From cd714e67a745b808845adcabe6756a44e371f40f Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 17 Nov 2015 21:42:36 +0000 Subject: [PATCH 01/11] '' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14255 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/doc2/Manual.html.html | 4 +- doc/doc2/Section_commands.html | 14 +-- doc/doc2/compute.html | 12 +-- doc/doc2/compute_cluster_atom.html | 16 +++ doc/doc2/compute_hexorder_atom.html | 54 ++++++----- doc/doc2/compute_orientorder_atom.html | 129 +++++++++++++++++++++++++ doc/doc2/fix.html | 7 +- 7 files changed, 192 insertions(+), 44 deletions(-) create mode 100644 doc/doc2/compute_orientorder_atom.html diff --git a/doc/doc2/Manual.html.html b/doc/doc2/Manual.html.html index c4c0509ea7..ffc08f8f2e 100644 --- a/doc/doc2/Manual.html.html +++ b/doc/doc2/Manual.html.html @@ -3,7 +3,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@

LAMMPS Documentation

-

31 Oct 2015 version +

6 Nov 2015 version

Version info:

diff --git a/doc/doc2/Section_commands.html b/doc/doc2/Section_commands.html index 6254a22fec..eb161f65cf 100644 --- a/doc/doc2/Section_commands.html +++ b/doc/doc2/Section_commands.html @@ -461,13 +461,13 @@ KOKKOS, o = USER-OMP, t = OPT. damage/atomdihedral/localdilatation/atomdisplace/atomerotate/asphereerotate/rigid erotate/sphereerotate/sphere/atomevent/displacegroup/groupgyrationgyration/chunk heat/fluxhexorder/atomimproper/localinertia/chunkkeke/atom -ke/rigidmsdmsd/chunkmsd/nongaussomega/chunkpair -pair/localpe (c)pe/atomplasticity/atompressure (c)property/atom -property/localproperty/chunkrdfreducereduce/regionslice -sna/atomsnad/atomsnav/atomstress/atomtemp (ck)temp/asphere -temp/comtemp/chunktemp/deformtemp/partial (c)temp/profiletemp/ramp -temp/regiontemp/spheretitorque/chunkvacfvcm/chunk -voronoi/atom +ke/rigidmsdmsd/chunkmsd/nongaussomega/chunkorientorder/atom +pairpair/localpe (c)pe/atomplasticity/atompressure (c) +property/atomproperty/localproperty/chunkrdfreducereduce/region +slicesna/atomsnad/atomsnav/atomstress/atomtemp (ck) +temp/aspheretemp/comtemp/chunktemp/deformtemp/partial (c)temp/profile +temp/ramptemp/regiontemp/spheretitorque/chunkvacf +vcm/chunkvoronoi/atom

These are additional compute styles in USER packages, which can be diff --git a/doc/doc2/compute.html b/doc/doc2/compute.html index fc5922bd60..0752ccf682 100644 --- a/doc/doc2/compute.html +++ b/doc/doc2/compute.html @@ -166,23 +166,19 @@ calculations accessed in the various ways described above.

Each compute style has its own doc page which describes its arguments and what it does. Here is an alphabetic list of compute styles available in LAMMPS. They are also given in more compact form in the -compute section of this page. +Compute section of this page.

There are also additional compute styles (not listed here) submitted by users which are included in the LAMMPS distribution. The list of these with links to the individual styles are given in the compute section of this page.

-

There are also additional accelerated compute styles (note listed -here) included in the LAMMPS distribution for faster performance on -CPUs and GPUs. The list of these with links to the individual styles -are given in the compute section of this -page. -

Examples: 

compute 1 all hexorder/atom 
-compute 1 all hexorder/atom n 4 
+compute 1 all hexorder/atom degree 4 nnn 4 cutoff 1.2

Description:

@@ -42,7 +43,7 @@ is a complex number (stored as two real numbers) defined as follows:

-

where the sum is over the n nearest neighbors +

where the sum is over the nnn nearest neighbors of the central atom. The angle theta is formed by the bond vector rij and the x axis. theta is calculated only using the x and y components, whereas the distance from the @@ -51,18 +52,30 @@ central atom is calculated using all three Neighbor atoms not in the group are included in the order parameter of atoms in the group.

-

The optional keyword n sets the degree of the order parameter. -The default value is 6. For a perfect hexagonal lattice, +

The optional keyword cutoff defines the distance cutoff +used when searching for neighbors. The default value, also +the maximum allowable value, is the cutoff specified +by the pair style. +

+

The optional keyword nnn defines the number of nearest +neighbors used to calculate qn. The default value is 6. +If the value is NULL, then all neighbors up to the +distance cutoff are used. +

+

The optional keyword degree sets the degree n of the order parameter. +The default value is 6. For a perfect hexagonal lattice with +nnn = 6, q6 = exp(6 i phi) for all atoms, where the constant 0 < phi < pi/3 -depends only on the orientation of the lattice relative to the x axis. +depends only on the orientation of the lattice relative to the x axis. In an isotropic liquid, local neighborhoods may still exhibit weak hexagonal symmetry, but because the orientational correlation decays quickly with distance, the value of phi will be different for -different atoms, and |<q6>| << 1. +different atoms, and so when q6 is averaged over all the atoms +in the system, |<q6>| << 1.

-

The value of qn will be zero for atoms not in the -specified compute group. If the atom has less than n neighbors (within -the potential cutoff), then qn is set to zero. +

The value of qn is set to zero for atoms not in the +specified compute group, as well as for atoms that have less than +nnn neighbors within the distance cutoff.

The neighbor list needed to compute this quantity is constructed each time the calculation is performed (i.e. each time a snapshot of atoms @@ -75,8 +88,8 @@ interactions between atoms in the same bond, angle, or dihedral. This is the default setting for the special_bonds command, and means those pairwise interactions do not appear in the neighbor list. Because this fix uses the neighbor list, it also means -those pairs will not be included in the order parameter. One way -to get around this, is to write a dump file, and use the +those pairs will not be included in the order parameter. This difficulty +can be circumvented by writing a dump file, and using the rerun command to compute the order parameter for snapshots in the dump file. The rerun script can use a special_bonds command that includes all pairs in @@ -85,26 +98,23 @@ the neighbor list.

Output info:

This compute calculates a per-atom array with 2 columns, giving the -real and imaginary parts of qn, respectively. +real and imaginary parts qn, a complex number restricted to the +unit disk of the complex plane i.e. Re(qn)^2 + Im(qn)^2 <= 1 .

These values can be accessed by any command that uses per-atom values from a compute as input. See Section_howto 15 for an overview of LAMMPS output options.

-

The per-atom array contain pairs of numbers representing the -real and imaginary parts of qn, a complex number subject to the -constraint |qn| <= 1. -

Restrictions: none

Related commands:

-

compute coord/atom, compute centro/atom +

compute orientorder/atom, compute coord/atom, compute centro/atom

Default:

-

The option default is n = 6. +

The option defaults are cutoff = pair style cutoff, nnn = 6, degree = 6

diff --git a/doc/doc2/compute_orientorder_atom.html b/doc/doc2/compute_orientorder_atom.html new file mode 100644 index 0000000000..d3f28d7c36 --- /dev/null +++ b/doc/doc2/compute_orientorder_atom.html @@ -0,0 +1,129 @@ + +
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
+ + + + + + +
+ +

compute orientorder/atom command +

+

Syntax: +

+
compute ID group-ID orientorder/atom keyword values ... 
+
+ +

Examples: +

+
compute 1 all orientorder/atom 
+compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5 
+
+

Description: +

+

Define a computation that calculates a set of bond-orientational +order parameters Ql for each atom in a group. These order parameters +were introduced by Steinhardt et al. as a way to +characterize the local orientational order in atomic structures. +For each atom, Ql is a real number defined as follows: +

+
+
+

The first equation defines the spherical harmonic order parameters. +These are complex number components of the 3D analog of the 2D order +parameter qn, which is implemented as LAMMPS compute +hexorder/atom. +The summation is over the nnn nearest +neighbors of the central atom. +The angles theta and phi are the standard spherical polar angles +defining the direction of the bond vector rij. +The second equation defines Ql, which is a +rotationally invariant scalar quantity obtained by summing +over all the components of degree l. +

+

The optional keyword cutoff defines the distance cutoff +used when searching for neighbors. The default value, also +the maximum allowable value, is the cutoff specified +by the pair style. +

+

The optional keyword nnn defines the number of nearest +neighbors used to calculate Ql. The default value is 12. +If the value is NULL, then all neighbors up to the +specified distance cutoff are used. +

+

The optional keyword degrees defines the list of order parameters to +be computed. The first argument nlvalues is the number of order +parameters. This is followed by that number of integers giving the +degree of each order parameter. Because Q2 and all odd-degree +order parameters are zero for atoms in cubic crystals +(see Steinhardt), the default order parameters +are Q4, Q6, Q8, Q10, and Q12. The correct +numerical values for commonly encountered high-symmetry +structures are given by Mickel et al. +

+

The value of Ql is set to zero for atoms not in the +specified compute group, as well as for atoms that have less than +nnn neighbors within the distance cutoff. +

+

The neighbor list needed to compute this quantity is constructed each +time the calculation is performed (i.e. each time a snapshot of atoms +is dumped). Thus it can be inefficient to compute/dump this quantity +too frequently. +

+

IMPORTANT NOTE: If you have a bonded system, then the settings of +special_bonds command can remove pairwise +interactions between atoms in the same bond, angle, or dihedral. This +is the default setting for the special_bonds +command, and means those pairwise interactions do not appear in the +neighbor list. Because this fix uses the neighbor list, it also means +those pairs will not be included in the order parameter. This difficulty +can be circumvented by writing a dump file, and using the +rerun command to compute the order parameter for snapshots +in the dump file. The rerun script can use a +special_bonds command that includes all pairs in +the neighbor list. +

+

Output info: +

+

This compute calculates a per-atom array with nlvalues columns, giving the +Ql values for each atom, which are real numbers on the range 0 <= Ql <= 1. +

+

These values can be accessed by any command that uses +per-atom values from a compute as input. See Section_howto +15 for an overview of LAMMPS output +options. +

+

Restrictions: none +

+

Related commands: +

+

compute coord/atom, compute centro/atom, compute hexorder/atom +

+

Default: +

+

The option defaults are cutoff = pair style cutoff, nnn = 12, degrees = 5 4 6 8 9 10 12 i.e. Q4, Q6, Q8, Q10, and Q12. +

+
+ + + +(Steinhardt) P. Steinhardt, D. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983). + + +

(Mickel) W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke, J. Chem. Phys. 138, 044501 (2013). +

+ diff --git a/doc/doc2/fix.html b/doc/doc2/fix.html index ad6b904b3b..4658079d8e 100644 --- a/doc/doc2/fix.html +++ b/doc/doc2/fix.html @@ -159,7 +159,7 @@ for further info.

Each fix style has its own documentation page which describes its arguments and what it does, as listed below. Here is an alphabetic list of fix styles available in LAMMPS. They are also given in more -compact form in the fix section of this +compact form in the Fix section of this page.

There are also additional fix styles (not listed here) submitted by @@ -167,11 +167,6 @@ users which are included in the LAMMPS distribution. The list of these with links to the individual styles are given in the fix section of this page.

-

There are also additional accelerated fix styles (not listed here) -included in the LAMMPS distribution for faster performance on CPUs and -GPUs. The list of these with links to the individual styles are given -in the fix section of this page. -