411,412,414,415,416,418,420,423,425,426,429,433,435,437,440,441,442,448,449],dependend:6,depflag:12,dephas:[418,437],depos:195,deposit:[],deprec:261,depth:[51,123,168,290,360,394],dequidt:9,der:[87,107,347,348,377,392,393,415,443],deriv:[6,7,8,38,56,63,87,120,138,164,182,192,194,205,213,226,229,231,232,233,234,235,251,257,261,265,287,288,290,295,296,299,325,327,335,339,347,352,357,358,362,371,375,376,380,392,393,405,407,415,443],derjagin:415,derlet:251,descend:169,descent:[7,325],descib:[40,261],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,110,113,116,118,120,121,123,124,128,129,132,135,137,138,142,143,144,146,147,156,161,164,167,172,173,174,181,182,183,184,185,186,188,191,192,193,194,195,197,198,206,207,210,211,212,213,214,215,216,218,219,220,224,228,229,230,233,240,248,251,253,258,259,260,261,262,263,270,274,275,278,279,280,281,282,283,284,285,286,287,288,293,295,296,298,303,318,319,321,324,325,326,327,328,332,335,336,338,340,341,342,344,345,346,347,348,349,352,355,357,358,360,361,362,364,369,370,371,372,373,374,375,376,377,378,379,380,383,389,390,391,392,393,394,395,396,397,404,405,406,407,408,409,410,411,414,415,416,418,420,421,423,424,426,427,433,436,437,440,448,449,450],descript:[],descriptor:[120,167,365],deserno:319,design:[0,3,6,7,8,11,13,14,15,17,118,126,129,143,178,191,197,198,229,230,251,252,271,285,290,336,337,338,341,344,349,351,357,377,378,379,381,382,390,393,407,432],desir:[2,3,6,7,11,12,14,15,16,18,33,40,50,59,71,88,91,112,117,121,126,144,157,166,179,192,194,203,205,206,213,214,215,219,229,247,255,256,257,258,261,265,270,273,278,281,282,283,284,289,296,310,315,318,319,321,324,326,327,328,353,355,363,378,379,406,408,410,419,420,421,423,427,432,437,438,440,441,448,449,450],desk:7,desktop:[4,6,7,10,12,17,168],despit:443,destabil:339,destre:312,destroi:[11,39,189,190],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,93,102,104,106,107,109,111,112,114,117,119,120,121,122,123,124,127,137,138,139,141,144,145,148,149,152,163,167,168,169,172,173,174,178,181,182,183,184,186,188,190,191,192,193,194,195,203,205,206,207,208,210,211,213,215,216,220,226,227,228,229,230,231,232,233,234,235,239,241,246,247,248,249,252,255,256,257,259,260,262,263,264,270,273,278,281,282,283,284,285,286,288,289,290,291,292,293,294,301,303,305,313,318,319,322,326,327,329,330,333,334,335,336,338,339,341,343,344,345,346,347,348,349,352,353,357,358,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,379,380,383,384,389,392,393,394,396,397,405,412,414,415,421,423,424,425,426,428,429,432,433,435,438,441,448,449,452],detect:[2,3,12,61,63,86,204,256,289,328,348,363,368,418,420,423,434,437,448],determ:333,determin:[1,3,6,8,12,15,39,40,42,51,57,58,59,61,62,68,71,87,102,107,109,112,118,119,121,132,133,142,143,144,166,167,168,169,170,171,175,176,177,180,181,182,183,184,185,186,187,188,192,194,195,198,200,205,208,209,211,213,214,219,224,226,227,229,234,235,246,247,249,251,253,257,260,267,268,269,270,271,272,278,281,282,283,285,291,292,295,296,297,298,299,300,301,313,318,319,321,327,329,330,333,335,336,343,348,352,354,355,359,361,365,373,380,384,393,394,404,407,411,415,420,423,424,426,428,430,433,437,439,440,447,448,449],detil:108,devan:[9,395],devanathan:410,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,210,233,255,260,261,264,335,339,357,382,425],devemi:9,deviat:[227,233,251,359],devic:[1,3,12,15,17,210,333],device_typ:333,devin:[262,348],devis:382,dfactor:168,dff:443,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,319],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,264],dhi:[59,166,194,256],dhug:[227,260],dhugoniot:[227,260],dia:380,diagnost:[],diagon:[3,6,83,120,121,192,229,257,270,293],diagonalstyl:396,diagram:[41,118,143,163,188,253],diallo:363,diam:[168,169,256,327],diamet:[3,6,40,113,144,167,168,169,173,174,213,256,270,278,294,296,327,347,360,361,367,371,394,412,415,423,424,433],diamond:[321,357,380],diamter:[40,256],dick:6,dicsuss:226,dictat:[179,227],did:[3,12,326,353,354,355,361,384,408,410,431],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,140,292,318],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,94,96,97,120,122,123,124,125,127,130,131,132,133,134,136,137,138,144,145,147,152,163,164,166,167,168,169,172,174,177,179,181,183,188,189,190,191,192,193,194,198,204,205,206,207,208,209,210,213,214,216,226,229,230,231,232,234,235,237,239,242,244,245,246,249,251,253,255,257,260,261,262,265,268,270,273,274,275,276,278,281,282,283,286,287,288,290,293,294,295,296,299,303,304,313,315,317,318,319,321,322,324,325,327,328,330,331,332,333,334,335,339,343,344,346,347,348,353,355,357,360,361,362,364,367,369,370,372,373,380,381,382,383,384,386,390,392,393,394,395,396,397,405,406,407,408,410,412,415,416,417,418,420,421,423,425,426,427,428,431,432,433,435,437,438,440,441,443,447,448,449,450],differenti:[1,3,6,29,164,318,349,390,409],difficult:[192,253,333,363,432],difficulti:[273,392],diffract:[],diffus:[],digit:[2,3,169,303],dih_table1:164,dih_table2:164,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:190,dihydrid:357,dij:273,dilat:[],dim1:3,dim2:3,dim:[3,59,71,122,125,126,127,130,131,132,133,134,136,144,166,184,194,211,296,321,380,426,447,448,449],dimdim:448,dimems:252,dimens:[],dimension:[3,39,112,118,120,122,124,125,126,127,130,131,132,133,134,136,143,165,181,184,228,252,290,321,324,328,390,423,433],dimensionless:[105,120,290,319,396,415],dimer:[6,270,380],dimgrai:169,dimstr:[41,188],dinola:[257,281],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,167,280,443],dir1:434,dir2:434,dir:[1,3,4,8,11,12,227,251,260,277,390,392,393,421,434,448],dirac:120,direc:390,direct:[],directli:[3,6,8,9,11,12,87,113,120,167,168,175,200,207,211,216,252,271,282,294,296,297,298,299,321,325,333,334,335,340,342,343,349,352,355,357,369,373,384,387,395,404,421,433,434,435,441,448],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,60,170,193,212,255,261,264,278,287,288,328,332,334,335,339,346,348,349,355,356,358,365,366,377,380,381,382,386,390,391,392,393,396,406,408,409,410,421,423,424,425,434,448],disabl:[3,12,16,290,368,421,436],disadvantag:[6,188],disallow:[194,229],disappear:425,discard:[2,3,41,71,184,188,291,299,420,425,426],discontinu:[9,164,326,375],discourag:380,discov:[13,291],discret:[6,8,40,42,168,169,213,216],discuss:[],disk:[6,84,85,137,165,195,205,256,421],disloc:70,disord:[39,70],disp:[],dispar:394,disperion:[352,373],dispers:[3,6,7,9,142,252,318,319,343,352,373,378,384,393,407],displac:[],displace_atom:[],displace_box:59,displacemet:426,displai:[11,13,22,37,44,55,152,163,167,168,305,313,346,405],dispters:3,dissip:[6,206,213,252,287,288,341,353,361,378,379,405],dissolut:189,dist:[6,69,91,108,117,167,253,269,354,404,418,449],distanc:[3,6,7,9,12,20,21,29,39,43,45,46,47,48,49,51,53,54,55,56,58,59,61,63,64,66,69,71,72,73,74,75,76,77,81,86,89,90,93,103,104,105,106,108,114,115,116,117,118,120,133,139,142,144,145,146,147,151,166,167,168,169,177,181,184,185,189,190,191,192,194,195,196,199,205,211,216,226,227,228,229,233,241,251,252,256,260,261,268,269,270,273,274,275,276,277,278,285,286,288,289,290,293,295,296,297,298,299,300,304,318,319,321,324,326,328,329,330,333,336,337,338,339,340,341,342,343,344,345,347,349,350,351,352,353,354,355,356,357,359,360,361,362,363,367,368,369,370,371,372,373,374,375,376,377,378,379,380,383,384,385,386,387,388,389,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,421,423,426,432,433,437,441,443,447,449],distinct:[6,198,267,318,394],distinguish:[6,86,120,219,357],distort:334,distrbut:334,distribut:[],distro:[111,346,389,390],ditto:[8,11,12,14,15,16,17,18,115,190,421],div:8,divd:117,diverg:[3,12,39,270,288,425,443,450],divid:[3,6,16,41,91,112,117,121,141,142,152,163,169,181,182,183,188,194,251,286,293,298,318,326,328,358,393,432,440,448],divis:[6,216,339,367,377,420,423,441,448],dl_poli:7,dlambda:138,dlammps_async_imd:210,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,168],dlammps_gzip:[3,12,167,168,289,423,424,428],dlammps_jpeg:[3,12,168],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,168],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,167],dlen:433,dlmp_intel_offload:[12,16],dlo:[59,166,194,256],dlvo:[7,347,415],dm_lb:216,dmax:[278,324],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,93,102,104,105,106,107,109,111,112,114,117,119,121,123,124,137,139,141,144,145,146,152,163,167,168,169,170,172,173,174,179,180,181,182,183,184,185,186,195,205,213,214,224,229,230,234,235,239,246,247,248,249,256,259,270,275,278,281,282,283,292,296,299,301,303,305,313,317,326,327,328,333,334,335,338,346,348,349,355,356,358,363,364,366,367,380,381,382,384,386,389,390,391,396,405,406,408,410,412,421,423,424,425,426,428,431,432,433,440,441,448,449,450,451],docuement:394,dodgerblu:169,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,29,33,38,39,41,50,54,56,59,62,63,67,70,71,87,88,91,104,110,117,118,123,124,127,132,134,138,143,144,145,146,148,150,152,157,163,164,166,167,168,169,172,178,179,181,184,187,188,190,191,192,194,198,200,202,205,206,209,211,213,214,216,219,225,229,230,231,232,234,235,246,247,248,249,257,258,259,263,265,268,270,278,281,283,285,286,290,293,294,295,298,299,300,301,306,307,309,310,312,317,318,319,320,321,327,328,329,334,335,336,337,338,339,341,343,344,345,347,348,349,350,352,353,354,355,356,357,359,360,361,362,364,365,366,367,368,371,372,374,375,376,378,379,380,381,382,384,390,391,392,393,394,396,397,398,399,400,401,402,403,404,406,407,408,409,410,411,412,414,415,416,418,419,420,421,423,424,425,426,427,430,431,433,434,435,436,437,440,441,443,448,452],doegenomestolif:7,doesn:[3,7,8,12,144,167,179,184,185,275,327,329,333,335,348,356,366,392,393,406,408,409,410,423,425],dof:[3,8,112,123,124,137,181,270,449],dof_per_atom:[124,181],dof_per_chunk:[124,181],doff:[327,423],doi:[6,193],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,118,133,143,146,166,168,169,172,179,188,192,194,195,209,212,216,229,230,253,265,270,290,295,296,318,319,328,333,354,384,418,420,423,427,440],domin:[1,357,437],don:[0,8,11,12,13,116,147,175,200,214,259,299,380,421,423],donadio:282,done:[1,3,6,7,8,12,14,15,16,17,18,19,38,39,41,56,59,62,71,138,141,144,147,164,168,169,178,179,181,183,184,185,186,188,189,190,191,192,194,195,203,205,210,211,213,214,221,229,234,235,246,247,249,250,252,253,254,259,267,270,271,273,278,281,282,283,285,287,288,301,303,317,318,319,326,328,329,332,333,335,343,355,364,365,366,373,379,380,384,392,404,407,412,418,419,420,421,424,427,428,431,441,443,448,449],donor:363,dot:[121,140,175,200,208,228],doti:[339,390],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,39,87,194,203,258,299,303,317,319,332,333,339,358,362,392,393,419,423,427,431,436,448,449],dover:178,down:[3,6,7,8,11,39,71,192,213,278,294,333,357,384,422],downhil:[324,325],download:[5,7,8,9,11,12,13,17,210,365,391],downsid:6,downward:267,dozen:[8,12,107,172,392,393],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:222,dproduct:336,dr_ewald:[118,271],drag:[],dragforc:216,drai:[227,260],drain:[209,294,326],dramat:[59,166,189,190,191,192,194,229,278,281,282,319,333,384,420],drautz:339,draw:168,drawback:259,drawn:[167,168,169,206,418],drayleigh:[227,260],dreid:[],drfourth:105,drho:[113,334,355],drift:[6,103,105,206,207,213,214,225,268,278,432,440,443],drive:[11,12,176,192,194,208,229,251,257,270,297,328],driven:[6,156],driver:[6,12,14,15,172,203,210],drop:[3,169,353],droplet:364,drsquar:105,drude:[],dry:202,dsecriptor:365,dsf:[],dsmc:[],dstyle:256,dt_collis:216,dt_lb:216,dt_md:216,dt_srd:278,dtilt:[59,194],dtneb:437,dtqm:260,dtype:[115,190],dual:[17,278,333],dudarev:143,due:[1,3,6,9,10,12,16,17,19,40,54,57,58,61,66,70,71,74,75,81,86,88,89,90,93,102,103,104,105,106,110,116,118,120,121,122,123,125,127,130,131,132,133,134,136,137,139,143,144,147,148,167,168,172,175,176,183,187,189,190,191,192,193,194,195,200,201,202,203,206,207,210,211,213,214,215,216,219,220,221,225,226,227,228,229,233,241,251,254,256,268,269,270,272,275,277,278,279,281,282,283,284,285,287,288,290,294,295,297,298,299,301,319,324,326,328,329,330,350,353,355,359,360,364,378,379,384,390,392,394,395,404,407,408,410,413,415,416,418,420,423,424,425,432,437,440,441,443,448,449],duffi:290,duin:[9,261,266,392,393],duke:319,dummi:[12,29,409],dump1:428,dump2:428,dump:[],dump_atom:8,dump_custom:8,dump_modifi:[],dumpcustom:8,dumptimestep:428,dunbrack:[6,20,150,344,435],dunweg:[213,215],duplic:[2,3,14,15,16,17,18,19,41,42,145,188,207,251,423,447],dupont:[5,7,13],durat:[37,55,122,123,125,126,127,129,130,131,132,133,136,137,163,169,181,205,265,290,313,361,405],dure:[2,3,6,8,9,12,16,17,38,39,41,56,71,87,126,145,148,164,167,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,196,199,200,201,202,203,204,205,206,207,208,209,210,211,213,214,215,216,217,218,219,220,221,222,223,225,226,228,229,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,319,326,328,332,333,353,377,384,393,407,418,419,421,423,426,428,430,431,433,435,437,438,441,448,451,452],dvector:8,dvlo:415,dvx:6,dx_lb:216,dy3:143,dyamic:12,dyanam:6,dyanmic:437,dynam:[],dynamo:[5,334,355,380],dyne:447,dyre:374,dysam:426,e28637:29,e_1:339,e_2:339,e_b:358,e_e:357,e_hbond:363,e_i:[6,339,358],e_j:[6,339],e_k:[339,357],e_kl:6,e_lj:[335,352],e_n:[339,357],e_nn:357,e_pr:357,e_rebo:335,e_tors:335,eaa:304,eaat:151,each:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,66,67,68,70,71,72,73,74,75,76,77,78,80,81,83,85,87,89,90,93,94,95,96,97,98,99,100,101,102,103,104,105,106,109,110,111,112,113,114,115,116,117,118,119,120,121,123,124,125,126,127,128,131,132,133,134,136,137,138,139,140,141,142,143,144,147,148,150,151,152,153,154,155,156,157,158,159,161,162,163,164,166,167,168,169,170,171,172,173,174,175,176,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,205,206,207,208,209,210,211,212,213,214,215,216,217,219,220,221,222,223,225,226,227,228,229,231,232,233,234,235,236,237,238,239,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,261,262,263,265,267,270,271,272,273,274,275,276,277,278,279,280,281,282,283,285,288,289,290,291,292,293,294,295,296,298,299,300,301,303,304,306,307,308,309,310,312,313,314,317,318,319,321,325,326,327,328,329,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,357,358,359,360,361,362,363,364,367,368,369,370,371,372,373,374,375,376,377,378,379,380,383,384,385,386,387,389,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,410,411,412,413,414,415,416,417,418,420,421,423,424,425,426,427,428,430,431,432,433,435,437,438,440,441,443,447,448,449,450,452],eacn:[41,188],eam0d:252,eam3d:252,eam:[],eam_databas:13,eam_gener:13,eangl:441,earli:[41,181,183,184,185,186,188,264,271],earlier:[7,8,12,59,169,328,361,380,384,437],earliest:437,earth:357,easi:[6,7,8,11,13,87,121,167,173,174,175,176,184,187,200,208,209,211,213,214,272,281,282,283,295,298,300,327,423,426,431,433,449],easier:[8,9,13,16,167,168,252],easili:[8,11,168,169,294,328,420,430,439,448],eastwood:[318,319],eat:151,eatom:301,eaxmpl:6,eba:21,ebb13:151,ebb:21,ebond:[198,214,440,441],ebt:151,ec_ii:380,ec_ij:380,ec_jj:380,echo:[],eco:[392,393],ecoa:[392,393],ecoul:[107,198,214,392,393,441],ecp:[357,423],edg:[2,3,6,41,59,71,118,142,143,146,147,168,177,184,211,272,295,298,299,300,301,321,423,426,433],edge_histo:142,edge_threshold:142,edih:441,edim:286,edip:[],edit:[3,8,12,13,14,15,16,17,18,19,443],editor:13,edu:[7,9,11,13,355,378,389,392,393],edward:[9,17],eebt:151,eff:[],effect:[1,2,3,6,8,9,11,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,43,45,46,47,48,49,51,53,54,56,66,71,74,75,81,89,90,93,103,104,105,106,1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333,420],espresso:[9,264],essenti:[8,11,12,27,88,125,126,127,130,131,132,133,134,136,153,182,233,252,294,319,335,349,369,410,428,441],essex:29,establish:[87,209],estim:[1,3,6,10,12,38,41,56,91,121,178,188,199,227,278,285,318,319,324,384,393,407,437,441],esu:447,esub:380,eta:[6,216,229,260,261,263,294,356,358,360,390,409,447],eta_dot:229,eta_ij:390,eta_ji:358,etag:[40,423],etail:441,etap:229,etap_dot:229,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,17,39,40,42,54,61,68,89,90,91,94,109,110,113,115,121,122,124,125,126,127,128,130,131,132,133,134,136,138,144,146,147,148,157,167,168,169,172,178,179,180,181,183,184,185,186,189,190,194,195,203,205,206,213,229,256,267,271,290,291,299,303,317,318,326,327,328,329,331,355,356,364,377,379,388,392,393,406,408,410,418,421,423,424,425,430,432,433,437,439,440,441,443,447,448,450,452],ethernet:18,etol:[326,328,418,437],etot0:260,etot:[6,94,96,97,110,121,130,169,198,214,227,260,440,441],eu2:143,eu3:143,euler:[326,328],eulerian:178,euqat:398,europhi:216,evalu:[2,3,11,12,38,56,71,87,88,91,107,117,120,124,134,142,144,167,168,169,173,174,175,176,178,180,181,182,183,184,185,186,187,194,200,206,208,209,211,212,213,214,252,258,261,272,281,282,283,292,295,298,300,301,303,318,319,324,326,333,384,390,407,418,419,421,425,426,428,430,431,432,433,437,439,441,448,449],evalut:[303,421],evan:[132,247],evanseck:[6,20,150,344,435],evapor:[],evaul:[8,326],evdwl:[107,392,393,441],even:[3,6,8,12,15,16,17,18,34,39,41,52,57,59,61,63,70,71,119,145,146,160,164,167,169,172,173,174,179,180,181,183,184,185,186,188,189,190,192,194,195,198,211,214,227,229,230,252,265,267,270,271,278,286,290,293,295,299,301,311,318,324,326,328,333,338,357,358,361,364,384,394,413,423,424,426,428,429,430,432,433,435,438,440,441,443,452],evenli:[3,41,121,164,188,216,367,413,423],event:[],eventu:[3,6,12,15,146,261,437],ever:[54,56,212,278],evera:[347,360,394,405],everi:[0,1,2,3,6,8,11,12,15,16,39,41,71,72,91,113,119,132,147,167,168,169,170,172,173,174,175,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,199,202,203,205,207,209,210,211,216,217,225,229,230,233,250,251,252,256,257,258,259,260,261,262,263,265,267,268,270,271,273,274,278,280,281,282,283,284,285,286,289,290,291,292,293,301,303,317,319,328,329,330,333,353,354,364,377,392,393,401,417,418,419,423,425,427,428,430,431,432,437,438,439,441,448,452],everyth:[8,107],everywher:[116,371],eviri:357,evolut:[207,216,253,418],evolv:[216,253,291],ewald:[2,3,5,6,7,8,12,88,110,118,121,291,318,319,326,340,342,343,349,352,357,369,373,387,395,405,407,425],ewald_disp:352,ewalddisp:3,exact:[22,41,44,71,138,147,152,188,191,206,207,213,214,215,256,265,266,278,290,305,318,346,425,430,437,450,452],exactli:[3,6,12,14,17,38,41,56,59,71,91,123,128,135,144,164,173,174,183,188,194,199,206,213,214,215,230,240,241,248,252,260,278,283,284,297,333,346,353,355,361,364,367,378,384,407,425,426,433,437,448],exager:443,examin:[6,8,191,252],examp:[421,448],exampl:[],exce:[3,6,16,17,18,41,58,71,146,181,184,185,188,192,194,199,202,229,252,278,326,333,423,448],exceed:[3,41,59,188,194,229,278,431],excel:357,except:[1,2,5,6,8,11,14,16,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,108,109,112,117,121,122,123,124,125,126,127,128,130,131,132,133,134,135,136,137,144,148,150,151,152,153,154,155,156,158,159,161,162,163,164,166,167,169,172,175,181,182,183,187,188,192,194,201,204,205,208,211,213,215,229,230,231,232,233,234,235,236,240,241,244,246,247,248,249,253,262,263,270,272,273,275,278,281,283,284,290,294,301,303,304,305,306,307,308,309,312,313,314,318,319,321,323,327,328,329,331,332,333,334,335,337,340,341,342,343,344,345,346,347,348,349,351,352,353,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,379,381,385,386,387,389,392,393,394,395,397,405,406,407,408,409,410,412,414,415,416,418,420,421,423,425,426,428,431,432,433,434,435,437,441,443,447,448,449,451],excess:357,exchang:[2,3,6,8,9,61,62,172,178,179,205,213,262,270,286,290,293,318,333,357,438],exchange:318,excit:[9,357],exclud:[3,6,9,12,16,17,63,71,112,120,124,131,132,148,167,181,184,189,190,217,225,255,268,270,285,296,301,326,327,329,341,361,364,378,379,384,404,435],exclus:[1,3,9,12,16,87,333,348,432],excurs:418,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,145,168,210,264,303,317,320,332,419,421,431,434,437,448],exemplari:206,exemplifi:357,exert:[6,211,214,265,297,298,299,319],exhaust:[178,332,448],exhibit:[229,325,357,432],exist:[3,6,7,8,11,12,13,37,55,59,68,70,144,145,163,168,169,172,177,187,190,192,195,205,255,256,258,301,304,306,307,309,313,322,327,333,364,392,413,419,421,423,424,425,434,435,436,448,449,450],exit:[2,3,11,12,41,57,167,188,317,332,421,422,431,440,448],exlanatori:3,exp:[],expand:[],expans:[12,120,167,434],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,102,125,136,142,164,188,200,205,207,226,251,257,259,260,265,270,301,319,329,346,380,384,418,421,423,425,428,432,437,448],expens:[6,10,71,169,251,255,270,290,301,318,319,329,333,421],experi:[6,13,15,17,187,195,210,219,228,257,269,270,324,328,353,384,432,437],experienc:[6,12,218,219],experiment:[318,333,437],expert:12,expertis:7,explain:[1,3,6,8,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,92,124,132,164,167,168,169,172,181,182,186,188,190,192,194,229,251,259,270,275,301,303,317,318,321,327,328,332,338,355,367,397,412,416,421,424,425,428,430,433,443,448,452],explan:[3,6,59,113,120,167,181,228,251,364,417,420,421,423,432],explanatori:[3,8,117,167,180,181,183,184,185,270,327,420,448],explantori:[3,266],explic:383,explicit:[6,9,11,22,44,77,87,113,116,138,152,173,174,194,305,323,335,336,339,344,346,355,357,368,378,411,417,420,424,427],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,109,112,122,131,134,142,144,150,151,153,154,155,156,158,159,161,162,164,167,169,175,184,187,194,201,204,206,208,213,229,231,232,233,234,235,236,244,246,247,249,259,260,262,270,272,273,281,283,284,290,294,304,306,307,308,309,312,314,327,333,334,335,337,340,341,342,343,344,345,346,347,348,349,350,352,353,354,355,356,358,359,360,361,362,363,364,367,368,369,370,371,372,373,374,375,376,377,378,381,384,385,386,387,389,394,395,397,398,399,400,401,402,403,405,406,407,408,409,410,411,412,414,415,416,423,425,432,433,435,436,443],explictli:[16,436],exploit:[9,15,17,253],explor:[118,143],expon:[3,261,263,355,360,363,377,383,395],exponenti:[87,390,406,416,437,448],expos:11,exposit:[178,353,354],express:[6,120,130,144,173,174,192,226,251,261,290,296,303,339,355,357,371,380,396,405,448],expressiont:339,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,94,97,98,107,109,117,119,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,172,175,176,179,186,187,193,196,200,203,204,205,207,208,209,211,213,215,227,229,233,241,251,252,268,269,270,272,274,275,277,281,282,283,284,285,287,288,290,292,295,299,300,360,380,393,394,396,440,441],extent:[1,3,41,45,57,71,142,146,167,177,184,188,211,297,300,318,321,335,407,420,423,426],exterior:[3,6,299],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,102,109,110,112,118,121,122,123,125,127,130,131,132,133,134,136,137,143,144,145,146,150,169,183,188,190,229,258,259,260,270,278,326,327,330,331,352,361,364,367,380,384,420,421,423,426,435,443,448],extract:[3,6,11,13,36,63,87,107,115,117,119,173,174,263,328,349,358,380,396,421,428,440],extract_atom:11,extract_comput:[11,421],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,168,192,194,229,288,357,409,443],extrema:377,extrins:178,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[140,292],f_a:[408,409,410],f_ave:117,f_c:409,f_f:410,f_fix_id:260,f_harm:288,f_i:390,f_id:[6,71,117,119,167,172,180,181,182,183,184,185,186,224,280,292,441,448],f_ij:390,f_indent:186,f_int:287,f_jj:91,f_k:390,f_langevin:290,f_max:[260,265],f_msst:227,f_r:[214,408,409,410],f_sigma:339,f_solid:288,f_ss:6,f_temp:214,face:[3,6,57,59,71,132,142,146,177,184,185,295,297,298,299,300,321,360,380,394,423,426],face_threshold:142,facet:142,facil:[0,12],facilit:[6,13],fact:[6,8,16,207,278,288,361,435],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,118,120,138,143,146,150,161,167,168,169,173,174,182,188,192,194,195,205,210,213,215,216,227,229,230,233,253,257,269,273,278,282,286,293,294,295,299,309,319,321,333,335,336,339,340,342,344,349,350,351,353,357,361,368,369,380,384,386,387,393,395,397,406,411,420,423,426,427,432,435,437,438,441,443,447,448],factori:[3,421],factoriz:318,fail:[3,11,12,59,148,192,195,318,326,328,351,393,421],fairli:[11,384,432,437],faken:73,falcon:210,fall:[3,6,169,183,256,421],fals:[86,301,303,448],fame:8,famili:420,familiar:[0,11],fan:390,far:[3,6,12,17,57,59,61,86,167,169,170,188,189,190,192,195,205,229,251,269,270,278,295,306,309,324,328,329,412,421,423,428,441],farago:213,farrel:[408,410],farther:167,fashion:[6,8,41,71,144,169,172,173,174,179,184,188,190,195,205,207,211,226,227,229,231,232,233,234,235,243,246,247,248,249,259,260,262,270,274,277,280,288,290,294,295,296,298,300,328,364,378,426,435,448,451],fasolino:366,fast:[6,7,9,12,13,17,39,167,238,260,291,318,319,341,378,379,405,407,425,430,432,441,449,452],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,105,109,112,122,131,150,151,153,154,155,156,158,159,161,162,164,167,169,172,175,187,188,201,204,208,212,213,229,231,232,233,234,235,236,244,246,247,249,257,261,262,270,272,273,278,281,283,285,287,290,294,304,306,307,308,309,312,314,318,319,330,331,333,334,335,337,339,340,341,342,343,344,345,346,347,348,349,352,353,355,356,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,381,385,386,387,389,394,395,397,405,406,407,408,409,410,412,414,415,416,418,432,436,443],fastest:[6,14,17,132,184,290,291,333,420],fatal:[3,440],fault:[70,393],faulti:12,fava:360,favor:191,favorit:7,fbmc:285,fcc:[],fcm:[243,448],fdirect:198,fdotr:365,fdti:87,fe2:143,fe3:143,fe_md_boundari:178,featu:8,featur:[],fecr:355,feedback:[7,210],feel:[7,210,211,219,251,299,301,328,384],felling:382,felt:299,femtosecond:447,fene:[],fennel:[349,369],fep:[],ferguson:[6,150,435],fermi:[1,12,15,130,333,410],fermion:[9,357],ferrand:[9,13],few:[1,3,4,5,6,7,10,11,12,13,14,17,18,39,170,180,181,182,183,184,185,186,214,229,256,259,261,273,292,318,326,327,328,335,420,423,428,432,434,448,450],fewer:[1,3,11,15,16,61,219,432],fewest:3,fextern:203,feynman:253,fff:421,ffield:[348,358,392,393],ffmpeg:[3,12,168],ffplai:168,fft:[1,3,7,12,14,15,88,109,110,121,252,318,319,432],fft_inc:[12,319],fft_lib:12,fft_path:12,fftbench:318,fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],fictiti:[6,175,176,200,203,207,253,269,349,369,373,404],field1:[424,428],field2:424,field:[],fifth:[275,386],figur:[1,3,8,11,12,260,420,421],fij:352,file0:251,file1:[11,13,251,289,303,327,428,430,434],file2:[11,13,289,303,327,428,430,434],file:[],filenam:[3,12,13,38,41,56,164,167,168,169,170,178,181,182,183,184,185,186,188,193,251,255,258,261,262,263,266,267,270,271,289,290,315,316,317,328,334,335,339,349,355,356,358,366,380,381,382,386,390,391,392,393,396,406,407,408,409,410,419,420,421,424,425,430,434,441,448,450,451,452],filennam:430,filep:[3,167,169,425,430,452],filepo:267,fill:[7,144,168,256,290,321,329,339,393,426],filter:[169,178],final_integr:8,final_integrate_respa:8,finchham:[6,126,351],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,117,147,164,170,179,191,192,202,205,228,251,257,265,269,324,326,328,329,349,364,369,373,380,405,407,443,448],find_custom:8,fine:[16,17,148,175,200,288,329,333,448],finer:[120,144,448],finest:318,finger:[144,166,226,426],finish:[6,11,41,188,303,315,317,318,330,332,333,412,428,448,449],finit:[],finni:[7,355,405],finvers:198,fiorin:[9,193],fire:[324,325,326,328,437],firebrick:169,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,103,104,105,112,116,117,121,129,132,138,140,142,143,145,146,147,151,164,167,168,169,170,172,179,181,182,183,184,185,186,188,191,194,205,206,211,216,226,227,228,229,251,253,258,259,260,262,267,270,273,274,275,276,278,279,280,287,288,289,290,292,296,301,303,304,310,321,326,327,328,329,332,333,334,335,338,339,340,342,344,346,348,349,355,357,358,361,362,365,366,368,369,373,378,379,380,382,384,386,390,392,393,396,404,406,407,408,409,410,418,419,420,421,423,424,425,428,430,432,435,436,437,440,441,443,448,449,450,452],fischer:[6,9,19,20,150,344,435],fit:[3,6,9,12,38,56,164,269,278,335,339,366,380,384,400,407,409,431,448],five:[73,130,260,327,339,381,423,437],fix:[],fix_adapt:[138,174,377],fix_atom_swap:205,fix_bal:62,fix_deposit:[3,179,205,256],fix_evapor:[179,205],fix_flux:178,fix_gcmc:[179,327],fix_gl:207,fix_gld:207,fix_grav:256,fix_id:[3,192,227,229,231,232,233,234,235,257,260],fix_modifi:[],fix_mov:[166,296],fix_nh:8,fix_npt:207,fix_nvt:[179,205],fix_poem:[3,6],fix_pour:[3,195],fix_qbmsst:9,fix_qeq:[3,348],fix_rattl:273,fix_reax_bond:392,fix_rigid:[219,338],fix_saed_vtk:271,fix_setforc:8,fix_shak:273,fix_srd:3,fix_styl:233,fix_temp_rescal:284,fixedpoint:[192,229],fixextern:203,fixid:178,fji:352,flag1:[197,331],flag2:[197,331],flag:[3,8,11,12,14,15,16,17,18,40,66,74,75,81,86,89,90,93,103,104,106,118,139,143,147,167,168,169,170,186,191,193,197,210,213,217,219,225,226,252,259,270,275,277,278,285,289,298,301,316,319,327,331,332,333,335,363,368,380,404,418,420,421,423,424,425,427,428,429,433,448],flag_buck:343,flag_coul:[343,352,373],flag_lj:[352,373],flagfld:[341,378,379],flaghi:[3,341,378,379],flaglog:[341,378,379],flagn:197,flagvf:[341,378,379],flat:[6,290,295,296,300],flavor:[2,7,12,384],fld:[9,295,341,378,379],flen:336,flex_press:336,flexibl:[3,6,8,145,168,181,184,193,207,230,286,293,357,409,441],flip:[3,6,194,229,297,298],floor:448,flop:12,floralwhit:169,flow:[],fluctuat:[6,64,87,192,205,206,213,216,229,233,251,252,288,290,312],fluid:[],fluid_veloc:220,flush:[3,169,440],flux:[],flv:168,fly:[7,9,12,41,168,172,178,195,198,270,273,291,339,441,443],fmackai:9,fmag:196,fmass:253,fmax:[326,441],fmomentum:198,fmsec:[2,169,213,214,226,229,257,270,281,282,432,442,447,449],fname:317,fno:12,fnorm:[326,441],fnpt:198,fnvt:198,foce:364,fock:336,focu:273,fogarti:[9,263,393],foil:[120,251,396],fold:[276,432],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,120,121,123,124,130,132,137,140,142,144,145,150,153,154,155,156,158,159,161,162,164,167,168,169,172,178,179,180,181,182,183,184,185,186,188,193,194,195,198,199,203,205,206,207,210,212,213,214,216,219,227,229,233,234,235,246,247,249,252,253,255,258,259,260,261,263,265,267,269,270,271,273,280,281,282,283,286,287,288,289,290,292,293,301,302,306,307,308,309,312,314,316,321,323,326,327,328,333,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,351,352,353,354,355,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,39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288,319,356,379,392,393,421,448],interf:333,interfac:[],interfer:[229,335],interg:[6,443],intergr:[432,436],interi:379,interior:[3,6,41,299,426],interlac:380,interleav:[6,144,431],intermedi:[6,12,59,168,228,251,312,328,421,422,431,435],intermix:418,intermolecular:335,intern:[0,2,3,5,6,9,11,16,20,21,24,28,32,35,36,39,40,42,63,87,99,101,118,121,124,126,143,151,164,168,169,172,173,174,178,190,194,198,210,222,223,227,229,233,252,270,274,304,306,309,312,316,326,327,398,399,407,421,423,425,428,437,440,441,447,448,449,450],internal_element_set:178,internal_quadratur:178,internet:212,interpenetr:380,interpentr:[399,400,402],interpol:[6,15,38,56,100,164,168,169,178,216,251,318,319,328,339,384,393,401,407,408],interpret:[2,6,11,168,183,361,397,418,421,437,448],interrupt:260,intersect:[3,6,118,169,299,301,426],intersert:299,interspers:326,interstiti:142,intertia:[3,93],interv:[3,6,91,182,213,260,265,266,401,418,437,448],intestieti:118,intial:[6,333,335],intiial:[41,428],intiti:[3,277],intra:270,intra_energi:205,intramolecular:[29,205],introduc:[6,9,168,229,260,265,270,312,318,334,349,357,369,373,377,406,437],introduct:[],intsal:16,intuit:321,inv:[118,143,271],invalid:[3,12,71,89,147,241,328,378,379,425],invari:120,invent:273,invers:[],invert:[6,148,252],invis:299,invoc:[142,191,333,421],invok:[1,3,6,7,8,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,59,63,66,71,74,75,81,87,88,89,90,93,103,104,106,109,110,111,112,117,122,131,138,139,142,144,145,147,148,150,151,153,154,155,156,158,159,161,162,164,167,168,169,170,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,196,197,199,200,201,202,203,204,205,206,208,209,210,211,213,214,215,216,217,218,219,220,221,222,223,225,226,228,229,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,261,262,263,264,265,266,267,268,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,304,306,307,308,309,312,314,317,318,319,320,321,326,328,333,334,335,337,340,341,342,343,344,345,347,348,349,352,353,355,356,358,359,360,361,362,363,364,365,367,369,370,371,372,373,374,375,376,377,378,379,381,384,385,386,387,389,394,395,396,397,406,407,408,409,410,412,413,414,415,416,417,420,421,422,424,426,428,431,432,434,435,437,440,441,443,448,449],invokd:3,involv:[3,6,7,8,12,63,108,115,116,117,124,148,172,189,205,216,255,258,263,278,318,325,326,328,338,354,360,406,408,410,419,420,426,428,432,437],ioff:[327,423],ion:[6,7,250,275,290,319,339,350,358,359,380,405,410,416,423,443],ionic:[6,9,340,342,350,357,358,387,443],ioniz:[9,348,357],iparam:[3,190],ipi:[],ipp:[],ir3:143,ir4:143,irregular:[6,41,58,188,192,194,229,270],irrelev:386,irrespect:[378,379],irrevers:198,isbn:415,isel:[318,319],isenthalp:[229,230,231,232],ismail:[318,319,343,373],isn:[3,8,11,12,209],iso:[3,192,198,214,229,230,231,232,233,234,235,257,265,270,443],isobar:[229,230,234,235],isodem:357,isol:[3,147,301],isomorph:253,isotherm:[205,229,230,234,235,257],isotrop:[6,213,257,318,319,341,360,378,379],isovolum:271,isralewitz:274,issu:[1,3,6,9,11,12,13,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,59,71,73,81,103,109,112,122,131,150,151,153,154,155,156,158,159,161,162,164,168,175,178,187,191,192,195,200,201,204,205,208,213,227,229,231,232,233,234,235,236,244,246,247,249,253,257,259,262,270,272,273,277,281,282,283,288,294,300,303,304,306,307,308,309,312,314,319,327,328,331,334,335,337,340,341,342,343,344,345,347,348,349,352,353,355,356,358,359,360,361,362,363,367,369,370,371,372,373,374,375,376,377,378,381,385,386,387,389,394,395,397,404,406,407,408,409,410,412,414,415,416,423,425,432,435,440,441,448,449],ital:[392,393],itali:13,item:[6,7,8,41,167,169,188],iter:[3,6,12,39,41,63,175,176,187,188,192,198,200,203,211,252,261,262,270,273,285,301,303,317,324,325,326,328,332,418,428,432,437,441,448],ith:[71,117,119,180,181,182,183,184,185,186,280,292,441,448],itself:[2,3,4,6,7,8,9,11,12,13,18,42,59,91,107,135,167,168,169,170,182,193,198,214,224,228,264,270,290,301,303,327,328,349,358,360,364,365,407,421,427,430,431,435,448,452],ityp:[3,115,116,144,177,190,263,413],itype1:116,itype2:116,itypen:116,ivector:8,ivori:169,ixcm:270,ixi:[42,93,270,327,448],ixx:[42,93,270,327,448],ixz:[42,93,270,327,448],iycm:270,iyi:[42,93,270,327,448],iyz:[42,93,270,327,448],izcm:270,izrailev:274,izumi:409,izz:[42,93,270,327,448],j0jt:91,j20:182,j_m:120,jac:[6,150,435],jackson:383,jacobi:3,jacobsen:325,jagreat:13,jame:[9,19],janssen:251,januari:380,jaramillo:[7,9,13,357],jarzynski:274,jatempl:9,jcc:9,jcp:295,jec:13,jeff:13,jello:229,jensen:[213,318],jeremi:[9,382],jerom:9,jewett:13,jiang:[214,443],jiao:[9,13],jiht:[7,9],jik:339,jim:7,jku:7,jmake:12,jmm:120,joannopoulo:227,job:[12,60,273,431],jochim:[229,230],john:[7,13],johnson:13,join:[6,426],joint:[3,255,363],jon:[9,70],jonathan:9,jone:[1,3,6,7,9,10,12,13,45,46,64,87,1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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso_e/atom command","compute meso_rho/atom command","compute meso_t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute sna/atom command","compute stress/atom command","compute temp command","compute temp/asphere command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":189,"default":[37,39,40,55,57,58,59,61,62,71,87,88,102,103,105,107,118,120,124,132,133,137,143,144,147,149,163,165,166,167,168,169,170,171,173,174,175,177,178,179,181,184,185,186,189,190,192,193,194,195,199,202,205,206,211,213,214,215,216,217,219,224,227,229,230,233,247,248,252,253,256,257,258,259,260,262,265,267,268,270,271,278,280,285,286,287,288,291,293,295,297,301,313,316,318,319,321,322,324,325,327,329,330,331,333,336,339,341,357,378,379,384,392,393,404,405,418,419,420,423,424,426,428,430,431,432,435,437,439,440,441,442,447,449,450,451],"function":448,"long":[340,342,343,344,345,349,351,352,369,373,377,387,395],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[173,174],addforc:175,addit:[12,13],addtorqu:176,adiabat:6,adp:334,airebo:335,alloi:355,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:177,arrai:6,aspher:[6,82,123,231,234,237,238,246],atc:[9,178],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,95,96,99,100,101,110,111,113,120,121,142,177,179,180,259,448],atom_modifi:39,atom_styl:40,attract:5,aveforc:187,awpmd:[9,336],balanc:[41,188],barostat:6,basal:67,beck:337,berendsen:[257,281],between:6,binary2txt:13,bodi:[6,8,42,68,239,338],bond:[8,13,69,189,190,191,266],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:339,born:[340,351],boundari:[7,57],box:[6,58,192],brownian:341,buck:[342,343,351],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,150,344,377],chunk:[6,66,71,75,90,93,104,106,114,124,139,141,181],citat:7,class2:[21,43,151,304,345],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[295,347,415],colvar:[9,13,193],com:[74,75,125],comb3:348,comb:[262,348],come:5,comm_modifi:61,comm_styl:62,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,445,446,447,448,449,450,451,452],common:3,comparison:1,compos:6,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,448],compute_modifi:102,condit:7,conduct:[6,286],constant:6,constraint:7,contact:76,coord:77,core:6,correl:182,cosin:[23,24,25,26,27,28,153],cossq:306,coul:[340,342,343,344,345,349,350,351,362,369,373,377,387,395],coupl:6,creat:190,create_atom:144,create_bond:145,create_box:146,createatom:13,creation:7,csld:282,csvr:282,cubic:371,cuda:[9,14,109,112,122,131,175,187,201,204,208,229,236,272,273,281,283,294,340,342,344,345,355,361,362,369,370,372,375,385,406,408],custom:8,cut:[49,336,342,345,349,352,357,359,369,370,377,383,387],cvff:307,damag:78,data2xmovi:13,data:6,databas:13,deby:[349,369],deform:[127,128,194],delete_atom:147,delete_bond:148,delta:24,deposit:195,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,16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\ No newline at end of file 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12,15,17,39,41,71,91,164,179,184,188,189,190,195,202,205,211,212,269,273,278,286,288,293,301,303,317,326,327,328,329,330,333,354,365,368,384,393,404,418,420,421,423,431,437,440,441],checkf:164,checkqeq:393,checku:164,chem:[6,13,20,21,25,39,40,43,45,46,87,88,112,121,150,151,161,193,198,206,207,214,216,228,229,230,247,248,253,257,260,262,270,274,278,281,282,285,286,287,288,295,304,312,314,318,319,325,328,335,340,344,345,348,349,350,352,353,357,359,360,362,363,369,373,374,377,380,383,384,387,404,411,432,435,437,443],chemic:[9,118,138,143,167,178,179,205,261,266,267,285,319,392,393,400],chemistri:[9,260,261,263,339,357,392,393],chen:290,cheng:348,chenoweth:[392,393],chenoweth_2008:[392,393],chi:[92,133,166,251,261,263,358,360,449],chiefli:391,child:8,chip:[7,12,17,333,436],chipot:193,chiral:312,chmod:[11,12],cho:380,chocol:[7,169],choic:[3,6,12,15,16,18,40,41,54,87,121,123,137,148,164,181,184,185,188,191,194,195,207,213,216,227,229,253,261,270,285,313,319,324,325,328,330,333,364,377,384,388,423,432,433,436,437,442,443,447],choos:[1,3,6,7,8,12,16,17,18,29,39,54,87,117,134,135,168,189,190,191,192,195,202,213,216,227,229,231,232,233,234,235,257,278,282,296,318,319,325,413,418,420,432,438],chose:[408,410],chosen:[2,3,6,12,17,120,144,147,156,164,168,174,179,192,195,202,205,206,214,216,227,229,233,253,256,267,278,282,285,286,291,293,294,300,319,320,325,333,357,361,367,368,371,395,408,418,432,437,443],chri:142,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[66,75,90,93,104,106,114,124,139,141,181],chute:[4,10,208],ciccotti:273,cieplak:[6,150,435],cii:182,cij:182,circular:[3,6,123,165],circumst:18,circumv:265,citat:[],cite:[3,7,8,12,213],cko:2,cl1:143,clarendon:[29,352],clarifi:[7,408,410],clariti:303,clark:387,class2:[],classic:[0,3,5,6,7,8,9,203,253,260,265,290,314,357],classifi:[9,405],claus:421,clean:[6,12,14,15,17,431],cleanli:[422,451],clear:[],clearli:7,clebsch:120,clermont:[9,13],clever:427,click:[2,11,22,37,44,55,144,152,163,168,210,305,313,328,346,405],client:[210,212],climb:[228,328,437],clinic:[7,13],clo:[133,166,449],clock:[12,418,437],clockwis:296,close:[3,6,11,12,13,39,41,67,121,147,167,190,191,192,207,214,216,229,247,270,273,296,299,317,319,322,324,325,328,333,335,339,349,350,380,384,410,427,433,443,445],closer:[3,41,116,142,166,167,188,192,196,287,328],closest:[190,251,270,293,360,394,404,413],cloud:443,clovertown:18,clsuter:72,clump1:[255,270],clump2:[255,270],clump3:[255,270],clump:270,cluster:[],clutter:[3,9],cmap:423,cmatrix:207,cmax:380,cmd:[11,12,253,434],cmin:380,cmm:[],cn1:182,cn2:182,cna:[],cnn:182,cnr:[9,13],cnt:[364,427],co2:[40,143,273,327],coars:[7,9,29,36,40,54,156,255,270,278,362,395,435],coarser:[319,448],coarsest:120,code:[],coeff:[3,7,8,12,21,22,33,44,50,150,151,152,157,304,305,310,346,364,368,384,397,423,425],coeffcient:423,coeffici:[],coefficienct:353,coefficient0:355,coefficient1:355,coeffieci:[6,337],coeffincientn:355,coexist:[9,205,357],cohes:[6,358,380],coincid:[205,299,344,378,379,418],cold:[6,129,209,329,443],coldest:286,coleman8:9,coleman:[9,118,143,271],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,93,98,104,106,114,124,132,139,141,144,167,169,181,193,219,225,255,265,268,270,301,318,327,329,347,367,423,430,436,452],collid:[199,278,300],colliex:143,collinear:[3,255],collis:[3,216,278,296,300,354,361,416],colllis:278,colloid:[],colombo:39,colon:[170,301,424],color1:169,color2:169,color:[3,9,41,167,168,169,188,206,260,265],column:[3,6,9,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,104,106,108,110,113,114,115,116,117,119,120,121,124,132,139,141,142,143,164,167,169,172,180,181,182,183,184,185,186,219,226,227,260,270,279,280,290,300,359,363,392,393,424,438,440,448],colvar:[],colvarmodul:12,com:[],comamnd:194,comand:[191,425],comannd:333,comb3:[],comb:[],comb_1:262,comb_2:262,combiant:350,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,92,108,115,123,137,167,168,178,183,210,219,229,253,259,282,291,299,302,304,318,319,321,325,333,347,349,350,357,358,364,376,377,396,406,408,410,415,426,431,443,448],come:[],comfort:[12,13],comm:[0,3,12,61,73,210,212,213,319,328,333,353,384,389,407],comm_modifi:[],comm_styl:[],command:[],comment:[2,7,11,12,38,56,150,164,167,214,270,290,327,328,334,355,356,358,368,380,386,393,396,406,407,408,409,410,420,421,423,443,448],commerci:7,commmand:[3,6,12,59,107,248,417,418,420,437,451],common:[],commonli:[3,6,12,17,25,57,59,105,146,167,168,170,314,362,371,396,408,410,423,426,435],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,147,148,168,169,188,189,190,192,193,194,210,212,216,218,219,220,229,252,259,261,262,263,270,278,290,301,318,329,330,331,333,354,388,420,421,425,432,433,450,452],communc:318,comp:[7,212,213,273,319,328,357,384,389,394,403,407,409],compact:[63,172,346,405],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,110,118,127,142,143,152,163,169,198,261,301,303,318,319,326,328,380,418,437,438,443,447],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,151,152,163,304,305,313,345,405],compat:[3,5,7,8,9,11,12,13,17,18,41,71,117,119,155,167,170,174,180,181,182,183,184,185,186,188,252,264,282,285,292,295,298,318,333,365,384,407,420,421,448],compens:[6,189,190,268,329,357],compet:289,competit:319,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,142,167,168,170,210,289,319,333,423,424,428],compl:17,complain:[12,17],complement:380,complementari:[7,349,369],complet:[3,6,9,12,15,41,59,71,169,184,188,193,219,253,256,259,278,289,291,303,317,328,333,358,412,418,423,428,431,435,437,440,443,448],complex:[6,8,11,12,13,25,40,42,62,120,132,144,145,216,299,316,328,357,407,421,423,426,448],compli:[285,289],complic:[6,7,9,12,13,179,205,421],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,93,94,97,104,105,106,107,108,109,110,112,113,117,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,136,137,139,140,141,167,168,169,175,176,180,181,182,183,184,185,186,187,191,192,194,195,200,203,208,212,213,216,219,221,225,226,228,229,230,233,234,235,246,247,249,250,252,253,254,257,268,270,272,273,274,275,278,281,282,283,285,292,293,298,299,300,318,321,325,326,327,328,333,353,357,361,378,379,396,423,424,433,441,448,449],componenet:6,composit:[6,179,216,355],compound:[348,357,358],compres:[71,114,181],compress:[3,6,59,71,114,147,167,168,169,181,194,227,233,257,260],compris:[40,299,367,394,412],compton:[118,143],comptu:[3,6],compuat:319,comput:[],computation:[3,6,189,190,290,339],computational:443,compute_arrai:8,compute_fep:[174,377],compute_group_group:205,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[118,271],compute_scalar:8,compute_temp:8,compute_ti:174,compute_vector:8,compute_xrd:143,concaten:[2,3,451],concav:299,concentr:355,concept:[6,124,134,181,432],conceptu:[3,6,71,132,192,194,328,349,364,380,428],concern:[6,73,87,206],concis:[11,289],conclud:12,concret:8,concurr:[9,16,319],conden:[290,408,410],condens:[6,126,290,335,351,355,369],condit:[],conducit:6,conduct:[],cone:426,confid:[3,437],config:[12,167,420],configfil:193,configur:[1,6,12,15,17,38,59,146,164,166,167,168,172,192,193,194,195,199,205,212,213,241,253,261,289,316,326,328,335,339,356,380,406,408,410,418,423,425,426,437],confin:[423,437],conflict:[3,40,384,421],conform:[3,6,13,59,191,192,228,269,274,289,312,328,357,435],confus:3,conjuct:353,conjug:[7,8,213,325,357,392,393],conjunct:[6,7,71,86,87,114,127,132,138,144,148,169,173,174,213,216,220,241,256,257,261,262,263,265,270,278,286,293,298,318,319,328,340,342,346,349,353,357,363,369,387,395,411,423,426,430,443,452],connect:[3,6,87,129,147,191,210,255,270,273,275,328,350,361,404,410,420,421,427,443],conput:3,consecut:[3,11,12,39,71,144,169,173,174,195,210,211,349,369,373,418,424,426],consequ:[1,6,290,368,437],conserv:[3,172,179,191,198,199,206,209,213,215,216,220,225,227,229,241,270,273,281,282,286,293,294,298,328,352,353,361,375,432,437],consid:[6,9,70,71,78,87,115,129,130,147,167,169,173,174,180,182,184,188,190,191,195,217,230,252,270,285,286,289,290,293,319,346,357,364,393,394,404,418,419,421,424,425,426,428,431,433,441,443,448],consider:[6,8,213,214,281,282,283,333,432],consist:[3,6,8,9,11,12,40,42,65,69,79,92,104,108,111,112,115,124,127,129,144,156,166,170,175,176,181,194,195,198,200,203,206,213,214,215,226,229,231,232,233,234,235,236,237,239,240,241,242,244,245,246,247,248,249,257,260,265,267,269,270,281,282,283,284,294,318,319,321,327,328,333,335,339,341,347,349,357,360,378,379,380,384,394,407,413,421,423,424,426,427,428,435,443,448],consistent_fe_initi:178,consit:270,constant:[],constitu:[3,6,219,270,295,299,347,394],constrain:[3,6,8,122,123,124,125,127,130,131,132,133,134,136,137,172,181,195,205,206,211,219,223,255,256,268,270,273,276,286,293,326,327,357,428,435,443],constraint:[],construct:[6,8,14,38,54,56,61,64,67,70,72,73,77,118,120,143,192,229,252,269,299,329,333,352,384,404,406,407,426,427,448],constructor:8,consult:393,consum:[1,265,388,448],consumpt:316,contact:[],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,116,118,120,124,132,142,143,144,146,150,152,163,164,167,168,169,170,172,173,174,178,180,181,182,183,184,185,186,188,193,195,200,207,211,212,213,214,216,227,241,251,252,255,256,258,260,263,267,270,271,278,285,289,290,299,300,303,317,319,327,328,331,332,334,335,336,339,348,349,352,355,356,357,364,365,380,386,390,391,392,393,396,406,407,408,409,410,411,418,419,420,421,423,424,425,426,428,430,432,435,437,440,441,443,448,450,452],content:[12,18,393,439,441],context:[3,6,8,12,17,117,169,189,190,195,255,267,294,325,415,423,430,439,447,448,449],contibut:70,contigu:420,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,103,104,140,169,172,173,174,179,181,182,183,184,185,186,188,191,192,193,194,195,205,206,207,209,210,211,213,214,215,221,226,227,229,231,232,233,234,235,246,247,248,249,254,256,259,260,270,271,274,277,278,280,287,288,290,296,299,303,317,332,333,339,353,354,371,374,392,393,394,409,418,421,423,425,426,431,437,440,441,448,450],continuum:[6,7,9,178,290],contour_integr:178,contract:[59,192,194,229,257,270],contradictori:3,contrain:273,contraint:241,contrari:[207,214],contrast:[1,6,42,55,64,129,194,301,415,451],contrib:290,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,93,102,104,106,107,108,109,110,112,114,117,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,174,179,180,181,182,183,184,185,186,192,205,213,216,219,220,224,230,247,248,255,256,264,267,270,271,273,292,318,326,328,336,353,354,355,357,364,378,379,384,392,393,435,441,443],contributor:12,control:[3,5,6,7,8,11,13,16,27,29,41,87,91,120,153,167,168,172,178,179,188,192,193,194,209,210,213,214,229,231,232,233,234,235,257,262,270,281,282,283,290,294,316,318,330,357,360,392,393,406,410,418,420,432,438,439],control_typ:178,controlfil:393,convect:91,conveni:[6,12,29,167,170,186,271,321,396,448],convent:[3,8,9,29,155,162,163,169,269,275,302,355,357,448],converg:[3,6,41,88,167,168,170,175,188,191,192,200,203,233,260,262,265,269,273,324,325,326,328,348,349,369,418,430,437],convers:[3,8,120,168,169,179,182,257,318,349,350,351,357,369,373,377,387,421,437,447],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,144,151,167,168,169,186,227,301,304,306,309,312,321,328,334,355,408,410,416,421,423,424,425,430,440,443,447,448,450,452],convex:299,convinc:[7,12],cooki:7,cool:[7,134,209,268],cooordin:167,cooper:[5,7],coord123:114,coord1:[3,114,181,184,185],coord2:[3,114,181,184,185],coord3:[3,114,181,184,185],coord:[],coordiat:326,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,93,103,104,106,113,114,116,120,127,133,139,141,142,144,148,166,167,168,169,170,172,175,180,181,183,184,185,188,189,190,191,192,193,194,195,198,200,201,203,205,208,209,210,211,212,213,214,226,228,229,231,232,234,235,247,250,251,252,255,256,257,267,268,270,272,273,274,275,276,277,278,280,288,289,290,297,298,300,301,321,326,327,328,333,334,335,338,356,418,423,424,426,428,431,433,437,443,448,449],coordn:[114,181],coorind:104,copi:[0,3,4,8,11,12,15,17,40,119,168,290,328,346,392,421],copper:416,coproccesor:16,coprocessor:[1,4,7,9,16,17,333,436],coproprocessor:17,copy_arrai:8,copyright:[7,8,255],coral:169,core:[],core_shel:126,coreshel:[6,9,342,349,351],cornel:[6,150,435],corner123i:113,corner123x:113,corner123z:113,corner1i:113,corner1x:113,corner1z:113,corner2i:113,corner2x:113,corner2z:113,corner3i:113,corner3x:113,corner3z:113,corner:[3,6,40,113,168,299,300,321,412,423],cornflowerblu:169,cornsilk:169,corpor:16,corr:348,correct:[3,6,9,11,12,16,17,59,87,88,102,110,116,126,131,138,168,194,207,213,229,230,247,255,257,260,289,295,299,318,328,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,351,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,414,415,416,423,438,441,443],correction_max_iter:178,correctli:[3,8,9,11,17,71,81,102,103,122,123,125,127,129,130,131,132,133,136,137,140,167,169,175,195,200,203,214,223,229,230,263,270,273,275,277,296,299,328,329,333,351,379,420,421,423,447,449],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,96,97,109,112,113,114,115,118,119,120,122,123,131,138,143,150,151,152,153,154,155,156,158,159,161,162,164,167,168,169,173,174,175,181,183,184,185,187,190,192,194,201,203,204,208,213,216,217,225,226,227,229,231,232,233,234,235,236,241,244,246,247,249,252,253,257,262,270,272,273,281,283,285,294,295,296,298,299,300,302,304,305,306,307,308,309,312,314,319,323,325,327,328,334,335,337,340,341,342,343,344,345,346,347,348,349,352,353,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,380,381,384,385,386,387,389,390,392,393,394,395,396,397,406,407,408,409,410,412,414,415,416,418,420,421,423,424,426,436,437,438,440,441,443,448],correspondingli:[378,379,432],cosin:[],cosineshift:27,cosmo:[207,212],cossq:[],cost:[1,6,10,11,12,17,39,41,71,109,118,121,143,168,169,181,184,185,188,189,190,202,229,262,290,318,319,331,349,369,373,384,406,420,432],costheta0:[406,408,410],costheta:390,costli:[11,88,207,329],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,93,104,106,109,112,114,124,134,139,141,157,167,168,169,173,174,179,181,182,184,188,194,203,212,259,260,261,265,268,270,272,278,279,285,289,290,291,295,299,301,303,310,315,317,324,326,329,333,336,359,363,364,392,393,419,420,421,423,425,427,430,431,439,443,448,449],coulomb:[3,5,6,7,8,9,10,12,14,15,18,88,107,108,121,145,149,261,263,291,318,319,326,333,340,342,343,344,345,348,349,350,351,352,357,361,362,364,369,373,377,384,387,392,393,395,405,410,411,415,428,435,441,443,447],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,41,63,68,77,91,114,116,117,132,142,148,175,176,179,181,183,184,185,187,188,195,200,202,205,211,229,241,256,273,281,282,299,319,326,327,328,330,333,359,363,384,441,448],counter:[296,418,429,431,437],counterbal:209,counterpart:[167,270,418],counterproduct:18,coupl:[],cours:[3,8,138,167,173,174,206,269,275,289,295,297,298,300,301,319,378,397,420,423,436,443,448,450],coval:[6,29,357,380,443],covari:207,cover:[6,71,164,169,178,216,357,367,412],coverag:[71,184],cpc:212,cpp:[1,3,6,8,9,11,12,13,87,167,173,174,203,273],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,169,172,198,214,291,316,319,333,346,405,418,436,437,440,441],cpuremain:441,cr2:143,cr3:143,crack:[4,329],crada:[5,7],crai:[5,7,13,18,167],crash:[3,329,443],craympi:333,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:178,create_faceset:178,create_nodeset:178,createatom:[],creation:[],crimson:169,critchlei:255,criteria:[3,116,145,168,169,189,190,191,224,326,389,412,425,428,448],criterion:[41,142,144,147,179,188,191,205,241,262,296,301,326,328,348,357,361,428,437,438],criterioni:437,critic:[48,49,227,285,290,326],cross:[3,12,22,71,89,123,152,167,168,180,184,190,194,226,228,247,270,275,277,286,293,305,321,328,344,353,354,355,362,363,364,369,371,373,390,395,408,410,423,427,433,450],crossov:1,crossterm:423,crozier:[0,7,13],crucial:260,crystal:[4,6,13,73,251,252,288,329,427,441,443],crystallin:[6,252,321,409,443],crystallis:285,crystallogr:[118,143],crystallograph:[321,441],crystallographi:[118,143,321],cs1:143,cs_chunk:6,cs_im:[40,423],cs_re:[40,423],csanyi:[120,391,396],cscl:380,csequ:6,csh:[11,12,346],cshrc:[11,12],csic:[356,406,408,410],csinfo:6,csisi:[356,406,408,410],csld:[],cst:355,cstherm:6,cstyle:420,csvr:[],ctcm:[334,355],ctemp_cor:198,cterm:274,ctr:9,ctype:11,cu1:143,cu2:143,cu3au:380,cube:[6,41,142,147,188,198,299,321,443],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:339,cummul:[3,6,186,189,190,191,193,202,207,213,215,278,281,282,283,284,286,293,363,441],cumul:[6,179,181,183,184,185,199,205,213,227,229,233,241,270,271,328],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,102,108,116,117,121,124,132,140,142,145,148,167,168,169,170,173,174,178,179,181,184,185,186,188,189,190,191,192,193,194,195,199,200,203,205,207,210,211,213,219,226,229,230,234,235,241,246,247,249,255,261,262,264,267,268,269,270,273,274,276,277,278,281,282,283,289,290,293,294,295,296,297,298,300,301,303,316,317,318,319,322,323,325,326,327,328,333,339,346,348,352,355,357,358,361,365,368,378,379,380,381,382,384,390,392,393,397,408,410,411,413,418,419,420,421,423,424,425,426,427,429,430,431,433,435,437,438,440,441,448,449,450,451,452],curv:[6,144,205,252],curvatur:[360,394,416],custom:[],cut0:421,cut1:432,cut2:432,cut:[],cuthi:[251,263],cutinn:[341,378,379],cutlo:[251,263],cutmax:390,cutoff1:[345,352,369,373,377,387,395],cutoff2:[340,342,343,345,351,352,369,373,377,387,395],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,108,115,116,120,142,145,147,190,191,196,251,260,261,263,265,267,270,278,291,295,299,301,318,319,326,329,330,331,333,334,335,336,337,338,339,340,341,342,343,344,345,347,349,350,351,352,353,354,355,356,357,358,359,360,362,363,364,365,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,392,393,394,395,396,397,398,399,400,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,421,425,428,432,443],cutoffa:356,cutoffc:356,cuu3:355,cval:143,cvd:285,cvel:274,cvff:[],cwiggl:[3,226,295,298,300,448],cyan:[2,168,169],cycl:[3,205,227,229,230,233],cyclic:[3,164],cygwin:12,cylind:[3,4,168,211,256,296,299,426],cylindr:[6,211,275,296],cypress:333,cyrot:339,cyrstal:252,d3q15:216,d3q19:216,d_double_doubl:15,d_e:290,d_flag2:259,d_flag:259,d_name:[113,167,259,280,433],d_single_doubl:15,d_single_singl:15,d_sx:259,d_sy:259,d_sz:259,daan:288,dai:12,daili:12,daivi:247,damag:[],dammak:265,damp:[3,6,172,177,213,214,215,220,229,230,233,257,260,265,270,281,282,294,296,297,325,326,328,340,342,344,349,352,357,361,369,377,387,395,405,411,437,443],damp_com:214,damp_drud:214,dampen:[270,443],dampflag:[296,361],dan:17,danger:[3,12,205,301,353,441],dangl:147,daniel:9,darden:[319,352],darkblu:169,darkcyan:169,darken:168,darkgoldenrod:169,darkgrai:169,darkgreen:169,darkkhaki:169,darkmagenta:169,darkolivegreen:169,darkorang:169,darkorchid:169,darkr:169,darksalmon:169,darkseagreen:169,darkslateblu:169,darkslategrai:169,darkturquois:169,darkviolet:169,dasgupta:261,dash:[361,440],dat:[6,91,164,178,419],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,271],dataset:271,datatyp:3,date:[0,6,12,13,392,393,448],datom1:115,datom2:115,datom3:115,datom4:115,datum:[3,6,42,65,68,69,79,92,108,115,167,182],davi:295,david:[9,19,318,319,408,410],daw:[355,390],dbg:14,dcd:[3,6,7,167,168,169,170,253,424,428],ddim:166,deactiv:377,dealt:212,debug:[6,7,11,12,13,14,17,118,143,144,253,258,316,318,333,365,384,413,421,422,425,430,433,440,448],deby:[],decai:[349,416],decid:[3,6,12,16,71,226,259,270,291,438],decipher:321,declin:278,decod:168,decompos:[87,396],decomposit:[3,5,7,18,62,178,253],decoupl:[6,443],decreas:[3,167,175,176,191,194,200,203,213,289,318],decrement:274,deepli:315,deeppink:169,deepskyblu:169,def:[12,13,421],defaul:61,defect:[6,70,142],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,150,151,152,153,154,155,156,158,159,161,162,163,164,165,166,167,168,169,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,198,199,200,203,204,205,208,211,212,213,214,215,216,224,226,228,229,230,231,232,233,234,235,237,238,239,242,244,245,246,247,248,249,251,252,253,255,256,257,259,261,263,268,270,271,272,273,276,278,280,281,282,283,284,286,287,288,290,292,293,295,296,297,298,299,300,301,303,304,305,306,307,308,309,312,313,314,316,318,319,321,323,325,326,327,328,329,330,331,332,333,335,336,337,338,340,341,342,343,344,345,346,347,349,350,352,353,354,356,357,359,360,361,362,363,364,365,367,369,370,371,372,373,374,375,376,377,378,379,383,384,385,386,387,389,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,420,421,423,424,426,427,428,429,432,433,434,435,437,438,440,441,443,444,445,446,447,448,449],definit:[2,3,6,8,12,13,78,80,116,120,169,181,182,183,184,185,186,194,211,233,271,280,292,295,298,300,302,313,316,327,336,339,347,357,367,390,396,412,421,423,425,432,434,447,448],defint:441,deform:[],deg2theta:143,deg:443,degener:[3,255],degrad:[8,18,252,319,432],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,94,96,97,99,101,102,112,122,123,124,125,126,127,128,129,130,131,132,133,134,136,137,143,144,150,151,154,155,162,164,166,168,181,191,198,205,207,208,213,214,219,229,230,233,234,235,246,247,249,253,255,269,270,273,281,282,283,288,304,306,309,312,314,326,352,355,363,433,441,443,449],degress:[124,181],del:437,delai:[3,6,12,329,354,441],deleg:364,delet:[2,3,7,8,12,54,57,60,63,142,147,148,172,181,182,183,184,185,186,189,191,202,205,229,271,281,282,301,303,317,327,329,332,384,423,424,426,434,435,440,444,446,448,449],delete_atom:[],delete_bond:[],delete_el:178,deli:166,delimit:[421,448],deloc:[230,357],delr:380,delt_lo:437,delta:[],delta_1:339,delta_3:339,delta_7:339,delta_conf:3,delta_ij:[380,390],delta_mu:[3,179],delta_pi:339,delta_r:390,delta_sigma:339,delx:166,delz:166,demand:265,demo:11,demon:250,demonstr:[260,380],den:256,dendrim:363,denniston:[9,216,218,219,220,252],denomin:[7,149],denot:[118,198,214,252,263,265,349,362,364,393],dens:[71,191,357],densiti:[3,6,7,9,18,40,41,59,100,116,120,130,142,144,173,174,178,181,184,185,188,194,203,216,219,222,223,252,256,257,261,290,295,321,323,327,334,339,355,380,381,382,390,394,399,401,402,403,423,432,433,441,447],depart:[0,7],departur:[227,260],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,108,109,112,113,114,115,119,120,122,127,131,132,138,144,145,150,151,152,153,154,155,156,158,159,161,162,163,164,166,167,168,169,172,173,174,175,176,179,181,183,184,186,187,188,190,192,200,201,204,207,208,209,211,213,214,216,218,219,226,229,231,232,233,234,235,236,244,246,247,249,251,262,265,267,270,272,273,278,281,282,283,285,287,289,290,292,294,295,298,299,300,301,303,304,305,306,307,308,309,312,314,319,321,326,327,329,330,331,333,334,335,337,338,339,340,341,342,343,344,345,346,347,348,349,350,352,353,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,380,381,383,385,386,387,389,390,392,393,394,395,396,397,405,406,407,408,409,410,411,412,414,415,416,418,420,423,425,426,429,433,435,437,440,441,442,448,449],dependend:6,depflag:12,dephas:[418,437],depos:195,deposit:[],deprec:261,depth:[51,123,168,290,360,394],dequidt:9,der:[87,107,347,348,377,392,393,415,443],deriv:[6,7,8,38,56,63,87,120,138,164,182,192,194,205,213,226,229,231,232,233,234,235,251,257,261,265,287,288,290,295,296,299,325,327,335,339,347,352,357,358,362,371,375,376,380,392,393,405,407,415,443],derjagin:415,derlet:251,descend:169,descent:[7,325],descib:[40,261],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,110,113,116,118,120,121,123,124,128,129,132,135,137,138,142,143,144,146,147,156,161,164,167,172,173,174,181,182,183,184,185,186,188,191,192,193,194,195,197,198,206,207,210,211,212,213,214,215,216,218,219,220,224,228,229,230,233,240,248,251,253,258,259,260,261,262,263,270,274,275,278,279,280,281,282,283,284,285,286,287,288,293,295,296,298,303,318,319,321,324,325,326,327,328,332,335,336,338,340,341,342,344,345,346,347,348,349,352,355,357,358,360,361,362,364,369,370,371,372,373,374,375,376,377,378,379,380,383,389,390,391,392,393,394,395,396,397,404,405,406,407,408,409,410,411,414,415,416,418,420,421,423,424,426,427,433,436,437,440,448,449,450],descript:[],descriptor:[120,167,365],deserno:319,design:[0,3,6,7,8,11,13,14,15,17,118,126,129,143,178,191,197,198,229,230,251,252,271,285,290,336,337,338,341,344,349,351,357,377,378,379,381,382,390,393,407,432],desir:[2,3,6,7,11,12,14,15,16,18,33,40,50,59,71,88,91,112,117,121,126,144,157,166,179,192,194,203,205,206,213,214,215,219,229,247,255,256,257,258,261,265,270,273,278,281,282,283,284,289,296,310,315,318,319,321,324,326,327,328,353,355,363,378,379,406,408,410,419,420,421,423,427,432,437,438,440,441,448,449,450],desk:7,desktop:[4,6,7,10,12,17,168],despit:443,destabil:339,destre:312,destroi:[11,39,189,190],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,93,102,104,106,107,109,111,112,114,117,119,120,121,122,123,124,127,137,138,139,141,144,145,148,149,152,163,167,168,169,172,173,174,178,181,182,183,184,186,188,190,191,192,193,194,195,203,205,206,207,208,210,211,213,215,216,220,226,227,228,229,230,231,232,233,234,235,239,241,246,247,248,249,252,255,256,257,259,260,262,263,264,270,273,278,281,282,283,284,285,286,288,289,290,291,292,293,294,301,303,305,313,318,319,322,326,327,329,330,333,334,335,336,338,339,341,343,344,345,346,347,348,349,352,353,357,358,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,379,380,383,384,389,392,393,394,396,397,405,412,414,415,421,423,424,425,426,428,429,432,433,435,438,441,448,449,452],detect:[2,3,12,61,63,86,204,256,289,328,348,363,368,418,420,423,434,437,448],determ:333,determin:[1,3,6,8,12,15,39,40,42,51,57,58,59,61,62,68,71,87,102,107,109,112,118,119,121,132,133,142,143,144,166,167,168,169,170,171,175,176,177,180,181,182,183,184,185,186,187,188,192,194,195,198,200,205,208,209,211,213,214,219,224,226,227,229,234,235,246,247,249,251,253,257,260,267,268,269,270,271,272,278,281,282,283,285,291,292,295,296,297,298,299,300,301,313,318,319,321,327,329,330,333,335,336,343,348,352,354,355,359,361,365,373,380,384,393,394,404,407,411,415,420,423,424,426,428,430,433,437,439,440,447,448,449],detil:108,devan:[9,395],devanathan:410,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,210,233,255,260,261,264,335,339,357,382,425],devemi:9,deviat:[227,233,251,359],devic:[1,3,12,15,17,210,333],device_typ:333,devin:[262,348],devis:382,dfactor:168,dff:443,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,319],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,264],dhi:[59,166,194,256],dhug:[227,260],dhugoniot:[227,260],dia:380,diagnost:[],diagon:[3,6,83,120,121,192,229,257,270,293],diagonalstyl:396,diagram:[41,118,143,163,188,253],diallo:363,diam:[168,169,256,327],diamet:[3,6,40,113,144,167,168,169,173,174,213,256,270,278,294,296,327,347,360,361,367,371,394,412,415,423,424,433],diamond:[321,357,380],diamter:[40,256],dick:6,dicsuss:226,dictat:[179,227],did:[3,12,326,353,354,355,361,384,408,410,431],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,140,292,318],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,94,96,97,120,122,123,124,125,127,130,131,132,133,134,136,137,138,144,145,147,152,163,164,166,167,168,169,172,174,177,179,181,183,188,189,190,191,192,193,194,198,204,205,206,207,208,209,210,213,214,216,226,229,230,231,232,234,235,237,239,242,244,245,246,249,251,253,255,257,260,261,262,265,268,270,273,274,275,276,278,281,282,283,286,287,288,290,293,294,295,296,299,303,304,313,315,317,318,319,321,322,324,325,327,328,330,331,332,333,334,335,339,343,344,346,347,348,353,355,357,360,361,362,364,367,369,370,372,373,380,381,382,383,384,386,390,392,393,394,395,396,397,405,406,407,408,410,412,415,416,417,418,420,421,423,425,426,427,428,431,432,433,435,437,438,440,441,443,447,448,449,450],differenti:[1,3,6,29,164,318,349,390,409],difficult:[192,253,333,363,432],difficulti:[273,392],diffract:[],diffus:[],digit:[2,3,169,303],dih_table1:164,dih_table2:164,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:190,dihydrid:357,dij:273,dilat:[],dim1:3,dim2:3,dim:[3,59,71,122,125,126,127,130,131,132,133,134,136,144,166,184,194,211,296,321,380,426,447,448,449],dimdim:448,dimems:252,dimens:[],dimension:[3,39,112,118,120,122,124,125,126,127,130,131,132,133,134,136,143,165,181,184,228,252,290,321,324,328,390,423,433],dimensionless:[105,120,290,319,396,415],dimer:[6,270,380],dimgrai:169,dimstr:[41,188],dinola:[257,281],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,167,280,443],dir1:434,dir2:434,dir:[1,3,4,8,11,12,227,251,260,277,390,392,393,421,434,448],dirac:120,direc:390,direct:[],directli:[3,6,8,9,11,12,87,113,120,167,168,175,200,207,211,216,252,271,282,294,296,297,298,299,321,325,333,334,335,340,342,343,349,352,355,357,369,373,384,387,395,404,421,433,434,435,441,448],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,60,170,193,212,255,261,264,278,287,288,328,332,334,335,339,346,348,349,355,356,358,365,366,377,380,381,382,386,390,391,392,393,396,406,408,409,410,421,423,424,425,434,448],disabl:[3,12,16,290,368,421,436],disadvantag:[6,188],disallow:[194,229],disappear:425,discard:[2,3,41,71,184,188,291,299,420,425,426],discontinu:[9,164,326,375],discourag:380,discov:[13,291],discret:[6,8,40,42,168,169,213,216],discuss:[],disk:[6,84,85,137,165,195,205,256,421],disloc:70,disord:[39,70],disp:[],dispar:394,disperion:[352,373],dispers:[3,6,7,9,142,252,318,319,343,352,373,378,384,393,407],displac:[],displace_atom:[],displace_box:59,displacemet:426,displai:[11,13,22,37,44,55,152,163,167,168,305,313,346,405],dispters:3,dissip:[6,206,213,252,287,288,341,353,361,378,379,405],dissolut:189,dist:[6,69,91,108,117,167,253,269,354,404,418,449],distanc:[3,6,7,9,12,20,21,29,39,43,45,46,47,48,49,51,53,54,55,56,58,59,61,63,64,66,69,71,72,73,74,75,76,77,81,86,89,90,93,103,104,105,106,108,114,115,116,117,118,120,133,139,142,144,145,146,147,151,166,167,168,169,177,181,184,185,189,190,191,192,194,195,196,199,205,211,216,226,227,228,229,233,241,251,252,256,260,261,268,269,270,273,274,275,276,277,278,285,286,288,289,290,293,295,296,297,298,299,300,304,318,319,321,324,326,328,329,330,333,336,337,338,339,340,341,342,343,344,345,347,349,350,351,352,353,354,355,356,357,359,360,361,362,363,367,368,369,370,371,372,373,374,375,376,377,378,379,380,383,384,385,386,387,388,389,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,421,423,426,432,433,437,441,443,447,449],distinct:[6,198,267,318,394],distinguish:[6,86,120,219,357],distort:334,distrbut:334,distribut:[],distro:[111,346,389,390],ditto:[8,11,12,14,15,16,17,18,115,190,421],div:8,divd:117,diverg:[3,12,39,270,288,425,443,450],divid:[3,6,16,41,91,112,117,121,141,142,152,163,169,181,182,183,188,194,251,286,293,298,318,326,328,358,393,432,440,448],divis:[6,216,339,367,377,420,423,441,448],dl_poli:7,dlambda:138,dlammps_async_imd:210,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,168],dlammps_gzip:[3,12,167,168,289,423,424,428],dlammps_jpeg:[3,12,168],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,168],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,167],dlen:433,dlmp_intel_offload:[12,16],dlo:[59,166,194,256],dlvo:[7,347,415],dm_lb:216,dmax:[278,324],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,93,102,104,105,106,107,109,111,112,114,117,119,121,123,124,137,139,141,144,145,146,152,163,167,168,169,170,172,173,174,179,180,181,182,183,184,185,186,195,205,213,214,224,229,230,234,235,239,246,247,248,249,256,259,270,275,278,281,282,283,292,296,299,301,303,305,313,317,326,327,328,333,334,335,338,346,348,349,355,356,358,363,364,366,367,380,381,382,384,386,389,390,391,396,405,406,408,410,412,421,423,424,425,426,428,431,432,433,440,441,448,449,450,451],docuement:394,dodgerblu:169,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,29,33,38,39,41,50,54,56,59,62,63,67,70,71,87,88,91,104,110,117,118,123,124,127,132,134,138,143,144,145,146,148,150,152,157,163,164,166,167,168,169,172,178,179,181,184,187,188,190,191,192,194,198,200,202,205,206,209,211,213,214,216,219,225,229,230,231,232,234,235,246,247,248,249,257,258,259,263,265,268,270,278,281,283,285,286,290,293,294,295,298,299,300,301,306,307,309,310,312,317,318,319,320,321,327,328,329,334,335,336,337,338,339,341,343,344,345,347,348,349,350,352,353,354,355,356,357,359,360,361,362,364,365,366,367,368,371,372,374,375,376,378,379,380,381,382,384,390,391,392,393,394,396,397,398,399,400,401,402,403,404,406,407,408,409,410,411,412,414,415,416,418,419,420,421,423,424,425,426,427,430,431,433,434,435,436,437,440,441,443,448,452],doegenomestolif:7,doesn:[3,7,8,12,144,167,179,184,185,275,327,329,333,335,348,356,366,392,393,406,408,409,410,423,425],dof:[3,8,112,123,124,137,181,270,449],dof_per_atom:[124,181],dof_per_chunk:[124,181],doff:[327,423],doi:[6,193],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,118,133,143,146,166,168,169,172,179,188,192,194,195,209,212,216,229,230,253,265,270,290,295,296,318,319,328,333,354,384,418,420,423,427,440],domin:[1,357,437],don:[0,8,11,12,13,116,147,175,200,214,259,299,380,421,423],donadio:282,done:[1,3,6,7,8,12,14,15,16,17,18,19,38,39,41,56,59,62,71,138,141,144,147,164,168,169,178,179,181,183,184,185,186,188,189,190,191,192,194,195,203,205,210,211,213,214,221,229,234,235,246,247,249,250,252,253,254,259,267,270,271,273,278,281,282,283,285,287,288,301,303,317,318,319,326,328,329,332,333,335,343,355,364,365,366,373,379,380,384,392,404,407,412,418,419,420,421,424,427,428,431,441,443,448,449],donor:363,dot:[121,140,175,200,208,228],doti:[339,390],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,39,87,194,203,258,299,303,317,319,332,333,339,358,362,392,393,419,423,427,431,436,448,449],dover:178,down:[3,6,7,8,11,39,71,192,213,278,294,333,357,384,422],downhil:[324,325],download:[5,7,8,9,11,12,13,17,210,365,391],downsid:6,downward:267,dozen:[8,12,107,172,392,393],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:222,dproduct:336,dr_ewald:[118,271],drag:[],dragforc:216,drai:[227,260],drain:[209,294,326],dramat:[59,166,189,190,191,192,194,229,278,281,282,319,333,384,420],drautz:339,draw:168,drawback:259,drawn:[167,168,169,206,418],drayleigh:[227,260],dreid:[],drfourth:105,drho:[113,334,355],drift:[6,103,105,206,207,213,214,225,268,278,432,440,443],drive:[11,12,176,192,194,208,229,251,257,270,297,328],driven:[6,156],driver:[6,12,14,15,172,203,210],drop:[3,169,353],droplet:364,drsquar:105,drude:[],dry:202,dsecriptor:365,dsf:[],dsmc:[],dstyle:256,dt_collis:216,dt_lb:216,dt_md:216,dt_srd:278,dtilt:[59,194],dtneb:437,dtqm:260,dtype:[115,190],dual:[17,278,333],dudarev:143,due:[1,3,6,9,10,12,16,17,19,40,54,57,58,61,66,70,71,74,75,81,86,88,89,90,93,102,103,104,105,106,110,116,118,120,121,122,123,125,127,130,131,132,133,134,136,137,139,143,144,147,148,167,168,172,175,176,183,187,189,190,191,192,193,194,195,200,201,202,203,206,207,210,211,213,214,215,216,219,220,221,225,226,227,228,229,233,241,251,254,256,268,269,270,272,275,277,278,279,281,282,283,284,285,287,288,290,294,295,297,298,299,301,319,324,326,328,329,330,350,353,355,359,360,364,378,379,384,390,392,394,395,404,407,408,410,413,415,416,418,420,423,424,425,432,437,440,441,443,448,449],duffi:290,duin:[9,261,266,392,393],duke:319,dummi:[12,29,409],dump1:428,dump2:428,dump:[],dump_atom:8,dump_custom:8,dump_modifi:[],dumpcustom:8,dumptimestep:428,dunbrack:[6,20,150,344,435],dunweg:[213,215],duplic:[2,3,14,15,16,17,18,19,41,42,145,188,207,251,423,447],dupont:[5,7,13],durat:[37,55,122,123,125,126,127,129,130,131,132,133,136,137,163,169,181,205,265,290,313,361,405],dure:[2,3,6,8,9,12,16,17,38,39,41,56,71,87,126,145,148,164,167,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,196,199,200,201,202,203,204,205,206,207,208,209,210,211,213,214,215,216,217,218,219,220,221,222,223,225,226,228,229,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,319,326,328,332,333,353,377,384,393,407,418,419,421,423,426,428,430,431,433,435,437,438,441,448,451,452],dvector:8,dvlo:415,dvx:6,dx_lb:216,dy3:143,dyamic:12,dyanam:6,dyanmic:437,dynam:[],dynamo:[5,334,355,380],dyne:447,dyre:374,dysam:426,e28637:29,e_1:339,e_2:339,e_b:358,e_e:357,e_hbond:363,e_i:[6,339,358],e_j:[6,339],e_k:[339,357],e_kl:6,e_lj:[335,352],e_n:[339,357],e_nn:357,e_pr:357,e_rebo:335,e_tors:335,eaa:304,eaat:151,each:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,66,67,68,70,71,72,73,74,75,76,77,78,80,81,83,85,87,89,90,93,94,95,96,97,98,99,100,101,102,103,104,105,106,109,110,111,112,113,114,115,116,117,118,119,120,121,123,124,125,126,127,128,131,132,133,134,136,137,138,139,140,141,142,143,144,147,148,150,151,152,153,154,155,156,157,158,159,161,162,163,164,166,167,168,169,170,171,172,173,174,175,176,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,205,206,207,208,209,210,211,212,213,214,215,216,217,219,220,221,222,223,225,226,227,228,229,231,232,233,234,235,236,237,238,239,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,261,262,263,265,267,270,271,272,273,274,275,276,277,278,279,280,281,282,283,285,288,289,290,291,292,293,294,295,296,298,299,300,301,303,304,306,307,308,309,310,312,313,314,317,318,319,321,325,326,327,328,329,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,357,358,359,360,361,362,363,364,367,368,369,370,371,372,373,374,375,376,377,378,379,380,383,384,385,386,387,389,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,410,411,412,413,414,415,416,417,418,420,421,423,424,425,426,427,428,430,431,432,433,435,437,438,440,441,443,447,448,449,450,452],eacn:[41,188],eam0d:252,eam3d:252,eam:[],eam_databas:13,eam_gener:13,eangl:441,earli:[41,181,183,184,185,186,188,264,271],earlier:[7,8,12,59,169,328,361,380,384,437],earliest:437,earth:357,easi:[6,7,8,11,13,87,121,167,173,174,175,176,184,187,200,208,209,211,213,214,272,281,282,283,295,298,300,327,423,426,431,433,449],easier:[8,9,13,16,167,168,252],easili:[8,11,168,169,294,328,420,430,439,448],eastwood:[318,319],eat:151,eatom:301,eaxmpl:6,eba:21,ebb13:151,ebb:21,ebond:[198,214,440,441],ebt:151,ec_ii:380,ec_ij:380,ec_jj:380,echo:[],eco:[392,393],ecoa:[392,393],ecoul:[107,198,214,392,393,441],ecp:[357,423],edg:[2,3,6,41,59,71,118,142,143,146,147,168,177,184,211,272,295,298,299,300,301,321,423,426,433],edge_histo:142,edge_threshold:142,edih:441,edim:286,edip:[],edit:[3,8,12,13,14,15,16,17,18,19,443],editor:13,edu:[7,9,11,13,355,378,389,392,393],edward:[9,17],eebt:151,eff:[],effect:[1,2,3,6,8,9,11,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,43,45,46,47,48,49,51,53,54,56,66,71,74,75,81,89,90,93,103,104,105,106,1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333,420],espresso:[9,264],essenti:[8,11,12,27,88,125,126,127,130,131,132,133,134,136,153,182,233,252,294,319,335,349,369,410,428,441],essex:29,establish:[87,209],estim:[1,3,6,10,12,38,41,56,91,121,178,188,199,227,278,285,318,319,324,384,393,407,437,441],esu:447,esub:380,eta:[6,216,229,260,261,263,294,356,358,360,390,409,447],eta_dot:229,eta_ij:390,eta_ji:358,etag:[40,423],etail:441,etap:229,etap_dot:229,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,17,39,40,42,54,61,68,89,90,91,94,109,110,113,115,121,122,124,125,126,127,128,130,131,132,133,134,136,138,144,146,147,148,157,167,168,169,172,178,179,180,181,183,184,185,186,189,190,194,195,203,205,206,213,229,256,267,271,290,291,299,303,317,318,326,327,328,329,331,355,356,364,377,379,388,392,393,406,408,410,418,421,423,424,425,430,432,433,437,439,440,441,443,447,448,450,452],ethernet:18,etol:[326,328,418,437],etot0:260,etot:[6,94,96,97,110,121,130,169,198,214,227,260,440,441],eu2:143,eu3:143,euler:[326,328],eulerian:178,euqat:398,europhi:216,evalu:[2,3,11,12,38,56,71,87,88,91,107,117,120,124,134,142,144,167,168,169,173,174,175,176,178,180,181,182,183,184,185,186,187,194,200,206,208,209,211,212,213,214,252,258,261,272,281,282,283,292,295,298,300,301,303,318,319,324,326,333,384,390,407,418,419,421,425,426,428,430,431,432,433,437,439,441,448,449],evalut:[303,421],evan:[132,247],evanseck:[6,20,150,344,435],evapor:[],evaul:[8,326],evdwl:[107,392,393,441],even:[3,6,8,12,15,16,17,18,34,39,41,52,57,59,61,63,70,71,119,145,146,160,164,167,169,172,173,174,179,180,181,183,184,185,186,188,189,190,192,194,195,198,211,214,227,229,230,252,265,267,270,271,278,286,290,293,295,299,301,311,318,324,326,328,333,338,357,358,361,364,384,394,413,423,424,426,428,429,430,432,433,435,438,440,441,443,452],evenli:[3,41,121,164,188,216,367,413,423],event:[],eventu:[3,6,12,15,146,261,437],ever:[54,56,212,278],evera:[347,360,394,405],everi:[0,1,2,3,6,8,11,12,15,16,39,41,71,72,91,113,119,132,147,167,168,169,170,172,173,174,175,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,199,202,203,205,207,209,210,211,216,217,225,229,230,233,250,251,252,256,257,258,259,260,261,262,263,265,267,268,270,271,273,274,278,280,281,282,283,284,285,286,289,290,291,292,293,301,303,317,319,328,329,330,333,353,354,364,377,392,393,401,417,418,419,423,425,427,428,430,431,432,437,438,439,441,448,452],everyth:[8,107],everywher:[116,371],eviri:357,evolut:[207,216,253,418],evolv:[216,253,291],ewald:[2,3,5,6,7,8,12,88,110,118,121,291,318,319,326,340,342,343,349,352,357,369,373,387,395,405,407,425],ewald_disp:352,ewalddisp:3,exact:[22,41,44,71,138,147,152,188,191,206,207,213,214,215,256,265,266,278,290,305,318,346,425,430,437,450,452],exactli:[3,6,12,14,17,38,41,56,59,71,91,123,128,135,144,164,173,174,183,188,194,199,206,213,214,215,230,240,241,248,252,260,278,283,284,297,333,346,353,355,361,364,367,378,384,407,425,426,433,437,448],exager:443,examin:[6,8,191,252],examp:[421,448],exampl:[],exce:[3,6,16,17,18,41,58,71,146,181,184,185,188,192,194,199,202,229,252,278,326,333,423,448],exceed:[3,41,59,188,194,229,278,431],excel:357,except:[1,2,5,6,8,11,14,16,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,108,109,112,117,121,122,123,124,125,126,127,128,130,131,132,133,134,135,136,137,144,148,150,151,152,153,154,155,156,158,159,161,162,163,164,166,167,169,172,175,181,182,183,187,188,192,194,201,204,205,208,211,213,215,229,230,231,232,233,234,235,236,240,241,244,246,247,248,249,253,262,263,270,272,273,275,278,281,283,284,290,294,301,303,304,305,306,307,308,309,312,313,314,318,319,321,323,327,328,329,331,332,333,334,335,337,340,341,342,343,344,345,346,347,348,349,351,352,353,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,379,381,385,386,387,389,392,393,394,395,397,405,406,407,408,409,410,412,414,415,416,418,420,421,423,425,426,428,431,432,433,434,435,437,441,443,447,448,449,451],excess:357,exchang:[2,3,6,8,9,61,62,172,178,179,205,213,262,270,286,290,293,318,333,357,438],exchange:318,excit:[9,357],exclud:[3,6,9,12,16,17,63,71,112,120,124,131,132,148,167,181,184,189,190,217,225,255,268,270,285,296,301,326,327,329,341,361,364,378,379,384,404,435],exclus:[1,3,9,12,16,87,333,348,432],excurs:418,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,145,168,210,264,303,317,320,332,419,421,431,434,437,448],exemplari:206,exemplifi:357,exert:[6,211,214,265,297,298,299,319],exhaust:[178,332,448],exhibit:[229,325,357,432],exist:[3,6,7,8,11,12,13,37,55,59,68,70,144,145,163,168,169,172,177,187,190,192,195,205,255,256,258,301,304,306,307,309,313,322,327,333,364,392,413,419,421,423,424,425,434,435,436,448,449,450],exit:[2,3,11,12,41,57,167,188,317,332,421,422,431,440,448],exlanatori:3,exp:[],expand:[],expans:[12,120,167,434],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,102,125,136,142,164,188,200,205,207,226,251,257,259,260,265,270,301,319,329,346,380,384,418,421,423,425,428,432,437,448],expens:[6,10,71,169,251,255,270,290,301,318,319,329,333,421],experi:[6,13,15,17,187,195,210,219,228,257,269,270,324,328,353,384,432,437],experienc:[6,12,218,219],experiment:[318,333,437],expert:12,expertis:7,explain:[1,3,6,8,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,92,124,132,164,167,168,169,172,181,182,186,188,190,192,194,229,251,259,270,275,301,303,317,318,321,327,328,332,338,355,367,397,412,416,421,424,425,428,430,433,443,448,452],explan:[3,6,59,113,120,167,181,228,251,364,417,420,421,423,432],explanatori:[3,8,117,167,180,181,183,184,185,270,327,420,448],explantori:[3,266],explic:383,explicit:[6,9,11,22,44,77,87,113,116,138,152,173,174,194,305,323,335,336,339,344,346,355,357,368,378,411,417,420,424,427],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,109,112,122,131,134,142,144,150,151,153,154,155,156,158,159,161,162,164,167,169,175,184,187,194,201,204,206,208,213,229,231,232,233,234,235,236,244,246,247,249,259,260,262,270,272,273,281,283,284,290,294,304,306,307,308,309,312,314,327,333,334,335,337,340,341,342,343,344,345,346,347,348,349,350,352,353,354,355,356,358,359,360,361,362,363,364,367,368,369,370,371,372,373,374,375,376,377,378,381,384,385,386,387,389,394,395,397,398,399,400,401,402,403,405,406,407,408,409,410,411,412,414,415,416,423,425,432,433,435,436,443],explictli:[16,436],exploit:[9,15,17,253],explor:[118,143],expon:[3,261,263,355,360,363,377,383,395],exponenti:[87,390,406,416,437,448],expos:11,exposit:[178,353,354],express:[6,120,130,144,173,174,192,226,251,261,290,296,303,339,355,357,371,380,396,405,448],expressiont:339,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,94,97,98,107,109,117,119,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,172,175,176,179,186,187,193,196,200,203,204,205,207,208,209,211,213,215,227,229,233,241,251,252,268,269,270,272,274,275,277,281,282,283,284,285,287,288,290,292,295,299,300,360,380,393,394,396,440,441],extent:[1,3,41,45,57,71,142,146,167,177,184,188,211,297,300,318,321,335,407,420,423,426],exterior:[3,6,299],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,102,109,110,112,118,121,122,123,125,127,130,131,132,133,134,136,137,143,144,145,146,150,169,183,188,190,229,258,259,260,270,278,326,327,330,331,352,361,364,367,380,384,420,421,423,426,435,443,448],extract:[3,6,11,13,36,63,87,107,115,117,119,173,174,263,328,349,358,380,396,421,428,440],extract_atom:11,extract_comput:[11,421],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,168,192,194,229,288,357,409,443],extrema:377,extrins:178,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[140,292],f_a:[408,409,410],f_ave:117,f_c:409,f_f:410,f_fix_id:260,f_harm:288,f_i:390,f_id:[6,71,117,119,167,172,180,181,182,183,184,185,186,224,280,292,441,448],f_ij:390,f_indent:186,f_int:287,f_jj:91,f_k:390,f_langevin:290,f_max:[260,265],f_msst:227,f_r:[214,408,409,410],f_sigma:339,f_solid:288,f_ss:6,f_temp:214,face:[3,6,57,59,71,132,142,146,177,184,185,295,297,298,299,300,321,360,380,394,423,426],face_threshold:142,facet:142,facil:[0,12],facilit:[6,13],fact:[6,8,16,207,278,288,361,435],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,118,120,138,143,146,150,161,167,168,169,173,174,182,188,192,194,195,205,210,213,215,216,227,229,230,233,253,257,269,273,278,282,286,293,294,295,299,309,319,321,333,335,336,339,340,342,344,349,350,351,353,357,361,368,369,380,384,386,387,393,395,397,406,411,420,423,426,427,432,435,437,438,441,443,447,448],factori:[3,421],factoriz:318,fail:[3,11,12,59,148,192,195,318,326,328,351,393,421],fairli:[11,384,432,437],faken:73,falcon:210,fall:[3,6,169,183,256,421],fals:[86,301,303,448],fame:8,famili:420,familiar:[0,11],fan:390,far:[3,6,12,17,57,59,61,86,167,169,170,188,189,190,192,195,205,229,251,269,270,278,295,306,309,324,328,329,412,421,423,428,441],farago:213,farrel:[408,410],farther:167,fashion:[6,8,41,71,144,169,172,173,174,179,184,188,190,195,205,207,211,226,227,229,231,232,233,234,235,243,246,247,248,249,259,260,262,270,274,277,280,288,290,294,295,296,298,300,328,364,378,426,435,448,451],fasolino:366,fast:[6,7,9,12,13,17,39,167,238,260,291,318,319,341,378,379,405,407,425,430,432,441,449,452],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,105,109,112,122,131,150,151,153,154,155,156,158,159,161,162,164,167,169,172,175,187,188,201,204,208,212,213,229,231,232,233,234,235,236,244,246,247,249,257,261,262,270,272,273,278,281,283,285,287,290,294,304,306,307,308,309,312,314,318,319,330,331,333,334,335,337,339,340,341,342,343,344,345,346,347,348,349,352,353,355,356,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,381,385,386,387,389,394,395,397,405,406,407,408,409,410,412,414,415,416,418,432,436,443],fastest:[6,14,17,132,184,290,291,333,420],fatal:[3,440],fault:[70,393],faulti:12,fava:360,favor:191,favorit:7,fbmc:285,fcc:[],fcm:[243,448],fdirect:198,fdotr:365,fdti:87,fe2:143,fe3:143,fe_md_boundari:178,featu:8,featur:[],fecr:355,feedback:[7,210],feel:[7,210,211,219,251,299,301,328,384],felling:382,felt:299,femtosecond:447,fene:[],fennel:[349,369],fep:[],ferguson:[6,150,435],fermi:[1,12,15,130,333,410],fermion:[9,357],ferrand:[9,13],few:[1,3,4,5,6,7,10,11,12,13,14,17,18,39,170,180,181,182,183,184,185,186,214,229,256,259,261,273,292,318,326,327,328,335,420,423,428,432,434,448,450],fewer:[1,3,11,15,16,61,219,432],fewest:3,fextern:203,feynman:253,fff:421,ffield:[348,358,392,393],ffmpeg:[3,12,168],ffplai:168,fft:[1,3,7,12,14,15,88,109,110,121,252,318,319,432],fft_inc:[12,319],fft_lib:12,fft_path:12,fftbench:318,fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],fictiti:[6,175,176,200,203,207,253,269,349,369,373,404],field1:[424,428],field2:424,field:[],fifth:[275,386],figur:[1,3,8,11,12,260,420,421],fij:352,file0:251,file1:[11,13,251,289,303,327,428,430,434],file2:[11,13,289,303,327,428,430,434],file:[],filenam:[3,12,13,38,41,56,164,167,168,169,170,178,181,182,183,184,185,186,188,193,251,255,258,261,262,263,266,267,270,271,289,290,315,316,317,328,334,335,339,349,355,356,358,366,380,381,382,386,390,391,392,393,396,406,407,408,409,410,419,420,421,424,425,430,434,441,448,450,451,452],filennam:430,filep:[3,167,169,425,430,452],filepo:267,fill:[7,144,168,256,290,321,329,339,393,426],filter:[169,178],final_integr:8,final_integrate_respa:8,finchham:[6,126,351],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,117,147,164,170,179,191,192,202,205,228,251,257,265,269,324,326,328,329,349,364,369,373,380,405,407,443,448],find_custom:8,fine:[16,17,148,175,200,288,329,333,448],finer:[120,144,448],finest:318,finger:[144,166,226,426],finish:[6,11,41,188,303,315,317,318,330,332,333,412,428,448,449],finit:[],finni:[7,355,405],finvers:198,fiorin:[9,193],fire:[324,325,326,328,437],firebrick:169,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,103,104,105,112,116,117,121,129,132,138,140,142,143,145,146,147,151,164,167,168,169,170,172,179,181,182,183,184,185,186,188,191,194,205,206,211,216,226,227,228,229,251,253,258,259,260,262,267,270,273,274,275,276,278,279,280,287,288,289,290,292,296,301,303,304,310,321,326,327,328,329,332,333,334,335,338,339,340,342,344,346,348,349,355,357,358,361,362,365,366,368,369,373,378,379,380,382,384,386,390,392,393,396,404,406,407,408,409,410,418,419,420,421,423,424,425,428,430,432,435,436,437,440,441,443,448,449,450,452],fischer:[6,9,19,20,150,344,435],fit:[3,6,9,12,38,56,164,269,278,335,339,366,380,384,400,407,409,431,448],five:[73,130,260,327,339,381,423,437],fix:[],fix_adapt:[138,174,377],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,179,256],fix_evapor:179,fix_flux:178,fix_gcmc:[179,327],fix_gl:207,fix_gld:207,fix_grav:256,fix_id:[3,192,227,229,231,232,233,234,235,257,260],fix_modifi:[],fix_mov:[166,296],fix_nh:8,fix_npt:207,fix_nvt:[179,205],fix_poem:[3,6],fix_pour:[3,195],fix_qbmsst:9,fix_qeq:[3,348],fix_rattl:273,fix_reax_bond:392,fix_rigid:[219,338],fix_saed_vtk:271,fix_setforc:8,fix_shak:273,fix_srd:3,fix_styl:233,fix_temp_rescal:284,fixedpoint:[192,229],fixextern:203,fixid:178,fji:352,flag1:[197,331],flag2:[197,331],flag:[3,8,11,12,14,15,16,17,18,40,66,74,75,81,86,89,90,93,103,104,106,118,139,143,147,167,168,169,170,186,191,193,197,210,213,217,219,225,226,252,259,270,275,277,278,285,289,298,301,316,319,327,331,332,333,335,363,368,380,404,418,420,421,423,424,425,427,428,429,433,448],flag_buck:343,flag_coul:[343,352,373],flag_lj:[352,373],flagfld:[341,378,379],flaghi:[3,341,378,379],flaglog:[341,378,379],flagn:197,flagvf:[341,378,379],flat:[6,290,295,296,300],flavor:[2,7,12,384],fld:[9,295,341,378,379],flen:336,flex_press:336,flexibl:[3,6,8,145,168,181,184,193,207,230,286,293,357,409,441],flip:[3,6,194,229,297,298],floor:448,flop:12,floralwhit:169,flow:[],fluctuat:[6,64,87,192,205,206,213,216,229,233,251,252,288,290,312],fluid:[],fluid_veloc:220,flush:[3,169,440],flux:[],flv:168,fly:[7,9,12,41,168,172,178,195,198,270,273,291,339,441,443],fmackai:9,fmag:196,fmass:253,fmax:[326,441],fmomentum:198,fmsec:[2,169,213,214,226,229,257,270,281,282,432,442,447,449],fname:317,fno:12,fnorm:[326,441],fnpt:198,fnvt:198,foce:364,fock:336,focu:273,fogarti:[9,263,393],foil:[120,251,396],fold:[276,432],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,120,121,123,124,130,132,137,140,142,144,145,150,153,154,155,156,158,159,161,162,164,167,168,169,172,178,179,180,181,182,183,184,185,186,188,193,194,195,198,199,203,205,206,207,210,212,213,214,216,219,227,229,233,234,235,246,247,249,252,253,255,258,259,260,261,263,265,267,269,270,271,273,280,281,282,283,286,287,288,289,290,292,293,301,302,306,307,308,309,312,314,316,321,323,326,327,328,333,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,351,352,353,354,355,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,393,394,395,3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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso_e/atom command","compute meso_rho/atom command","compute meso_t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute sna/atom command","compute stress/atom command","compute temp command","compute temp/asphere command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":189,"default":[37,39,40,55,57,58,59,61,62,71,87,88,102,103,105,107,118,120,124,132,133,137,143,144,147,149,163,165,166,167,168,169,170,171,173,174,175,177,178,179,181,184,185,186,189,190,192,193,194,195,199,202,205,206,211,213,214,215,216,217,219,224,227,229,230,233,247,248,252,253,256,257,258,259,260,262,265,267,268,270,271,278,280,285,286,287,288,291,293,295,297,301,313,316,318,319,321,322,324,325,327,329,330,331,333,336,339,341,357,378,379,384,392,393,404,405,418,419,420,423,424,426,428,430,431,432,435,437,439,440,441,442,447,449,450,451],"function":448,"long":[340,342,343,344,345,349,351,352,369,373,377,387,395],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[173,174],addforc:175,addit:[12,13],addtorqu:176,adiabat:6,adp:334,airebo:335,alloi:355,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:177,arrai:6,aspher:[6,82,123,231,234,237,238,246],atc:[9,178],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,95,96,99,100,101,110,111,113,120,121,142,177,179,180,259,448],atom_modifi:39,atom_styl:40,attract:5,aveforc:187,awpmd:[9,336],balanc:[41,188],barostat:6,basal:67,beck:337,berendsen:[257,281],between:6,binary2txt:13,bodi:[6,8,42,68,239,338],bond:[8,13,69,189,190,191,266],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:339,born:[340,351],boundari:[7,57],box:[6,58,192],brownian:341,buck:[342,343,351],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,150,344,377],chunk:[6,66,71,75,90,93,104,106,114,124,139,141,181],citat:7,class2:[21,43,151,304,345],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[295,347,415],colvar:[9,13,193],com:[74,75,125],comb3:348,comb:[262,348],come:5,comm_modifi:61,comm_styl:62,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,445,446,447,448,449,450,451,452],common:3,comparison:1,compos:6,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,448],compute_modifi:102,condit:7,conduct:[6,286],constant:6,constraint:7,contact:76,coord:77,core:6,correl:182,cosin:[23,24,25,26,27,28,153],cossq:306,coul:[340,342,343,344,345,349,350,351,362,369,373,377,387,395],coupl:6,creat:190,create_atom:144,create_bond:145,create_box:146,createatom:13,creation:7,csld:282,csvr:282,cubic:371,cuda:[9,14,109,112,122,131,175,187,201,204,208,229,236,272,273,281,283,294,340,342,344,345,355,361,362,369,370,372,375,385,406,408],custom:8,cut:[49,336,342,345,349,352,357,359,369,370,377,383,387],cvff:307,damag:78,data2xmovi:13,data:6,databas:13,deby:[349,369],deform:[127,128,194],delete_atom:147,delete_bond:148,delta:24,deposit:195,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,16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86,187,188,189,190,192,193,194,195,196,198,199,200,201,202,203,204,205,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300],state:280,stationari:223,stop:[173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,192,193,194,195,196,198,199,200,201,202,203,204,205,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300],store:[279,280],strategi:1,streitz:349,stress:121,structur:2,style:[1,2,6,8],submit:8,suffix:436,summari:6,swap:[179,191],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,252,253,254,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,445,446,447,448,449,450,451,452],system:6,tabl:[0,6,38,56,164,407,408],tad:437,taitwat:[402,403],temp:[122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,281,282,283,284],temper:438,temperatur:6,tersoff:[408,409,410],test:11,tfmc:285,thermal:[6,286],thermo:[6,439],thermo_modifi:440,thermo_styl:441,thermodynam:[6,8],thermostat:6,thole:411,time:[6,186],timestep:442,tip3p:6,tip4p:[6,349,369,373,377],tip:12,tmd:289,tool:13,torqu:139,transform:198,tri:[245,412],triclin:6,tstat:353,ttm:290,tune:291,type:7,umbrella:314,uncomput:444,undump:445,unfix:446,unit:447,user:[9,12,14,16,18],vacf:140,valu:[6,448],variabl:[6,8,448],variou:1,vcm:141,vector:[6,292,448],veloc:449,version:[0,5,12],via:12,vim:13,viscos:[6,293],viscou:[220,294],visual:6,voronoi:142,vtk:271,wall:[6,295,296,297,298,299,300],warn:3,water:6,weight:183,what:[7,12],wolf:[340,349],wrapper:11,write:6,write_data:450,write_dump:451,write_restart:452,xmgrace:13,xmovi:13,xrd:143,yukawa:[414,415],zbl:[410,416]}}) \ No newline at end of file diff --git a/doc/set.html b/doc/set.html index d0c30f8dca..c90a9530f2 100644 --- a/doc/set.html +++ b/doc/set.html @@ -148,67 +148,67 @@ 
     type value = atom type
-    value can be an atom-style variable (see below)
-  type/fraction values = type fraction seed
-    type = new atom type
-    fraction = fraction of selected atoms to set to new atom type
-    seed = random # seed (positive integer)
-  mol value = molecule ID
-    value can be an atom-style variable (see below)
-  x,*y*,*z* value = atom coordinate (distance units)
-    value can be an atom-style variable (see below)
-  charge value = atomic charge (charge units)
-    value can be an atom-style variable (see below)
-  dipole values = x y z
-    x,y,z = orientation of dipole moment vector
-    any of x,y,z can be an atom-style variable (see below)
-  dipole/random value = seed Dlen
-    seed = random # seed (positive integer) for dipole moment orientations
-    Dlen = magnitude of dipole moment (dipole units)
-  quat values = a b c theta
-    a,b,c = unit vector to rotate particle around via right-hand rule
-    theta = rotation angle (degrees)
-    any of a,b,c,theta can be an atom-style variable (see below)
-  quat/random value = seed
-    seed = random # seed (positive integer) for quaternion orientations
-  diameter value = diameter of spherical particle (distance units)
-    value can be an atom-style variable (see below)
-  shape value = Sx Sy Sz
-    Sx,Sy,Sz = 3 diameters of ellipsoid (distance units)
-  length value = len
-    len = length of line segment (distance units)
-    len can be an atom-style variable (see below)
-  tri value = side
-    side = side length of equilateral triangle (distance units)
-    side can be an atom-style variable (see below)
-  theta value = angle (degrees)
-    angle = orientation of line segment with respect to x-axis
-    angle can be an atom-style variable (see below)
-  angmom values = Lx Ly Lz
-    Lx,Ly,Lz = components of angular momentum vector (distance-mass-velocity units)
-    any of Lx,Ly,Lz can be an atom-style variable (see below)
-  mass value = per-atom mass (mass units)
-    value can be an atom-style variable (see below)
-  density value = particle density for sphere or ellipsoid (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)
-    value can be an atom-style variable (see below)
-  volume value = particle volume for Peridynamic particle (distance^3 units)
-    value can be an atom-style variable (see below)
-  image nx ny nz
-    nx,ny,nz = which periodic image of the simulation box the atom is in
-  bond value = bond type for all bonds between selected atoms
-  angle value = angle type for all angles between selected atoms
-  dihedral value = dihedral type for all dihedrals between selected atoms
-  improper value = improper type for all impropers between selected atoms
-  meso_e value = energy of SPH particles (need units)
-    value can be an atom-style variable (see below)
-  meso_cv value = heat capacity of SPH particles (need units)
-    value can be an atom-style variable (see below)
-  meso_rho value = density of SPH particles (need units)
-    value can be an atom-style variable (see below)
-  i_name value = value for custom integer vector with name
-    value can be an atom-style variable (see below)
-  d_name value = value for custom floating-point vector with name
-    value can be an atom-style variable (see below)
+  value can be an atom-style variable (see below)
+type/fraction values = type fraction seed
+  type = new atom type
+  fraction = fraction of selected atoms to set to new atom type
+  seed = random # seed (positive integer)
+mol value = molecule ID
+  value can be an atom-style variable (see below)
+x,*y*,*z* value = atom coordinate (distance units)
+  value can be an atom-style variable (see below)
+charge value = atomic charge (charge units)
+  value can be an atom-style variable (see below)
+dipole values = x y z
+  x,y,z = orientation of dipole moment vector
+  any of x,y,z can be an atom-style variable (see below)
+dipole/random value = seed Dlen
+  seed = random # seed (positive integer) for dipole moment orientations
+  Dlen = magnitude of dipole moment (dipole units)
+quat values = a b c theta
+  a,b,c = unit vector to rotate particle around via right-hand rule
+  theta = rotation angle (degrees)
+  any of a,b,c,theta can be an atom-style variable (see below)
+quat/random value = seed
+  seed = random # seed (positive integer) for quaternion orientations
+diameter value = diameter of spherical particle (distance units)
+  value can be an atom-style variable (see below)
+shape value = Sx Sy Sz
+  Sx,Sy,Sz = 3 diameters of ellipsoid (distance units)
+length value = len
+  len = length of line segment (distance units)
+  len can be an atom-style variable (see below)
+tri value = side
+  side = side length of equilateral triangle (distance units)
+  side can be an atom-style variable (see below)
+theta value = angle (degrees)
+  angle = orientation of line segment with respect to x-axis
+  angle can be an atom-style variable (see below)
+angmom values = Lx Ly Lz
+  Lx,Ly,Lz = components of angular momentum vector (distance-mass-velocity units)
+  any of Lx,Ly,Lz can be an atom-style variable (see below)
+mass value = per-atom mass (mass units)
+  value can be an atom-style variable (see below)
+density value = particle density for sphere or ellipsoid (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)
+  value can be an atom-style variable (see below)
+volume value = particle volume for Peridynamic particle (distance^3 units)
+  value can be an atom-style variable (see below)
+image nx ny nz
+  nx,ny,nz = which periodic image of the simulation box the atom is in
+bond value = bond type for all bonds between selected atoms
+angle value = angle type for all angles between selected atoms
+dihedral value = dihedral type for all dihedrals between selected atoms
+improper value = improper type for all impropers between selected atoms
+meso_e value = energy of SPH particles (need units)
+  value can be an atom-style variable (see below)
+meso_cv value = heat capacity of SPH particles (need units)
+  value can be an atom-style variable (see below)
+meso_rho value = density of SPH particles (need units)
+  value can be an atom-style variable (see below)
+i_name value = value for custom integer vector with name
+  value can be an atom-style variable (see below)
+d_name value = value for custom floating-point vector with name
+  value can be an atom-style variable (see below)
    diff --git a/doc/shell.html b/doc/shell.html index eaf88c7f39..16b6175091 100644 --- a/doc/shell.html +++ b/doc/shell.html @@ -136,19 +136,19 @@ 
     cd arg = dir
-    dir = directory to change to
-  mkdir args = dir1 dir2 ...
-    dir1,dir2 = one or more directories to create
-  mv args = old new
-    old = old filename
-    new = new filename
-  rm args = file1 file2 ...
-    file1,file2 = one or more filenames to delete
-  rmdir args = dir1 dir2 ...
-    dir1,dir2 = one or more directories to delete
-  putenv args = var1=value1 var2=value2
-    var=value = one of more definitions of environment variables
-  anything else is passed as a command to the shell for direct execution
+  dir = directory to change to
+mkdir args = dir1 dir2 ...
+  dir1,dir2 = one or more directories to create
+mv args = old new
+  old = old filename
+  new = new filename
+rm args = file1 file2 ...
+  file1,file2 = one or more filenames to delete
+rmdir args = dir1 dir2 ...
+  dir1,dir2 = one or more directories to delete
+putenv args = var1=value1 var2=value2
+  var=value = one of more definitions of environment variables
+anything else is passed as a command to the shell for direct execution
    diff --git a/doc/special_bonds.html b/doc/special_bonds.html index a716bcd37a..a8b97e9d4d 100644 --- a/doc/special_bonds.html +++ b/doc/special_bonds.html @@ -137,19 +137,19 @@ 
     amber values = none
-  charmm values = none
-  dreiding values = none
-  fene values = none
-  lj/coul values = w1,w2,w3
-    w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones and Coulombic interactions
-  lj values = w1,w2,w3
-    w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions
-  coul values = w1,w2,w3
-    w1,w2,w3 = weights (0.0 to 1.0) on pairwise Coulombic interactions
-  angle value = yes or no
-  dihedral value = yes or no
-  extra value = N
-    N = number of extra 1-2,1-3,1-4 interactions to save space for
+charmm values = none
+dreiding values = none
+fene values = none
+lj/coul values = w1,w2,w3
+  w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones and Coulombic interactions
+lj values = w1,w2,w3
+  w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions
+coul values = w1,w2,w3
+  w1,w2,w3 = weights (0.0 to 1.0) on pairwise Coulombic interactions
+angle value = yes or no
+dihedral value = yes or no
+extra value = N
+  N = number of extra 1-2,1-3,1-4 interactions to save space for

    Examples:

    special_bonds amber
diff --git a/doc/tad.html b/doc/tad.html
index aa0bff9b8e..843fc4a7bb 100644
--- a/doc/tad.html
+++ b/doc/tad.html
@@ -144,20 +144,20 @@
 
 
     min values = etol ftol maxiter maxeval
-    etol = stopping tolerance for energy (energy units)
-    ftol = stopping tolerance for force (force units)
-    maxiter = max iterations of minimize
-    maxeval = max number of force/energy evaluations
-  neb values = ftol N1 N2 Nevery
-    etol = stopping tolerance for energy (energy units)
-    ftol = stopping tolerance for force (force units)
-    N1 = max # of iterations (timesteps) to run initial NEB
-    N2 = max # of iterations (timesteps) to run barrier-climbing NEB
-    Nevery = print NEB statistics every this many timesteps
-  neb_style value = quickmin or fire
-  neb_step value = dtneb
-    dtneb = timestep for NEB damped dynamics minimization
-  neb_log value = file where NEB statistics are printed
+  etol = stopping tolerance for energy (energy units)
+  ftol = stopping tolerance for force (force units)
+  maxiter = max iterations of minimize
+  maxeval = max number of force/energy evaluations
+neb values = ftol N1 N2 Nevery
+  etol = stopping tolerance for energy (energy units)
+  ftol = stopping tolerance for force (force units)
+  N1 = max # of iterations (timesteps) to run initial NEB
+  N2 = max # of iterations (timesteps) to run barrier-climbing NEB
+  Nevery = print NEB statistics every this many timesteps
+neb_style value = quickmin or fire
+neb_step value = dtneb
+  dtneb = timestep for NEB damped dynamics minimization
+neb_log value = file where NEB statistics are printed
    diff --git a/doc/thermo_style.html b/doc/thermo_style.html index 5195ac1a5c..981a09b10c 100644 --- a/doc/thermo_style.html +++ b/doc/thermo_style.html @@ -137,70 +137,70 @@ 
     one args = none
-  multi args = none
-  custom args = list of keywords
-    possible keywords = step, elapsed, elaplong, dt, time,
-                        cpu, tpcpu, spcpu, cpuremain, part,
-                        atoms, temp, press, pe, ke, etotal, enthalpy,
-                        evdwl, ecoul, epair, ebond, eangle, edihed, eimp,
-                        emol, elong, etail,
-                        vol, density, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
-                     xy, xz, yz, xlat, ylat, zlat,
-                        bonds, angles, dihedrals, impropers,
-                     pxx, pyy, pzz, pxy, pxz, pyz,
-                     fmax, fnorm, nbuild, ndanger,
-                     cella, cellb, cellc, cellalpha, cellbeta, cellgamma,
-                     c_ID, c_ID[I], c_ID[I][J],
-                        f_ID, f_ID[I], f_ID[I][J],
-                        v_name
-      step = timestep
-      elapsed = timesteps since start of this run
-      elaplong = timesteps since start of initial run in a series of runs
-      dt = timestep size
-      time = simulation time
-      cpu = elapsed CPU time in seconds
-      tpcpu = time per CPU second
-      spcpu = timesteps per CPU second
-      cpuremain = estimated CPU time remaining in run
-      part = which partition (0 to Npartition-1) this is
-      atoms = # of atoms
-      temp = temperature
-      press = pressure
-      pe = total potential energy
-      ke = kinetic energy
-      etotal = total energy (pe + ke)
-      enthalpy = enthalpy (etotal + press*vol)
-      evdwl = VanderWaal pairwise energy
-      ecoul = Coulombic pairwise energy
-      epair = pairwise energy (evdwl + ecoul + elong + etail)
-      ebond = bond energy
-      eangle = angle energy
-      edihed = dihedral energy
-      eimp = improper energy
-      emol = molecular energy (ebond + eangle + edihed + eimp)
-      elong = long-range kspace energy
-      etail = VanderWaal energy long-range tail correction
-      vol = volume
-      density = mass density of system
-      lx,ly,lz = box lengths in x,y,z
-      xlo,xhi,ylo,yhi,zlo,zhi = box boundaries
-      xy,xz,yz = box tilt for triclinic (non-orthogonal) simulation boxes
-      xlat,ylat,zlat = lattice spacings as calculated by lattice command
-      bonds,angles,dihedrals,impropers = # of these interactions defined
-      pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor
-      fmax = max component of force on any atom in any dimension
-      fnorm = length of force vector for all atoms
-      nbuild = # of neighbor list builds
-      ndanger = # of dangerous neighbor list builds
-      cella,cellb,cellc = periodic cell lattice constants a,b,c
-      cellalpha, cellbeta, cellgamma = periodic cell angles alpha,beta,gamma
-      c_ID = global scalar value calculated by a compute with ID
-      c_ID[I] = Ith component of global vector calculated by a compute with ID
-      c_ID[I][J] = I,J component of global array calculated by a compute with ID
-      f_ID = global scalar value calculated by a fix with ID
-      f_ID[I] = Ith component of global vector calculated by a fix with ID
-      f_ID[I][J] = I,J component of global array calculated by a fix with ID
-      v_name = scalar value calculated by an equal-style variable with name
+multi args = none
+custom args = list of keywords
+  possible keywords = step, elapsed, elaplong, dt, time,
+                      cpu, tpcpu, spcpu, cpuremain, part,
+                      atoms, temp, press, pe, ke, etotal, enthalpy,
+                      evdwl, ecoul, epair, ebond, eangle, edihed, eimp,
+                      emol, elong, etail,
+                      vol, density, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
+                   xy, xz, yz, xlat, ylat, zlat,
+                      bonds, angles, dihedrals, impropers,
+                   pxx, pyy, pzz, pxy, pxz, pyz,
+                   fmax, fnorm, nbuild, ndanger,
+                   cella, cellb, cellc, cellalpha, cellbeta, cellgamma,
+                   c_ID, c_ID[I], c_ID[I][J],
+                      f_ID, f_ID[I], f_ID[I][J],
+                      v_name
+    step = timestep
+    elapsed = timesteps since start of this run
+    elaplong = timesteps since start of initial run in a series of runs
+    dt = timestep size
+    time = simulation time
+    cpu = elapsed CPU time in seconds
+    tpcpu = time per CPU second
+    spcpu = timesteps per CPU second
+    cpuremain = estimated CPU time remaining in run
+    part = which partition (0 to Npartition-1) this is
+    atoms = # of atoms
+    temp = temperature
+    press = pressure
+    pe = total potential energy
+    ke = kinetic energy
+    etotal = total energy (pe + ke)
+    enthalpy = enthalpy (etotal + press*vol)
+    evdwl = VanderWaal pairwise energy
+    ecoul = Coulombic pairwise energy
+    epair = pairwise energy (evdwl + ecoul + elong + etail)
+    ebond = bond energy
+    eangle = angle energy
+    edihed = dihedral energy
+    eimp = improper energy
+    emol = molecular energy (ebond + eangle + edihed + eimp)
+    elong = long-range kspace energy
+    etail = VanderWaal energy long-range tail correction
+    vol = volume
+    density = mass density of system
+    lx,ly,lz = box lengths in x,y,z
+    xlo,xhi,ylo,yhi,zlo,zhi = box boundaries
+    xy,xz,yz = box tilt for triclinic (non-orthogonal) simulation boxes
+    xlat,ylat,zlat = lattice spacings as calculated by lattice command
+    bonds,angles,dihedrals,impropers = # of these interactions defined
+    pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor
+    fmax = max component of force on any atom in any dimension
+    fnorm = length of force vector for all atoms
+    nbuild = # of neighbor list builds
+    ndanger = # of dangerous neighbor list builds
+    cella,cellb,cellc = periodic cell lattice constants a,b,c
+    cellalpha, cellbeta, cellgamma = periodic cell angles alpha,beta,gamma
+    c_ID = global scalar value calculated by a compute with ID
+    c_ID[I] = Ith component of global vector calculated by a compute with ID
+    c_ID[I][J] = I,J component of global array calculated by a compute with ID
+    f_ID = global scalar value calculated by a fix with ID
+    f_ID[I] = Ith component of global vector calculated by a fix with ID
+    f_ID[I][J] = I,J component of global array calculated by a fix with ID
+    v_name = scalar value calculated by an equal-style variable with name
    diff --git a/doc/variable.html b/doc/variable.html index d3867fa481..ab9808a4d7 100644 --- a/doc/variable.html +++ b/doc/variable.html @@ -138,60 +138,60 @@ 
     delete = no args
-  index args = one or more strings
-  loop args = N
-    N = integer size of loop, loop from 1 to N inclusive
-  loop args = N pad
-    N = integer size of loop, loop from 1 to N inclusive
-    pad = all values will be same length, e.g. 001, 002, ..., 100
-  loop args = N1 N2
-    N1,N2 = loop from N1 to N2 inclusive
-  loop args = N1 N2 pad
-    N1,N2 = loop from N1 to N2 inclusive
-    pad = all values will be same length, e.g. 050, 051, ..., 100
-  world args = one string for each partition of processors
-  universe args = one or more strings
-  uloop args = N
-    N = integer size of loop
-  uloop args = N pad
-    N = integer size of loop
-    pad = all values will be same length, e.g. 001, 002, ..., 100
-  string arg = one string
-  format args = vname fstr
-    vname = name of equal-style variable to evaluate
-    fstr = C-style format string
-  getenv arg = one string
-  file arg = filename
-  atomfile arg = filename
-  python arg = function
-  equal or atom args = one formula containing numbers, thermo keywords, math operations, group functions, atom values and vectors, compute/fix/variable references
-    numbers = 0.0, 100, -5.4, 2.8e-4, etc
-    constants = PI
-    thermo keywords = vol, ke, press, etc from thermo_style
-    math operators = (), -x, x+y, x-y, x*y, x/y, x^y, x%y,
-                     x == y, x != y, x &lt y, x &lt= y, x &gt y, x &gt= y, x && y, x || y, !x
-    math functions = sqrt(x), exp(x), ln(x), log(x), abs(x),
-                     sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x),
-                     random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x)
-                     ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z),
-                  stride(x,y,z), stride2(x,y,z,a,b,c),
-                  vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)
-    group functions = count(group), mass(group), charge(group),
-                   xcm(group,dim), vcm(group,dim), fcm(group,dim),
-                   bound(group,dir), gyration(group), ke(group),
-                   angmom(group,dim), torque(group,dim),
-                      inertia(group,dimdim), omega(group,dim)
-    region functions = count(group,region), mass(group,region), charge(group,region),
-                   xcm(group,dim,region), vcm(group,dim,region), fcm(group,dim,region),
-                   bound(group,dir,region), gyration(group,region), ke(group,reigon),
-                   angmom(group,dim,region), torque(group,dim,region),
-                   inertia(group,dimdim,region), omega(group,dim,region)
-    special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x)
-    atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]
-    atom vector = id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q
-    compute references = c_ID, c_ID[i], c_ID[i][j]
-    fix references = f_ID, f_ID[i], f_ID[i][j]
-    variable references = v_name, v_name[i]
+index args = one or more strings
+loop args = N
+  N = integer size of loop, loop from 1 to N inclusive
+loop args = N pad
+  N = integer size of loop, loop from 1 to N inclusive
+  pad = all values will be same length, e.g. 001, 002, ..., 100
+loop args = N1 N2
+  N1,N2 = loop from N1 to N2 inclusive
+loop args = N1 N2 pad
+  N1,N2 = loop from N1 to N2 inclusive
+  pad = all values will be same length, e.g. 050, 051, ..., 100
+world args = one string for each partition of processors
+universe args = one or more strings
+uloop args = N
+  N = integer size of loop
+uloop args = N pad
+  N = integer size of loop
+  pad = all values will be same length, e.g. 001, 002, ..., 100
+string arg = one string
+format args = vname fstr
+  vname = name of equal-style variable to evaluate
+  fstr = C-style format string
+getenv arg = one string
+file arg = filename
+atomfile arg = filename
+python arg = function
+equal or atom args = one formula containing numbers, thermo keywords, math operations, group functions, atom values and vectors, compute/fix/variable references
+  numbers = 0.0, 100, -5.4, 2.8e-4, etc
+  constants = PI
+  thermo keywords = vol, ke, press, etc from thermo_style
+  math operators = (), -x, x+y, x-y, x*y, x/y, x^y, x%y,
+                   x == y, x != y, x &lt y, x &lt= y, x &gt y, x &gt= y, x && y, x || y, !x
+  math functions = sqrt(x), exp(x), ln(x), log(x), abs(x),
+                   sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x),
+                   random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x)
+                   ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z),
+                stride(x,y,z), stride2(x,y,z,a,b,c),
+                vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)
+  group functions = count(group), mass(group), charge(group),
+                 xcm(group,dim), vcm(group,dim), fcm(group,dim),
+                 bound(group,dir), gyration(group), ke(group),
+                 angmom(group,dim), torque(group,dim),
+                    inertia(group,dimdim), omega(group,dim)
+  region functions = count(group,region), mass(group,region), charge(group,region),
+                 xcm(group,dim,region), vcm(group,dim,region), fcm(group,dim,region),
+                 bound(group,dir,region), gyration(group,region), ke(group,reigon),
+                 angmom(group,dim,region), torque(group,dim,region),
+                 inertia(group,dimdim,region), omega(group,dim,region)
+  special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x)
+  atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]
+  atom vector = id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q
+  compute references = c_ID, c_ID[i], c_ID[i][j]
+  fix references = f_ID, f_ID[i], f_ID[i][j]
+  variable references = v_name, v_name[i]
    diff --git a/doc/velocity.html b/doc/velocity.html index aa82e906d3..32ca817d6f 100644 --- a/doc/velocity.html +++ b/doc/velocity.html @@ -137,21 +137,21 @@ 
     create args = temp seed
-    temp = temperature value (temperature units)
-    seed = random # seed (positive integer)
-  set args = vx vy vz
-    vx,vy,vz = velocity value or NULL (velocity units)
-    any of vx,vy,vz van be a variable (see below)
-  scale arg = temp
-    temp = temperature value (temperature units)
-  ramp args = vdim vlo vhi dim clo chi
-    vdim = vx or vy or vz
-    vlo,vhi = lower and upper velocity value (velocity units)
-    dim = x or y or z
-    clo,chi = lower and upper coordinate bound (distance units)
-  zero arg = linear or angular
-    linear = zero the linear momentum
-    angular = zero the angular momentum
+  temp = temperature value (temperature units)
+  seed = random # seed (positive integer)
+set args = vx vy vz
+  vx,vy,vz = velocity value or NULL (velocity units)
+  any of vx,vy,vz van be a variable (see below)
+scale arg = temp
+  temp = temperature value (temperature units)
+ramp args = vdim vlo vhi dim clo chi
+  vdim = vx or vy or vz
+  vlo,vhi = lower and upper velocity value (velocity units)
+  dim = x or y or z
+  clo,chi = lower and upper coordinate bound (distance units)
+zero arg = linear or angular
+  linear = zero the linear momentum
+  angular = zero the angular momentum
    • zero or more keyword/value pairs may be appended
      • @@ -159,15 +159,15 @@ 
     dist value = uniform or gaussian
-  sum value = no or yes
-  mom value = no or yes
-  rot value = no or yes
-  temp value = temperature compute ID
-  bias value = no or yes
-  loop value = all or local or geom
-  rigid value = fix-ID
-    fix-ID = ID of rigid body fix
-  units value = box or lattice
+sum value = no or yes
+mom value = no or yes
+rot value = no or yes
+temp value = temperature compute ID
+bias value = no or yes
+loop value = all or local or geom
+rigid value = fix-ID
+  fix-ID = ID of rigid body fix
+units value = box or lattice
    diff --git a/doc/write_data.html b/doc/write_data.html index dcc68346d3..cb8e4e6bbd 100644 --- a/doc/write_data.html +++ b/doc/write_data.html @@ -138,9 +138,9 @@ 
     nocoeff = do not write out force field info
-  pair value = ii or ij
-    ii = write one line of pair coefficient info per atom type
-    ij = write one line of pair coefficient info per IJ atom type pair
+pair value = ii or ij
+  ii = write one line of pair coefficient info per atom type
+  ij = write one line of pair coefficient info per IJ atom type pair
    diff --git a/doc/write_restart.html b/doc/write_restart.html index d5b7a00b2c..e9eccb74a2 100644 --- a/doc/write_restart.html +++ b/doc/write_restart.html @@ -138,9 +138,9 @@ 
     fileper arg = Np
-    Np = write one file for every this many processors
-  nfile arg = Nf
-    Nf = write this many files, one from each of Nf processors
+  Np = write one file for every this many processors
+nfile arg = Nf
+  Nf = write this many files, one from each of Nf processors