forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13663 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
689a20f66d
commit
b4ad6888a0
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@ -436,8 +436,8 @@ package</A>.
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<TR ALIGN="center"><TD ><A HREF = "fix_imd.html">imd</A></TD><TD ><A HREF = "fix_ipi.html">ipi</A></TD><TD ><A HREF = "fix_langevin_eff.html">langevin/eff</A></TD><TD ><A HREF = "fix_lb_fluid.html">lb/fluid</A></TD><TD ><A HREF = "fix_lb_momentum.html">lb/momentum</A></TD><TD ><A HREF = "fix_lb_pc.html">lb/pc</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_lb_rigid_pc_sphere.html">lb/rigid/pc/sphere</A></TD><TD ><A HREF = "fix_lb_viscous.html">lb/viscous</A></TD><TD ><A HREF = "fix_meso.html">meso</A></TD><TD ><A HREF = "fix_meso_stationary.html">meso/stationary</A></TD><TD ><A HREF = "fix_nh_eff.html">nph/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">npt/eff</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_nve_eff.html">nve/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">nvt/eff</A></TD><TD ><A HREF = "fix_nvt_sllod_eff.html">nvt/sllod/eff</A></TD><TD ><A HREF = "fix_phonon.html">phonon</A></TD><TD ><A HREF = "fix_pimd.html">pimd</A></TD><TD ><A HREF = "fix_qeq_reax.html">qeq/reax</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_qmmm.html">qmmm</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/c/bonds</A></TD><TD ><A HREF = "fix_reaxc_species.html">reax/c/species</A></TD><TD ><A HREF = "fix_smd.html">smd</A></TD><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A></TD><TD ><A HREF = "fix_ti_rs.html">ti/rs</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_ti_spring.html">ti/spring</A></TD><TD ><A HREF = "fix_ttm.html">ttm/mod</A>
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<TR ALIGN="center"><TD ><A HREF = "fix_qmmm.html">qmmm</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/c/bonds</A></TD><TD ><A HREF = "fix_reaxc_species.html">reax/c/species</A></TD><TD ><A HREF = "fix_saed_vtk.html">saed/vtk</A></TD><TD ><A HREF = "fix_smd.html">smd</A></TD><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_ti_rs.html">ti/rs</A></TD><TD ><A HREF = "fix_ti_spring.html">ti/spring</A></TD><TD ><A HREF = "fix_ttm.html">ttm/mod</A>
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</TD></TR></TABLE></DIV>
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<HR>
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@ -472,7 +472,8 @@ package</A>.
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</P>
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR ALIGN="center"><TD ><A HREF = "compute_ackland_atom.html">ackland/atom</A></TD><TD ><A HREF = "compute_basal_atom.html">basal/atom</A></TD><TD ><A HREF = "compute_fep.html">fep</A></TD><TD ><A HREF = "compute_ke_eff.html">ke/eff</A></TD><TD ><A HREF = "compute_ke_atom_eff.html">ke/atom/eff</A></TD><TD ><A HREF = "compute_meso_e_atom.html">meso_e/atom</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_meso_rho_atom.html">meso_rho/atom</A></TD><TD ><A HREF = "compute_meso_t_atom.html">meso_t/atom</A></TD><TD ><A HREF = "compute_temp_eff.html">temp/eff</A></TD><TD ><A HREF = "compute_temp_deform_eff.html">temp/deform/eff</A></TD><TD ><A HREF = "compute_temp_region_eff.html">temp/region/eff</A></TD><TD ><A HREF = "compute_temp_rotate.html">temp/rotate</A>
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<TR ALIGN="center"><TD ><A HREF = "compute_meso_rho_atom.html">meso_rho/atom</A></TD><TD ><A HREF = "compute_meso_t_atom.html">meso_t/atom</A></TD><TD ><A HREF = "compute_saed.html">saed</A></TD><TD ><A HREF = "compute_temp_eff.html">temp/eff</A></TD><TD ><A HREF = "compute_temp_deform_eff.html">temp/deform/eff</A></TD><TD ><A HREF = "compute_temp_region_eff.html">temp/region/eff</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_temp_rotate.html">temp/rotate</A></TD><TD ><A HREF = "compute_xrd.html">xrd</A>
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</TD></TR></TABLE></DIV>
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<HR>
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|
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@ -624,6 +624,7 @@ package"_Section_start.html#start_3.
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"qmmm"_fix_qmmm.html,
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"reax/c/bonds"_fix_reax_bonds.html,
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"reax/c/species"_fix_reaxc_species.html,
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"saed/vtk"_fix_saed_vtk.html,
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"smd"_fix_smd.html,
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"temp/rescale/eff"_fix_temp_rescale_eff.html,
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"ti/rs"_fix_ti_rs.html,
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@ -721,10 +722,12 @@ package"_Section_start.html#start_3.
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"meso_e/atom"_compute_meso_e_atom.html,
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"meso_rho/atom"_compute_meso_rho_atom.html,
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"meso_t/atom"_compute_meso_t_atom.html,
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"saed"_compute_saed.html,
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"temp/eff"_compute_temp_eff.html,
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"temp/deform/eff"_compute_temp_deform_eff.html,
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"temp/region/eff"_compute_temp_region_eff.html,
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"temp/rotate"_compute_temp_rotate.html :tb(c=6,ea=c)
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"temp/rotate"_compute_temp_rotate.html,
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"xrd"_compute_xrd.html :tb(c=6,ea=c)
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:line
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|
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@ -126,6 +126,7 @@ on how to build LAMMPS with both kinds of auxiliary libraries.
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<TR ALIGN="center"><TD >USER-CG-CMM</TD><TD > coarse-graining model</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "pair_sdk.html">pair_style lj/sdk</A></TD><TD > USER/cg-cmm</TD><TD > <A HREF = "http://lammps.sandia.gov/pictures.html#cg">cg</A></TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >USER-COLVARS</TD><TD > collective variables</TD><TD > Fiorin & Henin & Kohlmeyer (3)</TD><TD > <A HREF = "fix_colvars.html">fix colvars</A></TD><TD > USER/colvars</TD><TD > <A HREF = "colvars">colvars</A></TD><TD > lib/colvars</TD></TR>
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<TR ALIGN="center"><TD >USER-CUDA</TD><TD > NVIDIA GPU styles</TD><TD > Christian Trott (U Tech Ilmenau)</TD><TD > <A HREF = "accelerate_cuda.html">Section accelerate</A></TD><TD > USER/cuda</TD><TD > -</TD><TD > lib/cuda</TD></TR>
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<TR ALIGN="center"><TD >USER-DIFFRACTION</TD><TD > virutal x-ray and electron diffraction</TD><TD > Shawn Coleman (ARL)</TD><TD ><A HREF = "compute_xrd.html">compute xrd</A></TD><TD > USER/diffraction</TD><TD > -</TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >USER-EFF</TD><TD > electron force field</TD><TD > Andres Jaramillo-Botero (Caltech)</TD><TD > <A HREF = "pair_eff.html">pair_style eff/cut</A></TD><TD > USER/eff</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#eff">eff</A></TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >USER-FEP</TD><TD > free energy perturbation</TD><TD > Agilio Padua (U Blaise Pascal Clermont-Ferrand)</TD><TD > <A HREF = "compute_fep.html">compute fep</A></TD><TD > USER/fep</TD><TD > -</TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >USER-INTEL</TD><TD > Vectorized CPU and Intel(R) coprocessor styles</TD><TD > W. Michael Brown (Intel)</TD><TD > <A HREF = "accelerate_intel.html">Section accelerate</A></TD><TD > examples/intel</TD><TD > -</TD><TD > -</TD></TR>
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@ -336,6 +337,24 @@ tu-ilmenau.de). Contact him directly if you have questions.
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</P>
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<HR>
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<H4>USER-DIFFRACTION package
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</H4>
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<P>This package contains the commands neeed to calculate x-ray and
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electron diffraction intensities based on kinematic diffraction
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theory.
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</P>
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<P>See these doc pages and their related commands to get started:
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</P>
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<UL><LI><A HREF = "compute_xrd.html">compute xrd</A>
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<LI><A HREF = "compute_saed.html">compute saed</A>
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<LI><A HREF = "fix_saed_vtk.html">fix saed/vtk</A>
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</UL>
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<P>The person who created this package is Shawn P. Coleman
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(shawn.p.coleman8.ctr at mail.mil) while at the University of
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Arkansas. Contact him directly if you have questions.
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</P>
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<HR>
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<H4>USER-EFF package
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</H4>
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<P>This package contains a LAMMPS implementation of the electron Force
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@ -118,6 +118,7 @@ USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpm
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USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cg-cmm, "cg"_cg, -
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USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (3), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
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USER-CUDA, NVIDIA GPU styles, Christian Trott (U Tech Ilmenau), "Section accelerate"_accelerate_cuda.html, USER/cuda, -, lib/cuda
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USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"compute xrd"_compute_xrd.html, USER/diffraction, -, -
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USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
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USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "compute fep"_compute_fep.html, USER/fep, -, -
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USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section accelerate"_accelerate_intel.html, examples/intel, -, -
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@ -323,6 +324,24 @@ tu-ilmenau.de). Contact him directly if you have questions.
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:line
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USER-DIFFRACTION package :h4
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This package contains the commands neeed to calculate x-ray and
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electron diffraction intensities based on kinematic diffraction
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theory.
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See these doc pages and their related commands to get started:
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"compute xrd"_compute_xrd.html
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"compute saed"_compute_saed.html
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"fix saed/vtk"_fix_saed_vtk.html :ul
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The person who created this package is Shawn P. Coleman
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(shawn.p.coleman8.ctr at mail.mil) while at the University of
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Arkansas. Contact him directly if you have questions.
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:line
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USER-EFF package :h4
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This package contains a LAMMPS implementation of the electron Force
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|
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@ -21,8 +21,7 @@
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<LI>lambda = wavelength of incident radiation (length units)
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<LI>type1 type2 ... typeN = chemical symbol of each atom type (see valid
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options below)
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<LI>type1 type2 ... typeN = chemical symbol of each atom type (see valid options below)
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<LI>zero or more keyword/value pairs may be appended
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@ -46,9 +45,9 @@ options below)
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</UL>
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<P><B>Examples:</B>
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</P>
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<P>compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
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compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
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</P>
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<PRE>compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
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compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
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</PRE>
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<PRE>fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
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fix saed/vtk 1 1 1 c_2 file Ni_000.saed
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</PRE>
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@ -71,8 +70,11 @@ position of each atom, fj are atomic scattering factors.
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</P>
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<P>Diffraction intensities are calculated on a three-dimensional mesh of
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reciprocal lattice nodes. The mesh spacing is defined either (I) by
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the entire simulation domain or (II) manually using selected values.
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the entire simulation domain or (II) manually using selected values as
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shown in the 2D diagram below.
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</P>
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<CENTER><A HREF = "saed_mesh.jpg"><IMG SRC = "JPG/saed_mesh_small.jpg"></A>
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</CENTER>
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<P>For a mesh defined by the simulation domain, a rectilinear grid is
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constructed with spacing <I>c</I>*inv(A) along each reciprocal lattice
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axis. Where A are the vectors corresponding to the edges of the
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@ -100,8 +102,11 @@ increase the cost of computation. Otherwise, <I>Zone</I> parameters will
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denote the z1=h, z2=k, and z3=l (in a global since) zone axis of an
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intersecting Ewald sphere. Diffraction intensities will only be
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computed at the intersection of the reciprocal lattice mesh and a
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<I>dR_Ewald</I> thick surface of the Ewald sphere.
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<I>dR_Ewald</I> thick surface of the Ewald sphere. See the example 3D
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intestiety data and the intersection of a <B>010</B> zone axis in the below image.
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</P>
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<CENTER><A HREF = "saed_ewald_intersect.jpg"><IMG SRC = "JPG/saed_ewald_intersect_small.jpg"></A>
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</CENTER>
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<P>The atomic scattering factors, fj, accounts for the reduction in
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diffraction intensity due to Compton scattering. Compute saed uses
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analytical approximations of the atomic scattering factors that vary
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@ -159,12 +164,12 @@ options.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "fix_saed_vtk.html">fix saed_vtk</A>
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<A HREF = "compute_xrd.html">compute xrd</A>
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<P><A HREF = "fix_saed_vtk.html">fix saed_vtk</A>, <A HREF = "compute_xrd.html">compute xrd</A>
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</P>
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<P><B>Default:</B>
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</P>
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<P>The option defaults are Kmax = 1.70, Zone 1 0 0, c 1 1 1, dR_Ewald = 0.01
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<P>The option defaults are Kmax = 1.70, Zone 1 0 0, c 1 1 1, dR_Ewald =
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0.01.
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</P>
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<HR>
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@ -15,8 +15,7 @@ compute ID group-ID saed lambda type1 type2 ... typeN keyword value ... :pre
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ID, group-ID are documented in "compute"_compute.html command :ulb,l
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saed = style name of this compute command :l
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lambda = wavelength of incident radiation (length units) :l
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type1 type2 ... typeN = chemical symbol of each atom type (see valid
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options below) :l
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type1 type2 ... typeN = chemical symbol of each atom type (see valid options below) :l
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zero or more keyword/value pairs may be appended :l
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keyword = {Kmax} or {Zone} or {dR_Ewald} or {c} or {manual} or {echo} :l
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@ -38,7 +37,7 @@ keyword = {Kmax} or {Zone} or {dR_Ewald} or {c} or {manual} or {echo} :l
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[Examples:]
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compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
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compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
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compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo :pre
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fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
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fix saed/vtk 1 1 1 c_2 file Ni_000.saed :pre
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@ -61,7 +60,10 @@ position of each atom, fj are atomic scattering factors.
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|
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Diffraction intensities are calculated on a three-dimensional mesh of
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reciprocal lattice nodes. The mesh spacing is defined either (I) by
|
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the entire simulation domain or (II) manually using selected values.
|
||||
the entire simulation domain or (II) manually using selected values as
|
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shown in the 2D diagram below.
|
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|
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:c,image(JPG/saed_mesh_small.jpg,saed_mesh.jpg)
|
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|
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For a mesh defined by the simulation domain, a rectilinear grid is
|
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constructed with spacing {c}*inv(A) along each reciprocal lattice
|
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|
|
@ -90,7 +92,10 @@ increase the cost of computation. Otherwise, {Zone} parameters will
|
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denote the z1=h, z2=k, and z3=l (in a global since) zone axis of an
|
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intersecting Ewald sphere. Diffraction intensities will only be
|
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computed at the intersection of the reciprocal lattice mesh and a
|
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{dR_Ewald} thick surface of the Ewald sphere.
|
||||
{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.
|
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|
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:c,image(JPG/saed_ewald_intersect_small.jpg,saed_ewald_intersect.jpg)
|
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|
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The atomic scattering factors, fj, accounts for the reduction in
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diffraction intensity due to Compton scattering. Compute saed uses
|
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|
@ -150,12 +155,12 @@ The compute_saed command does not work for triclinic cells.
|
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|
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[Related commands:]
|
||||
|
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"fix saed_vtk"_fix_saed_vtk.html
|
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"compute xrd"_compute_xrd.html
|
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"fix saed_vtk"_fix_saed_vtk.html, "compute xrd"_compute_xrd.html
|
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|
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[Default:]
|
||||
|
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The option defaults are Kmax = 1.70, Zone 1 0 0, c 1 1 1, dR_Ewald = 0.01
|
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The option defaults are Kmax = 1.70, Zone 1 0 0, c 1 1 1, dR_Ewald =
|
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0.01.
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:line
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@ -170,4 +175,3 @@ Volume C: Mathematical and Chemical Tables, 554-95 (2004).
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:link(Fox)
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[(Fox)] Fox, O'Keefe, Tabbernor, Acta Crystallogr. A, 45, 786-93
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(1989).
|
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|
||||
|
|
|
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|
|
@ -21,8 +21,7 @@
|
|||
|
||||
<LI>lambda = wavelength of incident radiation (length units)
|
||||
|
||||
<LI>type1 type2 ... typeN = chemical symbol of each atom type (see valid
|
||||
options below)
|
||||
<LI>type1 type2 ... typeN = chemical symbol of each atom type (see valid options below)
|
||||
|
||||
<LI>zero or more keyword/value pairs may be appended
|
||||
|
||||
|
|
@ -44,12 +43,12 @@ options below)
|
|||
</UL>
|
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<P><B>Examples:</B>
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</P>
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<P>compute 1 all xrd 1.541838 Al O 2Theta 0.087 0.87 c 1 1 1 LP 1 echo
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<PRE>compute 1 all xrd 1.541838 Al O 2Theta 0.087 0.87 c 1 1 1 LP 1 echo
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compute 2 all xrd 1.541838 Al O 2Theta 10 100 c 0.05 0.05 0.05 LP 1 manual
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</P>
|
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<P>fix 1 all ave/histo 1 1 1 0.087 0.87 250 c_1<B>1</B> mode vector weights c_1<B>2</B> file Rad2Theta.xrd
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fix 2 all ave/histo 1 1 1 10 100 250 c_2<B>1</B> mode vector weights c_2<B>2</B> file Deg2Theta.xrd
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</P>
|
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</PRE>
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<PRE>fix 1 all ave/histo 1 1 1 0.087 0.87 250 c_1[1] mode vector weights c_1[2] file Rad2Theta.xrd
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fix 2 all ave/histo 1 1 1 10 100 250 c_2[1] mode vector weights c_2[2] file Deg2Theta.xrd
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</PRE>
|
||||
<PRE>
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
|
|
@ -78,8 +77,11 @@ the <I>LP</I> switch.
|
|||
</P>
|
||||
<P>Diffraction intensities are calculated on a three-dimensional mesh of
|
||||
reciprocal lattice nodes. The mesh spacing is defined either (I)
|
||||
by the entire simulation domain or (II) manually using selected values.
|
||||
by the entire simulation domain or (II) manually using selected values as
|
||||
shown in the 2D diagram below.
|
||||
</P>
|
||||
<CENTER><A HREF = "xrd_mesh.jpg"><IMG SRC = "JPG/xrd_mesh_small.jpg"></A>
|
||||
</CENTER>
|
||||
<P>For a mesh defined by the simulation domain, a rectilinear grid is
|
||||
constructed with spacing <I>c</I>*inv(A) along each reciprocal lattice
|
||||
axis. Where A are the vectors corresponding to the edges of the
|
||||
|
|
@ -89,23 +91,24 @@ average of the (inversed) box lengths with periodic boundary conditions.
|
|||
Meshes defined by the simulation domain must contain at least one periodic
|
||||
boundary.
|
||||
</P>
|
||||
<P>If the <I>manual</I> flag is included, the mesh of reciprocal lattice nodes
|
||||
will defined using the <I>c</I> values for the spacing along each reciprocal
|
||||
lattice axis. Note that manual mapping of the reciprocal space mesh is
|
||||
good for comparing diffraction results from multiple simulations; however
|
||||
it can reduce the likelihood that Bragg reflections will be satisfied
|
||||
unless small spacing parameters <B><0.05 Angstrom^(-1)</B> are implemented.
|
||||
Meshes with manual spacing do not require a periodic boundary.
|
||||
<P>If the <I>manual</I> flag is included, the mesh of reciprocal lattice nodes
|
||||
will defined using the <I>c</I> values for the spacing along each
|
||||
reciprocal lattice axis. Note that manual mapping of the reciprocal
|
||||
space mesh is good for comparing diffraction results from multiple
|
||||
simulations; however it can reduce the likelihood that Bragg
|
||||
reflections will be satisfied unless small spacing parameters (< 0.05
|
||||
Angstrom^(-1)) are implemented. Meshes with manual spacing do not
|
||||
require a periodic boundary.
|
||||
</P>
|
||||
<P>The limits of the reciprocal lattice mesh are determined by range of
|
||||
scattering angles explored. The <I>2Theta</I> parameters allows the user to
|
||||
reduce the scattering angle range to only the region of interest which
|
||||
reduces the cost of the computation.
|
||||
<P>The limits of the reciprocal lattice mesh are determined by range of
|
||||
scattering angles explored. The <I>2Theta</I> parameters allows the user
|
||||
to reduce the scattering angle range to only the region of interest
|
||||
which reduces the cost of the computation.
|
||||
</P>
|
||||
<P>The atomic scattering factors, fj, accounts for the reduction in
|
||||
diffraction intensity due to Compton scattering. Compute xrd uses
|
||||
analytical approximations of the atomic scattering factors that vary
|
||||
for each atom type (type1 type2 ... typeN) and angle of diffraction.
|
||||
<P>The atomic scattering factors, fj, accounts for the reduction in
|
||||
diffraction intensity due to Compton scattering. Compute xrd uses
|
||||
analytical approximations of the atomic scattering factors that vary
|
||||
for each atom type (type1 type2 ... typeN) and angle of diffraction.
|
||||
The analytic approximation is computed using the formula
|
||||
<A HREF = "#Colliex">(Colliex)</A>:
|
||||
</P>
|
||||
|
|
@ -183,12 +186,13 @@ options.
|
|||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "compute_ave_histo.html">fix ave/histo</A>
|
||||
<P><A HREF = "compute_ave_histo.html">fix ave/histo</A>,
|
||||
<A HREF = "compute_saed.html">compute saed</A>
|
||||
</P>
|
||||
<P><B>Default:</B>
|
||||
</P>
|
||||
<P>The option defaults are 2Theta = 1 179 (degrees), c = 1 1 1, LP = 1, no manual flag, no echo flag
|
||||
<P>The option defaults are 2Theta = 1 179 (degrees), c = 1 1 1, LP = 1,
|
||||
no manual flag, no echo flag.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
|
|
|
|||
|
|
@ -15,8 +15,7 @@ compute ID group-ID xrd lambda type1 type2 ... typeN keyword value ... :pre
|
|||
ID, group-ID are documented in "compute"_compute.html command :ulb,l
|
||||
xrd = style name of this compute command :l
|
||||
lambda = wavelength of incident radiation (length units) :l
|
||||
type1 type2 ... typeN = chemical symbol of each atom type (see valid
|
||||
options below) :l
|
||||
type1 type2 ... typeN = chemical symbol of each atom type (see valid options below) :l
|
||||
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {2Theta} or {c} or {LP} or {manual} or {echo} :l
|
||||
|
|
@ -36,10 +35,10 @@ keyword = {2Theta} or {c} or {LP} or {manual} or {echo} :l
|
|||
[Examples:]
|
||||
|
||||
compute 1 all xrd 1.541838 Al O 2Theta 0.087 0.87 c 1 1 1 LP 1 echo
|
||||
compute 2 all xrd 1.541838 Al O 2Theta 10 100 c 0.05 0.05 0.05 LP 1 manual
|
||||
compute 2 all xrd 1.541838 Al O 2Theta 10 100 c 0.05 0.05 0.05 LP 1 manual :pre
|
||||
|
||||
fix 1 all ave/histo 1 1 1 0.087 0.87 250 c_1[1] mode vector weights c_1[2] file Rad2Theta.xrd
|
||||
fix 2 all ave/histo 1 1 1 10 100 250 c_2[1] mode vector weights c_2[2] file Deg2Theta.xrd
|
||||
fix 1 all ave/histo 1 1 1 0.087 0.87 250 c_1\[1\] mode vector weights c_1\[2\] file Rad2Theta.xrd
|
||||
fix 2 all ave/histo 1 1 1 10 100 250 c_2\[1\] mode vector weights c_2\[2\] file Deg2Theta.xrd :pre
|
||||
|
||||
:pre
|
||||
|
||||
|
|
@ -66,7 +65,11 @@ the {LP} switch.
|
|||
|
||||
Diffraction intensities are calculated on a three-dimensional mesh of
|
||||
reciprocal lattice nodes. The mesh spacing is defined either (I)
|
||||
by the entire simulation domain or (II) manually using selected values.
|
||||
by the entire simulation domain or (II) manually using selected values as
|
||||
shown in the 2D diagram below.
|
||||
|
||||
:c,image(JPG/xrd_mesh_small.jpg,xrd_mesh.jpg)
|
||||
|
||||
|
||||
For a mesh defined by the simulation domain, a rectilinear grid is
|
||||
constructed with spacing {c}*inv(A) along each reciprocal lattice
|
||||
|
|
@ -77,23 +80,24 @@ average of the (inversed) box lengths with periodic boundary conditions.
|
|||
Meshes defined by the simulation domain must contain at least one periodic
|
||||
boundary.
|
||||
|
||||
If the {manual} flag is included, the mesh of reciprocal lattice nodes
|
||||
will defined using the {c} values for the spacing along each reciprocal
|
||||
lattice axis. Note that manual mapping of the reciprocal space mesh is
|
||||
good for comparing diffraction results from multiple simulations; however
|
||||
it can reduce the likelihood that Bragg reflections will be satisfied
|
||||
unless small spacing parameters [<0.05 Angstrom^(-1)] are implemented.
|
||||
Meshes with manual spacing do not require a periodic boundary.
|
||||
If the {manual} flag is included, the mesh of reciprocal lattice nodes
|
||||
will defined using the {c} values for the spacing along each
|
||||
reciprocal lattice axis. Note that manual mapping of the reciprocal
|
||||
space mesh is good for comparing diffraction results from multiple
|
||||
simulations; however it can reduce the likelihood that Bragg
|
||||
reflections will be satisfied unless small spacing parameters (< 0.05
|
||||
Angstrom^(-1)) are implemented. Meshes with manual spacing do not
|
||||
require a periodic boundary.
|
||||
|
||||
The limits of the reciprocal lattice mesh are determined by range of
|
||||
scattering angles explored. The {2Theta} parameters allows the user to
|
||||
reduce the scattering angle range to only the region of interest which
|
||||
reduces the cost of the computation.
|
||||
The limits of the reciprocal lattice mesh are determined by range of
|
||||
scattering angles explored. The {2Theta} parameters allows the user
|
||||
to reduce the scattering angle range to only the region of interest
|
||||
which reduces the cost of the computation.
|
||||
|
||||
The atomic scattering factors, fj, accounts for the reduction in
|
||||
diffraction intensity due to Compton scattering. Compute xrd uses
|
||||
analytical approximations of the atomic scattering factors that vary
|
||||
for each atom type (type1 type2 ... typeN) and angle of diffraction.
|
||||
The atomic scattering factors, fj, accounts for the reduction in
|
||||
diffraction intensity due to Compton scattering. Compute xrd uses
|
||||
analytical approximations of the atomic scattering factors that vary
|
||||
for each atom type (type1 type2 ... typeN) and angle of diffraction.
|
||||
The analytic approximation is computed using the formula
|
||||
"(Colliex)"_#Colliex:
|
||||
|
||||
|
|
@ -172,12 +176,13 @@ The compute_xrd command does not work for triclinic cells.
|
|||
|
||||
[Related commands:]
|
||||
|
||||
"fix ave/histo"_compute_ave_histo.html
|
||||
"fix ave/histo"_compute_ave_histo.html,
|
||||
"compute saed"_compute_saed.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The option defaults are 2Theta = 1 179 (degrees), c = 1 1 1, LP = 1, no manual flag, no echo flag
|
||||
The option defaults are 2Theta = 1 179 (degrees), c = 1 1 1, LP = 1,
|
||||
no manual flag, no echo flag.
|
||||
|
||||
:line
|
||||
|
||||
|
|
|
|||
|
|
@ -66,7 +66,7 @@
|
|||
string = text to print as 2nd line of output file
|
||||
<I>title3</I> arg = string
|
||||
string = text to print as 3rd line of output file, only for vector mode
|
||||
<I>weights</I> arg = c_ID, c_ID[N], f_ID, f_ID[N], v_name
|
||||
<I>weights</I> arg = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_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
|
||||
|
|
@ -294,14 +294,14 @@ describes the six values that are printed at the first of each section
|
|||
of output. The third describes the 4 values printed for each bin in
|
||||
the histogram.
|
||||
</P>
|
||||
<P>If the <I>weights</I> keyword is specified, the fix will compute a weighted
|
||||
histogram using per-bin weights specified by the <I>weights</I> argument. As
|
||||
normal, the bin locations will be will be generated based off value1.
|
||||
However, instead of each binned value contributing 1 to the bin
|
||||
location, the contributing ammount is assigned the weights
|
||||
argument. Only a single value1 and weights argument pair can be can be
|
||||
used for each fix ave/histo. The length of value1 must match the
|
||||
lenght of the weights arguemnt.
|
||||
<P>If the <I>weights</I> keyword is specified, the fix will generate a weighted
|
||||
histogram using data from the assigned value1 and weights argument.
|
||||
As normal, the bin locations will be will be generated based off value1.
|
||||
However, instead of each binned value contributing 1 to the bin location,
|
||||
the contributing ammount is assigned the weights argument. Only a single
|
||||
value1 and weights argument pair can be can be used for each fix
|
||||
ave/histo. The length of value1 must match the lenght of the weights
|
||||
arguemnt.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
|
|
|
|||
|
|
@ -52,7 +52,7 @@ keyword = {mode} or {file} or {ave} or {start} or {beyond} or {overwrite} or {ti
|
|||
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
|
||||
{weights} arg = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name
|
||||
{weights} arg = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_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
|
||||
|
|
@ -279,14 +279,14 @@ describes the six values that are printed at the first of each section
|
|||
of output. The third describes the 4 values printed for each bin in
|
||||
the histogram.
|
||||
|
||||
If the {weights} keyword is specified, the fix will compute a weighted
|
||||
histogram using per-bin weights specified by the {weights} argument. As
|
||||
normal, the bin locations will be will be generated based off value1.
|
||||
However, instead of each binned value contributing 1 to the bin
|
||||
location, the contributing ammount is assigned the weights
|
||||
argument. Only a single value1 and weights argument pair can be can be
|
||||
used for each fix ave/histo. The length of value1 must match the
|
||||
lenght of the weights arguemnt.
|
||||
If the {weights} keyword is specified, the fix will generate a weighted
|
||||
histogram using data from the assigned value1 and weights argument.
|
||||
As normal, the bin locations will be will be generated based off value1.
|
||||
However, instead of each binned value contributing 1 to the bin location,
|
||||
the contributing ammount is assigned the weights argument. Only a single
|
||||
value1 and weights argument pair can be can be used for each fix
|
||||
ave/histo. The length of value1 must match the lenght of the weights
|
||||
arguemnt.
|
||||
|
||||
:line
|
||||
|
||||
|
|
|
|||
|
|
@ -42,9 +42,9 @@
|
|||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<P>compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
|
||||
compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
|
||||
</P>
|
||||
<PRE>compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
|
||||
compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
|
||||
</PRE>
|
||||
<PRE>fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
|
||||
fix saed/vtk 1 1 1 c_2 file Ni_000.saed
|
||||
</PRE>
|
||||
|
|
@ -69,11 +69,11 @@ specified values may represent calculations performed by saed computes
|
|||
which store their own "group" definitions.
|
||||
</P>
|
||||
<P>Fix saed/vtk is designed to work only with <A HREF = "compute_saed.txt">compute_saed</A>
|
||||
values.
|
||||
</P>
|
||||
<P>compute 3 top saed 0.0251 Al O
|
||||
fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed
|
||||
values, e.g.
|
||||
</P>
|
||||
<PRE>compute 3 top saed 0.0251 Al O
|
||||
fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed
|
||||
</PRE>
|
||||
<HR>
|
||||
|
||||
<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify on what
|
||||
|
|
|
|||
|
|
@ -35,7 +35,7 @@ keyword = {file} or {ave} or {start} or {file} or {overwrite}:l
|
|||
[Examples:]
|
||||
|
||||
compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
|
||||
compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
|
||||
compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo :pre
|
||||
|
||||
fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
|
||||
fix saed/vtk 1 1 1 c_2 file Ni_000.saed :pre
|
||||
|
|
@ -61,10 +61,10 @@ specified values may represent calculations performed by saed computes
|
|||
which store their own "group" definitions.
|
||||
|
||||
Fix saed/vtk is designed to work only with "compute_saed"_compute_saed.txt
|
||||
values.
|
||||
values, e.g.
|
||||
|
||||
compute 3 top saed 0.0251 Al O
|
||||
fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed
|
||||
fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed :pre
|
||||
|
||||
:line
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue