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\documentclass[12pt]{article}
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\begin{document}
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$$
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\mathbf{J}
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= \sum_i e_i \mathbf{v}_i
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+ \sum_{i<j} \left( \mathbf{f}_{ij} \cdot \mathbf{v}_j \right) \mathbf{x}_{ij}
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= \sum_i e_i \mathbf{v}_i
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+ \frac{1}{2} \sum_{i<j} \left( \mathbf{f}_{ij} \cdot \left(\mathbf{v}_i + \mathbf{v}_j \right) \right) \mathbf{x}_{ij}
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$$
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\end{document}
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\documentclass[12pt]{article}
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\begin{document}
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$$
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\kappa = \frac{V}{k_B T^2} \int_0^\infty \langle J_x(0) J_x(t) \rangle \, dt
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= \frac{V}{3 k_B T^2} \int_0^\infty \langle \mathbf{J}(0) \cdot \mathbf{J}(t) \rangle \, dt
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$$
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\end{document}
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#!/usr/bin/python
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"""
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function:
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parse the block of thermo data in a lammps logfile and perform auto- and
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cross correlation of the specified column data. The total sum of the
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correlation is also computed which can be converted to an integral by
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multiplying by the timestep.
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output:
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standard output contains column data for the auto- & cross correlations
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plus the total sum of each. Note, only the upper triangle of the
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correlation matrix is computed.
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usage:
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correlate.py [-c col] <-c col2> <-s max_correlation_time> [logfile]
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"""
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import sys
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import re
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import array
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# parse command line
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maxCorrelationTime = 0
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cols = array.array("I")
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nCols = 0
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args = sys.argv[1:]
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index = 0
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while index < len(args):
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arg = args[index]
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index += 1
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if (arg == "-c"):
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cols.append(int(args[index])-1)
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nCols += 1
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index += 1
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elif (arg == "-s"):
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maxCorrelationTime = int(args[index])
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index += 1
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else :
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filename = arg
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if (nCols < 1): raise RuntimeError, 'no data columns requested'
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data = [array.array("d")]
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for s in range(1,nCols) : data.append( array.array("d") )
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# read data block from log file
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start = False
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input = open(filename)
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nSamples = 0
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pattern = re.compile('\d')
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line = input.readline()
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while line :
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columns = line.split()
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if (columns and pattern.match(columns[0])) :
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for i in range(nCols):
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data[i].append( float(columns[cols[i]]) )
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nSamples += 1
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start = True
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else :
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if (start) : break
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line = input.readline()
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print "# read :",nSamples," samples of ", nCols," data"
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if( maxCorrelationTime < 1): maxCorrelationTime = int(nSamples/2);
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# correlate and integrate
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correlationPairs = []
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for i in range(0,nCols):
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for j in range(i,nCols): # note only upper triangle of the correlation matrix
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correlationPairs.append([i,j])
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header = "# "
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for k in range(len(correlationPairs)):
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i = str(correlationPairs[k][0]+1)
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j = str(correlationPairs[k][1]+1)
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header += " C"+i+j+" sum_C"+i+j
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print header
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nCorrelationPairs = len(correlationPairs)
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sum = [0.0] * nCorrelationPairs
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for s in range(maxCorrelationTime) :
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correlation = [0.0] * nCorrelationPairs
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nt = nSamples-s
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for t in range(0,nt) :
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for p in range(nCorrelationPairs):
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i = correlationPairs[p][0]
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j = correlationPairs[p][1]
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correlation[p] += data[i][t]*data[j][s+t]
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output = ""
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for p in range(0,nCorrelationPairs):
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correlation[p] /= nt
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sum[p] += correlation[p]
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output += str(correlation[p]) + " " + str(sum[p]) + " "
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print output
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@ -343,10 +343,10 @@ description:
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</P>
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</P>
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<DIV ALIGN=center><TABLE BORDER=1 >
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<DIV ALIGN=center><TABLE BORDER=1 >
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||||||
<TR ALIGN="center"><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD></TR>
|
<TR ALIGN="center"><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_pe.html">pe</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD></TR>
|
<TR ALIGN="center"><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_pe.html">pe</A></TD></TR>
|
||||||
<TR ALIGN="center"><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD></TR>
|
<TR ALIGN="center"><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD></TR>
|
||||||
<TR ALIGN="center"><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD></TR>
|
<TR ALIGN="center"><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD></TR>
|
||||||
<TR ALIGN="center"><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A>
|
<TR ALIGN="center"><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A>
|
||||||
</TD></TR></TABLE></DIV>
|
</TD></TR></TABLE></DIV>
|
||||||
|
|
||||||
<P>These are compute styles contributed by users, which can be used if
|
<P>These are compute styles contributed by users, which can be used if
|
||||||
|
|
|
||||||
|
|
@ -462,6 +462,7 @@ description:
|
||||||
"erotate/asphere"_compute_erotate_asphere.html,
|
"erotate/asphere"_compute_erotate_asphere.html,
|
||||||
"erotate/sphere"_compute_erotate_sphere.html,
|
"erotate/sphere"_compute_erotate_sphere.html,
|
||||||
"group/group"_compute_group_group.html,
|
"group/group"_compute_group_group.html,
|
||||||
|
"heat/flux"_compute_heat_flux.html,
|
||||||
"ke"_compute_ke.html,
|
"ke"_compute_ke.html,
|
||||||
"ke/atom"_compute_ke_atom.html,
|
"ke/atom"_compute_ke_atom.html,
|
||||||
"pe"_compute_pe.html,
|
"pe"_compute_pe.html,
|
||||||
|
|
|
||||||
|
|
@ -117,6 +117,7 @@ available in LAMMPS:
|
||||||
<LI><A HREF = "compute_erotate_asphere.html">erotate/asphere</A> - rotational energy of aspherical particles
|
<LI><A HREF = "compute_erotate_asphere.html">erotate/asphere</A> - rotational energy of aspherical particles
|
||||||
<LI><A HREF = "compute_erotate_sphere.html">erotate/sphere</A> - rotational energy of spherical particles
|
<LI><A HREF = "compute_erotate_sphere.html">erotate/sphere</A> - rotational energy of spherical particles
|
||||||
<LI><A HREF = "compute_group_group.html">group/group</A> - energy/force between two groups of atoms
|
<LI><A HREF = "compute_group_group.html">group/group</A> - energy/force between two groups of atoms
|
||||||
|
<LI><A HREF = "compute_heat_flux.html">heat/flux</A> - heat flux through a group of atoms
|
||||||
<LI><A HREF = "compute_ke.html">ke</A> - translational kinetic energy
|
<LI><A HREF = "compute_ke.html">ke</A> - translational kinetic energy
|
||||||
<LI><A HREF = "compute_ke_atom.html">ke/atom</A> - kinetic energy for each atom
|
<LI><A HREF = "compute_ke_atom.html">ke/atom</A> - kinetic energy for each atom
|
||||||
<LI><A HREF = "compute_pe.html">pe</A> - potential energy
|
<LI><A HREF = "compute_pe.html">pe</A> - potential energy
|
||||||
|
|
|
||||||
|
|
@ -114,6 +114,7 @@ available in LAMMPS:
|
||||||
"erotate/asphere"_compute_erotate_asphere.html - rotational energy of aspherical particles
|
"erotate/asphere"_compute_erotate_asphere.html - rotational energy of aspherical particles
|
||||||
"erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles
|
"erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles
|
||||||
"group/group"_compute_group_group.html - energy/force between two groups of atoms
|
"group/group"_compute_group_group.html - energy/force between two groups of atoms
|
||||||
|
"heat/flux"_compute_heat_flux.html - heat flux through a group of atoms
|
||||||
"ke"_compute_ke.html - translational kinetic energy
|
"ke"_compute_ke.html - translational kinetic energy
|
||||||
"ke/atom"_compute_ke_atom.html - kinetic energy for each atom
|
"ke/atom"_compute_ke_atom.html - kinetic energy for each atom
|
||||||
"pe"_compute_pe.html - potential energy
|
"pe"_compute_pe.html - potential energy
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,147 @@
|
||||||
|
<HTML>
|
||||||
|
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
|
||||||
|
</CENTER>
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
<HR>
|
||||||
|
|
||||||
|
<H3>compute heat/flux command
|
||||||
|
</H3>
|
||||||
|
<P><B>Syntax:</B>
|
||||||
|
</P>
|
||||||
|
<PRE>compute ID group-ID heat/flux pe-ID
|
||||||
|
</PRE>
|
||||||
|
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
||||||
|
<LI>heat/flux = style name of this compute command
|
||||||
|
<LI>pe-ID = ID of a compute that calculates per-atom potential energy
|
||||||
|
</UL>
|
||||||
|
<P><B>Examples:</B>
|
||||||
|
</P>
|
||||||
|
<PRE>compute myFlux all heat/flux myPE
|
||||||
|
</PRE>
|
||||||
|
<P><B>Description:</B>
|
||||||
|
</P>
|
||||||
|
<P>Define a computation that calculates the heat flux vector based on
|
||||||
|
interactions between atoms in the specified group. This can be used
|
||||||
|
by itself to measure the heat flux between a hot and cold reservoir of
|
||||||
|
particles or to calculate a thermal conductivity using the Green-Kubo
|
||||||
|
formalism.
|
||||||
|
</P>
|
||||||
|
<P>The compute takes a <I>pe-ID</I> argument which is the ID of a <A HREF = "compute_pe_atom.html">compute
|
||||||
|
pe/atom</A> that calculates per-atom potential
|
||||||
|
energy. It should be defined for the same group used by compute
|
||||||
|
heat/flux, though LAMMPS does not check for this.
|
||||||
|
</P>
|
||||||
|
<P>The Green-Kubo formulas relate the ensemble average of the
|
||||||
|
auto-correlation of the heat flux J to the thermal conductivity kappa.
|
||||||
|
</P>
|
||||||
|
<CENTER><IMG SRC = "Eqs/heat_flux_k.jpg">
|
||||||
|
</CENTER>
|
||||||
|
<CENTER><IMG SRC = "Eqs/heat_flux_J.jpg">
|
||||||
|
</CENTER>
|
||||||
|
<P>Ei is the per-atom energy (potential and kinetic). The potential term
|
||||||
|
is calculated by the compute <I>pe-ID</I> specified as an argument to
|
||||||
|
the compute heat/flux command.
|
||||||
|
</P>
|
||||||
|
<P>IMPORTANT NOTE: The per-atom potential energy calculated by the
|
||||||
|
<I>pe-ID</I> compute should only include pairwise energy, to be consistent
|
||||||
|
with the full heat-flux calculation. Thus if any bonds, angles, etc
|
||||||
|
exist in the system, the compute should limit its calculation to only
|
||||||
|
the pair contribution. E.g. it could be defined as
|
||||||
|
</P>
|
||||||
|
<PRE>compute myPE all pe/atom pair
|
||||||
|
</PRE>
|
||||||
|
<P>Note that if <I>pair</I> is not listed as the last argument, it will be
|
||||||
|
included by default, but so will other contributions such as bond,
|
||||||
|
angle, etc.
|
||||||
|
</P>
|
||||||
|
<P>The heat flux J is calculated by this compute for pairwise
|
||||||
|
interactions for any I,J pair where one of the 2 atoms in is the
|
||||||
|
compute group. It can be output every so many timesteps (e.g. via the
|
||||||
|
thermo_style custom command). Then as post-processing steps, an
|
||||||
|
autocorrelation can be performed, its integral estimated, and the
|
||||||
|
Green-Kubo formula evaluated.
|
||||||
|
</P>
|
||||||
|
<P>Here is an example of this procedure. First a LAMMPS input script for
|
||||||
|
solid Ar is appended below. A Python script
|
||||||
|
<A HREF = "Scripts/correlate.py">correlate.py</A> is also given, which calculates
|
||||||
|
the autocorrelation of the flux output in the logfile flux.log,
|
||||||
|
produced by the LAMMPS run. It is invoked as
|
||||||
|
</P>
|
||||||
|
<PRE>correlate.py flux.log -c 3 -s 200
|
||||||
|
</PRE>
|
||||||
|
<P>The resulting data lists the autocorrelation in column 1 and the
|
||||||
|
integral of the autocorrelation in column 2. The integral of the
|
||||||
|
correlation needs to be multiplied by V/(kB T^2) times the sample
|
||||||
|
interval and the appropriate unit conversion factors. For real
|
||||||
|
<A HREF = "units.html">units</A> in LAMMPS, this is 2917703220.0 in this case. The
|
||||||
|
final thermal conductivity value obtained is 0.25 W/mK.
|
||||||
|
</P>
|
||||||
|
<P><B>Output info:</B>
|
||||||
|
</P>
|
||||||
|
<P>This compute calculates a vector of length 6. The 6 components are
|
||||||
|
the x, y, z components of the full heat flux, followed by the x, y, z
|
||||||
|
components of just the convective portion of the flux, which is the
|
||||||
|
energy per atom times the velocity of the atom.
|
||||||
|
</P>
|
||||||
|
<P>The vector values calculated by this compute are "extensive", meaning
|
||||||
|
they scale with the number of atoms in the simulation. They should be
|
||||||
|
divided by the appropriate volume to get a flux.
|
||||||
|
</P>
|
||||||
|
<P><B>Restrictions:</B>
|
||||||
|
</P>
|
||||||
|
<P>Only pairwise interactions, as defined by the pair_style command, are
|
||||||
|
included in this calculation.
|
||||||
|
</P>
|
||||||
|
<P>To use this compute you must define an atom_style, such as dpd or
|
||||||
|
granular, that communicates the velocites of ghost atoms.
|
||||||
|
</P>
|
||||||
|
<P><B>Related commands:</B> none
|
||||||
|
</P>
|
||||||
|
<P><B>Default:</B> none
|
||||||
|
</P>
|
||||||
|
<HR>
|
||||||
|
|
||||||
|
<H4>Sample LAMMPS input script
|
||||||
|
</H4>
|
||||||
|
<PRE>atom_style dpd
|
||||||
|
units real
|
||||||
|
dimension 3
|
||||||
|
boundary p p p
|
||||||
|
lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
|
||||||
|
region box block 0 4 0 4 0 4
|
||||||
|
create_box 1 box
|
||||||
|
create_atoms 1 box
|
||||||
|
mass 1 39.948
|
||||||
|
pair_style lj/cut 13.0
|
||||||
|
pair_coeff * * 0.2381 3.405
|
||||||
|
group every region box
|
||||||
|
velocity all create 70 102486 mom yes rot yes dist gaussian
|
||||||
|
timestep 4.0
|
||||||
|
thermo 10
|
||||||
|
</PRE>
|
||||||
|
<PRE># ------------- Equilibration and thermalisation ----------------
|
||||||
|
</PRE>
|
||||||
|
<PRE>fix NPT all npt 70 70 10 xyz 0.0 0.0 100.0 drag 0.2
|
||||||
|
run 8000
|
||||||
|
unfix NPT
|
||||||
|
</PRE>
|
||||||
|
<PRE># --------------- Equilibration in nve -----------------
|
||||||
|
</PRE>
|
||||||
|
<PRE>fix NVE all nve
|
||||||
|
run 8000
|
||||||
|
</PRE>
|
||||||
|
<PRE># -------------- Flux calculation in nve ---------------
|
||||||
|
</PRE>
|
||||||
|
<PRE>reset_timestep 0
|
||||||
|
compute flux all heat_flux
|
||||||
|
log flux.log
|
||||||
|
variable J equal c_flux<B>1</B>/vol
|
||||||
|
thermo_style custom step temp v_J
|
||||||
|
run 100000
|
||||||
|
</PRE>
|
||||||
|
</HTML>
|
||||||
|
|
@ -0,0 +1,142 @@
|
||||||
|
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||||
|
|
||||||
|
:link(lws,http://lammps.sandia.gov)
|
||||||
|
:link(ld,Manual.html)
|
||||||
|
:link(lc,Section_commands.html#comm)
|
||||||
|
|
||||||
|
:line
|
||||||
|
|
||||||
|
compute heat/flux command :h3
|
||||||
|
|
||||||
|
[Syntax:]
|
||||||
|
|
||||||
|
compute ID group-ID heat/flux pe-ID :pre
|
||||||
|
|
||||||
|
ID, group-ID are documented in "compute"_compute.html command
|
||||||
|
heat/flux = style name of this compute command
|
||||||
|
pe-ID = ID of a compute that calculates per-atom potential energy :ul
|
||||||
|
|
||||||
|
[Examples:]
|
||||||
|
|
||||||
|
compute myFlux all heat/flux myPE :pre
|
||||||
|
|
||||||
|
[Description:]
|
||||||
|
|
||||||
|
Define a computation that calculates the heat flux vector based on
|
||||||
|
interactions between atoms in the specified group. This can be used
|
||||||
|
by itself to measure the heat flux between a hot and cold reservoir of
|
||||||
|
particles or to calculate a thermal conductivity using the Green-Kubo
|
||||||
|
formalism.
|
||||||
|
|
||||||
|
The compute takes a {pe-ID} argument which is the ID of a "compute
|
||||||
|
pe/atom"_compute_pe_atom.html that calculates per-atom potential
|
||||||
|
energy. Normally, it should be defined for the same group used by
|
||||||
|
compute heat/flux, though LAMMPS does not check for this.
|
||||||
|
|
||||||
|
The Green-Kubo formulas relate the ensemble average of the
|
||||||
|
auto-correlation of the heat flux J to the thermal conductivity kappa.
|
||||||
|
|
||||||
|
:c,image(Eqs/heat_flux_k.jpg)
|
||||||
|
|
||||||
|
:c,image(Eqs/heat_flux_J.jpg)
|
||||||
|
|
||||||
|
Ei is the per-atom energy (potential and kinetic). The potential
|
||||||
|
portion is calculated by the compute {pe-ID} specified as an argument
|
||||||
|
to the compute heat/flux command.
|
||||||
|
|
||||||
|
IMPORTANT NOTE: The per-atom potential energy calculated by the
|
||||||
|
{pe-ID} compute should only include pairwise energy, to be consistent
|
||||||
|
with the second virial-like term in the formula for J. Thus if any
|
||||||
|
bonds, angles, etc exist in the system, the compute should limit its
|
||||||
|
calculation to only the pair contribution. E.g. it could be defined
|
||||||
|
as follows. Note that if {pair} is not listed as the last argument,
|
||||||
|
it will be included by default, but so will other contributions such
|
||||||
|
as bond, angle, etc.
|
||||||
|
|
||||||
|
compute myPE all pe/atom pair :pre
|
||||||
|
|
||||||
|
The second term of the heat flux equation for J is calculated by
|
||||||
|
compute heat/flux for pairwise interactions for any I,J pair where one
|
||||||
|
of the 2 atoms in is the compute group. It can be output every so
|
||||||
|
many timesteps (e.g. via the thermo_style custom command). Then as
|
||||||
|
post-processing steps, an autocorrelation can be performed, its
|
||||||
|
integral estimated, and the Green-Kubo formula evaluated.
|
||||||
|
|
||||||
|
Here is an example of this procedure. First a LAMMPS input script for
|
||||||
|
solid Ar is appended below. A Python script
|
||||||
|
"correlate.py"_Scripts/correlate.py is also given, which calculates
|
||||||
|
the autocorrelation of the flux output in the logfile flux.log,
|
||||||
|
produced by the LAMMPS run. It is invoked as
|
||||||
|
|
||||||
|
correlate.py flux.log -c 3 -s 200 :pre
|
||||||
|
|
||||||
|
The resulting data lists the autocorrelation in column 1 and the
|
||||||
|
integral of the autocorrelation in column 2. The integral of the
|
||||||
|
correlation needs to be multiplied by V/(kB T^2) times the sample
|
||||||
|
interval and the appropriate unit conversion factors. For real
|
||||||
|
"units"_units.html in LAMMPS, this is 2917703220.0 in this case. The
|
||||||
|
final thermal conductivity value obtained is 0.25 W/mK.
|
||||||
|
|
||||||
|
[Output info:]
|
||||||
|
|
||||||
|
This compute calculates a vector of length 6. The 6 components are
|
||||||
|
the x, y, z components of the full heat flux, followed by the x, y, z
|
||||||
|
components of just the convective portion of the flux, which is the
|
||||||
|
energy per atom times the velocity of the atom.
|
||||||
|
|
||||||
|
The vector values calculated by this compute are "extensive", meaning
|
||||||
|
they scale with the number of atoms in the simulation. They should be
|
||||||
|
divided by the appropriate volume to get a flux.
|
||||||
|
|
||||||
|
[Restrictions:]
|
||||||
|
|
||||||
|
Only pairwise interactions, as defined by the pair_style command, are
|
||||||
|
included in this calculation.
|
||||||
|
|
||||||
|
To use this compute you must define an atom_style, such as dpd or
|
||||||
|
granular, that communicates the velocites of ghost atoms.
|
||||||
|
|
||||||
|
[Related commands:] none
|
||||||
|
|
||||||
|
[Default:] none
|
||||||
|
|
||||||
|
:line
|
||||||
|
|
||||||
|
Sample LAMMPS input script :h4
|
||||||
|
|
||||||
|
atom_style dpd
|
||||||
|
units real
|
||||||
|
dimension 3
|
||||||
|
boundary p p p
|
||||||
|
lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
|
||||||
|
region box block 0 4 0 4 0 4
|
||||||
|
create_box 1 box
|
||||||
|
create_atoms 1 box
|
||||||
|
mass 1 39.948
|
||||||
|
pair_style lj/cut 13.0
|
||||||
|
pair_coeff * * 0.2381 3.405
|
||||||
|
group every region box
|
||||||
|
velocity all create 70 102486 mom yes rot yes dist gaussian
|
||||||
|
timestep 4.0
|
||||||
|
thermo 10 :pre
|
||||||
|
|
||||||
|
# ------------- Equilibration and thermalisation ---------------- :pre
|
||||||
|
|
||||||
|
fix NPT all npt 70 70 10 xyz 0.0 0.0 100.0 drag 0.2
|
||||||
|
run 8000
|
||||||
|
unfix NPT :pre
|
||||||
|
|
||||||
|
# --------------- Equilibration in nve ----------------- :pre
|
||||||
|
|
||||||
|
fix NVE all nve
|
||||||
|
run 8000 :pre
|
||||||
|
|
||||||
|
# -------------- Flux calculation in nve --------------- :pre
|
||||||
|
|
||||||
|
reset_timestep 0
|
||||||
|
compute flux all heat_flux
|
||||||
|
log flux.log
|
||||||
|
variable J equal c_flux[1]/vol
|
||||||
|
thermo_style custom step temp v_J
|
||||||
|
run 100000 :pre
|
||||||
|
|
||||||
|
|
@ -0,0 +1,225 @@
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
|
DE-AC04-93AL85000 with Sandia Corporation, the U.S. Government retains
|
||||||
|
certain rights in this software. This software is distributed under
|
||||||
|
the GNU General Public License.
|
||||||
|
|
||||||
|
See the README file in the top-level LAMMPS directory.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
Contributing authors: Reese Jones (Sandia)
|
||||||
|
Philip Howell (Siemens)
|
||||||
|
Vikas Varsney (Air Force Research Laboratory)
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#include "math.h"
|
||||||
|
#include "string.h"
|
||||||
|
#include "compute_heat_flux.h"
|
||||||
|
#include "atom.h"
|
||||||
|
#include "atom_vec.h"
|
||||||
|
#include "update.h"
|
||||||
|
#include "force.h"
|
||||||
|
#include "pair.h"
|
||||||
|
#include "modify.h"
|
||||||
|
#include "group.h"
|
||||||
|
#include "neighbor.h"
|
||||||
|
#include "neigh_list.h"
|
||||||
|
#include "neigh_request.h"
|
||||||
|
#include "error.h"
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
|
enum{DUMMY0,INVOKED_SCALAR,INVOKED_VECTOR,DUMMMY3,INVOKED_PERATOM};
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
ComputeHeatFlux::ComputeHeatFlux(LAMMPS *lmp, int narg, char **arg) :
|
||||||
|
Compute(lmp, narg, arg)
|
||||||
|
{
|
||||||
|
if (narg != 4) error->all("Illegal compute heat/flux command");
|
||||||
|
|
||||||
|
vector_flag = 1;
|
||||||
|
size_vector = 6;
|
||||||
|
extvector = 1;
|
||||||
|
|
||||||
|
// store pe/atom ID used by heat flux computation
|
||||||
|
// insure it is valid for pe/atom computation
|
||||||
|
|
||||||
|
int n = strlen(arg[3]) + 1;
|
||||||
|
id_atomPE = new char[n];
|
||||||
|
strcpy(id_atomPE,arg[3]);
|
||||||
|
|
||||||
|
int icompute = modify->find_compute(id_atomPE);
|
||||||
|
if (icompute < 0) error->all("Could not find compute heat/flux pe/atom ID");
|
||||||
|
if (modify->compute[icompute]->peatomflag == 0)
|
||||||
|
error->all("Compute heat/flux compute ID does not compute pe/atom");
|
||||||
|
|
||||||
|
vector = new double[6];
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
ComputeHeatFlux::~ComputeHeatFlux()
|
||||||
|
{
|
||||||
|
delete [] vector;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void ComputeHeatFlux::init()
|
||||||
|
{
|
||||||
|
// error checks
|
||||||
|
|
||||||
|
if (atom->avec->ghost_velocity == 0)
|
||||||
|
error->all("Compute heat/flux requires ghost atoms store velocity");
|
||||||
|
|
||||||
|
if (force->pair == NULL || force->pair->single_enable == 0)
|
||||||
|
error->all("Pair style does not support compute heat/flux");
|
||||||
|
|
||||||
|
int icompute = modify->find_compute(id_atomPE);
|
||||||
|
if (icompute < 0)
|
||||||
|
error->all("Pe/atom ID for compute heat/flux does not exist");
|
||||||
|
atomPE = modify->compute[icompute];
|
||||||
|
|
||||||
|
pair = force->pair;
|
||||||
|
cutsq = force->pair->cutsq;
|
||||||
|
|
||||||
|
// need an occasional half neighbor list
|
||||||
|
|
||||||
|
int irequest = neighbor->request((void *) this);
|
||||||
|
neighbor->requests[irequest]->pair = 0;
|
||||||
|
neighbor->requests[irequest]->compute = 1;
|
||||||
|
neighbor->requests[irequest]->occasional = 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void ComputeHeatFlux::init_list(int id, NeighList *ptr)
|
||||||
|
{
|
||||||
|
list = ptr;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void ComputeHeatFlux::compute_vector()
|
||||||
|
{
|
||||||
|
int i,j,ii,jj,inum,jnum,itype,jtype;
|
||||||
|
double xtmp,ytmp,ztmp,delx,dely,delz;
|
||||||
|
double rsq,eng,fpair,factor_coul,factor_lj,factor;
|
||||||
|
double fdotv,massone,ke,pe;
|
||||||
|
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||||
|
|
||||||
|
invoked_vector = update->ntimestep;
|
||||||
|
|
||||||
|
double **x = atom->x;
|
||||||
|
double **v = atom->v;
|
||||||
|
int *type = atom->type;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
int nall = nlocal + atom->nghost;
|
||||||
|
double *special_coul = force->special_coul;
|
||||||
|
double *special_lj = force->special_lj;
|
||||||
|
int newton_pair = force->newton_pair;
|
||||||
|
|
||||||
|
// invoke half neighbor list (will copy or build if necessary)
|
||||||
|
|
||||||
|
neighbor->build_one(list->index);
|
||||||
|
|
||||||
|
inum = list->inum;
|
||||||
|
ilist = list->ilist;
|
||||||
|
numneigh = list->numneigh;
|
||||||
|
firstneigh = list->firstneigh;
|
||||||
|
|
||||||
|
// heat flux J = \sum_i e_i v_i + \sum_{i<j} (f_ij . v_j) x_ij
|
||||||
|
|
||||||
|
// virial-like contribution
|
||||||
|
// loop over neighbors of my atoms
|
||||||
|
// require either i or j be in compute group
|
||||||
|
|
||||||
|
double Jv[3] = {0.0,0.0,0.0};
|
||||||
|
|
||||||
|
for (ii = 0; ii < inum; ii++) {
|
||||||
|
i = ilist[ii];
|
||||||
|
xtmp = x[i][0];
|
||||||
|
ytmp = x[i][1];
|
||||||
|
ztmp = x[i][2];
|
||||||
|
itype = type[i];
|
||||||
|
jlist = firstneigh[i];
|
||||||
|
jnum = numneigh[i];
|
||||||
|
|
||||||
|
for (jj = 0; jj < jnum; jj++) {
|
||||||
|
j = jlist[jj];
|
||||||
|
|
||||||
|
if (j < nall) factor_coul = factor_lj = 1.0;
|
||||||
|
else {
|
||||||
|
factor_coul = special_coul[j/nall];
|
||||||
|
factor_lj = special_lj[j/nall];
|
||||||
|
j %= nall;
|
||||||
|
}
|
||||||
|
|
||||||
|
if (!(mask[i] & groupbit) && !(mask[j] & groupbit)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
jtype = type[j];
|
||||||
|
|
||||||
|
if (rsq < cutsq[itype][jtype]) {
|
||||||
|
eng = pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
|
||||||
|
|
||||||
|
if (newton_pair || j < nlocal) factor = 1.0;
|
||||||
|
else factor = 0.5;
|
||||||
|
|
||||||
|
// symmetrize velocities
|
||||||
|
|
||||||
|
double vx = 0.5*(v[i][0]+v[j][0]);
|
||||||
|
double vy = 0.5*(v[i][1]+v[j][1]);
|
||||||
|
double vz = 0.5*(v[i][2]+v[j][2]);
|
||||||
|
fdotv = factor * fpair * (delx*vx + dely*vy + delz*vz);
|
||||||
|
|
||||||
|
Jv[0] += fdotv*delx;
|
||||||
|
Jv[1] += fdotv*dely;
|
||||||
|
Jv[2] += fdotv*delz;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// energy convection contribution
|
||||||
|
// uses per-atom potential energy
|
||||||
|
|
||||||
|
if (!(atomPE->invoked_flag & INVOKED_PERATOM)) {
|
||||||
|
atomPE->compute_peratom();
|
||||||
|
atomPE->invoked_flag |= INVOKED_PERATOM;
|
||||||
|
}
|
||||||
|
|
||||||
|
double *mass = atom->mass;
|
||||||
|
double *rmass = atom->rmass;
|
||||||
|
double mvv2e = force->mvv2e;
|
||||||
|
|
||||||
|
double Jc[3] = {0.0,0.0,0.0};
|
||||||
|
|
||||||
|
for (int i = 0; i < nlocal; i++) {
|
||||||
|
if (mask[i] & groupbit) {
|
||||||
|
massone = (rmass) ? rmass[i] : mass[type[i]];
|
||||||
|
ke = mvv2e * 0.5 * massone *
|
||||||
|
(v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
|
||||||
|
pe = atomPE->scalar_atom[i];
|
||||||
|
eng = pe + ke;
|
||||||
|
Jc[0] += v[i][0]*eng;
|
||||||
|
Jc[1] += v[i][1]*eng;
|
||||||
|
Jc[2] += v[i][2]*eng;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// total flux
|
||||||
|
|
||||||
|
double data[6] = {Jv[0]+Jc[0],Jv[1]+Jc[1],Jv[2]+Jc[2],
|
||||||
|
Jc[0],Jc[1],Jc[2]};
|
||||||
|
MPI_Allreduce(data,vector,6,MPI_DOUBLE,MPI_SUM,world);
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,39 @@
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||||
|
certain rights in this software. This software is distributed under
|
||||||
|
the GNU General Public License.
|
||||||
|
|
||||||
|
See the README file in the top-level LAMMPS directory.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifndef COMPUTE_HEATFLUX_H
|
||||||
|
#define COMPUTE_HEATFLUX_H
|
||||||
|
|
||||||
|
#include "compute.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class ComputeHeatFlux : public Compute {
|
||||||
|
public:
|
||||||
|
ComputeHeatFlux(class LAMMPS *, int, char **);
|
||||||
|
~ComputeHeatFlux();
|
||||||
|
void init();
|
||||||
|
void init_list(int, class NeighList *);
|
||||||
|
void compute_vector();
|
||||||
|
|
||||||
|
private:
|
||||||
|
double **cutsq;
|
||||||
|
class Pair *pair;
|
||||||
|
class NeighList *list;
|
||||||
|
class Compute *atomPE;
|
||||||
|
char *id_atomPE;
|
||||||
|
};
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif
|
||||||
|
|
@ -81,6 +81,7 @@ CommandStyle(write_restart,WriteRestart)
|
||||||
#include "compute_coord_atom.h"
|
#include "compute_coord_atom.h"
|
||||||
#include "compute_displace_atom.h"
|
#include "compute_displace_atom.h"
|
||||||
#include "compute_group_group.h"
|
#include "compute_group_group.h"
|
||||||
|
#include "compute_heat_flux.h"
|
||||||
#include "compute_ke.h"
|
#include "compute_ke.h"
|
||||||
#include "compute_ke_atom.h"
|
#include "compute_ke_atom.h"
|
||||||
#include "compute_pe.h"
|
#include "compute_pe.h"
|
||||||
|
|
@ -106,6 +107,7 @@ ComputeStyle(cna/atom,ComputeCNAAtom)
|
||||||
ComputeStyle(coord/atom,ComputeCoordAtom)
|
ComputeStyle(coord/atom,ComputeCoordAtom)
|
||||||
ComputeStyle(displace/atom,ComputeDisplaceAtom)
|
ComputeStyle(displace/atom,ComputeDisplaceAtom)
|
||||||
ComputeStyle(group/group,ComputeGroupGroup)
|
ComputeStyle(group/group,ComputeGroupGroup)
|
||||||
|
ComputeStyle(heat/flux,ComputeHeatFlux)
|
||||||
ComputeStyle(ke,ComputeKE)
|
ComputeStyle(ke,ComputeKE)
|
||||||
ComputeStyle(ke/atom,ComputeKEAtom)
|
ComputeStyle(ke/atom,ComputeKEAtom)
|
||||||
ComputeStyle(pe,ComputePE)
|
ComputeStyle(pe,ComputePE)
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue