diff --git a/doc/Manual.html b/doc/Manual.html index 861b99a289..982db83274 100644 --- a/doc/Manual.html +++ b/doc/Manual.html @@ -1,150 +1,46 @@ - - - - - - - - - LAMMPS Documentation — LAMMPS-ICMS 28 July 2015 version documentation - + + + +LAMMPS-ICMS Users Manual + + + + - - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
- - - +
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
- -
-
-
- -
- - - -
-
-
- -

-

LAMMPS Documentation

-
-

27 Jul 2015 version

-
-
-

Version info:

-

The LAMMPS “version” is the date when it was released, such as 1 May + + + + +

+ +

+ +

LAMMPS-ICMS Documentation +

+

4 Aug 2015 version +

+

Version info: +

+

The LAMMPS "version" is the date when it was released, such as 1 May 2010. LAMMPS is updated continuously. Whenever we fix a bug or add a -feature, we release it immediately, and post a notice on this page of the WWW site. Each dated copy of LAMMPS contains all the +feature, we release it immediately, and post a notice on this page of +the WWW site. Each dated copy of LAMMPS contains all the features and bug-fixes up to and including that version date. The version date is printed to the screen and logfile every time you run LAMMPS. It is also in the file src/version.h and in the LAMMPS directory name created when you unpack a tarball, and at the top of -the first page of the manual (this page).

+the first page of the manual (this page). +

+
  • If you browse the HTML doc pages on the LAMMPS WWW site, they always +describe the most current version of LAMMPS.

    LAMMPS-ICMS is an experimental variant of LAMMPS with additional features made available for testing before they will be submitted @@ -159,296 +55,437 @@ development will be halted except for important bugfixes until all features of LAMMPS-ICMS fully compatible with the upstream version or replaced by alternate implementations.

    +
  • If you browse the HTML doc pages included in your tarball, they +describe the version you have. -
      -
    • If you browse the HTML doc pages on the LAMMPS WWW site, they always -describe the most current version of LAMMPS.
      • -
    • If you browse the HTML doc pages included in your tarball, they -describe the version you have.
      • -
    • The PDF file on the WWW site or in the tarball is updated -about once per month. This is because it is large, and we don’t want -it to be part of every patch.
      • -
    • There is also a Developer.pdf file in the doc +
    • The PDF file on the WWW site or in the tarball is updated +about once per month. This is because it is large, and we don't want +it to be part of every patch. + +
    • There is also a Developer.pdf file in the doc directory, which describes the internal structure and algorithms of -LAMMPS.
      • -
    -

    LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel -Simulator.

    -

    LAMMPS is a classical molecular dynamics simulation code designed to +LAMMPS. +

+

LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel +Simulator. +

+

LAMMPS is a classical molecular dynamics simulation code designed to run efficiently on parallel computers. It was developed at Sandia National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely -under the terms of the GNU Public License (GPL).

-

The primary developers of LAMMPS are Steve Plimpton, Aidan +under the terms of the GNU Public License (GPL). +

+

The primary developers of LAMMPS are Steve Plimpton, Aidan Thompson, and Paul Crozier who can be contacted at -sjplimp,athomps,pscrozi at sandia.gov. The LAMMPS WWW Site at -http://lammps.sandia.gov has more information about the code and its -uses.

-
-

The LAMMPS documentation is organized into the following sections. If +sjplimp,athomps,pscrozi at sandia.gov. The LAMMPS WWW Site at +http://lammps.sandia.gov has more information about the code and its +uses. +

+ + + + +
+ +

The LAMMPS documentation is organized into the following sections. If you find errors or omissions in this manual or have suggestions for useful information to add, please send an email to the developers so -we can improve the LAMMPS documentation.

-

Once you are familiar with LAMMPS, you may want to bookmark this page at Section_commands.html#comm since -it gives quick access to documentation for all LAMMPS commands.

-

PDF file of the entire manual, generated by -htmldoc

-
- -
-
-
-
-

Indices and tables

- -
+we can improve the LAMMPS documentation. +

+

Once you are familiar with LAMMPS, you may want to bookmark this +page at Section_commands.html#comm since +it gives quick access to documentation for all LAMMPS commands. +

+

PDF file of the entire manual, generated by +htmldoc +

+

+

+
  1. +Introduction + + +
  2. Getting started + + +
  3. Commands + + +
  4. Packages + + +
  5. Accelerating LAMMPS performance + + +
  6. How-to discussions + + +
  7. Example problems + +
  8. Performance & scalability + +
  9. Additional tools + +
  10. Modifying & extending LAMMPS + + +
  11. Python interface + + +
  12. Errors + + +
  13. Future and history + + + +
-
-
- - -
-
- -
- -
- - - - - - - - - - - - - - - - - - - - - \ No newline at end of file + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/doc/Manual.txt b/doc/Manual.txt index 51e3e11a4c..d49b7c3d40 100644 --- a/doc/Manual.txt +++ b/doc/Manual.txt @@ -1,7 +1,7 @@ LAMMPS-ICMS Users Manual - + @@ -21,7 +21,7 @@

LAMMPS-ICMS Documentation :c,h3 -27 Jul 2015 version :c,h4 +4 Aug 2015 version :c,h4 Version info: :h4 @@ -100,7 +100,7 @@ it gives quick access to documentation for all LAMMPS commands. .. toctree:: :maxdepth: 2 - :numbered: + :numbered: // comment Section_intro Section_start @@ -120,8 +120,8 @@ it gives quick access to documentation for all LAMMPS commands. Indices and tables ================== -* :ref:`genindex` -* :ref:`search` +* :ref:`genindex` // comment +* :ref:`search` // comment END_RST --> diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 2748b05f8b..b8bcf0b55d 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -758,12 +758,12 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.

LAMMPS is built with the appropriate package.

-++++--- @@ -806,14 +806,21 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.

- + - + + + + + + + + + -
adapt/fep reax/c/species saed/vtk smdtemp/rescale/effsmd/adjust/dt
ti/rs
smd/integrate/tlsphsmd/integrate/ulsphsmd/move/triangulated/surfacesmd/setvelsmd/tlsph/reference/configurationsmd/wall/surface
temp/rescale/effti/rs ti/spring ttm/mod     
@@ -920,12 +927,12 @@ KOKKOS, o = USER-OMP, t = OPT.

used if LAMMPS is built with the appropriate package.

---++-++ @@ -938,16 +945,37 @@ used if LA - - - + + + - + + + + + + + + + + + + + + + + + + + + + + + + - -
ackland/atom
meso_rho/atom meso_t/atom saedtemp/drudetemp/efftemp/deform/effsmd/contact/radiussmd/damagesmd/hourglass/error
temp/region/eff
smd/internal/energysmd/plastic/strainsmd/plastic/strain/ratesmd/rhosmd/tlsph/defgradsmd/tlsph/dt
smd/tlsph/num/neighssmd/tlsph/shapesmd/tlsph/strainsmd/tlsph/strain/ratesmd/tlsph/stresssmd/triangle/mesh/vertices
smd/ulsph/num/neighssmd/ulsph/strainsmd/ulsph/strain/ratesmd/ulpsh/stresssmd/voltemp/drude
temp/efftemp/deform/efftemp/region/eff temp/rotate xrd    
@@ -1110,10 +1138,10 @@ KOKKOS, o = USER-OMP, t = OPT.

if LAMMPS is built with the appropriate package.

---+++ @@ -1144,19 +1172,24 @@ if LAMMPS + + + + + - + - + - + diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 725a734cdc..1c5a8e0289 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -633,6 +633,13 @@ package"_Section_start.html#start_3. "reax/c/species"_fix_reaxc_species.html, "saed/vtk"_fix_saed_vtk.html, "smd"_fix_smd.html, +"smd/adjust/dt"_fix_smd_adjust_dt.html, +"smd/integrate/tlsph"_fix_smd_integrate_tlsph.html, +"smd/integrate/ulsph"_fix_smd_integrate_ulsph.html, +"smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html, +"smd/setvel"_fix_smd_setvel.html, +"smd/tlsph/reference/configuration"_fix_smd_tlsph_reference_configuration.html, +"smd/wall/surface"_fix_smd_wall_surface.html, "temp/rescale/eff"_fix_temp_rescale_eff.html, "ti/rs"_fix_ti_rs.html, "ti/spring"_fix_ti_spring.html, @@ -730,6 +737,26 @@ package"_Section_start.html#start_3. "meso_rho/atom"_compute_meso_rho_atom.html, "meso_t/atom"_compute_meso_t_atom.html, "saed"_compute_saed.html, +"smd/contact/radius"_compute_smd_contact_radius.html, +"smd/damage"_compute_smd_damage.html, +"smd/hourglass/error"_compute_smd_hourglass_error.html, +"smd/internal/energy"_compute_smd_internal_energy.html, +"smd/plastic/strain"_compute_smd_plastic_strain.html, +"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html, +"smd/rho"_compute_smd_rho.html, +"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html, +"smd/tlsph/dt"_compute_smd_tlsph_dt.html, +"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html, +"smd/tlsph/shape"_compute_smd_tlsph_shape.html, +"smd/tlsph/strain"_compute_smd_tlsph_strain.html, +"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html, +"smd/tlsph/stress"_compute_smd_tlsph_stress.html, +"smd/triangle/mesh/vertices"_compute_smd_triangle_mesh_vertices.html, +"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html, +"smd/ulsph/strain"_compute_smd_ulsph_strain.html, +"smd/ulsph/strain/rate"_compute_smd_ulsph_strain/rate.html, +"smd/ulpsh/stress"_compute_smd_ulpsh_stress.html, +"smd/vol"_compute_smd_vol.html, "temp/drude"_compute_temp_drude.html, "temp/eff"_compute_temp_eff.html, "temp/deform/eff"_compute_temp_deform_eff.html, @@ -884,6 +911,10 @@ package"_Section_start.html#start_3. "meam/sw/spline"_pair_meam_sw_spline.html, "quip"_pair_quip.html, "reax/c"_pair_reax_c.html, +"smd/hertz"_pair_smd_hertz.html, +"smd/tlsph"_pair_smd_tlsph.html, +"smd/triangulated/surface"_pair_smd_triangulated_surface.html, +"smd/ulsph"_pair_smd_ulsph.html, "sph/heatconduction"_pair_sph_heatconduction.html, "sph/idealgas"_pair_sph_idealgas.html, "sph/lj"_pair_sph_lj.html, diff --git a/doc/Section_packages.html b/doc/Section_packages.html index 98a805ea2e..13c55323ae 100644 --- a/doc/Section_packages.html +++ b/doc/Section_packages.html @@ -98,7 +98,8 @@
  • 4.18. USER-QMMM package
  • 4.19. USER-QTB package
  • 4.20. USER-REAXC package
    • -
  • 4.21. USER-SPH package
    • +
  • 4.21. USER-SMD package
    • +
  • 4.22. USER-SPH package
  • 5. Accelerating LAMMPS performance
    • @@ -828,7 +829,21 @@ on how to build LAMMPS with both kinds of auxiliary libraries.

    - + + + + + + + + + @@ -839,7 +854,7 @@ on how to build LAMMPS with both kinds of auxiliary libraries.

    - + @@ -881,7 +896,7 @@ See the src/package/Makefile.lammps file for info on where to download the library. Section start of the manual also gives details on how to build LAMMPS with both kinds of auxiliary libraries.

    -

    More details on each package, from the USER-*/README file is given +

    More details on each package, from the USER-*/README file is given below.

    @@ -1115,7 +1130,7 @@ Western Ontario. Contact them directly if you have questions.

    4.14. USER-MISC package

    The files in this package are a potpourri of (mostly) unrelated features contributed to LAMMPS by users. Each feature is a single -pair of files (*.cpp and *.h).

    +pair of files (*.cpp and *.h).

    More information about each feature can be found by reading its doc page in the LAMMPS doc directory. The doc page which lists all LAMMPS input script commands is as follows:

    @@ -1237,8 +1252,20 @@ Aidan Thompson at Sandia (athomps at sandia.gov), if you have questions.

    +
    +

    4.21. USER-SMD package

    +

    This package implements smoothed Mach dynamics (SMD) in +LAMMPS. Currently, the package has the following features:

    +

    ???

    +

    See the file doc/USER/smd/SPH_user_guide.pdf to get started.

    +

    There are example scripts for using this package in examples/USER/smd.

    +

    The person who created this package is Georg Ganzenmuller at the +Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in +Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if +you have questions.

    +
    -

    4.21. USER-SPH package

    +

    4.22. USER-SPH package

    This package implements smoothed particle hydrodynamics (SPH) in LAMMPS. Currently, the package has the following features:

     args = none for any style except body and hybrid
@@ -241,19 +241,23 @@ quantities.
    - + + + + + - + - + - + @@ -293,6 +297,12 @@ per-particle mass and volume.

    The meso style is for smoothed particle hydrodynamics (SPH) particles which store a density (rho), energy (e), and heat capacity (cv).

    +

    The smd style is for a general formulation of Smooth Particle +Hydrodynamics. Both fluids and solids can be modeled. Particles +store the mass and volume of an integration point, a kernel diameter +used for calculating the field variables (e.g. stress and deformation) +and a contact radius for calculating repulsive forces which prevent +individual physical bodies from penetretating each other.

    The wavepacket style is similar to electron, but the electrons may consist of several Gaussian wave packets, summed up with coefficients cs= (cs_re,cs_im). Each of the wave packets is treated as a separate diff --git a/doc/atom_style.txt b/doc/atom_style.txt index 4750cbfbdd..78e8232409 100644 --- a/doc/atom_style.txt +++ b/doc/atom_style.txt @@ -14,7 +14,8 @@ atom_style style args :pre style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \ {electron} or {ellipsoid} or {full} or {line} or {meso} or \ - {molecular} or {peri} or {sphere} or {tri} or {template} or {hybrid} :ulb,l + {molecular} or {peri} or {smd} or {sphere} or {tri} or \ + {template} or {hybrid} :ulb,l args = none for any style except {body} and {hybrid} {body} args = bstyle bstyle-args bstyle = style of body particles @@ -76,6 +77,7 @@ quantities. {meso} | rho, e, cv | SPH particles | {molecular} | bonds, angles, dihedrals, impropers | uncharged molecules | {peri} | mass, volume | mesocopic Peridynamic models | +{smd} | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles | {sphere} | diameter, mass, angular velocity | granular models | {template} | template index, template atom | small molecules with fixed topology | {tri} | corner points, angular momentum | rigid bodies | @@ -123,6 +125,13 @@ The {meso} style is for smoothed particle hydrodynamics (SPH) particles which store a density (rho), energy (e), and heat capacity (cv). +The {smd} style is for a general formulation of Smooth Particle +Hydrodynamics. Both fluids and solids can be modeled. Particles +store the mass and volume of an integration point, a kernel diameter +used for calculating the field variables (e.g. stress and deformation) +and a contact radius for calculating repulsive forces which prevent +individual physical bodies from penetretating each other. + The {wavepacket} style is similar to {electron}, but the electrons may consist of several Gaussian wave packets, summed up with coefficients cs= (cs_re,cs_im). Each of the wave packets is treated as a separate diff --git a/doc/compute_smd_contact_radius.html b/doc/compute_smd_contact_radius.html new file mode 100644 index 0000000000..e8e2782796 --- /dev/null +++ b/doc/compute_smd_contact_radius.html @@ -0,0 +1,235 @@ + + + + + + + + + + + compute smd/contact_radius command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    compute smd/contact_radius command

    +
    +

    Syntax

    +
    compute ID group-ID smd/contact_radius
+
    +
    +
      +
    • ID, group-ID are documented in compute command
      • +
    • smd/contact_radius = style name of this compute command
      • +
    +
    +
    +

    Examples

    +
    compute 1 all smd/contact_radius
+
    +
    +
    +
    +

    Description

    +

    Define a computation which outputs the contact radius, i.e., the radius used to prevent particles from penetrating each other. +The contact radius is used only to prevent particles belonging to different physical bodies from penetrating each other. It is used by the contact pair styles, +e.g., smd/hertz and smd/tri_surface.

    +

    See this PDF guide to using Smooth Mach Dynamics in +LAMMPS.

    +

    The value of the contact radius will be 0.0 for particles not in the +specified compute group.

    +

    Output info:

    +

    This compute calculates a per-particle vector, which can be accessed by +any command that uses per-particle values from a compute as input. See +Section_howto 15 for an overview of +LAMMPS output options.

    +

    The per-particle vector values will be in distance units.

    +
    +
    +

    Restrictions

    +

    This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS section for more info.

    +
    + +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/compute_smd_contact_radius.txt b/doc/compute_smd_contact_radius.txt new file mode 100644 index 0000000000..fea13fcfc3 --- /dev/null +++ b/doc/compute_smd_contact_radius.txt @@ -0,0 +1,53 @@ +"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 smd/contact_radius command :h3 + +[Syntax:] + +compute ID group-ID smd/contact_radius :pre + +ID, group-ID are documented in "compute"_compute.html command +smd/contact_radius = style name of this compute command :ul + +[Examples:] + +compute 1 all smd/contact_radius :pre + +[Description:] + +Define a computation which outputs the contact radius, i.e., the radius used to prevent particles from penetrating each other. +The contact radius is used only to prevent particles belonging to different physical bodies from penetrating each other. It is used by the contact pair styles, +e.g., smd/hertz and smd/tri_surface. + +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in +LAMMPS. + +The value of the contact radius will be 0.0 for particles not in the +specified compute group. + +[Output info:] + +This compute calculates a per-particle vector, which can be accessed by +any command that uses per-particle values from a compute as input. See +"Section_howto 15"_Section_howto.html#howto_15 for an overview of +LAMMPS output options. + +The per-particle vector values will be in distance "units"_units.html. + +[Restrictions:] + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +[Related commands:] + +"dump custom"_dump.html smd/hertz smd/tri_surface + +[Default:] none diff --git a/doc/compute_smd_damage.html b/doc/compute_smd_damage.html new file mode 100644 index 0000000000..4442785ed7 --- /dev/null +++ b/doc/compute_smd_damage.html @@ -0,0 +1,232 @@ + + + + + + + + + + + compute smd/damage command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    compute smd/damage command

    +
    +

    Syntax

    +
    compute ID group-ID smd/damage
+
    +
    +
      +
    • ID, group-ID are documented in compute command
      • +
    • smd/damage = style name of this compute command
      • +
    +
    +
    +

    Examples

    +
    compute 1 all smd/damage
+
    +
    +
    +
    +

    Description

    +

    Define a computation that calculates the damage status of SPH particles +according to the damage model which is defined via the SMD SPH pair styles, e.g., the maximum plastic strain failure criterion.

    +

    See this PDF guide to use Smooth Mach Dynamics in LAMMPS.

    +

    Output Info:

    +

    This compute calculates a per-particle vector, which can be accessed by +any command that uses per-particle values from a compute as input. See +How-to discussions, section 6.15 +for an overview of LAMMPS output options.

    +

    The per-particle values are dimensionless an in the range of zero to one.

    +
    +
    +

    Restrictions

    +

    This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS +section for more info.

    +
    + +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/compute_smd_damage.txt b/doc/compute_smd_damage.txt new file mode 100644 index 0000000000..0d92132a25 --- /dev/null +++ b/doc/compute_smd_damage.txt @@ -0,0 +1,48 @@ +"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 smd/damage command :h3 + +[Syntax:] + +compute ID group-ID smd/damage :pre + +ID, group-ID are documented in "compute"_compute.html command +smd/damage = style name of this compute command :ul + +[Examples:] + +compute 1 all smd/damage :pre + +[Description:] + +Define a computation that calculates the damage status of SPH particles +according to the damage model which is defined via the SMD SPH pair styles, e.g., the maximum plastic strain failure criterion. + +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS. + +[Output Info:] + +This compute calculates a per-particle vector, which can be accessed by +any command that uses per-particle values from a compute as input. See +"How-to discussions, section 6.15"_Section_howto.html#howto_15 +for an overview of LAMMPS output options. + +The per-particle values are dimensionless an in the range of zero to one. + +[Restrictions:] + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info. + +[Related commands:] + +"smd/plastic_strain"_compute_smd_plastic_strain.html, "smd/tlsph_stress"_compute_smd_tlsph_stress.html + +[Default:] none diff --git a/doc/compute_smd_hourglass_error.html b/doc/compute_smd_hourglass_error.html new file mode 100644 index 0000000000..da6ff46a4c --- /dev/null +++ b/doc/compute_smd_hourglass_error.html @@ -0,0 +1,239 @@ + + + + + + + + + + + compute smd/hourglass_error command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    compute smd/hourglass_error command

    +
    +

    Syntax

    +
    compute ID group-ID smd/hourglass_error
+
    +
    +
      +
    • ID, group-ID are documented in compute command
      • +
    • smd/hourglass_error = style name of this compute command
      • +
    +
    +
    +

    Examples

    +
    compute 1 all smd/hourglass_error
+
    +
    +
    +
    +

    Description

    +

    Define a computation which outputs the error of the approximated +relative separation with respect to the actual relative separation of +the particles i and j. Ideally, if the deformation gradient is exact, +and there exists a unique mapping between all particles’ positions +within the neighborhood of the central node and the deformation gradient, +the approximated relative separation will coincide with the actual relative +separation of the particles i and j in the deformed configuration. +This compute is only really useful for debugging the hourglass control mechanim which is part of the Total-Lagrangian SPH pair style.

    +

    See this PDF guide to use Smooth Mach Dynamics in LAMMPS.

    +

    Output Info:

    +

    This compute calculates a per-particle vector, which can be accessed by +any command that uses per-particle values from a compute as input. See +How-to discussions, section 6.15 +for an overview of LAMMPS output options.

    +

    The per-particle vector values will are dimensionless. See units.

    +
    +
    +

    Restrictions

    +

    This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS +section for more info.

    +

    This quantity will be computed only for particles which interact with tlsph pair style.

    +

    Related Commands:

    +

    smd/tlsph_defgrad

    +
    +
    +

    Default

    +
    +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/compute_smd_hourglass_error.txt b/doc/compute_smd_hourglass_error.txt new file mode 100644 index 0000000000..ba87db467a --- /dev/null +++ b/doc/compute_smd_hourglass_error.txt @@ -0,0 +1,57 @@ +"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 smd/hourglass_error command :h3 + +[Syntax:] + +compute ID group-ID smd/hourglass_error :pre + +ID, group-ID are documented in "compute"_compute.html command +smd/hourglass_error = style name of this compute command :ul + +[Examples:] + +compute 1 all smd/hourglass_error :pre + +[Description:] + +Define a computation which outputs the error of the approximated +relative separation with respect to the actual relative separation of +the particles i and j. Ideally, if the deformation gradient is exact, +and there exists a unique mapping between all particles' positions +within the neighborhood of the central node and the deformation gradient, +the approximated relative separation will coincide with the actual relative +separation of the particles i and j in the deformed configuration. +This compute is only really useful for debugging the hourglass control mechanim which is part of the Total-Lagrangian SPH pair style. + +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS. + +[Output Info:] + +This compute calculates a per-particle vector, which can be accessed by +any command that uses per-particle values from a compute as input. See +"How-to discussions, section 6.15"_Section_howto.html#howto_15 +for an overview of LAMMPS output options. + +The per-particle vector values will are dimensionless. See "units"_units.html. + +[Restrictions:] + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info. + +This quantity will be computed only for particles which interact with tlsph pair style. + +[Related Commands:] + +"smd/tlsph_defgrad"_compute_smd_tlsph_defgrad.html + +[Default:] + diff --git a/doc/compute_smd_internal_energy.html b/doc/compute_smd_internal_energy.html new file mode 100644 index 0000000000..aa4bc9a3cf --- /dev/null +++ b/doc/compute_smd_internal_energy.html @@ -0,0 +1,231 @@ + + + + + + + + + + + compute smd/internal_energy command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    compute smd/internal_energy command

    +
    +

    Syntax

    +
    compute ID group-ID smd/internal_energy
+
    +
    +
      +
    • ID, group-ID are documented in compute command
      • +
    • smd/smd/internal_energy = style name of this compute command
      • +
    +
    +
    +

    Examples

    +
    compute 1 all smd/internal_energy
+
    +
    +
    +
    +

    Description

    +

    Define a computation which outputs the per-particle enthalpy, i.e., the sum of potential energy and heat.

    +

    See this PDF guide to use Smooth Mach Dynamics in LAMMPS.

    +

    Output Info:

    +

    This compute calculates a per-particle vector, which can be accessed by +any command that uses per-particle values from a compute as input. See +How-to discussions, section 6.15 +for an overview of LAMMPS output options.

    +

    The per-particle vector values will be given in units of energy.

    +
    +
    +

    Restrictions

    +

    This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS +section for more info. This compute can only be used for particles which interact via the +updated Lagrangian or total Lagrangian SPH pair styles.

    +

    Related Commands:

    +
    +
    +

    Default

    +
    +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/compute_smd_internal_energy.txt b/doc/compute_smd_internal_energy.txt new file mode 100644 index 0000000000..d52a3936ad --- /dev/null +++ b/doc/compute_smd_internal_energy.txt @@ -0,0 +1,49 @@ +"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 smd/internal_energy command :h3 + +[Syntax:] + +compute ID group-ID smd/internal_energy :pre + +ID, group-ID are documented in "compute"_compute.html command +smd/smd/internal_energy = style name of this compute command :ul + +[Examples:] + +compute 1 all smd/internal_energy :pre + +[Description:] + +Define a computation which outputs the per-particle enthalpy, i.e., the sum of potential energy and heat. + +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS. + +[Output Info:] + +This compute calculates a per-particle vector, which can be accessed by +any command that uses per-particle values from a compute as input. See +"How-to discussions, section 6.15"_Section_howto.html#howto_15 +for an overview of LAMMPS output options. + +The per-particle vector values will be given in "units"_units.html of energy. + +[Restrictions:] + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info. This compute can only be used for particles which interact via the +updated Lagrangian or total Lagrangian SPH pair styles. + + +[Related Commands:] + + + +[Default:] diff --git a/doc/compute_smd_plastic_strain.html b/doc/compute_smd_plastic_strain.html new file mode 100644 index 0000000000..b98731a41d --- /dev/null +++ b/doc/compute_smd_plastic_strain.html @@ -0,0 +1,234 @@ + + + + + + + + + + + compute smd/plastic_strain command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    compute smd/plastic_strain command

    +
    +

    Syntax

    +
    compute ID group-ID smd/plastic_strain
+
    +
    +
      +
    • ID, group-ID are documented in compute command
      • +
    • smd/plastic_strain = style name of this compute command
      • +
    +
    +
    +

    Examples

    +
    compute 1 all smd/plastic_strain
+
    +
    +
    +
    +

    Description

    +

    Define a computation that outputs the equivalent plastic strain per particle. +This command is only meaningful if a material model with plasticity is defined.

    +

    See this PDF guide to use Smooth Mach Dynamics in LAMMPS.

    +

    Output Info:

    +

    This compute calculates a per-particle vector, which can be accessed by +any command that uses per-particle values from a compute as input. See +How-to discussions, section 6.15 +for an overview of LAMMPS output options.

    +

    The per-particle values will be given dimensionless. See units.

    +
    +
    +

    Restrictions

    +

    This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS +section for more info. This compute can only be used for particles which interact via the +updated Lagrangian or total Lagrangian SPH pair styles.

    +
    + +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/compute_smd_plastic_strain.txt b/doc/compute_smd_plastic_strain.txt new file mode 100644 index 0000000000..0951677ee8 --- /dev/null +++ b/doc/compute_smd_plastic_strain.txt @@ -0,0 +1,51 @@ +"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 smd/plastic_strain command :h3 + +[Syntax:] + +compute ID group-ID smd/plastic_strain :pre + +ID, group-ID are documented in "compute"_compute.html command +smd/plastic_strain = style name of this compute command :ul + +[Examples:] + +compute 1 all smd/plastic_strain :pre + +[Description:] + +Define a computation that outputs the equivalent plastic strain per particle. +This command is only meaningful if a material model with plasticity is defined. + + +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS. + +[Output Info:] + +This compute calculates a per-particle vector, which can be accessed by +any command that uses per-particle values from a compute as input. See +"How-to discussions, section 6.15"_Section_howto.html#howto_15 +for an overview of LAMMPS output options. + +The per-particle values will be given dimensionless. See "units"_units.html. + +[Restrictions:] + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info. This compute can only be used for particles which interact via the +updated Lagrangian or total Lagrangian SPH pair styles. + +[Related commands:] + +"smd/plastic_strain_rate"_compute_smd_tlsph_strain.html, "smd/tlsph_strain_rate"_compute_smd_tlsph_strain_rate.html, +"smd/tlsph_strain"_compute_smd_tlsph_strain.html + +[Default:] none \ No newline at end of file diff --git a/doc/compute_smd_plastic_strain_rate.html b/doc/compute_smd_plastic_strain_rate.html new file mode 100644 index 0000000000..a41b2f8bd7 --- /dev/null +++ b/doc/compute_smd_plastic_strain_rate.html @@ -0,0 +1,234 @@ + + + + + + + + + + + compute smd/plastic_strain_rate command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    compute smd/plastic_strain_rate command

    +
    +

    Syntax

    +
    compute ID group-ID smd/plastic_strain_rate
+
    +
    +
      +
    • ID, group-ID are documented in compute command
      • +
    • smd/plastic_strain_rate = style name of this compute command
      • +
    +
    +
    +

    Examples

    +
    compute 1 all smd/plastic_strain_rate
+
    +
    +
    +
    +

    Description

    +

    Define a computation that outputs the time rate of the equivalent plastic strain. +This command is only meaningful if a material model with plasticity is defined.

    +

    See this PDF guide to use Smooth Mach Dynamics in LAMMPS.

    +

    Output Info:

    +

    This compute calculates a per-particle vector, which can be accessed by +any command that uses per-particle values from a compute as input. See +How-to discussions, section 6.15 +for an overview of LAMMPS output options.

    +

    The per-particle values will be given in units of one over time.

    +
    +
    +

    Restrictions

    +

    This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS +section for more info. This compute can only be used for particles which interact via the +updated Lagrangian or total Lagrangian SPH pair styles.

    +
    + +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/compute_smd_plastic_strain_rate.txt b/doc/compute_smd_plastic_strain_rate.txt new file mode 100644 index 0000000000..8879a63786 --- /dev/null +++ b/doc/compute_smd_plastic_strain_rate.txt @@ -0,0 +1,50 @@ +"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 smd/plastic_strain_rate command :h3 + +[Syntax:] + +compute ID group-ID smd/plastic_strain_rate :pre + +ID, group-ID are documented in "compute"_compute.html command +smd/plastic_strain_rate = style name of this compute command :ul + +[Examples:] + +compute 1 all smd/plastic_strain_rate :pre + +[Description:] + +Define a computation that outputs the time rate of the equivalent plastic strain. +This command is only meaningful if a material model with plasticity is defined. + +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS. + +[Output Info:] + +This compute calculates a per-particle vector, which can be accessed by +any command that uses per-particle values from a compute as input. See +"How-to discussions, section 6.15"_Section_howto.html#howto_15 +for an overview of LAMMPS output options. + +The per-particle values will be given in "units"_units.html of one over time. + +[Restrictions:] + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info. This compute can only be used for particles which interact via the +updated Lagrangian or total Lagrangian SPH pair styles. + +[Related commands:] + +"smd/plastic_strain"_compute_smd_plastic_strain.html, "smd/tlsph_strain_rate"_compute_smd_tlsph_strain_rate.html, +"smd/tlsph_strain"_compute_smd_tlsph_strain.html + +[Default:] none \ No newline at end of file diff --git a/doc/compute_smd_rho.html b/doc/compute_smd_rho.html new file mode 100644 index 0000000000..ed99b71cfd --- /dev/null +++ b/doc/compute_smd_rho.html @@ -0,0 +1,233 @@ + + + + + + + + + + + compute smd/rho command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    compute smd/rho command

    +
    +

    Syntax

    +
    compute ID group-ID smd/rho
+
    +
    +
      +
    • ID, group-ID are documented in compute command
      • +
    • smd/rho = style name of this compute command
      • +
    +
    +
    +

    Examples

    +
    compute 1 all smd/rho
+
    +
    +
    +
    +

    Description

    +

    Define a computation that calculates the per-particle mass density. +The mass density is the mass of a particle which is constant during +the course of a simulation, divided by its volume, which can change due to mechanical deformation.

    +

    See this PDF guide to use Smooth Mach Dynamics in LAMMPS.

    +

    Output info:

    +

    This compute calculates a per-particle vector, which can be accessed by +any command that uses per-particle values from a compute as input. See +How-to discussions, section 6.15 +for an overview of LAMMPS output options.

    +

    The per-particle values will be in units of mass over volume.

    +
    +
    +

    Restrictions

    +

    This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS +section for more info.

    +
    + +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/compute_smd_rho.txt b/doc/compute_smd_rho.txt new file mode 100644 index 0000000000..3ae8c7e7a6 --- /dev/null +++ b/doc/compute_smd_rho.txt @@ -0,0 +1,49 @@ +"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 smd/rho command :h3 + +[Syntax:] + +compute ID group-ID smd/rho :pre + +ID, group-ID are documented in "compute"_compute.html command +smd/rho = style name of this compute command :ul + +[Examples:] + +compute 1 all smd/rho :pre + +[Description:] + +Define a computation that calculates the per-particle mass density. +The mass density is the mass of a particle which is constant during +the course of a simulation, divided by its volume, which can change due to mechanical deformation. + +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS. + +[Output info:] + +This compute calculates a per-particle vector, which can be accessed by +any command that uses per-particle values from a compute as input. See +"How-to discussions, section 6.15"_Section_howto.html#howto_15 +for an overview of LAMMPS output options. + +The per-particle values will be in "units"_units.html of mass over volume. + +[Restrictions:] + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info. + +[Related commands:] + +"smd/vol"_compute_smd_vol.html + +[Default:] none diff --git a/doc/compute_smd_tlsph_defgrad.html b/doc/compute_smd_tlsph_defgrad.html new file mode 100644 index 0000000000..3c76fd812f --- /dev/null +++ b/doc/compute_smd_tlsph_defgrad.html @@ -0,0 +1,236 @@ + + + + + + + + + + + compute smd/tlsph_defgrad command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    compute smd/tlsph_defgrad command

    +
    +

    Syntax

    +
    compute ID group-ID smd/tlsph_defgrad
+
    +
    +
      +
    • ID, group-ID are documented in compute command
      • +
    • smd/tlsph_defgrad = style name of this compute command
      • +
    +
    +
    +

    Examples

    +
    compute 1 all smd/tlsph_defgrad
+
    +
    +
    +
    +

    Description

    +

    Define a computation that calculates the deformation gradient. +It is only meaningful for particles which interact according to the Total-Lagrangian SPH pair style.

    +

    See this PDF guide to use Smooth Mach Dynamics in +LAMMPS.

    +

    Output info:

    +

    This compute outputss a per-particle vector of vectors (tensors), which can be +accessed by any command that uses per-particle values from a compute as input. See +How-to discussions, section 6.15 +for an overview of LAMMPS output options.

    +

    The per-particle vector values will be given dimensionless. See units. +The per-particle vector has 10 entries. The first nine entries correspond to the xx, xy, xz, yx, yy, yz, zx, zy, zz components +of the asymmetric deformation gradient tensor. The tenth entry is the determinant of the deformation gradient.

    +
    +
    +

    Restrictions

    +

    This compute is part of the USER-SMD package. It is only enabled if LAMMPS was +built with that package. See the Making LAMMPS +section for more info. TThis compute can only be used for particles which interact via the +total Lagrangian SPH pair style.

    +
    + +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/compute_smd_tlsph_defgrad.txt b/doc/compute_smd_tlsph_defgrad.txt new file mode 100644 index 0000000000..e7c3514a63 --- /dev/null +++ b/doc/compute_smd_tlsph_defgrad.txt @@ -0,0 +1,53 @@ +"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 smd/tlsph_defgrad command :h3 + +[Syntax:] + +compute ID group-ID smd/tlsph_defgrad :pre + +ID, group-ID are documented in "compute"_compute.html command +smd/tlsph_defgrad = style name of this compute command :ul + +[Examples:] + +compute 1 all smd/tlsph_defgrad :pre + +[Description:] + +Define a computation that calculates the deformation gradient. +It is only meaningful for particles which interact according to the Total-Lagrangian SPH pair style. + +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in +LAMMPS. + +[Output info:] + +This compute outputss a per-particle vector of vectors (tensors), which can be +accessed by any command that uses per-particle values from a compute as input. See +"How-to discussions, section 6.15"_Section_howto.html#howto_15 +for an overview of LAMMPS output options. + +The per-particle vector values will be given dimensionless. See "units"_units.html. +The per-particle vector has 10 entries. The first nine entries correspond to the xx, xy, xz, yx, yy, yz, zx, zy, zz components +of the asymmetric deformation gradient tensor. The tenth entry is the determinant of the deformation gradient. + + +[Restrictions:] + +This compute is part of the USER-SMD package. It is only enabled if LAMMPS was +built with that package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info. TThis compute can only be used for particles which interact via the +total Lagrangian SPH pair style. + +[Related commands:] + +"smd/hourglass_error"_compute_smd_hourglass_error.html + +[Default:] none diff --git a/doc/compute_smd_tlsph_dt.html b/doc/compute_smd_tlsph_dt.html new file mode 100644 index 0000000000..cf96deef6d --- /dev/null +++ b/doc/compute_smd_tlsph_dt.html @@ -0,0 +1,237 @@ + + + + + + + + + + + compute smd/tlsph_dt command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    compute smd/tlsph_dt command

    +
    +

    Syntax

    +
    compute ID group-ID smd/tlsph_dt
+
    +
    +
      +
    • ID, group-ID are documented in compute command
      • +
    • smd/tlsph_dt = style name of this compute command
      • +
    +
    +
    +

    Examples

    +
    compute 1 all smd/tlsph_dt
+
    +
    +
    +
    +

    Description

    +

    Define a computation that outputs the CFL-stable time increment per particle. +This time increment is essentially given by the speed of sound, divided by the SPH smoothing length. +Because both the speed of sound and the smoothing length typically change during the course of a simulation, +the stable time increment needs to be recomputed every time step. +This calculation is performed automatically in the relevant SPH pair styles and this compute only serves to make the +stable time increment accessible for output purposes.

    +

    See this PDF guide to using Smooth Mach Dynamics in LAMMPS.

    +

    Output info:

    +

    This compute calculates a per-particle vector, which can be accessed by +any command that uses per-particle values from a compute as input. See +How-to discussions, section 6.15 +for an overview of LAMMPS output options.

    +

    The per-particle values will be given in units of time.

    +
    +
    +

    Restrictions

    +

    This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS +section for more info.

    +

    This compute can only be used for particles interacting with the Total-Lagrangian SPH pair style.

    +
    + +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/compute_smd_tlsph_dt.txt b/doc/compute_smd_tlsph_dt.txt new file mode 100644 index 0000000000..10cdd1a75a --- /dev/null +++ b/doc/compute_smd_tlsph_dt.txt @@ -0,0 +1,54 @@ +"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 smd/tlsph_dt command :h3 + +[Syntax:] + +compute ID group-ID smd/tlsph_dt :pre + +ID, group-ID are documented in "compute"_compute.html command +smd/tlsph_dt = style name of this compute command :ul + +[Examples:] + +compute 1 all smd/tlsph_dt :pre + +[Description:] + +Define a computation that outputs the CFL-stable time increment per particle. +This time increment is essentially given by the speed of sound, divided by the SPH smoothing length. +Because both the speed of sound and the smoothing length typically change during the course of a simulation, +the stable time increment needs to be recomputed every time step. +This calculation is performed automatically in the relevant SPH pair styles and this compute only serves to make the +stable time increment accessible for output purposes. + +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS. + +[Output info:] + +This compute calculates a per-particle vector, which can be accessed by +any command that uses per-particle values from a compute as input. See +"How-to discussions, section 6.15"_Section_howto.html#howto_15 +for an overview of LAMMPS output options. + +The per-particle values will be given in "units"_units.html of time. + +[Restrictions:] + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info. + +This compute can only be used for particles interacting with the Total-Lagrangian SPH pair style. + +[Related commands:] + +"smd/adjust_dt"_fix_smd_adjust_dt.html + +[Default:] none diff --git a/doc/compute_smd_tlsph_num_neighs.html b/doc/compute_smd_tlsph_num_neighs.html new file mode 100644 index 0000000000..e2f6d1d7a8 --- /dev/null +++ b/doc/compute_smd_tlsph_num_neighs.html @@ -0,0 +1,233 @@ + + + + + + + + + + + compute smd/tlsph_num_neighs command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    compute smd/tlsph_num_neighs command

    +
    +

    Syntax

    +
    compute ID group-ID smd/tlsph_num_neighs
+
    +
    +
      +
    • ID, group-ID are documented in compute command
      • +
    • smd/tlsph_num_neighs = style name of this compute command
      • +
    +
    +
    +

    Examples

    +
    compute 1 all smd/tlsph_num_neighs
+
    +
    +
    +
    +

    Description

    +

    Define a computation that calculates the number of particles +inside of the smoothing kernel radius for particles interacting via the Total-Lagrangian SPH pair style.

    +

    See this PDF guide to using Smooth Mach Dynamics in LAMMPS.

    +

    Output info:

    +

    This compute calculates a per-particle vector, which can be accessed by +any command that uses per-particle values from a compute as input. See +How-to discussions, section 6.15 +for an overview of LAMMPS output options.

    +

    The per-particle values are dimensionless. See units.

    +
    +
    +

    Restrictions

    +

    This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS +section for more info.

    +

    This quantity will be computed only for particles which interact with the Total-Lagrangian pair style.

    +
    + +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/compute_smd_tlsph_num_neighs.txt b/doc/compute_smd_tlsph_num_neighs.txt new file mode 100644 index 0000000000..b699710597 --- /dev/null +++ b/doc/compute_smd_tlsph_num_neighs.txt @@ -0,0 +1,50 @@ +"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 smd/tlsph_num_neighs command :h3 + +[Syntax:] + +compute ID group-ID smd/tlsph_num_neighs :pre + +ID, group-ID are documented in "compute"_compute.html command +smd/tlsph_num_neighs = style name of this compute command :ul + +[Examples:] + +compute 1 all smd/tlsph_num_neighs :pre + +[Description:] + +Define a computation that calculates the number of particles +inside of the smoothing kernel radius for particles interacting via the Total-Lagrangian SPH pair style. + +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS. + +[Output info:] + +This compute calculates a per-particle vector, which can be accessed by +any command that uses per-particle values from a compute as input. See +"How-to discussions, section 6.15"_Section_howto.html#howto_15 +for an overview of LAMMPS output options. + +The per-particle values are dimensionless. See "units"_units.html. + +[Restrictions:] + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info. + +This quantity will be computed only for particles which interact with the Total-Lagrangian pair style. + +[Related commands:] + +"smd/ulsph_num_neighs"_compute_smd/ulsph_num_neighs.html + +[Default:] none diff --git a/doc/compute_smd_tlsph_shape.html b/doc/compute_smd_tlsph_shape.html new file mode 100644 index 0000000000..7eb8549906 --- /dev/null +++ b/doc/compute_smd_tlsph_shape.html @@ -0,0 +1,235 @@ + + + + + + + + + + + compute smd/tlsph_shape command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    compute smd/tlsph_shape command

    +
    +

    Syntax

    +
    compute ID group-ID smd/tlsph_shape
+
    +
    +
      +
    • ID, group-ID are documented in compute command
      • +
    • smd/tlsph_shape = style name of this compute command
      • +
    +
    +
    +

    Examples

    +
    compute 1 all smd/tlsph_shape
+
    +
    +
    +
    +

    Description

    +

    Define a computation that outputs the current shape of the volume associated with a particle as a rotated ellipsoid. +It is only meaningful for particles which interact according to the Total-Lagrangian SPH pair style.

    +

    See this PDF guide to use Smooth Mach Dynamics in LAMMPS.

    +

    Output info:

    +

    This compute calculates a per-particle vector of vectors, which can be +accessed by any command that uses per-particle values from a compute as input. See +How-to discussions, section 6.15 +for an overview of LAMMPS output options.

    +

    The per-particle vector has 7 entries. The first three entries correspond to the lengths of the ellipsoid’s axes and have units of length. +These axis valus are computed as the contact radius times the xx, yy, or zz components of the Green-Lagrange strain tensor associated with the particle. +The next 4 values are quaternions (order: q, x, y, z) which describe the spatial rotation of the particle relative to its initial state.

    +
    +
    +

    Restrictions

    +

    This compute is part of the USER-SMD package. It is only enabled if LAMMPS was +built with that package. See the Making LAMMPS +section for more info.

    +

    This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style.

    +
    + +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/compute_smd_tlsph_shape.txt b/doc/compute_smd_tlsph_shape.txt new file mode 100644 index 0000000000..a9a69b05e1 --- /dev/null +++ b/doc/compute_smd_tlsph_shape.txt @@ -0,0 +1,52 @@ +"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 smd/tlsph_shape command :h3 + +[Syntax:] + +compute ID group-ID smd/tlsph_shape :pre + +ID, group-ID are documented in "compute"_compute.html command +smd/tlsph_shape = style name of this compute command :ul + +[Examples:] + +compute 1 all smd/tlsph_shape :pre + +[Description:] + +Define a computation that outputs the current shape of the volume associated with a particle as a rotated ellipsoid. +It is only meaningful for particles which interact according to the Total-Lagrangian SPH pair style. + +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS. + +[Output info:] + +This compute calculates a per-particle vector of vectors, which can be +accessed by any command that uses per-particle values from a compute as input. See +"How-to discussions, section 6.15"_Section_howto.html#howto_15 +for an overview of LAMMPS output options. + +The per-particle vector has 7 entries. The first three entries correspond to the lengths of the ellipsoid's axes and have units of length. +These axis valus are computed as the contact radius times the xx, yy, or zz components of the Green-Lagrange strain tensor associated with the particle. +The next 4 values are quaternions (order: q, x, y, z) which describe the spatial rotation of the particle relative to its initial state. + +[Restrictions:] + +This compute is part of the USER-SMD package. It is only enabled if LAMMPS was +built with that package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info. + +This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style. + +[Related commands:] + +"smd/contact_radius"_compute_smd_contact_radius.html + +[Default:] none diff --git a/doc/compute_smd_tlsph_strain.html b/doc/compute_smd_tlsph_strain.html new file mode 100644 index 0000000000..dd438fb94e --- /dev/null +++ b/doc/compute_smd_tlsph_strain.html @@ -0,0 +1,236 @@ + + + + + + + + + + + compute smd/tlsph_strain command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    compute smd/tlsph_strain command

    +
    +

    Syntax

    +
    compute ID group-ID smd/tlsph_strain
+
    +
    +
      +
    • ID, group-ID are documented in compute command
      • +
    • smd/tlsph_strain = style name of this compute command
      • +
    +
    +
    +

    Examples

    +
    compute 1 all smd/tlsph_strain
+
    +
    +
    +
    +

    Description

    +

    Define a computation that calculates the Green-Lagrange strain tensor for particles interacting via the Total-Lagrangian SPH pair style.

    +

    See this PDF guide to using Smooth Mach Dynamics in LAMMPS.

    +

    Output info:

    +

    This compute calculates a per-particle vector of vectors (tensors), +which can be accessed by any command that uses per-particle values +from a compute as input. See +How-to discussions, section 6.15

    +
    +
    for an overview of LAMMPS output options.
    +

    The per-particle tensor values will be given dimensionless. See units.

    +

    The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components +of the symmetric strain tensor.

    +
    +
    +

    Restrictions

    +

    This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS +section for more info.

    +

    This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style.

    +
    + +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/compute_smd_tlsph_strain.txt b/doc/compute_smd_tlsph_strain.txt new file mode 100644 index 0000000000..7624a90bda --- /dev/null +++ b/doc/compute_smd_tlsph_strain.txt @@ -0,0 +1,53 @@ +"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 smd/tlsph_strain command :h3 + +[Syntax:] + +compute ID group-ID smd/tlsph_strain :pre + +ID, group-ID are documented in "compute"_compute.html command +smd/tlsph_strain = style name of this compute command :ul + +[Examples:] + +compute 1 all smd/tlsph_strain :pre + +[Description:] + +Define a computation that calculates the Green-Lagrange strain tensor for particles interacting via the Total-Lagrangian SPH pair style. + +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS. + +[Output info:] + +This compute calculates a per-particle vector of vectors (tensors), +which can be accessed by any command that uses per-particle values +from a compute as input. See +"How-to discussions, section 6.15"_Section_howto.html#howto_15 + for an overview of LAMMPS output options. + +The per-particle tensor values will be given dimensionless. See "units"_units.html. + +The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components +of the symmetric strain tensor. + +[Restrictions:] + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info. + +This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style. + +[Related commands:] + +"smd/tlsph_strain_rate"_compute_smd_tlsph_strain_rate.html, "smd/tlsph_stress"_compute_smd_tlsph_stress.html + +[Default:] none diff --git a/doc/compute_smd_tlsph_strain_rate.html b/doc/compute_smd_tlsph_strain_rate.html new file mode 100644 index 0000000000..8147685ef3 --- /dev/null +++ b/doc/compute_smd_tlsph_strain_rate.html @@ -0,0 +1,234 @@ + + + + + + + + + + + compute smd/tlsph_strain_rate command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    compute smd/tlsph_strain_rate command

    +
    +

    Syntax

    +
    compute ID group-ID smd/tlsph_strain_rate
+
    +
    +
      +
    • ID, group-ID are documented in compute command
      • +
    • smd/tlsph_strain_rate = style name of this compute command
      • +
    +
    +
    +

    Examples

    +
    compute 1 all smd/tlsph_strain_rate
+
    +
    +
    +
    +

    Description

    +

    Define a computation that calculates the rate of the strain tensor for particles interacting via the Total-Lagrangian SPH pair style.

    +

    See this PDF guide to using Smooth Mach Dynamics in LAMMPS.

    +

    Output info:

    +

    This compute calculates a per-particle vector of vectors (tensors), which can be +accessed by any command that uses per-particle values from a compute as input. See +How-to discussions, section 6.15 +for an overview of LAMMPS output options.

    +

    The values will be given in units of one over time.

    +

    The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components +of the symmetric strain rate tensor.

    +
    +
    +

    Restrictions

    +

    This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS +section for more info.

    +

    This quantity will be computed only for particles which interact with Total-Lagrangian SPH pair style.

    +
    + +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/compute_smd_tlsph_strain_rate.txt b/doc/compute_smd_tlsph_strain_rate.txt new file mode 100644 index 0000000000..e9b81b709e --- /dev/null +++ b/doc/compute_smd_tlsph_strain_rate.txt @@ -0,0 +1,53 @@ +"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 smd/tlsph_strain_rate command :h3 + +[Syntax:] + +compute ID group-ID smd/tlsph_strain_rate :pre + +ID, group-ID are documented in "compute"_compute.html command +smd/tlsph_strain_rate = style name of this compute command :ul + +[Examples:] + +compute 1 all smd/tlsph_strain_rate :pre + +[Description:] + +Define a computation that calculates the rate of the strain tensor for particles interacting via the Total-Lagrangian SPH pair style. + +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS. + +[Output info:] + +This compute calculates a per-particle vector of vectors (tensors), which can be +accessed by any command that uses per-particle values from a compute as input. See +"How-to discussions, section 6.15"_Section_howto.html#howto_15 +for an overview of LAMMPS output options. + +The values will be given in "units"_units.html of one over time. + +The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components +of the symmetric strain rate tensor. + +[Restrictions:] + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info. + + +This quantity will be computed only for particles which interact with Total-Lagrangian SPH pair style. + +[Related commands:] + +"smd/tlsph_strain"_compute_smd_tlsph_strain.html, "smd/tlsph_stress"_compute_smd_tlsph_stress.html + +[Default:] none diff --git a/doc/compute_smd_tlsph_stress.html b/doc/compute_smd_tlsph_stress.html new file mode 100644 index 0000000000..ebab7f4924 --- /dev/null +++ b/doc/compute_smd_tlsph_stress.html @@ -0,0 +1,235 @@ + + + + + + + + + + + compute smd/tlsph_stress command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    compute smd/tlsph_stress command

    +
    +

    Syntax

    +
    compute ID group-ID smd/tlsph_stress
+
    +
    +
      +
    • ID, group-ID are documented in compute command
      • +
    • smd/tlsph_stress = style name of this compute command
      • +
    +
    +
    +

    Examples

    +
    compute 1 all smd/tlsph_stress
+
    +
    +
    +
    +

    Description

    +

    Define a computation that outputs the Cauchy stress tensor for particles interacting via the Total-Lagrangian SPH pair style.

    +

    See this PDF guide to using Smooth Mach Dynamics in LAMMPS.

    +

    Output info:

    +

    This compute calculates a per-particle vector of vectors (tensors), which can be +accessed by any command that uses per-particle values from a compute as input. See +How-to discussions, section 6.15 +for an overview of LAMMPS output options.

    +

    The values will be given in units of pressure.

    +

    The per-particle vector has 7 entries. The first six entries correspond to the xx, yy, zz, xy, xz and yz components +of the symmetric Cauchy stress tensor. The seventh entry is the second invariant of the stress tensor, i.e., +the von Mises equivalent stress.

    +
    +
    +

    Restrictions

    +

    This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS +section for more info.

    +

    This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style.

    +
    + +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/compute_smd_tlsph_stress.txt b/doc/compute_smd_tlsph_stress.txt new file mode 100644 index 0000000000..9c8dab6b0a --- /dev/null +++ b/doc/compute_smd_tlsph_stress.txt @@ -0,0 +1,53 @@ +"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 smd/tlsph_stress command :h3 + +[Syntax:] + +compute ID group-ID smd/tlsph_stress :pre + +ID, group-ID are documented in "compute"_compute.html command +smd/tlsph_stress = style name of this compute command :ul + +[Examples:] + +compute 1 all smd/tlsph_stress :pre + +[Description:] + +Define a computation that outputs the Cauchy stress tensor for particles interacting via the Total-Lagrangian SPH pair style. + +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS. + +[Output info:] + +This compute calculates a per-particle vector of vectors (tensors), which can be +accessed by any command that uses per-particle values from a compute as input. See +"How-to discussions, section 6.15"_Section_howto.html#howto_15 +for an overview of LAMMPS output options. + +The values will be given in "units"_units.html of pressure. + +The per-particle vector has 7 entries. The first six entries correspond to the xx, yy, zz, xy, xz and yz components +of the symmetric Cauchy stress tensor. The seventh entry is the second invariant of the stress tensor, i.e., +the von Mises equivalent stress. + +[Restrictions:] + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info. + +This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style. + +[Related commands:] + +"smd/tlsph_strain"_compute_smd_tlsph_strain.html, "smd/tlsph_strain_rate"_compute_smd_tlsph_strain_rate.html + +[Default:] none diff --git a/doc/compute_smd_triangle_mesh_vertices.html b/doc/compute_smd_triangle_mesh_vertices.html new file mode 100644 index 0000000000..8a9e78ac85 --- /dev/null +++ b/doc/compute_smd_triangle_mesh_vertices.html @@ -0,0 +1,238 @@ + + + + + + + + + + + compute smd/triangle_mesh_vertices — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    compute smd/triangle_mesh_vertices

    +
    +

    Syntax

    +
    compute ID group-ID smd/triangle_mesh_vertices
+
    +
    +
      +
    • ID, group-ID are documented in compute command
      • +
    • smd/triangle_mesh_vertices = style name of this compute command
      • +
    +
    +
    +

    Examples

    +
    compute 1 all smd/triangle_mesh_vertices
+
    +
    +
    +
    +

    Description

    +

    Define a computation that returns the coordinates of the vertices +corresponding to the triangle-elements of a mesh created by the `fix smd/wall_surface <ls_>`_.

    +

    See this PDF guide to using Smooth Mach Dynamics in LAMMPS.

    +

    Output info:

    +

    This compute returns a per-particle vector of vectors, which can be +accessed by any command that uses per-particle values from a compute as +input. See How-to discussions, section 6.15 +for an overview of LAMMPS output options.

    +

    The per-particle vector has nine entries, (x1/y1/z1), (x2/y2/z2), and (x3/y3/z3) corresponding +to the first, second, and third vertex of each triangle.

    +

    It is only meaningful to use this compute for a group of particles which is created via the +`fix smd/wall_surface <ls_>`_ command.

    +

    The output of this compute can be used with the dump2vtk_tris tool to generate a VTK representation of the +smd/wall_surace mesh for visualization purposes.

    +

    The values will be given in units of distance.

    +
    +
    +

    Restrictions

    +

    This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS +section for more info.

    +
    + +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/compute_smd_triangle_mesh_vertices.txt b/doc/compute_smd_triangle_mesh_vertices.txt new file mode 100644 index 0000000000..9d7740c7ec --- /dev/null +++ b/doc/compute_smd_triangle_mesh_vertices.txt @@ -0,0 +1,59 @@ +"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) + +:link(ls,fix_smd_wall_surface.html) + +:line + +compute smd/triangle_mesh_vertices :h3 + +[Syntax:] + +compute ID group-ID smd/triangle_mesh_vertices :pre + +ID, group-ID are documented in "compute"_compute.html command +smd/triangle_mesh_vertices = style name of this compute command :ul + +[Examples:] + +compute 1 all smd/triangle_mesh_vertices :pre + +[Description:] + +Define a computation that returns the coordinates of the vertices +corresponding to the triangle-elements of a mesh created by the "fix smd/wall_surface"_ls. + +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS. + +[Output info:] + +This compute returns a per-particle vector of vectors, which can be +accessed by any command that uses per-particle values from a compute as +input. See "How-to discussions, section 6.15"_Section_howto.html#howto_15 +for an overview of LAMMPS output options. + +The per-particle vector has nine entries, (x1/y1/z1), (x2/y2/z2), and (x3/y3/z3) corresponding +to the first, second, and third vertex of each triangle. + +It is only meaningful to use this compute for a group of particles which is created via the +"fix smd/wall_surface"_ls command. + +The output of this compute can be used with the dump2vtk_tris tool to generate a VTK representation of the +smd/wall_surace mesh for visualization purposes. + +The values will be given in "units"_units.html of distance. + +[Restrictions:] + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info. + +[Related commands:] + +"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html, "smd/wall_surface"_ls + +[Default:] none diff --git a/doc/compute_smd_ulsph_num_neighs.html b/doc/compute_smd_ulsph_num_neighs.html new file mode 100644 index 0000000000..ffc061a8f5 --- /dev/null +++ b/doc/compute_smd_ulsph_num_neighs.html @@ -0,0 +1,232 @@ + + + + + + + + + + + compute smd/ulsph_num_neighs command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    compute smd/ulsph_num_neighs command

    +
    +

    Syntax

    +
    compute ID group-ID smd/ulsph_num_neighs
+
    +
    +
      +
    • ID, group-ID are documented in compute command
      • +
    • smd/ulsph_num_neighs = style name of this compute command
      • +
    +
    +
    +

    Examples

    +
    compute 1 all smd/ulsph_num_neighs
+
    +
    +
    +
    +

    Description

    +

    Define a computation that returns the number of neighbor particles +inside of the smoothing kernel radius for particles interacting via the updated Lagrangian SPH pair style.

    +

    See this PDF guide to using Smooth Mach Dynamics in LAMMPS.

    +

    Output info:

    +

    This compute returns a per-particle vector, which can be accessed by +any command that uses per-particle values from a compute as input. See +Section_howto 15 for an overview of +LAMMPS output options.

    +

    The per-particle values will be given dimentionless, see units.

    +
    +
    +

    Restrictions

    +

    This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS +section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style.

    +
    + +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/compute_smd_ulsph_num_neighs.txt b/doc/compute_smd_ulsph_num_neighs.txt new file mode 100644 index 0000000000..00020f13c5 --- /dev/null +++ b/doc/compute_smd_ulsph_num_neighs.txt @@ -0,0 +1,48 @@ +"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 smd/ulsph_num_neighs command :h3 + +[Syntax:] + +compute ID group-ID smd/ulsph_num_neighs :pre + +ID, group-ID are documented in "compute"_compute.html command +smd/ulsph_num_neighs = style name of this compute command :ul + +[Examples:] + +compute 1 all smd/ulsph_num_neighs :pre + +[Description:] + +Define a computation that returns the number of neighbor particles +inside of the smoothing kernel radius for particles interacting via the updated Lagrangian SPH pair style. + +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS. + +[Output info:] + +This compute returns a per-particle vector, which can be accessed by +any command that uses per-particle values from a compute as input. See +"Section_howto 15"_Section_howto.html#howto_15 for an overview of +LAMMPS output options. + +The per-particle values will be given dimentionless, see "units"_units.html. + +[Restrictions:] + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_2 +section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style. + +[Related commands:] + +smd/tlsph_num_neighs + +[Default:] none diff --git a/doc/compute_smd_ulsph_strain.html b/doc/compute_smd_ulsph_strain.html new file mode 100644 index 0000000000..e879467282 --- /dev/null +++ b/doc/compute_smd_ulsph_strain.html @@ -0,0 +1,234 @@ + + + + + + + + + + + compute smd/ulsph_strain command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    compute smd/ulsph_strain command

    +
    +

    Syntax

    +
    compute ID group-ID smd/ulsph_strain
+
    +
    +
      +
    • ID, group-ID are documented in compute command
      • +
    • smd/ulsph_strain = style name of this compute command
      • +
    +
    +
    +

    Examples

    +
    compute 1 all smd/ulsph_strain
+
    +
    +
    +
    +

    Description

    +

    Define a computation that outputs the logarithmic strain tensor. +for particles interacting via the updated Lagrangian SPH pair style.

    +

    See this PDF guide to using Smooth Mach Dynamics in LAMMPS.

    +

    Output info:

    +

    This compute calculates a per-particle tensor, which can be accessed by +any command that uses per-particle values from a compute as input. See +Section_howto 15 for an overview of +LAMMPS output options.

    +

    The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components +of the symmetric strain rate tensor.

    +

    The per-particle tensor values will be given dimensionless, see units.

    +
    +
    +

    Restrictions

    +

    This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS +section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style.

    +
    + +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/compute_smd_ulsph_strain.txt b/doc/compute_smd_ulsph_strain.txt new file mode 100644 index 0000000000..e8418389d8 --- /dev/null +++ b/doc/compute_smd_ulsph_strain.txt @@ -0,0 +1,51 @@ +"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 smd/ulsph_strain command :h3 + +[Syntax:] + +compute ID group-ID smd/ulsph_strain :pre + +ID, group-ID are documented in "compute"_compute.html command +smd/ulsph_strain = style name of this compute command :ul + +[Examples:] + +compute 1 all smd/ulsph_strain :pre + +[Description:] + +Define a computation that outputs the logarithmic strain tensor. +for particles interacting via the updated Lagrangian SPH pair style. + +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS. + +[Output info:] + +This compute calculates a per-particle tensor, which can be accessed by +any command that uses per-particle values from a compute as input. See +"Section_howto 15"_Section_howto.html#howto_15 for an overview of +LAMMPS output options. + +The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components +of the symmetric strain rate tensor. + +The per-particle tensor values will be given dimensionless, see "units"_units.html. + +[Restrictions:] + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style. + +[Related commands:] + +smd/tlsph_strain + +[Default:] none diff --git a/doc/compute_smd_ulsph_strain_rate.html b/doc/compute_smd_ulsph_strain_rate.html new file mode 100644 index 0000000000..34d7dc2060 --- /dev/null +++ b/doc/compute_smd_ulsph_strain_rate.html @@ -0,0 +1,234 @@ + + + + + + + + + + + compute smd/ulsph_strain_rate command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    compute smd/ulsph_strain_rate command

    +
    +

    Syntax

    +
    compute ID group-ID smd/ulsph_strain_rate
+
    +
    +
      +
    • ID, group-ID are documented in compute command
      • +
    • smd/ulsph_strain_rate = style name of this compute command
      • +
    +
    +
    +

    Examples

    +
    compute 1 all smd/ulsph_strain_rate
+
    +
    +
    +
    +

    Description

    +

    Define a computation that outputs the rate of the logarithmic strain tensor +for particles interacting via the updated Lagrangian SPH pair style.

    +

    See this PDF guide to using Smooth Mach Dynamics in LAMMPS.

    +

    Output info:

    +

    This compute calculates a per-particle vector of vectors (tensors), which +can be accessed by any command that uses per-particle values from a compute +as input. See Section_howto 15 for an overview of +LAMMPS output options.

    +

    The values will be given in units of one over time.

    +

    The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components +of the symmetric strain rate tensor.

    +
    +
    +

    Restrictions

    +

    This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS +section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style.

    +
    + +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/compute_smd_ulsph_strain_rate.txt b/doc/compute_smd_ulsph_strain_rate.txt new file mode 100644 index 0000000000..4d5fb952cb --- /dev/null +++ b/doc/compute_smd_ulsph_strain_rate.txt @@ -0,0 +1,52 @@ +"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 smd/ulsph_strain_rate command :h3 + +[Syntax:] + +compute ID group-ID smd/ulsph_strain_rate :pre + +ID, group-ID are documented in "compute"_compute.html command +smd/ulsph_strain_rate = style name of this compute command :ul + +[Examples:] + +compute 1 all smd/ulsph_strain_rate :pre + +[Description:] + +Define a computation that outputs the rate of the logarithmic strain tensor +for particles interacting via the updated Lagrangian SPH pair style. + +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS. + +[Output info:] + +This compute calculates a per-particle vector of vectors (tensors), which +can be accessed by any command that uses per-particle values from a compute +as input. See "Section_howto 15"_Section_howto.html#howto_15 for an overview of +LAMMPS output options. + +The values will be given in "units"_units.html of one over time. + +The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components +of the symmetric strain rate tensor. + +[Restrictions:] + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_2 +section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style. + + +[Related commands:] + +smd/utsph_strain_rate + +[Default:] none diff --git a/doc/compute_smd_ulsph_stress.html b/doc/compute_smd_ulsph_stress.html new file mode 100644 index 0000000000..b3ca6eeb44 --- /dev/null +++ b/doc/compute_smd_ulsph_stress.html @@ -0,0 +1,237 @@ + + + + + + + + + + + compute smd/ulsph_stress command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    compute smd/ulsph_stress command

    +
    +

    Syntax

    +
    compute ID group-ID smd/ulsph_stress
+
    +
    +
      +
    • ID, group-ID are documented in compute command
      • +
    • smd/ulsph_stress = style name of this compute command
      • +
    +
    +
    +

    Examples

    +
    compute 1 all smd/ulsph_stress
+
    +
    +
    +
    +

    Description

    +

    Define a computation that outputs the Cauchy stress tensor.

    +

    See this PDF guide to using Smooth Mach Dynamics in LAMMPS.

    +

    Output info:

    +

    This compute calculates a per-particle vector of vectors (tensors), +which can be accessed by any command that uses per-particle values +from a compute as input. See Section_howto 15 +for an overview of LAMMPS output options.

    +

    The values will be given in units of pressure.

    +

    The per-particle vector has 7 entries. The first six entries correspond to the xx, yy, zz, xy, xz, yz components +of the symmetric Cauchy stress tensor. The seventh entry is the second invariant of the stress tensor, i.e., +the von Mises equivalent stress.

    +
    +
    +

    Restrictions

    +

    This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS +section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style.

    +
    + +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/compute_smd_ulsph_stress.txt b/doc/compute_smd_ulsph_stress.txt new file mode 100644 index 0000000000..84a987a8e7 --- /dev/null +++ b/doc/compute_smd_ulsph_stress.txt @@ -0,0 +1,53 @@ +"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 smd/ulsph_stress command :h3 + +[Syntax:] + +compute ID group-ID smd/ulsph_stress :pre + +ID, group-ID are documented in "compute"_compute.html command +smd/ulsph_stress = style name of this compute command :ul + +[Examples:] + +compute 1 all smd/ulsph_stress :pre + +[Description:] + +Define a computation that outputs the Cauchy stress tensor. + +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS. + +[Output info:] + +This compute calculates a per-particle vector of vectors (tensors), +which can be accessed by any command that uses per-particle values +from a compute as input. See "Section_howto 15"_Section_howto.html#howto_15 +for an overview of LAMMPS output options. + +The values will be given in "units"_units.html of pressure. + +The per-particle vector has 7 entries. The first six entries correspond to the xx, yy, zz, xy, xz, yz components +of the symmetric Cauchy stress tensor. The seventh entry is the second invariant of the stress tensor, i.e., +the von Mises equivalent stress. + +[Restrictions:] + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style. + + +[Related commands:] + +"smd/ulsph_strain"_compute_smd_ulsph_strain.html, "smd/ulsph_strain_rate"_compute_smd_ulsph_strain_rate.html +"smd/tlsph_stress"_compute_smd_tlsph_stress.html :pre + +[Default:] none diff --git a/doc/compute_smd_vol.html b/doc/compute_smd_vol.html new file mode 100644 index 0000000000..02b2ce77c1 --- /dev/null +++ b/doc/compute_smd_vol.html @@ -0,0 +1,236 @@ + + + + + + + + + + + compute smd/vol command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    compute smd/vol command

    +
    +

    Syntax

    +
    compute ID group-ID smd/vol
+
    +
    +
      +
    • ID, group-ID are documented in compute command
      • +
    • smd/vol = style name of this compute command
      • +
    +
    +
    +

    Examples

    +
    compute 1 all smd/vol
+
    +
    +
    +
    +

    Description

    +

    Define a computation that provides the per-particle volume and the sum of the per-particle volumes of the +group for which the fix is defined.

    +

    See this PDF guide to using Smooth Mach Dynamics in +LAMMPS.

    +

    Output info:

    +

    This compute calculates a per-particle vector, which can be accessed by +any command that uses per-particle values from a compute as input. See +How-to discussions, section 6.15 +for an overview of LAMMPS output options.

    +

    The per-particle vector values will be given in units of volume.

    +

    Additionally, the compute returns a scalar, which is the sum of the per-particle volumes of the +group for which the fix is defined.

    +
    +
    +

    Restrictions

    +

    This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS

    +
    +
    section for more info.
    +
    + +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/compute_smd_vol.txt b/doc/compute_smd_vol.txt new file mode 100644 index 0000000000..1e0ab786bf --- /dev/null +++ b/doc/compute_smd_vol.txt @@ -0,0 +1,52 @@ +"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 smd/vol command :h3 + +[Syntax:] + +compute ID group-ID smd/vol :pre + +ID, group-ID are documented in "compute"_compute.html command +smd/vol = style name of this compute command :ul + +[Examples:] + +compute 1 all smd/vol :pre + +[Description:] + +Define a computation that provides the per-particle volume and the sum of the per-particle volumes of the +group for which the fix is defined. + +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in +LAMMPS. + +[Output info:] + +This compute calculates a per-particle vector, which can be accessed by +any command that uses per-particle values from a compute as input. See +"How-to discussions, section 6.15"_Section_howto.html#howto_15 +for an overview of LAMMPS output options. + +The per-particle vector values will be given in "units"_units.html of volume. + +Additionally, the compute returns a scalar, which is the sum of the per-particle volumes of the +group for which the fix is defined. + +[Restrictions:] + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 + section for more info. + +[Related commands:] + +"smd/rho"_compute_smd_rho.html + +[Default:] none diff --git a/doc/doc2/Section_commands.html b/doc/doc2/Section_commands.html index 8a8444e6ad..427f4b8253 100644 --- a/doc/doc2/Section_commands.html +++ b/doc/doc2/Section_commands.html @@ -438,8 +438,9 @@ package. - - + +
    awpmd/cut
    meam/sw/spline quip reax/csmd/hertz
    smd/tlsphsmd/triangulated/surfacesmd/ulsph sph/heatconduction
    sph/idealgas
    sph/idealgas sph/lj sph/rhosum sph/taitwater
    sph/taitwater/morris
    sph/taitwater/morris srp tersoff/table (o) thole
    tip4p/long/soft (o)
    tip4p/long/soft (o)      
    USER-SPH
    USER-SMDsmoothed Mach dynamicsGeorg Ganzenmuller (EMI)userguide.pdfUSER/smd
      +
    • +
    +
      +
    • +
    +
    USER-SPH smoothed particle hydrodynamics Georg Ganzenmuller (EMI) userguide.pdf
     
            mass, volume mesocopic Peridynamic models
    sphere
    smdvolume, kernel diameter, contact radius, masssolid and fluid SPH particles
    sphere diameter, mass, angular velocity granular models
    template
    template template index, template atom small molecules with fixed topology
    tri
    tri corner points, angular momentum rigid bodies
    wavepacket
    wavepacket charge, spin, eradius, etag, cs_re, cs_im AWPMD
    langevin/efflb/fluidlb/momentumlb/pclb/rigid/pc/spherelb/viscous
    mesomeso/stationarynph/effnpt/effnve/effnvt/eff
    nvt/sllod/effphononpimdqbmsstqeq/reaxqmmm
    qtbreax/c/bondsreax/c/speciessaed/vtksmdtemp/rescale/eff
    ti/rsti/springttm/mod +
    qtbreax/c/bondsreax/c/speciessaed/vtksmdsmd/adjust/dt
    smd/integrate/tlsphsmd/integrate/ulsphsmd/move/triangulated/surfacesmd/setvelsmd/tlsph/reference/configurationsmd/wall/surface
    temp/rescale/effti/rsti/springttm/mod
    @@ -474,8 +475,11 @@ package.

    - - + + + +
    ackland/atombasal/atomfepke/effke/atom/effmeso_e/atom
    meso_rho/atommeso_t/atomsaedtemp/drudetemp/efftemp/deform/eff
    temp/region/efftemp/rotatexrd +
    meso_rho/atommeso_t/atomsaedsmd/contact/radiussmd/damagesmd/hourglass/error
    smd/internal/energysmd/plastic/strainsmd/plastic/strain/ratesmd/rhosmd/tlsph/defgradsmd/tlsph/dt
    smd/tlsph/num/neighssmd/tlsph/shapesmd/tlsph/strainsmd/tlsph/strain/ratesmd/tlsph/stresssmd/triangle/mesh/vertices
    smd/ulsph/num/neighssmd/ulsph/strainsmd/ulsph/strain/ratesmd/ulpsh/stresssmd/voltemp/drude
    temp/efftemp/deform/efftemp/region/efftemp/rotatexrd
    @@ -530,7 +534,8 @@ package. listlj/charmm/coul/long/soft (o)lj/cut/coul/cut/soft (o)lj/cut/coul/long/soft (o) lj/cut/dipole/sf (go)lj/cut/soft (o)lj/cut/tip4p/long/soft (o)lj/sdk (gko) lj/sdk/coul/long (go)lj/sdk/coul/msm (o)lj/sf (o)meam/spline -meam/sw/splinequipreax/csph/heatconduction +meam/sw/splinequipreax/csmd/hertz +smd/tlsphsmd/triangulated/surfacesmd/ulsphsph/heatconduction sph/idealgassph/ljsph/rhosumsph/taitwater sph/taitwater/morrissrptersoff/table (o)thole tip4p/long/soft (o) diff --git a/doc/doc2/Section_packages.html b/doc/doc2/Section_packages.html index 4b9bd92756..9f91d29dd7 100644 --- a/doc/doc2/Section_packages.html +++ b/doc/doc2/Section_packages.html @@ -140,6 +140,7 @@ on how to build LAMMPS with both kinds of auxiliary libraries. USER-QTB quantum nuclear effects Yuan Shen (Stanford) fix qtb fix_qbmsst qtb - - USER-QUIP QUIP/libatoms interface Albert Bartok-Partay (U Cambridge) pair_style quip USER/quip - lib/quip USER-REAXC C version of ReaxFF Metin Aktulga (LBNL) pair_style reaxc reax - - +USER-SMD smoothed Mach dynamics Georg Ganzenmuller (EMI) userguide.pdf USER/smd - - USER-SPH smoothed particle hydrodynamics Georg Ganzenmuller (EMI) userguide.pdf USER/sph sph - @@ -639,6 +640,22 @@ questions.

    +

    USER-SMD package +

    +

    This package implements smoothed Mach dynamics (SMD) in +LAMMPS. Currently, the package has the following features: +

    +

    ??? +

    +

    See the file doc/USER/smd/SPH_user_guide.pdf to get started. +

    +

    There are example scripts for using this package in examples/USER/smd. +

    +

    The person who created this package is Georg Ganzenmuller at the +Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in +Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if +you have questions. +

    USER-SPH package

    This package implements smoothed particle hydrodynamics (SPH) in diff --git a/doc/doc2/USER/atc/man_add_molecule.html b/doc/doc2/USER/atc/man_add_molecule.html new file mode 100644 index 0000000000..99270c7276 --- /dev/null +++ b/doc/doc2/USER/atc/man_add_molecule.html @@ -0,0 +1,59 @@ + + + + +ATC: fix_modify AtC add_molecule + + + + + +

    +
    + + +

    fix_modify AtC add_molecule

    +syntax

    +

    fix_modify_AtC add_molecule <small|large> <TAG> <GROUP_NAME>
    +

    + +

    +examples

    +

    group WATERGROUP type 1 2
    + fix_modify AtC add_molecule small water WATERGROUP
    +

    +

    +description

    +

    Associates a tag with all molecules corresponding to a specified group.
    +

    +

    +restrictions

    +

    +related

    +

    +default

    +

    No defaults for this command.

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_add_species.html b/doc/doc2/USER/atc/man_add_species.html new file mode 100644 index 0000000000..95192034d9 --- /dev/null +++ b/doc/doc2/USER/atc/man_add_species.html @@ -0,0 +1,59 @@ + + + + +ATC: fix_modify AtC add_species + + + + + + +
    + + +

    fix_modify AtC add_species

    +syntax

    +

    fix_modify_AtC add_species <TAG> <group|type> <ID>
    +

    + +

    +examples

    +

    fix_modify AtC add_species gold type 1
    + group GOLDGROUP type 1
    + fix_modify AtC add_species gold group GOLDGROUP

    +

    +description

    +

    Associates a tag with all atoms of a specified type or within a specified group.
    +

    +

    +restrictions

    +

    +related

    +

    +default

    +

    No defaults for this command.

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_atom_element_map.html b/doc/doc2/USER/atc/man_atom_element_map.html new file mode 100644 index 0000000000..3073c0f920 --- /dev/null +++ b/doc/doc2/USER/atc/man_atom_element_map.html @@ -0,0 +1,52 @@ + + + + +ATC: fix_modify AtC atom_element_map + + + + + + +
    + + +

    fix_modify AtC atom_element_map

    +syntax

    +

    fix_modify AtC atom_element_map <eulerian|lagrangian> <frequency>
    +

    + +

    +examples

    +

    fix_modify atc atom_element_map eulerian 100

    +

    +description

    +

    Changes frame of reference from eulerian to lagrangian and sets the frequency for which the map from atoms to elements is reformed and all the attendant data is recalculated.

    +

    +restrictions

    +

    Cannot change map type after initialization.

    +

    +related

    +

    +default

    +

    lagrangian

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_atom_weight.html b/doc/doc2/USER/atc/man_atom_weight.html new file mode 100644 index 0000000000..18b0dcae6e --- /dev/null +++ b/doc/doc2/USER/atc/man_atom_weight.html @@ -0,0 +1,61 @@ + + + + +ATC: fix_modify AtC atom_weight + + + + + + +
    + + +

    fix_modify AtC atom_weight

    +syntax

    +

    fix_modify AtC atom_weight <method> <arguments>

    + +

    +examples

    +

    fix_modify atc atom_weight constant myatoms 11.8
    + fix_modify atc atom_weight lattice
    + fix_modify atc atom_weight read-in atm_wt_file.txt
    +

    +

    +description

    +

    Command for assigning the value of atomic weights used for atomic integration in atom-continuum coupled simulations.

    +

    +restrictions

    +

    Use of lattice option requires a lattice type and parameter is already specified.

    +

    +related

    +

    +default

    +

    lattice

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_atomic_charge.html b/doc/doc2/USER/atc/man_atomic_charge.html new file mode 100644 index 0000000000..718f8a433f --- /dev/null +++ b/doc/doc2/USER/atc/man_atomic_charge.html @@ -0,0 +1,51 @@ + + + + +ATC: fix_modify AtC atomic_charge + + + + + + +
    + + +

    fix_modify AtC atomic_charge

    +syntax

    +

    fix_modify AtC <include | omit> atomic_charge

    + +

    +examples

    +

    fix_modify atc compute include atomic_charge

    +

    +description

    +

    Determines whether AtC tracks the total charge as a finite element field

    +

    +restrictions

    +

    Required for: electrostatics

    +

    +related

    +

    +default

    +

    if the atom charge is defined, default is on, otherwise default is off

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_boundary.html b/doc/doc2/USER/atc/man_boundary.html new file mode 100644 index 0000000000..3e877355f1 --- /dev/null +++ b/doc/doc2/USER/atc/man_boundary.html @@ -0,0 +1,48 @@ + + + + +ATC: fix_modify AtC boundary + + + + + + +
    + + +

    fix_modify AtC boundary

    +syntax

    +

    fix_modify AtC boundary type <atom-type-id>

    + +

    +examples

    +

    fix_modify AtC boundary type ghost_atoms

    +

    +description

    +

    Command to define the atoms that represent the ficticious boundary internal to the FE mesh. For fully overlapped MD/FE domains with periodic boundary conditions no boundary atoms should be defined.

    +

    +restrictions

    +

    +default

    +

    none

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_boundary_dynamics.html b/doc/doc2/USER/atc/man_boundary_dynamics.html new file mode 100644 index 0000000000..87696b8b43 --- /dev/null +++ b/doc/doc2/USER/atc/man_boundary_dynamics.html @@ -0,0 +1,46 @@ + + + + +ATC: fix_modify AtC boundary_dynamics + + + + + + +
    + + +

    fix_modify AtC boundary_dynamics

    +syntax

    +

    fix_modify AtC boundary_dynamics < on | damped_harmonic | prescribed | coupled | none > [args]
    +

    +

    +description

    +

    Sets different schemes for controlling boundary atoms. On will integrate the boundary atoms using the velocity-verlet algorithm. Damped harmonic uses a mass/spring/dashpot for the boundary atoms with added arguments of the damping and spring constants followed by the ratio of the boundary type mass to the desired mass. Prescribed forces the boundary atoms to follow the finite element displacement. Coupled does the same.

    +

    +restrictions

    +

    Boundary atoms must be specified. When using swaps between internal and boundary atoms, the initial configuration must have already correctly partitioned the two.

    +

    +related

    +

    +default

    +

    prescribed on

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_boundary_faceset.html b/doc/doc2/USER/atc/man_boundary_faceset.html new file mode 100644 index 0000000000..2e96330d6c --- /dev/null +++ b/doc/doc2/USER/atc/man_boundary_faceset.html @@ -0,0 +1,47 @@ + + + + +ATC: fix_modify AtC boundary_faceset + + + + + + +
    + + +

    fix_modify AtC boundary_faceset

    +syntax

    +

    fix_modify AtC boundary_faceset <is | add> [args]

    +

    +examples

    +

    fix_modify AtC boundary_faceset is obndy

    +

    +description

    +

    This command species the faceset name when using a faceset to compute the MD/FE boundary fluxes. The faceset must already exist.

    +

    +restrictions

    +

    This is only valid when fe_md_boundary is set to faceset.

    +

    +related

    +

    +default

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_boundary_integral.html b/doc/doc2/USER/atc/man_boundary_integral.html new file mode 100644 index 0000000000..3e78f12963 --- /dev/null +++ b/doc/doc2/USER/atc/man_boundary_integral.html @@ -0,0 +1,53 @@ + + + + +ATC: fix_modify AtC output boundary_integral + + + + + + +
    + + +

    fix_modify AtC output boundary_integral

    +syntax

    +

    fix_modify AtC output boundary_integral [field] faceset [name]

    + +

    +examples

    +

    fix_modify AtC output boundary_integral stress faceset loop1
    +

    +

    +description

    +

    Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file

    +

    +restrictions

    +

    Must be used with the hardy/field type of AtC fix ( see fix atc command )

    +

    +related

    +

    +default

    +

    none

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_consistent_fe_initialization.html b/doc/doc2/USER/atc/man_consistent_fe_initialization.html new file mode 100644 index 0000000000..2f3bf4a6cf --- /dev/null +++ b/doc/doc2/USER/atc/man_consistent_fe_initialization.html @@ -0,0 +1,51 @@ + + + + +ATC: fix_modify AtC consistent_fe_initialization + + + + + + +
    + + +

    fix_modify AtC consistent_fe_initialization

    +syntax

    +

    fix_modify AtC consistent_fe_initialization <on | off>

    + +

    +examples

    +

    fix_modify atc consistent_fe_initialization on

    +

    +description

    +

    Determines whether AtC initializes FE intrinsic fields (e.g., temperature) to match the projected MD values. This is particularly useful for fully overlapping simulations.

    +

    +restrictions

    +

    Can be used with: thermal, two_temperature. Cannot be used with time filtering on. Does not include boundary nodes.

    +

    +related

    +

    +default

    +

    Default is off

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_contour_integral.html b/doc/doc2/USER/atc/man_contour_integral.html new file mode 100644 index 0000000000..c321605e88 --- /dev/null +++ b/doc/doc2/USER/atc/man_contour_integral.html @@ -0,0 +1,54 @@ + + + + +ATC: fix_modify AtC output contour_integral + + + + + + +
    + + +

    fix_modify AtC output contour_integral

    +syntax

    +

    fix_modify AtC output contour_integral [field] faceset [name] <axis [x | y | z ]>

    + +

    +examples

    +

    fix_modify AtC output contour_integral stress faceset loop1
    +

    +

    +description

    +

    Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file

    +

    +restrictions

    +

    Must be used with the hardy/field type of AtC fix ( see fix atc command )

    +

    +related

    +

    +default

    +

    none

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_control.html b/doc/doc2/USER/atc/man_control.html new file mode 100644 index 0000000000..af0236f30e --- /dev/null +++ b/doc/doc2/USER/atc/man_control.html @@ -0,0 +1,72 @@ + + + + +ATC: fix_modify AtC control + + + + + + +
    + + +

    fix_modify AtC control

    +syntax

    +

    fix_modify AtC control <physics_type> <solution_parameter>

    +


    +

    + +

    fix_modify AtC transfer <physics_type> control max_iterations <max_iterations>
    +

    + +

    fix_modify AtC transfer <physics_type> control tolerance <tolerance>
    +

    + +

    +examples

    +

    fix_modify AtC control thermal max_iterations 10
    + fix_modify AtC control momentum tolerance 1.e-5
    +

    +

    +description

    +

    Sets the numerical parameters for the matrix solvers used in the specified control algorithm. Many solution approaches require iterative solvers, and these methods enable users to provide the maximum number of iterations and the relative tolerance.

    +

    +restrictions

    +

    only for be used with specific controllers : thermal, momentum
    + They are ignored if a lumped solution is requested

    +

    +related

    +

    +default

    +

    max_iterations is the number of rows in the matrix
    + tolerance is 1.e-10

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_control_momentum.html b/doc/doc2/USER/atc/man_control_momentum.html new file mode 100644 index 0000000000..805c12567a --- /dev/null +++ b/doc/doc2/USER/atc/man_control_momentum.html @@ -0,0 +1,68 @@ + + + + +ATC: fix_modify AtC control momentum + + + + + + +
    + + +

    fix_modify AtC control momentum

    +syntax

    +

    fix_modify AtC control momentum none
    +

    +

    fix_modify AtC control momentum rescale <frequency>
    +

    + +

    fix_modify AtC control momentum glc_displacement
    +

    +

    fix_modify AtC control momentum glc_velocity
    +

    +

    fix_modify AtC control momentum hoover
    +

    +

    fix_modify AtC control momentum flux [faceset face_set_id, interpolate]

    + +

    +examples

    +

    fix_modify AtC control momentum glc_velocity
    + fix_modify AtC control momentum flux faceset bndy_faces
    +

    +

    +description

    +

    +restrictions

    +

    only to be used with specific transfers : elastic
    + rescale not valid with time filtering activated

    +

    +related

    +

    +default

    +

    none

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_control_thermal.html b/doc/doc2/USER/atc/man_control_thermal.html new file mode 100644 index 0000000000..301297f306 --- /dev/null +++ b/doc/doc2/USER/atc/man_control_thermal.html @@ -0,0 +1,76 @@ + + + + +ATC: fix_modify AtC control thermal + + + + + + +
    + + +

    fix_modify AtC control thermal

    +syntax

    +

    fix_modify AtC control thermal <control_type> <optional_args>

    + +

    fix_modify AtC control thermal rescale <frequency>
    +

    + +

    fix_modify AtC control thermal hoover
    +

    +

    fix_modify AtC control thermal flux <boundary_integration_type(optional)> <face_set_id(optional)>
    +

    + +

    +examples

    +

    fix_modify AtC control thermal none
    + fix_modify AtC control thermal rescale 10
    + fix_modify AtC control thermal hoover
    + fix_modify AtC control thermal flux
    + fix_modify AtC control thermal flux faceset bndy_faces
    +

    +

    +description

    +

    Sets the energy exchange mechansim from the finite elements to the atoms, managed through a control algorithm. Rescale computes a scale factor for each atom to match the finite element temperature. Hoover is a Gaussian least-constraint isokinetic thermostat enforces that the nodal restricted atomic temperature matches the finite element temperature. Flux is a similar mode, but rather adds energy to the atoms based on conservation of energy. Hoover and flux allows the prescription of sources or fixed temperatures on the atoms.

    +

    +restrictions

    +

    only for be used with specific transfers : thermal (rescale, hoover, flux), two_temperature (flux)
    + rescale not valid with time filtering activated

    +

    +related

    +

    +default

    +

    none
    + rescale frequency is 1
    + flux boundary_integration_type is interpolate

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_control_thermal_correction_max_iterations.html b/doc/doc2/USER/atc/man_control_thermal_correction_max_iterations.html new file mode 100644 index 0000000000..8a511019f9 --- /dev/null +++ b/doc/doc2/USER/atc/man_control_thermal_correction_max_iterations.html @@ -0,0 +1,53 @@ + + + + +ATC: fix_modify AtC control thermal correction_max_iterations + + + + + + +
    + + +

    fix_modify AtC control thermal correction_max_iterations

    +syntax

    +

    fix_modify AtC control thermal correction_max_iterations <max_iterations>

    + +

    +examples

    +

    fix_modify AtC control thermal correction_max_iterations 10
    +

    +

    +description

    +

    Sets the maximum number of iterations to compute the 2nd order in time correction term for lambda with the fractional step method. The method uses the same tolerance as the controller's matrix solver.

    +

    +restrictions

    +

    only for use with thermal physics using the fractional step method.

    +

    +related

    +

    +default

    +

    correction_max_iterations is 20

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_decomposition.html b/doc/doc2/USER/atc/man_decomposition.html new file mode 100644 index 0000000000..15725073d3 --- /dev/null +++ b/doc/doc2/USER/atc/man_decomposition.html @@ -0,0 +1,55 @@ + + + + +ATC: fix_modify AtC decomposition + + + + + + +
    + + +

    fix_modify AtC decomposition

    +syntax

    +

    fix_modify AtC decomposition <type>

    + +

    +examples

    +

    fix_modify atc decomposition distributed_memory
    +

    +

    +description

    +

    Command for assigning the distribution of work and memory for parallel runs.

    +

    +restrictions

    +

    replicated_memory is appropriate for simulations were the number of nodes << number of atoms

    +

    +related

    +

    +default

    +

    replicated_memory

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_electron_integration.html b/doc/doc2/USER/atc/man_electron_integration.html new file mode 100644 index 0000000000..b14c14d86d --- /dev/null +++ b/doc/doc2/USER/atc/man_electron_integration.html @@ -0,0 +1,56 @@ + + + + +ATC: fix_modify AtC extrinsic electron_integration + + + + + + +
    + + +

    fix_modify AtC extrinsic electron_integration

    +syntax

    +

    fix_modify AtC extrinsic electron_integration <integration_type> <num_subcyle_steps(optional)>
    +

    + +

    +examples

    +

    fix_modify AtC extrinsic electron_integration implicit
    + fix_modify AtC extrinsic electron_integration explicit 100
    +

    +

    +description

    +

    Switches between integration scheme for the electron temperature. The number of subcyling steps used to integrate the electron temperature 1 LAMMPS timestep can be manually adjusted to capture fast electron dynamics.

    +

    +restrictions

    +

    For use only with two_temperature type of AtC fix ( see fix atc command )
    +

    +

    +default

    +

    implicit
    + subcycle_steps = 1

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_equilibrium_start.html b/doc/doc2/USER/atc/man_equilibrium_start.html new file mode 100644 index 0000000000..3723cf98bf --- /dev/null +++ b/doc/doc2/USER/atc/man_equilibrium_start.html @@ -0,0 +1,50 @@ + + + + +ATC: fix_modify AtC equilibrium_start + + + + + + +
    + + +

    fix_modify AtC equilibrium_start

    +syntax

    +

    fix_modify AtC equilibrium_start <on|off>

    +

    +examples

    +

    fix_modify atc equilibrium_start on
    +

    +

    +description

    +

    Starts filtered calculations assuming they start in equilibrium, i.e. perfect finite element force balance.

    +

    +restrictions

    +

    only needed before filtering is begun

    +

    +related

    +

    see fix_modify AtC filter

    +

    +default

    +

    on

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_extrinsic_exchange.html b/doc/doc2/USER/atc/man_extrinsic_exchange.html new file mode 100644 index 0000000000..8f6533ad64 --- /dev/null +++ b/doc/doc2/USER/atc/man_extrinsic_exchange.html @@ -0,0 +1,50 @@ + + + + +ATC: fix_modify AtC extrinsic exchange + + + + + + +
    + + +

    fix_modify AtC extrinsic exchange

    +syntax

    +

    fix_modify AtC extrinsic exchange <on|off>

    +

    +examples

    +

    fix_modify AtC extrinsic exchange on
    +

    +

    +description

    +

    Switches energy exchange between the MD system and electron system on and off

    +

    +restrictions

    +

    Only valid for use with two_temperature type of AtC fix.

    +

    +related

    +

    see fix atc command

    +

    +default

    +

    on

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_fe_md_boundary.html b/doc/doc2/USER/atc/man_fe_md_boundary.html new file mode 100644 index 0000000000..06bca2b337 --- /dev/null +++ b/doc/doc2/USER/atc/man_fe_md_boundary.html @@ -0,0 +1,50 @@ + + + + +ATC: fix_modify AtC fe_md_boundary + + + + + + +
    + + +

    fix_modify AtC fe_md_boundary

    +syntax

    +

    fix_modify AtC fe_md_boundary <faceset | interpolate | no_boundary> [args]

    +

    +examples

    +

    fix_modify atc fe_md_boundary interpolate
    +

    +

    +description

    +

    Specifies different methods for computing fluxes between between the MD and FE integration regions. Faceset defines a faceset separating the MD and FE regions and uses finite element face quadrature to compute the flux. Interpolate uses a reconstruction scheme to approximate the flux, which is more robust but less accurate if the MD/FE boundary does correspond to a faceset. No boundary results in no fluxes between the systems being computed.

    +

    +restrictions

    +

    If faceset is used, all the AtC non-boundary atoms must lie within and completely fill the domain enclosed by the faceset.

    +

    +related

    +

    see for how to specify the faceset name.

    +

    +default

    +

    Interpolate.

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_fem_mesh.html b/doc/doc2/USER/atc/man_fem_mesh.html new file mode 100644 index 0000000000..2abd84d6ce --- /dev/null +++ b/doc/doc2/USER/atc/man_fem_mesh.html @@ -0,0 +1,25 @@ + + +ATC: fix_modify AtC fem create mesh + + + +

    fix_modify AtC fem create mesh

    +syntax

    +fix_modify AtC fem create mesh <nx> <ny> <nz> <region-id> <f|p> <f|p> <f|p> +

    +examples

    + fix_modify AtC fem create mesh 10 1 1 feRegion p p p

    +description

    +Creates a uniform mesh in a rectangular region

    +restrictions

    +creates only uniform rectangular grids in a rectangular region

    +related

    +

    +default

    +none
    Generated on Mon Aug 17 09:35:16 2009 for ATC by  + +doxygen 1.3.9.1
    + + diff --git a/doc/doc2/USER/atc/man_filter_scale.html b/doc/doc2/USER/atc/man_filter_scale.html new file mode 100644 index 0000000000..975f87e949 --- /dev/null +++ b/doc/doc2/USER/atc/man_filter_scale.html @@ -0,0 +1,55 @@ + + + + +ATC: fix_modify AtC filter scale + + + + + + +
    + + +

    fix_modify AtC filter scale

    +syntax

    +

    fix_modify AtC filter scale <scale>
    +

    + +

    +examples

    +

    fix_modify AtC filter scale 10.0
    +

    +

    +description

    +

    Filters the MD dynamics to construct a more appropriate continuous field. Equilibrating first filters the time derivatives without changing the dynamics to provide a better initial condition to the filtered dynamics

    +

    +restrictions

    +

    only for be used with specific transfers: thermal, two_temperature

    +

    +related

    +

    fix_modify AtC filter fix_modify AtC filter type

    +

    +default

    +

    0.

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_filter_type.html b/doc/doc2/USER/atc/man_filter_type.html new file mode 100644 index 0000000000..8d9dbd3d12 --- /dev/null +++ b/doc/doc2/USER/atc/man_filter_type.html @@ -0,0 +1,51 @@ + + + + +ATC: fix_modify AtC filter type + + + + + + +
    + + +

    fix_modify AtC filter type

    +syntax

    +

    fix_modify AtC filter type <exponential | step | no_filter>
    +

    +

    +examples

    +

    fix_modify AtC filter type exponential
    +

    +

    +description

    +

    Specifies the type of time filter used.

    +

    +restrictions

    +

    only for be used with specific transfers: thermal, two_temperature

    +

    +related

    +

    fix_modify AtC filter fix_modify AtC filter scale

    +

    +default

    +

    No default.

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_fix_atc.html b/doc/doc2/USER/atc/man_fix_atc.html new file mode 100644 index 0000000000..e710c28ed2 --- /dev/null +++ b/doc/doc2/USER/atc/man_fix_atc.html @@ -0,0 +1,254 @@ + + + + +ATC: fix atc command + + + + + + +
    + + +

    fix atc command

    +syntax

    +

    fix <fixID> <group> atc <type> <parameter_file>

    + +

    +examples

    +

    fix AtC internal atc thermal Ar_thermal.dat
    + fix AtC internal atc two_temperature Ar_ttm.mat
    + fix AtC internal atc hardy
    + fix AtC internal atc field
    +

    +

    +description

    +

    This fix is the beginning to creating a coupled FE/MD simulation and/or an on-the-fly estimation of continuum fields. The coupled versions of this fix do Verlet integration and the /post-processing does not. After instantiating this fix, several other fix_modify commands will be needed to set up the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions.

    +

    The following coupling example is typical, but non-exhaustive:
    +

    +

    # ... commands to create and initialize the MD system
    +

    +

    # initial fix to designate coupling type and group to apply it to
    + # tag group physics material_file
    + fix AtC internal atc thermal Ar_thermal.mat
    +
    + # create a uniform 12 x 2 x 2 mesh that covers region contain the group
    + # nx ny nz region periodicity
    + fix_modify AtC mesh create 12 2 2 mdRegion f p p
    +
    + # specify the control method for the type of coupling
    + # physics control_type
    + fix_modify AtC thermal control flux
    +
    + # specify the initial values for the empirical field "temperature"
    + # field node_group value
    + fix_modify AtC initial temperature all 30.
    +
    + # create an output stream for nodal fields
    + # filename output_frequency
    + fix_modify AtC output atc_fe_output 100
    +
    +

    +

    run 1000
    +

    +

    likewise for this post-processing example:
    +

    +

    # ... commands to create and initialize the MD system
    +

    +

    # initial fix to designate post-processing and the group to apply it to
    + # no material file is allowed nor required
    + fix AtC internal atc hardy
    +
    + # for hardy fix, specific kernel function (function type and range) to # be used as a localization function
    + fix AtC kernel quartic_sphere 10.0
    +
    + # create a uniform 1 x 1 x 1 mesh that covers region contain the group
    + # with periodicity this effectively creats a system average
    + fix_modify AtC mesh create 1 1 1 box p p p
    +
    + # change from default lagrangian map to eulerian
    + # refreshed every 100 steps
    + fix_modify AtC atom_element_map eulerian 100
    +
    + # start with no field defined
    + # add mass density, potential energy density, stress and temperature
    + fix_modify AtC fields add density energy stress temperature
    +
    + # create an output stream for nodal fields
    + # filename output_frequency
    + fix_modify AtC output nvtFE 100 text
    +

    +

    run 1000
    +

    +

    the mesh's linear interpolation functions can be used as the localization function
    + by using the field option:
    +

    +

    fix AtC internal atc field
    +
    + fix_modify AtC mesh create 1 1 1 box p p p
    +
    + ...
    +
    +

    +

    Note coupling and post-processing can be combined in the same simulations using separate fixes.
    + For detailed exposition of the theory and algorithms please see:
    +

    + +

    Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes The finite element method , Dover 2003, for the basics of FE simulation.

    +

    +restrictions

    +

    Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc.

    +

    Currently,

    + +

    +related

    +

    fix_modify commands for setup:
    +

    + +

    fix_modify commands for boundary and initial conditions:
    +

    + +

    fix_modify commands for control and filtering:
    +

    + +

    fix_modify commands for output:
    +

    + +

    fix_modify commands for post-processing:
    +

    + +

    miscellaneous fix_modify commands:
    +

    + +

    Note: a set of example input files with the attendant material files are included with this package

    +

    +default

    +

    none

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_fix_flux.html b/doc/doc2/USER/atc/man_fix_flux.html new file mode 100644 index 0000000000..d8369a8785 --- /dev/null +++ b/doc/doc2/USER/atc/man_fix_flux.html @@ -0,0 +1,53 @@ + + + + +ATC: fix_modify AtC fix_flux + + + + + + +
    + + +

    fix_modify AtC fix_flux

    +syntax

    +

    fix_modify AtC fix_flux <field> <face_set> <value | function>

    + +

    +examples

    +

    fix_modify atc fix_flux temperature faceSet 10.0
    +

    +

    +description

    +

    Command for fixing normal fluxes e.g. heat_flux. This command only prescribes the normal component of the physical flux, e.g. heat (energy) flux. The units are in AtC units, i.e. derived from the LAMMPS length, time, and mass scales.

    +

    +restrictions

    +

    Only normal fluxes (Neumann data) can be prescribed.

    +

    +related

    +

    see fix_modify AtC unfix_flux

    +

    +default

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_fix_nodes.html b/doc/doc2/USER/atc/man_fix_nodes.html new file mode 100644 index 0000000000..cf5c93590a --- /dev/null +++ b/doc/doc2/USER/atc/man_fix_nodes.html @@ -0,0 +1,56 @@ + + + + +ATC: fix_modify AtC fix + + + + + + +
    + + +

    fix_modify AtC fix

    +syntax

    +

    fix_modify AtC fix <field> <nodeset> <constant | function>

    + +

    +examples

    +

    fix_modify AtC fix temperature groupNAME 10.
    + fix_modify AtC fix temperature groupNAME 0 0 0 10.0 0 0 1.0
    +

    +

    +description

    +

    Creates a constraint on the values of the specified field at specified nodes.

    +

    +restrictions

    +

    keyword 'all' reserved in nodeset name

    +

    +related

    +

    see fix_modify AtC unfix

    +

    +default

    +

    none

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_hardy_computes.html b/doc/doc2/USER/atc/man_hardy_computes.html new file mode 100644 index 0000000000..c16550742b --- /dev/null +++ b/doc/doc2/USER/atc/man_hardy_computes.html @@ -0,0 +1,67 @@ + + + + +ATC: fix_modify AtC computes + + + + + + +
    + + +

    fix_modify AtC computes

    +syntax

    +

    fix_modify AtC computes <add | delete> [per-atom compute id] <volume | number>
    +

    + +

    +examples

    +

    compute virial all stress/atom
    + fix_modify AtC computes add virial volume
    + fix_modify AtC computes delete virial
    +
    + compute centrosymmetry all centro/atom
    + fix_modify AtC computes add centrosymmetry number
    +

    +

    +description

    +

    Calculates continuum fields corresponding to specified per-atom computes created by LAMMPS
    +

    +

    +restrictions

    +

    Must be used with the hardy/field type of AtC fix ( see fix atc command )
    + Per-atom compute must be specified before corresponding continuum field can be requested
    +

    +

    +related

    +

    See manual page for compute

    +

    +default

    +

    No defaults exist for this command

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_hardy_fields.html b/doc/doc2/USER/atc/man_hardy_fields.html new file mode 100644 index 0000000000..1f55fd5e37 --- /dev/null +++ b/doc/doc2/USER/atc/man_hardy_fields.html @@ -0,0 +1,83 @@ + + + + +ATC: fix_modify AtC fields + + + + + + +
    + + +

    fix_modify AtC fields

    +syntax

    +

    fix_modify AtC fields <all | none>
    + fix_modify AtC fields <add | delete> <list_of_fields>
    +

    + +

    +examples

    +

    fix_modify AtC fields add velocity temperature

    +

    +description

    +

    Allows modification of the fields calculated and output by the transfer class. The commands are cumulative, e.g.
    + fix_modify AtC fields none
    + followed by
    + fix_modify AtC fields add velocity temperature
    + will only output the velocity and temperature fields.

    +

    +restrictions

    +

    Must be used with the hardy/field type of AtC fix, see fix atc command. Currently, the stress and heat flux formulas are only correct for central force potentials, e.g. Lennard-Jones and EAM but not Stillinger-Weber.

    +

    +related

    +

    See fix_modify AtC gradients , fix_modify AtC rates and fix_modify AtC computes

    +

    +default

    +

    By default, no fields are output

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_hardy_gradients.html b/doc/doc2/USER/atc/man_hardy_gradients.html new file mode 100644 index 0000000000..708fecbca1 --- /dev/null +++ b/doc/doc2/USER/atc/man_hardy_gradients.html @@ -0,0 +1,57 @@ + + + + +ATC: fix_modify AtC gradients + + + + + + +
    + + +

    fix_modify AtC gradients

    +syntax

    +

    fix_modify AtC gradients <add | delete> <list_of_fields>
    +

    + +

    +examples

    +

    fix_modify AtC gradients add temperature velocity stress
    + fix_modify AtC gradients delete velocity
    +

    +

    +description

    +

    Requests calculation and ouput of gradients of the fields from the transfer class. These gradients will be with regard to spatial or material coordinate for eulerian or lagrangian analysis, respectively, as specified by atom_element_map (see fix_modify AtC atom_element_map )

    +

    +restrictions

    +

    Must be used with the hardy/field type of AtC fix ( see fix atc command )

    +

    +related

    +

    +default

    +

    No gradients are calculated by default

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_hardy_kernel.html b/doc/doc2/USER/atc/man_hardy_kernel.html new file mode 100644 index 0000000000..3d81b367dd --- /dev/null +++ b/doc/doc2/USER/atc/man_hardy_kernel.html @@ -0,0 +1,65 @@ + + + + +ATC: fix_modify AtC kernel + + + + + + +
    + + +

    fix_modify AtC kernel

    +syntax

    +

    fix_modify AtC kernel <type> <parameters>

    + +

    +examples

    +

    fix_modify AtC kernel cell 1.0 1.0 1.0
    + fix_modify AtC kernel quartic_sphere 10.0

    +

    +description

    +

    +restrictions

    +

    Must be used with the hardy AtC fix
    + For bar kernel types, half-width oriented along x-direction
    + For cylinder kernel types, cylindrical axis is assumed to be in z-direction
    + ( see fix atc command )

    +

    +related

    +

    +default

    +

    No default

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_hardy_on_the_fly.html b/doc/doc2/USER/atc/man_hardy_on_the_fly.html new file mode 100644 index 0000000000..d140cf6840 --- /dev/null +++ b/doc/doc2/USER/atc/man_hardy_on_the_fly.html @@ -0,0 +1,60 @@ + + + + +ATC: fix_modify AtC on_the_fly + + + + + + +
    + + +

    fix_modify AtC on_the_fly

    +syntax

    +

    fix_modify AtC on_the_fly <bond | kernel> <optional on | off>
    + - bond | kernel (keyword) = specifies on-the-fly calculation of bond or kernel matrix elements
    +

    + +

    +examples

    +

    fix_modify AtC on_the_fly bond on
    + fix_modify AtC on_the_fly kernel
    + fix_modify AtC on_the_fly kernel off
    +

    +

    +description

    +

    Overrides normal mode of pre-calculating and storing bond pair-to-node a nd kernel atom-to-node matrices. If activated, will calculate elements of t hese matrices during repeated calls of field computations (i.e. "on-the-fly") and not store them for future use.
    + on flag is optional - if omitted, on_the_fly will be activated for the s pecified matrix. Can be deactivated using off flag.
    +

    +

    +restrictions

    +

    Must be used with the hardy/field type of AtC fix ( see fix atc command )

    +

    +related

    +

    +default

    +

    By default, on-the-fly calculation is not active (i.e. off). However, code does a memory allocation check to determine if it can store all needed bond and kernel matrix ele ments. If this allocation fails, on-the-fly is activated.
    +

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_hardy_rates.html b/doc/doc2/USER/atc/man_hardy_rates.html new file mode 100644 index 0000000000..ab0315cb65 --- /dev/null +++ b/doc/doc2/USER/atc/man_hardy_rates.html @@ -0,0 +1,58 @@ + + + + +ATC: fix_modify AtC rates + + + + + + +
    + + +

    fix_modify AtC rates

    +syntax

    +

    fix_modify AtC rates <add | delete> <list_of_fields>
    +

    + +

    +examples

    +

    fix_modify AtC rates add temperature velocity stress
    + fix_modify AtC rates delete stress
    +

    +

    +description

    +

    Requests calculation and ouput of rates (time derivatives) of the fields from the transfer class. For eulerian analysis (see fix_modify AtC atom_element_map ), these rates are the partial time derivatives of the nodal fields, not the full (material) time derivatives.
    +

    +

    +restrictions

    +

    Must be used with the hardy/field type of AtC fix ( see fix atc command )

    +

    +related

    +

    +default

    +

    No rates are calculated by default

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_initial.html b/doc/doc2/USER/atc/man_initial.html new file mode 100644 index 0000000000..c0a0be3852 --- /dev/null +++ b/doc/doc2/USER/atc/man_initial.html @@ -0,0 +1,51 @@ + + + + +ATC: fix_modify AtC initial + + + + + + +
    + + +

    fix_modify AtC initial

    +syntax

    +

    fix_modify AtC initial <field> <nodeset> <constant | function>

    + +

    +examples

    +

    fix_modify atc initial temperature groupNAME 10.

    +

    +description

    +

    Sets the initial values for the specified field at the specified nodes.

    +

    +restrictions

    +

    keyword 'all' reserved in nodeset name

    +

    +default

    +

    none

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_internal_atom_integrate.html b/doc/doc2/USER/atc/man_internal_atom_integrate.html new file mode 100644 index 0000000000..b15bf71aad --- /dev/null +++ b/doc/doc2/USER/atc/man_internal_atom_integrate.html @@ -0,0 +1,40 @@ + + + + +ATC: fix_modify AtC internal_atom_integrate + + + + + + +
    + + +

    fix_modify AtC internal_atom_integrate

    +syntax

    +

    fix_modify AtC internal_atom_integrate <on | off> fix_modify AtC internal_atom_integrate on

    +

    +description

    +

    Has AtC perform time integration for the atoms in the group on which it operates. This does not include boundary atoms.

    +

    +default

    +

    on for coupling methods, off for post-processors off

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_internal_element_set.html b/doc/doc2/USER/atc/man_internal_element_set.html new file mode 100644 index 0000000000..31bee57860 --- /dev/null +++ b/doc/doc2/USER/atc/man_internal_element_set.html @@ -0,0 +1,52 @@ + + + + +ATC: fix_modify AtC internal_element_set + + + + + + +
    + + +

    fix_modify AtC internal_element_set

    +syntax

    +

    fix_modify AtC internal_element_set <element-set-name>

    + +

    +examples

    +

    fix_modify AtC internal_element_set myElementSet fix_modify AtC internal_element_set off

    +

    +description

    +

    Enables AtC to base the region for internal atoms to be an element set. If no ghost atoms are used, all the AtC atoms must be constrained to remain in this element set by the user, e.g., with walls. If boundary atoms are used in conjunction with Eulerian atom maps AtC will partition all atoms of a boundary or internal type to be of type internal if they are in the internal region or to be of type boundary otherwise.

    +

    +restrictions

    +

    If boundary atoms are used in conjunction with Eulerian atom maps, the Eulerian reset frequency must be an integer multiple of the Lammps reneighbor frequency

    +

    +related

    +

    see atom_element_map_type and boundary

    +

    +default

    +

    off

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_internal_quadrature.html b/doc/doc2/USER/atc/man_internal_quadrature.html new file mode 100644 index 0000000000..172187c298 --- /dev/null +++ b/doc/doc2/USER/atc/man_internal_quadrature.html @@ -0,0 +1,50 @@ + + + + +ATC: fix_modify AtC internal_quadrature + + + + + + +
    + + +

    fix_modify AtC internal_quadrature

    +syntax

    +

    fix_modify atc internal_quadrature <on | off> [region]

    +

    +examples

    +

    fix_modify atc internal_quadrature off

    +

    +description

    +

    Command to use or not use atomic quadrature on internal elements fully filled with atoms. By turning the internal quadrature off these elements do not contribute to the governing PDE and the fields at the internal nodes follow the weighted averages of the atomic data.

    +

    +optional

    +

    Optional region tag specifies which finite element nodes will be treated as being within the MD region. This option is only valid with internal_quadrature off.

    +

    +restrictions

    +

    +related

    +

    +default

    +

    on

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_kernel_function.html b/doc/doc2/USER/atc/man_kernel_function.html new file mode 100644 index 0000000000..08ec827dec --- /dev/null +++ b/doc/doc2/USER/atc/man_kernel_function.html @@ -0,0 +1,64 @@ + + + + +ATC: fix_modify AtC kernel + + + + + + +
    + + +

    fix_modify AtC kernel

    +syntax

    +

    fix_modify AtC kernel <type> <parameters>

    + +

    +examples

    +

    fix_modify AtC kernel cell 1.0 1.0 1.0 fix_modify AtC kernel quartic_sphere 10.0

    +

    +description

    +

    +restrictions

    +

    Must be used with the hardy AtC fix
    + For bar kernel types, half-width oriented along x-direction
    + For cylinder kernel types, cylindrical axis is assumed to be in z-direction
    + ( see fix atc command )

    +

    +related

    +

    +default

    +

    No default

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_localized_lambda.html b/doc/doc2/USER/atc/man_localized_lambda.html new file mode 100644 index 0000000000..5dadb9d730 --- /dev/null +++ b/doc/doc2/USER/atc/man_localized_lambda.html @@ -0,0 +1,48 @@ + + + + +ATC: fix_modify AtC control localized_lambda + + + + + + +
    + + +

    fix_modify AtC control localized_lambda

    +syntax

    +

    fix_modify AtC control localized_lambda <on|off>

    +

    +examples

    +

    fix_modify atc control localized_lambda on
    +

    +

    +description

    +

    Turns on localization algorithms for control algorithms to restrict the influence of FE coupling or boundary conditions to a region near the boundary of the MD region. Control algorithms will not affect atoms in elements not possessing faces on the boundary of the region. Flux-based control is localized via row-sum lumping while quantity control is done by solving a truncated matrix equation.

    +

    +restrictions

    +

    +related

    +

    +default

    +

    Default is off.

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_lumped_lambda_solve.html b/doc/doc2/USER/atc/man_lumped_lambda_solve.html new file mode 100644 index 0000000000..bb3f8cfde8 --- /dev/null +++ b/doc/doc2/USER/atc/man_lumped_lambda_solve.html @@ -0,0 +1,47 @@ + + + + +ATC: fix_modify AtC control lumped_lambda_solve + + + + + + +
    + + +

    fix_modify AtC control lumped_lambda_solve

    +syntax

    +

    fix_modify AtC control lumped_lambda_solve <on|off>

    +

    +examples

    +

    fix_modify atc control lumped_lambda_solve on
    +

    +

    +description

    +

    Command to use or not use lumped matrix for lambda solve

    +

    +restrictions

    +

    +related

    +

    +default

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_mask_direction.html b/doc/doc2/USER/atc/man_mask_direction.html new file mode 100644 index 0000000000..01ca9d192b --- /dev/null +++ b/doc/doc2/USER/atc/man_mask_direction.html @@ -0,0 +1,47 @@ + + + + +ATC: fix_modify AtC control mask_direction + + + + + + +
    + + +

    fix_modify AtC control mask_direction

    +syntax

    +

    fix_modify AtC control mask_direction <direction> <on|off>

    +

    +examples

    +

    fix_modify atc control mask_direction 0 on
    +

    +

    +description

    +

    Command to mask out certain dimensions from the atomic regulator

    +

    +restrictions

    +

    +related

    +

    +default

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_mass_matrix.html b/doc/doc2/USER/atc/man_mass_matrix.html new file mode 100644 index 0000000000..5f543fc20c --- /dev/null +++ b/doc/doc2/USER/atc/man_mass_matrix.html @@ -0,0 +1,51 @@ + + + + +ATC: fix_modify AtC mass_matrix + + + + + + +
    + + +

    fix_modify AtC mass_matrix

    +syntax

    +

    fix_modify AtC mass_matrix <fe | md_fe>

    + +

    +examples

    +

    fix_modify atc mass_matrix fe

    +

    +description

    +

    Determines whether AtC uses the FE mass matrix based on Gaussian quadrature or based on atomic quadrature in the MD region. This is useful for fully overlapping simulations to improve efficiency.

    +

    +restrictions

    +

    Should not be used unless the FE region is contained within the MD region, otherwise the method will be unstable and inaccurate

    +

    +related

    +

    +default

    +

    Default is off

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_material.html b/doc/doc2/USER/atc/man_material.html new file mode 100644 index 0000000000..9867e90f77 --- /dev/null +++ b/doc/doc2/USER/atc/man_material.html @@ -0,0 +1,49 @@ + + + + +ATC: fix_modify AtC material + + + + + + +
    + + +

    fix_modify AtC material

    +syntax

    +

    fix_modify AtC material [elementset_name] [material_id]
    +

    +

    +examples

    +

    fix_modify AtC material gap_region 2

    +

    +description

    +

    Sets the material model in elementset_name to be of type material_id.

    +

    +restrictions

    +

    The element set must already be created and the material must be specified in the material file given the the atc fix on construction

    +

    +related

    +

    +default

    +

    All elements default to the first material in the material file.

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_mesh_add_to_nodeset.html b/doc/doc2/USER/atc/man_mesh_add_to_nodeset.html new file mode 100644 index 0000000000..cf5ad52f60 --- /dev/null +++ b/doc/doc2/USER/atc/man_mesh_add_to_nodeset.html @@ -0,0 +1,51 @@ + + + + +ATC: fix_modify AtC mesh add_to_nodeset + + + + + + +
    + + +

    fix_modify AtC mesh add_to_nodeset

    +syntax

    +

    fix_modify AtC mesh add_to_nodeset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>

    + +

    +examples

    +

    fix_modify AtC mesh add_to_nodeset lbc -11.9 -11 -12 12 -12 12

    +

    +description

    +

    Command to add nodes to an already existing FE nodeset.

    +

    +restrictions

    +

    +related

    +

    +default

    +

    Coordinates are assumed to be in lattice units.

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_mesh_create.html b/doc/doc2/USER/atc/man_mesh_create.html new file mode 100644 index 0000000000..efaf7f4307 --- /dev/null +++ b/doc/doc2/USER/atc/man_mesh_create.html @@ -0,0 +1,56 @@ + + + + +ATC: fix_modify AtC mesh create + + + + + + +
    + + +

    fix_modify AtC mesh create

    +syntax

    +

    fix_modify AtC mesh create <nx> <ny> <nz> <region-id> <f|p> <f|p> <f|p>
    +

    + +

    +examples

    +

    fix_modify AtC mesh create 10 1 1 feRegion p p p
    +

    +

    +description

    +

    Creates a uniform mesh in a rectangular region

    +

    +restrictions

    +

    Creates only uniform rectangular grids in a rectangular region

    +

    +related

    +

    fix_modify AtC mesh quadrature

    +

    +default

    +

    When created, mesh defaults to gauss2 (2-point Gaussian) quadrature. Use "mesh quadrature" command to change quadrature style.

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_mesh_create_elementset.html b/doc/doc2/USER/atc/man_mesh_create_elementset.html new file mode 100644 index 0000000000..51bdae4faa --- /dev/null +++ b/doc/doc2/USER/atc/man_mesh_create_elementset.html @@ -0,0 +1,52 @@ + + + + +ATC: fix_modify AtC mesh create_elementset + + + + + + +
    + + +

    fix_modify AtC mesh create_elementset

    +syntax

    +

    fix_modify AtC create_elementset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>

    + +

    +examples

    +

    fix_modify AtC mesh create_elementset middle -4.1 4.1 -100 100 -100 1100

    +

    +description

    +

    Command to assign an id to a set of FE elements to be used subsequently in defining material and mesh-based operations.

    +

    +restrictions

    +

    Only viable for rectangular grids.

    +

    +related

    +

    +default

    +

    Coordinates are assumed to be in lattice units.

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_mesh_create_faceset_box.html b/doc/doc2/USER/atc/man_mesh_create_faceset_box.html new file mode 100644 index 0000000000..163a6b442c --- /dev/null +++ b/doc/doc2/USER/atc/man_mesh_create_faceset_box.html @@ -0,0 +1,54 @@ + + + + +ATC: fix_modify AtC mesh create_faceset box + + + + + + +
    + + +

    fix_modify AtC mesh create_faceset box

    +syntax

    +

    fix_modify AtC mesh create_faceset <id> box <xmin> <xmax> <ymin> <ymax> <zmin> <zmax> <in|out> [units]

    + +

    +examples

    +

    fix_modify AtC mesh create_faceset obndy box -4.0 4.0 -12 12 -12 12 out

    +

    +description

    +

    Command to assign an id to a set of FE faces.

    +

    +restrictions

    +

    Only viable for rectangular grids.

    +

    +related

    +

    +default

    +

    The default options are units = lattice and the use of outer faces

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_mesh_create_faceset_plane.html b/doc/doc2/USER/atc/man_mesh_create_faceset_plane.html new file mode 100644 index 0000000000..3ca1108d1a --- /dev/null +++ b/doc/doc2/USER/atc/man_mesh_create_faceset_plane.html @@ -0,0 +1,54 @@ + + + + +ATC: fix_modify AtC mesh create_faceset plane + + + + + + +
    + + +

    fix_modify AtC mesh create_faceset plane

    +syntax

    +

    fix_modify AtC mesh create_faceset <id> plane <x|y|z> <val1> <x|y|z> <lval2> <uval2> [units]

    + +

    +examples

    +

    fix_modify AtC mesh create_faceset xyplane plane y 0 x -4 0

    +

    +description

    +

    Command to assign an id to a set of FE faces.

    +

    +restrictions

    +

    Only viable for rectangular grids.

    +

    +related

    +

    +default

    +

    The default option is units = lattice.

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_mesh_create_nodeset.html b/doc/doc2/USER/atc/man_mesh_create_nodeset.html new file mode 100644 index 0000000000..9d5d155654 --- /dev/null +++ b/doc/doc2/USER/atc/man_mesh_create_nodeset.html @@ -0,0 +1,51 @@ + + + + +ATC: fix_modify AtC mesh create_nodeset + + + + + + +
    + + +

    fix_modify AtC mesh create_nodeset

    +syntax

    +

    fix_modify AtC mesh create_nodeset <id> <xmin> <xmax> <ymin> <ymax> <zmin> <zmax>

    + +

    +examples

    +

    fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -12 12 -12 12

    +

    +description

    +

    Command to assign an id to a set of FE nodes to be used subsequently in defining boundary conditions.

    +

    +restrictions

    +

    +related

    +

    +default

    +

    Coordinates are assumed to be in lattice units.

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_mesh_delete_elements.html b/doc/doc2/USER/atc/man_mesh_delete_elements.html new file mode 100644 index 0000000000..cc269c8e65 --- /dev/null +++ b/doc/doc2/USER/atc/man_mesh_delete_elements.html @@ -0,0 +1,50 @@ + + + + +ATC: fix_modify AtC mesh delete_elements + + + + + + +
    + + +

    fix_modify AtC mesh delete_elements

    +syntax

    +

    fix_modify AtC mesh delete_elements <element_set>

    + +

    +examples

    +

    fix_modify AtC delete_elements gap

    +

    +description

    +

    Deletes a group of elements from the mesh.

    +

    +restrictions

    +

    +related

    +

    +default

    +

    none

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_mesh_nodeset_to_elementset.html b/doc/doc2/USER/atc/man_mesh_nodeset_to_elementset.html new file mode 100644 index 0000000000..45d03fc986 --- /dev/null +++ b/doc/doc2/USER/atc/man_mesh_nodeset_to_elementset.html @@ -0,0 +1,53 @@ + + + + +ATC: fix_modify AtC mesh nodeset_to_elementset + + + + + + +
    + + +

    fix_modify AtC mesh nodeset_to_elementset

    +syntax

    +

    fix_modify AtC nodeset_to_elementset <nodeset_id> <elementset_id> <max/min>

    + +

    +examples

    +

    fix_modify AtC mesh nodeset_to_elementset myNodeset myElementset min

    +

    +description

    +

    Command to create an elementset from an existing nodeset. Either the minimal element set of elements with all nodes in the set, or maximal element set with all elements with at least one node in the set, can be created

    +

    +restrictions

    +

    None.

    +

    +related

    +

    +default

    +

    Unless specified, the maximal element set is created

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_mesh_output.html b/doc/doc2/USER/atc/man_mesh_output.html new file mode 100644 index 0000000000..be1b4c194f --- /dev/null +++ b/doc/doc2/USER/atc/man_mesh_output.html @@ -0,0 +1,49 @@ + + + + +ATC: fix_modify AtC mesh output + + + + + + +
    + + +

    fix_modify AtC mesh output

    +syntax

    +

    fix_modify AtC mesh output <file_prefix>

    +

    +examples

    +

    fix_modify AtC mesh output meshData
    +

    +

    +description

    +

    Command to output mesh and associated data: nodesets, facesets, and elementsets. This data is only output once upon initialization since currently the mesh is static. Creates (binary, "gold" format) Ensight output of mesh data.

    +

    +restrictions

    +

    none

    +

    +related

    +

    +default

    +

    none

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_mesh_quadrature.html b/doc/doc2/USER/atc/man_mesh_quadrature.html new file mode 100644 index 0000000000..d5291d99db --- /dev/null +++ b/doc/doc2/USER/atc/man_mesh_quadrature.html @@ -0,0 +1,51 @@ + + + + +ATC: fix_modify AtC mesh quadrature + + + + + + +
    + + +

    fix_modify AtC mesh quadrature

    +syntax

    +

    fix_modify AtC mesh quadrature <quad>

    + +

    +examples

    +

    fix_modify AtC mesh quadrature face

    +

    +description

    +

    (Re-)assigns the quadrature style for the existing mesh.

    +

    +restrictions

    +

    +related

    +

    fix_modify AtC mesh create

    +

    +default

    +

    none

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_mesh_read.html b/doc/doc2/USER/atc/man_mesh_read.html new file mode 100644 index 0000000000..a497a2ed04 --- /dev/null +++ b/doc/doc2/USER/atc/man_mesh_read.html @@ -0,0 +1,52 @@ + + + + +ATC: fix_modify AtC mesh read + + + + + + +
    + + +

    fix_modify AtC mesh read

    +syntax

    +

    fix_modify AtC mesh read <filename> <f|p> <f|p> <f|p>

    + +

    +examples

    +

    fix_modify AtC mesh read myComponent.mesh p p p
    + fix_modify AtC mesh read myOtherComponent.exo

    +

    +description

    +

    Reads a mesh from a text or exodus file, and assigns periodic boundary conditions if needed.

    +

    +restrictions

    +

    +related

    +

    +default

    +

    periodicity flags are false by default

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_mesh_write.html b/doc/doc2/USER/atc/man_mesh_write.html new file mode 100644 index 0000000000..21754a1e68 --- /dev/null +++ b/doc/doc2/USER/atc/man_mesh_write.html @@ -0,0 +1,50 @@ + + + + +ATC: fix_modify AtC mesh write + + + + + + +
    + + +

    fix_modify AtC mesh write

    +syntax

    +

    fix_modify AtC mesh write <filename>

    + +

    +examples

    +

    fix_modify AtC mesh write myMesh.mesh
    +

    +

    +description

    +

    Writes a mesh to a text file.

    +

    +restrictions

    +

    +related

    +

    +default

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_momentum_time_integration.html b/doc/doc2/USER/atc/man_momentum_time_integration.html new file mode 100644 index 0000000000..3b987f70ef --- /dev/null +++ b/doc/doc2/USER/atc/man_momentum_time_integration.html @@ -0,0 +1,60 @@ + + + + +ATC: fix_modify AtC time_integration (momentum) + + + + + + +
    + + +

    fix_modify AtC time_integration (momentum)

    +syntax

    +

    fix_modify AtC time_integration <descriptor>
    +

    + +

    various time integration methods for the finite elements
    +

    +

    +description

    +

    verlet - atomic velocity update with 2nd order Verlet, nodal temperature update with 2nd order Verlet, kinetostats based on controlling force
    + fractional_step - atomic velocity update with 2nd order Verlet, mixed nodal momentum update, 2nd order Verlet for continuum and exact 2nd order Verlet for atomic contributions, kinetostats based on controlling discrete momentum changes
    + gear - atomic velocity update with 2nd order Verlet, nodal temperature update with 3rd or 4th order Gear, kinetostats based on controlling power
    +

    +

    +examples

    +

    fix_modify atc time_integration verlet
    + fix_modify atc time_integration fractional_step
    +

    +

    +description

    +

    +related

    +

    see fix atc command

    +

    +default

    +

    none

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_output.html b/doc/doc2/USER/atc/man_output.html new file mode 100644 index 0000000000..3129ff30c9 --- /dev/null +++ b/doc/doc2/USER/atc/man_output.html @@ -0,0 +1,63 @@ + + + + +ATC: fix_modify AtC output + + + + + + +
    + + +

    fix_modify AtC output

    +syntax

    +

    fix_modify AtC output <filename_prefix> <frequency> [text | full_text | binary | vector_components | tensor_components ] fix_modify AtC output index [step | time ]

    + +

    +examples

    +

    fix_modify AtC output heatFE 100
    + fix_modify AtC output hardyFE 1 text tensor_components
    + fix_modify AtC output hardyFE 10 text binary tensor_components
    + fix_modify AtC output index step
    +

    +

    +description

    +

    Creates text and/or binary (Ensight, "gold" format) output of nodal/mesh data which is transfer/physics specific. Output indexed by step or time is possible.

    +

    +restrictions

    +

    +related

    +

    see fix atc command

    +

    +default

    +

    no default format output indexed by time

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_output_elementset.html b/doc/doc2/USER/atc/man_output_elementset.html new file mode 100644 index 0000000000..be259388ba --- /dev/null +++ b/doc/doc2/USER/atc/man_output_elementset.html @@ -0,0 +1,54 @@ + + + + +ATC: fix_modify AtC output elementset + + + + + + +
    + + +

    fix_modify AtC output elementset

    +syntax

    +

    fix_modify AtC output volume_integral <eset_name> <field> {`

    + +

    +examples

    +

    fix_modify AtC output eset1 mass_density
    +

    +

    +description

    +

    Performs volume integration of specified field over elementset and outputs resulting variable values to GLOBALS file.

    +

    +restrictions

    +

    +related

    +

    see fix atc command

    +

    +default

    +

    none

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_output_nodeset.html b/doc/doc2/USER/atc/man_output_nodeset.html new file mode 100644 index 0000000000..db76c8008e --- /dev/null +++ b/doc/doc2/USER/atc/man_output_nodeset.html @@ -0,0 +1,55 @@ + + + + +ATC: fix_modify AtC output nodeset + + + + + + +
    + + +

    fix_modify AtC output nodeset

    +syntax

    +

    fix_modify AtC output nodeset <nodeset_name> <operation>

    + +

    +examples

    +

    fix_modify AtC output nodeset nset1 sum
    +

    +

    +description

    +

    Performs operation over the nodes belonging to specified nodeset and outputs resulting variable values to GLOBALS file.

    +

    +restrictions

    +

    +related

    +

    see fix atc command

    +

    +default

    +

    none

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_pair_interactions.html b/doc/doc2/USER/atc/man_pair_interactions.html new file mode 100644 index 0000000000..d46dcb1234 --- /dev/null +++ b/doc/doc2/USER/atc/man_pair_interactions.html @@ -0,0 +1,50 @@ + + + + +ATC: fix_modify AtC pair_interactions/bond_interactions + + + + + + +
    + + +

    fix_modify AtC pair_interactions/bond_interactions

    +syntax

    +

    fix_modify AtC pair_interactions <on|off>
    + fix_modify AtC bond_interactions <on|off>
    +

    +

    +examples

    +

    fix_modify AtC bond_interactions on
    +

    +

    +description

    +

    include bonds and/or pairs in the stress and heat flux computations

    +

    +restrictions

    +

    +related

    +

    +default

    +

    pair interactions: on, bond interactions: off

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_poisson_solver.html b/doc/doc2/USER/atc/man_poisson_solver.html new file mode 100644 index 0000000000..d69d74db1a --- /dev/null +++ b/doc/doc2/USER/atc/man_poisson_solver.html @@ -0,0 +1,53 @@ + + + + +ATC: fix_modify AtC poisson_solver + + + + + + +
    + + +

    fix_modify AtC poisson_solver

    +syntax

    +

    fix_modify AtC poisson_solver mesh create <nx> <ny> <nz> <region-id> <f|p> <f|p> <f|p>

    + +

    +examples

    +

    fix_modify AtC poisson_solver mesh create 10 1 1 feRegion p p p

    +

    +description

    +

    Creates a uniform mesh in a rectangular region

    +

    +restrictions

    +

    creates only uniform rectangular grids in a rectangular region

    +

    +related

    +

    +default

    +

    none

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_read_restart.html b/doc/doc2/USER/atc/man_read_restart.html new file mode 100644 index 0000000000..96168fccc7 --- /dev/null +++ b/doc/doc2/USER/atc/man_read_restart.html @@ -0,0 +1,51 @@ + + + + +ATC: fix_modify AtC read_restart + + + + + + +
    + + +

    fix_modify AtC read_restart

    +syntax

    +

    fix_modify AtC read_restart [file_name]
    +

    +

    +examples

    +

    fix_modify AtC read_restart ATC_state
    +

    +

    +description

    +

    Reads the current state of the fields from a named text-based restart file.

    +

    +restrictions

    +

    The restart file only contains fields and their time derivatives. The reference positions of the atoms and the commands that initialize the fix are not saved e.g. an identical mesh containing the same atoms will have to be recreated.

    +

    +related

    +

    see write_restart fix_modify AtC write_restart

    +

    +default

    +

    none

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_remove_molecule.html b/doc/doc2/USER/atc/man_remove_molecule.html new file mode 100644 index 0000000000..054291efda --- /dev/null +++ b/doc/doc2/USER/atc/man_remove_molecule.html @@ -0,0 +1,54 @@ + + + + +ATC: fix_modify AtC remove_molecule + + + + + + +
    + + +

    fix_modify AtC remove_molecule

    +syntax

    +

    fix_modify_AtC remove_molecule <TAG>
    +

    + +

    +examples

    +

    fix_modify AtC remove_molecule water
    +

    +

    +description

    +

    Removes tag designated for tracking a specified set of molecules.
    +

    +

    +restrictions

    +

    +related

    +

    +default

    +

    No defaults for this command.

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_remove_source.html b/doc/doc2/USER/atc/man_remove_source.html new file mode 100644 index 0000000000..d1d249eb76 --- /dev/null +++ b/doc/doc2/USER/atc/man_remove_source.html @@ -0,0 +1,52 @@ + + + + +ATC: fix_modify AtC remove_source + + + + + + +
    + + +

    fix_modify AtC remove_source

    +syntax

    +

    fix_modify AtC remove_source <field> <element_set>

    + +

    +examples

    +

    fix_modify atc remove_source temperature groupNAME

    +

    +description

    +

    Remove a domain source.

    +

    +restrictions

    +

    keyword 'all' reserved in element_set name

    +

    +related

    +

    see fix_modify AtC source

    +

    +default

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_remove_species.html b/doc/doc2/USER/atc/man_remove_species.html new file mode 100644 index 0000000000..ba94a52658 --- /dev/null +++ b/doc/doc2/USER/atc/man_remove_species.html @@ -0,0 +1,54 @@ + + + + +ATC: fix_modify AtC remove_species + + + + + + +
    + + +

    fix_modify AtC remove_species

    +syntax

    +

    fix_modify_AtC delete_species <TAG>
    +

    + +

    +examples

    +

    fix_modify AtC remove_species gold
    +

    +

    +description

    +

    Removes tag designated for tracking a specified species.
    +

    +

    +restrictions

    +

    +related

    +

    +default

    +

    No defaults for this command.

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_reset_atomic_reference_positions.html b/doc/doc2/USER/atc/man_reset_atomic_reference_positions.html new file mode 100644 index 0000000000..cb82f61bbb --- /dev/null +++ b/doc/doc2/USER/atc/man_reset_atomic_reference_positions.html @@ -0,0 +1,49 @@ + + + + +ATC: fix_modify AtC reset_atomic_reference_positions + + + + + + +
    + + +

    fix_modify AtC reset_atomic_reference_positions

    +syntax

    +

    fix_modify AtC reset_atomic_reference_positions

    +

    +examples

    +

    fix_modify atc reset_atomic_reference_positions

    +

    +description

    +

    Resets the atomic positions ATC uses to perform point to field operations. In can be used to use perfect lattice sites in ATC but a thermalized or deformed lattice in LAMMPS.

    +

    +restrictions

    +

    +

    +related

    +

    +

    +default

    +

    Default is off

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_reset_time.html b/doc/doc2/USER/atc/man_reset_time.html new file mode 100644 index 0000000000..35d75ccb97 --- /dev/null +++ b/doc/doc2/USER/atc/man_reset_time.html @@ -0,0 +1,65 @@ + + + + +ATC: fix_modify AtC reset_time + + + + + + +
    + + +

    fix_modify AtC reset_time

    +syntax

    +

    fix_modify AtC reset_time

    +

    +examples

    +

    fix_modify atc reset_time 0.0
    +

    +

    +description

    +

    Resets the simulation time counter.

    +

    +restrictions

    +

    +related

    +

    +default

    +

    +syntax

    +

    fix_modify AtC kernel_bandwidth

    +

    +examples

    +

    fix_modify atc reset_time 8
    +

    +

    +description

    +

    Sets a maximum parallel bandwidth for the kernel functions during parallel communication. If the command is not issued, the default will be to assume the bandwidth of the kernel matrix corresponds to the number of sampling locations.

    +

    +restrictions

    +

    Only is used if kernel functions are being used.

    +

    +related

    +

    +default

    +

    Number of sample locations.

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_sample_frequency.html b/doc/doc2/USER/atc/man_sample_frequency.html new file mode 100644 index 0000000000..13f468b222 --- /dev/null +++ b/doc/doc2/USER/atc/man_sample_frequency.html @@ -0,0 +1,52 @@ + + + + +ATC: fix_modify AtC sample_frequency + + + + + + +
    + + +

    fix_modify AtC sample_frequency

    +syntax

    +

    fix_modify AtC sample_frequency [freq]

    + +

    +examples

    +

    fix_modify AtC sample_frequency 10

    +

    +description

    +

    Specifies a frequency at which fields are computed for the case where time filters are being applied.

    +

    +restrictions

    +

    Must be used with the hardy/field AtC fix ( see fix atc command ) and is only relevant when time filters are being used.

    +

    +related

    +

    +

    +default

    +

    none

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_set.html b/doc/doc2/USER/atc/man_set.html new file mode 100644 index 0000000000..d104e535b6 --- /dev/null +++ b/doc/doc2/USER/atc/man_set.html @@ -0,0 +1,56 @@ + + + + +ATC: fix_modify AtC set + + + + + + +
    + + +

    fix_modify AtC set

    +syntax

    +

    fix_modify AtC set reference_potential_energy <value_or_filename(optional)>

    + +

    +examples

    +

    fix_modify AtC set reference_potential_energy
    + fix_modify AtC set reference_potential_energy -0.05
    + fix_modify AtC set reference_potential_energy myPEvalues
    +

    +

    +description

    +

    Used to set various quantities for the post-processing algorithms. It sets the zero point for the potential energy density using the value provided for all nodes, or from the current configuration of the lattice if no value is provided, or values provided within the specified filename.

    +

    +restrictions

    +

    Must be used with the hardy/field type of AtC fix ( see fix atc command )

    +

    +related

    +

    +default

    +

    Defaults to lammps zero point i.e. isolated atoms

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_source.html b/doc/doc2/USER/atc/man_source.html new file mode 100644 index 0000000000..833b2a866f --- /dev/null +++ b/doc/doc2/USER/atc/man_source.html @@ -0,0 +1,53 @@ + + + + +ATC: fix_modify AtC source + + + + + + +
    + + +

    fix_modify AtC source

    +syntax

    +

    fix_modify AtC source <field> <element_set> <value | function>

    + +

    +examples

    +

    fix_modify atc source temperature middle temporal_ramp 10. 0.

    +

    +description

    +

    Add domain sources to the mesh. The units are consistent with LAMMPS's units for mass, length and time and are defined by the PDE being solved, e.g. for thermal transfer the balance equation is for energy and source is energy per time.

    +

    +restrictions

    +

    keyword 'all' reserved in element_set name

    +

    +related

    +

    see fix_modify AtC remove_source

    +

    +default

    +

    none

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_source_integration.html b/doc/doc2/USER/atc/man_source_integration.html new file mode 100644 index 0000000000..70f62d2e57 --- /dev/null +++ b/doc/doc2/USER/atc/man_source_integration.html @@ -0,0 +1,46 @@ + + + + +ATC: fix_modify AtC source_integration + + + + + + +
    + + +

    fix_modify AtC source_integration

    +syntax

    +

    fix_modify AtC source_integration < fe | atom>

    +

    +examples

    +

    fix_modify atc source_integration atom

    +

    +description

    +

    +restrictions

    +

    +related

    +

    +default

    +

    Default is fe

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_temperature_definition.html b/doc/doc2/USER/atc/man_temperature_definition.html new file mode 100644 index 0000000000..f4fb21471c --- /dev/null +++ b/doc/doc2/USER/atc/man_temperature_definition.html @@ -0,0 +1,47 @@ + + + + +ATC: fix_modify AtC temperature_definition + + + + + + +
    + + +

    fix_modify AtC temperature_definition

    +syntax

    +

    fix_modify AtC temperature_definition <kinetic|total>

    +

    +examples

    +

    fix_modify atc temperature_definition kinetic
    +

    +

    +description

    +

    Change the definition for the atomic temperature used to create the finite element temperature. The kinetic option is based only on the kinetic energy of the atoms while the total option uses the total energy (kinetic + potential) of an atom.

    +

    +restrictions

    +

    This command is only valid when using thermal coupling. Also, while not a formal restriction, the user should ensure that associating a potential energy with each atom makes physical sense for the total option to be meaningful.

    +

    +default

    +

    kinetic

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_thermal_time_integration.html b/doc/doc2/USER/atc/man_thermal_time_integration.html new file mode 100644 index 0000000000..c2f636134f --- /dev/null +++ b/doc/doc2/USER/atc/man_thermal_time_integration.html @@ -0,0 +1,59 @@ + + + + +ATC: fix_modify AtC time_integration (thermal) + + + + + + +
    + + +

    fix_modify AtC time_integration (thermal)

    +syntax

    +

    fix_modify AtC time_integration <descriptor>
    +

    + +

    various time integration methods for the finite elements
    +

    +

    +description

    +

    gear - atomic velocity update with 2nd order Verlet, nodal temperature update with 3rd or 4th order Gear, thermostats based on controlling power
    + fractional_step - atomic velocity update with 2nd order Verlet, mixed nodal temperature update, 3/4 Gear for continuum and 2 Verlet for atomic contributions, thermostats based on controlling discrete energy changes
    +

    +

    +examples

    +

    fix_modify atc time_integration gear
    + fix_modify atc time_integration fractional_step
    +

    +

    +description

    +

    +related

    +

    see fix atc command

    +

    +default

    +

    none

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_time_filter.html b/doc/doc2/USER/atc/man_time_filter.html new file mode 100644 index 0000000000..ec70fed871 --- /dev/null +++ b/doc/doc2/USER/atc/man_time_filter.html @@ -0,0 +1,57 @@ + + + + +ATC: fix_modify AtC filter + + + + + + +
    + + +

    fix_modify AtC filter

    +syntax

    +

    fix_modify AtC filter <on | off | equilibrate>
    +

    + +

    +examples

    +

    fix_modify atc transfer filter on
    +

    +

    +description

    +

    Filters the MD dynamics to construct a more appropriate continuous field. Equilibrating first filters the time derivatives without changing the dynamics to provide a better initial condition to the filtered dynamics

    +

    +restrictions

    +

    only for be used with specific transfers: thermal, two_temperature

    +

    +related

    +

    fix_modify AtC filter scale
    + fix_modify AtC equilibrium_start

    +

    +default

    +

    off

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_track_displacement.html b/doc/doc2/USER/atc/man_track_displacement.html new file mode 100644 index 0000000000..8f729cffe3 --- /dev/null +++ b/doc/doc2/USER/atc/man_track_displacement.html @@ -0,0 +1,48 @@ + + + + +ATC: fix_modify AtC track_displacement + + + + + + +
    + + +

    fix_modify AtC track_displacement

    +syntax

    +

    fix_modify AtC track_displacement <on/off>
    +

    +

    +examples

    +

    fix_modify atc track_displacement on
    +

    +

    +description

    +

    Determines whether displacement is tracked or not. For solids problems this is a useful quantity, but for fluids it is not relevant.

    +

    +restrictions

    +

    Some constitutive models require the displacement field

    +

    +default

    +

    on

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_unfix_flux.html b/doc/doc2/USER/atc/man_unfix_flux.html new file mode 100644 index 0000000000..b2a19a7fd0 --- /dev/null +++ b/doc/doc2/USER/atc/man_unfix_flux.html @@ -0,0 +1,52 @@ + + + + +ATC: fix_modify AtC unfix_flux + + + + + + +
    + + +

    fix_modify AtC unfix_flux

    +syntax

    +

    fix_modify AtC fix_flux <field> <face_set> <value | function>

    + +

    +examples

    +

    fix_modify atc unfix_flux temperature faceSet
    +

    +

    +description

    +

    Command for removing prescribed normal fluxes e.g. heat_flux, stress.

    +

    +restrictions

    +

    +related

    +

    see fix_modify AtC unfix_flux

    +

    +default

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_unfix_nodes.html b/doc/doc2/USER/atc/man_unfix_nodes.html new file mode 100644 index 0000000000..498d549f9e --- /dev/null +++ b/doc/doc2/USER/atc/man_unfix_nodes.html @@ -0,0 +1,53 @@ + + + + +ATC: fix_modify AtC unfix + + + + + + +
    + + +

    fix_modify AtC unfix

    +syntax

    +

    fix_modify AtC unfix <field> <nodeset>

    + +

    +examples

    +

    fix_modify AtC unfix temperature groupNAME

    +

    +description

    +

    Removes constraint on field values for specified nodes.

    +

    +restrictions

    +

    keyword 'all' reserved in nodeset name

    +

    +related

    +

    see fix_modify AtC fix

    +

    +default

    +

    none

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_write_atom_weights.html b/doc/doc2/USER/atc/man_write_atom_weights.html new file mode 100644 index 0000000000..939506a28e --- /dev/null +++ b/doc/doc2/USER/atc/man_write_atom_weights.html @@ -0,0 +1,53 @@ + + + + +ATC: fix_modify AtC write_atom_weights + + + + + + +
    + + +

    fix_modify AtC write_atom_weights

    +syntax

    +

    fix_modify AtC write_atom_weights <filename> <frequency>

    + +

    +examples

    +

    fix_modify atc write_atom_weights atm_wt_file.txt 10
    +

    +

    +description

    +

    Command for writing the values of atomic weights to a specified file.

    +

    +restrictions

    +

    +related

    +

    +default

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/atc/man_write_restart.html b/doc/doc2/USER/atc/man_write_restart.html new file mode 100644 index 0000000000..6ea350d5e8 --- /dev/null +++ b/doc/doc2/USER/atc/man_write_restart.html @@ -0,0 +1,51 @@ + + + + +ATC: fix_modify AtC write_restart + + + + + + +
    + + +

    fix_modify AtC write_restart

    +syntax

    +

    fix_modify AtC write_restart [file_name]
    +

    +

    +examples

    +

    fix_modify AtC write_restart restart.mydata
    +

    +

    +description

    +

    Dumps the current state of the fields to a named text-based restart file. This done when the command is invoked and not repeated, unlike the similar lammps command.

    +

    +restrictions

    +

    The restart file only contains fields and their time derivatives. The reference positions of the atoms and the commands that initialize the fix are not saved e.g. an identical mesh containing the same atoms will have to be recreated.

    +

    +related

    +

    see read_restart fix_modify AtC read_restart

    +

    +default

    +

    none

    +
    +
    Generated on 21 Aug 2013 for ATC by  + +doxygen 1.6.1
    + + diff --git a/doc/doc2/USER/smd/SMD_user_guide.pdf b/doc/doc2/USER/smd/SMD_user_guide.pdf new file mode 100644 index 0000000000..50a5b7bb66 Binary files /dev/null and b/doc/doc2/USER/smd/SMD_user_guide.pdf differ diff --git a/doc/doc2/USER/sph/SPH_LAMMPS_userguide.pdf b/doc/doc2/USER/sph/SPH_LAMMPS_userguide.pdf new file mode 100755 index 0000000000..7ca4a72910 Binary files /dev/null and b/doc/doc2/USER/sph/SPH_LAMMPS_userguide.pdf differ diff --git a/doc/doc2/atom_style.html b/doc/doc2/atom_style.html index 6c690b135f..a8a9cc45d8 100644 --- a/doc/doc2/atom_style.html +++ b/doc/doc2/atom_style.html @@ -15,7 +15,7 @@ 

    atom_style style args
    -

    The units for these quantities depend on the unit style; see the units command for details. diff --git a/doc/doc2/set.html b/doc/doc2/set.html index e314b1f62c..1d5aa86924 100644 --- a/doc/doc2/set.html +++ b/doc/doc2/set.html @@ -23,7 +23,7 @@

  • keyword = type or type/fraction or mol or x or y or z or charge or dipole or dipole/random or quat or quat/random or diameter or shape or length or tri or theta or angmom or mass or density or volume or image or bond or angle or dihedral or improper or - meso_e or meso_cv or meso_rho or i_name or d_name + meso_e or meso_cv or meso_rho or smd_contact_radius or smd_mass_density or i_name or d_name 
      type value = atom type
     value can be an atom-style variable (see below)
@@ -83,10 +83,12 @@
     value can be an atom-style variable (see below)
   meso_rho value = density of SPH particles (need units)
     value can be an atom-style variable (see below)
-  i_name value = value for custom integer vector with name
-    value can be an atom-style variable (see below)
-  d_name value = value for custom floating-point vector with name
+  smd_contact_radius = radius for short range interactions, i.e. contact and friction
     value can be an atom-style variable (see below) 
+  smd_mass_density = set particle mass based on volume by providing a mass density
+    value can be an atom-style variable (see below)
+  i_name value = value for custom integer vector with name
+  d_name value = value for custom floating-point vector with name
    @@ -316,6 +318,20 @@ assumed to be in mass/distance^2 units). If none of these cases are valid, then the mass is set to the density value directly (the input density is assumed to be in mass units).

    +

    Keyword smd_mass_density also sets the mass of all selected +particles, but it is only applicable to the Smooth Mach Dynamics +package USER-SMD. This command assumes that the particle volume has +already been correctly set and calculates particle mass from the +provided mass density value. +

    +

    Keyword smd_contact_radius only applies to simulations with the +Smooth Mach Dynamics package USER-SMD. This command sets an +interaction radius for computing short-range interactions, +e.g. repulsive forces to prevent different individual physical bodies +from penetrating each other. Note that the SPH smoothing kernel +diameter used for computing long range, nonlocal interactions, is set +using the diameter keyword. +

    Keyword volume sets the volume of all selected particles. Currently, only the atom_style peri command defines particles with a volume attribute. Note that this command does not @@ -331,8 +347,7 @@ the simulation. The flags can be output with atom snapshots via the nx,ny,nz, then the current image value for that dimension is unchanged. For non-periodic dimensions only a value of 0 can be specified. This keyword does not allow use of atom-style variables. -

    -

    This command can be useful after a system has been equilibrated and +This command can be useful after a system has been equilibrated and atoms have diffused one or more box lengths in various directions. This command can then reset the image values for atoms so that they are effectively inside the simulation box, e.g if a diffusion diff --git a/doc/fix_gcmc.html b/doc/fix_gcmc.html index cf26a12cc8..891119487b 100644 --- a/doc/fix_gcmc.html +++ b/doc/fix_gcmc.html @@ -178,7 +178,7 @@ fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk

    This fix performs grand canonical Monte Carlo (GCMC) exchanges of atoms or molecules of the given type with an imaginary ideal gas reservoir at the specified T and chemical potential (mu) as discussed in -(Frenkel). If used with the fix nvt command, +(Frenkel). If used with the fix nvt command, simulations in the grand canonical ensemble (muVT, constant chemical potential, constant volume, and constant temperature) can be performed. Specific uses include computing isotherms in microporous @@ -249,13 +249,9 @@ coordinates are chosen at a random position within the current simulation cell or region, and new atom velocities are randomly chosen from the specified temperature distribution given by T. Relative coordinates for atoms in a molecule are taken from the template -molecule provided by the user, with the origin of the relative -coordinates coinciding with the chosen insertion point. This means -that if the origin of the template molecule coordinate system -lies far from the center of the template molecule, -the inserted molecule will lie far from the insertion point. -A random initial rotation is used in -the case of molecule insertions.

    +molecule provided by the user. The center of mass of the molecule +is placed at the insertion point. The orientation of the molecule +is chosen at random by rotating about this point.

    Individual atoms are inserted, unless the mol keyword is used. It specifies a template-ID previously defined using the molecule command, which reads a file that defines the @@ -278,11 +274,9 @@ the angle in degrees. Rotations are performed by generating a random point on the unit sphere and a random rotation angle on the range [0,maxangle). The molecule is then rotated by that angle about an axis passing through the molecule center of mass. The axis is parallel -to the unit vector defined by the point on the unit sphere. The -same procedure is used for randomly rotating molecules when they -are inserted, except that the rotation axis passes through whatever -origin is used for the molecule template, and the maximum angle is -360 degrees.

    +to the unit vector defined by the point on the unit sphere. +The same procedure is used for randomly rotating molecules when they +are inserted, except that the maximum angle is 360 degrees.

    Note that fix GCMC does not use configurational bias MC or any other kind of sampling of intramolecular degrees of freedom. Inserted molecules can have different orientations, but they will all diff --git a/doc/fix_smd.rst b/doc/fix_smd.rst new file mode 100644 index 0000000000..62d215a648 --- /dev/null +++ b/doc/fix_smd.rst @@ -0,0 +1,168 @@ +.. index:: fix smd + +fix smd command +=============== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID smd type values keyword values + +* ID, group-ID are documented in :doc:`fix ` command +* smd = style name of this fix command +* mode = *cvel* or *cfor* to select constant velocity or constant force SMD +.. parsed-literal:: + + *cvel* values = K vel + K = spring constant (force/distance units) + vel = velocity of pulling (distance/time units) + *cfor* values = force + force = pulling force (force units) + +* keyword = *tether* or *couple* +.. parsed-literal:: + + *tether* values = x y z R0 + x,y,z = point to which spring is tethered + R0 = distance of end of spring from tether point (distance units) + *couple* values = group-ID2 x y z R0 + group-ID2 = 2nd group to couple to fix group with a spring + x,y,z = direction of spring, automatically computed with 'auto' + R0 = distance of end of spring (distance units) + + + +Examples +"""""""" + +.. parsed-literal:: + + fix pull cterm smd cvel 20.0 -0.00005 tether NULL NULL 100.0 0.0 + fix pull cterm smd cvel 20.0 -0.0001 tether 25.0 25 25.0 0.0 + fix stretch cterm smd cvel 20.0 0.0001 couple nterm auto auto auto 0.0 + fix pull cterm smd cfor 5.0 tether 25.0 25.0 25.0 0.0 + +Description +""""""""""" + +This fix implements several options of steered MD (SMD) as reviewed in +:ref:`(Izrailev) `, which allows to induce conformational changes +in systems and to compute the potential of mean force (PMF) along the +assumed reaction coordinate :ref:`(Park) ` based on Jarzynski's +equality :ref:`(Jarzynski) `. This fix borrows a lot from :doc:`fix spring ` and :doc:`fix setforce `. + +You can apply a moving spring force to a group of atoms (*tether* +style) or between two groups of atoms (*couple* style). The spring +can then be used in either constant velocity (*cvel*) mode or in +constant force (*cfor*) mode to induce transitions in your systems. +When running in *tether* style, you may need some way to fix some +other part of the system (e.g. via :doc:`fix spring/self `) + +The *tether* style attaches a spring between a point at a distance of +R0 away from a fixed point *x,y,z* and the center of mass of the fix +group of atoms. A restoring force of magnitude K (R - R0) Mi / M is +applied to each atom in the group where *K* is the spring constant, Mi +is the mass of the atom, and M is the total mass of all atoms in the +group. Note that *K* thus represents the total force on the group of +atoms, not a per-atom force. + +In *cvel* mode the distance R is incremented or decremented +monotonously according to the pulling (or pushing) velocity. +In *cfor* mode a constant force is added and the actual distance +in direction of the spring is recorded. + +The *couple* style links two groups of atoms together. The first +group is the fix group; the second is specified by group-ID2. The +groups are coupled together by a spring that is at equilibrium when +the two groups are displaced by a vector in direction *x,y,z* with +respect to each other and at a distance R0 from that displacement. +Note that *x,y,z* only provides a direction and will be internally +normalized. But since it represents the *absolute* displacement of +group-ID2 relative to the fix group, (1,1,0) is a different spring +than (-1,-1,0). For each vector component, the displacement can be +described with the *auto* parameter. In this case the direction is +recomputed in every step, which can be useful for steering a local +process where the whole object undergoes some other change. When the +relative positions and distance between the two groups are not in +equilibrium, the same spring force described above is applied to atoms +in each of the two groups. + +For both the *tether* and *couple* styles, any of the x,y,z values can +be specified as NULL which means do not include that dimension in the +distance calculation or force application. + +For constant velocity pulling (*cvel* mode), the running integral +over the pulling force in direction of the spring is recorded and +can then later be used to compute the potential of mean force (PMF) +by averaging over multiple independent trajectories along the same +pulling path. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +The fix stores the direction of the spring, current pulling target +distance and the running PMF to :doc:`binary restart files `. +See the :doc:`read_restart ` command for info on how to +re-specify a fix in an input script that reads a restart file, so that +the operation of the fix continues in an uninterrupted fashion. + +None of the :doc:`fix_modify ` options are relevant to this +fix. + +This fix computes a vector list of 7 quantities, which can be accessed +by various :ref:`output commands `. The +quantities in the vector are in this order: the x-, y-, and +z-component of the pulling force, the total force in direction of the +pull, the equilibrium distance of the spring, the distance between the +two reference points, and finally the accumulated PMF (the sum of +pulling forces times displacement). + +The force is the total force on the group of atoms by the spring. In +the case of the *couple* style, it is the force on the fix group +(group-ID) or the negative of the force on the 2nd group (group-ID2). +The vector values calculated by this fix are "extensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`fix drag `, :doc:`fix spring `, +:doc:`fix spring/self `, +:doc:`fix spring/rg ` + +**Default:** none + + +---------- + + +.. _Israilev: + + + +**(Izrailev)** Izrailev, Stepaniants, Isralewitz, Kosztin, Lu, Molnar, +Wriggers, Schulten. Computational Molecular Dynamics: Challenges, +Methods, Ideas, volume 4 of Lecture Notes in Computational Science and +Engineering, pp. 39-65. Springer-Verlag, Berlin, 1998. + +**(Park)** +Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004) + +**(Jarzynski)** +Jarzynski, Phys. Rev. Lett. 78, 2690 (1997) + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/fix_smd_adjust_dt.html b/doc/fix_smd_adjust_dt.html new file mode 100644 index 0000000000..c3eeb9930d --- /dev/null +++ b/doc/fix_smd_adjust_dt.html @@ -0,0 +1,240 @@ + + + + + + + + + + + fix smd/adjust_dt command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

    + + + + +
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    +

    fix smd/adjust_dt command

    +
    +

    Syntax

    +
    fix ID group-ID smd/adjust_dt arg
+
    +
    +
      +
    • ID, group-ID are documented in fix command
      • +
    • smd/adjust_dt = style name of this fix command
      • +
    • arg = s_fact
      • +
    +
    +s_fact = safety factor
+
    +
    +
    +

    Examples

    +
    fix 1 all smd/adjust_dt 0.1
+
    +
    +
    +
    +

    Description

    +

    The fix calculates a new stable time increment for use with the SMD time integrators.

    +

    The stable time increment is based on multiple conditions. For the SPH pair styles, a +CFL criterion (Courant, Friedrichs & Lewy, 1928) is evaluated, which determines the the speed of +sound cannot propagate further than a typical spacing between particles within a single time step to ensure +no information is lost. For the contact pair styles, a linear analysis of the pair potential determines a +stable maximum time step.

    +

    This fix inquires the minimum stable time increment across all particles contained in the group for which this +fix is defined. An additional safety factor s_fact is applied to the time increment.

    +

    See this PDF guide to use Smooth Mach Dynamics in LAMMPS.

    +
    +
    +

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Currently, no part of USER-SMD supports restarting nor minimization.

    +
    +
    +

    Restrictions

    +

    This fix is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS +section for more info.

    +
    + +
    + + +
    +
    + + +
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    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/fix_smd_adjust_dt.txt b/doc/fix_smd_adjust_dt.txt new file mode 100644 index 0000000000..1d967e6147 --- /dev/null +++ b/doc/fix_smd_adjust_dt.txt @@ -0,0 +1,55 @@ +"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 + +fix smd/adjust_dt command :h3 + +[Syntax:] + +fix ID group-ID smd/adjust_dt arg :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +smd/adjust_dt = style name of this fix command :l +arg = {s_fact} :l + {s_fact} = safety factor :pre + +:ule + +[Examples:] + +fix 1 all smd/adjust_dt 0.1 :pre + +[Description:] + +The fix calculates a new stable time increment for use with the SMD time integrators. + +The stable time increment is based on multiple conditions. For the SPH pair styles, a +CFL criterion (Courant, Friedrichs & Lewy, 1928) is evaluated, which determines the the speed of +sound cannot propagate further than a typical spacing between particles within a single time step to ensure +no information is lost. For the contact pair styles, a linear analysis of the pair potential determines a +stable maximum time step. + +This fix inquires the minimum stable time increment across all particles contained in the group for which this +fix is defined. An additional safety factor {s_fact} is applied to the time increment. + +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS. + +[Restart, fix_modify, output, run start/stop, minimize info:] + +Currently, no part of USER-SMD supports restarting nor minimization. + +[Restrictions:] + +This fix is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info. + +[Related commands:] + +"smd/tlsph_dt"_compute_smd_tlsph_dt.html + +[Default:] none diff --git a/doc/fix_smd_integrate_tlsph.html b/doc/fix_smd_integrate_tlsph.html new file mode 100644 index 0000000000..3a794ace3c --- /dev/null +++ b/doc/fix_smd_integrate_tlsph.html @@ -0,0 +1,238 @@ + + + + + + + + + + + fix smd/integrate_tlsph command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    fix smd/integrate_tlsph command

    +
    +

    Syntax

    +
    fix ID group-ID smd/integrate_tlsph keyword values
+
    +
    +
      +
    • ID, group-ID are documented in fix command
      • +
    • smd/integrate_tlsph = style name of this fix command
      • +
    • zero or more keyword/value pairs may be appended
      • +
    • keyword = limit_velocity
      • +
    +
    +limit_velocity value = max_vel
+  max_vel = maximum allowed velocity
+
    +
    +
    +

    Examples

    +
    fix 1 all smd/integrate_tlsph
+fix 1 all smd/integrate_tlsph limit_velocity 1000
+
    +
    +
    +
    +

    Description

    +

    The fix performs explicit time integration for particles which interact according with the Total-Lagrangian SPH pair style.

    +

    See this PDF guide to using Smooth Mach Dynamics in LAMMPS.

    +

    The limit_velocity keyword will control the velocity, scaling the norm of +the velocity vector to max_vel in case it exceeds this velocity limit.

    +
    +
    +

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.

    +
    +
    +

    Restrictions

    +

    This fix is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS +section for more info.

    +
    + +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/fix_smd_integrate_tlsph.txt b/doc/fix_smd_integrate_tlsph.txt new file mode 100644 index 0000000000..091836c658 --- /dev/null +++ b/doc/fix_smd_integrate_tlsph.txt @@ -0,0 +1,54 @@ +"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 + +fix smd/integrate_tlsph command :h3 + +[Syntax:] + +fix ID group-ID smd/integrate_tlsph keyword values :pre + +ID, group-ID are documented in "fix"_fix.html command +smd/integrate_tlsph = style name of this fix command +zero or more keyword/value pairs may be appended :ul + +keyword = {limit_velocity} :l + + {limit_velocity} value = max_vel + max_vel = maximum allowed velocity :pre + +:ule + +[Examples:] + +fix 1 all smd/integrate_tlsph +fix 1 all smd/integrate_tlsph limit_velocity 1000 :pre + +[Description:] + +The fix performs explicit time integration for particles which interact according with the Total-Lagrangian SPH pair style. + +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS. + +The {limit_velocity} keyword will control the velocity, scaling the norm of +the velocity vector to max_vel in case it exceeds this velocity limit. + +[Restart, fix_modify, output, run start/stop, minimize info:] + +Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs. + +[Restrictions:] + +This fix is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info. + +[Related commands:] + +"smd/integrate_ulsph"_fix_smd_integrate_ulsph.html + +[Default:] none diff --git a/doc/fix_smd_integrate_ulsph.html b/doc/fix_smd_integrate_ulsph.html new file mode 100644 index 0000000000..a804d22467 --- /dev/null +++ b/doc/fix_smd_integrate_ulsph.html @@ -0,0 +1,246 @@ + + + + + + + + + + + fix smd/integrate_ulsph command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    fix smd/integrate_ulsph command

    +
    +

    Syntax

    +
    fix ID group-ID smd/integrate_ulsph keyword
+
    +
    +
      +
    • ID, group-ID are documented in fix command
      • +
    • smd/integrate_ulsph = style name of this fix command
      • +
    • zero or more keyword/value pairs may be appended
      • +
    +

    keyword = adjust_radius or limit_velocity

    +
    +
    adjust_radius values = adjust_radius_factor min_nn max_nn
    +
    adjust_radius_factor = factor which scale the smooth/kernel radius +min_nn = minimum number of neighbors +max_nn = maximum number of neighbors
    +
    limit_velocity values = max_velocity
    +
    max_velocity = maximum allowed velocity.
    +
    +
    +
    +

    Examples

    +
    fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50
+
    +
    +
    fix 1 all smd/integrate_ulsph limit_velocity 1000
+
    +
    +
    +
    +

    Description

    +

    The fix performs explicit time integration for particles which interact with the updated Lagrangian SPH pair style. +See this PDF guide to using Smooth Mach Dynamics in LAMMPS.

    +

    The adjust_radius keyword activates dynamic adjustment of the per-particle SPH smoothing kernel radius such that the number of neighbors per particles remains +within the interval min_nn to max_nn. The parameter adjust_radius_factor determines the amount of adjustment per timestep. Typical values are +*adjust_radius_factor*=1.02, *min_nn*=15, and *max_nn*=20.

    +

    The limit_velocity keyword will control the velocity, scaling the norm of +the velocity vector to max_vel in case it exceeds this velocity limit.

    +
    +
    +

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.

    +
    +
    +

    Restrictions

    +

    This fix is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS +section for more info.

    +
    + +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/fix_smd_integrate_ulsph.txt b/doc/fix_smd_integrate_ulsph.txt new file mode 100644 index 0000000000..c9667465d8 --- /dev/null +++ b/doc/fix_smd_integrate_ulsph.txt @@ -0,0 +1,60 @@ +"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 + +fix smd/integrate_ulsph command :h3 + +[Syntax:] + +fix ID group-ID smd/integrate_ulsph keyword :pre + +ID, group-ID are documented in "fix"_fix.html command +smd/integrate_ulsph = style name of this fix command +zero or more keyword/value pairs may be appended :ul + +keyword = adjust_radius or limit_velocity + +adjust_radius values = adjust_radius_factor min_nn max_nn + adjust_radius_factor = factor which scale the smooth/kernel radius + min_nn = minimum number of neighbors + max_nn = maximum number of neighbors +limit_velocity values = max_velocity + max_velocity = maximum allowed velocity. + + +[Examples:] + +fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50 :pre +fix 1 all smd/integrate_ulsph limit_velocity 1000 :pre + +[Description:] + +The fix performs explicit time integration for particles which interact with the updated Lagrangian SPH pair style. +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS. + +The {adjust_radius} keyword activates dynamic adjustment of the per-particle SPH smoothing kernel radius such that the number of neighbors per particles remains +within the interval {min_nn} to {max_nn}. The parameter {adjust_radius_factor} determines the amount of adjustment per timestep. Typical values are +{adjust_radius_factor}=1.02, {min_nn}=15, and {max_nn}=20. + +The {limit_velocity} keyword will control the velocity, scaling the norm of +the velocity vector to max_vel in case it exceeds this velocity limit. + +[Restart, fix_modify, output, run start/stop, minimize info:] + +Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs. + +[Restrictions:] + +This fix is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info. + +[Related commands:] + + + +[Default:] none diff --git a/doc/fix_smd_move_triangulated_surface.html b/doc/fix_smd_move_triangulated_surface.html new file mode 100644 index 0000000000..78315cb519 --- /dev/null +++ b/doc/fix_smd_move_triangulated_surface.html @@ -0,0 +1,257 @@ + + + + + + + + + + + fix smd/move_tri_surf command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
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    + +
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    +

    fix smd/move_tri_surf command

    +
    +

    Syntax

    +
    fix ID group-ID smd/move_tri_surf keyword
+
    +
    +
      +
    • ID, group-ID are documented in fix command
      • +
    • smd/move_tri_surf keyword = style name of this fix command
      • +
    • keyword = **LINEAR* or **WIGGLE* or **ROTATE*
      • +
    +
    **LINEAR* args = Vx Vy Vz
+   Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL
+**WIGGLE* args = Vx Vy Vz max_travel
+   vx,vy,vz = components of velocity vector (velocity units), any component can be specified as NULL
+   max_travel = wiggle amplitude
+**ROTATE* args = Px Py Pz Rx Ry Rz period
+   Px,Py,Pz = origin point of axis of rotation (distance units)
+   Rx,Ry,Rz = axis of rotation vector
+   period = period of rotation (time units)
+
    +
    +
    +
    +

    Examples

    +
    fix 1 tool smd/move_tri_surf *LINEAR 20 20 10
+fix 2 tool smd/move_tri_surf *WIGGLE 20 20 10
+fix 2 tool smd/move_tri_surf *ROTATE 0 0 0 5 2 1
+
    +
    +
    +
    +

    Description

    +

    This fix applies only to rigid surfaces read from .STL files via fix smd/wall_surface . +It updates position and velocity for the particles in the group each timestep without regard to forces on the particles. +The rigid surfaces can thus be moved along simple trajectories during the simulation.

    +

    The **LINEAR* style moves particles with the specified constant velocity +vector V = (Vx,Vy,Vz). This style also sets the velocity of each particle +to V = (Vx,Vy,Vz).

    +

    The **WIGGLE* style moves particles in an oscillatory fashion. +Particles are moved along (vx, vy, vz) with constant velocity until a +displacement of max_travel is reached. Then, the velocity vector is +reversed. This process is repeated.

    +

    The **ROTATE* style rotates particles around a rotation axis R = (Rx,Ry,Rz) that +goes through a point P = (Px,Py,Pz). The period of the rotation is also +specified. This style also sets the velocity of each particle to (omega cross +Rperp) where omega is its angular velocity around the rotation axis and +Rperp is a perpendicular vector from the rotation axis to the particle.

    +

    See this PDF guide to using Smooth Mach Dynamics in LAMMPS.

    +
    +
    +

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.

    +
    +
    +

    Restrictions

    +

    This fix is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS +section for more info.

    +
    + +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/fix_smd_move_triangulated_surface.txt b/doc/fix_smd_move_triangulated_surface.txt new file mode 100644 index 0000000000..6a4306de29 --- /dev/null +++ b/doc/fix_smd_move_triangulated_surface.txt @@ -0,0 +1,75 @@ +"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 + +fix smd/move_tri_surf command :h3 + +[Syntax:] + +fix ID group-ID smd/move_tri_surf keyword :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +smd/move_tri_surf keyword = style name of this fix command :l +keyword = {*LINEAR} or {*WIGGLE} or {*ROTATE} :l + + {*LINEAR} args = Vx Vy Vz + Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL + {*WIGGLE} args = Vx Vy Vz max_travel + vx,vy,vz = components of velocity vector (velocity units), any component can be specified as NULL + max_travel = wiggle amplitude + {*ROTATE} args = Px Py Pz Rx Ry Rz period + Px,Py,Pz = origin point of axis of rotation (distance units) + Rx,Ry,Rz = axis of rotation vector + period = period of rotation (time units) :pre + +:ule + +[Examples:] + +fix 1 tool smd/move_tri_surf *LINEAR 20 20 10 +fix 2 tool smd/move_tri_surf *WIGGLE 20 20 10 +fix 2 tool smd/move_tri_surf *ROTATE 0 0 0 5 2 1 :pre + +[Description:] + +This fix applies only to rigid surfaces read from .STL files via fix "smd/wall_surface"_fix_smd_wall_surface.html . +It updates position and velocity for the particles in the group each timestep without regard to forces on the particles. +The rigid surfaces can thus be moved along simple trajectories during the simulation. + +The {*LINEAR} style moves particles with the specified constant velocity +vector V = (Vx,Vy,Vz). This style also sets the velocity of each particle +to V = (Vx,Vy,Vz). + +The {*WIGGLE} style moves particles in an oscillatory fashion. +Particles are moved along (vx, vy, vz) with constant velocity until a +displacement of max_travel is reached. Then, the velocity vector is +reversed. This process is repeated. + +The {*ROTATE} style rotates particles around a rotation axis R = (Rx,Ry,Rz) that +goes through a point P = (Px,Py,Pz). The period of the rotation is also +specified. This style also sets the velocity of each particle to (omega cross +Rperp) where omega is its angular velocity around the rotation axis and +Rperp is a perpendicular vector from the rotation axis to the particle. + +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS. + +[Restart, fix_modify, output, run start/stop, minimize info:] + +Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs. + +[Restrictions:] + +This fix is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info. + + +[Related commands:] + +"smd/triangle_mesh_vertices"_compute_smd_triangle_mesh_vertices.html, "smd/wall_surface"_fix_smd_wall_surface.html + +[Default:] none diff --git a/doc/fix_smd_setvel.html b/doc/fix_smd_setvel.html new file mode 100644 index 0000000000..f4e8f5759c --- /dev/null +++ b/doc/fix_smd_setvel.html @@ -0,0 +1,263 @@ + + + + + + + + + + + fix smd/setvel command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    fix smd/setvel command

    +
    +

    Syntax

    +
    fix ID group-ID smd/setvel vx vy vz keyword value ...
+
    +
    +
      +
    • ID, group-ID are documented in fix command
      • +
    • smd/setvel = style name of this fix command
      • +
    • vx,vy,vz = velocity component values
      • +
    • any of vx,vy,vz can be a variable (see below)
      • +
    • zero or more keyword/value pairs may be appended to args
      • +
    • keyword = region
      • +
    +
    +region value = region-ID
+  region-ID = ID of region particles must be in to have their velocities set
+
    +
    +
    +

    Examples

    +
    fix top_velocity top_group setvel 1.0 0.0 0.0
+
    +
    +
    +
    +

    Description

    +

    Set each component of velocity on each particle in the group to the specified +values vx,vy,vz, regardless of the forces acting on the particle. This command can +be used to impose velocity boundary conditions.

    +

    Any of the vx,vy,vz values can be specified as NULL which means do not +alter the velocity component in that dimension.

    +

    This fix is indented to be used together with a time integration fix.

    +

    Any of the 3 quantities defining the velocity components can be specified +as an equal-style or atom-style variable, namely vx, +vy, vz. If the value is a variable, it should be specified as +v_name, where name is the variable name. In this case, the variable +will be evaluated each timestep, and its value used to determine the +force component.

    +

    Equal-style variables can specify formulas with various mathematical +functions, and include thermo_style command +keywords for the simulation box parameters and timestep and elapsed +time. Thus it is easy to specify a time-dependent velocity field.

    +

    Atom-style variables can specify the same formulas as equal-style +variables but can also include per-atom values, such as atom +coordinates. Thus it is easy to specify a spatially-dependent velocity +field with optional time-dependence as well.

    +

    If the region keyword is used, the particle must also be in the +specified geometric region in order to have its velocity set by this command.

    +
    +
    +
    +

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Currently, no part of USER-SMD supports restarting nor minimization +None of the fix_modify options +are relevant to this fix.

    +

    This fix computes a global 3-vector of forces, which can be accessed +by various output commands. This is the +total force on the group of atoms. The vector values calculated by this +fix are “extensive”.

    +

    No parameter of this fix can be used with the start/stop keywords of +the run command.

    +
    +
    +

    Restrictions

    +

    This fix is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS +section for more info.

    +

    Related commands: none

    +

    Default: none

    +
    +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/fix_smd_setvel.txt b/doc/fix_smd_setvel.txt new file mode 100644 index 0000000000..6d96e79723 --- /dev/null +++ b/doc/fix_smd_setvel.txt @@ -0,0 +1,84 @@ +"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 + +fix smd/setvel command :h3 + +[Syntax:] + +fix ID group-ID smd/setvel vx vy vz keyword value ... :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +smd/setvel = style name of this fix command :l +vx,vy,vz = velocity component values :l +any of vx,vy,vz can be a variable (see below) :l +zero or more keyword/value pairs may be appended to args :l +keyword = {region} :l + {region} value = region-ID + region-ID = ID of region particles must be in to have their velocities set :pre +:ule + +[Examples:] + +fix top_velocity top_group setvel 1.0 0.0 0.0 :pre + +[Description:] + +Set each component of velocity on each particle in the group to the specified +values vx,vy,vz, regardless of the forces acting on the particle. This command can +be used to impose velocity boundary conditions. + +Any of the vx,vy,vz values can be specified as NULL which means do not +alter the velocity component in that dimension. + +This fix is indented to be used together with a time integration fix. + +Any of the 3 quantities defining the velocity components can be specified +as an equal-style or atom-style "variable"_variable.html, namely {vx}, +{vy}, {vz}. If the value is a variable, it should be specified as +v_name, where name is the variable name. In this case, the variable +will be evaluated each timestep, and its value used to determine the +force component. + +Equal-style variables can specify formulas with various mathematical +functions, and include "thermo_style"_thermo_style.html command +keywords for the simulation box parameters and timestep and elapsed +time. Thus it is easy to specify a time-dependent velocity field. + +Atom-style variables can specify the same formulas as equal-style +variables but can also include per-atom values, such as atom +coordinates. Thus it is easy to specify a spatially-dependent velocity +field with optional time-dependence as well. + +If the {region} keyword is used, the particle must also be in the +specified geometric "region"_region.html in order to have its velocity set by this command. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +Currently, no part of USER-SMD supports restarting nor minimization +None of the "fix_modify"_fix_modify.html options +are relevant to this fix. + +This fix computes a global 3-vector of forces, which can be accessed +by various "output commands"_Section_howto.html#howto_15. This is the +total force on the group of atoms. The vector values calculated by this +fix are "extensive". + +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. + +[Restrictions:] + +This fix is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info. + +[Related commands:] none + +[Default:] none diff --git a/doc/fix_smd_tlsph_reference_configuration.html b/doc/fix_smd_tlsph_reference_configuration.html new file mode 100644 index 0000000000..b4af1d92e0 --- /dev/null +++ b/doc/fix_smd_tlsph_reference_configuration.html @@ -0,0 +1,190 @@ + + + + + + + + + + + <no title> — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/log.lammps b/doc/fix_smd_tlsph_reference_configuration.txt similarity index 100% rename from tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/log.lammps rename to doc/fix_smd_tlsph_reference_configuration.txt diff --git a/doc/fix_smd_wall_surface.html b/doc/fix_smd_wall_surface.html new file mode 100644 index 0000000000..67166e4765 --- /dev/null +++ b/doc/fix_smd_wall_surface.html @@ -0,0 +1,244 @@ + + + + + + + + + + + fix smd/wall_surface command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    fix smd/wall_surface command

    +
    +

    Syntax

    +
    fix ID group-ID smd/wall_surface arg type mol-ID
+
    +
    +
      +
    • ID, group-ID are documented in fix command
      • +
    • smd/wall_surface = style name of this fix command
      • +
    • arg = file
      • +
    +
    +file = file name of a triangular mesh in stl format
+
    +
      +
    • type = particle type to be given to the new particles created by this fix
      • +
    • mol-ID = molecule-ID to be given to the new particles created by this fix (must be >= 65535)
      • +
    +
    +
    +

    Examples

    +
    fix stl_surf all smd/wall_surface tool.stl 2 65535
+
    +
    +
    +
    +

    Description

    +

    This fix creates reads a traingulated surface from a file in .STL format. +For each triangle, a new particle is created which stores the barycenter of the triangle and the vertex positions. +The radius of the new particle is that of the minimum circle which encompasses the triangle vertices.

    +

    The triangulated surface can be used as a complex rigid wall via the smd/tri_surface pair style. +It is possible to move the triangulated surface via the smd/move_tri_surf fix style.

    +

    Immediately after a .STL file has been read, the simulation needs to be run for 0 timesteps in order to properly register the new particles +in the system. See the “funnel_flow” example in the USER-SMD examples directory.

    +

    See this PDF guide to use Smooth Mach Dynamics in LAMMPS.

    +
    +
    +

    Restart, fix_modify, output, run start/stop, minimize info

    +

    Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.

    +
    +
    +

    Restrictions

    +

    This fix is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS +section for more info. The molecule ID given to the particles created by this fix have to be equal to or larger than 65535.

    +

    Within each .STL file, only a single triangulated object must be present, even though the STL format allows for the possibility of multiple objects in one file.

    +
    + +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/fix_smd_wall_surface.txt b/doc/fix_smd_wall_surface.txt new file mode 100644 index 0000000000..cc0f4340af --- /dev/null +++ b/doc/fix_smd_wall_surface.txt @@ -0,0 +1,58 @@ +"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 + +fix smd/wall_surface command :h3 + +[Syntax:] + +fix ID group-ID smd/wall_surface arg type mol-ID :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +smd/wall_surface = style name of this fix command :l +arg = {file} :l + {file} = file name of a triangular mesh in stl format :pre +type = particle type to be given to the new particles created by this fix :l +mol-ID = molecule-ID to be given to the new particles created by this fix (must be >= 65535) :l + +:ule + +[Examples:] + +fix stl_surf all smd/wall_surface tool.stl 2 65535 :pre + +[Description:] + +This fix creates reads a traingulated surface from a file in .STL format. +For each triangle, a new particle is created which stores the barycenter of the triangle and the vertex positions. +The radius of the new particle is that of the minimum circle which encompasses the triangle vertices. + +The triangulated surface can be used as a complex rigid wall via the "smd/tri_surface"_pair_smd_triangulated_surface.html pair style. +It is possible to move the triangulated surface via the "smd/move_tri_surf"_fix_smd_move_triangulated_surface.html fix style. + +Immediately after a .STL file has been read, the simulation needs to be run for 0 timesteps in order to properly register the new particles +in the system. See the "funnel_flow" example in the USER-SMD examples directory. + +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS. + +[Restart, fix_modify, output, run start/stop, minimize info:] + +Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs. + +[Restrictions:] + +This fix is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info. The molecule ID given to the particles created by this fix have to be equal to or larger than 65535. + +Within each .STL file, only a single triangulated object must be present, even though the STL format allows for the possibility of multiple objects in one file. + +[Related commands:] + +"smd/triangle_mesh_vertices"_compute_smd_triangle_mesh_vertices.html, "smd/move_tri_surf"_fix_smd_move_triangulated_surface.html, "smd/tri_surface"_pair_smd_triangulated_surface.html + +[Default:] none diff --git a/doc/genindex.html b/doc/genindex.html index b2d51fcaf5..2592e637a5 100644 --- a/doc/genindex.html +++ b/doc/genindex.html @@ -499,8 +499,6 @@
    compute msd
    - -
    compute msd/chunk
    @@ -541,6 +539,8 @@
    compute property/atom
    +
    +
    compute property/chunk
    @@ -566,6 +566,82 @@ +
    compute smd/contact_radius +
    + + +
    compute smd/damage +
    + + +
    compute smd/hourglass_error +
    + + +
    compute smd/internal_energy +
    + + +
    compute smd/plastic_strain +
    + + +
    compute smd/plastic_strain_rate +
    + + +
    compute smd/rho +
    + + +
    compute smd/tlsph_defgrad +
    + + +
    compute smd/tlsph_dt +
    + + +
    compute smd/tlsph_num_neighs +
    + + +
    compute smd/tlsph_shape +
    + + +
    compute smd/tlsph_strain +
    + + +
    compute smd/tlsph_strain_rate +
    + + +
    compute smd/tlsph_stress +
    + + +
    compute smd/ulsph_num_neighs +
    + + +
    compute smd/ulsph_strain +
    + + +
    compute smd/ulsph_strain_rate +
    + + +
    compute smd/ulsph_stress +
    + + +
    compute smd/vol +
    + +
    compute sna/atom
    @@ -1053,8 +1129,6 @@
    fix nve/asphere/noforce
    -
    -
    fix nve/body
    @@ -1067,6 +1141,8 @@
    fix nve/limit
    +
    +
    fix nve/line
    @@ -1204,6 +1280,30 @@ +
    fix smd/adjust_dt +
    + + +
    fix smd/integrate_tlsph +
    + + +
    fix smd/integrate_ulsph +
    + + +
    fix smd/move_tri_surf +
    + + +
    fix smd/setvel +
    + + +
    fix smd/wall_surface +
    + +
    fix spring
    @@ -1675,8 +1775,6 @@
    pair_style lj/sdk
    -
    -
    pair_style lj/sf
    @@ -1685,6 +1783,8 @@
    pair_style lj/smooth
    +
    +
    pair_style lj/smooth/linear
    @@ -1750,6 +1850,22 @@ +
    pair_style smd/hertz +
    + + +
    pair_style smd/tlsph +
    + + +
    pair_style smd/tri_surface +
    + + +
    pair_style smd/ulsph +
    + +
    pair_style snap
    diff --git a/doc/pair_smd_hertz.html b/doc/pair_smd_hertz.html new file mode 100644 index 0000000000..481a032699 --- /dev/null +++ b/doc/pair_smd_hertz.html @@ -0,0 +1,233 @@ + + + + + + + + + + + pair_style smd/hertz command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    pair_style smd/hertz command

    +
    +

    Syntax

    +
    pair_style smd/hertz scale_factor
+
    +
    +
    +
    +

    Examples

    +

    pair_style smd/hertz 1.0 +pair_coeff 1 1 <contact_stiffness>

    +
    +
    +

    Description

    +

    The smd/hertz style calculates contact forces between SPH particles belonging to different physical bodies.

    +

    The contact forces are calculated using a Hertz potential, which evaluates the overlap between two particles +(whose spatial extents are defined via its contact radius). +The effect is that a particles cannot penetrate into each other. +The parameter <contact_stiffness> has units of pressure and should equal roughly one half +of the Young’s modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particles.

    +

    The parameter scale_factor can be used to scale the particles’ contact radii. This can be useful to control how close +particles can approach each other. Usually, *scale_factor*=1.0.

    +
    +

    Mixing, shift, table, tail correction, restart, rRESPA info:

    +

    No mixing is performed automatically. +Currently, no part of USER-SMD supports restarting nor minimization. +rRESPA does not apply to this pair style.

    +
    +
    +
    +

    Restrictions

    +

    This fix is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS +section for more info.

    +
    + +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/pair_smd_hertz.txt b/doc/pair_smd_hertz.txt new file mode 100644 index 0000000000..5d6784bb12 --- /dev/null +++ b/doc/pair_smd_hertz.txt @@ -0,0 +1,56 @@ +"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 + +pair_style smd/hertz command :h3 + +[Syntax:] + +pair_style smd/hertz scale_factor :pre + +[Examples:] + +pair_style smd/hertz 1.0 +pair_coeff 1 1 + +[Description:] + +The {smd/hertz} style calculates contact forces between SPH particles belonging to different physical bodies. + +The contact forces are calculated using a Hertz potential, which evaluates the overlap between two particles +(whose spatial extents are defined via its contact radius). +The effect is that a particles cannot penetrate into each other. +The parameter has units of pressure and should equal roughly one half +of the Young's modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particles. + +The parameter {scale_factor} can be used to scale the particles' contact radii. This can be useful to control how close +particles can approach each other. Usually, {scale_factor}=1.0. + +:line + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +No mixing is performed automatically. +Currently, no part of USER-SMD supports restarting nor minimization. +rRESPA does not apply to this pair style. + +:line + +[Restrictions:] + +This fix is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info. + +[Related commands:] + +"pair_coeff"_pair_coeff.html + +[Default:] none + +:line + diff --git a/doc/pair_smd_tlsph.html b/doc/pair_smd_tlsph.html new file mode 100644 index 0000000000..7a32ec3900 --- /dev/null +++ b/doc/pair_smd_tlsph.html @@ -0,0 +1,243 @@ + + + + + + + + + + + pair_style smd/tlsph command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    pair_style smd/tlsph command

    +
    +

    Syntax

    +
    pair_style smd/tlsph args
+
    +
    +
    +
    +

    Examples

    +

    pair_style smd/tlsph

    +
    +
    +

    Description

    +

    The smd/tlsph style computes particle interactions according to continuum mechanics constitutive laws and a Total-Lagrangian Smooth-Particle Hydrodynamics algorithm.

    +

    This pair style is invoked with the following command:

    +
    pair_style smd/tlsph
+pair_coeff i j *COMMON rho0 E nu Q1 Q2 hg Cp &
+               *END
+
    +
    +

    Here, i and j denote the LAMMPS particle types for which this pair style is +defined. Note that i and j must be equal, i.e., no tlsph cross interactions +between different particle types are allowed. +In contrast to the usual LAMMPS pair coeff definitions, which are given solely a +number of floats and integers, the tlsph pair coeff definition is organised using +keywords. These keywords mark the beginning of different sets of parameters for particle properties, +material constitutive models, and damage models. The pair coeff line must be terminated with +the **END* keyword. The use the line continuation operator & is recommended. A typical +invocation of the tlsph for a solid body would consist of an equation of state for computing +the pressure (the diagonal components of the stress tensor), and a material model to compute shear +stresses (the off-diagonal components of the stress tensor). Damage and failure models can also be added.

    +

    Please see the SMD user guide for a complete listing of the possible keywords and material models.

    +
    +

    Mixing, shift, table, tail correction, restart, rRESPA info:

    +

    No mixing is performed automatically. +Currently, no part of USER-SMD supports restarting nor minimization. +rRESPA does not apply to this pair style.

    +
    +
    +
    +

    Restrictions

    +

    This fix is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS +section for more info.

    +
    + +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/pair_smd_tlsph.txt b/doc/pair_smd_tlsph.txt new file mode 100644 index 0000000000..a81d2e25c1 --- /dev/null +++ b/doc/pair_smd_tlsph.txt @@ -0,0 +1,67 @@ +"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 + +pair_style smd/tlsph command :h3 + +[Syntax:] + +pair_style smd/tlsph args :pre + +[Examples:] + +pair_style smd/tlsph + + +[Description:] + +The {smd/tlsph} style computes particle interactions according to continuum mechanics constitutive laws and a Total-Lagrangian Smooth-Particle Hydrodynamics algorithm. + +This pair style is invoked with the following command: + +pair_style smd/tlsph +pair_coeff i j *COMMON rho0 E nu Q1 Q2 hg Cp & + *END :pre + +Here, {i} and {j} denote the {LAMMPS} particle types for which this pair style is +defined. Note that {i} and {j} must be equal, i.e., no {tlsph} cross interactions +between different particle types are allowed. +In contrast to the usual {LAMMPS} {pair coeff} definitions, which are given solely a +number of floats and integers, the {tlsph} {pair coeff} definition is organised using +keywords. These keywords mark the beginning of different sets of parameters for particle properties, +material constitutive models, and damage models. The {pair coeff} line must be terminated with +the {*END} keyword. The use the line continuation operator {&} is recommended. A typical +invocation of the {tlsph} for a solid body would consist of an equation of state for computing +the pressure (the diagonal components of the stress tensor), and a material model to compute shear +stresses (the off-diagonal components of the stress tensor). Damage and failure models can also be added. + +Please see the "SMD user guide"_USER/smd/SMD_LAMMPS_userguide.pdf for a complete listing of the possible keywords and material models. + +:line + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +No mixing is performed automatically. +Currently, no part of USER-SMD supports restarting nor minimization. +rRESPA does not apply to this pair style. + +:line + +[Restrictions:] + +This fix is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info. + +[Related commands:] + +"pair_coeff"_pair_coeff.html + +[Default:] none + +:line + diff --git a/doc/pair_smd_triangulated_surface.html b/doc/pair_smd_triangulated_surface.html new file mode 100644 index 0000000000..8ea0d5514e --- /dev/null +++ b/doc/pair_smd_triangulated_surface.html @@ -0,0 +1,234 @@ + + + + + + + + + + + pair_style smd/tri_surface command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    pair_style smd/tri_surface command

    +
    +

    Syntax

    +
    pair_style smd/tri_surface scale_factor
+
    +
    +
    +
    +

    Examples

    +

    pair_style smd/tri_surface 1.0 +pair_coeff 1 1 <contact_stiffness>

    +
    +
    +

    Description

    +

    The smd/tri_surface style calculates contact forces between SPH particles and a rigid wall boundary defined via the +smd/wall_surface fix.

    +

    The contact forces are calculated using a Hertz potential, which evaluates the overlap between a particle +(whose spatial extents are defined via its contact radius) and the triangle. +The effect is that a particle cannot penetrate into the triangular surface. +The parameter <contact_stiffness> has units of pressure and should equal roughly one half +of the Young’s modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particle

    +

    The parameter scale_factor can be used to scale the particles’ contact radii. This can be useful to control how close +particles can approach the triangulated surface. Usually, *scale_factor*=1.0.

    +
    +

    Mixing, shift, table, tail correction, restart, rRESPA info:

    +

    No mixing is performed automatically. +Currently, no part of USER-SMD supports restarting nor minimization. +rRESPA does not apply to this pair style.

    +
    +
    +
    +

    Restrictions

    +

    This fix is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS +section for more info.

    +
    + +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/pair_smd_triangulated_surface.txt b/doc/pair_smd_triangulated_surface.txt new file mode 100644 index 0000000000..bfc0e806ac --- /dev/null +++ b/doc/pair_smd_triangulated_surface.txt @@ -0,0 +1,57 @@ +"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 + +pair_style smd/tri_surface command :h3 + +[Syntax:] + +pair_style smd/tri_surface scale_factor :pre + +[Examples:] + +pair_style smd/tri_surface 1.0 +pair_coeff 1 1 + +[Description:] + +The {smd/tri_surface} style calculates contact forces between SPH particles and a rigid wall boundary defined via the +"smd/wall_surface"_fix_smd_wall_surface.html fix. + +The contact forces are calculated using a Hertz potential, which evaluates the overlap between a particle +(whose spatial extents are defined via its contact radius) and the triangle. +The effect is that a particle cannot penetrate into the triangular surface. +The parameter has units of pressure and should equal roughly one half +of the Young's modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particle + +The parameter {scale_factor} can be used to scale the particles' contact radii. This can be useful to control how close +particles can approach the triangulated surface. Usually, {scale_factor}=1.0. + +:line + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +No mixing is performed automatically. +Currently, no part of USER-SMD supports restarting nor minimization. +rRESPA does not apply to this pair style. + +:line + +[Restrictions:] + +This fix is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info. + +[Related commands:] + +"pair_coeff"_pair_coeff.html + +[Default:] none + +:line + diff --git a/doc/pair_smd_ulsph.html b/doc/pair_smd_ulsph.html new file mode 100644 index 0000000000..ab5961b393 --- /dev/null +++ b/doc/pair_smd_ulsph.html @@ -0,0 +1,248 @@ + + + + + + + + + + + pair_style smd/ulsph command — LAMMPS 15 May 2015 version documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    + +
    +
    +
    + +
    +

    pair_style smd/ulsph command

    +
    +

    Syntax

    +
    pair_style smd/ulsph args
+
    +
    +
      +
    • these keywords must be given
      • +
    +

    keyword = **DENSITY_SUMMATION* or **DENSITY_CONTINUITY* and **VELOCITY_GRADIENT* or **NO_VELOCITY_GRADIENT* and **GRADIENT_CORRECTION* or **NO_GRADIENT_CORRECTION*

    +
    +
    +

    Examples

    +

    pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION

    +
    +
    +

    Description

    +

    The smd/ulsph style computes particle interactions according to continuum mechanics constitutive laws and an updated Lagrangian Smooth-Particle Hydrodynamics algorithm.

    +

    This pair style is invoked similar to the following command:

    +
    pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION
+pair_coeff i j *COMMON rho0 c0 Q1 Cp hg &
+               *END
+
    +
    +

    Here, i and j denote the LAMMPS particle types for which this pair style is +defined. Note that i and j can be different, i.e., ulsph cross interactions +between different particle types are allowed. However, i–i respectively j–j pair_coeff lines have to preceed a cross interaction. +In contrast to the usual LAMMPS pair coeff definitions, which are given solely a +number of floats and integers, the ulsph pair coeff definition is organised using +keywords. These keywords mark the beginning of different sets of parameters for particle properties, +material constitutive models, and damage models. The pair coeff line must be terminated with +the **END* keyword. The use the line continuation operator & is recommended. A typical +invocation of the ulsph for a solid body would consist of an equation of state for computing +the pressure (the diagonal components of the stress tensor), and a material model to compute shear +stresses (the off-diagonal components of the stress tensor).

    +

    Note that the use of *GRADIENT_CORRECTION can lead to severe numerical instabilities. For a general fluid simulation, *NO_GRADIENT_CORRECTION is recommended.

    +

    Please see the SMD user guide for a complete listing of the possible keywords and material models.

    +
    +

    Mixing, shift, table, tail correction, restart, rRESPA info:

    +

    No mixing is performed automatically. +Currently, no part of USER-SMD supports restarting nor minimization. +rRESPA does not apply to this pair style.

    +
    +
    +
    +

    Restrictions

    +

    This fix is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS +section for more info.

    +
    + +
    + + +
    +
    + + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/pair_smd_ulsph.txt b/doc/pair_smd_ulsph.txt new file mode 100644 index 0000000000..d4c9fc41fa --- /dev/null +++ b/doc/pair_smd_ulsph.txt @@ -0,0 +1,71 @@ +"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 + +pair_style smd/ulsph command :h3 + +[Syntax:] + +pair_style smd/ulsph args :pre + +these keywords must be given :l +keyword = {*DENSITY_SUMMATION} or {*DENSITY_CONTINUITY} and {*VELOCITY_GRADIENT} or {*NO_VELOCITY_GRADIENT} and {*GRADIENT_CORRECTION} or {*NO_GRADIENT_CORRECTION} + +[Examples:] + +pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION + +[Description:] + +The {smd/ulsph} style computes particle interactions according to continuum mechanics constitutive laws and an updated Lagrangian Smooth-Particle Hydrodynamics algorithm. + +This pair style is invoked similar to the following command: + +pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION +pair_coeff i j *COMMON rho0 c0 Q1 Cp hg & + *END :pre + +Here, {i} and {j} denote the {LAMMPS} particle types for which this pair style is +defined. Note that {i} and {j} can be different, i.e., {ulsph} cross interactions +between different particle types are allowed. However, {i}--{i} respectively {j}--{j} pair_coeff lines have to preceed a cross interaction. +In contrast to the usual {LAMMPS} {pair coeff} definitions, which are given solely a +number of floats and integers, the {ulsph} {pair coeff} definition is organised using +keywords. These keywords mark the beginning of different sets of parameters for particle properties, +material constitutive models, and damage models. The {pair coeff} line must be terminated with +the {*END} keyword. The use the line continuation operator {&} is recommended. A typical +invocation of the {ulsph} for a solid body would consist of an equation of state for computing +the pressure (the diagonal components of the stress tensor), and a material model to compute shear +stresses (the off-diagonal components of the stress tensor). + +Note that the use of *GRADIENT_CORRECTION can lead to severe numerical instabilities. For a general fluid simulation, *NO_GRADIENT_CORRECTION is recommended. + +Please see the "SMD user guide"_USER/smd/SMD_LAMMPS_userguide.pdf for a complete listing of the possible keywords and material models. + +:line + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +No mixing is performed automatically. +Currently, no part of USER-SMD supports restarting nor minimization. +rRESPA does not apply to this pair style. + +:line + +[Restrictions:] + +This fix is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info. + +[Related commands:] + +"pair_coeff"_pair_coeff.html + +[Default:] none + +:line + diff --git a/doc/prd.html b/doc/prd.html index 07420fc597..01557ac623 100644 --- a/doc/prd.html +++ b/doc/prd.html @@ -153,8 +153,8 @@ vel values = loop dist loop = all or local or geom, used in dephasing dist = uniform or gaussian, used in dephasing -time value = step or clock - step = simulation runs for N timesteps on each replica (default) +time value = steps or clock + steps = simulation runs for N timesteps on each replica (default) clock = simulation runs for N timesteps across all replicas @@ -171,11 +171,11 @@ prd 5000 100 10 10 100 1 54982 min 0.1 0.1 100 200 replicas of a system. One or more replicas can be used. The total number of steps N to run can be interpreted in one of two ways; see discussion of the time keyword below.

    -

    PRD is described in this paper by Art Voter. It is a method +

    PRD is described in this paper by Art Voter. It is a method for performing accelerated dynamics that is suitable for infrequent-event systems that obey first-order kinetics. A good overview of accelerated dynamics methods for such systems in given in -this review paper from the same group. To quote from the +this review paper from the same group. To quote from the paper: “The dynamical evolution is characterized by vibrational excursions within a potential basin, punctuated by occasional transitions between basins.” The transition probability is @@ -268,7 +268,7 @@ dynamics have been performed. Note that N only includes the dynamics of stages 2 and 3, not the steps taken during dephasing or the minimization iterations of quenching. The specified N is interpreted in one of two ways, depending on the time keyword. If -the time value is step, which is the default, then each replica +the time value is steps, which is the default, then each replica runs for N timesteps. If the time value is clock, then the simulation runs until N aggregate timesteps across all replicas have elapsed. This aggregate time is the “clock” time defined below, which @@ -392,7 +392,7 @@ include the “ave” fixes such as

    Default

    The option defaults are min = 0.1 0.1 40 50, no temp setting, vel = -geom gaussian, and time = step.

    +geom gaussian, and time = steps.

    (Voter) Voter, Phys Rev B, 57, 13985 (1998).

    (Voter2) Voter, Montalenti, Germann, Annual Review of Materials diff --git a/doc/prd.txt b/doc/prd.txt index 9f601fc884..b4f5184e1d 100644 --- a/doc/prd.txt +++ b/doc/prd.txt @@ -31,8 +31,8 @@ keyword = {min} or {temp} or {vel} :l {vel} values = loop dist loop = {all} or {local} or {geom}, used in dephasing dist = {uniform} or {gaussian}, used in dephasing - {time} value = {step} or {clock} - {step} = simulation runs for N timesteps on each replica (default) + {time} value = {steps} or {clock} + {steps} = simulation runs for N timesteps on each replica (default) {clock} = simulation runs for N timesteps across all replicas :pre :ule @@ -158,7 +158,7 @@ dynamics have been performed. Note that {N} only includes the dynamics of stages 2 and 3, not the steps taken during dephasing or the minimization iterations of quenching. The specified {N} is interpreted in one of two ways, depending on the {time} keyword. If -the {time} value is {step}, which is the default, then each replica +the {time} value is {steps}, which is the default, then each replica runs for {N} timesteps. If the {time} value is {clock}, then the simulation runs until {N} aggregate timesteps across all replicas have elapsed. This aggregate time is the "clock" time defined below, which @@ -310,7 +310,7 @@ dt/reset"_fix_dt_reset.html and "fix deposit"_fix_deposit.html. [Default:] The option defaults are min = 0.1 0.1 40 50, no temp setting, vel = -geom gaussian, and time = step. +geom gaussian, and time = steps. :line diff --git a/doc/read_data.html b/doc/read_data.html index 01d1b92d48..0ffe97755e 100644 --- a/doc/read_data.html +++ b/doc/read_data.html @@ -610,8 +610,8 @@ box the atom is in. These may be important to include for some kinds of analysis.

    --++ @@ -653,19 +653,22 @@ of analysis.

    - + + + + - + - + - + - + @@ -695,6 +698,8 @@ of analysis.

  • eradius = electron radius (or fixed-core radius)
  • etag = integer ID of electron that each wavepacket belongs to
  • cs_re,cs_im = real/imaginary parts of wavepacket coefficients
    • +
  • kernel_radius = ??? (distance units)
    • +
  • contact_radius = ??? (distance units)

    • The units for these quantities depend on the unit style; see the units command for details.

    diff --git a/doc/read_data.txt b/doc/read_data.txt index 2483699664..f3bd1e5f3f 100644 --- a/doc/read_data.txt +++ b/doc/read_data.txt @@ -535,6 +535,7 @@ line: atom-ID molecule-ID atom-type lineflag density x y z meso: atom-ID atom-type rho e cv x y z molecular: atom-ID molecule-ID atom-type x y z peri: atom-ID atom-type volume density x y z +smd: atom-ID atom-type molecule volume mass kernel_radius contact_radius x y z sphere: atom-ID atom-type diameter density x y z template: atom-ID molecule-ID template-index template-atom atom-type x y z tri: atom-ID molecule-ID atom-type triangleflag density x y z @@ -565,7 +566,9 @@ cv = heat capacity (need units) for SPH particles spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP) eradius = electron radius (or fixed-core radius) etag = integer ID of electron that each wavepacket belongs to -cs_re,cs_im = real/imaginary parts of wavepacket coefficients :ul +cs_re,cs_im = real/imaginary parts of wavepacket coefficients +kernel_radius = ??? (distance units) +contact_radius = ??? 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check:[3,6,8,11,12,15,17,39,41,71,91,164,179,184,188,189,190,195,202,205,211,212,269,273,278,286,288,293,301,303,317,326,327,328,329,330,333,354,365,368,384,393,404,418,420,421,423,431,437,440,441],checkf:164,checkqeq:393,checku:164,chem:[6,13,20,21,25,39,40,43,45,46,87,88,112,121,150,151,161,193,198,206,207,214,216,228,229,230,247,248,253,257,260,262,270,274,278,281,282,285,286,287,288,295,304,312,314,318,319,325,328,335,340,344,345,348,349,350,352,353,357,359,360,362,363,369,373,374,377,380,383,384,387,404,411,432,435,437,443],chemic:[9,118,138,143,167,178,179,205,261,266,267,285,319,392,393,400],chemistri:[9,260,261,263,339,357,392,393],chen:290,cheng:348,chenoweth:[392,393],chenoweth_2008:[392,393],chi:[92,133,166,251,261,263,358,360,449],chiefli:391,child:8,chip:[7,12,17,333,436],chipot:193,chiral:312,chmod:[11,12],cho:380,chocol:[7,169],choic:[3,6,12,15,16,18,40,41,54,87,121,123,137,148,164,181,184,185,188,191,194,195,207,213,216,227,229,253,261,270,285,313,319,324,325,328,330,333,364,377,384,388,423,432,433,436,437,442,443,447],choos:[1,3,6,7,8,12,16,17,18,29,39,54,87,117,134,135,168,189,190,191,192,195,202,213,216,227,229,231,232,233,234,235,257,278,282,296,318,319,325,413,418,420,432,438],chose:[408,410],chosen:[2,3,6,12,17,120,144,147,156,164,168,174,179,192,195,202,205,206,214,216,227,229,233,253,256,267,278,282,285,286,291,293,294,300,319,320,325,333,357,361,367,368,371,395,408,418,432,437,443],chri:142,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[66,75,90,93,104,106,114,124,139,141,181],chute:[4,10,208],ciccotti:273,cieplak:[6,150,435],cii:182,cij:182,circular:[3,6,123,165],circumst:18,circumv:265,citat:[],cite:[3,7,8,12,213],cko:2,cl1:143,clarendon:[29,352],clarifi:[7,408,410],clariti:303,clark:387,class2:[],classic:[0,3,5,6,7,8,9,203,253,260,265,290,314,357],classifi:[9,405],claus:421,clean:[6,12,14,15,17,431],cleanli:[422,451],clear:[],clearli:7,clebsch:120,clermont:[9,13],clever:427,click:[2,11,22,37,44,55,144,152,163,168,210,305,313,328,346,405],client:[210,212],climb:[228,328,437],clinic:[7,13],clo:[133,166,449],clock:[12,418,437],clockwis:296,close:[3,6,11,12,13,39,41,67,121,147,167,190,191,192,207,214,216,229,247,270,273,296,299,317,319,322,324,325,328,333,335,339,349,350,380,384,410,427,433,443,445],closer:[3,41,116,142,166,167,188,192,196,287,328],closest:[190,251,270,293,360,394,404,413],cloud:443,clovertown:18,clsuter:72,clump1:[255,270],clump2:[255,270],clump3:[255,270],clump:270,cluster:[],clutter:[3,9],cmap:423,cmatrix:207,cmax:380,cmd:[11,12,253,434],cmin:380,cmm:[],cn1:182,cn2:182,cna:[],cnn:182,cnr:[9,13],cnt:[364,427],co2:[40,143,273,327],coars:[7,9,29,36,40,54,156,255,270,278,362,395,435],coarser:[319,448],coarsest:120,code:[],coeff:[3,7,8,12,21,22,33,44,50,150,151,152,157,304,305,310,346,364,368,384,397,423,425],coeffcient:423,coeffici:[],coefficienct:353,coefficient0:355,coefficient1:355,coeffieci:[6,337],coeffincientn:355,coexist:[9,205,357],cohes:[6,358,380],coincid:[205,299,344,378,379,418],cold:[6,129,209,329,443],coldest:286,coleman8:9,coleman:[9,118,143,271],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,93,98,104,106,114,124,132,139,141,144,167,169,181,193,219,225,255,265,268,270,301,318,327,329,347,367,423,430,436,452],collid:[199,278,300],colliex:143,collinear:[3,255],collis:[3,216,278,296,300,354,361,416],colllis:278,colloid:[],colombo:39,colon:[170,301,424],color1:169,color2:169,color:[3,9,41,167,168,169,188,206,260,265],column:[3,6,9,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,104,106,108,110,113,114,115,116,117,119,120,121,124,132,139,141,142,143,164,167,169,172,180,181,182,183,184,185,186,219,226,227,260,270,279,280,290,300,359,363,392,393,424,438,440,448],colvar:[],colvarmodul:12,com:[],comamnd:194,comand:[191,425],comannd:333,comb3:[],comb:[],comb_1:262,comb_2:262,combiant:350,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,92,108,115,123,137,167,168,178,183,210,219,229,253,259,282,291,299,302,304,318,319,321,325,333,347,349,350,357,358,364,376,377,396,406,408,410,415,426,431,443,448],come:[],comfort:[12,13],comm:[0,3,12,61,73,210,212,213,319,328,333,353,384,389,407],comm_modifi:[],comm_styl:[],command:[],comment:[2,7,11,12,38,56,150,164,167,214,270,290,327,328,334,355,356,358,368,380,386,393,396,406,407,408,409,410,420,421,423,443,448],commerci:7,commmand:[3,6,12,59,107,248,417,418,420,437,451],common:[],commonli:[3,6,12,17,25,57,59,105,146,167,168,170,314,362,371,396,408,410,423,426,435],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,147,148,168,169,188,189,190,192,193,194,210,212,216,218,219,220,229,252,259,261,262,263,270,278,290,301,318,329,330,331,333,354,388,420,421,425,432,433,450,452],communc:318,comp:[7,212,213,273,319,328,357,384,389,394,403,407,409],compact:[63,172,346,405],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,110,118,127,142,143,152,163,169,198,261,301,303,318,319,326,328,380,418,437,438,443,447],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,151,152,163,304,305,313,345,405],compat:[3,5,7,8,9,11,12,13,17,18,41,71,117,119,155,167,170,174,180,181,182,183,184,185,186,188,252,264,282,285,292,295,298,318,333,365,384,407,420,421,448],compens:[6,189,190,268,329,357],compet:289,competit:319,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,142,167,168,170,210,289,319,333,423,424,428],compl:17,complain:[12,17],complement:380,complementari:[7,349,369],complet:[3,6,9,12,15,41,59,71,169,184,188,193,219,253,256,259,278,289,291,303,317,328,333,358,412,418,423,428,431,435,437,440,443,448],complex:[6,8,11,12,13,25,40,42,62,120,132,144,145,216,299,316,328,357,407,421,423,426,448],compli:[285,289],complic:[6,7,9,12,13,179,205,421],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,93,94,97,104,105,106,107,108,109,110,112,113,117,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,136,137,139,140,141,167,168,169,175,176,180,181,182,183,184,185,186,187,191,192,194,195,200,203,208,212,213,216,219,221,225,226,228,229,230,233,234,235,246,247,249,250,252,253,254,257,268,270,272,273,274,275,278,281,282,283,285,292,293,298,299,300,318,321,325,326,327,328,333,353,357,361,378,379,396,423,424,433,441,448,449],componenet:6,composit:[6,179,216,355],compound:[348,357,358],compres:[71,114,181],compress:[3,6,59,71,114,147,167,168,169,181,194,227,233,257,260],compris:[40,299,367,394,412],compton:[118,143],comptu:[3,6],compuat:319,comput:[],computation:[3,6,189,190,290,339],computational:443,compute_arrai:8,compute_fep:[174,377],compute_group_group:205,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[118,271],compute_scalar:8,compute_temp:8,compute_ti:174,compute_vector:8,compute_xrd:143,concaten:[2,3,451],concav:299,concentr:355,concept:[6,124,134,181,432],conceptu:[3,6,71,132,192,194,328,349,364,380,428],concern:[6,73,87,206],concis:[11,289],conclud:12,concret:8,concurr:[9,16,319],conden:[290,408,410],condens:[6,126,290,335,351,355,369],condit:[],conducit:6,conduct:[],cone:426,confid:[3,437],config:[12,167,420],configfil:193,configur:[1,6,12,15,17,38,59,146,164,166,167,168,172,192,193,194,195,199,205,212,213,241,253,261,289,316,326,328,335,339,356,380,406,408,410,418,423,425,426,437],confin:[423,437],conflict:[3,40,384,421],conform:[3,6,13,59,191,192,228,269,274,289,312,328,357,435],confus:3,conjuct:353,conjug:[7,8,213,325,357,392,393],conjunct:[6,7,71,86,87,114,127,132,138,144,148,169,173,174,213,216,220,241,256,257,261,262,263,265,270,278,286,293,298,318,319,328,340,342,346,349,353,357,363,369,384,387,395,411,423,426,430,443,452],connect:[3,6,87,129,147,191,210,255,270,273,275,328,350,361,404,410,420,421,427,443],conput:3,consecut:[3,11,12,39,71,144,169,173,174,195,210,211,349,369,373,418,424,426],consequ:[1,6,290,368,437],conserv:[3,172,179,191,198,199,206,209,213,215,216,220,225,227,229,241,270,273,281,282,286,293,294,298,328,352,353,361,375,432,437],consid:[6,9,70,71,78,87,115,129,130,147,167,169,173,174,180,182,184,188,190,191,195,217,230,252,270,285,286,289,290,293,319,346,357,364,393,394,404,418,419,421,424,425,426,428,431,433,441,443,448],consider:[6,8,213,214,281,282,283,333,432],consist:[3,6,8,9,11,12,40,42,65,69,79,92,104,108,111,112,115,124,127,129,144,156,166,170,175,176,181,194,195,198,200,203,206,213,214,215,226,229,231,232,233,234,235,236,237,239,240,241,242,244,245,246,247,248,249,257,260,265,267,269,270,281,282,283,284,294,318,319,321,327,328,333,335,339,341,347,349,357,360,364,378,379,380,384,394,407,413,421,423,424,426,427,428,435,443,448],consistent_fe_initi:178,consit:270,constant:[],constitu:[3,6,219,270,295,299,347,394],constrain:[3,6,8,122,123,124,125,127,130,131,132,133,134,136,137,172,181,195,205,206,211,219,223,255,256,268,270,273,276,286,293,326,327,357,428,435,443],constraint:[],construct:[6,8,14,38,54,56,61,64,67,70,72,73,77,118,120,143,192,229,252,269,299,329,333,352,384,404,406,407,426,427,448],constructor:8,consult:393,consum:[1,265,388,448],consumpt:316,contact:[],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,116,118,120,124,132,142,143,144,146,150,152,163,164,167,168,169,170,172,173,174,178,180,181,182,183,184,185,186,188,193,195,200,207,211,212,213,214,216,227,241,251,252,255,256,258,260,263,267,270,271,278,285,289,290,299,300,303,317,319,327,328,331,332,334,335,336,339,348,349,352,355,356,357,364,365,380,386,390,391,392,393,396,406,407,408,409,410,411,418,419,420,421,423,424,425,426,428,430,432,435,437,440,441,443,448,450,452],content:[12,18,393,439,441],context:[3,6,8,12,17,117,169,189,190,195,255,267,294,325,415,423,430,439,447,448,449],contibut:70,contigu:420,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,103,104,140,169,172,173,174,179,181,182,183,184,185,186,188,191,192,193,194,195,205,206,207,209,210,211,213,214,215,221,226,227,229,231,232,233,234,235,246,247,248,249,254,256,259,260,270,271,274,277,278,280,287,288,290,296,299,303,317,332,333,339,353,354,371,374,392,393,394,409,418,421,423,425,426,431,437,440,441,448,450],continuum:[6,7,9,178,290],contour_integr:178,contract:[59,192,194,229,257,270],contradictori:3,contrain:273,contraint:241,contrari:[207,214],contrast:[1,6,42,55,64,129,194,301,415,451],contrib:290,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,93,102,104,106,107,108,109,110,112,114,117,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,174,179,180,181,182,183,184,185,186,192,205,213,216,219,220,224,230,247,248,255,256,264,267,270,271,273,292,318,326,328,336,353,354,355,357,364,378,379,384,392,393,435,441,443],contributor:12,control:[3,5,6,7,8,11,13,16,27,29,41,87,91,120,153,167,168,172,178,179,188,192,193,194,209,210,213,214,229,231,232,233,234,235,257,262,270,281,282,283,290,294,316,318,330,357,360,392,393,406,410,418,420,432,438,439],control_typ:178,controlfil:393,convect:91,conveni:[6,12,29,167,170,186,271,321,396,448],convent:[3,8,9,29,155,162,163,169,269,275,302,355,357,448],converg:[3,6,41,88,167,168,170,175,188,191,192,200,203,233,260,262,265,269,273,324,325,326,328,348,349,369,418,430,437],convers:[3,8,120,168,169,179,182,257,318,349,350,351,357,369,373,377,387,421,437,447],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,144,151,167,168,169,186,227,301,304,306,309,312,321,328,334,355,408,410,416,421,423,424,425,430,440,443,447,448,450,452],convex:299,convinc:[7,12],cooki:7,cool:[7,134,209,268],cooordin:167,cooper:[5,7],coord123:114,coord1:[3,114,181,184,185],coord2:[3,114,181,184,185],coord3:[3,114,181,184,185],coord:[],coordiat:326,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,93,103,104,106,113,114,116,120,127,133,139,141,142,144,148,166,167,168,169,170,172,175,180,181,183,184,185,188,189,190,191,192,193,194,195,198,200,201,203,205,208,209,210,211,212,213,214,226,228,229,231,232,234,235,247,250,251,252,255,256,257,267,268,270,272,273,274,275,276,277,278,280,288,289,290,297,298,300,301,321,326,327,328,333,334,335,338,356,418,423,424,426,428,431,433,437,443,448,449],coordn:[114,181],coorind:104,copi:[0,3,4,8,11,12,15,17,40,119,168,290,328,346,392,421],copper:416,coproccesor:16,coprocessor:[1,4,7,9,16,17,333,436],coproprocessor:17,copy_arrai:8,copyright:[7,8,255],coral:169,core:[],core_shel:126,coreshel:[6,9,342,349,351],cornel:[6,150,435],corner123i:113,corner123x:113,corner123z:113,corner1i:113,corner1x:113,corner1z:113,corner2i:113,corner2x:113,corner2z:113,corner3i:113,corner3x:113,corner3z:113,corner:[3,6,40,113,168,299,300,321,412,423],cornflowerblu:169,cornsilk:169,corpor:16,corr:348,correct:[3,6,9,11,12,16,17,59,87,88,102,110,116,126,131,138,168,194,207,213,229,230,247,255,257,260,289,295,299,318,328,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,351,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,414,415,416,423,438,441,443],correction_max_iter:178,correctli:[3,8,9,11,17,71,81,102,103,122,123,125,127,129,130,131,132,133,136,137,140,167,169,175,195,200,203,214,223,229,230,263,270,273,275,277,296,299,328,329,333,351,379,420,421,423,447,449],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,96,97,109,112,113,114,115,118,119,120,122,123,131,138,143,150,151,152,153,154,155,156,158,159,161,162,164,167,168,169,173,174,175,181,183,184,185,187,190,192,194,201,203,204,208,213,216,217,225,226,227,229,231,232,233,234,235,236,241,244,246,247,249,252,253,257,262,270,272,273,281,283,285,294,295,296,298,299,300,302,304,305,306,307,308,309,312,314,319,323,325,327,328,334,335,337,340,341,342,343,344,345,346,347,348,349,352,353,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,380,381,384,385,386,387,389,390,392,393,394,395,396,397,406,407,408,409,410,412,414,415,416,418,420,421,423,424,426,436,437,438,440,441,443,448],correspondingli:[378,379,432],cosin:[],cosineshift:27,cosmo:[207,212],cossq:[],cost:[1,6,10,11,12,17,39,41,71,109,118,121,143,168,169,181,184,185,188,189,190,202,229,262,290,318,319,331,349,369,373,384,406,420,432],costheta0:[406,408,410],costheta:390,costli:[11,88,207,329],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,93,104,106,109,112,114,124,134,139,141,157,167,168,169,173,174,179,181,182,184,188,194,203,212,259,260,261,265,268,270,272,278,279,285,289,290,291,295,299,301,303,310,315,317,324,326,329,333,336,359,363,364,392,393,419,420,421,423,425,427,430,431,439,443,448,449],coulomb:[3,5,6,7,8,9,10,12,14,15,18,88,107,108,121,145,149,261,263,291,318,319,326,333,340,342,343,344,345,348,349,350,351,352,357,361,362,364,369,373,377,384,387,392,393,395,405,410,411,415,428,435,441,443,447],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,41,63,68,77,91,114,116,117,132,142,148,175,176,179,181,183,184,185,187,188,195,200,202,205,211,229,241,256,273,281,282,299,319,326,327,328,330,333,359,363,384,441,448],counter:[296,418,429,431,437],counterbal:209,counterpart:[167,270,418],counterproduct:18,coupl:[],cours:[3,8,138,167,173,174,206,269,275,289,295,297,298,300,301,319,378,397,420,423,436,443,448,450],coval:[6,29,357,380,443],covari:207,cover:[6,71,164,169,178,216,357,367,412],coverag:[71,184],cpc:212,cpp:[1,3,6,8,9,11,12,13,87,167,173,174,203,273],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,169,172,198,214,291,316,319,333,346,405,418,436,437,440,441],cpuremain:441,cr2:143,cr3:143,crack:[4,329],crada:[5,7],crai:[5,7,13,18,167],crash:[3,329,443],craympi:333,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:178,create_faceset:178,create_nodeset:178,createatom:[],creation:[],crimson:169,critchlei:255,criteria:[3,116,145,168,169,189,190,191,224,326,389,412,425,428,448],criterion:[41,142,144,147,179,188,191,205,241,262,296,301,326,328,348,357,361,428,437,438],criterioni:437,critic:[48,49,227,285,290,326],cross:[3,12,22,71,89,123,152,167,168,180,184,190,194,226,228,247,270,275,277,286,293,305,321,328,344,353,354,355,362,363,364,369,371,373,390,395,408,410,423,427,433,450],crossov:1,crossterm:423,crozier:[0,7,13],crucial:260,crystal:[4,6,13,73,251,252,288,329,427,441,443],crystallin:[6,252,321,409,443],crystallis:285,crystallogr:[118,143],crystallograph:[321,441],crystallographi:[118,143,321],cs1:143,cs_chunk:6,cs_im:[40,423],cs_re:[40,423],csanyi:[120,391,396],cscl:380,csequ:6,csh:[11,12,346],cshrc:[11,12],csic:[356,406,408,410],csinfo:6,csisi:[356,406,408,410],csld:[],cst:355,cstherm:6,cstyle:420,csvr:[],ctcm:[334,355],ctemp_cor:198,cterm:274,ctr:9,ctype:11,cu1:143,cu2:143,cu3au:380,cube:[6,41,142,147,188,198,299,321,443],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:339,cummul:[3,6,186,189,190,191,193,202,207,213,215,278,281,282,283,284,286,293,363,441],cumul:[6,179,181,183,184,185,199,205,213,227,229,233,241,270,271,328],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,102,108,116,117,121,124,132,140,142,145,148,167,168,169,170,173,174,178,179,181,184,185,186,188,189,190,191,192,193,194,195,199,200,203,205,207,210,211,213,219,226,229,230,234,235,241,246,247,249,255,261,262,264,267,268,269,270,273,274,276,277,278,281,282,283,289,290,293,294,295,296,297,298,300,301,303,316,317,318,319,322,323,325,326,327,328,333,339,346,348,352,355,357,358,361,365,368,378,379,380,381,382,384,390,392,393,397,408,410,411,413,418,419,420,421,423,424,425,426,427,429,430,431,433,435,437,438,440,441,448,449,450,451,452],curv:[6,144,205,252],curvatur:[360,394,416],custom:[],cut0:421,cut1:432,cut2:432,cut:[],cuthi:[251,263],cutinn:[341,378,379],cutlo:[251,263],cutmax:390,cutoff1:[345,352,369,373,377,387,395],cutoff2:[340,342,343,345,351,352,369,373,377,387,395],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,108,115,116,120,142,145,147,190,191,196,251,260,261,263,265,267,270,278,291,295,299,301,318,319,326,329,330,331,333,334,335,336,337,338,339,340,341,342,343,344,345,347,349,350,351,352,353,354,355,356,357,358,359,360,362,363,364,365,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,392,393,394,395,396,397,398,399,400,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,421,425,428,432,443],cutoffa:356,cutoffc:356,cuu3:355,cval:143,cvd:285,cvel:274,cvff:[],cwiggl:[3,226,295,298,300,448],cyan:[2,168,169],cycl:[3,205,227,229,230,233],cyclic:[3,164],cygwin:12,cylind:[3,4,168,211,256,296,299,426],cylindr:[6,211,275,296],cypress:333,cyrot:339,cyrstal:252,d3q15:216,d3q19:216,d_double_doubl:15,d_e:290,d_flag2:259,d_flag:259,d_name:[113,167,259,280,433],d_single_doubl:15,d_single_singl:15,d_sx:259,d_sy:259,d_sz:259,daan:288,dai:12,daili:12,daivi:247,damag:[],dammak:265,damp:[3,6,172,177,213,214,215,220,229,230,233,257,260,265,270,281,282,294,296,297,325,326,328,340,342,344,349,352,357,361,369,377,387,395,405,411,437,443],damp_com:214,damp_drud:214,dampen:[270,443],dampflag:[296,361],dan:17,danger:[3,12,205,301,353,441],dangl:147,daniel:9,darden:[319,352],darkblu:169,darkcyan:169,darken:168,darkgoldenrod:169,darkgrai:169,darkgreen:169,darkkhaki:169,darkmagenta:169,darkolivegreen:169,darkorang:169,darkorchid:169,darkr:169,darksalmon:169,darkseagreen:169,darkslateblu:169,darkslategrai:169,darkturquois:169,darkviolet:169,dasgupta:261,dash:[361,440],dat:[6,91,164,178,419],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,271],dataset:271,datatyp:3,date:[0,6,12,13,392,393,448],datom1:115,datom2:115,datom3:115,datom4:115,datum:[3,6,42,65,68,69,79,92,108,115,167,182],davi:295,david:[9,19,318,319,408,410],daw:[355,390],dbg:14,dcd:[3,6,7,167,168,169,170,253,424,428],ddim:166,deactiv:377,dealt:212,debug:[6,7,11,12,13,14,17,118,143,144,253,258,316,318,333,365,384,413,421,422,425,430,433,440,448],deby:[],decai:[349,416],decid:[3,6,12,16,71,226,259,270,291,438],decipher:321,declin:278,decod:168,decompos:[87,396],decomposit:[3,5,7,18,62,178,253],decoupl:[6,443],decreas:[3,167,175,176,191,194,200,203,213,289,318],decrement:274,deepli:315,deeppink:169,deepskyblu:169,def:[12,13,421],defaul:61,defect:[6,70,142],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,150,151,152,153,154,155,156,158,159,161,162,163,164,165,166,167,168,169,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,198,199,200,203,204,205,208,211,212,213,214,215,216,224,226,228,229,230,231,232,233,234,235,237,238,239,242,244,245,246,247,248,249,251,252,253,255,256,257,259,261,263,268,270,271,272,273,276,278,280,281,282,283,284,286,287,288,290,292,293,295,296,297,298,299,300,301,303,304,305,306,307,308,309,312,313,314,316,318,319,321,323,325,326,327,328,329,330,331,332,333,335,336,337,338,340,341,342,343,344,345,346,347,349,350,352,353,354,356,357,359,360,361,362,363,364,365,367,369,370,371,372,373,374,375,376,377,378,379,383,384,385,386,387,389,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,420,421,423,424,426,427,428,429,432,433,434,435,437,438,440,441,443,444,445,446,447,448,449],definit:[2,3,6,8,12,13,78,80,116,120,169,181,182,183,184,185,186,194,211,233,271,280,292,295,298,300,302,313,316,327,336,339,347,357,367,390,396,412,421,423,425,432,434,447,448],defint:441,deform:[],deg2theta:143,deg:443,degener:[3,255],degrad:[8,18,252,319,432],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,94,96,97,99,101,102,112,122,123,124,125,126,127,128,129,130,131,132,133,134,136,137,143,144,150,151,154,155,162,164,166,168,181,191,198,205,207,208,213,214,219,229,230,233,234,235,246,247,249,253,255,269,270,273,281,282,283,288,304,306,309,312,314,326,352,355,363,433,441,443,449],degress:[124,181],del:437,delai:[3,6,12,329,354,441],deleg:364,delet:[2,3,7,8,12,54,57,60,63,142,147,148,172,181,182,183,184,185,186,189,191,202,205,229,271,281,282,301,303,317,327,329,332,384,423,424,426,434,435,440,444,446,448,449],delete_atom:[],delete_bond:[],delete_el:178,deli:166,delimit:[421,448],deloc:[230,357],delr:380,delt_lo:437,delta:[],delta_1:339,delta_3:339,delta_7:339,delta_conf:3,delta_ij:[380,390],delta_mu:[3,179],delta_pi:339,delta_r:390,delta_sigma:339,delx:166,delz:166,demand:265,demo:11,demon:250,demonstr:[260,380],den:256,dendrim:363,denniston:[9,216,218,219,220,252],denomin:[7,149],denot:[118,198,214,252,263,265,349,362,364,393],dens:[71,191,357],densiti:[3,6,7,9,18,40,41,59,100,116,120,130,142,144,173,174,178,181,184,185,188,194,203,216,219,222,223,252,256,257,261,290,295,321,323,327,334,339,355,380,381,382,390,394,399,401,402,403,423,432,433,441,447],depart:[0,7],departur:[227,260],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,108,109,112,113,114,115,119,120,122,127,131,132,138,144,145,150,151,152,153,154,155,156,158,159,161,162,163,164,166,167,168,169,172,173,174,175,176,179,181,183,184,186,187,188,190,192,200,201,204,207,208,209,211,213,214,216,218,219,226,229,231,232,233,234,235,236,244,246,247,249,251,262,265,267,270,272,273,278,281,282,283,285,287,289,290,292,294,295,298,299,300,301,303,304,305,306,307,308,309,312,314,319,321,326,327,329,330,331,333,334,335,337,338,339,340,341,342,343,344,345,346,347,348,349,350,352,353,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,380,381,383,385,386,387,389,390,392,393,394,395,396,397,405,406,407,408,409,410,411,412,414,415,416,418,420,423,425,426,429,433,435,437,440,441,442,448,449],dependend:6,depflag:12,dephas:[418,437],depos:195,deposit:[],deprec:261,depth:[51,123,168,290,360,394],dequidt:9,der:[87,107,347,348,377,392,393,415,443],deriv:[6,7,8,38,56,63,87,120,138,164,182,192,194,205,213,226,229,231,232,233,234,235,251,257,261,265,287,288,290,295,296,299,325,327,335,339,347,352,357,358,362,371,375,376,380,392,393,405,407,415,443],derjagin:415,derlet:251,descend:169,descent:[7,325],descib:[40,261],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,110,113,116,118,120,121,123,124,128,129,132,135,137,138,142,143,144,146,147,156,161,164,167,172,173,174,181,182,183,184,185,186,188,191,192,193,194,195,197,198,206,207,210,211,212,213,214,215,216,218,219,220,224,228,229,230,233,240,248,251,253,258,259,260,261,262,263,270,274,275,278,279,280,281,282,283,284,285,286,287,288,293,295,296,298,303,318,319,321,324,325,326,327,328,332,335,336,338,340,341,342,344,345,346,347,348,349,352,355,357,358,360,361,362,364,369,370,371,372,373,374,375,376,377,378,379,380,383,389,390,391,392,393,394,395,396,397,404,405,406,407,408,409,410,411,414,415,416,418,420,421,423,424,426,427,433,436,437,440,448,449,450],descript:[],descriptor:[120,167,365],deserno:319,design:[0,3,6,7,8,11,13,14,15,17,118,126,129,143,178,191,197,198,229,230,251,252,271,285,290,336,337,338,341,344,349,351,357,377,378,379,381,382,390,393,407,432],desir:[2,3,6,7,11,12,14,15,16,18,33,40,50,59,71,88,91,112,117,121,126,144,157,166,179,192,194,203,205,206,213,214,215,219,229,247,255,256,257,258,261,265,270,273,278,281,282,283,284,289,296,310,315,318,319,321,324,326,327,328,353,355,363,378,379,406,408,410,419,420,421,423,427,432,437,438,440,441,448,449,450],desk:7,desktop:[4,6,7,10,12,17,168],despit:443,destabil:339,destre:312,destroi:[11,39,189,190],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,93,102,104,106,107,109,111,112,114,117,119,120,121,122,123,124,127,137,138,139,141,144,145,148,149,152,163,167,168,169,172,173,174,178,181,182,183,184,186,188,190,191,192,193,194,195,203,205,206,207,208,210,211,213,215,216,220,226,227,228,229,230,231,232,233,234,235,239,241,246,247,248,249,252,255,256,257,259,260,262,263,264,270,273,278,281,282,283,284,285,286,288,289,290,291,292,293,294,301,303,305,313,318,319,322,326,327,329,330,333,334,335,336,338,339,341,343,344,345,346,347,348,349,352,353,357,358,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,379,380,383,384,389,392,393,394,396,397,405,412,414,415,421,423,424,425,426,428,429,432,433,435,438,441,448,449,452],detect:[2,3,12,61,63,86,204,256,289,328,348,363,368,418,420,423,434,437,448],determ:333,determin:[1,3,6,8,12,15,39,40,42,51,57,58,59,61,62,68,71,87,102,107,109,112,118,119,121,132,133,142,143,144,166,167,168,169,170,171,175,176,177,180,181,182,183,184,185,186,187,188,192,194,195,198,200,205,208,209,211,213,214,219,224,226,227,229,234,235,246,247,249,251,253,257,260,267,268,269,270,271,272,278,281,282,283,285,291,292,295,296,297,298,299,300,301,313,318,319,321,327,329,330,333,335,336,343,348,352,354,355,359,361,364,365,373,380,384,393,394,404,407,411,415,420,423,424,426,428,430,433,437,439,440,447,448,449],detil:108,devan:[9,395],devanathan:410,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,210,233,255,260,261,264,335,339,357,382,425],devemi:9,deviat:[227,233,251,359],devic:[1,3,12,15,17,210,333],device_typ:333,devin:[262,348],devis:382,dfactor:168,dff:443,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,319],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,264],dhi:[59,166,194,256],dhug:[227,260],dhugoniot:[227,260],dia:380,diagnost:[],diagon:[3,6,83,120,121,192,229,257,270,293],diagonalstyl:396,diagram:[41,118,143,163,188,253],diallo:363,diam:[168,169,256,327],diamet:[3,6,40,113,144,167,168,169,173,174,213,256,270,278,294,296,327,347,360,361,367,371,394,412,415,423,424,433],diamond:[321,357,380],diamter:[40,256],dick:6,dicsuss:226,dictat:[179,227],did:[3,12,326,353,354,355,361,384,408,410,431],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,140,292,318],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,94,96,97,120,122,123,124,125,127,130,131,132,133,134,136,137,138,144,145,147,152,163,164,166,167,168,169,172,174,177,179,181,183,188,189,190,191,192,193,194,198,204,205,206,207,208,209,210,213,214,216,226,229,230,231,232,234,235,237,239,242,244,245,246,249,251,253,255,257,260,261,262,265,268,270,273,274,275,276,278,281,282,283,286,287,288,290,293,294,295,296,299,303,304,313,315,317,318,319,321,322,324,325,327,328,330,331,332,333,334,335,339,343,344,346,347,348,353,355,357,360,361,362,364,367,369,370,372,373,380,381,382,383,384,386,390,392,393,394,395,396,397,405,406,407,408,410,412,415,416,417,418,420,421,423,425,426,427,428,431,432,433,435,437,438,440,441,443,447,448,449,450],differenti:[1,3,6,29,164,318,349,390,409],difficult:[192,253,333,363,432],difficulti:[273,392],diffract:[],diffus:[],digit:[2,3,169,303],dih_table1:164,dih_table2:164,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:190,dihydrid:357,dij:273,dilat:[],dim1:3,dim2:3,dim:[3,59,71,122,125,126,127,130,131,132,133,134,136,144,166,184,194,211,296,321,380,426,447,448,449],dimdim:448,dimems:252,dimens:[],dimension:[3,39,112,118,120,122,124,125,126,127,130,131,132,133,134,136,143,165,181,184,228,252,290,321,324,328,390,423,433],dimensionless:[105,120,290,319,396,415],dimer:[6,270,380],dimgrai:169,dimstr:[41,188],dinola:[257,281],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,167,280,443],dir1:434,dir2:434,dir:[1,3,4,8,11,12,227,251,260,277,390,392,393,421,434,448],dirac:120,direc:390,direct:[],directli:[3,6,8,9,11,12,87,113,120,167,168,175,200,207,211,216,252,271,282,294,296,297,298,299,321,325,333,334,335,340,342,343,349,352,355,357,369,373,384,387,395,404,421,433,434,435,441,448],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,60,170,193,212,255,261,264,278,287,288,328,332,334,335,339,346,348,349,355,356,358,365,366,377,380,381,382,386,390,391,392,393,396,406,408,409,410,421,423,424,425,434,448],disabl:[3,12,16,290,368,421,436],disadvantag:[6,188],disallow:[194,229],disappear:425,discard:[2,3,41,71,184,188,291,299,420,425,426],discontinu:[9,164,326,375],discourag:380,discov:[13,291],discret:[6,8,40,42,168,169,213,216],discuss:[],disk:[6,84,85,137,165,195,205,256,421],disloc:70,disord:[39,70],disp:[],dispar:394,disperion:[352,373],dispers:[3,6,7,9,142,252,318,319,343,352,373,378,384,393,407],displac:[],displace_atom:[],displace_box:59,displacemet:426,displai:[11,13,22,37,44,55,152,163,167,168,305,313,346,405],dispters:3,dissip:[6,206,213,252,287,288,341,353,361,378,379,405],dissolut:189,dist:[6,69,91,108,117,167,253,269,354,404,418,449],distanc:[3,6,7,9,12,20,21,29,39,43,45,46,47,48,49,51,53,54,55,56,58,59,61,63,64,66,69,71,72,73,74,75,76,77,81,86,89,90,93,103,104,105,106,108,114,115,116,117,118,120,133,139,142,144,145,146,147,151,166,167,168,169,177,181,184,185,189,190,191,192,194,195,196,199,205,211,216,226,227,228,229,233,241,251,252,256,260,261,268,269,270,273,274,275,276,277,278,285,286,288,289,290,293,295,296,297,298,299,300,304,318,319,321,324,326,328,329,330,333,336,337,338,339,340,341,342,343,344,345,347,349,350,351,352,353,354,355,356,357,359,360,361,362,363,367,368,369,370,371,372,373,374,375,376,377,378,379,380,383,384,385,386,387,388,389,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,421,423,426,432,433,437,441,443,447,449],distinct:[6,198,267,318,394],distinguish:[6,86,120,219,357],distort:334,distrbut:334,distribut:[],distro:[111,346,389,390],ditto:[8,11,12,14,15,16,17,18,115,190,421],div:8,divd:117,diverg:[3,12,39,270,288,425,443,450],divid:[3,6,16,41,91,112,117,121,141,142,152,163,169,181,182,183,188,194,251,286,293,298,318,326,328,358,393,432,440,448],divis:[6,216,339,367,377,420,423,441,448],dl_poli:7,dlambda:138,dlammps_async_imd:210,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,168],dlammps_gzip:[3,12,167,168,289,423,424,428],dlammps_jpeg:[3,12,168],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,168],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,167],dlen:433,dlmp_intel_offload:[12,16],dlo:[59,166,194,256],dlvo:[7,347,415],dm_lb:216,dmax:[278,324],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,93,102,104,105,106,107,109,111,112,114,117,119,121,123,124,137,139,141,144,145,146,152,163,167,168,169,170,172,173,174,179,180,181,182,183,184,185,186,195,205,213,214,224,229,230,234,235,239,246,247,248,249,256,259,270,275,278,281,282,283,292,296,299,301,303,305,313,317,326,327,328,333,334,335,338,346,348,349,355,356,358,363,364,366,367,380,381,382,384,386,389,390,391,396,405,406,408,410,412,421,423,424,425,426,428,431,432,433,440,441,448,449,450,451],docuement:394,dodgerblu:169,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,29,33,38,39,41,50,54,56,59,62,63,67,70,71,87,88,91,104,110,117,118,123,124,127,132,134,138,143,144,145,146,148,150,152,157,163,164,166,167,168,169,172,178,179,181,184,187,188,190,191,192,194,198,200,202,205,206,209,211,213,214,216,219,225,229,230,231,232,234,235,246,247,248,249,257,258,259,263,265,268,270,278,281,283,285,286,290,293,294,295,298,299,300,301,306,307,309,310,312,317,318,319,320,321,327,328,329,334,335,336,337,338,339,341,343,344,345,347,348,349,350,352,353,354,355,356,357,359,360,361,362,364,365,366,367,368,371,372,374,375,376,378,379,380,381,382,384,390,391,392,393,394,396,397,398,399,400,401,402,403,404,406,407,408,409,410,411,412,414,415,416,418,419,420,421,423,424,425,426,427,430,431,433,434,435,436,437,440,441,443,448,452],doegenomestolif:7,doesn:[3,7,8,12,144,167,179,184,185,275,327,329,333,335,348,356,366,392,393,406,408,409,410,423,425],dof:[3,8,112,123,124,137,181,270,449],dof_per_atom:[124,181],dof_per_chunk:[124,181],doff:[327,423],doi:[6,193],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,118,133,143,146,166,168,169,172,179,188,192,194,195,209,212,216,229,230,253,265,270,290,295,296,318,319,328,333,354,384,418,420,423,427,440],domin:[1,357,437],don:[0,8,11,12,13,116,147,175,200,214,259,299,380,421,423],donadio:282,done:[1,3,6,7,8,12,14,15,16,17,18,19,38,39,41,56,59,62,71,138,141,144,147,164,168,169,178,179,181,183,184,185,186,188,189,190,191,192,194,195,203,205,210,211,213,214,221,229,234,235,246,247,249,250,252,253,254,259,267,270,271,273,278,281,282,283,285,287,288,301,303,317,318,319,326,328,329,332,333,335,343,355,364,365,366,373,379,380,384,392,404,407,412,418,419,420,421,424,427,428,431,441,443,448,449],donor:363,dot:[121,140,175,200,208,228],doti:[339,390],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,39,87,194,203,258,299,303,317,319,332,333,339,358,362,392,393,419,423,427,431,436,448,449],dover:178,down:[3,6,7,8,11,39,71,192,213,278,294,333,357,384,422],downhil:[324,325],download:[5,7,8,9,11,12,13,17,210,365,391],downsid:6,downward:267,dozen:[8,12,107,172,392,393],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:222,dproduct:336,dr_ewald:[118,271],drag:[],dragforc:216,drai:[227,260],drain:[209,294,326],dramat:[59,166,189,190,191,192,194,229,278,281,282,319,333,384,420],drautz:339,draw:168,drawback:259,drawn:[167,168,169,206,418],drayleigh:[227,260],dreid:[],drfourth:105,drho:[113,334,355],drift:[6,103,105,206,207,213,214,225,268,278,432,440,443],drive:[11,12,176,192,194,208,229,251,257,270,297,328],driven:[6,156],driver:[6,12,14,15,172,203,210],drop:[3,169,353],droplet:364,drsquar:105,drude:[],dry:202,dsecriptor:365,dsf:[],dsmc:[],dstyle:256,dt_collis:216,dt_lb:216,dt_md:216,dt_srd:278,dtilt:[59,194],dtneb:437,dtqm:260,dtype:[115,190],dual:[17,278,333],dudarev:143,due:[1,3,6,9,10,12,16,17,19,40,54,57,58,61,66,70,71,74,75,81,86,88,89,90,93,102,103,104,105,106,110,116,118,120,121,122,123,125,127,130,131,132,133,134,136,137,139,143,144,147,148,167,168,172,175,176,183,187,189,190,191,192,193,194,195,200,201,202,203,206,207,210,211,213,214,215,216,219,220,221,225,226,227,228,229,233,241,251,254,256,268,269,270,272,275,277,278,279,281,282,283,284,285,287,288,290,294,295,297,298,299,301,319,324,326,328,329,330,350,353,355,359,360,364,378,379,384,390,392,394,395,404,407,408,410,413,415,416,418,420,423,424,425,432,437,440,441,443,448,449],duffi:290,duin:[9,261,266,392,393],duke:319,dummi:[12,29,409],dump1:428,dump2:428,dump:[],dump_atom:8,dump_custom:8,dump_modifi:[],dumpcustom:8,dumptimestep:428,dunbrack:[6,20,150,344,435],dunweg:[213,215],duplic:[2,3,14,15,16,17,18,19,41,42,145,188,207,251,423,447],dupont:[5,7,13],durat:[37,55,122,123,125,126,127,129,130,131,132,133,136,137,163,169,181,205,265,290,313,361,405],dure:[2,3,6,8,9,12,16,17,38,39,41,56,71,87,126,145,148,164,167,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,196,199,200,201,202,203,204,205,206,207,208,209,210,211,213,214,215,216,217,218,219,220,221,222,223,225,226,228,229,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,319,326,328,332,333,353,377,384,393,407,418,419,421,423,426,428,430,431,433,435,437,438,441,448,451,452],dvector:8,dvlo:415,dvx:6,dx_lb:216,dy3:143,dyamic:12,dyanam:6,dyanmic:437,dynam:[],dynamo:[5,334,355,380],dyne:447,dyre:374,dysam:426,e28637:29,e_1:339,e_2:339,e_b:358,e_e:357,e_hbond:363,e_i:[6,339,358],e_j:[6,339],e_k:[339,357],e_kl:6,e_lj:[335,352],e_n:[339,357],e_nn:357,e_pr:357,e_rebo:335,e_tors:335,eaa:304,eaat:151,each:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,66,67,68,70,71,72,73,74,75,76,77,78,80,81,83,85,87,89,90,93,94,95,96,97,98,99,100,101,102,103,104,105,106,109,110,111,112,113,114,115,116,117,118,119,120,121,123,124,125,126,127,128,131,132,133,134,136,137,138,139,140,141,142,143,144,147,148,150,151,152,153,154,155,156,157,158,159,161,162,163,164,166,167,168,169,170,171,172,173,174,175,176,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,205,206,207,208,209,210,211,212,213,214,215,216,217,219,220,221,222,223,225,226,227,228,229,231,232,233,234,235,236,237,238,239,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,261,262,263,265,267,270,271,272,273,274,275,276,277,278,279,280,281,282,283,285,288,289,290,291,292,293,294,295,296,298,299,300,301,303,304,306,307,308,309,310,312,313,314,317,318,319,321,325,326,327,328,329,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,357,358,359,360,361,362,363,364,367,368,369,370,371,372,373,374,375,376,377,378,379,380,383,384,385,386,387,389,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,410,411,412,413,414,415,416,417,418,420,421,423,424,425,426,427,428,430,431,432,433,435,437,438,440,441,443,447,448,449,450,452],eacn:[41,188],eam0d:252,eam3d:252,eam:[],eam_databas:13,eam_gener:13,eangl:441,earli:[41,181,183,184,185,186,188,264,271],earlier:[7,8,12,59,169,328,361,380,384,437],earliest:437,earth:357,easi:[6,7,8,11,13,87,121,167,173,174,175,176,184,187,200,208,209,211,213,214,272,281,282,283,295,298,300,327,423,426,431,433,449],easier:[8,9,13,16,167,168,252],easili:[8,11,168,169,294,328,420,430,439,448],eastwood:[318,319],eat:151,eatom:301,eaxmpl:6,eba:21,ebb13:151,ebb:21,ebond:[198,214,440,441],ebt:151,ec_ii:380,ec_ij:380,ec_jj:380,echo:[],eco:[392,393],ecoa:[392,393],ecoul:[107,198,214,392,393,441],ecp:[357,423],edg:[2,3,6,41,59,71,118,142,143,146,147,168,177,184,211,272,295,298,299,300,301,321,423,426,433],edge_histo:142,edge_threshold:142,edih:441,edim:286,edip:[],edit:[3,8,12,13,14,15,16,17,18,19,443],editor:13,edu:[7,9,11,13,355,378,389,392,393],edward:[9,17],eebt:151,eff:[],effect:[1,2,3,6,8,9,11,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,43,45,46,47,48,49,51,53,54,56,66,71,74,75,8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0,274,278,281,282,283,284,286,289,290,293,297,300,301,317,318,327,328,332,333,353,355,360,394,396,397,411,413,418,421,423,424,425,426,428,430,431,435,439,441,443,448,452],end_of_step:8,endbondtors:[3,151,157,423],endif:8,energet:[191,335,393],energi:[0,1,2,3,4,5,6,7,8,9,12,13,20,21,23,24,25,26,27,28,29,30,31,32,35,36,38,40,43,45,46,47,48,49,51,53,54,56,63,65,69,82,83,84,85,86,87,88,91,94,95,96,97,98,99,101,102,107,108,109,110,112,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,144,148,150,151,152,153,154,155,156,158,159,161,162,163,164,167,169,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,304,306,307,308,309,312,314,318,319,324,325,326,328,329,333,334,335,337,338,339,340,341,342,343,344,345,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,389,390,392,393,394,395,396,397,398,399,404,405,406,407,408,409,410,412,413,414,415,416,418,421,423,428,432,433,435,437,439,440,441,443,447,448,451],energy_update_freq:393,enforc:[6,57,58,104,166,167,168,170,172,179,191,194,229,250,252,262,270,273,303,318,369,420,448,449],enforce2d:[],eng:[11,65,69,108,167,203,301,303,348,382],eng_previ:303,engin:[178,194,255,274,287,355,381],engr:[392,393],enhanc:[174,178,418],enlarg:[59,168],enough:[3,40,61,86,144,145,147,188,214,256,260,265,270,291,295,296,299,329,333,349,388,423,427,428],enpub:355,ensembl:[],ensight:6,ensur:[3,6,120,167,179,192,205,206,229,289,319,339,354,377,404,406],enter:[57,134,358,437],enthalpi:[231,232,355,440,441,448],entir:[0,2,3,6,11,14,15,41,42,63,88,109,110,112,116,118,121,124,143,144,169,172,173,174,181,184,185,188,191,193,202,205,206,209,213,214,225,229,231,232,233,234,235,251,253,255,268,270,276,290,292,303,333,352,373,384,407,423,431,432],entireti:[367,412],entiti:[6,8,40,42,167,270],entri:[3,8,38,42,56,65,69,79,92,108,115,118,142,164,169,183,184,185,193,260,301,327,339,356,380,386,393,396,406,407,408,409,410],entropi:437,entry1:[38,56,169,346,407],entry2:169,entryn:169,enumer:[145,167],enumuer:6,env:333,environ:[1,3,6,11,12,16,17,18,168,207,212,251,333,334,339,346,348,356,357,390,408,420,434,448],epair:[107,169,359,363,392,393,441],epen:[392,393],epfl:[207,212],epp:352,epq:352,eps0:415,eps14:377,epsilon0:410,epsilon:[3,6,36,45,46,50,53,54,87,150,173,174,205,270,278,295,299,324,326,338,344,345,347,349,350,351,352,360,362,363,364,367,368,369,370,371,372,373,374,375,376,377,383,387,394,395,400,406,412,414,415,432,443,447],epsilon_0:416,epsilon_14:344,epsilon_:394,epsilon_d:350,epsilon_i:[360,384,394],epsilon_i_:394,epsilon_i_a:[360,394],epsilon_i_b:[360,394],epsilon_i_c:[360,394],epsilon_ij:384,epsilon_j:[360,384,394],epsilon_j_:394,epsilon_j_a:[360,394],epsilon_j_b:[360,394],epsilon_j_c:[360,394],epsilon_lj:394,epton:389,eqch:139,eqeq:[392,393],eqp:352,eqq:352,equal:[2,3,6,8,11,12,17,39,41,54,63,65,68,69,76,79,86,87,91,92,108,110,115,117,119,121,123,138,140,144,168,169,172,173,174,175,176,179,182,183,186,187,188,192,194,195,200,205,206,208,209,211,213,214,216,219,220,226,227,233,243,251,253,256,258,260,261,262,265,267,269,270,272,274,281,282,283,286,287,288,290,292,293,295,298,300,301,303,317,326,328,329,330,332,333,348,353,359,360,363,378,383,390,392,393,394,396,397,407,412,416,419,420,421,423,425,426,430,431,434,437,439,441,448,449],equat:[3,6,7,8,9,91,112,118,143,152,163,172,192,198,199,207,213,214,216,219,227,228,229,230,233,247,251,253,260,261,265,273,278,286,290,293,295,296,298,300,312,318,319,347,352,353,357,358,361,366,378,379,380,384,394,399,400,402,403,411,416,443],equi:230,equidist:228,equil:[3,261,322,430,452],equilater:433,equilibr:[3,4,5,6,7,9,59,91,144,172,179,182,191,192,205,227,229,230,247,248,260,261,262,263,286,287,288,293,348,349,392,393,419,433],equilibria:293,equilibribum:[189,190],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,127,128,151,153,192,194,205,206,207,214,216,229,233,247,260,265,269,273,274,275,278,285,286,288,293,304,306,309,312,348,380,386,443],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:178,equival:[6,12,13,59,142,146,169,183,186,192,194,205,213,229,247,257,269,270,298,353,357,408,410,423,426,431,432,441,443],equlibrium:6,equliibr:[261,263],er3:143,eradiu:[40,113,357,423],eras:[272,287],erat:[194,379],erc:349,erfc:[349,369,384],erforc:113,erg:447,erhart:[179,355,408,410],ermscal:336,ernst:9,eror:3,eros:380,erose_form:380,erot:[],errata:[408,410],erratum:295,erron:3,error:[],erta:361,ervel:[113,423],escap:[195,443],especi:[8,11,16,132,144,172,179,188,205,260,265,268,269,333,420],espresso:[9,264],essenti:[8,11,12,27,88,125,126,127,130,131,132,133,134,136,153,182,233,252,294,319,335,349,369,410,428,441],essex:29,establish:[87,209],estim:[1,3,6,10,12,38,41,56,91,121,178,188,199,227,278,285,318,319,324,384,393,407,437,441],esu:447,esub:380,eta:[6,216,229,260,261,263,294,356,358,360,390,409,447],eta_dot:229,eta_ij:390,eta_ji:358,etag:[40,423],etail:441,etap:229,etap_dot:229,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,17,39,40,42,54,61,68,89,90,91,94,109,110,113,115,121,122,124,125,126,127,128,130,131,132,133,134,136,138,144,146,147,148,157,167,168,169,172,178,179,180,181,183,184,185,186,189,190,194,195,203,205,206,213,229,256,267,271,290,291,299,303,317,318,326,327,328,329,331,355,356,364,377,379,388,392,393,406,408,410,418,421,423,424,425,430,432,433,437,439,440,441,443,447,448,450,452],ethernet:18,etol:[326,328,418,437],etot0:260,etot:[6,94,96,97,110,121,130,169,198,214,227,260,440,441],eu2:143,eu3:143,euler:[326,328],eulerian:178,euqat:398,europhi:216,evalu:[2,3,11,12,38,56,71,87,88,91,107,117,120,124,134,142,144,167,168,169,173,174,175,176,178,180,181,182,183,184,185,186,187,194,200,206,208,209,211,212,213,214,252,258,261,272,281,282,283,292,295,298,300,301,303,318,319,324,326,333,384,390,407,418,419,421,425,426,428,430,431,432,433,437,439,441,448,449],evalut:[303,421],evan:[132,247],evanseck:[6,20,150,344,435],evapor:[],evaul:[8,326],evdwl:[107,392,393,441],even:[3,6,8,12,15,16,17,18,34,39,41,52,57,59,61,63,70,71,119,145,146,160,164,167,169,172,173,174,179,180,181,183,184,185,186,188,189,190,192,194,195,198,211,214,227,229,230,252,265,267,270,271,278,286,290,293,295,299,301,311,318,324,326,328,333,338,357,358,361,364,384,394,413,423,424,426,428,429,430,432,433,435,438,440,441,443,452],evenli:[3,41,121,164,188,216,367,413,423],event:[],eventu:[3,6,12,15,146,261,437],ever:[54,56,212,278],evera:[347,360,394,405],everi:[0,1,2,3,6,8,11,12,15,16,39,41,71,72,91,113,119,132,147,167,168,169,170,172,173,174,175,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,199,202,203,205,207,209,210,211,216,217,225,229,230,233,250,251,252,256,257,258,259,260,261,262,263,265,267,268,270,271,273,274,278,280,281,282,283,284,285,286,289,290,291,292,293,301,303,317,319,328,329,330,333,353,354,364,377,392,393,401,417,418,419,423,425,427,428,430,431,432,437,438,439,441,448,452],everyth:[8,107],everywher:[116,371],eviri:357,evolut:[207,216,253,418],evolv:[216,253,291],ewald:[2,3,5,6,7,8,12,88,110,118,121,291,318,319,326,340,342,343,349,352,357,369,373,387,395,405,407,425],ewald_disp:352,ewalddisp:3,exact:[22,41,44,71,138,147,152,188,191,206,207,213,214,215,256,265,266,278,290,305,318,346,425,430,437,450,452],exactli:[3,6,12,14,17,38,41,56,59,71,91,123,128,135,144,164,173,174,183,188,194,199,206,213,214,215,230,240,241,248,252,260,278,283,284,297,333,346,353,355,361,364,367,378,384,407,425,426,433,437,448],exager:443,examin:[6,8,191,252],examp:[421,448],exampl:[],exce:[3,6,16,17,18,41,58,71,146,181,184,185,188,192,194,199,202,229,252,278,326,333,423,448],exceed:[3,41,59,188,194,229,278,431],excel:357,except:[1,2,5,6,8,11,14,16,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,108,109,112,117,121,122,123,124,125,126,127,128,130,131,132,133,134,135,136,137,144,148,150,151,152,153,154,155,156,158,159,161,162,163,164,166,167,169,172,175,181,182,183,187,188,192,194,201,204,205,208,211,213,215,229,230,231,232,233,234,235,236,240,241,244,246,247,248,249,253,262,263,270,272,273,275,278,281,283,284,290,294,301,303,304,305,306,307,308,309,312,313,314,318,319,321,323,327,328,329,331,332,333,334,335,337,340,341,342,343,344,345,346,347,348,349,351,352,353,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,379,381,385,386,387,389,392,393,394,395,397,405,406,407,408,409,410,412,414,415,416,418,420,421,423,425,426,428,431,432,433,434,435,437,441,443,447,448,449,451],excess:357,exchang:[2,3,6,8,9,61,62,172,178,179,205,213,262,270,286,290,293,318,333,357,438],exchange:318,excit:[9,357],exclud:[3,6,9,12,16,17,63,71,112,120,124,131,132,148,167,181,184,189,190,217,225,255,268,270,285,296,301,326,327,329,341,361,364,378,379,384,404,435],exclus:[1,3,9,12,16,87,333,348,384,432],excurs:418,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,145,168,210,264,303,317,320,332,419,421,431,434,437,448],exemplari:206,exemplifi:357,exert:[6,211,214,265,297,298,299,319],exhaust:[178,332,448],exhibit:[229,325,357,432],exist:[3,6,7,8,11,12,13,37,55,59,68,70,144,145,163,168,169,172,177,187,190,192,195,205,255,256,258,301,304,306,307,309,313,322,327,333,364,392,413,419,421,423,424,425,434,435,436,448,449,450],exit:[2,3,11,12,41,57,167,188,317,332,421,422,431,440,448],exlanatori:3,exp:[],expand:[],expans:[12,120,167,434],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,102,125,136,142,164,188,200,205,207,226,251,257,259,260,265,270,301,319,329,346,380,384,418,421,423,425,428,432,437,448],expens:[6,10,71,169,251,255,270,290,301,318,319,329,333,421],experi:[6,13,15,17,187,195,210,219,228,257,269,270,324,328,353,384,432,437],experienc:[6,12,218,219],experiment:[318,333,437],expert:12,expertis:7,explain:[1,3,6,8,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,92,124,132,164,167,168,169,172,181,182,186,188,190,192,194,229,251,259,270,275,301,303,317,318,321,327,328,332,338,355,367,397,412,416,421,424,425,428,430,433,443,448,452],explan:[3,6,59,113,120,167,181,228,251,364,417,420,421,423,432],explanatori:[3,8,117,167,180,181,183,184,185,270,327,420,448],explantori:[3,266],explic:383,explicit:[6,9,11,22,44,77,87,113,116,138,152,173,174,194,305,323,335,336,339,344,346,355,357,368,378,411,417,420,424,427],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,109,112,122,131,134,142,144,150,151,153,154,155,156,158,159,161,162,164,167,169,175,184,187,194,201,204,206,208,213,229,231,232,233,234,235,236,244,246,247,249,259,260,262,270,272,273,281,283,284,290,294,304,306,307,308,309,312,314,327,333,334,335,337,340,341,342,343,344,345,346,347,348,349,350,352,353,354,355,356,358,359,360,361,362,363,364,367,368,369,370,371,372,373,374,375,376,377,378,381,384,385,386,387,389,394,395,397,398,399,400,401,402,403,405,406,407,408,409,410,411,412,414,415,416,423,425,432,433,435,436,443],explictli:[16,436],exploit:[9,15,17,253],explor:[118,143],expon:[3,261,263,355,360,363,377,383,395],exponenti:[87,390,406,416,437,448],expos:11,exposit:[178,353,354],express:[6,120,130,144,173,174,192,226,251,261,290,296,303,339,355,357,371,380,396,405,448],expressiont:339,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,94,97,98,107,109,117,119,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,172,175,176,179,186,187,193,196,200,203,204,205,207,208,209,211,213,215,227,229,233,241,251,252,268,269,270,272,274,275,277,281,282,283,284,285,287,288,290,292,295,299,300,360,380,393,394,396,440,441],extent:[1,3,41,45,57,71,142,146,167,177,184,188,211,297,300,318,321,335,407,420,423,426],exterior:[3,6,299],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,102,109,110,112,118,121,122,123,125,127,130,131,132,133,134,136,137,143,144,145,146,150,169,183,188,190,229,258,259,260,270,278,326,327,330,331,352,361,364,367,380,384,420,421,423,426,435,443,448],extract:[3,6,11,13,36,63,87,107,115,117,119,173,174,263,328,349,358,380,396,421,428,440],extract_atom:11,extract_comput:[11,421],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,168,192,194,229,288,357,409,443],extrema:377,extrins:178,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[140,292],f_a:[408,409,410],f_ave:117,f_c:409,f_f:410,f_fix_id:260,f_harm:288,f_i:390,f_id:[6,71,117,119,167,172,180,181,182,183,184,185,186,224,280,292,441,448],f_ij:390,f_indent:186,f_int:287,f_jj:91,f_k:390,f_langevin:290,f_max:[260,265],f_msst:227,f_r:[214,408,409,410],f_sigma:339,f_solid:288,f_ss:6,f_temp:214,face:[3,6,57,59,71,132,142,146,177,184,185,295,297,298,299,300,321,360,380,394,423,426],face_threshold:142,facet:142,facil:[0,12],facilit:[6,13],fact:[6,8,16,207,278,288,361,435],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,118,120,138,143,146,150,161,167,168,169,173,174,182,188,192,194,195,205,210,213,215,216,227,229,230,233,253,257,269,273,278,282,286,293,294,295,299,309,319,321,333,335,336,339,340,342,344,349,350,351,353,357,361,364,368,369,380,384,386,387,393,395,397,406,411,420,423,426,427,432,435,437,438,441,443,447,448],factori:[3,421],factoriz:318,fail:[3,11,12,59,148,192,195,318,326,328,351,393,421],fairli:[11,384,432,437],faken:73,falcon:210,fall:[3,6,169,183,256,421],fals:[86,301,303,448],fame:8,famili:420,familiar:[0,11],fan:390,far:[3,6,12,17,57,59,61,86,167,169,170,188,189,190,192,195,205,229,251,269,270,278,295,306,309,324,328,329,412,421,423,428,441],farago:213,farrel:[408,410],farther:167,fashion:[6,8,41,71,144,169,172,173,174,179,184,188,190,195,205,207,211,226,227,229,231,232,233,234,235,243,246,247,248,249,259,260,262,270,274,277,280,288,290,294,295,296,298,300,328,364,378,426,435,448,451],fasolino:366,fast:[6,7,9,12,13,17,39,167,238,260,291,318,319,341,378,379,405,407,425,430,432,441,449,452],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,105,109,112,122,131,150,151,153,154,155,156,158,159,161,162,164,167,169,172,175,187,188,201,204,208,212,213,229,231,232,233,234,235,236,244,246,247,249,257,261,262,270,272,273,278,281,283,285,287,290,294,304,306,307,308,309,312,314,318,319,330,331,333,334,335,337,339,340,341,342,343,344,345,346,347,348,349,352,353,355,356,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,381,385,386,387,389,394,395,397,405,406,407,408,409,410,412,414,415,416,418,432,436,443],fastest:[6,14,17,132,184,290,291,333,420],fatal:[3,440],fault:[70,393],faulti:12,fava:360,favor:191,favorit:7,fbmc:285,fcc:[],fcm:[243,448],fdirect:198,fdotr:365,fdti:87,fe2:143,fe3:143,fe_md_boundari:178,featu:8,featur:[],fecr:355,feedback:[7,210],feel:[7,210,211,219,251,299,301,328,384],felling:382,felt:299,femtosecond:447,fene:[],fennel:[349,369],fep:[],ferguson:[6,150,435],fermi:[1,12,15,130,333,410],fermion:[9,357],ferrand:[9,13],few:[1,3,4,5,6,7,10,11,12,13,14,17,18,39,170,180,181,182,183,184,185,186,214,229,256,259,261,273,292,318,326,327,328,335,420,423,428,432,434,448,450],fewer:[1,3,11,15,16,61,219,432],fewest:3,fextern:203,feynman:253,fff:421,ffield:[348,358,392,393],ffmpeg:[3,12,168],ffplai:168,fft:[1,3,7,12,14,15,88,109,110,121,252,318,319,432],fft_inc:[12,319],fft_lib:12,fft_path:12,fftbench:318,fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],fictiti:[6,175,176,200,203,207,253,269,349,369,373,404],field1:[424,428],field2:424,field:[],fifth:[275,386],figur:[1,3,8,11,12,260,420,421],fij:352,file0:251,file1:[11,13,251,289,303,327,428,430,434],file2:[11,13,289,303,327,428,430,434],file:[],filenam:[3,12,13,38,41,56,164,167,168,169,170,178,181,182,183,184,185,186,188,193,251,255,258,261,262,263,266,267,270,271,289,290,315,316,317,328,334,335,339,349,355,356,358,366,380,381,382,386,390,391,392,393,396,406,407,408,409,410,419,420,421,424,425,430,434,441,448,450,451,452],filennam:430,filep:[3,167,169,425,430,452],filepo:267,fill:[7,144,168,256,290,321,329,339,393,426],filter:[169,178],final_integr:8,final_integrate_respa:8,finchham:[6,126,351],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,117,147,164,170,179,191,192,202,205,228,251,257,265,269,324,326,328,329,349,364,369,373,380,405,407,443,448],find_custom:8,fine:[16,17,148,175,200,288,329,333,448],finer:[120,144,448],finest:318,finger:[144,166,226,426],finish:[6,11,41,188,303,315,317,318,330,332,333,412,428,448,449],finit:[],finni:[7,355,405],finvers:198,fiorin:[9,193],fire:[324,325,326,328,437],firebrick:169,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,103,104,105,112,116,117,121,129,132,138,140,142,143,145,146,147,151,164,167,168,169,170,172,179,181,182,183,184,185,186,188,191,194,205,206,211,216,226,227,228,229,251,253,258,259,260,262,267,270,273,274,275,276,278,279,280,287,288,289,290,292,296,301,303,304,310,321,326,327,328,329,332,333,334,335,338,339,340,342,344,346,348,349,355,357,358,361,362,365,366,368,369,373,378,379,380,382,384,386,390,392,393,396,404,406,407,408,409,410,418,419,420,421,423,424,425,428,430,432,435,436,437,440,441,443,448,449,450,452],fischer:[6,9,19,20,150,344,435],fit:[3,6,9,12,38,56,164,269,278,335,339,366,380,384,400,407,409,431,448],five:[73,130,260,327,339,381,423,437],fix:[],fix_adapt:[138,174,377],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,179,256],fix_evapor:179,fix_flux:178,fix_gcmc:[179,327],fix_gl:207,fix_gld:207,fix_grav:256,fix_id:[3,192,227,229,231,232,233,234,235,257,260],fix_modifi:[],fix_mov:[166,296],fix_nh:8,fix_npt:207,fix_nvt:[179,205],fix_poem:[3,6],fix_pour:[3,195],fix_qbmsst:9,fix_qeq:[3,348],fix_rattl:273,fix_reax_bond:392,fix_rigid:[219,338],fix_saed_vtk:271,fix_setforc:8,fix_shak:273,fix_srd:3,fix_styl:233,fix_temp_rescal:284,fixedpoint:[192,229],fixextern:203,fixid:178,fji:352,flag1:[197,331],flag2:[197,331],flag:[3,8,11,12,14,15,16,17,18,40,66,74,75,81,86,89,90,93,103,104,106,118,139,143,147,167,168,169,170,186,191,193,197,210,213,217,219,225,226,252,259,270,275,277,278,285,289,298,301,316,319,327,331,332,333,335,363,368,380,404,418,420,421,423,424,425,427,428,429,433,448],flag_buck:343,flag_coul:[343,352,373],flag_lj:[352,373],flagfld:[341,378,379],flaghi:[3,341,378,379],flaglog:[341,378,379],flagn:197,flagvf:[341,378,379],flat:[6,290,295,296,300],flavor:[2,7,12],fld:[9,295,341,378,379],flen:336,flex_press:336,flexibl:[3,6,8,145,168,181,184,193,207,230,286,293,357,409,441],flip:[3,6,194,229,297,298],floor:448,flop:12,floralwhit:169,flow:[],fluctuat:[6,64,87,192,205,206,213,216,229,233,251,252,288,290,312],fluid:[],fluid_veloc:220,flush:[3,169,440],flux:[],flv:168,fly:[7,9,12,41,168,172,178,195,198,270,273,291,339,441,443],fmackai:9,fmag:196,fmass:253,fmax:[326,441],fmomentum:198,fmsec:[2,169,213,214,226,229,257,270,281,282,432,442,447,449],fname:317,fno:12,fnorm:[326,441],fnpt:198,fnvt:198,foce:364,fock:336,focu:273,fogarti:[9,263,393],foil:[120,251,396],fold:[276,432],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,120,121,123,124,130,132,137,140,142,144,145,150,153,154,155,156,158,159,161,162,164,167,168,169,172,178,179,180,181,182,183,184,185,186,188,193,194,195,198,199,203,205,206,207,210,212,213,214,216,219,227,229,233,234,235,246,247,249,252,253,255,258,259,260,261,263,265,267,269,270,271,273,280,281,282,283,286,287,288,289,290,292,293,301,302,306,307,308,309,312,314,316,321,323,326,327,328,333,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,351,352,353,354,355,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,3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3,71,143,253,285,288,319,356,379,392,393,421,448],interf:333,interfac:[],interfer:[229,335],interg:[6,443],intergr:[432,436],interi:379,interior:[3,6,41,299,426],interlac:380,interleav:[6,144,431],intermedi:[6,12,59,168,228,251,312,328,421,422,431,435],intermix:418,intermolecular:335,intern:[0,2,3,5,6,9,11,16,20,21,24,28,32,35,36,39,40,42,63,87,99,101,118,121,124,126,143,151,164,168,169,172,173,174,178,190,194,198,210,222,223,227,229,233,252,270,274,304,306,309,312,316,326,327,398,399,407,421,423,425,428,437,440,441,447,448,449,450],internal_element_set:178,internal_quadratur:178,internet:212,interpenetr:380,interpentr:[399,400,402],interpol:[6,15,38,56,100,164,168,169,178,216,251,318,319,328,339,384,393,401,407,408],interpret:[2,6,11,168,183,361,397,418,421,437,448],interrupt:260,intersect:[3,6,118,169,299,301,426],intersert:299,interspers:326,interstiti:142,intertia:[3,93],interv:[3,6,91,182,213,260,265,266,401,418,437,448],intestieti:118,intial:[6,333,335],intiial:[41,428],intiti:[3,277],intra:270,intra_energi:205,intramolecular:[29,205],introduc:[6,9,168,229,260,265,270,312,318,334,349,357,369,373,377,406,437],introduct:[],intsal:16,intuit:321,inv:[118,143,271],invalid:[3,12,71,89,147,241,328,378,379,425],invari:120,invent:273,invers:[],invert:[6,148,252],invis:299,invoc:[142,191,333,421],invok:[1,3,6,7,8,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,59,63,66,71,74,75,81,87,88,89,90,93,103,104,106,109,110,111,112,117,122,131,138,139,142,144,145,147,148,150,151,153,154,155,156,158,159,161,162,164,167,168,169,170,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,196,197,199,200,201,202,203,204,205,206,208,209,210,211,213,214,215,216,217,218,219,220,221,222,223,225,226,228,229,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,261,262,263,264,265,266,267,268,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,304,306,307,308,309,312,314,317,318,319,320,321,326,328,333,334,335,337,340,341,342,343,344,345,347,348,349,352,353,355,356,358,359,360,361,362,363,364,365,367,369,370,371,372,373,374,375,376,377,378,379,381,384,385,386,387,389,394,395,396,397,406,407,408,409,410,412,413,414,415,416,417,420,421,422,424,426,428,431,432,434,435,437,440,441,443,448,449],invokd:3,involv:[3,6,7,8,12,63,108,115,116,117,124,148,172,189,205,216,255,258,263,278,318,325,326,328,338,354,360,406,408,410,419,420,426,428,432,437],ioff:[327,423],ion:[6,7,250,275,290,319,339,350,358,359,380,405,410,416,423,443],ionic:[6,9,340,342,350,357,358,387,443],ioniz:[9,348,357],iparam:[3,190],ipi:[],ipp:[],ir3:143,ir4:143,irregular:[6,41,58,188,192,194,229,270],irrelev:386,irrespect:[378,379],irrevers:198,isbn:415,isel:[318,319],isenthalp:[229,230,231,232],ismail:[318,319,343,373],isn:[3,8,11,12,209],iso:[3,192,198,214,229,230,231,232,233,234,235,257,265,270,443],isobar:[229,230,234,235],isodem:357,isol:[3,147,301],isomorph:253,isotherm:[205,229,230,234,235,257],isotrop:[6,213,257,318,319,341,360,378,379],isovolum:271,isralewitz:274,issu:[1,3,6,9,11,12,13,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,59,71,73,81,103,109,112,122,131,150,151,153,154,155,156,158,159,161,162,164,168,175,178,187,191,192,195,200,201,204,205,208,213,227,229,231,232,233,234,235,236,244,246,247,249,253,257,259,262,270,272,273,277,281,282,283,288,294,300,303,304,306,307,308,309,312,314,319,327,328,331,334,335,337,340,341,342,343,344,345,347,348,349,352,353,355,356,358,359,360,361,362,363,367,369,370,371,372,373,374,375,376,377,378,381,385,386,387,389,394,395,397,404,406,407,408,409,410,412,414,415,416,423,425,432,435,440,441,448,449],ital:[392,393],itali:13,item:[6,7,8,41,167,169,188],iter:[3,6,12,39,41,63,175,176,187,188,192,198,200,203,211,252,261,262,270,273,285,301,303,317,324,325,326,328,332,418,428,432,437,441,448],ith:[71,117,119,180,181,182,183,184,185,186,280,292,441,448],itself:[2,3,4,6,7,8,9,11,12,13,18,42,59,91,107,135,167,168,169,170,182,193,198,214,224,228,264,270,290,301,303,327,328,349,358,360,364,365,407,421,427,430,431,435,448,452],ityp:[3,115,116,144,177,190,263,413],itype1:116,itype2:116,itypen:116,ivector:8,ivori:169,ixcm:270,ixi:[42,93,270,327,448],ixx:[42,93,270,327,448],ixz:[42,93,270,327,448],iycm:270,iyi:[42,93,270,327,448],iyz:[42,93,270,327,448],izcm:270,izrailev:274,izumi:409,izz:[42,93,270,327,448],j0jt:91,j20:182,j_m:120,jac:[6,150,435],jackson:383,jacobi:3,jacobsen:325,jagreat:13,jame:[9,19],janssen:251,januari:380,jaramillo:[7,9,13,357],jarzynski:274,jatempl:9,jcc:9,jcp:295,jec:13,jeff:13,jello:229,jensen:[213,318],jeremi:[9,382],jerom:9,jewett:13,jiang:[214,443],jiao:[9,13],jiht:[7,9],jik:339,jim:7,jku:7,jmake:12,jmm:120,joannopoulo:227,job:[12,60,273,431],jochim:[229,230],john:[7,13],johnson:13,join:[6,426],joint:[3,255,363],jon:[9,70],jonathan:9,jone:[1,3,6,7,9,10,12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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso_e/atom command","compute meso_rho/atom command","compute meso_t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute sna/atom command","compute stress/atom command","compute temp command","compute temp/asphere command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":189,"default":[37,39,40,55,57,58,59,61,62,71,87,88,102,103,105,107,118,120,124,132,133,137,143,144,147,149,163,165,166,167,168,169,170,171,173,174,175,177,178,179,181,184,185,186,189,190,192,193,194,195,199,202,205,206,211,213,214,215,216,217,219,224,227,229,230,233,247,248,252,253,256,257,258,259,260,262,265,267,268,270,271,278,280,285,286,287,288,291,293,295,297,301,313,316,318,319,321,322,324,325,327,329,330,331,333,336,339,341,357,378,379,384,392,393,404,405,418,419,420,423,424,426,428,430,431,432,435,437,439,440,441,442,447,449,450,451],"function":448,"long":[340,342,343,344,345,349,351,352,369,373,377,387,395],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[173,174],addforc:175,addit:[12,13],addtorqu:176,adiabat:6,adp:334,airebo:335,alloi:355,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:177,arrai:6,aspher:[6,82,123,231,234,237,238,246],atc:[9,178],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,95,96,99,100,101,110,111,113,120,121,142,177,179,180,259,448],atom_modifi:39,atom_styl:40,attract:5,aveforc:187,awpmd:[9,336],balanc:[41,188],barostat:6,basal:67,beck:337,berendsen:[257,281],between:6,binary2txt:13,bodi:[6,8,42,68,239,338],bond:[8,13,69,189,190,191,266],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:339,born:[340,351],boundari:[7,57],box:[6,58,192],brownian:341,buck:[342,343,351],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,150,344,377],chunk:[6,66,71,75,90,93,104,106,114,124,139,141,181],citat:7,class2:[21,43,151,304,345],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[295,347,415],colvar:[9,13,193],com:[74,75,125],comb3:348,comb:[262,348],come:5,comm_modifi:61,comm_styl:62,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,445,446,447,448,449,450,451,452],common:3,comparison:1,compos:6,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,448],compute_modifi:102,condit:7,conduct:[6,286],constant:6,constraint:7,contact:76,coord:77,core:6,correl:182,cosin:[23,24,25,26,27,28,153],cossq:306,coul:[340,342,343,344,345,349,350,351,362,369,373,377,387,395],coupl:6,creat:190,create_atom:144,create_bond:145,create_box:146,createatom:13,creation:7,csld:282,csvr:282,cubic:371,cuda:[9,14,109,112,122,131,175,187,201,204,208,229,236,272,273,281,283,294,340,342,344,345,355,361,362,369,370,372,375,385,406,408],custom:8,cut:[49,336,342,345,349,352,357,359,369,370,377,383,387],cvff:307,damag:78,data2xmovi:13,data:6,databas:13,deby:[349,369],deform:[127,128,194],delete_atom:147,delete_bond:148,delta:24,deposit:195,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,16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\ No newline at end of file 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64,189,199,211,214,225,312,370,400,462,469],acceptor:390,access:[0,3,6,7,8,9,11,12,16,40,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,85,88,89,90,91,92,93,95,96,99,100,101,103,104,105,106,107,108,110,111,112,113,114,115,117,118,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,151,152,153,154,155,156,157,159,160,161,162,163,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,219,220,221,222,223,224,225,226,227,228,229,230,231,233,235,236,237,238,239,240,241,242,243,245,246,247,248,249,253,256,257,258,259,260,261,262,263,264,265,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,299,302,303,304,305,306,307,308,309,310,311,313,314,315,316,317,319,320,321,322,323,324,325,326,327,345,360,386,388,390,391,407,419,420,428,451,452,455,460,472,479],accidenti:339,accler:16,accommod:197,accomod:249,accompani:8,accomplish:[16,214,237,263],accord:[64,71,121,127,130,188,199,209,210,236,249,272,280,294,296,314,315,317,322,323,325,326,327,356,360,384,388,399,402,417,424,426,428,430,431,433,434,435,463,468,479],accordingli:[11,14,143,157,168,356,405,406],account:[3,6,9,87,118,162,163,172,183,202,203,219,230,231,233,249,254,255,266,267,269,271,275,281,290,291,293,302,303,304,305,308,309,310,313,317,320,335,354,376,388,396,400,405,406,407,451,468,480],accuml:[3,290,313,320],accumul:[1,6,8,15,71,192,202,233,290,294,319,343,360,460,478],accur:[1,3,6,15,17,38,41,56,147,208,247,285,290,293,305,313,320,326,328,346,366,384,387,388,411,421,436,438,439,441,468,479],accuraci:[1,3,6,12,41,187,189,208,227,249,282,293,318,328,345,346,352,384,411,419,420,438,444,463,468,474,479,482],ach:345,achiev:[1,3,6,16,17,18,41,208,227,249,250,272,273,280,345,391,463],achiv:18,acid:9,ackland1:382,ackland2:382,ackland:[],acknowledg:[],acml:12,aco:479,acolor:[188,189],acoust:272,acquir:[3,6,58,61,62,167,210,212,214,249,415,459,474],across:[1,2,3,6,9,12,13,15,41,57,61,65,68,69,71,79,92,107,108,115,117,152,166,168,201,203,204,205,208,219,229,290,291,295,313,317,320,326,330,355,360,449,454,457,458,462,471],act:[3,6,108,149,218,228,231,232,233,234,236,239,248,290,299,312,314,315,317,326,327,328,353,368,379,387,388,390,421,435],acta:[118,163,361],action:[2,6,11,12,71,226,231,315,474],activ:[5,8,11,12,13,14,55,59,87,162,199,213,226,230,233,239,248,270,290,297,316,343,404,436,448,476,479],actual:[1,3,6,8,12,56,62,122,147,187,189,193,194,207,209,210,218,233,234,267,271,277,285,294,305,307,308,309,310,312,318,327,328,345,356,387,389,399,405,406,451,452,463,464,472,479],adam:[345,346],adapt:[],add:[0,1,3,5,6,7,8,9,11,12,13,14,15,16,17,18,19,40,42,71,87,91,102,114,117,119,162,164,165,187,188,192,193,194,195,196,198,200,201,202,203,204,205,206,210,213,218,220,223,227,228,229,231,233,235,236,240,247,248,249,250,251,252,253,254,255,266,267,268,269,271,279,289,290,292,293,302,304,308,310,311,315,316,317,319,321,322,326,328,346,348,352,354,362,367,369,372,376,384,391,396,407,411,414,420,422,452,454,455,460,462,464,466,474],add_molecul:198,add_speci:198,add_to_nodeset:198,addforc:[],addit:[],addition:[6,8,16,139,305,327,387,421],address:[7,8,11,188,232],addtorqu:[],adequ:[305,318,345,355,463],adher:29,adhikari:236,adiabat:[],adiam:[188,189],adjac:[39,164,355,411,438,439,468,469],adjiman:410,adjust:[2,3,6,16,17,41,59,118,143,144,147,148,151,152,157,158,163,168,187,188,201,208,212,214,230,233,237,241,245,246,249,250,253,267,271,274,276,277,280,281,282,283,288,290,297,305,309,313,318,320,321,322,324,325,327,345,346,353,355,360,362,381,405,406,441,464,480],adjust_dt:128,adjust_radiu:297,adjust_radius_factor:297,admiss:253,adof:[144,201],adopt:[289,474],adp:[],adri:[9,286,419,420],adust:158,advanc:[3,230,366,449,460],advantag:[1,6,8,11,14,18,39,40,41,208,360,383,463,468],advect:[3,6,305],advertis:8,advis:[355,418],afer:3,affect:[1,6,10,14,15,16,17,40,60,61,71,88,117,141,148,162,168,189,194,201,202,203,204,205,206,209,210,211,212,214,215,223,229,231,233,239,246,250,251,252,254,255,261,266,267,269,290,291,303,317,327,339,345,351,352,353,355,356,357,360,384,405,406,411,451,452,454,457,459,462,464],affin:[16,17,18,214,360,375],afil:227,aforement:18,afresh:[278,462,479],afshar:380,after:[2,3,5,6,8,9,11,12,15,16,21,22,33,39,40,41,44,50,57,58,59,61,63,71,143,144,145,146,147,148,151,152,153,154,156,157,164,165,167,168,171,172,177,186,187,188,189,190,192,193,194,198,199,201,202,208,209,210,211,212,214,218,225,236,237,238,239,240,245,246,247,249,254,255,261,266,267,269,272,276,280,288,290,293,301,306,308,309,310,312,313,314,315,316,320,322,324,328,331,332,337,344,350,351,353,354,356,358,359,360,361,362,366,373,375,382,383,384,385,391,392,393,404,405,406,407,408,409,413,417,419,420,427,437,439,440,441,449,451,453,454,455,456,457,459,460,462,464,466,468,471,472,474,478,479,480,481,482,483],afterrun:462,afterward:3,afterword:41,ag1:163,ag2:163,again:[6,11,12,17,62,140,144,146,150,158,187,189,214,229,276,331,344,355,405,406,449,451,452,454,456,461,468,470,479,481],against:[11,12,13,64,215,355,419,420],aggreg:[6,12,65,68,69,79,92,108,115,229,245,288,290,303,449,480],aggress:[229,468],agilio:[9,13],agre:[3,8,184,353,362,393,420],agreement:[5,7],ahd:390,ahead:324,aidan:[0,5,7,9,13],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:188,akohlmei:[7,9,13,190,230],aktulga:[7,9,283,420],al2o3_001:[118,291],al3:163,ala:236,alain:9,alat:[271,407],alb:[417,439,441],albeit:289,albert:9,alchem:[87,158],alcohol:320,alcu:[361,366],alcu_eam:417,alderton:379,alejandr:[249,250],alessandro:13,algorithm:[0,1,6,7,8,9,41,61,189,198,208,211,214,236,238,239,261,273,290,293,312,313,317,320,325,351,352,353,357,360,384,406,424,426,449,451,468],alia:12,alias:[1,346],aliceblu:189,align:[6,12,29,41,71,166,184,204,208,231,348,454,457,474],alkali:384,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,152,157,158,159,160,161,162,163,164,165,166,167,168,170,172,177,183,184,187,188,189,190,192,193,194,195,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,242,244,245,247,249,250,251,252,253,254,255,256,257,258,259,260,261,262,264,265,266,267,268,269,270,271,272,273,275,276,277,278,279,280,281,282,283,285,286,287,288,289,290,291,292,293,294,295,296,297,301,302,304,305,306,307,308,309,312,313,314,315,316,317,318,319,320,322,323,324,325,326,327,328,329,330,331,332,335,340,343,344,345,346,347,348,350,353,354,355,356,357,359,360,361,362,363,365,366,367,369,370,371,372,373,375,376,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,400,404,405,406,407,408,409,410,411,412,413,414,416,417,418,419,420,421,422,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,446,447,448,449,451,452,453,454,455,456,457,458,459,461,462,463,464,465,466,467,468,469,471,472,474,478,479,480,481,482,483],allen:[29,87,379,387],allentildeslei:87,allign:3,allindex:329,alloc:[3,5,6,8,9,11,12,60,223,319,354,356,360,415,420,454,462],allocat:3,alloi:[],allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,108,143,144,157,162,163,164,166,172,183,184,187,188,189,190,192,193,195,197,198,199,201,202,203,204,205,206,208,210,211,212,213,214,215,219,220,223,225,226,227,228,230,233,236,239,240,244,246,249,250,271,275,277,278,279,280,284,290,291,293,294,296,297,301,305,312,313,314,315,317,318,319,320,321,322,328,330,332,340,345,346,348,353,354,355,356,359,360,363,366,367,368,369,370,371,376,382,384,388,389,390,391,400,405,406,411,417,420,421,424,426,435,444,446,449,452,454,456,457,458,459,460,461,464,466,467,468,471,472,479,480],almost:[2,3,12,60,231,280,317,346,357,360,435],alo:376,alon:[6,7,211,286,419,420,452],alond:13,along:[6,8,9,12,29,40,87,118,163,164,186,187,188,211,231,236,237,241,246,248,280,290,293,294,298,302,303,312,316,317,323,326,328,348,351,352,353,355,376,379,388,391,394,396,400,407,419,420,438,454,457,464,465,479],alonso:[408,409],alpha:[6,51,193,236,272,280,285,353,361,364,367,376,380,382,383,385,390,395,396,407,412,416,440,442,472,474],alpha_:442,alpha_c:404,alpha_i:[427,442],alpha_ialpha_j:442,alpha_lj:404,alphabet:[2,3,22,37,44,55,63,172,183,192,332,340,354,373,436,454],alphanumer:[3,63,192,279,287,330,354,479],alreadi:[3,7,8,12,42,164,165,167,197,201,204,205,208,210,214,240,278,280,305,328,354,355,380,389,391,398,406,435,444,447,450,454,455,459,464,479],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,54,55,56,58,59,61,63,66,71,73,75,77,81,87,89,90,93,103,104,105,106,107,112,114,116,117,119,140,141,142,143,144,145,146,147,148,150,151,152,153,154,156,157,158,159,160,161,162,164,165,166,167,168,170,172,183,184,185,187,188,189,190,192,193,194,195,197,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,220,223,224,225,226,227,229,230,233,234,235,236,246,247,249,250,251,252,253,254,255,260,263,264,266,267,268,269,271,272,273,275,276,277,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,298,299,302,303,305,308,309,310,311,312,316,317,318,319,321,323,326,328,330,332,337,340,343,345,346,348,349,350,353,354,355,356,357,359,360,366,370,371,373,377,378,379,380,382,383,384,387,388,390,391,392,400,404,405,407,411,413,415,416,417,418,421,422,424,430,431,433,434,435,436,437,438,439,440,441,442,449,451,452,453,454,455,456,457,458,459,461,462,463,464,466,467,468,469,472,473,474,475,477,478,479,480,481,483],alter:[3,6,8,9,11,12,41,59,142,143,144,145,147,150,151,152,153,156,157,164,168,187,188,190,193,194,201,209,210,211,212,214,248,249,285,288,290,292,299,305,313,320,327,352,355,391,454,459,461,464,479,480,483],alter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,76,77,116,122,140,239,271,293,303,354,413,419,420,454],centro:[],centroid:[3,273,443,464],cerda:345,ceriotti2:227,ceriotti:[13,227,232],certain:[1,2,3,6,8,12,17,39,71,113,117,119,168,187,188,200,201,202,203,204,205,206,211,223,224,290,292,306,319,330,337,344,356,391,411,420,442,456,460,474,479],certainli:231,cerutti:346,cfg:[3,6,7,13,187,188,189,190],cfile:420,cfl:[128,295],cfor:294,cg_type:422,cgiko:2,cgikot:2,cgkio:2,cgko:2,cgkot:2,cgo:2,cgot:2,ch2:293,ch2lmp:[],ch3:293,chain3:356,chain:[],challeng:[6,294],chalopin:285,champaign:[230,345,346,405],chandler:[361,382],chandrasekhar:[6,396],chang:[1,2,3,6,8,9,11,12,14,15,16,17,39,40,41,46,55,57,59,62,71,80,87,116,126,128,146,147,148,164,165,166,168,184,186,187,188,189,190,192,193,194,195,196,198,199,204,205,207,208,209,210,211,212,213,214,215,219,220,222,224,227,229,230,231,233,235,236,237,239,245,246,247,249,250,251,252,253,254,255,261,266,267,268,269,271,272,276,277,279,280,284,287,288,289,290,292,293,294,305,308,309,310,311,313,314,315,316,317,318,320,323,326,328,346,351,353,355,358,360,380,384,388,391,405,406,407,411,419,420,436,449,450,451,452,454,455,456,457,458,459,460,462,463,464,465,466,469,472,475,477,478,479,480,481],change_box:[],changeabl:187,channel:[4,195],chapter:[273,346],charact:[2,3,6,12,38,41,56,63,184,187,188,189,190,192,208,279,287,330,354,359,384,395,417,419,420,438,451,452,456,461,462,479,481,482,483],character:[6,67,70,116,140,427,449,468],characterist:[234,305,314],charg:[1,3,4,5,6,7,9,11,15,40,87,88,113,118,163,164,187,190,192,193,194,199,215,220,225,279,281,282,283,287,307,320,345,346,354,367,369,375,376,378,379,382,384,385,391,396,400,404,414,419,420,436,441,442,444,446,447,454,455,459,464,466,474,478,479],charmm2lammp:13,charmm:[],chartreus:189,cheap:305,cheaper:[219,387,421],check:[3,6,8,11,12,15,17,39,41,71,91,184,199,204,208,209,210,215,222,225,231,232,289,293,305,313,315,320,328,330,344,353,354,355,356,357,360,381,392,395,411,420,435,449,451,452,454,462,468,471,472],checkf:184,checkqeq:420,checku:184,chem:[6,13,20,21,25,39,40,43,45,46,87,88,112,141,170,171,181,213,218,226,227,234,236,248,249,250,267,268,273,277,280,282,290,294,305,308,309,312,313,314,315,322,331,339,341,345,346,352,355,362,367,371,372,375,376,377,379,380,384,386,387,389,390,396,400,401,404,407,410,411,414,435,442,463,466,468,474],chemic:[9,118,158,163,187,198,199,225,281,286,287,312,346,419,420,431],chemistri:[9,280,281,283,366,384,419,420],chen:317,cheng:375,chenoweth:[419,420],chenoweth_2008:[419,420],chi:[92,153,186,271,281,283,385,387,480],chiefli:418,child:8,chip:[7,12,17,360,467],chipot:213,chiral:339,chmod:[11,12],cho:407,chocol:[7,189],choic:[3,6,12,15,16,18,40,41,54,87,141,143,157,168,184,201,204,205,208,211,214,215,227,233,236,247,249,273,281,290,312,340,346,351,352,355,357,360,391,404,411,415,454,463,464,467,468,473,474,478],choos:[1,3,6,7,8,12,16,17,18,29,39,54,87,117,154,155,188,209,210,211,212,215,222,233,236,247,249,251,252,253,254,255,277,305,309,323,345,346,352,444,449,451,463,469],chose:[439,441],chosen:[2,3,6,12,17,140,164,167,176,184,188,194,199,212,215,222,225,226,234,236,247,249,253,273,276,287,305,309,312,313,318,320,321,327,346,347,352,360,384,388,394,395,398,422,439,449,463,468,474],chri:162,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[66,75,90,93,104,106,114,144,159,161,201],chute:[4,10,228],ciccotti:293,cieplak:[6,170,466],cii:202,cij:202,circl:301,circular:[3,6,143,185],circumst:18,circumv:285,citat:[],cite:[3,7,8,12,233],cko:2,cl1:163,clarendon:[29,379],clarifi:[7,439,441],clariti:330,clark:414,class2:[],classic:[0,3,5,6,7,8,9,223,273,280,285,317,341,384],classifi:[9,436],claus:452,clean:[6,12,14,15,17,462],cleanli:[453,482],clear:[],clearli:7,clebsch:140,clermont:[9,13],clever:458,click:[2,11,22,37,44,55,164,172,183,188,230,332,340,355,373,436],client:[230,232],climb:[248,355,468],clinic:[7,13],clo:[153,186,480],clock:[12,449,468],clockwis:323,close:[3,6,11,12,13,39,41,67,141,167,187,210,211,212,227,234,236,249,267,290,293,323,326,344,346,349,351,352,355,360,362,366,376,377,407,411,423,425,441,458,464,474,476],closer:[3,41,116,162,186,187,208,212,216,314,355],closest:[210,271,290,320,387,421,435,444],cloud:474,clovertown:18,clsuter:72,clump1:[275,290],clump2:[275,290],clump3:[275,290],clump:290,cluster:[],clutter:[3,9],cmap:454,cmatrix:227,cmax:407,cmd:[11,12,273,465],cmin:407,cmm:[],cn1:202,cn2:202,cna:[],cnn:202,cnr:[9,13],cnt:[391,458],co2:[40,163,293,354],coars:[7,9,29,36,40,54,176,275,290,305,389,422,466],coarser:[346,479],coarsest:140,code:[],coeff:[3,7,8,12,21,22,33,44,50,170,171,172,177,331,332,337,373,391,395,411,424,426,428,454,456],coeffcient:454,coeffici:[],coefficienct:380,coefficient0:382,coefficient1:382,coeffieci:[6,364],coeffincientn:382,coexist:[9,225,384],cohes:[6,385,407],coincid:[122,326,371,405,406,449],cold:[6,149,229,356,474],coldest:313,coleman8:9,coleman:[9,118,163,291],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,93,98,104,106,114,144,152,159,161,164,187,189,201,213,239,245,275,285,288,290,328,345,354,356,374,394,454,461,467,483],collid:[219,305,327],colliex:163,collinear:[3,275],collis:[3,236,305,323,327,381,388,447],colllis:305,colloid:[],colombo:39,colon:[190,328,455],color1:189,color2:189,color:[3,9,41,187,188,189,208,226,280,285],column:[3,6,9,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,104,106,108,110,113,114,115,116,117,119,140,141,144,152,159,161,162,163,184,187,189,192,200,201,202,203,204,205,206,239,246,247,280,290,306,307,317,327,386,390,419,420,455,469,471,479],colvar:[],colvarmodul:12,com:[],comamnd:214,comand:[211,456],comannd:360,comb3:[],comb:[],comb_1:282,comb_2:282,combiant:377,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,92,108,115,143,157,187,188,198,203,230,239,249,273,279,309,318,326,329,331,345,346,348,352,360,374,376,377,384,385,391,403,404,427,437,439,441,446,457,462,474,479],come:[],comfort:[12,13],comm:[0,3,12,61,73,230,232,233,346,355,360,380,411,416,438],comm_modifi:[],comm_styl:[],command:[],comment:[2,7,11,12,38,56,170,184,187,234,290,317,354,355,361,382,383,385,395,407,413,420,427,437,438,439,440,441,451,452,454,474,479],commerci:7,commmand:[3,6,12,59,107,268,448,449,451,468,482],common:[],commonli:[3,6,12,17,25,57,59,105,166,187,188,190,341,389,398,427,439,441,454,457,466],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,167,168,188,189,208,209,210,212,213,214,230,232,236,238,239,240,249,272,279,281,282,283,290,305,317,328,345,356,357,358,360,381,415,451,452,456,463,464,481,483],communc:345,comp:[7,232,233,293,346,355,384,411,416,421,434,438,440],compact:[63,192,373,436],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,110,118,147,162,163,172,183,189,218,281,328,330,345,346,353,355,407,449,468,469,474,478],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,171,172,183,331,332,340,372,436],compat:[3,5,7,8,9,11,12,13,17,18,41,71,117,119,175,187,190,194,200,201,202,203,204,205,206,208,272,284,309,312,319,322,325,345,360,392,411,438,451,452,479],compens:[6,209,210,288,356,384],compet:316,competit:346,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,162,187,188,190,230,316,346,360,454,455,459],compl:17,complain:[12,17],complement:407,complementari:[7,376,396],complet:[3,6,9,12,15,41,59,71,189,204,208,213,239,273,276,279,305,316,318,330,344,355,360,385,424,426,443,449,454,459,462,466,468,471,474,479],complex:[6,8,11,12,13,25,40,42,62,140,152,164,165,236,301,326,343,355,384,438,452,454,457,479],compli:[312,316],complic:[6,7,9,12,13,199,225,452],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,93,94,97,104,105,106,107,108,109,110,112,113,117,127,130,131,132,133,136,137,138,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,156,157,159,160,161,187,188,189,195,196,200,201,202,203,204,205,206,207,211,212,214,215,220,223,228,232,233,236,239,241,245,246,248,249,250,253,254,255,266,267,269,270,272,273,274,277,288,290,292,293,294,298,299,302,305,308,309,310,312,319,320,325,326,327,345,348,352,353,354,355,360,380,384,388,405,406,424,426,427,454,455,464,472,479,480],componenet:6,composit:[6,199,236,382],compound:[375,384,385],compres:[71,114,201],compress:[3,6,59,71,114,167,187,188,189,201,214,247,253,277,280],compris:[40,326,394,421,443],compton:[118,163],comptu:[3,6],compuat:346,comput:[],computation:[3,6,209,210,317,366],computational:474,compute_arrai:8,compute_fep:[194,404],compute_group_group:225,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[118,291],compute_scalar:8,compute_temp:8,compute_ti:194,compute_vector:8,compute_xrd:163,concaten:[2,3,482],concav:326,concentr:382,concept:[6,144,154,201,463],conceptu:[3,6,71,152,212,214,355,376,391,407,459],concern:[6,73,87,226],concis:[11,316],conclud:12,concret:8,concurr:[9,16,346],conden:[317,439,441],condens:[6,146,317,362,378,382,396],condit:[],conducit:6,conduct:[],cone:457,confid:[3,468],config:[12,187,451],configfil:213,configur:[1,2,6,12,15,17,38,59,122,166,184,186,187,188,192,212,213,214,215,219,225,232,233,261,273,281,316,343,353,355,362,366,383,407,437,439,441,449,454,456,457,468],confin:[454,468],conflict:[3,40,411,452],conform:[3,6,13,59,211,212,248,289,294,316,339,355,384,466],confus:3,conjuct:380,conjug:[7,8,233,352,384,419,420],conjunct:[6,7,71,86,87,114,147,152,158,164,168,189,193,194,233,236,240,261,276,277,281,282,283,285,290,305,313,320,325,345,346,355,367,369,373,376,380,384,390,396,411,414,422,442,454,457,461,474,483],connect:[3,6,87,149,167,211,230,275,290,293,302,355,377,388,435,441,451,452,458,474],conput:3,consecut:[3,11,12,39,71,164,189,193,194,215,230,231,376,396,400,449,455,457],consequ:[1,6,317,395,468],conserv:[3,192,199,211,218,219,226,229,233,235,236,240,245,247,249,261,290,293,308,309,313,320,321,325,355,379,380,388,402,463,468],consid:[6,9,70,71,78,87,115,149,150,167,187,189,193,194,200,202,204,208,210,211,215,237,250,272,290,312,313,316,317,320,346,373,384,391,420,421,435,449,450,452,455,456,457,459,462,464,472,474,479],consider:[6,8,233,234,308,309,310,360,463],consist:[3,6,8,9,11,12,40,42,65,69,79,92,104,108,111,112,115,144,147,149,164,176,186,190,195,196,201,214,215,218,220,223,226,233,234,235,246,249,251,252,253,254,255,256,257,259,260,261,262,264,265,266,267,268,269,277,280,285,287,289,290,308,309,310,311,321,345,346,348,354,355,360,362,366,368,374,376,384,387,391,405,406,407,411,421,424,426,438,444,452,454,455,457,458,459,466,474,479],consistent_fe_initi:198,consit:290,constant:[],constitu:[3,6,239,290,322,326,374,421],constitut:[424,426],constrain:[3,6,8,142,143,144,145,147,150,151,152,153,154,156,157,192,201,215,225,226,231,239,243,275,276,288,290,293,303,313,320,353,354,384,459,466,474],constraint:[],construct:[6,8,14,38,54,56,61,64,67,70,72,73,77,118,140,163,212,249,272,289,326,356,360,379,411,435,437,438,457,458,479],constructor:8,consult:420,consum:[1,285,415,479],consumpt:343,contact:[],contact_stiff:[423,425],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,116,118,140,144,152,162,163,164,166,170,172,183,184,187,188,189,190,192,193,194,198,200,201,202,203,204,205,206,208,213,215,220,227,231,232,233,234,236,247,261,271,272,275,276,278,280,283,287,290,291,295,305,312,316,317,326,327,330,344,346,354,355,358,359,361,362,363,366,375,376,379,382,383,384,391,392,407,413,417,418,419,420,427,437,438,439,440,441,442,449,450,451,452,454,455,456,457,459,461,463,466,468,471,472,474,479,481,483],content:[12,18,420,470,472],context:[3,6,8,12,17,117,189,209,210,215,275,287,321,352,446,454,461,470,478,479,480],contibut:70,contigu:451,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,103,104,160,189,192,193,194,199,201,202,203,204,205,206,208,211,212,213,214,215,225,226,227,229,230,231,233,234,235,241,246,247,249,251,252,253,254,255,266,267,268,269,274,276,279,280,290,291,294,304,305,307,314,315,317,323,326,330,344,359,360,366,380,381,398,401,419,420,421,424,426,440,449,452,454,456,457,462,468,471,472,479,481],continuum:[6,7,9,198,317,424,426],contour_integr:198,contract:[59,212,214,249,277,290],contradictori:3,contrain:293,contraint:261,contrari:[227,234],contrast:[1,6,42,55,64,149,214,328,424,426,446,482],contrib:317,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,93,102,104,106,107,108,109,110,112,114,117,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,194,199,200,201,202,203,204,205,206,212,225,233,236,239,240,244,250,267,268,275,276,284,287,290,291,293,319,345,353,355,363,380,381,382,384,391,405,406,411,419,420,466,472,474],contributor:12,control:[3,5,6,7,8,11,13,16,27,29,41,87,91,122,140,173,187,188,192,198,199,208,212,213,214,229,230,233,234,249,251,252,253,254,255,277,282,290,296,297,308,309,310,317,321,343,345,357,384,387,419,420,423,425,437,441,449,451,463,469,470],control_typ:198,controlfil:420,convect:91,conveni:[6,12,29,187,190,206,291,348,427,479],convent:[3,8,9,29,175,182,183,189,289,302,329,382,384,479],converg:[3,6,41,88,187,188,190,195,208,211,212,220,223,253,280,282,285,289,293,351,352,353,355,375,376,396,449,461,468],convers:[3,8,140,188,189,199,202,277,345,376,377,378,384,396,400,404,414,452,468,478],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,164,171,187,188,189,206,247,328,331,333,336,339,348,355,361,382,439,441,447,452,454,455,456,461,471,474,478,479,481,483],convex:326,convinc:[7,12],cooki:7,cool:[7,154,229,288],cooordin:187,cooper:[5,7],coord123:114,coord1:[3,114,201,204,205],coord2:[3,114,201,204,205],coord3:[3,114,201,204,205],coord:[],coordiat:353,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,93,103,104,106,113,114,116,134,140,147,153,159,161,162,164,168,186,187,188,189,190,192,195,200,201,203,204,205,208,209,210,211,212,213,214,215,218,220,221,223,225,228,229,230,231,232,233,234,246,248,249,251,252,254,255,267,270,271,272,275,276,277,287,288,290,292,293,294,299,302,303,304,305,307,315,316,317,324,325,327,328,348,353,354,355,360,361,362,365,383,449,454,455,457,459,462,464,468,474,479,480],coordn:[114,201],coorind:104,copi:[0,3,4,8,11,12,15,17,40,119,188,317,355,373,419,452],copper:447,coproccesor:16,coprocessor:[1,4,7,9,16,17,360,467],coproprocessor:17,copy_arrai:8,copyright:[7,8,275],coral:189,core:[],core_shel:146,coreshel:[6,9,369,376,378],cornel:[6,170,466],corner123i:113,corner123x:113,corner123z:113,corner1i:113,corner1x:113,corner1z:113,corner2i:113,corner2x:113,corner2z:113,corner3i:113,corner3x:113,corner3z:113,corner:[3,6,40,113,188,326,327,348,443,454],cornflowerblu:189,cornsilk:189,corpor:16,corr:375,correct:[3,6,9,11,12,16,17,59,87,88,102,110,116,146,151,158,188,214,227,233,249,250,267,275,277,280,316,322,326,345,355,361,362,363,364,365,366,367,368,369,370,371,372,374,375,376,377,378,379,380,381,382,383,384,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,443,445,446,447,454,469,472,474],correction_max_iter:198,correctli:[3,8,9,11,17,71,81,102,103,142,143,145,147,149,150,151,152,153,156,157,160,187,189,195,215,220,223,234,243,249,250,283,290,293,302,304,323,326,355,356,360,378,406,451,452,454,464,478,480],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,43,44,45,46,47,48,49,51,53,54,56,70,71,87,96,97,109,112,113,114,115,118,119,127,130,131,132,133,134,136,137,138,140,142,143,151,158,163,170,171,172,173,174,175,176,178,179,181,182,184,187,188,189,193,194,195,201,203,204,205,207,210,212,214,221,223,224,228,233,236,237,245,246,247,249,251,252,253,254,255,256,261,264,266,267,269,272,273,277,282,290,292,293,308,310,312,321,322,323,325,326,327,329,331,332,333,334,335,336,339,341,346,350,352,354,355,361,362,364,367,368,369,370,371,372,373,374,375,376,379,380,382,383,384,385,386,387,388,389,390,391,394,396,397,398,399,400,401,402,403,404,405,407,408,411,412,413,414,416,417,419,420,421,422,427,428,437,438,439,440,441,443,445,446,447,449,451,452,454,455,457,467,468,469,471,472,474,479],correspondingli:[405,406,463],cosin:[],cosineshift:27,cosmo:[227,232],cossq:[],cost:[1,6,10,11,12,17,39,41,71,109,118,141,163,188,189,201,204,205,208,209,210,222,249,282,317,345,346,358,376,396,400,411,437,451,463],costheta0:[437,439,441],costheta:417,costli:[11,88,227,356],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,93,104,106,109,112,114,144,154,159,161,177,187,188,189,193,194,199,201,202,204,208,214,223,232,279,280,281,285,288,290,292,305,306,312,316,317,318,322,326,328,330,337,342,344,351,353,356,360,363,386,390,391,419,420,450,451,452,454,456,458,461,462,470,474,479,480],coulomb:[3,5,6,7,8,9,10,12,14,15,18,88,107,108,141,165,169,281,283,318,345,346,353,360,367,369,370,371,372,375,376,377,378,379,384,388,389,391,396,400,404,411,414,419,420,422,436,441,442,446,459,466,472,474,478],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,41,63,68,77,91,114,116,117,152,162,168,195,196,199,201,203,204,205,207,208,215,220,222,225,231,249,261,276,293,308,309,326,346,353,354,355,357,360,386,390,411,472,479],counter:[323,449,460,462,468],counterbal:229,counterpart:[187,290,449],counterproduct:18,coupl:[],courant:295,cours:[3,8,126,128,158,187,193,194,226,289,302,316,322,324,325,327,328,346,405,428,451,454,467,474,479,481],coval:[6,29,384,407,474],covari:227,cover:[6,71,184,189,198,236,384,394,443],coverag:[71,204],cpc:232,cpp:[1,3,6,8,9,11,12,13,87,187,193,194,223,293],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,189,192,218,234,318,343,346,360,373,436,449,467,468,471,472],cpuremain:472,cr2:163,cr3:163,crack:[4,356],crada:[5,7],crai:[5,7,13,18,187],crash:[3,356,474],craympi:360,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:198,create_faceset:198,create_nodeset:198,createatom:[],creation:[],crimson:189,critchlei:275,criteria:[3,116,165,188,189,209,210,211,244,353,416,443,456,459,479],criterion:[41,121,162,164,167,199,208,211,225,261,282,295,323,328,353,355,375,384,388,459,468,469],criterioni:468,critic:[48,49,247,312,317,353],cross:[3,12,22,71,89,143,172,187,188,200,204,210,214,246,248,267,290,298,302,304,313,320,332,348,355,371,380,381,382,389,390,391,396,398,400,417,422,424,426,439,441,454,458,464,481],crossov:1,crossterm:454,crozier:[0,7,13],crucial:280,crystal:[4,6,13,73,271,272,315,356,458,472,474],crystallin:[6,272,348,440,474],crystallis:312,crystallogr:[118,163],crystallograph:[348,472],crystallographi:[118,163,348],cs1:163,cs_chunk:6,cs_im:[40,454],cs_re:[40,454],csanyi:[140,418,427],cscl:407,csequ:6,csh:[11,12,373],cshrc:[11,12],csic:[383,437,439,441],csinfo:6,csisi:[383,437,439,441],csld:[],cst:382,cstherm:6,cstyle:451,csvr:[],ctcm:[361,382],ctemp_cor:218,cterm:294,ctr:9,ctype:11,cu1:163,cu2:163,cu3au:407,cube:[6,41,162,167,208,218,326,348,474],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:366,cummul:[3,6,206,209,210,211,213,222,227,233,235,305,308,309,310,311,313,320,390,472],cumul:[6,199,201,203,204,205,219,225,233,247,249,253,261,290,291,355],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,102,108,116,117,130,141,144,152,160,162,165,168,187,188,189,190,193,194,198,199,201,204,205,206,208,209,210,211,212,213,214,215,219,220,223,225,227,230,231,233,239,246,249,250,254,255,261,266,267,269,275,281,282,284,287,288,289,290,293,294,295,296,297,298,299,301,303,304,305,308,309,310,316,317,320,321,322,323,324,325,327,328,330,343,344,345,346,349,350,352,353,354,355,360,366,373,375,379,382,384,385,388,392,395,405,406,407,408,409,411,417,419,420,423,424,425,426,428,439,441,442,444,449,450,451,452,454,455,456,457,458,460,461,462,464,466,468,469,471,472,479,480,481,482,483],curv:[6,164,225,272],curvatur:[387,421,447],custom:[],cut0:452,cut1:463,cut2:463,cut:[],cuthi:[271,283],cutinn:[368,405,406],cutlo:[271,283],cutmax:417,cutoff1:[372,379,396,400,404,414,422],cutoff2:[367,369,370,372,378,379,396,400,404,414,422],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,108,115,116,140,162,165,167,210,211,216,271,280,281,283,285,287,290,305,318,322,326,328,345,346,353,356,357,358,360,361,362,363,364,365,366,367,368,369,370,371,372,374,376,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,419,420,421,422,427,428,429,430,431,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,452,456,459,463,474],cutoffa:383,cutoffc:383,cuu3:382,cval:163,cvd:312,cvel:294,cvff:[],cwiggl:[3,246,322,325,327,479],cyan:[2,188,189],cycl:[3,225,247,249,250,253],cyclic:[3,184],cygwin:12,cylind:[3,4,188,231,276,323,326,457],cylindr:[6,231,302,323],cypress:360,cyrot:366,cyrstal:272,d3q15:236,d3q19:236,d_double_doubl:15,d_e:317,d_flag2:279,d_flag:279,d_name:[113,187,279,307,464],d_single_doubl:15,d_single_singl:15,d_sx:279,d_sy:279,d_sz:279,daan:315,dai:12,daili:12,daivi:267,damag:[],dammak:285,damp:[3,6,192,197,233,234,235,240,249,250,253,277,280,285,290,308,309,321,323,324,352,353,355,367,369,371,376,379,384,388,396,404,414,422,436,442,468,474],damp_com:234,damp_drud:234,dampen:[290,474],dampflag:[323,388],dan:17,danger:[3,12,225,328,380,472],dangl:167,daniel:9,darden:[346,379],darkblu:189,darkcyan:189,darken:188,darkgoldenrod:189,darkgrai:189,darkgreen:189,darkkhaki:189,darkmagenta:189,darkolivegreen:189,darkorang:189,darkorchid:189,darkr:189,darksalmon:189,darkseagreen:189,darkslateblu:189,darkslategrai:189,darkturquois:189,darkviolet:189,dasgupta:281,dash:[388,471],dat:[6,91,184,198,450],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,291],dataset:291,datatyp:3,date:[0,6,12,13,419,420,479],datom1:115,datom2:115,datom3:115,datom4:115,datum:[3,6,42,65,68,69,79,92,108,115,187,202],davi:322,david:[9,19,345,346,439,441],daw:[382,417],dbg:14,dcd:[3,6,7,187,188,189,190,273,455,459],ddim:186,deactiv:404,dealt:232,debug:[6,7,11,12,13,14,17,118,122,163,164,273,278,343,345,360,392,411,444,452,453,456,461,464,471,479],deby:[],decai:[376,447],decid:[3,6,12,16,71,246,279,290,318,469],decipher:348,declin:305,decod:188,decompos:[87,427],decomposit:[3,5,7,18,62,198,273],decoupl:[6,474],decreas:[3,187,195,196,211,214,220,223,233,316,345],decrement:294,deepli:342,deeppink:189,deepskyblu:189,def:[12,13,452],defaul:61,defect:[6,70,162],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,170,171,172,173,174,175,176,178,179,181,182,183,184,185,186,187,188,189,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,218,219,220,223,224,225,228,231,232,233,234,235,236,244,246,248,249,250,251,252,253,254,255,257,258,259,262,264,265,266,267,268,269,271,272,273,275,276,277,279,281,283,288,290,291,292,293,295,299,303,305,307,308,309,310,311,313,314,315,317,319,320,322,323,324,325,326,327,328,330,331,332,333,334,335,336,339,340,341,343,345,346,348,350,352,353,354,355,356,357,358,359,360,362,363,364,365,367,368,369,370,371,372,373,374,376,377,379,380,381,383,384,386,387,388,389,390,391,392,394,396,397,398,399,400,401,402,403,404,405,406,410,411,412,413,414,416,417,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,451,452,454,455,457,458,459,460,463,464,465,466,468,469,471,472,474,475,476,477,478,479,480],definit:[2,3,6,8,12,13,78,80,116,140,189,201,202,203,204,205,206,214,231,253,291,307,319,322,325,327,329,340,343,354,363,366,374,384,394,417,424,426,427,443,452,454,456,463,465,478,479],defint:472,deform:[],deg2theta:163,deg:474,degener:[3,275],degrad:[8,18,272,346,463],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,94,96,97,99,101,102,112,142,143,144,145,146,147,148,149,150,151,152,153,154,156,157,163,164,170,171,174,175,182,184,186,188,201,211,218,225,227,228,233,234,239,249,250,253,254,255,266,267,269,273,275,289,290,293,308,309,310,315,331,333,336,339,341,353,379,382,390,464,472,474,480],degress:[144,201],del:468,delai:[3,6,12,356,381,472],deleg:391,delet:[2,3,7,8,12,54,57,60,63,162,167,168,192,201,202,203,204,205,206,209,211,222,225,249,291,308,309,328,330,344,354,356,359,411,454,455,457,465,466,471,475,477,479,480],delete_atom:[],delete_bond:[],delete_el:198,deli:186,delimit:[452,479],deloc:[250,384],delr:407,delt_lo:468,delta:[],delta_1:366,delta_3:366,delta_7:366,delta_conf:3,delta_ij:[407,417],delta_mu:[3,199],delta_pi:366,delta_r:417,delta_sigma:366,delx:186,delz:186,demand:285,demo:11,demon:270,demonstr:[280,407],den:276,dendrim:390,denniston:[9,236,238,239,240,272],denomin:[7,169],denot:[118,218,234,272,283,285,376,389,391,420,424,426],dens:[71,211,384],densiti:[3,6,7,9,18,40,41,59,100,116,126,140,150,162,164,193,194,198,201,204,205,208,214,223,236,239,242,243,272,276,277,281,317,322,348,350,354,361,366,382,407,408,409,417,421,430,432,433,434,454,463,464,472,478],density_continu:426,density_summ:426,depart:[0,7],departur:[247,280],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,108,109,112,113,114,115,119,140,142,147,151,152,158,164,165,170,171,172,173,174,175,176,178,179,181,182,183,184,186,187,188,189,192,193,194,195,196,199,201,203,204,206,207,208,210,212,220,221,224,227,228,229,231,233,234,236,238,239,246,249,251,252,253,254,255,256,264,266,267,269,271,282,285,287,290,292,293,299,305,308,309,310,312,314,316,317,319,321,322,325,326,327,328,330,331,332,333,334,335,336,339,341,346,348,353,354,356,357,358,360,361,362,364,365,366,367,368,369,370,371,372,373,374,375,376,377,379,380,382,383,384,385,386,387,388,389,390,391,394,396,397,398,399,400,401,402,403,404,405,407,408,410,412,413,414,416,417,419,420,421,422,427,428,436,437,438,439,440,441,442,443,445,446,447,449,451,454,456,457,460,464,466,468,471,472,473,479,480],dependend:6,depflag:12,dephas:[449,468],depos:215,deposit:[],deprec:281,depth:[51,143,188,317,387,421],dequidt:9,der:[87,107,374,375,404,419,420,446,474],deriv:[6,7,8,38,56,63,87,140,158,184,202,212,214,225,233,246,249,251,252,253,254,255,271,277,281,285,314,315,317,322,323,326,352,354,362,366,374,379,384,385,389,398,402,403,407,419,420,436,438,446,474],derjagin:446,derlet:271,descend:189,descent:[7,352],descib:[40,281],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,110,113,116,118,130,140,141,143,144,148,149,152,155,157,158,162,163,164,166,167,176,181,184,187,192,193,194,201,202,203,204,205,206,208,211,212,213,214,215,217,218,226,227,230,231,232,233,234,235,236,238,239,240,244,248,249,250,253,260,268,271,273,278,279,280,281,282,283,290,294,302,305,306,307,308,309,310,311,312,313,314,315,320,322,323,325,330,345,346,348,351,352,353,354,355,359,362,363,365,367,368,369,371,372,373,374,375,376,379,382,384,385,387,388,389,391,396,397,398,399,400,401,402,403,404,405,406,407,410,416,417,418,419,420,421,422,427,428,435,436,437,438,439,440,441,442,445,446,447,449,451,452,454,455,457,458,464,467,468,471,479,480,481],descript:[],descriptor:[140,187,392],deserno:346,design:[0,3,6,7,8,11,13,14,15,17,118,146,149,163,198,211,217,218,249,250,271,272,291,312,317,363,364,365,368,371,376,378,384,404,405,406,408,409,417,420,438,463],desir:[2,3,6,7,11,12,14,15,16,18,33,40,50,59,71,88,91,112,117,141,146,164,177,186,199,212,214,223,225,226,233,234,235,239,249,267,275,276,277,278,281,285,290,293,305,308,309,310,311,316,323,337,342,345,346,348,351,353,354,355,380,382,390,405,406,437,439,441,450,451,452,454,458,463,468,469,471,472,479,480,481],desk:7,desktop:[4,6,7,10,12,17,188],despit:474,destabil:366,destre:339,destroi:[11,39,209,210],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,93,102,104,106,107,109,111,112,114,117,119,140,141,142,143,144,147,157,158,159,161,164,165,168,169,172,183,187,188,189,192,193,194,198,201,202,203,204,206,208,210,211,212,213,214,215,223,225,226,227,228,230,231,233,235,236,240,246,247,248,249,250,251,252,253,254,255,259,261,266,267,268,269,272,275,276,277,279,280,282,283,284,290,293,305,308,309,310,311,312,313,315,316,317,318,319,320,321,328,330,332,340,345,346,349,353,354,356,357,360,361,362,363,365,366,368,370,371,372,373,374,375,376,379,380,384,385,387,388,389,390,391,394,396,397,398,399,400,401,402,403,404,405,406,407,410,411,416,419,420,421,427,428,436,443,445,446,452,454,455,456,457,459,460,463,464,466,469,472,479,480,483],detect:[2,3,12,61,63,86,224,276,316,355,375,390,395,449,451,454,465,468,479],determ:360,determin:[1,3,6,8,12,15,39,40,42,51,57,58,59,61,62,68,71,87,102,107,109,112,118,119,127,141,152,153,162,163,164,186,187,188,189,190,191,195,196,197,200,201,202,203,204,205,206,207,208,212,214,215,218,220,225,228,229,231,233,234,239,244,246,247,249,254,255,266,267,269,271,273,277,280,287,288,289,290,291,292,295,297,299,305,308,309,310,312,318,319,322,323,324,325,326,327,328,340,345,346,348,354,356,357,360,362,363,370,375,379,381,382,386,388,391,392,400,407,411,420,421,435,438,442,446,451,454,455,457,459,461,464,468,470,471,478,479,480],detil:108,devan:[9,422],devanathan:441,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,230,253,275,280,281,284,362,366,384,409,456],devemi:9,deviat:[247,253,271,386],devic:[1,3,12,15,17,230,360],device_typ:360,devin:[282,375],devis:409,dfactor:188,dff:474,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,346],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,284],dhi:[59,186,214,276],dhug:[247,280],dhugoniot:[247,280],dia:407,diagnost:[],diagon:[3,6,83,140,141,212,249,277,290,320,424,426],diagonalstyl:427,diagram:[41,118,163,183,208,273],diallo:390,diam:[188,189,276,354],diamet:[3,6,40,113,164,187,188,189,193,194,233,276,290,305,321,323,354,374,387,388,394,398,421,443,446,454,455,464],diamond:[348,384,407],diamter:[40,276],dick:6,dicsuss:246,dictat:[199,247],did:[3,12,353,380,381,382,388,411,439,441,462],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,160,319,345],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,94,96,97,120,140,142,143,144,145,147,150,151,152,153,154,156,157,158,164,165,167,172,183,184,186,187,188,189,192,194,197,199,201,203,208,209,210,211,212,213,214,218,224,225,226,227,228,229,230,233,234,236,246,249,250,251,252,254,255,257,259,262,264,265,266,269,271,273,275,277,280,281,282,285,288,290,293,294,302,303,305,308,309,310,313,314,315,317,320,321,322,323,326,330,331,340,342,344,345,346,348,349,351,352,354,355,357,358,359,360,361,362,366,370,371,373,374,375,380,382,384,387,388,389,391,394,396,397,399,400,407,408,409,410,411,413,417,419,420,421,422,423,424,426,427,428,436,437,438,439,441,443,446,447,448,449,451,452,454,456,457,458,459,462,463,464,466,468,469,471,472,474,478,479,480,481],differenti:[1,3,6,29,184,345,376,417,440],difficult:[212,273,360,390,463],difficulti:[293,419],diffract:[],diffus:[],digit:[2,3,189,330],dih_table1:184,dih_table2:184,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:210,dihydrid:384,dij:293,dilat:[],dim1:3,dim2:3,dim:[3,59,71,142,145,146,147,150,151,152,153,154,156,164,186,204,214,231,323,348,407,457,478,479,480],dimdim:479,dimems:272,dimens:[],dimension:[3,39,112,118,140,142,144,145,146,147,150,151,152,153,154,156,163,185,201,204,248,272,317,348,351,355,417,454,464],dimensionless:[105,121,122,124,127,129,131,136,140,317,346,427,446],dimentionless:135,dimer:[6,290,407],dimgrai:189,dimstr:[41,208],dinola:[277,308],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,187,307,474],dir1:465,dir2:465,dir:[1,3,4,8,11,12,247,271,280,304,417,419,420,452,465,479],dirac:140,direc:417,direct:[],directli:[3,6,8,9,11,12,87,113,140,187,188,195,220,227,231,236,272,291,309,321,323,324,325,326,348,352,360,361,362,367,369,370,376,379,382,384,396,400,411,414,422,435,452,464,465,466,472,479],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,60,190,213,232,275,281,284,301,305,314,315,355,359,361,362,366,373,375,376,382,383,385,392,393,404,407,408,409,413,417,418,419,420,427,437,439,440,441,452,454,455,456,465,479],disabl:[3,12,16,317,395,452,467],disadvantag:[6,208],disallow:[214,249],disappear:456,discard:[2,3,41,71,204,208,318,326,451,456,457],discontinu:[9,184,353,402],discourag:407,discov:[13,318],discret:[6,8,40,42,188,189,233,236],discuss:[],disk:[6,84,85,157,185,215,225,276,452],disloc:70,disord:[39,70],disp:[],dispar:421,disperion:[379,400],dispers:[3,6,7,9,162,272,345,346,370,379,400,405,411,420,438],displac:[],displace_atom:[],displace_box:59,displacemet:457,displai:[11,13,22,37,44,55,172,183,187,188,332,340,373,436],dispters:3,dissip:[6,226,233,272,314,315,368,380,388,405,406,436],dissolut:209,dist:[6,69,91,108,117,187,273,289,381,435,449,480],distanc:[3,6,7,9,12,20,21,29,39,43,45,46,47,48,49,51,53,54,55,56,58,59,61,63,64,66,69,71,72,73,74,75,76,77,81,86,89,90,93,103,104,105,106,108,114,115,116,117,118,120,134,140,153,159,162,164,165,166,167,171,186,187,188,189,197,201,204,205,209,210,211,212,214,215,216,219,225,231,236,246,247,248,249,253,261,271,272,276,280,281,288,289,290,293,294,298,302,303,304,305,312,313,315,316,317,320,322,323,324,325,326,327,331,345,346,348,351,353,355,356,357,360,363,364,365,366,367,368,369,370,371,372,374,376,377,378,379,380,381,382,383,384,386,387,388,389,390,394,395,396,397,398,399,400,401,402,403,404,405,406,407,410,411,412,413,414,415,416,417,419,420,421,422,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,449,452,454,457,463,464,468,472,474,478,480],distinct:[6,218,287,345,421],distinguish:[6,86,140,239,384],distort:361,distrbut:361,distribut:[],distro:[111,373,416,417],ditto:[8,11,12,14,15,16,17,18,115,210,452],div:8,divd:117,diverg:[3,12,39,290,315,456,474,481],divid:[3,6,16,41,91,112,117,126,128,141,161,162,172,183,189,201,202,203,208,214,271,313,320,325,345,353,355,385,420,463,471,479],divis:[6,236,366,394,404,451,454,472,479],dl_poli:7,dlambda:158,dlammps_async_imd:230,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,188],dlammps_gzip:[3,12,187,188,316,454,455,459],dlammps_jpeg:[3,12,188],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,188],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,187],dlen:464,dlmp_intel_offload:[12,16],dlo:[59,186,214,276],dlvo:[7,374,446],dm_lb:236,dmax:[305,351],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,93,102,104,105,106,107,109,111,112,114,117,119,141,143,144,157,159,161,164,165,166,172,183,187,188,189,190,192,193,194,199,200,201,202,203,204,205,206,215,225,233,234,244,249,250,254,255,259,266,267,268,269,276,279,290,302,305,308,309,310,319,32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,92,108,115,118,127,130,131,132,133,134,136,137,138,162,184,189,203,204,205,213,280,328,354,366,383,407,413,420,427,437,438,439,440,441],entropi:468,entry1:[38,56,189,373,438],entry2:189,entryn:189,enumer:[165,187],enumuer:6,env:360,environ:[1,3,6,11,12,16,17,18,188,227,232,271,360,361,366,373,375,383,384,417,439,451,465,479],epair:[107,189,386,390,419,420,472],epen:[419,420],epfl:[227,232],epp:379,epq:379,eps0:446,eps14:404,epsilon0:441,epsilon:[3,6,36,45,46,50,53,54,87,170,193,194,225,290,305,322,326,351,353,365,371,372,374,376,377,378,379,387,389,390,391,394,395,396,397,398,399,400,401,402,403,404,410,414,421,422,431,437,443,445,446,463,474,478],epsilon_0:447,epsilon_14:371,epsilon_:421,epsilon_d:377,epsilon_i:[387,411,421],epsilon_i_:421,epsilon_i_a:[387,421],epsilon_i_b:[387,421],epsilon_i_c:[387,421],epsilon_ij:411,epsilon_j:[387,411,421],epsilon_j_:421,epsilon_j_a:[387,421],epsilon_j_b:[387,421],epsilon_j_c:[387,421],epsilon_lj:421,epton:416,eqch:159,eqeq:[419,420],eqp:379,eqq:379,equal:[2,3,6,8,11,12,17,39,41,54,63,65,68,69,76,79,86,87,91,92,108,110,115,117,119,141,143,158,160,164,188,189,192,193,194,195,196,199,202,203,206,207,208,212,214,215,220,225,226,228,229,231,233,234,236,239,240,246,247,253,263,271,273,276,278,280,281,282,285,287,289,290,292,294,299,301,308,309,310,313,314,315,317,319,320,322,325,327,328,330,344,353,355,356,357,359,360,375,380,386,387,390,405,410,417,419,420,421,423,424,425,427,428,438,443,447,450,451,452,454,456,457,461,462,465,468,470,472,479,480],equat:[3,6,7,8,9,91,112,118,163,172,183,192,212,218,219,227,233,234,236,239,247,248,249,250,253,267,271,273,280,281,285,293,305,313,317,320,322,323,325,327,339,345,346,374,379,380,384,385,388,393,405,406,407,411,421,424,426,430,431,433,434,442,447,474],equi:250,equidist:248,equil:[3,281,349,461,483],equilater:464,equilibr:[3,4,5,6,7,9,59,91,164,192,199,202,211,212,225,247,249,250,267,268,280,281,282,283,313,314,315,320,375,376,419,420,450,464],equilibria:320,equilibribum:[209,210],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,147,148,171,173,212,214,225,226,227,234,236,249,253,267,280,285,289,293,294,302,305,312,313,315,320,331,333,336,339,375,407,413,474],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:198,equival:[6,12,13,59,124,125,133,138,162,166,189,203,206,212,214,225,233,249,267,277,289,290,325,380,384,439,441,454,457,462,463,472,474],equlibrium:6,equliibr:[281,283],er3:163,eradiu:[40,113,384,454],eras:[292,314],erat:[214,406],erc:376,erfc:[376,396,411],erforc:113,erg:478,erhart:[199,382,439,441],ermscal:363,ernst:9,eror:3,eros:407,erose_form:407,erot:[],errata:[439,441],erratum:322,erron:3,error:[],erta:388,ervel:[113,454],escap:[215,474],especi:[8,11,16,152,164,192,199,208,225,280,285,288,289,360,451],espresso:[9,284],essenti:[8,11,12,27,88,128,145,146,147,150,151,152,153,154,156,173,202,253,272,321,346,362,376,396,441,459,472],essex:29,establish:[87,229],estim:[1,3,6,10,12,38,41,56,91,141,198,208,219,247,305,312,345,346,351,411,420,438,468,472],esu:478,esub:407,eta:[6,236,249,280,281,283,321,383,385,387,417,440,478],eta_dot:249,eta_ij:417,eta_ji:385,etag:[40,454],etail:472,etap:249,etap_dot:249,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,17,39,40,42,54,61,68,89,90,91,94,109,110,113,115,141,142,144,145,146,147,148,150,151,152,153,154,156,158,164,166,167,168,177,187,188,189,192,198,199,200,201,203,204,205,206,209,210,214,215,223,225,226,233,249,276,287,291,317,318,326,330,344,345,353,354,355,356,358,382,383,391,404,406,415,419,420,437,439,441,449,452,454,455,456,461,463,464,468,470,471,472,474,478,479,481,483],ethernet:18,etol:[353,355,449,468],etot0:280,etot:[6,94,96,97,110,141,150,189,218,234,247,280,471,472],eu2:163,eu3:163,euler:[353,355],eulerian:198,euqat:429,europhi:236,evalu:[2,3,11,12,38,56,71,87,88,91,107,117,140,144,154,162,164,187,188,189,193,194,195,196,198,200,201,202,203,204,205,206,207,214,220,226,228,229,231,232,233,234,272,278,281,292,295,299,308,309,310,319,322,325,327,328,330,345,346,351,353,360,411,417,423,425,438,449,450,452,456,457,459,461,462,463,464,468,470,472,479,480],evalut:[330,452],evan:[152,267],evanseck:[6,20,170,371,466],evapor:[],evaul:[8,353],evdwl:[107,419,420,472],even:[3,6,8,12,15,16,17,18,34,39,41,52,57,59,61,63,70,71,119,165,166,180,184,187,189,192,193,194,199,200,201,203,204,205,206,208,209,210,212,214,215,218,231,234,247,249,250,272,285,287,290,291,301,305,313,317,320,322,326,328,338,345,351,353,355,360,365,384,385,388,391,411,421,444,454,455,457,459,460,461,463,464,466,469,471,472,474,483],evenli:[3,41,141,184,208,236,394,444,454],event:[],eventu:[3,6,12,15,166,281,468],ever:[54,56,232,305],evera:[374,387,421,436],everi:[0,1,2,3,6,8,11,12,15,16,39,41,71,72,91,113,119,128,152,167,187,188,189,190,192,193,194,195,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,214,215,219,222,223,225,227,229,230,231,236,237,245,249,250,253,270,271,272,276,277,278,279,280,281,282,283,285,287,288,290,291,293,294,305,307,308,309,310,311,312,313,316,317,318,319,320,328,330,344,346,355,356,357,360,380,381,391,404,419,420,432,448,449,450,454,456,458,459,461,462,463,468,469,470,472,479,483],everyth:[8,107],everywher:[116,398],eviri:384,evolut:[227,236,273,449],evolv:[236,273,318],ewald:[2,3,5,6,7,8,12,88,110,118,141,318,345,346,353,367,369,370,376,379,384,396,400,414,422,436,438,456],ewald_disp:379,ewalddisp:3,exact:[22,41,44,71,122,158,167,172,208,211,226,227,233,234,235,276,285,286,305,317,332,345,373,456,461,468,481,483],exactli:[3,6,12,14,17,38,41,56,59,71,91,143,148,155,164,184,193,194,203,208,214,219,226,233,234,235,250,260,261,268,272,280,305,310,311,324,360,373,380,382,388,391,394,405,411,438,456,457,464,468,479],exager:474,examin:[6,8,211,272],examp:[452,479],exampl:[],exce:[3,6,16,17,18,41,58,71,166,201,204,205,208,212,214,219,222,249,272,296,297,305,353,360,454,479],exceed:[3,41,59,208,214,249,305,462],excel:384,except:[1,2,5,6,8,11,14,16,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,108,109,112,117,141,142,143,144,145,146,147,148,150,151,152,153,154,155,156,157,164,168,170,171,172,173,174,175,176,178,179,181,182,183,184,186,187,189,192,195,201,202,203,207,208,212,214,221,224,225,228,231,233,235,249,250,251,252,253,254,255,256,260,261,264,266,267,268,269,273,282,283,290,292,293,302,305,308,310,311,317,321,328,330,331,332,333,334,335,336,339,340,341,345,346,348,350,354,355,356,358,359,360,361,362,364,367,368,369,370,371,372,373,374,375,376,378,379,380,382,383,384,385,386,387,388,389,390,391,394,396,397,398,399,400,401,402,403,404,405,406,408,412,413,414,416,419,420,421,422,428,436,437,438,439,440,441,443,445,446,447,449,451,452,454,456,457,459,462,463,464,465,466,468,472,474,478,479,480,482],excess:384,exchang:[2,3,6,8,9,61,62,192,198,199,225,233,282,290,313,317,320,345,360,384,469],exchange:345,excit:[9,384],exclud:[3,6,9,12,16,17,63,71,112,140,144,151,152,168,187,201,204,209,210,237,245,275,288,290,312,323,328,353,354,356,368,388,391,405,406,411,435,466],exclus:[1,3,9,12,16,87,360,375,411,463],excurs:449,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,165,188,230,284,330,344,347,359,450,452,462,465,468,479],exemplari:226,exemplifi:384,exert:[6,231,234,285,324,325,326,346],exhaust:[198,359,479],exhibit:[249,352,384,463],exist:[3,6,7,8,11,12,13,37,55,59,68,70,122,164,165,183,188,189,192,197,207,210,212,215,225,275,276,278,328,331,333,334,336,340,349,354,360,391,419,444,450,452,454,455,456,465,466,467,479,480,481],exit:[2,3,11,12,41,57,187,208,344,359,452,453,462,471,479],exlanatori:3,exp:[],expand:[],expans:[12,140,187,465],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,102,145,156,162,184,208,220,225,227,246,271,277,279,280,285,290,328,346,356,373,407,411,449,452,454,456,459,463,468,479],expens:[6,10,71,189,271,275,290,317,328,345,346,356,360,452],experi:[6,13,15,17,207,215,230,239,248,277,289,290,351,355,380,411,463,468],experienc:[6,12,238,239],experiment:[345,360,468],expert:12,expertis:7,explain:[1,3,6,8,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,92,144,152,184,187,188,189,192,201,202,206,208,210,212,214,249,271,279,290,302,328,330,344,345,348,354,355,359,365,382,394,428,443,447,452,455,456,459,461,464,474,479,483],explan:[3,6,59,113,140,187,201,248,271,391,448,451,452,454,463],explanatori:[3,8,117,187,200,201,203,204,205,290,354,451,479],explantori:[3,286],explic:410,explicit:[6,9,11,22,44,77,87,113,116,158,172,193,194,214,296,297,332,350,362,363,366,371,373,382,384,395,405,442,448,451,455,458],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,109,112,142,151,154,162,164,170,171,173,174,175,176,178,179,181,182,184,187,189,195,204,207,214,221,224,226,228,233,249,251,252,253,254,255,256,264,266,267,269,279,280,282,290,292,293,308,310,311,317,321,331,333,334,335,336,339,341,354,360,361,362,364,367,368,369,370,371,372,373,374,375,376,377,379,380,381,382,383,385,386,387,388,389,390,391,394,395,396,397,398,399,400,401,402,403,404,405,408,411,412,413,414,416,421,422,428,429,430,431,432,433,434,436,437,438,439,440,441,442,443,445,446,447,454,456,463,464,466,467,474],explictli:[16,467],exploit:[9,15,17,273],explor:[118,163],expon:[3,281,283,382,387,390,404,410,422],exponenti:[87,417,437,447,468,479],expos:11,exposit:[198,380,381],express:[6,140,150,164,193,194,212,246,271,281,317,323,330,366,382,384,398,407,427,436,479],expressiont:366,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,94,97,98,107,109,117,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,192,195,196,199,206,207,213,216,220,223,224,225,227,228,229,231,233,235,247,249,253,261,271,272,288,289,290,292,294,299,302,304,308,309,310,311,312,314,315,317,319,322,326,327,387,407,420,421,427,471,472],extent:[1,3,41,45,57,71,162,166,187,197,204,208,231,324,327,345,348,362,423,425,438,451,454,457],exterior:[3,6,326],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,102,109,110,112,118,141,142,143,145,147,150,151,152,153,154,156,157,163,164,165,166,170,189,203,208,210,249,278,279,280,290,305,353,354,357,358,379,388,391,394,407,411,451,452,454,457,466,474,479],extract:[3,6,11,13,36,63,87,107,115,117,119,193,194,283,355,376,385,407,427,452,459,471],extract_atom:11,extract_comput:[11,452],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,188,212,214,249,315,384,440,474],extrema:404,extrins:198,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[160,319],f_a:[439,440,441],f_ave:117,f_c:440,f_f:441,f_fix_id:280,f_harm:315,f_i:417,f_id:[6,71,117,119,187,192,200,201,202,203,204,205,206,244,307,319,472,479],f_ij:417,f_indent:206,f_int:314,f_jj:91,f_k:417,f_langevin:317,f_max:[280,285],f_msst:247,f_r:[234,439,440,441],f_sigma:366,f_solid:315,f_ss:6,f_temp:234,face:[3,6,57,59,71,152,162,166,197,204,205,322,324,325,326,327,348,387,407,421,454,457],face_threshold:162,facet:162,facil:[0,12],facilit:[6,13],fact:[6,8,16,227,305,315,388,466],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,118,140,158,163,166,170,181,187,188,189,193,194,202,208,212,214,215,225,230,233,235,236,247,249,250,253,273,277,289,293,295,297,305,309,313,320,321,322,326,336,346,348,360,362,363,366,367,369,371,376,377,378,380,384,388,391,395,396,407,411,413,414,420,422,428,437,442,451,454,457,458,463,466,468,469,472,474,478,479],factori:[3,452],factoriz:345,fail:[3,11,12,59,168,212,215,345,353,355,378,420,452],failur:[121,424],fairli:[11,411,463,468],faken:73,falcon:230,fall:[3,6,189,203,276,452],fals:[86,328,330,479],fame:8,famili:451,familiar:[0,11],fan:417,far:[3,6,12,17,57,59,61,86,187,189,190,208,209,210,212,215,249,271,289,290,305,322,333,336,351,355,356,443,452,454,459,472],farago:233,farrel:[439,441],farther:187,fashion:[6,8,41,71,164,189,192,193,194,199,204,208,210,215,225,227,231,246,247,249,251,252,253,254,255,263,266,267,268,269,279,280,282,290,294,298,304,307,315,317,321,322,323,325,327,355,391,405,457,466,479,482],fasolino:393,fast:[6,7,9,12,13,17,39,187,258,280,318,345,346,368,405,406,436,438,456,461,463,472,480,483],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,105,109,112,142,151,170,171,173,174,175,176,178,179,181,182,184,187,189,192,195,207,208,221,224,228,232,233,249,251,252,253,254,255,256,264,266,267,269,277,281,282,290,292,293,305,308,310,312,314,317,321,331,333,334,335,336,339,341,345,346,357,358,360,361,362,364,366,367,368,369,370,371,372,373,374,375,376,379,380,382,383,385,386,387,388,389,390,391,394,396,397,398,399,400,401,402,403,404,405,408,412,413,414,416,421,422,428,436,437,438,439,440,441,443,445,446,447,449,463,467,474],fastest:[6,14,17,152,204,317,318,360,451],fatal:[3,471],fault:[70,420],faulti:12,fava:387,favor:211,favorit:7,fbmc:312,fcc:[],fcm:[263,479],fdirect:218,fdotr:392,fdti:87,fe2:163,fe3:163,fe_md_boundari:198,featu:8,featur:[],fecr:382,feedback:[7,230],feel:[7,230,231,239,271,326,328,355,411],felling:409,felt:326,femtosecond:478,fene:[],fennel:[376,396],fep:[],ferguson:[6,170,466],fermi:[1,12,15,150,360,441],fermion:[9,384],ferrand:[9,13],few:[1,3,4,5,6,7,10,11,12,13,14,17,18,39,190,200,201,202,203,204,205,206,234,249,276,279,281,293,319,345,353,354,355,362,451,454,459,463,465,479,481],fewer:[1,3,11,15,16,61,239,463],fewest:3,fextern:223,feynman:273,fff:452,ffield:[375,385,419,420],ffmpeg:[3,12,188],ffplai:188,fft:[1,3,7,12,14,15,88,109,110,141,272,345,346,463],fft_inc:[12,346],fft_lib:12,fft_path:12,fftbench:345,fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],fictiti:[6,195,196,220,223,227,273,289,376,396,400,435],field1:[455,459],field2:455,field:[],fifth:[302,413],figur:[1,3,8,11,12,280,451,452],fij:379,file0:271,file1:[11,13,271,316,330,354,459,461,465],file2:[11,13,316,330,354,459,461,465],file:[],filenam:[3,12,13,38,41,56,184,187,188,189,190,198,201,202,203,204,205,206,208,213,271,275,278,281,282,283,286,287,290,291,316,317,342,343,344,355,361,362,366,376,382,383,385,393,407,408,409,413,417,418,419,420,427,437,438,439,440,441,450,451,452,455,456,461,465,472,479,481,482,483],filennam:461,filep:[3,187,189,456,461,483],filepo:287,fill:[7,164,188,276,317,348,356,366,420,457],filter:[189,198],final_integr:8,final_integrate_respa:8,finchham:[6,146,378],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,117,167,184,190,199,211,212,222,225,248,271,277,285,289,351,353,355,356,376,391,396,400,407,436,438,474,479],find_custom:8,fine:[16,17,168,195,220,315,356,360,479],finer:[140,164,479],finest:345,finger:[164,186,246,457],finish:[6,11,41,208,330,342,344,345,357,359,360,443,459,479,480],finit:[],finni:[7,382,436],finvers:218,fiorin:[9,213],fire:[351,352,353,355,468],firebrick:189,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,103,104,105,112,116,117,127,130,133,134,138,141,149,152,158,160,162,163,165,166,167,171,184,187,188,189,190,192,199,201,202,203,204,205,206,208,211,214,225,226,231,236,246,247,248,249,271,273,278,279,280,282,287,290,293,294,302,303,305,306,307,314,315,316,317,319,323,328,330,331,337,348,353,354,355,356,359,360,361,362,365,366,367,369,371,373,375,376,382,384,385,388,389,392,393,395,396,400,405,406,407,409,411,413,417,419,420,427,435,437,438,439,440,441,449,450,451,452,454,455,456,459,461,463,466,467,468,471,472,474,479,480,481,483],fischer:[6,9,19,20,170,371,466],fit:[3,6,9,12,38,56,184,289,305,362,366,393,407,411,431,438,440,462,479],five:[73,150,280,354,366,408,454,468],fix:[],fix_adapt:[158,194,404],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,199,276],fix_evapor:199,fix_flux:198,fix_gcmc:[199,354],fix_gl:227,fix_gld:227,fix_grav:276,fix_id:[3,212,247,249,251,252,253,254,255,277,280],fix_modifi:[],fix_mov:[186,323],fix_nh:8,fix_npt:227,fix_nvt:[199,225],fix_poem:[3,6],fix_pour:[3,215],fix_qbmsst:9,fix_qeq:[3,375],fix_rattl:293,fix_reax_bond:419,fix_rigid:[239,365],fix_saed_vtk:291,fix_setforc:8,fix_shak:293,fix_srd:3,fix_styl:253,fix_temp_rescal:311,fixedpoint:[212,249],fixextern:223,fixid:198,fji:379,flag1:[217,358],flag2:[217,358],flag:[3,8,11,12,14,15,16,17,18,40,66,74,75,81,86,89,90,93,103,104,106,118,159,163,167,187,188,189,190,206,211,213,217,230,233,237,239,245,246,272,279,290,302,304,305,312,316,325,328,343,346,354,358,359,360,362,390,395,407,435,449,451,452,454,455,456,458,459,460,464,479],flag_buck:370,flag_coul:[370,379,400],flag_lj:[379,400],flagfld:[368,405,406],flaghi:[3,368,405,406],flaglog:[368,405,406],flagn:217,flagvf:[368,405,406],flat:[6,317,322,323,327],flavor:[2,7,12],fld:[9,322,368,405,406],flen:363,flex_press:363,flexibl:[3,6,8,165,188,201,204,213,227,250,313,320,384,440,472],flip:[3,6,214,249,324,325],floor:479,flop:12,floralwhit:189,flow:[],fluctuat:[6,64,87,212,225,226,233,236,249,253,271,272,315,317,339],fluid:[],fluid_veloc:240,flush:[3,189,471],flux:[],flv:188,fly:[7,9,12,41,188,192,198,215,218,290,293,318,366,472,474],fmackai:9,fmag:216,fmass:273,fmax:[353,472],fmomentum:218,fmsec:[2,189,233,234,246,249,277,290,308,309,463,473,478,480],fname:344,fno:12,fnorm:[353,472],fnpt:218,fnvt:218,foce:391,fock:363,focu:293,fogarti:[9,283,420],foil:[140,271,427],fold:[303,463],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,140,141,143,144,150,152,157,160,162,164,165,170,173,174,175,176,178,179,181,182,184,187,188,189,192,198,199,200,201,202,203,204,205,206,208,213,214,215,218,219,223,225,226,227,230,232,233,234,236,239,247,249,253,254,255,266,267,269,272,273,275,278,279,280,281,283,285,287,289,290,291,293,307,308,309,310,313,314,315,316,317,319,320,328,329,333,334,335,336,339,341,343,348,350,353,354,355,360,361,362,363,364,365,366,367,368,369,370,371,372,374,375,376,377,378,379,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,416,417,418,419,420,421,422,424,426,427,428,429,430,431,432,433,434,435,437,438,439,440,441,442,443,445,446,447,449,451,452,454,455,456,457,459,461,462,463,466,468,469,470,474,479,480,482],foo:[4,8,11,12,187,188,223,452,465,479],foot:6,footprint:[12,360],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:239,forcefield:[289,390],forcegroup:236,forcezero:351,ford:379,forestgreen:189,forev:71,forget:[234,474],forgiv:249,form:[2,3,6,8,12,16,19,22,44,54,63,66,74,75,77,81,87,89,90,93,103,104,106,116,140,141,158,159,168,172,189,192,193,194,210,226,227,233,235,239,246,267,272,283,285,289,290,317,322,326,331,332,339,350,352,354,355,362,363,366,373,382,384,386,390,391,395,407,409,413,414,417,419,420,421,427,428,436,438,439,440,441,446,448,451,452,454,459,464,471,474,479],formal:[6,78,80,91,226,227,233,249,273,305,313],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,172,184,187,188,189,190,201,203,204,205,206,208,210,272,275,279,281,283,286,290,291,301,316,317,328,329,332,350,354,355,361,362,366,373,382,385,395,407,409,418,419,420,422,427,438,444,451,452,454,455,456,459,470,471,472,479,481],former:[6,12,16,39,41,189,208,317,321,366,368,460,466,479],formerli:[7,13],formul:[1,40,64,141,195,220,233,249,267,281,283,289,293,316,345,362,366,382,384,387,407,416],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,87,89,90,91,94,96,97,106,112,118,141,142,143,144,145,146,147,148,150,151,152,153,154,155,156,157,163,164,169,171,172,183,187,193,194,195,196,201,202,203,206,207,214,220,228,229,231,233,234,246,271,272,278,287,292,299,303,305,308,309,310,319,322,325,327,328,330,331,332,334,340,348,354,362,363,365,366,371,372,373,374,379,380,382,383,387,388,389,390,392,395,396,398,399,400,402,403,405,406,407,410,411,412,421,422,428,436,437,439,440,441,445,446,447,450,454,457,464,471,472,478,479,480],forth:[1,6,11,12,13,14,15,359,452,457,461],fortran:[3,6,9,11,12,13,223,382,391,407,419,420],fortun:8,forward:[3,8,87,344,355,360],foster:[366,416,417],foul:167,found:[3,6,9,12,73,158,187,211,213,225,230,236,272,312,318,330,344,356,373,376,379,449,455,456,471],four:[6,11,54,81,103,104,140,160,247,317,339,354,355,449],fourier:[],fourth:[6,105,289,302,312,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7,119,307],input:[],input_doubl:3,inquir:295,insensit:12,insert:[3,5,7,8,12,59,164,192,215,225,231,276,345,427,435,452,458,474],insid:[2,3,6,8,11,71,129,135,164,187,189,200,204,205,215,216,222,225,231,236,239,276,290,305,322,324,325,326,327,328,343,348,398,452,453,454,456,457,464,468,479],insight:[6,13],instabl:[236,379,426],instal:[],instanc:[6,11,213,227,324,386,391,411,417,452,474],instantan:[6,63,211,212,226,227,249,253,272,277,280,285,287,290,312,460,472],instanti:[6,11,12,198,391,451],instead:[1,3,6,8,9,11,12,13,17,18,40,41,59,63,70,71,90,117,143,146,168,184,187,194,201,203,204,205,206,208,212,213,233,236,239,240,272,278,288,290,307,325,343,345,346,349,356,360,369,370,382,395,397,404,407,449,457,461,468,470,474,479],institut:[9,230,275],instruct:[3,6,8,11,12,13,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,109,112,142,151,162,170,171,173,174,175,176,178,179,181,182,184,185,188,195,207,221,224,228,233,249,251,252,253,254,255,256,264,266,267,269,282,290,292,293,308,310,321,331,333,334,335,336,339,341,346,360,361,362,364,367,368,369,370,371,372,374,375,376,379,380,382,383,385,386,387,388,389,390,391,394,396,397,398,399,400,401,402,403,404,405,408,412,413,414,416,421,422,428,437,438,439,440,441,443,445,446,447,463,474],insuffici:[3,6,12],insult:249,insur:[3,6,11,12,17,39,40,61,73,102,104,164,165,184,187,188,189,195,209,210,215,220,221,222,223,225,228,233,245,278,279,288,290,305,317,322,326,327,328,330,344,354,356,360,374,387,391,415,421,438,451,452,454,455,459,462,463,471,472,479,480],int_max:3,integ:[3,6,8,11,12,39,40,42,64,68,70,71,113,115,117,119,140,162,164,167,168,170,174,175,179,184,186,187,188,189,199,201,204,205,209,210,211,215,217,223,225,226,227,230,233,234,235,236,272,275,276,279,280,285,290,305,307,309,312,316,317,335,345,348,368,380,381,394,407,419,420,424,426,427,449,451,452,454,462,463,464,468,471,479,480],integr:[],integrate_ulsph:296,intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,8,12,13,36,226,418,454],intens:[1,3,6,9,63,66,74,75,86,89,90,91,93,103,104,105,106,112,114,116,117,118,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,159,160,161,163,192,201,202,203,204,205,206,208,209,210,211,219,222,229,239,247,249,253,287,290,291,305,313,317,319,320,471,472],intepol:479,inter:[14,18,42,61,62,144,167,168,187,211,233,235,248,282,290,345,355,366,464,474,479,481,483],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,37,39,42,44,50,54,55,57,61,63,65,69,77,79,87,88,92,107,108,110,112,115,116,122,123,124,125,127,128,129,130,131,132,133,135,136,137,138,140,141,143,157,158,162,165,166,167,168,169,170,172,176,177,183,187,192,193,194,209,210,211,224,225,230,231,233,235,239,261,271,273,275,281,283,289,290,296,297,305,306,312,317,321,322,323,326,327,332,333,334,336,340,345,346,353,354,355,356,357,358,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,414,416,417,420,421,422,424,426,427,428,435,436,437,439,440,441,442,443,444,445,446,447,449,452,454,456,458,459,463,464,466,471,472,474,481],interatom:[3,4,7,164,187,248,314,315,361,366,382,384,392,407,440,479],intercept:118,interchang:6,interconnect:18,interconvert:384,intereract:39,interesect:326,interest:[1,5,7,8,9,11,13,71,163,273,312,315,346,383,406,419,420,452,479],interf:360,interfac:[],interfer:[249,362],interg:[6,474],intergr:[463,467],interi:406,interior:[3,6,41,326,457],interlac:407,interleav:[6,164,462],intermedi:[6,12,59,188,248,271,339,355,452,453,462,466],intermix:449,intermolecular:362,intern:[0,2,3,5,6,9,11,16,20,21,24,28,32,35,36,39,40,42,63,87,99,101,118,141,144,146,163,171,184,188,189,192,193,194,198,210,214,218,230,242,243,247,249,253,272,290,294,331,333,336,339,343,353,354,429,430,438,452,454,456,459,468,471,472,478,479,480,481],internal_element_set:198,internal_quadratur:198,internet:232,interpenetr:407,interpentr:[430,431,433],interpol:[6,15,38,56,100,184,188,189,198,236,271,345,346,355,366,411,420,432,438,439],interpret:[2,6,11,188,203,388,428,449,452,468,479],interrupt:280,intersect:[3,6,118,189,326,328,457],intersert:326,interspers:353,interstiti:162,intertia:[3,93],interv:[3,6,91,202,233,280,285,286,297,432,449,468,479],intestieti:118,intial:[6,360,362],intiial:[41,459],intiti:[3,304],intra:290,intra_energi:225,intramolecular:[29,225],introduc:[6,9,188,249,280,285,290,339,345,361,376,384,396,400,404,437,468],introduct:[],intsal:16,intuit:348,inv:[118,163,291],invalid:[3,12,71,89,167,261,355,405,406,456],invari:[133,138,140],invent:293,invers:[],invert:[6,168,272],invis:326,invoc:[162,211,360,424,426,452],invok:[1,3,6,7,8,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,59,63,66,71,74,75,81,87,88,89,90,93,103,104,106,109,110,111,112,117,142,151,158,159,162,164,165,167,168,170,171,173,174,175,176,178,179,181,182,184,187,188,189,190,192,193,194,195,196,197,198,199,200,201,2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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso_e/atom command","compute meso_rho/atom command","compute meso_t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact_radius command","compute smd/damage command","compute smd/hourglass_error command","compute smd/internal_energy command","compute smd/plastic_strain command","compute smd/plastic_strain_rate command","compute smd/rho command","compute smd/tlsph_defgrad command","compute smd/tlsph_dt command","compute smd/tlsph_num_neighs command","compute smd/tlsph_shape command","compute smd/tlsph_strain command","compute smd/tlsph_strain_rate command","compute smd/tlsph_stress command","compute smd/triangle_mesh_vertices","compute smd/ulsph_num_neighs command","compute smd/ulsph_strain command","compute smd/ulsph_strain_rate command","compute smd/ulsph_stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute temp command","compute temp/asphere command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":209,"default":[37,39,40,55,57,58,59,61,62,71,87,88,102,103,105,107,118,122,123,140,144,152,153,157,163,164,167,169,183,185,186,187,188,189,190,191,193,194,195,197,198,199,201,204,205,206,209,210,212,213,214,215,219,222,225,226,231,233,234,235,236,237,239,244,247,249,250,253,267,268,272,273,276,277,278,279,280,282,285,287,288,290,291,305,307,312,313,314,315,318,320,322,324,328,340,343,345,346,348,349,351,352,354,356,357,358,360,363,366,368,384,405,406,411,419,420,435,436,449,450,451,454,455,457,459,461,462,463,466,468,470,471,472,473,478,480,481,482],"function":479,"long":[367,369,370,371,372,376,378,379,396,400,404,414,422],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[193,194],addforc:195,addit:[12,13],addtorqu:196,adiabat:6,adjust_dt:295,adp:361,airebo:362,alloi:382,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:197,arrai:6,aspher:[6,82,143,251,254,257,258,266],atc:[9,198],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,95,96,99,100,101,110,111,113,140,141,162,197,199,200,279,479],atom_modifi:39,atom_styl:40,attract:5,aveforc:207,awpmd:[9,363],balanc:[41,208],barostat:6,basal:67,beck:364,berendsen:[277,308],between:6,binary2txt:13,bodi:[6,8,42,68,259,365],bond:[8,13,69,209,210,211,286],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:366,born:[367,378],boundari:[7,57],box:[6,58,212],brownian:368,buck:[369,370,378],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,170,371,404],chunk:[6,66,71,75,90,93,104,106,114,144,159,161,201],citat:7,class2:[21,43,171,331,372],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[322,374,446],colvar:[9,13,213],com:[74,75,145],comb3:375,comb:[282,375],come:5,comm_modifi:61,comm_styl:62,command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,475,476,477,478,479,480,481,482,483],common:3,comparison:1,compos:6,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,479],compute_modifi:102,condit:7,conduct:[6,313],constant:6,constraint:7,contact:76,contact_radiu:120,coord:77,core:6,correl:202,cosin:[23,24,25,26,27,28,173],cossq:333,coul:[367,369,370,371,372,376,377,378,389,396,400,404,414,422],coupl:6,creat:210,create_atom:164,create_bond:165,create_box:166,createatom:13,creation:7,csld:309,csvr:309,cubic:398,cuda:[9,14,109,112,142,151,195,207,221,224,228,249,256,292,293,308,310,321,367,369,371,372,382,388,389,396,397,399,402,412,437,439],custom:8,cut:[49,363,369,372,376,379,384,386,396,397,404,410,414],cvff:334,damag:[78,121],data2xmovi:13,data:6,databas:13,deby:[376,396],deform:[147,148,214],delete_atom:167,delete_bond:168,delta:24,deposit:215,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,475,476,477,478,479,480,481,482,483],diagnost:7,diel:377,dielectr:169,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:172,dihedral_styl:[2,170,171,173,174,175,176,177,178,179,180,181,182,183,184],dilat:80,dimens:185,dipol:[6,29,379],direct:218,discuss:6,disp:6,displac:[81,86],displace_atom:186,distribut:[7,12],document:0,dpd:380,drag:216,dreid:[6,390],drude:[6,9,149,217,218,234],dsf:[376,396],dsmc:381,dump:[6,8,187,188,190],dump_modifi:189,dynam:281,eam:[13,382],echo:191,edip:383,eff:[9,13,96,97,148,150,155,235,250,260,268,311,384],efield:220,eim:385,elast:6,emac:13,enforce2d:221,ensembl:7,erot:[82,83,84,85],error:3,evapor:222,event:86,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,467,468,469,470,471,472,473,475,476,477,478,479,480,481,482,483],exp:[27,173],expand:[46,399],extend:[8,11],extern:223,fcc:271,featur:[7,8],fene:[45,46],fep:[9,13,87,194],field:[6,7],file:6,finit:6,fix:[2,6,8,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,479],fix_modifi:[193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327],flow:6,fluid:236,flux:91,forc:[6,7,306],fourier:[30,31,174,335],freez:224,from:[6,11],futur:5,gauss:386,gaybern:387,gcmc:225,gener:[1,6,7,13],get:12,gld:226,gle:227,global:6,gpu:[15,364,367,369,371,372,374,376,379,380,382,386,387,389,396,397,399,410,412,421,422,428,437,438,445,446],gran:[323,388],granular:6,graviti:228,gromac:389,group2ndx:329,group:[88,328,479],gyrat:[89,90],harmon:[32,47,48,49,175,178,322,336,413],hbond:390,heat:[91,229],heatconduct:429,helix:176,hertz:[388,423],histo:203,histori:[5,388],hook:388,hourglass_error:122,how:6,hybrid:[33,50,177,337,391],idealga:430,imag:[187,188],imd:230,implicit:371,improp:[8,92],improper_coeff:332,improper_styl:[2,331,333,334,335,336,337,338,339,340,341],includ:342,inclus:8,indent:231,indic:0,individu:2,induc:6,inertia:93,info:[0,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,343],input:[2,6,8],instal:11,integr:[6,7],integrate_tlsph:296,integrate_ulsph:297,intel:[9,16,371,387,396,437],interfac:[6,11],internal_energi:123,introduct:7,invers:218,ipi:232,ipp:13,jul:0,jump:344,kate:13,keyword:411,kim:392,kokko:17,kspace:[2,8,318],kspace_modifi:345,kspace_styl:[6,346],label:347,lammp:[0,1,2,6,7,8,11,12],langevin:[233,234,235],lattic:348,lcbop:393,librari:[6,11,12],limit:[261,310],line:[12,262,394],linear:403,lineforc:241,list:[2,395],lj1043:322,lj126:322,lj93:322,lj96:397,lmp2arc:13,lmp2cfg:13,lmp2vmd:13,local:[6,65,68,69,79,92,108,115],log:349,lubric:405,lubricateu:406,make:12,mass:350,math:479,matlab:13,meam:[407,408,409],measur:1,meso:[242,243],meso_:99,meso_rho:100,meso_t:101,messag:3,micelle2d:13,mie:410,min_modifi:351,min_styl:352,minim:[8,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,353],misc:9,mod:[317,440],model:[6,7],modifi:8,molecul:354,molfil:[9,187,190],moltempl:13,momentum:[237,245],morri:434,mors:[51,390,412],move:246,move_tri_surf:298,movi:[187,188],mpi:11,msd:[103,104,105],msi2lmp:13,msm:[367,369,371,376,396],msst:247,multi:[6,7,178],multipl:6,nb3b:413,neb:[248,355],neigh_modifi:356,neighbor:357,nemd:6,newton:358,next:359,nharmon:179,noforc:[258,263],non:[6,7],none:[34,52,180,338,415],nongauss:105,nonlinear:53,nph:[249,250,251,252,290],nphug:253,npt:[249,250,254,255,290],nve:[256,257,258,259,260,261,262,263,264,265,290],nvt:[249,250,266,267,268,269,290],omega:106,omp:[9,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,43,45,46,47,48,49,51,53,54,56,170,171,173,174,175,176,178,179,181,182,184,228,249,251,252,253,254,255,256,264,266,267,269,282,331,333,334,335,336,339,341,361,362,364,367,368,369,370,371,372,374,375,376,377,379,380,382,385,386,387,388,389,390,391,394,396,397,398,399,400,401,402,403,404,405,408,409,412,413,414,416,421,422,428,437,438,439,440,441,443,445,446,447],onewai:270,open:7,oper:479,opl:181,opt:[19,371,382,396,400,412],optim:1,option:[6,8,12],orient:271,orthogon:6,other:6,output:[6,7,8,12,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327],overlai:391,overview:11,packag:[1,9,12,14,15,16,17,18,19,360],pair:[6,107,108],pair_coeff:373,pair_modifi:411,pair_styl:[2,361,362,363,364,365,366,367,368,369,370,371,372,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,445,446,447],pair_writ:444,pairwis:8,parallel:11,paramet:6,pars:2,partial:151,particl:[6,7,42],partit:448,past:5,per:6,perform:[1,10],peri:416,period:25,phonon:[9,13,272],pimd:273,piston:324,planeforc:274,plastic:111,plastic_strain:124,plastic_strain_r:125,pmb:416,poem:275,point:281,polariz:6,poli:[368,405,406],polym:13,polymorph:417,post:7,potenti:[2,6,8],pour:276,pppm:6,prd:449,pre:7,press:277,pressur:112,previou:12,print:[278,450],problem:[3,4],process:[6,7],processor:451,profil:152,properti:[6,113,114,115,279],pymol_aspher:13,python:[11,13,452],qbmsst:280,qeq:[281,282,283],qmmm:[9,284],qtb:[9,285],quadrat:182,quantiti:6,quartic:[35,54],quip:418,quit:453,ramp:153,rattl:293,rdf:116,read_data:454,read_dump:455,read_restart:456,reax:[13,283,286,287,419,420],reaxc:9,rebo:362,recent:288,reduc:117,refer:479,reflect:325,region:[8,117,154,155,326,457,479],relat:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,43,44,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,83,84,85,86,87,89,91,92,93,94,95,96,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,181,182,183,184,185,186,187,188,189,190,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,222,224,225,226,227,228,229,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,285,286,287,288,290,291,292,294,295,296,297,298,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,339,340,341,342,343,344,345,346,348,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,459,460,461,462,463,464,466,467,468,469,470,471,472,473,475,476,477,479,480,481,482,483],relax:212,replic:458,replica:[6,7],report:3,requir:12,rerun:459,rescal:[310,311],reset:219,reset_timestep:460,resquar:421,restart2data:13,restart:[6,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,461],restrain:289,restrict:[14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,475,476,477,478,479,480,481,482,483],rho:126,rhosum:432,rigid:[6,83,98,239,290],ring:339,rotat:156,rule:2,run:[6,11,12,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327,462],run_styl:463,scalabl:10,scalar:6,screen:12,script:[2,6,8,11,12],sdk:[36,422],self:304,serial:11,set:[6,464],setforc:292,setvel:299,shake:293,share:[11,12],shell:[6,465],shield:281,shift:[26,27,48,49,173],simpl:31,simul:6,size:6,slater:281,slice:119,sllod:[267,268],small:290,smd:[9,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,294,295,296,297,298,299,301,423,424,425,426],smooth:[402,403],sna:140,snad:140,snap:427,snapshot:6,snav:140,soft:[404,428],solver:2,sourc:7,spatial:[204,205],spc:6,speci:287,special:[7,411,479],special_bond:466,sph:[9,429,430,431,432,433,434],sphere:[84,85,157,205,239,252,255,264,269],spheric:6,spline:[408,409],spring:[302,303,304,315],squar:28,srd:[305,327],srp:435,standard:9,start:[12,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327],state:307,stationari:243,stop:[193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,218,219,220,221,222,223,224,225,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,322,323,324,325,326,327],store:[306,307],strategi:1,streitz:376,stress:141,structur:2,style:[1,2,6,8],submit:8,suffix:467,summari:6,swap:[199,211],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,272,273,274,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,475,476,477,478,479,480,481,482,483],system:6,tabl:[0,6,38,56,184,438,439],tad:468,taitwat:[433,434],temp:[142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,308,309,310,311],temper:469,temperatur:6,tersoff:[439,440,441],test:11,tfmc:312,thermal:[6,313],thermo:[6,470],thermo_modifi:471,thermo_styl:472,thermodynam:[6,8],thermostat:6,thole:442,time:[6,206],timestep:473,tip3p:6,tip4p:[6,376,396,400,404],tip:12,tlsph:424,tlsph_defgrad:127,tlsph_dt:128,tlsph_num_neigh:129,tlsph_shape:130,tlsph_strain:131,tlsph_strain_rat:132,tlsph_stress:133,tmd:316,tool:13,torqu:159,transform:218,tri:[265,443],tri_surfac:425,triangle_mesh_vertic:134,triclin:6,tstat:380,ttm:317,tune:318,type:7,ulsph:426,ulsph_num_neigh:135,ulsph_strain:136,ulsph_strain_r:137,ulsph_stress:138,umbrella:341,uncomput:475,undump:476,unfix:477,unit:478,user:[9,12,14,16,18],vacf:160,valu:[6,479],variabl:[6,8,479],variou:1,vcm:161,vector:[6,319,479],veloc:480,version:[0,5,12],via:12,vim:13,viscos:[6,320],viscou:[240,321],visual:6,vol:139,voronoi:162,vtk:291,wall:[6,322,323,324,325,326,327],wall_surfac:301,warn:3,water:6,weight:203,what:[7,12],wolf:[367,376],wrapper:11,write:6,write_data:481,write_dump:482,write_restart:483,xmgrace:13,xmovi:13,xrd:163,yukawa:[445,446],zbl:[441,447]}}) \ No newline at end of file diff --git a/doc/set.html b/doc/set.html index c90a9530f2..35f68d97c8 100644 --- a/doc/set.html +++ b/doc/set.html @@ -141,7 +141,7 @@
  • keyword = type or type/fraction or mol or x or y or z or charge or dipole or dipole/random or quat or quat/random or diameter or shape or length or tri or theta or angmom or mass or density or volume or image or

    bond or angle or dihedral or improper or -meso_e or meso_cv or meso_rho or i_name or d_name

    +meso_e or meso_cv or meso_rho or smd_contact_radius or smd_mass_density or i_name or d_name

    • @@ -205,10 +205,12 @@ value can be an atom-style variable (see below) meso_rho value = density of SPH particles (need units) value can be an atom-style variable (see below) +smd_contact_radius = radius for short range interactions, i.e. contact and friction + value can be an atom-style variable (see below) +smd_mass_density = set particle mass based on volume by providing a mass density + value can be an atom-style variable (see below) i_name value = value for custom integer vector with name - value can be an atom-style variable (see below) d_name value = value for custom floating-point vector with name - value can be an atom-style variable (see below)
    @@ -405,6 +407,18 @@ mass is set from the density and triangle area (the input density is assumed to be in mass/distance^2 units). If none of these cases are valid, then the mass is set to the density value directly (the input density is assumed to be in mass units).

    +

    Keyword smd_mass_density also sets the mass of all selected +particles, but it is only applicable to the Smooth Mach Dynamics +package USER-SMD. This command assumes that the particle volume has +already been correctly set and calculates particle mass from the +provided mass density value.

    +

    Keyword smd_contact_radius only applies to simulations with the +Smooth Mach Dynamics package USER-SMD. This command sets an +interaction radius for computing short-range interactions, +e.g. repulsive forces to prevent different individual physical bodies +from penetrating each other. Note that the SPH smoothing kernel +diameter used for computing long range, nonlocal interactions, is set +using the diameter keyword.

    Keyword volume sets the volume of all selected particles. Currently, only the atom_style peri command defines particles with a volume attribute. Note that this command does not @@ -418,8 +432,8 @@ the simulation. The flags can be output with atom snapshots via the dump command. If a value of NULL is specified for any of nx,ny,nz, then the current image value for that dimension is unchanged. For non-periodic dimensions only a value of 0 can be -specified. This keyword does not allow use of atom-style variables.

    -

    This command can be useful after a system has been equilibrated and +specified. This keyword does not allow use of atom-style variables. +This command can be useful after a system has been equilibrated and atoms have diffused one or more box lengths in various directions. This command can then reset the image values for atoms so that they are effectively inside the simulation box, e.g if a diffusion diff --git a/doc/set.txt b/doc/set.txt index 6eb7b17a55..6a4e66dd95 100644 --- a/doc/set.txt +++ b/doc/set.txt @@ -21,7 +21,9 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \ {length} or {tri} or {theta} or {angmom} or \ {mass} or {density} or {volume} or {image} or {bond} or {angle} or {dihedral} or {improper} or - {meso_e} or {meso_cv} or {meso_rho} or {i_name} or {d_name} :l + {meso_e} or {meso_cv} or {meso_rho} or \ + {smd_contact_radius} or {smd_mass_density} or \ + {i_name} or {d_name} :l {type} value = atom type value can be an atom-style variable (see below) {type/fraction} values = type fraction seed @@ -80,10 +82,12 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \ value can be an atom-style variable (see below) {meso_rho} value = density of SPH particles (need units) value can be an atom-style variable (see below) - {i_name} value = value for custom integer vector with name + {smd_contact_radius} = radius for short range interactions, i.e. contact and friction + value can be an atom-style variable (see below) + {smd_mass_density} = set particle mass based on volume by providing a mass density value can be an atom-style variable (see below) - {d_name} value = value for custom floating-point vector with name - value can be an atom-style variable (see below) :pre + {i_name} value = value for custom integer vector with name + {d_name} value = value for custom floating-point vector with name :pre :ule [Examples:] @@ -312,6 +316,20 @@ assumed to be in mass/distance^2 units). If none of these cases are valid, then the mass is set to the density value directly (the input density is assumed to be in mass units). +Keyword {smd_mass_density} also sets the mass of all selected +particles, but it is only applicable to the Smooth Mach Dynamics +package USER-SMD. This command assumes that the particle volume has +already been correctly set and calculates particle mass from the +provided mass density value. + +Keyword {smd_contact_radius} only applies to simulations with the +Smooth Mach Dynamics package USER-SMD. This command sets an +interaction radius for computing short-range interactions, +e.g. repulsive forces to prevent different individual physical bodies +from penetrating each other. Note that the SPH smoothing kernel +diameter used for computing long range, nonlocal interactions, is set +using the {diameter} keyword. + Keyword {volume} sets the volume of all selected particles. Currently, only the "atom_style peri"_atom_style.html command defines particles with a volume attribute. Note that this command does not @@ -327,7 +345,6 @@ the simulation. The flags can be output with atom snapshots via the nx,ny,nz, then the current image value for that dimension is unchanged. For non-periodic dimensions only a value of 0 can be specified. This keyword does not allow use of atom-style variables. - This command can be useful after a system has been equilibrated and atoms have diffused one or more box lengths in various directions. This command can then reset the image values for atoms so that they diff --git a/examples/USER/smd/README b/examples/USER/smd/README new file mode 100644 index 0000000000..3fc953cfc4 --- /dev/null +++ b/examples/USER/smd/README @@ -0,0 +1,7 @@ +SMOOTH MACH DYNAMICS Examples + +aluminum_strip_pull : a 2d strip of aluminum is elongated until failure +fluid_structure_interaction : multiple solid objects interact with fluid flow, 2d +funnel_flow: fluid flows through a complex 3d object read from a .STL file +rubber_rings_3d: two solid bodies impact each other and deform +rubber_strip_pull: a 2d check for the correctness of linear elasticity diff --git a/examples/USER/smd/aluminum_strip_pull/aluminum_strip_pull.lmp b/examples/USER/smd/aluminum_strip_pull/aluminum_strip_pull.lmp new file mode 100644 index 0000000000..aa348119da --- /dev/null +++ b/examples/USER/smd/aluminum_strip_pull/aluminum_strip_pull.lmp @@ -0,0 +1,139 @@ +#################################################################################################### +# +# TLSPH example: elongate a 2d strip of aluminum py pulling its ends apart +# +# unit sytem: GPa / mm / ms +# +#################################################################################################### + + +#################################################################################################### +# MATERIAL PARAMETERS +#################################################################################################### +variable E equal 70.0 # Young's modulus +variable nu equal 0.3 # Poisson ratio +variable rho equal 1 # initial mass density +variable q1 equal 0.56 # standard artificial viscosity linear coefficient +variable q2 equal 0.0 # standard artificial viscosity quadratic coefficient +variable hg equal 10.0 # hourglass control coefficient +variable cp equal 1.0 # heat capacity of material -- not used here + +variable JC_A equal 0.3241 # Johnson Cook arameters +variable JC_B equal 0.1138 +variable JC_N equal 0.42 +variable JC_C equal 0 #0.002 +variable JC_M equal 1.34 +variable JC_epsdot0 equal 1.0e-3 # 1/s = 1/(1000 ms) +variable Troom equal 298.15 +variable Tmelt equal 500.15 + +variable eosC0 equal 0.0 # Polynomial EOS parameters +variable eosC1 equal 74.2 +variable eosC2 equal 60.5 +variable eosC3 equal 36.5 +variable eosC4 equal 1.96 +variable eosC5 equal 0.0 +variable eosC6 equal 0.0 + +#################################################################################################### +# INITIALIZE LAMMPS +#################################################################################################### +dimension 2 +units si +boundary sm sm p # simulation box boundaries +atom_style smd +atom_modify map array +comm_modify vel yes +neigh_modify every 10 delay 0 check yes # re-build neighbor list every 10 steps +newton off + +#################################################################################################### +# CREATE INITIAL GEOMETRY +#################################################################################################### +variable l0 equal 1.0 # lattice spacing for creating particles +lattice sq ${l0} +region box block -10 10 -10 10 -0.1 0.1 units box +create_box 1 box +create_atoms 1 box +group tlsph type 1 + + +#################################################################################################### +# DISCRETIZATION PARAMETERS +#################################################################################################### +variable h equal 2.01*${l0} # SPH smoothing kernel radius +variable vol_one equal ${l0}^2 # volume of one particle -- assuming unit thickness +variable skin equal ${h} # Verlet list range +neighbor ${skin} bin +set group all volume ${vol_one} +set group all smd_mass_density ${rho} +set group all diameter ${h} # set SPH kernel radius + +#################################################################################################### +# DEFINE VELOCITY BOUNDARY CONDITIONS +#################################################################################################### +variable vel0 equal 0.02 # pull velocity +region top block EDGE EDGE 9.0 EDGE EDGE EDGE units box +region bot block EDGE EDGE EDGE -9.1 EDGE EDGE units box +group top region top +group bot region bot +variable vel_up equal ${vel0}*(1.0-exp(-0.01*time)) +variable vel_down equal -v_vel_up +fix veltop_fix top smd/setvelocity 0 v_vel_up 0 +fix velbot_fix bot smd/setvelocity 0 v_vel_down 0 + +#################################################################################################### +# INTERACTION PHYSICS / MATERIAL MODEL +# We use polynomial EOS for the pressure and the Johnson Cook strength model +# An integration point fails (cannot support tension anymore) if the plastic strain exceeds 0.5. +#################################################################################################### +pair_style smd/tlsph +pair_coeff 1 1 *COMMON ${rho} ${E} ${nu} ${q1} ${q2} ${hg} ${cp} & + *EOS_POLYNOMIAL ${eosC0} ${eosC1} ${eosC2} ${eosC3} ${eosC4} ${eosC5} ${eosC6} & + *JOHNSON_COOK ${JC_A} ${JC_B} ${JC_N} ${JC_C} ${JC_epsdot0} ${Troom} ${Tmelt} ${JC_M} & + *FAILURE_MAX_PLASTIC_STRAIN 1.2 & + *END + +#################################################################################################### +# TIME INTEGRATION +#################################################################################################### +fix dtfix tlsph smd/adjust_dt 0.1 # dynamically adjust time increment every step +fix integration_fix tlsph smd/integrate_tlsph + +#################################################################################################### +# SPECIFY TRAJECTORY OUTPUT +#################################################################################################### +compute dt_atom all smd/tlsph_dt +compute p all smd/plastic_strain +compute epsdot all smd/plastic_strain_rate +compute S all smd/tlsph_stress # Cauchy stress tensor +compute D all smd/tlsph_strain_rate +compute E all smd/tlsph_strain +compute nn all smd/tlsph_num_neighs # number of neighbors for each particle +compute shape all smd/tlsph_shape +compute damage all smd/damage +dump dump_id all custom 100 dump.LAMMPS id type x y z & + c_S[1] c_S[2] c_S[3] c_S[4] c_S[5] c_S[6] c_S[7] c_nn c_p & + c_E[1] c_E[2] c_E[3] c_E[4] c_E[5] c_E[6] & + c_shape[1] c_shape[2] c_shape[3] c_shape[4] c_shape[5] c_shape[6] c_shape[7] & + c_D[1] c_D[2] c_D[4] c_damage radius c_epsdot & + vx vy vz c_dt_atom +dump_modify dump_id first yes + +#################################################################################################### +# STATUS OUTPUT +#################################################################################################### +variable stress equal 0.5*(f_velbot_fix[2]-f_veltop_fix[2])/20 +variable length equal xcm(top,y)-xcm(bot,y) +variable strain equal (v_length-${length})/${length} # engineering strain +variable time equal f_dtfix +fix stress_curve all print 10 "${time} ${strain} ${stress}" file stress_strain.dat screen no + +thermo 100 +thermo_style custom step dt f_dtfix time v_strain + +#################################################################################################### +# RUN SIMULATION +#################################################################################################### +#fix 2 all enforce2d +run 25000 diff --git a/examples/USER/smd/fluid_structure_interaction/fluid_structure_interaction.lmp b/examples/USER/smd/fluid_structure_interaction/fluid_structure_interaction.lmp new file mode 100644 index 0000000000..d3ca496f0a --- /dev/null +++ b/examples/USER/smd/fluid_structure_interaction/fluid_structure_interaction.lmp @@ -0,0 +1,156 @@ +#################################################################################################### +# +# combined TLSPH / ULSPH example +# +# A column of water is placed in a container and allowed to collapse unter the +# influence of gravity. Several solid objects are also placed in the container. +# The water flow pushes the solid objects around until the sytem comes to halt due to +# viscous damping. The solid objects have a lower mass density than water and finally float on +# the water surface. +# +# Water is modelled using the Updated Lagrangian formalism. Solid bodies are modelled using the +# Total Lagrangian formalism. Contact forces between container, solid bodies, and water prevent +# mutual penetration of these physical entities. +# +# unit sytem: GPa / mm / ms +# +#################################################################################################### + +#################################################################################################### +# MATERIAL PARAMETERS +#################################################################################################### +variable rho_water equal 1000 # mass density water +variable rho_obj equal 300 # mass density solid objects +variable c0 equal 10.0 # speed of sound for water +variable E equal 5*${c0}*${c0}*${rho_water} # Young's modulus for solid objects +variable nu equal 0.3 # Poisson ratio for solid objects +variable sigma_yield equal 0.1*${E} # plastic yield stress for solid objects +variable hardening_parameter equal 0 # plastic hardening parameter for solid objects +variable contact_stiffness equal 2.5*${c0}^2*${rho_water} # contact force amplitude +variable q1 equal 1.0 # artificial viscosity +variable q2 equal 0.0 # artificial viscosity +variable Hg equal 10 # Hourglass control coefficient for solid objects +variable Cp equal 1.0 # heat capacity -- not used here + +#################################################################################################### +# INITIALIZE LAMMPS +#################################################################################################### +units si +dimension 2 +boundary sm sm p +atom_style smd +neigh_modify every 5 delay 0 check yes +comm_modify vel yes +newton off +atom_modify map array +comm_style tiled + +#################################################################################################### +# CREATE INITIAL GEOMETRY +#################################################################################################### +# create simulation box, a container, and a water column +variable l0 equal 0.05 # initial particle lattice spacing +region box block 0 6 0 8 -0.01 0.01 units box +create_box 3 box +region water block 0.25 1 0.25 4 EDGE EDGE units box +region container block 0.15 5.85 0.15 8 -0.01 0.01 units box side out # container +lattice sq ${l0} +create_atoms 1 region water +group water type 1 +create_atoms 3 region container +group container type 3 + +# create some solid objects to be pushed around +region obj1 prism 2 2.6 0.25 0.85 EDGE EDGE 0.3 0 0 units box +region obj2 block 3 3.6 0.25 0.85 EDGE EDGE units box +region obj3 sphere 4.3 0.5 0 0.25 units box +create_atoms 2 region obj1 +create_atoms 2 region obj2 +create_atoms 2 region obj3 +group solids type 2 +group tlsph type 2 + +#################################################################################################### +# DISCRETIZATION PARAMETERS +#################################################################################################### +variable h equal 2.5*${l0} # SPH kernel diameter +variable vol_one equal ${l0}^2 # initial particle volume for 2d simulation +set group all diameter ${h} +set group all smd_contact_radius ${l0} +set group all volume ${vol_one} +set group all smd_mass_density ${rho_water} +set group solids smd_mass_density ${rho_obj} +variable contact_scale equal 1.5 # scale factor to increase contact gap between bodies +variable skin equal ${h} # Verlet list range +neighbor ${skin} bin + +#################################################################################################### +# DEFINE BOUNDARY CONDITIONS +# +# note that the the particles constituting the container are simply not integrated in time, +# thus these particles never move. This is equivalent to a fixed displacement boundary condition. +#################################################################################################### +fix gfix all gravity -9.81 vector 0 1 0 # add gravity + +#################################################################################################### +# INTERACTION PHYSICS / MATERIAL MODEL +# 3 different pair styles are used: +# - updated Lagrangian SPH for water +# - total Lagrangian SPH for solid objects +# - a repulsive Hertzian potential for contact forces between different physical bodies +#################################################################################################### +pair_style hybrid/overlay smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION & + smd/tlsph smd/hertz ${contact_scale} +pair_coeff 1 1 smd/ulsph *COMMON ${rho_water} ${c0} ${q1} ${Cp} 0 & + *EOS_TAIT 7.0 & + *END +pair_coeff 2 2 smd/tlsph *COMMON ${rho_obj} ${E} ${nu} ${q1} ${q2} ${Hg} ${Cp} & + *STRENGTH_LINEAR_PLASTIC ${sigma_yield} ${hardening_parameter} & + *EOS_LINEAR & + *END +pair_coeff 3 3 none +pair_coeff 1 2 smd/hertz ${contact_stiffness} +pair_coeff 1 3 smd/hertz ${contact_stiffness} +pair_coeff 2 3 smd/hertz ${contact_stiffness} +pair_coeff 2 2 smd/hertz ${contact_stiffness} + +#################################################################################################### +# TIME INTEGRATION +#################################################################################################### +fix dtfix tlsph smd/adjust_dt 0.1 # dynamically adjust time increment every step +fix integration_fix_water water smd/integrate_ulsph adjust_radius 1.01 10 15 +fix integration_fix_solids solids smd/integrate_tlsph + +#################################################################################################### +# SPECIFY TRAJECTORY OUTPUT +#################################################################################################### +compute eint all smd/internal_energy +compute contact_radius all smd/contact_radius +compute S solids smd/tlsph_stress +compute nn water smd/ulsph_num_neighs +compute epl solids smd/plastic_strain +compute vol all smd/volume +compute rho all smd/rho + +dump dump_id all custom 100 dump.LAMMPS id type x y & + fx fy vx vy c_eint c_contact_radius mol & + c_S[1] c_S[2] c_S[4] mass radius c_epl c_vol c_rho c_nn proc +dump_modify dump_id first yes + + +#################################################################################################### +# STATUS OUTPUT +#################################################################################################### +compute alleint all reduce sum c_eint +variable etot equal pe+ke+c_alleint+f_gfix # total energy of the system +thermo 100 +thermo_style custom step ke pe v_etot c_alleint f_dtfix dt +thermo_modify lost ignore + +#################################################################################################### +# RUN SIMULATION +#################################################################################################### +fix balance_fix all balance 1000 0.9 rcb # load balancing for MPI +run 40000 + + diff --git a/examples/USER/smd/funnel_flow/boundary.stl b/examples/USER/smd/funnel_flow/boundary.stl new file mode 100644 index 0000000000..6c3921a82c --- /dev/null +++ b/examples/USER/smd/funnel_flow/boundary.stl @@ -0,0 +1,66306 @@ +solid Georgs Murmelbahn + facet normal 0.97540827284 -0.1710498719 -0.1389987144 + outer loop + vertex -1.410104E+01 5.1169753E+00 5.2342388E-04 + vertex -1.499841E+01 2.1865206E-04 -7.371949E-05 + vertex -1.546703E+01 1.2308852E+00 -4.803006E+00 + endloop + endfacet + facet normal -0.9838960828 -0.1770521446 0.02451604144 + outer loop + vertex 1.4773485E+01 5.7567939E-01 -4.965230E+00 + vertex 1.5000771E+01 1.5329637E-04 -4.200466E-09 + vertex 1.4060464E+01 5.2256358E+00 7.3727574E-04 + endloop + endfacet + facet normal -0.9832167034 -0.1821107288 0.0109816468 + outer loop 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a/examples/USER/smd/funnel_flow/funnel_flow.lmp b/examples/USER/smd/funnel_flow/funnel_flow.lmp new file mode 100644 index 0000000000..b688fcb95e --- /dev/null +++ b/examples/USER/smd/funnel_flow/funnel_flow.lmp @@ -0,0 +1,130 @@ +#################################################################################################### +# +# ULSPH example: water flow through a complex geometry read from a .STL file +# +# The boundary dump file (see below) can be converted into VTK format using the conversion +# tool dump2vtk_tris from the tools/smd directory. +# +# unit sytem: GPa / mm / ms +# +#################################################################################################### + + +#################################################################################################### +# MATERIAL PARAMETERS +#################################################################################################### +variable c0 equal 10.0 # speed of sound for fluid +variable rho equal 1.0e-6 # initial mass density +variable q1 equal 0.06 # standard artificial viscosity linear coefficient +variable q2 equal 0.0 # standard artificial viscosity quadratic coefficient +variable hg equal 0.0 # hourglass control coefficient +variable cp equal 1.0 # heat capacity of material -- not used here +variable K equal ${c0}*${rho}^2 +variable contact_stiffness equal 0.1*${K} + +#################################################################################################### +# INITIALIZE LAMMPS +#################################################################################################### +dimension 3 +units si +boundary f f f # simulation box boundaries +atom_style smd +atom_modify map array +comm_modify vel yes +comm_style tiled +neigh_modify every 10 delay 0 check yes exclude type 2 2 one 10000 +newton off + +#################################################################################################### +# CREATE INITIAL GEOMETRY +#################################################################################################### +variable l0 equal 5.0 # lattice spacing for creating particles +lattice sc ${l0} +region box block -110 60 -30 220 -90 130 units box +create_box 2 box +region particles cylinder y 0 -30 47 135 200 units box +create_atoms 1 region particles +group water type 1 + +#################################################################################################### +# DISCRETIZATION PARAMETERS +#################################################################################################### +variable h equal 2.01*${l0} # SPH smoothing kernel radius +variable vol_one equal ${l0}^3 # volume of one particle -- assuming unit thickness +variable skin equal 0.1*${h} # Verlet list range +neighbor ${skin} bin +variable cr equal ${l0}/2 +set group all smd_contact_radius ${cr} +set group all volume ${vol_one} +set group all smd_mass_density ${rho} +set group all diameter ${h} # set SPH kernel radius + +#################################################################################################### +# DEFINE GRAVITY BOUNDARY CONDITION +#################################################################################################### +fix gfix all gravity 0.01 vector 0.0 -1. 0.0 + +#################################################################################################### +# INTERACTION PHYSICS / MATERIAL MODEL +# We use polynomial EOS for the pressure and the Johnson Cook strength model +# An integration point fails (cannot support tension anymore) if the plastic strain exceeds 0.5. +#################################################################################################### +pair_style hybrid/overlay smd/tri_surface 1.0 & + smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION +pair_coeff 1 1 smd/ulsph *COMMON ${rho} ${c0} ${q1} ${cp} ${hg} & + *EOS_TAIT 2 & + *END +pair_coeff 2 2 none +pair_coeff 1 2 smd/tri_surface ${contact_stiffness} + + + +#################################################################################################### +# LOAD STL SURFACE +#################################################################################################### +fix stl_surface_fix all smd/wall_surface boundary.stl 2 65535 +run 0 # This is important! Always run for 0 timesteps directly after loading STL file! +group surface type 2 + +#################################################################################################### +# TIME INTEGRATION +#################################################################################################### +fix force_fix surface setforce 0 0 0 +fix dtfix all smd/adjust_dt 0.1 # dynamically adjust time increment every step +fix integration_fix all smd/integrate_ulsph adjust_radius 1.01 10 15 + +#################################################################################################### +# SPECIFY TRAJECTORY OUTPUT +#################################################################################################### +variable dumpFreq equal 100 +compute rho all smd/rho +compute nn all smd/ulsph_num_neighs # number of neighbors for each particle +compute contact_radius all smd/contact_radius +compute surface_coords surface smd/triangle_vertices + + +dump dump_id water custom ${dumpFreq} dump.LAMMPS id type x y z vx vy vz & + c_rho c_nn c_contact_radius proc +dump_modify dump_id first yes + +dump surf_dump surface custom 999999999 surface.LAMMPS id type mol x y z & + c_surface_coords[1] c_surface_coords[2] c_surface_coords[3] & + c_surface_coords[4] c_surface_coords[5] c_surface_coords[6] & + c_surface_coords[7] c_surface_coords[8] c_surface_coords[9] +dump_modify surf_dump first yes + +#################################################################################################### +# STATUS OUTPUT +#################################################################################################### +compute eint all smd/internal_energy +compute alleint all reduce sum c_eint +variable etot equal pe+ke+c_alleint+f_gfix # total energy of the system +thermo 100 +thermo_style custom step dt f_dtfix pe ke v_etot + +#################################################################################################### +# RUN SIMULATION +#################################################################################################### +balance 1.1 rcb +fix balance_fix all balance 1000 1.1 rcb +run 20000 diff --git a/examples/USER/smd/rubber_rings_3d/rubber_rings_3d.lmp b/examples/USER/smd/rubber_rings_3d/rubber_rings_3d.lmp new file mode 100644 index 0000000000..c8270e5dbc --- /dev/null +++ b/examples/USER/smd/rubber_rings_3d/rubber_rings_3d.lmp @@ -0,0 +1,112 @@ + +#################################################################################################### +# +# TLSPH example: Two rubber rings impact each other. +# +# unit sytem: GPa / mm / ms +# +#################################################################################################### + +#################################################################################################### +# MATERIAL PARAMETERS +#################################################################################################### +variable rho equal 1 # initial mass density +variable E equal 1.0 # Young's modulus +variable nu equal 0.3 # Poisson ratio +variable sigma_yield equal 0.051 # plastic yield stress +variable contact_stiffness equal 0.2 # contact stress for contact force between rings +variable q1 equal 0.06 # standard artificial viscosity linear coefficient +variable q2 equal 0.0 # standard artificial viscosity quadratic coefficient +variable hg equal 10.0 # hourglass control coefficient +variable cp equal 1.0 # heat capacity of material -- not used here + +#################################################################################################### +# INITIALIZE LAMMPS +#################################################################################################### +dimension 3 +units si +boundary sm sm sm # simulation box boundaries +atom_style smd +atom_modify map array +comm_modify vel yes +neigh_modify every 10 delay 0 check yes # re-build neighbor list every 10 steps +newton off + +#################################################################################################### +# READ GEOMETRY +#################################################################################################### +read_data washer_hex_adjusted.data # read geometry of one rubber ring from file +replicate 2 1 1 +region right block 12.2 EDGE EDGE EDGE EDGE EDGE units box +group right region right +group left subtract all right +set group left type 1 +set group right type 2 +group tlsph union left right + +#################################################################################################### +# DISCRETIZATION PARAMETERS +#################################################################################################### +variable l0 equal 0.3 # we need to set a length scale for the neighbor list skin +variable skin equal 4.0*${l0} # Verlet list range +neighbor ${skin} bin +set group all smd_contact_radius 1.0 + + +#################################################################################################### +# DEFINE INITIAL VELOCITY BOUNDARY CONDITIONS +#################################################################################################### +variable vel equal 100.0 # initial velocity +velocity left set ${vel} 0 0 sum no units box +velocity right set -${vel} 0 0 sum no units box + +#################################################################################################### +# INTERACTION PHYSICS / MATERIAL MODEL +# One rubber ring is linear elastic, the other rubber ring is elastic-ideal plastic. +# Contact forces between both rubber rings are used to realize physical contact. +#################################################################################################### +pair_style hybrid/overlay smd/tlsph smd/hertz 1.0 # activate Total-Lagrangian SPH +pair_coeff 1 1 smd/tlsph *COMMON ${rho} ${E} ${nu} ${q1} ${q2} ${hg} ${cp} & + *STRENGTH_LINEAR & + *EOS_LINEAR & + *END +pair_coeff 2 2 smd/tlsph *COMMON ${rho} ${E} ${nu} ${q1} ${q2} ${hg} ${cp} & + *STRENGTH_LINEAR_PLASTIC ${sigma_yield} 0.0 & + *EOS_LINEAR & + *END +pair_coeff 1 1 smd/hertz ${contact_stiffness} +pair_coeff 2 2 smd/hertz ${contact_stiffness} +pair_coeff 1 2 smd/hertz ${contact_stiffness} + +#################################################################################################### +# TIME INTEGRATION +#################################################################################################### +fix dtfix tlsph smd/adjust_dt 0.1 # dynamically adjust time increment every step +fix integration_fix tlsph smd/integrate_tlsph + +#################################################################################################### +# SPECIFY TRAJECTORY OUTPUT +#################################################################################################### +variable dumpFreq equal 30 +compute S all smd/tlsph_stress # Cauchy stress tensor +compute nn all smd/tlsph_num_neighs # number of neighbors for each particle +compute cr all smd/contact_radius +compute p all smd/plastic_strain +compute eint all smd/internal_energy +compute alleint all reduce sum c_eint +variable etot equal c_alleint+ke+pe + +dump dump_id all custom ${dumpFreq} dump.LAMMPS id type x y z vx vy vz & + c_S[1] c_S[2] c_S[3] c_S[4] c_S[5] c_S[6] c_S[7] c_nn c_cr proc c_p radius +dump_modify dump_id first yes + +#################################################################################################### +# STATUS OUTPUT +#################################################################################################### +thermo 100 +thermo_style custom step dt f_dtfix ke pe c_alleint v_etot + +#################################################################################################### +# PERFORM INITIAL LOAD BALANCING AND RUN SIMULATION +#################################################################################################### +run 5000 diff --git a/examples/USER/smd/rubber_rings_3d/washer_hex_adjusted.data b/examples/USER/smd/rubber_rings_3d/washer_hex_adjusted.data new file mode 100644 index 0000000000..586c97cd99 --- /dev/null +++ b/examples/USER/smd/rubber_rings_3d/washer_hex_adjusted.data @@ -0,0 +1,973 @@ +COMMENT +480 atoms +2 atom types +-12.000000 12.200000 xlo xhi +-12.000000 12.200000 ylo yhi +-0.500000 5.550000 zlo zhi + +Atoms + +1 1 1 3.08893 6.17786e-06 1.89656 0.497594 -7.30824 -5.99772 0.833333 -7.30824 -5.99772 0.833333 +2 1 1 3.08893 6.17786e-06 1.2877 0.497594 -7.30824 -5.99772 2.5 -7.30824 -5.99772 2.5 +3 1 1 3.08893 6.17786e-06 1.89656 0.497594 -7.30824 -5.99772 4.16667 -7.30824 -5.99772 4.16667 +4 1 1 3.08893 6.17786e-06 1.91673 0.497593 -8.33791 -4.4567 0.833333 -8.33791 -4.4567 0.833333 +5 1 1 3.08893 6.17786e-06 1.32763 0.497593 -8.33791 -4.4567 2.5 -8.33791 -4.4567 2.5 +6 1 1 3.08893 6.17786e-06 1.91673 0.497593 -8.33791 -4.4567 4.16667 -8.33791 -4.4567 4.16667 +7 1 1 3.08893 6.17786e-06 1.89354 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--- /dev/null +++ b/examples/USER/smd/rubber_strip_pull/plot.gpl @@ -0,0 +1,13 @@ +#!/usr/bin/gnuplot + +set grid +set key top left +set xlabel "yy strain" +set ylabel "yy stress [GPa]" +plot [0:0.1] "stress_strain.dat" w p ti "engineering stress from simulation", 1.1*x ti "analytic true stress with E=1.1 GPa" + +pause -1 + +set terminal postscript color enhanced lw 2 +set out "stress_strain.ps" +replot diff --git a/examples/USER/smd/rubber_strip_pull/rubber_strip_pull.lmp b/examples/USER/smd/rubber_strip_pull/rubber_strip_pull.lmp new file mode 100644 index 0000000000..88a7c896a5 --- /dev/null +++ b/examples/USER/smd/rubber_strip_pull/rubber_strip_pull.lmp @@ -0,0 +1,109 @@ +#################################################################################################### +# +# TLSPH example: elongate a 2d strip of a linear elastic material py pulling its ends apart +# +# unit sytem: GPa / mm / ms +# +#################################################################################################### + + +#################################################################################################### +# MATERIAL PARAMETERS +#################################################################################################### +variable E equal 1.0 # Young's modulus +variable nu equal 0.3 # Poisson ratio +variable rho equal 1 # initial mass density +variable q1 equal 0.06 # standard artificial viscosity linear coefficient +variable q2 equal 0.0 # standard artificial viscosity quadratic coefficient +variable hg equal 10.0 # hourglass control coefficient +variable cp equal 1.0 # heat capacity of material -- not used here + +#################################################################################################### +# INITIALIZE LAMMPS +#################################################################################################### +dimension 2 +units si +boundary sm sm p # simulation box boundaries +atom_style smd +atom_modify map array +comm_modify vel yes +neigh_modify every 10 delay 0 check yes # re-build neighbor list every 10 steps +newton off + +#################################################################################################### +# CREATE INITIAL GEOMETRY +#################################################################################################### +variable l0 equal 1.0 # lattice spacing for creating particles +lattice sq ${l0} +region box block -10 10 -10 10 -0.1 0.1 units box +create_box 1 box +create_atoms 1 box +group tlsph type 1 + + +#################################################################################################### +# DISCRETIZATION PARAMETERS +#################################################################################################### +variable h equal 2.01*${l0} # SPH smoothing kernel radius +variable vol_one equal ${l0}^2 # volume of one particle -- assuming unit thickness +variable skin equal ${h} # Verlet list range +neighbor ${skin} bin +set group all volume ${vol_one} +set group all smd_mass_density ${rho} +set group all diameter ${h} # set SPH kernel radius + +#################################################################################################### +# DEFINE VELOCITY BOUNDARY CONDITIONS +#################################################################################################### +variable vel0 equal 0.005 # pull velocity +region top block EDGE EDGE 9.0 EDGE EDGE EDGE units box +region bot block EDGE EDGE EDGE -9.1 EDGE EDGE units box +group top region top +group bot region bot +variable vel_up equal ${vel0}*(1.0-exp(-0.01*time)) +variable vel_down equal -v_vel_up +fix veltop_fix top smd/setvelocity 0 v_vel_up 0 +fix velbot_fix bot smd/setvelocity 0 v_vel_down 0 + +#################################################################################################### +# INTERACTION PHYSICS / MATERIAL MODEL +#################################################################################################### +pair_style smd/tlsph +pair_coeff 1 1 *COMMON ${rho} ${E} ${nu} ${q1} ${q2} ${hg} ${cp} & + *STRENGTH_LINEAR & + *EOS_LINEAR & + *END + +#################################################################################################### +# TIME INTEGRATION +#################################################################################################### +fix dtfix tlsph smd/adjust_dt 0.1 # dynamically adjust time increment every step +fix integration_fix tlsph smd/integrate_tlsph + +#################################################################################################### +# SPECIFY TRAJECTORY OUTPUT +#################################################################################################### +compute S all smd/tlsph_stress # Cauchy stress tensor +compute E all smd/tlsph_strain # Green-Lagrange strain tensor +compute nn all smd/tlsph_num_neighs # number of neighbors for each particle +dump dump_id all custom 10 dump.LAMMPS id type x y z vx vy vz & + c_S[1] c_S[2] c_S[4] c_nn & + c_E[1] c_E[2] c_E[4] & + vx vy vz +dump_modify dump_id first yes + +#################################################################################################### +# STATUS OUTPUT +#################################################################################################### +variable stress equal 0.5*(f_velbot_fix[2]-f_veltop_fix[2])/20 # stress = force / initial width +variable length equal xcm(top,y)-xcm(bot,y) +variable strain equal (v_length-${length})/${length} # engineering strain +fix stress_curve all print 10 "${strain} ${stress}" file stress_strain.dat screen no + +thermo 100 +thermo_style custom step dt f_dtfix v_strain + +#################################################################################################### +# RUN SIMULATION +#################################################################################################### +run 2500 diff --git a/lib/README b/lib/README index 508de508e8..a7a41f00f2 100644 --- a/lib/README +++ b/lib/README @@ -45,7 +45,7 @@ quip interface to QUIP/libAtoms framework, USER-QUIP package from Albert Bartok-Partay and Gabor Csanyi (U Cambridge) reax ReaxFF potential, REAX package from Adri van Duin (Penn State) and Aidan Thompson (Sandia) -quip interface to QUIP/libAtoms framework, USER-QUIP package - from Albert Bartok-Partay and Gabor Csanyi (U Cambridge) +smd hooks to Eigen library, used by USER-SMD package + from Georg Ganzenmueller (Ernst Mach Institute, Germany) voronoi hooks to the Voro++ library, used by compute voronoi/atom command from Daniel Schwen (LANL) diff --git a/src/Makefile b/src/Makefile index e2e59dead0..823acbec83 100644 --- a/src/Makefile +++ b/src/Makefile @@ -48,7 +48,7 @@ PACKAGE = asphere body class2 colloid coreshell dipole fld gpu granular kim \ PACKUSER = user-atc user-awpmd user-cg-cmm user-colvars user-cuda \ user-diffraction user-drude user-eff user-fep user-intel user-lb \ user-misc user-molfile user-omp user-phonon user-qmmm user-qtb \ - user-quip user-reaxc user-sph + user-quip user-reaxc user-smd user-sph PACKLIB = gpu kim kokkos meam poems python reax voronoi \ user-atc user-awpmd user-colvars user-cuda user-molfile \ diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp index a7a39cdda7..12c0768500 100644 --- a/src/PERI/pair_peri_ves.cpp +++ b/src/PERI/pair_peri_ves.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Contributing authors: Ezwanur Rahman, J.T. Foster (UTSA) + Contributing authors: Rezwanur Rahman, J.T. Foster (UTSA) ------------------------------------------------------------------------- */ #include "math.h" diff --git a/src/REPLICA/prd.cpp b/src/REPLICA/prd.cpp index 35fb181a7a..de3447db98 100644 --- a/src/REPLICA/prd.cpp +++ b/src/REPLICA/prd.cpp @@ -333,11 +333,11 @@ void PRD::command(int narg, char **arg) // decrement clock by random time at which 1 or more events occurred int frac_t_event = t_event; - for (int i = 0; i <= fix_event->ncoincident; i++) { + for (int i = 0; i < fix_event->ncoincident; i++) { int frac_rand = static_cast (random_clock->uniform() * t_event); frac_t_event = MIN(frac_t_event,frac_rand); } - int decrement = frac_t_event*universe->nworlds; + int decrement = (t_event - frac_t_event)*universe->nworlds; clock -= decrement; // share event across replicas @@ -508,6 +508,7 @@ void PRD::dephase() if (compute_event->compute_scalar() > 0.0) { fix_event->restore_state_dephase(); update->ntimestep -= t_dephase; + log_event(); } else { fix_event->restore_state_quench(); done = 1; diff --git a/src/USER-SMD/Install.sh b/src/USER-SMD/Install.sh new file mode 100644 index 0000000000..73f6146c4e --- /dev/null +++ b/src/USER-SMD/Install.sh @@ -0,0 +1,64 @@ +# Install/unInstall package files in LAMMPS +# mode = 0/1/2 for uninstall/install/update + +mode=$1 + +# arg1 = file, arg2 = file it depends on + +action () { + if (test $mode = 0) then + rm -f ../$1 + elif (! cmp -s $1 ../$1) then + if (test -z "$2" || test -e ../$2) then + cp $1 .. + if (test $mode = 2) then + echo " updating src/$1" + fi + fi + elif (test -n "$2") then + if (test ! -e ../$2) then + rm -f ../$1 + fi + fi +} + +# all package files with no dependencies + +for file in *.cpp *.h; do + action $file +done + +# edit 2 Makefile.package files to include/exclude package info + +if (test $1 = 1) then + + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*smd[^ \t]* //g' ../Makefile.package + sed -i -e 's|^PKG_INC =[ \t]*|&-I..\/..\/lib\/smd |' ../Makefile.package + sed -i -e 's|^PKG_PATH =[ \t]*|&-L..\/..\/lib\/smd$(LIBOBJDIR) |' ../Makefile.package + #sed -i -e 's|^PKG_LIB =[ \t]*|&-lsmd |' ../Makefile.package + sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(smd_SYSINC) |' ../Makefile.package + sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(smd_SYSLIB) |' ../Makefile.package + sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(smd_SYSPATH) |' ../Makefile.package + fi + + if (test -e ../Makefile.package.settings) then + sed -i -e '/^include.*smd.*$/d' ../Makefile.package.settings + # multiline form needed for BSD sed on Macs +# sed -i -e '4 i \ +#include ..\/..\/lib\/smd\/Makefile.lammps +#' ../Makefile.package.settings + + fi + +elif (test $1 = 0) then + + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*smd[^ \t]* //g' ../Makefile.package + fi + + if (test -e ../Makefile.package.settings) then + sed -i -e '/^include.*smd.*$/d' ../Makefile.package.settings + fi + +fi diff --git a/src/USER-SMD/README b/src/USER-SMD/README new file mode 100644 index 0000000000..91961c4923 --- /dev/null +++ b/src/USER-SMD/README @@ -0,0 +1,7 @@ +Smooth Mach Dynamics -- Smooth Particle Hydrodynamics for solids and fluids + +The person who created this package is Georg Ganzenmuller at the +Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in +Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if +you have questions. + diff --git a/src/USER-SMD/atom_vec_smd.cpp b/src/USER-SMD/atom_vec_smd.cpp new file mode 100644 index 0000000000..f9af5d3d92 --- /dev/null +++ b/src/USER-SMD/atom_vec_smd.cpp @@ -0,0 +1,1288 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#include "math.h" +#include "stdlib.h" +#include "string.h" +#include "atom_vec_smd.h" +#include "atom.h" +#include "comm.h" +#include "domain.h" +#include "modify.h" +#include "force.h" +#include "fix.h" +#include "fix_adapt.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace MathConst; +#define NMAT_FULL 9 +#define NMAT_SYMM 6 + +/* ---------------------------------------------------------------------- */ + +AtomVecSMD::AtomVecSMD(LAMMPS *lmp) : + AtomVec(lmp) { + molecular = 0; + + comm_x_only = 0; + comm_f_only = 0; + size_forward = 6; // variables that are changed by time integration + size_reverse = 4; // f[3] + de + size_border = 31; + size_velocity = 6; // v + vest + size_data_atom = 13; // 7 + 3 x0 + 3 x + size_data_vel = 4; + xcol_data = 11; + + atom->radius_flag = 1; + atom->rmass_flag = 1; + atom->vfrac_flag = 1; + atom->contact_radius_flag = 1; + atom->molecule_flag = 1; + atom->smd_data_9_flag = 1; + atom->e_flag = 1; + atom->vest_flag = 1; + atom->smd_stress_flag = 1; + atom->eff_plastic_strain_flag = 1; + atom->x0_flag = 1; + atom->damage_flag = 1; + atom->eff_plastic_strain_rate_flag = 1; + + forceclearflag = 1; + + atom->smd_flag = 1; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSMD::init() { + AtomVec::init(); + + // do nothing here +} + +/* ---------------------------------------------------------------------- + grow atom arrays + n = 0 grows arrays by a chunk + n > 0 allocates arrays to size n + ------------------------------------------------------------------------- */ + +void AtomVecSMD::grow(int n) { + if (n == 0) + grow_nmax(); + else + nmax = n; + atom->nmax = nmax; + if (nmax < 0 || nmax > MAXSMALLINT) + error->one(FLERR, "Per-processor system is too big"); + + //printf("in grow, nmax is now %d\n", nmax); + + tag = memory->grow(atom->tag, nmax, "atom:tag"); + type = memory->grow(atom->type, nmax, "atom:type"); + mask = memory->grow(atom->mask, nmax, "atom:mask"); + image = memory->grow(atom->image, nmax, "atom:image"); + x = memory->grow(atom->x, nmax, 3, "atom:x"); + v = memory->grow(atom->v, nmax, 3, "atom:v"); + + f = memory->grow(atom->f, nmax * comm->nthreads, 3, "atom:f"); + de = memory->grow(atom->de, nmax * comm->nthreads, "atom:de"); + + vfrac = memory->grow(atom->vfrac, nmax, "atom:vfrac"); + rmass = memory->grow(atom->rmass, nmax, "atom:rmass"); + x0 = memory->grow(atom->x0, nmax, 3, "atom:x0"); + radius = memory->grow(atom->radius, nmax, "atom:radius"); + contact_radius = memory->grow(atom->contact_radius, nmax, "atom:contact_radius"); + molecule = memory->grow(atom->molecule, nmax, "atom:molecule"); + smd_data_9 = memory->grow(atom->smd_data_9, nmax, NMAT_FULL, "atom:defgrad_old"); + e = memory->grow(atom->e, nmax, "atom:e"); + vest = memory->grow(atom->vest, nmax, 3, "atom:vest"); + tlsph_stress = memory->grow(atom->smd_stress, nmax, NMAT_SYMM, "atom:tlsph_stress"); + eff_plastic_strain = memory->grow(atom->eff_plastic_strain, nmax, "atom:eff_plastic_strain"); + eff_plastic_strain_rate = memory->grow(atom->eff_plastic_strain_rate, nmax, "atom:eff_plastic_strain_rate"); + damage = memory->grow(atom->damage, nmax, "atom:damage"); + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax); +} + +/* ---------------------------------------------------------------------- + reset local array ptrs + ------------------------------------------------------------------------- */ + +void AtomVecSMD::grow_reset() { + tag = atom->tag; + type = atom->type; + mask = atom->mask; + image = atom->image; + x = atom->x; + v = atom->v; + f = atom->f; + radius = atom->radius; + rmass = atom->rmass; + + molecule = atom->molecule; + vfrac = atom->vfrac; + x0 = atom->x0; + contact_radius = atom->contact_radius; + molecule = atom->molecule; + smd_data_9 = atom->smd_data_9; + e = atom->e; + de = atom->de; + tlsph_stress = atom->smd_stress; + eff_plastic_strain = atom->eff_plastic_strain; + eff_plastic_strain_rate = atom->eff_plastic_strain_rate; + damage = atom->damage; + vest = atom->vest; +} + +/* ---------------------------------------------------------------------- + copy atom I info to atom J + ------------------------------------------------------------------------- */ + +void AtomVecSMD::copy(int i, int j, int delflag) { + tag[j] = tag[i]; + type[j] = type[i]; + mask[j] = mask[i]; + image[j] = image[i]; + x[j][0] = x[i][0]; + x[j][1] = x[i][1]; + x[j][2] = x[i][2]; + v[j][0] = v[i][0]; + v[j][1] = v[i][1]; + v[j][2] = v[i][2]; + + vfrac[j] = vfrac[i]; + rmass[j] = rmass[i]; + x0[j][0] = x0[i][0]; + x0[j][1] = x0[i][1]; + x0[j][2] = x0[i][2]; + radius[j] = radius[i]; + contact_radius[j] = contact_radius[i]; + molecule[j] = molecule[i]; + e[j] = e[i]; + eff_plastic_strain[j] = eff_plastic_strain[i]; + eff_plastic_strain_rate[j] = eff_plastic_strain_rate[i]; + vest[j][0] = vest[i][0]; + vest[j][1] = vest[i][1]; + vest[j][2] = vest[i][2]; + + for (int k = 0; k < NMAT_FULL; k++) { + smd_data_9[j][k] = smd_data_9[i][k]; + } + + for (int k = 0; k < NMAT_SYMM; k++) { + tlsph_stress[j][k] = tlsph_stress[i][k]; + } + + damage[j] = damage[i]; + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + modify->fix[atom->extra_grow[iextra]]->copy_arrays(i, j, delflag); +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSMD::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) { + error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on"); + return -1; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSMD::pack_comm_vel(int n, int *list, double *buf, int pbc_flag, int *pbc) { + // communicate quantities to ghosts, which are changed by time-integration AND are required on ghost atoms. + + //no need to pack stress or defgrad information here, as these quantities are not required for ghost atoms. + // Inside pair_style tlsph, these quantities are computed and communicated to ghosts. + + // no need to communicate x0 here, as it is not changed by time integration + // if x0 is changed when the ref config is updated, this communication is performed in the fix_integrate/tlsph + // similarily, rmass could be removed here. + // radius should be communicated here for future time-integration of the radius with ulsph (not implemented yet) + int i, j, m; + double dx, dy, dz, dvx, dvy, dvz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0]; + buf[m++] = x[j][1]; + buf[m++] = x[j][2]; //3 + buf[m++] = radius[j]; + buf[m++] = vfrac[j]; // 5 + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; // 8 + + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; // 11 + buf[m++] = e[j]; // 12 + + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0] * domain->xprd; + dy = pbc[1] * domain->yprd; + dz = pbc[2] * domain->zprd; + } else { + dx = pbc[0] * domain->xprd + pbc[5] * domain->xy + pbc[4] * domain->xz; + dy = pbc[1] * domain->yprd + pbc[3] * domain->yz; + dz = pbc[2] * domain->zprd; + } + if (!deform_vremap) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = radius[j]; + buf[m++] = vfrac[j]; + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; // 8 + + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; // 11 + buf[m++] = e[j]; // 12 + + } + } else { + dvx = pbc[0] * h_rate[0] + pbc[5] * h_rate[5] + pbc[4] * h_rate[4]; + dvy = pbc[1] * h_rate[1] + pbc[3] * h_rate[3]; + dvz = pbc[2] * h_rate[2]; +// printf("\ndvx = %f, dvy=%f, dvz=%f\n", dvx, dvy, dvz); +// printf("dx = %f, dy=%f, dz=%f\n", dx, dy, dz); + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = radius[j]; + buf[m++] = vfrac[j]; + if (mask[i] & deform_groupbit) { + buf[m++] = v[j][0] + dvx; + buf[m++] = v[j][1] + dvy; + buf[m++] = v[j][2] + dvz; + buf[m++] = vest[j][0] + dvx; + buf[m++] = vest[j][1] + dvy; + buf[m++] = vest[j][2] + dvz; + } else { + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; // 8 + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; // 11 + } + + buf[m++] = e[j]; // 12 + + } + } + } + + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSMD::pack_comm_hybrid(int n, int *list, double *buf) { + int i, j, m; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = radius[j]; + buf[m++] = vfrac[j]; + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; + buf[m++] = e[j]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSMD::unpack_comm(int n, int first, double *buf) { + error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on"); +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSMD::unpack_comm_vel(int n, int first, double *buf) { + int i, m, last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + x[i][0] = buf[m++]; + x[i][1] = buf[m++]; + x[i][2] = buf[m++]; //3 + radius[i] = buf[m++]; + vfrac[i] = buf[m++]; // 5 + v[i][0] = buf[m++]; + v[i][1] = buf[m++]; + v[i][2] = buf[m++]; // 8 + + vest[i][0] = buf[m++]; + vest[i][1] = buf[m++]; + vest[i][2] = buf[m++]; // 11 + e[i] = buf[m++]; + + } +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSMD::unpack_comm_hybrid(int n, int first, double *buf) { + int i, m, last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + radius[i] = buf[m++]; + vfrac[i] = buf[m++]; + vest[i][0] = buf[m++]; + vest[i][1] = buf[m++]; + vest[i][2] = buf[m++]; + e[i] = buf[m++]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSMD::pack_reverse(int n, int first, double *buf) { + int i, m, last; + + printf("in pack_reverse\n"); + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + buf[m++] = f[i][0]; + buf[m++] = f[i][1]; + buf[m++] = f[i][2]; + buf[m++] = de[i]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSMD::pack_reverse_hybrid(int n, int first, double *buf) { + int i, m, last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + buf[m++] = de[i]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSMD::unpack_reverse(int n, int *list, double *buf) { + int i, j, m; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + f[j][0] += buf[m++]; + f[j][1] += buf[m++]; + f[j][2] += buf[m++]; + de[j] += buf[m++]; + } +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSMD::unpack_reverse_hybrid(int n, int *list, double *buf) { + int i, j, m; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + de[j] += buf[m++]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSMD::pack_border(int n, int *list, double *buf, int pbc_flag, int *pbc) { + error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on"); + return -1; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSMD::pack_border_vel(int n, int *list, double *buf, int pbc_flag, int *pbc) { + int i, j, m; + double dx, dy, dz, dvx, dvy, dvz; + + //printf("AtomVecSMD::pack_border_vel\n"); + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0]; + buf[m++] = x[j][1]; + buf[m++] = x[j][2]; // 3 + buf[m++] = x0[j][0]; + buf[m++] = x0[j][1]; + buf[m++] = x0[j][2]; // 6 + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + buf[m++] = ubuf(molecule[j]).d; // 10 + buf[m++] = radius[j]; + buf[m++] = rmass[j]; + buf[m++] = vfrac[j]; + buf[m++] = contact_radius[j]; + buf[m++] = e[j]; + buf[m++] = eff_plastic_strain[j]; // 16 + + for (int k = 0; k < NMAT_FULL; k++) { + buf[m++] = smd_data_9[j][k]; + } // 25 + + for (int k = 0; k < NMAT_SYMM; k++) { + buf[m++] = tlsph_stress[j][k]; + } // 31 + + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; // 34 + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; // 37 + } + } else { + + if (domain->triclinic == 0) { + dx = pbc[0] * domain->xprd; + dy = pbc[1] * domain->yprd; + dz = pbc[2] * domain->zprd; + } else { + dx = pbc[0]; + dy = pbc[1]; + dz = pbc[2]; + } + if (!deform_vremap) { + //printf("dx = %f\n", dx); + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; // 3 + buf[m++] = x0[j][0]; // this is correct + buf[m++] = x0[j][1]; + buf[m++] = x0[j][2]; // 6 + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + buf[m++] = ubuf(molecule[j]).d; // 10 + buf[m++] = radius[j]; + buf[m++] = rmass[j]; + buf[m++] = vfrac[j]; + buf[m++] = contact_radius[j]; + buf[m++] = e[j]; + buf[m++] = eff_plastic_strain[j]; // 17 + + for (int k = 0; k < NMAT_FULL; k++) { + buf[m++] = smd_data_9[j][k]; + } // 26 + + for (int k = 0; k < NMAT_SYMM; k++) { + buf[m++] = tlsph_stress[j][k]; + } // 32 + + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; // 35 + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; // 38 + + } + } else { + dvx = pbc[0] * h_rate[0] + pbc[5] * h_rate[5] + pbc[4] * h_rate[4]; + dvy = pbc[1] * h_rate[1] + pbc[3] * h_rate[3]; + dvz = pbc[2] * h_rate[2]; +// printf("\ndvx = %f, dvy=%f, dvz=%f\n", dvx, dvy, dvz); +// printf("dx = %f, dy=%f, dz=%f\n", dx, dy, dz); + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; // 3 + buf[m++] = x0[j][0]; + buf[m++] = x0[j][1]; + buf[m++] = x0[j][2]; // 6 + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + buf[m++] = ubuf(molecule[j]).d; // 10 + buf[m++] = radius[j]; + buf[m++] = rmass[j]; + buf[m++] = vfrac[j]; + buf[m++] = contact_radius[j]; + buf[m++] = e[j]; + buf[m++] = eff_plastic_strain[j]; // 16 + + for (int k = 0; k < NMAT_FULL; k++) { + buf[m++] = smd_data_9[j][k]; + } // 25 + + for (int k = 0; k < NMAT_SYMM; k++) { + buf[m++] = tlsph_stress[j][k]; + } // 31 + + if (mask[i] & deform_groupbit) { + buf[m++] = v[j][0] + dvx; + buf[m++] = v[j][1] + dvy; + buf[m++] = v[j][2] + dvz; // 34 + buf[m++] = vest[j][0] + dvx; + buf[m++] = vest[j][1] + dvy; + buf[m++] = vest[j][2] + dvz; // 37 + + } else { + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; // 34 + buf[m++] = vest[j][0]; + buf[m++] = vest[j][1]; + buf[m++] = vest[j][2]; // 37 + } + + } + } + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]->pack_border(n, list, &buf[m]); + + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSMD::pack_border_hybrid(int n, int *list, double *buf) { + int i, j, m; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + + buf[m++] = x0[j][0]; + buf[m++] = x0[j][1]; + buf[m++] = x0[j][2]; // 3 + buf[m++] = ubuf(molecule[j]).d; // 4 + buf[m++] = radius[j]; + buf[m++] = rmass[j]; + buf[m++] = vfrac[j]; + buf[m++] = contact_radius[j]; + buf[m++] = e[j]; + buf[m++] = eff_plastic_strain[j]; // 11 + + for (int k = 0; k < NMAT_FULL; k++) { + buf[m++] = smd_data_9[j][k]; + } // 20 + + for (int k = 0; k < NMAT_SYMM; k++) { + buf[m++] = tlsph_stress[j][k]; + } // 26 + + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSMD::unpack_border(int n, int first, double *buf) { + error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on"); +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSMD::unpack_border_vel(int n, int first, double *buf) { + int i, m, last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + if (i == nmax) + grow(0); + x[i][0] = buf[m++]; + x[i][1] = buf[m++]; + x[i][2] = buf[m++]; // 3 + x0[i][0] = buf[m++]; + x0[i][1] = buf[m++]; + x0[i][2] = buf[m++]; // 6 + tag[i] = (tagint) ubuf(buf[m++]).i; + type[i] = (int) ubuf(buf[m++]).i; + mask[i] = (int) ubuf(buf[m++]).i; + molecule[i] = (int) ubuf(buf[m++]).i; // 10 + + radius[i] = buf[m++]; + rmass[i] = buf[m++]; + vfrac[i] = buf[m++]; + contact_radius[i] = buf[m++]; + e[i] = buf[m++]; + eff_plastic_strain[i] = buf[m++]; // 16 + + for (int k = 0; k < NMAT_FULL; k++) { + smd_data_9[i][k] = buf[m++]; + } // 25 + + for (int k = 0; k < NMAT_SYMM; k++) { + tlsph_stress[i][k] = buf[m++]; + } // 31 + + v[i][0] = buf[m++]; + v[i][1] = buf[m++]; + v[i][2] = buf[m++]; // 34 + vest[i][0] = buf[m++]; + vest[i][1] = buf[m++]; + vest[i][2] = buf[m++]; // 37 + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]->unpack_border(n, first, &buf[m]); +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSMD::unpack_border_hybrid(int n, int first, double *buf) { + int i, m, last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + x0[i][0] = buf[m++]; + x0[i][1] = buf[m++]; + x0[i][2] = buf[m++]; // 3 + molecule[i] = (int) ubuf(buf[m++]).i; // 4 + radius[i] = buf[m++]; + rmass[i] = buf[m++]; + vfrac[i] = buf[m++]; + contact_radius[i] = buf[m++]; + e[i] = buf[m++]; + eff_plastic_strain[i] = buf[m++]; // 11 + + for (int k = 0; k < NMAT_FULL; k++) { + smd_data_9[i][k] = buf[m++]; + } // 20 + + for (int k = 0; k < NMAT_SYMM; k++) { + tlsph_stress[i][k] = buf[m++]; + } // 26 + } + return m; +} + +/* ---------------------------------------------------------------------- + pack data for atom I for sending to another proc + xyz must be 1st 3 values, so comm::exchange() can test on them + ------------------------------------------------------------------------- */ + +int AtomVecSMD::pack_exchange(int i, double *buf) { + int m = 1; + + //printf("in AtomVecSMD::pack_exchange tag %d\n", tag[i]); + + buf[m++] = x[i][0]; + buf[m++] = x[i][1]; + buf[m++] = x[i][2]; // 3 + buf[m++] = x0[i][0]; + buf[m++] = x0[i][1]; + buf[m++] = x0[i][2]; // 6 + buf[m++] = ubuf(tag[i]).d; + buf[m++] = ubuf(type[i]).d; + buf[m++] = ubuf(mask[i]).d; + buf[m++] = ubuf(image[i]).d; + buf[m++] = ubuf(molecule[i]).d; // 11 + buf[m++] = radius[i]; + buf[m++] = rmass[i]; + buf[m++] = vfrac[i]; + buf[m++] = contact_radius[i]; + buf[m++] = e[i]; + buf[m++] = eff_plastic_strain[i]; // 18 + buf[m++] = eff_plastic_strain_rate[i]; // 19 + + for (int k = 0; k < NMAT_FULL; k++) { + buf[m++] = smd_data_9[i][k]; + } // 27 + + for (int k = 0; k < NMAT_SYMM; k++) { + buf[m++] = tlsph_stress[i][k]; + } // 33 + + buf[m++] = v[i][0]; + buf[m++] = v[i][1]; + buf[m++] = v[i][2]; // 36 + buf[m++] = vest[i][0]; + buf[m++] = vest[i][1]; + buf[m++] = vest[i][2]; // 39 + + buf[m++] = damage[i]; + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i, &buf[m]); + + buf[0] = m; + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSMD::unpack_exchange(double *buf) { + int nlocal = atom->nlocal; + if (nlocal == nmax) + grow(0); + + int m = 1; + + x[nlocal][0] = buf[m++]; + x[nlocal][1] = buf[m++]; + x[nlocal][2] = buf[m++]; // 3 + x0[nlocal][0] = buf[m++]; + x0[nlocal][1] = buf[m++]; + x0[nlocal][2] = buf[m++]; // 6 + tag[nlocal] = (tagint) ubuf(buf[m++]).i; + type[nlocal] = (int) ubuf(buf[m++]).i; + mask[nlocal] = (int) ubuf(buf[m++]).i; + image[nlocal] = (imageint) ubuf(buf[m++]).i; + molecule[nlocal] = (int) ubuf(buf[m++]).i; // 11 + + radius[nlocal] = buf[m++]; + rmass[nlocal] = buf[m++]; + vfrac[nlocal] = buf[m++]; + contact_radius[nlocal] = buf[m++]; + e[nlocal] = buf[m++]; + eff_plastic_strain[nlocal] = buf[m++]; // 18 + eff_plastic_strain_rate[nlocal] = buf[m++]; // 19 + + for (int k = 0; k < NMAT_FULL; k++) { + smd_data_9[nlocal][k] = buf[m++]; + } // 27 + + for (int k = 0; k < NMAT_SYMM; k++) { + tlsph_stress[nlocal][k] = buf[m++]; + } // 33 + + v[nlocal][0] = buf[m++]; + v[nlocal][1] = buf[m++]; + v[nlocal][2] = buf[m++]; // 36 + vest[nlocal][0] = buf[m++]; + vest[nlocal][1] = buf[m++]; + vest[nlocal][2] = buf[m++]; // 39 + + damage[nlocal] = buf[m++]; //40 + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + m += modify->fix[atom->extra_grow[iextra]]->unpack_exchange(nlocal, &buf[m]); + + atom->nlocal++; + return m; +} + +/* ---------------------------------------------------------------------- + size of restart data for all atoms owned by this proc + include extra data stored by fixes + ------------------------------------------------------------------------- */ + +int AtomVecSMD::size_restart() { + int i; + + int nlocal = atom->nlocal; + int n = 43 * nlocal; // count pack_restart + 1 (size of buffer) + + if (atom->nextra_restart) + for (int iextra = 0; iextra < atom->nextra_restart; iextra++) + for (i = 0; i < nlocal; i++) + n += modify->fix[atom->extra_restart[iextra]]->size_restart(i); + + return n; +} + +/* ---------------------------------------------------------------------- + pack atom I's data for restart file including extra quantities + xyz must be 1st 3 values, so that read_restart can test on them + molecular types may be negative, but write as positive + ------------------------------------------------------------------------- */ +int AtomVecSMD::pack_restart(int i, double *buf) { + int m = 1; // 1 + + buf[m++] = x[i][0]; + buf[m++] = x[i][1]; + buf[m++] = x[i][2]; // 4 + buf[m++] = x0[i][0]; + buf[m++] = x0[i][1]; + buf[m++] = x0[i][2]; // 7 + buf[m++] = ubuf(tag[i]).d; + buf[m++] = ubuf(type[i]).d; + buf[m++] = ubuf(mask[i]).d; // 10 + buf[m++] = ubuf(image[i]).d; + buf[m++] = ubuf(molecule[i]).d; + buf[m++] = radius[i]; + buf[m++] = rmass[i]; + buf[m++] = vfrac[i]; // 15 + buf[m++] = contact_radius[i]; + buf[m++] = e[i]; + buf[m++] = eff_plastic_strain[i]; + buf[m++] = eff_plastic_strain_rate[i]; // 19 + + for (int k = 0; k < NMAT_FULL; k++) { + buf[m++] = smd_data_9[i][k]; + } // 28 + + for (int k = 0; k < NMAT_SYMM; k++) { + buf[m++] = tlsph_stress[i][k]; + } // 34 + + buf[m++] = v[i][0]; + buf[m++] = v[i][1]; + buf[m++] = v[i][2]; // 37 + buf[m++] = vest[i][0]; + buf[m++] = vest[i][1]; + buf[m++] = vest[i][2]; // 40 + + buf[m++] = damage[i]; // 41 + + if (atom->nextra_restart) + for (int iextra = 0; iextra < atom->nextra_restart; iextra++) + m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i, &buf[m]); + + buf[0] = m; + return m; +} + +/* ---------------------------------------------------------------------- + unpack data for one atom from restart file including extra quantities + ------------------------------------------------------------------------- */ + +int AtomVecSMD::unpack_restart(double *buf) { + int nlocal = atom->nlocal; + if (nlocal == nmax) { + grow(0); + if (atom->nextra_store) + memory->grow(atom->extra, nmax, atom->nextra_store, "atom:extra"); + } + + int m = 1; + + x[nlocal][0] = buf[m++]; + x[nlocal][1] = buf[m++]; + x[nlocal][2] = buf[m++]; // 3 + x0[nlocal][0] = buf[m++]; + x0[nlocal][1] = buf[m++]; + x0[nlocal][2] = buf[m++]; // 6 + tag[nlocal] = (tagint) ubuf(buf[m++]).i; + type[nlocal] = (int) ubuf(buf[m++]).i; + mask[nlocal] = (int) ubuf(buf[m++]).i; + image[nlocal] = (imageint) ubuf(buf[m++]).i; + molecule[nlocal] = (int) ubuf(buf[m++]).i; // 11 + + radius[nlocal] = buf[m++]; + rmass[nlocal] = buf[m++]; + vfrac[nlocal] = buf[m++]; //14 + contact_radius[nlocal] = buf[m++]; //15 + e[nlocal] = buf[m++]; + eff_plastic_strain[nlocal] = buf[m++]; // 18 + eff_plastic_strain_rate[nlocal] = buf[m++]; // 29 + + for (int k = 0; k < NMAT_FULL; k++) { + smd_data_9[nlocal][k] = buf[m++]; + } // 28 + + for (int k = 0; k < NMAT_SYMM; k++) { + tlsph_stress[nlocal][k] = buf[m++]; + } // 34 + + v[nlocal][0] = buf[m++]; + v[nlocal][1] = buf[m++]; + v[nlocal][2] = buf[m++]; // 37 + vest[nlocal][0] = buf[m++]; + vest[nlocal][1] = buf[m++]; + vest[nlocal][2] = buf[m++]; // 40 + + damage[nlocal] = buf[m++]; //41 + + //printf("nlocal in restart is %d\n", nlocal); + + double **extra = atom->extra; + if (atom->nextra_store) { + int size = static_cast(buf[0]) - m; + for (int i = 0; i < size; i++) + extra[nlocal][i] = buf[m++]; + } + + atom->nlocal++; + + //printf("returning m=%d in unpack_restart\n", m); + + return m; +} + +/* ---------------------------------------------------------------------- + create one atom of itype at coord + set other values to defaults + ------------------------------------------------------------------------- */ + +void AtomVecSMD::create_atom(int itype, double *coord) { + int nlocal = atom->nlocal; + if (nlocal == nmax) { + printf("nlocal = %d, nmax = %d, calling grow\n", nlocal, nmax); + grow(0); + printf("... finished growing\n"); + } + + tag[nlocal] = 0; + type[nlocal] = itype; + x[nlocal][0] = coord[0]; + x[nlocal][1] = coord[1]; + x[nlocal][2] = coord[2]; + x0[nlocal][0] = coord[0]; + x0[nlocal][1] = coord[1]; + x0[nlocal][2] = coord[2]; + mask[nlocal] = 1; + image[nlocal] = ((imageint) IMGMAX << IMG2BITS) | ((imageint) IMGMAX << IMGBITS) | IMGMAX; + v[nlocal][0] = 0.0; + v[nlocal][1] = 0.0; + v[nlocal][2] = 0.0; + vest[nlocal][0] = 0.0; + vest[nlocal][1] = 0.0; + vest[nlocal][2] = 0.0; + + vfrac[nlocal] = 1.0; + rmass[nlocal] = 1.0; + radius[nlocal] = 0.5; + contact_radius[nlocal] = 0.5; + molecule[nlocal] = 1; + e[nlocal] = 0.0; + eff_plastic_strain[nlocal] = 0.0; + eff_plastic_strain_rate[nlocal] = 0.0; + + for (int k = 0; k < NMAT_FULL; k++) { + smd_data_9[nlocal][k] = 0.0; + } + smd_data_9[nlocal][0] = 1.0; // xx + smd_data_9[nlocal][4] = 1.0; // yy + smd_data_9[nlocal][8] = 1.0; // zz + + for (int k = 0; k < NMAT_SYMM; k++) { + tlsph_stress[nlocal][k] = 0.0; + } + + damage[nlocal] = 0.0; + + atom->nlocal++; +} + +/* ---------------------------------------------------------------------- + unpack one line from Atoms section of data file + initialize other atom quantities + ------------------------------------------------------------------------- */ + +void AtomVecSMD::data_atom(double *coord, imageint imagetmp, char **values) { + int nlocal = atom->nlocal; + if (nlocal == nmax) + grow(0); + + tag[nlocal] = ATOTAGINT(values[0]); + + type[nlocal] = atoi(values[1]); + if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) + error->one(FLERR, "Invalid atom type in Atoms section of data file"); + + molecule[nlocal] = atoi(values[2]); + if (molecule[nlocal] <= 0) + error->one(FLERR, "Invalid molecule in Atoms section of data file"); + + vfrac[nlocal] = atof(values[3]); + if (vfrac[nlocal] < 0.0) + error->one(FLERR, "Invalid volume in Atoms section of data file"); + + rmass[nlocal] = atof(values[4]); + if (rmass[nlocal] == 0.0) + error->one(FLERR, "Invalid mass in Atoms section of data file"); + + radius[nlocal] = atof(values[5]); + if (radius[nlocal] < 0.0) + error->one(FLERR, "Invalid radius in Atoms section of data file"); + + contact_radius[nlocal] = atof(values[6]); + if (contact_radius[nlocal] < 0.0) + error->one(FLERR, "Invalid contact radius in Atoms section of data file"); + + e[nlocal] = 0.0; + + x0[nlocal][0] = atof(values[7]); + x0[nlocal][1] = atof(values[8]); + x0[nlocal][2] = atof(values[9]); + + x[nlocal][0] = coord[0]; + x[nlocal][1] = coord[1]; + x[nlocal][2] = coord[2]; + + image[nlocal] = imagetmp; + + mask[nlocal] = 1; + v[nlocal][0] = 0.0; + v[nlocal][1] = 0.0; + v[nlocal][2] = 0.0; + vest[nlocal][0] = 0.0; + vest[nlocal][1] = 0.0; + vest[nlocal][2] = 0.0; + + damage[nlocal] = 0.0; + + eff_plastic_strain[nlocal] = 0.0; + eff_plastic_strain_rate[nlocal] = 0.0; + + for (int k = 0; k < NMAT_FULL; k++) { + smd_data_9[nlocal][k] = 0.0; + } + + for (int k = 0; k < NMAT_SYMM; k++) { + tlsph_stress[nlocal][k] = 0.0; + } + + smd_data_9[nlocal][0] = 1.0; // xx + smd_data_9[nlocal][4] = 1.0; // yy + smd_data_9[nlocal][8] = 1.0; // zz + + atom->nlocal++; +} + +/* ---------------------------------------------------------------------- + unpack hybrid quantities from one line in Atoms section of data file + initialize other atom quantities for this sub-style + ------------------------------------------------------------------------- */ + +int AtomVecSMD::data_atom_hybrid(int nlocal, char **values) { + error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style tlsph"); + return -1; +} + +/* ---------------------------------------------------------------------- + unpack one line from Velocities section of data file + ------------------------------------------------------------------------- */ + +void AtomVecSMD::data_vel(int m, char **values) { + v[m][0] = atof(values[0]); + v[m][1] = atof(values[1]); + v[m][2] = atof(values[2]); + vest[m][0] = atof(values[0]); + vest[m][1] = atof(values[1]); + vest[m][2] = atof(values[2]); +} + +/* ---------------------------------------------------------------------- + unpack hybrid quantities from one line in Velocities section of data file + ------------------------------------------------------------------------- */ + +int AtomVecSMD::data_vel_hybrid(int m, char **values) { + error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style tlsph"); + return 0; +} + +/* ---------------------------------------------------------------------- + pack atom info for data file including 3 image flags + ------------------------------------------------------------------------- */ + +void AtomVecSMD::pack_data(double **buf) { + int nlocal = atom->nlocal; + for (int i = 0; i < nlocal; i++) { + buf[i][0] = ubuf(tag[i]).d; + buf[i][1] = ubuf(type[i]).d; + buf[i][2] = ubuf(molecule[i]).d; + buf[i][3] = vfrac[i]; + buf[i][4] = rmass[i]; + buf[i][5] = radius[i]; + buf[i][6] = contact_radius[i]; + + buf[i][7] = x[i][0]; + buf[i][8] = x[i][1]; + buf[i][9] = x[i][2]; + + buf[i][10] = ubuf((image[i] & IMGMASK) - IMGMAX).d; + buf[i][11] = ubuf((image[i] >> IMGBITS & IMGMASK) - IMGMAX).d; + buf[i][12] = ubuf((image[i] >> IMG2BITS) - IMGMAX).d; + } +} + +/* ---------------------------------------------------------------------- + pack hybrid atom info for data file + ------------------------------------------------------------------------- */ + +int AtomVecSMD::pack_data_hybrid(int i, double *buf) { + error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style tlsph"); + return -1; +} + +/* ---------------------------------------------------------------------- + write atom info to data file including 3 image flags + ------------------------------------------------------------------------- */ + +void AtomVecSMD::write_data(FILE *fp, int n, double **buf) { + for (int i = 0; i < n; i++) + fprintf(fp, + TAGINT_FORMAT + " %d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n", (tagint) ubuf(buf[i][0]).i, + (int) ubuf(buf[i][1]).i, (int) ubuf(buf[i][2]).i, buf[i][3], buf[i][4], buf[i][5], buf[i][6], buf[i][7], buf[i][8], + buf[i][9], (int) ubuf(buf[i][7]).i, (int) ubuf(buf[i][8]).i, (int) ubuf(buf[i][9]).i); +} + +/* ---------------------------------------------------------------------- + write hybrid atom info to data file + ------------------------------------------------------------------------- */ + +int AtomVecSMD::write_data_hybrid(FILE *fp, double *buf) { + error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style tlsph"); + return -1; +} + +/* ---------------------------------------------------------------------- + pack velocity info for data file + ------------------------------------------------------------------------- */ + +void AtomVecSMD::pack_vel(double **buf) { + int nlocal = atom->nlocal; + for (int i = 0; i < nlocal; i++) { + buf[i][0] = ubuf(tag[i]).d; + buf[i][1] = v[i][0]; + buf[i][2] = v[i][1]; + buf[i][3] = v[i][2]; + } +} + +/* ---------------------------------------------------------------------- + pack hybrid velocity info for data file + ------------------------------------------------------------------------- */ + +int AtomVecSMD::pack_vel_hybrid(int i, double *buf) { + error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style tlsph"); + return 0; +} + +/* ---------------------------------------------------------------------- + write velocity info to data file + ------------------------------------------------------------------------- */ + +void AtomVecSMD::write_vel(FILE *fp, int n, double **buf) { + for (int i = 0; i < n; i++) + fprintf(fp, TAGINT_FORMAT + " %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e\n", (tagint) ubuf(buf[i][0]).i, buf[i][1], buf[i][2], buf[i][3], + buf[i][4], buf[i][5], buf[i][6]); +} + +/* ---------------------------------------------------------------------- + write hybrid velocity info to data file + ------------------------------------------------------------------------- */ + +int AtomVecSMD::write_vel_hybrid(FILE *fp, double *buf) { + error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style tlsph"); + return 3; +} + +/* ---------------------------------------------------------------------- + return # of bytes of allocated memory + ------------------------------------------------------------------------- */ + +bigint AtomVecSMD::memory_usage() { + bigint bytes = 0; + + if (atom->memcheck("tag")) + bytes += memory->usage(tag, nmax); + if (atom->memcheck("type")) + bytes += memory->usage(type, nmax); + if (atom->memcheck("molecule")) + bytes += memory->usage(molecule, nmax); + if (atom->memcheck("mask")) + bytes += memory->usage(mask, nmax); + if (atom->memcheck("image")) + bytes += memory->usage(image, nmax); + if (atom->memcheck("x")) + bytes += memory->usage(x, nmax, 3); + if (atom->memcheck("v")) + bytes += memory->usage(v, nmax, 3); + if (atom->memcheck("vest")) + bytes += memory->usage(vest, nmax, 3); + if (atom->memcheck("f")) + bytes += memory->usage(f, nmax * comm->nthreads, 3); + + if (atom->memcheck("radius")) + bytes += memory->usage(radius, nmax); + if (atom->memcheck("contact_radius")) + bytes += memory->usage(contact_radius, nmax); + if (atom->memcheck("vfrac")) + bytes += memory->usage(vfrac, nmax); + if (atom->memcheck("rmass")) + bytes += memory->usage(rmass, nmax); + if (atom->memcheck("eff_plastic_strain")) + bytes += memory->usage(eff_plastic_strain, nmax); + if (atom->memcheck("eff_plastic_strain_rate")) + bytes += memory->usage(eff_plastic_strain_rate, nmax); + if (atom->memcheck("e")) + bytes += memory->usage(e, nmax); + if (atom->memcheck("de")) + bytes += memory->usage(de, nmax); + + if (atom->memcheck("smd_data_9")) + bytes += memory->usage(smd_data_9, nmax, NMAT_FULL); + if (atom->memcheck("tlsph_stress")) + bytes += memory->usage(tlsph_stress, nmax, NMAT_SYMM); + + if (atom->memcheck("damage")) + bytes += memory->usage(damage, nmax); + + return bytes; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSMD::force_clear(int n, size_t nbytes) { + //printf("clearing force on atom %d", n); + memset(&de[n], 0, nbytes); + memset(&f[0][0], 0, 3 * nbytes); +} diff --git a/src/USER-SMD/atom_vec_smd.h b/src/USER-SMD/atom_vec_smd.h new file mode 100644 index 0000000000..c79c60c352 --- /dev/null +++ b/src/USER-SMD/atom_vec_smd.h @@ -0,0 +1,125 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef ATOM_CLASS + +AtomStyle(smd,AtomVecSMD) + +#else + +#ifndef LMP_ATOM_VEC_SMD_H +#define LMP_ATOM_VEC_SMD_H + +#include "atom_vec.h" + +namespace LAMMPS_NS { + +class AtomVecSMD : public AtomVec { + public: + AtomVecSMD(class LAMMPS *); + ~AtomVecSMD() {} + void init(); + void grow(int); + void grow_reset(); + void copy(int, int, int); + void force_clear(int, size_t); + int pack_comm(int, int *, double *, int, int *); + int pack_comm_vel(int, int *, double *, int, int *); + int pack_comm_hybrid(int, int *, double *); + void unpack_comm(int, int, double *); + void unpack_comm_vel(int, int, double *); + int unpack_comm_hybrid(int, int, double *); + int pack_reverse(int, int, double *); + int pack_reverse_hybrid(int, int, double *); + void unpack_reverse(int, int *, double *); + int unpack_reverse_hybrid(int, int *, double *); + int pack_border(int, int *, double *, int, int *); + int pack_border_vel(int, int *, double *, int, int *); + int pack_border_hybrid(int, int *, double *); + void unpack_border(int, int, double *); + void unpack_border_vel(int, int, double *); + int unpack_border_hybrid(int, int, double *); + int pack_exchange(int, double *); + int unpack_exchange(double *); + int size_restart(); + int pack_restart(int, double *); + int unpack_restart(double *); + void create_atom(int, double *); + void data_atom(double *, imageint, char **); + int data_atom_hybrid(int, char **); + void data_vel(int, char **); + int data_vel_hybrid(int, char **); + void pack_data(double **); + int pack_data_hybrid(int, double *); + void write_data(FILE *, int, double **); + int write_data_hybrid(FILE *, double *); + void pack_vel(double **); + int pack_vel_hybrid(int, double *); + void write_vel(FILE *, int, double **); + int write_vel_hybrid(FILE *, double *); + bigint memory_usage(); + + private: + tagint *tag; + int *type,*mask; + imageint *image; + double **x,**v,**f; + double *radius,*rmass; + + int *molecule; + double *vfrac,**x0,*contact_radius, **smd_data_9, *e, *de, **vest; + double **tlsph_stress; + double *eff_plastic_strain; + double *damage; + double *eff_plastic_strain_rate; + + +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Per-processor system is too big + +The number of owned atoms plus ghost atoms on a single +processor must fit in 32-bit integer. + +E: Invalid atom type in Atoms section of data file + +Atom types must range from 1 to specified # of types. + +E: Invalid radius in Atoms section of data file + +Radius must be >= 0.0. + +E: Invalid density in Atoms section of data file + +Density value cannot be <= 0.0. + +*/ diff --git a/src/USER-SMD/compute_smd_contact_radius.cpp b/src/USER-SMD/compute_smd_contact_radius.cpp new file mode 100644 index 0000000000..865031addb --- /dev/null +++ b/src/USER-SMD/compute_smd_contact_radius.cpp @@ -0,0 +1,109 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#include "string.h" +#include "compute_smd_contact_radius.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeSMDContactRadius::ComputeSMDContactRadius(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) +{ + if (narg != 3) error->all(FLERR,"Illegal compute smd/contact_radius command"); + if (atom->contact_radius_flag != 1) error->all(FLERR,"compute smd/contact_radius command requires atom_style with contact_radius (e.g. smd)"); + + peratom_flag = 1; + size_peratom_cols = 0; + + nmax = 0; + contact_radius_vector = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputeSMDContactRadius::~ComputeSMDContactRadius() +{ + memory->sfree(contact_radius_vector); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDContactRadius::init() +{ + + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style,"smd/contact_radius") == 0) count++; + if (count > 1 && comm->me == 0) + error->warning(FLERR,"More than one compute smd/contact_radius"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDContactRadius::compute_peratom() +{ + invoked_peratom = update->ntimestep; + + // grow rhoVector array if necessary + + if (atom->nlocal > nmax) { + memory->sfree(contact_radius_vector); + nmax = atom->nmax; + contact_radius_vector = (double *) memory->smalloc(nmax*sizeof(double),"atom:contact_radius_vector"); + vector_atom = contact_radius_vector; + } + + double *contact_radius = atom->contact_radius; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + contact_radius_vector[i] = contact_radius[i]; + } + else { + contact_radius_vector[i] = 0.0; + } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array +------------------------------------------------------------------------- */ + +double ComputeSMDContactRadius::memory_usage() +{ + double bytes = nmax * sizeof(double); + return bytes; +} diff --git a/src/USER-SMD/compute_smd_contact_radius.h b/src/USER-SMD/compute_smd_contact_radius.h new file mode 100644 index 0000000000..9acb8e3b17 --- /dev/null +++ b/src/USER-SMD/compute_smd_contact_radius.h @@ -0,0 +1,55 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(smd/contact_radius,ComputeSMDContactRadius) + +#else + +#ifndef LMP_COMPUTE_SMD_CONTACT_RADIUS_H +#define LMP_COMPUTE_SMD_CONTACT_RADIUS_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeSMDContactRadius : public Compute { + public: + ComputeSMDContactRadius(class LAMMPS *, int, char **); + ~ComputeSMDContactRadius(); + void init(); + void compute_peratom(); + double memory_usage(); + + private: + int nmax; + double *contact_radius_vector; +}; + +} + +#endif +#endif diff --git a/src/USER-SMD/compute_smd_damage.cpp b/src/USER-SMD/compute_smd_damage.cpp new file mode 100644 index 0000000000..95d7bee3be --- /dev/null +++ b/src/USER-SMD/compute_smd_damage.cpp @@ -0,0 +1,109 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#include "string.h" +#include "compute_smd_damage.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeSMDDamage::ComputeSMDDamage(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) +{ + if (narg != 3) error->all(FLERR,"Illegal compute smd/damage command"); + if (atom->damage_flag != 1) error->all(FLERR,"compute smd/damage command requires atom_style with damage (e.g. smd)"); + + peratom_flag = 1; + size_peratom_cols = 0; + + nmax = 0; + damage_vector = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputeSMDDamage::~ComputeSMDDamage() +{ + memory->sfree(damage_vector); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDDamage::init() +{ + + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style,"smd/damage") == 0) count++; + if (count > 1 && comm->me == 0) + error->warning(FLERR,"More than one compute smd/damage"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDDamage::compute_peratom() +{ + invoked_peratom = update->ntimestep; + + // grow rhoVector array if necessary + + if (atom->nlocal > nmax) { + memory->sfree(damage_vector); + nmax = atom->nmax; + damage_vector = (double *) memory->smalloc(nmax*sizeof(double),"atom:damage_vector"); + vector_atom = damage_vector; + } + + double *damage = atom->damage; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + damage_vector[i] = damage[i]; + } + else { + damage_vector[i] = 0.0; + } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array +------------------------------------------------------------------------- */ + +double ComputeSMDDamage::memory_usage() +{ + double bytes = nmax * sizeof(double); + return bytes; +} diff --git a/src/USER-SMD/compute_smd_damage.h b/src/USER-SMD/compute_smd_damage.h new file mode 100644 index 0000000000..1259788ec4 --- /dev/null +++ b/src/USER-SMD/compute_smd_damage.h @@ -0,0 +1,55 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(smd/damage,ComputeSMDDamage) + +#else + +#ifndef LMP_COMPUTE_SMD_DAMAGE_H +#define LMP_COMPUTE_SMD_DAMAGE_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeSMDDamage : public Compute { + public: + ComputeSMDDamage(class LAMMPS *, int, char **); + ~ComputeSMDDamage(); + void init(); + void compute_peratom(); + double memory_usage(); + + private: + int nmax; + double *damage_vector; +}; + +} + +#endif +#endif diff --git a/src/USER-SMD/compute_smd_hourglass_error.cpp b/src/USER-SMD/compute_smd_hourglass_error.cpp new file mode 100644 index 0000000000..ae6ffee0e1 --- /dev/null +++ b/src/USER-SMD/compute_smd_hourglass_error.cpp @@ -0,0 +1,112 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#include "string.h" +#include "compute_smd_hourglass_error.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" +#include "pair.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeSMDHourglassError::ComputeSMDHourglassError(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) { + if (narg != 3) + error->all(FLERR, "Illegal compute smd/hourglass_error command"); + if (atom->smd_flag != 1) + error->all(FLERR, "compute smd/hourglass_error command requires atom_style with hourglass_error (e.g. smd)"); + + peratom_flag = 1; + size_peratom_cols = 0; + + nmax = 0; + hourglass_error_vector = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputeSMDHourglassError::~ComputeSMDHourglassError() { + memory->sfree(hourglass_error_vector); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDHourglassError::init() { + + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style, "smd/hourglass_error") == 0) + count++; + if (count > 1 && comm->me == 0) + error->warning(FLERR, "More than one compute smd/hourglass_error"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDHourglassError::compute_peratom() { + invoked_peratom = update->ntimestep; + + // grow output Vector array if necessary + + if (atom->nlocal > nmax) { + memory->sfree(hourglass_error_vector); + nmax = atom->nmax; + hourglass_error_vector = (double *) memory->smalloc(nmax * sizeof(double), "atom:hourglass_error_vector"); + vector_atom = hourglass_error_vector; + } + + int itmp = 0; + double *hourglass_error = (double *) force->pair->extract("smd/tlsph/hourglass_error_ptr", itmp); + if (hourglass_error == NULL) { + error->all(FLERR, "compute smd/hourglass_error failed to access hourglass_error array"); + } + + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + hourglass_error_vector[i] = hourglass_error[i]; + } else { + hourglass_error_vector[i] = 0.0; + } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array + ------------------------------------------------------------------------- */ + +double ComputeSMDHourglassError::memory_usage() { + double bytes = nmax * sizeof(double); + return bytes; +} diff --git a/src/USER-SMD/compute_smd_hourglass_error.h b/src/USER-SMD/compute_smd_hourglass_error.h new file mode 100644 index 0000000000..fdfbfae641 --- /dev/null +++ b/src/USER-SMD/compute_smd_hourglass_error.h @@ -0,0 +1,55 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(smd/hourglass_error,ComputeSMDHourglassError) + +#else + +#ifndef LMP_COMPUTE_SMD_HOURGLASS_ERROR_H +#define LMP_COMPUTE_SMD_HOURGLASS_ERROR_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeSMDHourglassError : public Compute { + public: + ComputeSMDHourglassError(class LAMMPS *, int, char **); + ~ComputeSMDHourglassError(); + void init(); + void compute_peratom(); + double memory_usage(); + + private: + int nmax; + double *hourglass_error_vector; +}; + +} + +#endif +#endif diff --git a/src/USER-SMD/compute_smd_internal_energy.cpp b/src/USER-SMD/compute_smd_internal_energy.cpp new file mode 100644 index 0000000000..9116df7011 --- /dev/null +++ b/src/USER-SMD/compute_smd_internal_energy.cpp @@ -0,0 +1,109 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#include "string.h" +#include "compute_smd_internal_energy.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeSMDInternalEnergy::ComputeSMDInternalEnergy(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) +{ + if (narg != 3) error->all(FLERR,"Illegal compute smd/internal_energy command"); + if (atom->e_flag != 1) error->all(FLERR,"compute smd/internal_energy command requires atom_style with internal_energy (e.g. smd)"); + + peratom_flag = 1; + size_peratom_cols = 0; + + nmax = 0; + internal_energy_vector = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputeSMDInternalEnergy::~ComputeSMDInternalEnergy() +{ + memory->sfree(internal_energy_vector); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDInternalEnergy::init() +{ + + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style,"smd/internal_energy") == 0) count++; + if (count > 1 && comm->me == 0) + error->warning(FLERR,"More than one compute smd/internal_energy"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDInternalEnergy::compute_peratom() +{ + invoked_peratom = update->ntimestep; + + // grow rhoVector array if necessary + + if (atom->nlocal > nmax) { + memory->sfree(internal_energy_vector); + nmax = atom->nmax; + internal_energy_vector = (double *) memory->smalloc(nmax*sizeof(double),"atom:internal_energy_vector"); + vector_atom = internal_energy_vector; + } + + double *e = atom->e; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + internal_energy_vector[i] = e[i]; + } + else { + internal_energy_vector[i] = 0.0; + } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array +------------------------------------------------------------------------- */ + +double ComputeSMDInternalEnergy::memory_usage() +{ + double bytes = nmax * sizeof(double); + return bytes; +} diff --git a/src/USER-SMD/compute_smd_internal_energy.h b/src/USER-SMD/compute_smd_internal_energy.h new file mode 100644 index 0000000000..4276a6ee60 --- /dev/null +++ b/src/USER-SMD/compute_smd_internal_energy.h @@ -0,0 +1,55 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(smd/internal_energy,ComputeSMDInternalEnergy) + +#else + +#ifndef LMP_COMPUTE_SMD_INTERNAL_ENERGY_H +#define LMP_COMPUTE_SMD_INTERNAL_ENERGY_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeSMDInternalEnergy : public Compute { + public: + ComputeSMDInternalEnergy(class LAMMPS *, int, char **); + ~ComputeSMDInternalEnergy(); + void init(); + void compute_peratom(); + double memory_usage(); + + private: + int nmax; + double *internal_energy_vector; +}; + +} + +#endif +#endif diff --git a/src/USER-SMD/compute_smd_plastic_strain.cpp b/src/USER-SMD/compute_smd_plastic_strain.cpp new file mode 100644 index 0000000000..734f40e267 --- /dev/null +++ b/src/USER-SMD/compute_smd_plastic_strain.cpp @@ -0,0 +1,109 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#include "string.h" +#include "compute_smd_plastic_strain.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeSMDPlasticStrain::ComputeSMDPlasticStrain(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) +{ + if (narg != 3) error->all(FLERR,"Illegal compute smd/plastic_strain command"); + if (atom->eff_plastic_strain_flag != 1) error->all(FLERR,"compute smd/plastic_strain command requires atom_style with plastic_strain (e.g. smd)"); + + peratom_flag = 1; + size_peratom_cols = 0; + + nmax = 0; + plastic_strain_vector = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputeSMDPlasticStrain::~ComputeSMDPlasticStrain() +{ + memory->sfree(plastic_strain_vector); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDPlasticStrain::init() +{ + + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style,"smd/plastic_strain") == 0) count++; + if (count > 1 && comm->me == 0) + error->warning(FLERR,"More than one compute smd/plastic_strain"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDPlasticStrain::compute_peratom() +{ + invoked_peratom = update->ntimestep; + + // grow rhoVector array if necessary + + if (atom->nlocal > nmax) { + memory->sfree(plastic_strain_vector); + nmax = atom->nmax; + plastic_strain_vector = (double *) memory->smalloc(nmax*sizeof(double),"atom:plastic_strain_vector"); + vector_atom = plastic_strain_vector; + } + + double *plastic_strain = atom->eff_plastic_strain; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + plastic_strain_vector[i] = plastic_strain[i]; + } + else { + plastic_strain_vector[i] = 0.0; + } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array +------------------------------------------------------------------------- */ + +double ComputeSMDPlasticStrain::memory_usage() +{ + double bytes = nmax * sizeof(double); + return bytes; +} diff --git a/src/USER-SMD/compute_smd_plastic_strain.h b/src/USER-SMD/compute_smd_plastic_strain.h new file mode 100644 index 0000000000..30b191ee2e --- /dev/null +++ b/src/USER-SMD/compute_smd_plastic_strain.h @@ -0,0 +1,55 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(smd/plastic_strain,ComputeSMDPlasticStrain) + +#else + +#ifndef LMP_COMPUTE_SMD_PLASTIC_STRAIN_H +#define LMP_COMPUTE_SMD_PLASTIC_STRAIN_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeSMDPlasticStrain : public Compute { + public: + ComputeSMDPlasticStrain(class LAMMPS *, int, char **); + ~ComputeSMDPlasticStrain(); + void init(); + void compute_peratom(); + double memory_usage(); + + private: + int nmax; + double *plastic_strain_vector; +}; + +} + +#endif +#endif diff --git a/src/USER-SMD/compute_smd_plastic_strain_rate.cpp b/src/USER-SMD/compute_smd_plastic_strain_rate.cpp new file mode 100644 index 0000000000..44a890bf82 --- /dev/null +++ b/src/USER-SMD/compute_smd_plastic_strain_rate.cpp @@ -0,0 +1,109 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#include "string.h" +#include "compute_smd_plastic_strain_rate.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeSMDPlasticStrainRate::ComputeSMDPlasticStrainRate(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) +{ + if (narg != 3) error->all(FLERR,"Illegal compute smd/plastic_strain command"); + if (atom->eff_plastic_strain_rate_flag != 1) error->all(FLERR,"compute smd/plastic_strain_rate command requires atom_style with plastic_strain_rate (e.g. smd)"); + + peratom_flag = 1; + size_peratom_cols = 0; + + nmax = 0; + plastic_strain_rate_vector = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputeSMDPlasticStrainRate::~ComputeSMDPlasticStrainRate() +{ + memory->sfree(plastic_strain_rate_vector); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDPlasticStrainRate::init() +{ + + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style,"smd/plastic_strain_rate") == 0) count++; + if (count > 1 && comm->me == 0) + error->warning(FLERR,"More than one compute smd/plastic_strain_rate"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDPlasticStrainRate::compute_peratom() +{ + invoked_peratom = update->ntimestep; + + // grow rhoVector array if necessary + + if (atom->nlocal > nmax) { + memory->sfree(plastic_strain_rate_vector); + nmax = atom->nmax; + plastic_strain_rate_vector = (double *) memory->smalloc(nmax*sizeof(double),"atom:plastic_strain_rate_vector"); + vector_atom = plastic_strain_rate_vector; + } + + double *plastic_strain_rate = atom->eff_plastic_strain_rate; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + plastic_strain_rate_vector[i] = plastic_strain_rate[i]; + } + else { + plastic_strain_rate_vector[i] = 0.0; + } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array +------------------------------------------------------------------------- */ + +double ComputeSMDPlasticStrainRate::memory_usage() +{ + double bytes = nmax * sizeof(double); + return bytes; +} diff --git a/src/USER-SMD/compute_smd_plastic_strain_rate.h b/src/USER-SMD/compute_smd_plastic_strain_rate.h new file mode 100644 index 0000000000..1d99ac0baa --- /dev/null +++ b/src/USER-SMD/compute_smd_plastic_strain_rate.h @@ -0,0 +1,55 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(smd/plastic_strain_rate,ComputeSMDPlasticStrainRate) + +#else + +#ifndef LMP_COMPUTE_SMD_PLASTIC_STRAIN_RATE_H +#define LMP_COMPUTE_SMD_PLASTIC_STRAIN_RATE_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeSMDPlasticStrainRate : public Compute { + public: + ComputeSMDPlasticStrainRate(class LAMMPS *, int, char **); + ~ComputeSMDPlasticStrainRate(); + void init(); + void compute_peratom(); + double memory_usage(); + + private: + int nmax; + double *plastic_strain_rate_vector; +}; + +} + +#endif +#endif diff --git a/src/USER-SMD/compute_smd_rho.cpp b/src/USER-SMD/compute_smd_rho.cpp new file mode 100644 index 0000000000..0e9ee9bb27 --- /dev/null +++ b/src/USER-SMD/compute_smd_rho.cpp @@ -0,0 +1,107 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#include "string.h" +#include "compute_smd_rho.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeSMDRho::ComputeSMDRho(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) { + if (narg != 3) + error->all(FLERR, "Illegal compute smd/rho command"); + if (atom->vfrac_flag != 1) + error->all(FLERR, "compute smd/rho command requires atom_style with volume (e.g. smd)"); + + peratom_flag = 1; + size_peratom_cols = 0; + + nmax = 0; + rhoVector = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputeSMDRho::~ComputeSMDRho() { + memory->sfree(rhoVector); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDRho::init() { + + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style, "smd/rho") == 0) + count++; + if (count > 1 && comm->me == 0) + error->warning(FLERR, "More than one compute smd/rho"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDRho::compute_peratom() { + invoked_peratom = update->ntimestep; + + // grow rhoVector array if necessary + + if (atom->nlocal > nmax) { + memory->sfree(rhoVector); + nmax = atom->nmax; + rhoVector = (double *) memory->smalloc(nmax * sizeof(double), "atom:rhoVector"); + vector_atom = rhoVector; + } + + double *vfrac = atom->vfrac; + double *rmass = atom->rmass; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + rhoVector[i] = rmass[i] / vfrac[i]; + } else { + rhoVector[i] = 0.0; + } + } + +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array + ------------------------------------------------------------------------- */ + +double ComputeSMDRho::memory_usage() { + double bytes = nmax * sizeof(double); + return bytes; +} diff --git a/src/USER-SMD/compute_smd_rho.h b/src/USER-SMD/compute_smd_rho.h new file mode 100644 index 0000000000..ce749c6466 --- /dev/null +++ b/src/USER-SMD/compute_smd_rho.h @@ -0,0 +1,55 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(smd/rho,ComputeSMDRho) + +#else + +#ifndef LMP_COMPUTE_SMD_RHO_H +#define LMP_COMPUTE_SMD_RHO_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeSMDRho : public Compute { + public: + ComputeSMDRho(class LAMMPS *, int, char **); + ~ComputeSMDRho(); + void init(); + void compute_peratom(); + double memory_usage(); + + private: + int nmax; + double *rhoVector; +}; + +} + +#endif +#endif diff --git a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp b/src/USER-SMD/compute_smd_tlsph_defgrad.cpp new file mode 100644 index 0000000000..7dcd7faca0 --- /dev/null +++ b/src/USER-SMD/compute_smd_tlsph_defgrad.cpp @@ -0,0 +1,138 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#include "string.h" +#include "compute_smd_tlsph_defgrad.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" +#include "pair.h" +#include +#include +#include "stdlib.h" +#include "string.h" +#include +using namespace Eigen; +using namespace std; +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeSMDTLSPHDefgrad::ComputeSMDTLSPHDefgrad(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) { + if (narg != 3) + error->all(FLERR, "Illegal compute smd/tlsph_defgrad command"); + + peratom_flag = 1; + size_peratom_cols = 10; + + nmax = 0; + defgradVector = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputeSMDTLSPHDefgrad::~ComputeSMDTLSPHDefgrad() { + memory->sfree(defgradVector); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDTLSPHDefgrad::init() { + + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style, "smd/tlsph_defgrad") == 0) + count++; + if (count > 1 && comm->me == 0) + error->warning(FLERR, "More than one compute smd/tlsph_defgrad"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDTLSPHDefgrad::compute_peratom() { + double **defgrad = atom->smd_data_9; + Matrix3d F; + invoked_peratom = update->ntimestep; + + // grow vector array if necessary + if (atom->nlocal > nmax) { + memory->destroy(defgradVector); + nmax = atom->nmax; + memory->create(defgradVector, nmax, size_peratom_cols, "defgradVector"); + array_atom = defgradVector; + } + + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + F(0, 0) = defgrad[i][0]; + F(0, 1) = defgrad[i][1]; + F(0, 2) = defgrad[i][2]; + F(1, 0) = defgrad[i][3]; + F(1, 1) = defgrad[i][4]; + F(1, 2) = defgrad[i][5]; + F(2, 0) = defgrad[i][6]; + F(2, 1) = defgrad[i][7]; + F(2, 2) = defgrad[i][8]; + + defgradVector[i][0] = F(0, 0); + defgradVector[i][1] = F(0, 1); + defgradVector[i][2] = F(0, 2); + defgradVector[i][3] = F(1, 0); + defgradVector[i][4] = F(1, 1); + defgradVector[i][5] = F(1, 2); + defgradVector[i][6] = F(2, 0); + defgradVector[i][7] = F(2, 1); + defgradVector[i][8] = F(2, 2); + defgradVector[i][9] = F.determinant(); + } else { + defgradVector[i][0] = 1.0; + defgradVector[i][1] = 0.0; + defgradVector[i][2] = 0.0; + defgradVector[i][3] = 0.0; + defgradVector[i][4] = 1.0; + defgradVector[i][5] = 0.0; + defgradVector[i][6] = 0.0; + defgradVector[i][7] = 0.0; + defgradVector[i][8] = 1.0; + defgradVector[i][9] = 1.0; + } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array + ------------------------------------------------------------------------- */ + +double ComputeSMDTLSPHDefgrad::memory_usage() { + double bytes = size_peratom_cols * nmax * sizeof(double); + return bytes; +} diff --git a/src/USER-SMD/compute_smd_tlsph_defgrad.h b/src/USER-SMD/compute_smd_tlsph_defgrad.h new file mode 100644 index 0000000000..c58fc5148d --- /dev/null +++ b/src/USER-SMD/compute_smd_tlsph_defgrad.h @@ -0,0 +1,55 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(smd/tlsph_defgrad,ComputeSMDTLSPHDefgrad) + +#else + +#ifndef LMP_COMPUTE_SMD_TLSPH_DEFGRAD_H +#define LMP_COMPUTE_SMD_TLSPH_DEFGRAD_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeSMDTLSPHDefgrad : public Compute { + public: + ComputeSMDTLSPHDefgrad(class LAMMPS *, int, char **); + ~ComputeSMDTLSPHDefgrad(); + void init(); + void compute_peratom(); + double memory_usage(); + + private: + int nmax; + double **defgradVector; +}; + +} + +#endif +#endif diff --git a/src/USER-SMD/compute_smd_tlsph_dt.cpp b/src/USER-SMD/compute_smd_tlsph_dt.cpp new file mode 100644 index 0000000000..fdb3c4feeb --- /dev/null +++ b/src/USER-SMD/compute_smd_tlsph_dt.cpp @@ -0,0 +1,115 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#include "string.h" +#include "compute_smd_tlsph_dt.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" +#include "pair.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeSMDTlsphDt::ComputeSMDTlsphDt(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) { + if (narg != 3) + error->all(FLERR, "Illegal compute smd/tlsph_dt command"); + if (atom->contact_radius_flag != 1) + error->all(FLERR, + "compute smd/tlsph_dt command requires atom_style with contact_radius (e.g. smd)"); + + peratom_flag = 1; + size_peratom_cols = 0; + + nmax = 0; + dt_vector = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputeSMDTlsphDt::~ComputeSMDTlsphDt() { + memory->sfree(dt_vector); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDTlsphDt::init() { + + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style, "smd/tlsph_dt") == 0) + count++; + if (count > 1 && comm->me == 0) + error->warning(FLERR, "More than one compute smd/tlsph_dt"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDTlsphDt::compute_peratom() { + invoked_peratom = update->ntimestep; + + // grow rhoVector array if necessary + + if (atom->nlocal > nmax) { + memory->sfree(dt_vector); + nmax = atom->nmax; + dt_vector = (double *) memory->smalloc(nmax * sizeof(double), + "atom:tlsph_dt_vector"); + vector_atom = dt_vector; + } + + int itmp = 0; + double *particle_dt = (double *) force->pair->extract("smd/tlsph/particle_dt_ptr", + itmp); + if (particle_dt == NULL) { + error->all(FLERR, + "compute smd/tlsph_dt failed to access particle_dt array"); + } + + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + dt_vector[i] = particle_dt[i]; + } else { + dt_vector[i] = 0.0; + } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array + ------------------------------------------------------------------------- */ + +double ComputeSMDTlsphDt::memory_usage() { + double bytes = nmax * sizeof(double); + return bytes; +} diff --git a/src/USER-SMD/compute_smd_tlsph_dt.h b/src/USER-SMD/compute_smd_tlsph_dt.h new file mode 100644 index 0000000000..0b258a1a7f --- /dev/null +++ b/src/USER-SMD/compute_smd_tlsph_dt.h @@ -0,0 +1,55 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(smd/tlsph_dt,ComputeSMDTlsphDt) + +#else + +#ifndef LMP_COMPUTE_SMD_TLSPH_DT_H +#define LMP_COMPUTE_SMD_TLSPH_DT_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeSMDTlsphDt : public Compute { + public: + ComputeSMDTlsphDt(class LAMMPS *, int, char **); + ~ComputeSMDTlsphDt(); + void init(); + void compute_peratom(); + double memory_usage(); + + private: + int nmax; + double *dt_vector; +}; + +} + +#endif +#endif diff --git a/src/USER-SMD/compute_smd_tlsph_num_neighs.cpp b/src/USER-SMD/compute_smd_tlsph_num_neighs.cpp new file mode 100644 index 0000000000..7b7b2ce07c --- /dev/null +++ b/src/USER-SMD/compute_smd_tlsph_num_neighs.cpp @@ -0,0 +1,107 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#include "string.h" +#include "compute_smd_tlsph_num_neighs.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" +#include "pair.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeSMDTLSPHNumNeighs::ComputeSMDTLSPHNumNeighs(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) { + if (narg != 3) + error->all(FLERR, "Illegal compute smd/tlsph_num_neighs command"); + + peratom_flag = 1; + size_peratom_cols = 0; + + nmax = 0; + numNeighsRefConfigOutput = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputeSMDTLSPHNumNeighs::~ComputeSMDTLSPHNumNeighs() { + memory->destroy(numNeighsRefConfigOutput); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDTLSPHNumNeighs::init() { + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style, "smd/tlsph_num_neighs") == 0) + count++; + if (count > 1 && comm->me == 0) + error->warning(FLERR, "More than one compute smd/tlsph_num_neighs"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDTLSPHNumNeighs::compute_peratom() { + invoked_peratom = update->ntimestep; + + if (atom->nlocal > nmax) { + memory->destroy(numNeighsRefConfigOutput); + nmax = atom->nmax; + memory->create(numNeighsRefConfigOutput, nmax, "tlsph/num_neighs:numNeighsRefConfigOutput"); + vector_atom = numNeighsRefConfigOutput; + } + + int *mask = atom->mask; + int nlocal = atom->nlocal; + + int itmp = 0; + int *numNeighsRefConfig = (int *) force->pair->extract("smd/tlsph/numNeighsRefConfig_ptr", itmp); + if (numNeighsRefConfig == NULL) { + error->all(FLERR, "compute smd/tlsph_num_neighs failed to access numNeighsRefConfig array"); + } + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + numNeighsRefConfigOutput[i] = numNeighsRefConfig[i]; + } else { + numNeighsRefConfigOutput[i] = 0.0; + } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array + ------------------------------------------------------------------------- */ + +double ComputeSMDTLSPHNumNeighs::memory_usage() { + double bytes = nmax * sizeof(double); + return bytes; +} diff --git a/src/USER-SMD/compute_smd_tlsph_num_neighs.h b/src/USER-SMD/compute_smd_tlsph_num_neighs.h new file mode 100644 index 0000000000..5b3613e05c --- /dev/null +++ b/src/USER-SMD/compute_smd_tlsph_num_neighs.h @@ -0,0 +1,69 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(smd/tlsph_num_neighs,ComputeSMDTLSPHNumNeighs) + +#else + +#ifndef LMP_COMPUTE_SMD_TLSPH_NUM_NEIGHS_H +#define LMP_COMPUTE_SMD_TLSPH_NUM_NEIGHS_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeSMDTLSPHNumNeighs : public Compute { + public: + ComputeSMDTLSPHNumNeighs(class LAMMPS *, int, char **); + ~ComputeSMDTLSPHNumNeighs(); + void init(); + void compute_peratom(); + double memory_usage(); + + private: + int nmax; + double *numNeighsRefConfigOutput; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +W: More than one compute ke/atom + +It is not efficient to use compute ke/atom more than once. + +*/ diff --git a/src/USER-SMD/compute_smd_tlsph_shape.cpp b/src/USER-SMD/compute_smd_tlsph_shape.cpp new file mode 100644 index 0000000000..d4e8c14b37 --- /dev/null +++ b/src/USER-SMD/compute_smd_tlsph_shape.cpp @@ -0,0 +1,137 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#include "string.h" +#include "compute_smd_tlsph_shape.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" +#include "pair.h" +#include +#include +#include "stdlib.h" +#include "string.h" +#include +#include +using namespace Eigen; +using namespace std; +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeSmdTlsphShape::ComputeSmdTlsphShape(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) { + if (narg != 3) + error->all(FLERR, "Illegal compute smd/tlsph_strain command"); + + peratom_flag = 1; + size_peratom_cols = 7; + + nmax = 0; + strainVector = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputeSmdTlsphShape::~ComputeSmdTlsphShape() { + memory->sfree(strainVector); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSmdTlsphShape::init() { + + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style, "smd/tlsph_strain") == 0) + count++; + if (count > 1 && comm->me == 0) + error->warning(FLERR, "More than one compute smd/tlsph_strain"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSmdTlsphShape::compute_peratom() { + double *contact_radius = atom->contact_radius; + invoked_peratom = update->ntimestep; + + // grow vector array if necessary + + if (atom->nlocal > nmax) { + memory->destroy(strainVector); + nmax = atom->nmax; + memory->create(strainVector, nmax, size_peratom_cols, "strainVector"); + array_atom = strainVector; + } + + int itmp = 0; + Matrix3d *R = (Matrix3d *) force->pair->extract("smd/tlsph/rotation_ptr", itmp); + if (R == NULL) { + error->all(FLERR, "compute smd/tlsph_shape failed to access rotation array"); + } + + Matrix3d *F = (Matrix3d *) force->pair->extract("smd/tlsph/Fincr_ptr", itmp); + if (F == NULL) { + error->all(FLERR, "compute smd/tlsph_shape failed to access deformation gradient array"); + } + + int *mask = atom->mask; + int nlocal = atom->nlocal; + Matrix3d E, eye; + eye.setIdentity(); + Quaterniond q; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + + E = 0.5 * (F[i].transpose() * F[i] - eye); // Green-Lagrange strain + strainVector[i][0] = contact_radius[i] * (1.0 + E(0, 0)); + strainVector[i][1] = contact_radius[i] * (1.0 + E(1, 1)); + strainVector[i][2] = contact_radius[i] * (1.0 + E(2, 2)); + + q = R[i]; // convert pure rotation matrix to quaternion + strainVector[i][3] = q.w(); + strainVector[i][4] = q.x(); + strainVector[i][5] = q.y(); + strainVector[i][6] = q.z(); + } else { + for (int j = 0; j < size_peratom_cols; j++) { + strainVector[i][j] = 0.0; + } + } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array + ------------------------------------------------------------------------- */ + +double ComputeSmdTlsphShape::memory_usage() { + double bytes = size_peratom_cols * nmax * sizeof(double); + return bytes; +} diff --git a/src/USER-SMD/compute_smd_tlsph_shape.h b/src/USER-SMD/compute_smd_tlsph_shape.h new file mode 100644 index 0000000000..673080e232 --- /dev/null +++ b/src/USER-SMD/compute_smd_tlsph_shape.h @@ -0,0 +1,55 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(smd/tlsph_shape,ComputeSmdTlsphShape) + +#else + +#ifndef LMP_COMPUTE_SMD_TLSPH_SHAPE_H +#define LMP_COMPUTE_SMD_TLSPH_SHAPE_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeSmdTlsphShape : public Compute { + public: + ComputeSmdTlsphShape(class LAMMPS *, int, char **); + ~ComputeSmdTlsphShape(); + void init(); + void compute_peratom(); + double memory_usage(); + + private: + int nmax; + double **strainVector; +}; + +} + +#endif +#endif diff --git a/src/USER-SMD/compute_smd_tlsph_strain.cpp b/src/USER-SMD/compute_smd_tlsph_strain.cpp new file mode 100644 index 0000000000..f191afeb2c --- /dev/null +++ b/src/USER-SMD/compute_smd_tlsph_strain.cpp @@ -0,0 +1,145 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#include "string.h" +#include "compute_smd_tlsph_strain.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" +#include "pair.h" +#include +#include +#include "stdlib.h" +#include "string.h" +#include +using namespace Eigen; +using namespace std; +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeSMDTLSPHstrain::ComputeSMDTLSPHstrain(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) { + if (narg != 3) + error->all(FLERR, "Illegal compute smd/tlsph_strain command"); + + peratom_flag = 1; + size_peratom_cols = 6; + + nmax = 0; + strainVector = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputeSMDTLSPHstrain::~ComputeSMDTLSPHstrain() { + memory->sfree(strainVector); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDTLSPHstrain::init() { + + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style, "smd/tlsph_strain") == 0) + count++; + if (count > 1 && comm->me == 0) + error->warning(FLERR, "More than one compute smd/tlsph_strain"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDTLSPHstrain::compute_peratom() { + double **defgrad0 = atom->smd_data_9; + + invoked_peratom = update->ntimestep; + + // grow vector array if necessary + + if (atom->nlocal > nmax) { + memory->destroy(strainVector); + nmax = atom->nmax; + memory->create(strainVector, nmax, size_peratom_cols, "strainVector"); + array_atom = strainVector; + } + + // copy data to output array + int itmp = 0; + Matrix3d *Fincr = (Matrix3d *) force->pair->extract("smd/tlsph/Fincr_ptr", itmp); + if (Fincr == NULL) { + error->all(FLERR, "compute smd/tlsph_strain failed to access Fincr array"); + } + + int *mask = atom->mask; + int nlocal = atom->nlocal; + Matrix3d E, eye, Ftotal, F0; + eye.setIdentity(); + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + + // old deformation gradient + F0(0, 0) = defgrad0[i][0]; + F0(0, 1) = defgrad0[i][1]; + F0(0, 2) = defgrad0[i][2]; + F0(1, 0) = defgrad0[i][3]; + F0(1, 1) = defgrad0[i][4]; + F0(1, 2) = defgrad0[i][5]; + F0(2, 0) = defgrad0[i][6]; + F0(2, 1) = defgrad0[i][7]; + F0(2, 2) = defgrad0[i][8]; + + // compute current total deformation gradient + Ftotal = F0 * Fincr[i]; // this is the total deformation gradient: reference deformation times incremental deformation + + + E = 0.5 * (Ftotal.transpose() * Ftotal - eye); // Green-Lagrange strain + strainVector[i][0] = E(0, 0); + strainVector[i][1] = E(1, 1); + strainVector[i][2] = E(2, 2); + strainVector[i][3] = E(0, 1); + strainVector[i][4] = E(0, 2); + strainVector[i][5] = E(1, 2); + } else { + for (int j = 0; j < size_peratom_cols; j++) { + strainVector[i][j] = 0.0; + } + } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array + ------------------------------------------------------------------------- */ + +double ComputeSMDTLSPHstrain::memory_usage() { + double bytes = size_peratom_cols * nmax * sizeof(double); + return bytes; +} diff --git a/src/USER-SMD/compute_smd_tlsph_strain.h b/src/USER-SMD/compute_smd_tlsph_strain.h new file mode 100644 index 0000000000..a42fcddde2 --- /dev/null +++ b/src/USER-SMD/compute_smd_tlsph_strain.h @@ -0,0 +1,55 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(smd/tlsph_strain,ComputeSMDTLSPHstrain) + +#else + +#ifndef LMP_COMPUTE_SMD_TLSPH_STRAIN_H +#define LMP_COMPUTE_SMD_TLSPH_STRAIN_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeSMDTLSPHstrain : public Compute { + public: + ComputeSMDTLSPHstrain(class LAMMPS *, int, char **); + ~ComputeSMDTLSPHstrain(); + void init(); + void compute_peratom(); + double memory_usage(); + + private: + int nmax; + double **strainVector; +}; + +} + +#endif +#endif diff --git a/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp b/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp new file mode 100644 index 0000000000..a9e909db10 --- /dev/null +++ b/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp @@ -0,0 +1,126 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#include "string.h" +#include "compute_smd_tlsph_strain_rate.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" +#include "pair.h" +#include +using namespace Eigen; +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeSMDTLSPHStrainRate::ComputeSMDTLSPHStrainRate(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) { + if (narg != 3) + error->all(FLERR, "Illegal compute smd/ulsph_strain_rate command"); + + peratom_flag = 1; + size_peratom_cols = 6; + + nmax = 0; + strain_rate_array = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputeSMDTLSPHStrainRate::~ComputeSMDTLSPHStrainRate() { + memory->sfree(strain_rate_array); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDTLSPHStrainRate::init() { + + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style, "smd/ulsph_strain_rate") == 0) + count++; + if (count > 1 && comm->me == 0) + error->warning(FLERR, "More than one compute smd/ulsph_strain_rate"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDTLSPHStrainRate::compute_peratom() { + invoked_peratom = update->ntimestep; + int *mol = atom->molecule; + + // grow vector array if necessary + + if (atom->nlocal > nmax) { + memory->destroy(strain_rate_array); + nmax = atom->nmax; + memory->create(strain_rate_array, nmax, size_peratom_cols, "stresstensorVector"); + array_atom = strain_rate_array; + } + + int ulsph_flag = 0; + int tlsph_flag = 0; + int itmp = 0; + Matrix3d *D = (Matrix3d *) force->pair->extract("smd/tlsph/strain_rate_ptr", itmp); + if (D == NULL) { + error->all(FLERR, + "compute smd/tlsph_strain_rate could not access strain rate. Are the matching pair styles present?"); + } + + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + + strain_rate_array[i][0] = D[i](0, 0); // xx + strain_rate_array[i][1] = D[i](1, 1); // yy + strain_rate_array[i][2] = D[i](2, 2); // zz + strain_rate_array[i][3] = D[i](0, 1); // xy + strain_rate_array[i][4] = D[i](0, 2); // xz + strain_rate_array[i][5] = D[i](1, 2); // yz + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array + ------------------------------------------------------------------------- */ + +double ComputeSMDTLSPHStrainRate::memory_usage() { + double bytes = size_peratom_cols * nmax * sizeof(double); + return bytes; +} + +/* + * deviator of a tensor + */ +Matrix3d ComputeSMDTLSPHStrainRate::Deviator(Matrix3d M) { + Matrix3d eye; + eye.setIdentity(); + eye *= M.trace() / 3.0; + return M - eye; +} diff --git a/src/USER-SMD/compute_smd_tlsph_strain_rate.h b/src/USER-SMD/compute_smd_tlsph_strain_rate.h new file mode 100644 index 0000000000..6332f03764 --- /dev/null +++ b/src/USER-SMD/compute_smd_tlsph_strain_rate.h @@ -0,0 +1,58 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(smd/tlsph_strain_rate,ComputeSMDTLSPHStrainRate) + +#else + +#ifndef LMP_COMPUTE_SMD_TLSPH_STRAIN_RATE_H +#define LMP_COMPUTE_SMD_TLSPH_STRAIN_RATE_H + +#include "compute.h" +#include +using namespace Eigen; + +namespace LAMMPS_NS { + +class ComputeSMDTLSPHStrainRate : public Compute { + public: + ComputeSMDTLSPHStrainRate(class LAMMPS *, int, char **); + ~ComputeSMDTLSPHStrainRate(); + void init(); + void compute_peratom(); + double memory_usage(); + Matrix3d Deviator(Matrix3d); + + private: + int nmax; + double **strain_rate_array; +}; + +} + +#endif +#endif diff --git a/src/USER-SMD/compute_smd_tlsph_stress.cpp b/src/USER-SMD/compute_smd_tlsph_stress.cpp new file mode 100644 index 0000000000..bd38b6af33 --- /dev/null +++ b/src/USER-SMD/compute_smd_tlsph_stress.cpp @@ -0,0 +1,131 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#include "string.h" +#include "compute_smd_tlsph_stress.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" +#include "pair.h" +#include +using namespace Eigen; +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeSMDTLSPHStress::ComputeSMDTLSPHStress(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) { + if (narg != 3) + error->all(FLERR, "Illegal compute smd/tlsph_stress command"); + + peratom_flag = 1; + size_peratom_cols = 7; + + nmax = 0; + stress_array = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputeSMDTLSPHStress::~ComputeSMDTLSPHStress() { + memory->sfree(stress_array); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDTLSPHStress::init() { + + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style, "smd/tlsph_stress") == 0) + count++; + if (count > 1 && comm->me == 0) + error->warning(FLERR, "More than one compute smd/tlsph_stress"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDTLSPHStress::compute_peratom() { + invoked_peratom = update->ntimestep; + Matrix3d stress_deviator; + double von_mises_stress; + + // grow vector array if necessary + + if (atom->nlocal > nmax) { + memory->destroy(stress_array); + nmax = atom->nmax; + memory->create(stress_array, nmax, size_peratom_cols, "stresstensorVector"); + array_atom = stress_array; + } + + int itmp = 0; + Matrix3d *T = (Matrix3d *) force->pair->extract("smd/tlsph/stressTensor_ptr", itmp); + if (T == NULL) { + error->all(FLERR, "compute smd/tlsph_stress could not access stress tensors. Are the matching pair styles present?"); + } + int nlocal = atom->nlocal; + int *mask = atom->mask; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + stress_deviator = Deviator(T[i]); + von_mises_stress = sqrt(3. / 2.) * stress_deviator.norm(); + stress_array[i][0] = T[i](0, 0); // xx + stress_array[i][1] = T[i](1, 1); // yy + stress_array[i][2] = T[i](2, 2); // zz + stress_array[i][3] = T[i](0, 1); // xy + stress_array[i][4] = T[i](0, 2); // xz + stress_array[i][5] = T[i](1, 2); // yz + stress_array[i][6] = von_mises_stress; + } else { + for (int j = 0; j < size_peratom_cols; j++) { + stress_array[i][j] = 0.0; + } + } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array + ------------------------------------------------------------------------- */ + +double ComputeSMDTLSPHStress::memory_usage() { + double bytes = size_peratom_cols * nmax * sizeof(double); + return bytes; +} + +/* + * deviator of a tensor + */ +Matrix3d ComputeSMDTLSPHStress::Deviator(Matrix3d M) { + Matrix3d eye; + eye.setIdentity(); + eye *= M.trace() / 3.0; + return M - eye; +} diff --git a/src/USER-SMD/compute_smd_tlsph_stress.h b/src/USER-SMD/compute_smd_tlsph_stress.h new file mode 100644 index 0000000000..5348584d04 --- /dev/null +++ b/src/USER-SMD/compute_smd_tlsph_stress.h @@ -0,0 +1,58 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(smd/tlsph_stress, ComputeSMDTLSPHStress) + +#else + +#ifndef LMP_COMPUTE_SMD_TLSPH_STRESS_H +#define LMP_COMPUTE_SMD_TLSPH_STRESS_H + +#include "compute.h" +#include +using namespace Eigen; + +namespace LAMMPS_NS { + +class ComputeSMDTLSPHStress : public Compute { + public: + ComputeSMDTLSPHStress(class LAMMPS *, int, char **); + ~ComputeSMDTLSPHStress(); + void init(); + void compute_peratom(); + double memory_usage(); + Matrix3d Deviator(Matrix3d); + + private: + int nmax; + double **stress_array; +}; + +} + +#endif +#endif diff --git a/src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp b/src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp new file mode 100644 index 0000000000..6e7bac76bc --- /dev/null +++ b/src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp @@ -0,0 +1,130 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#include "string.h" +#include "compute_smd_triangle_mesh_vertices.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" +#include "pair.h" +#include +#include +#include "stdlib.h" +#include "string.h" +#include +using namespace Eigen; +using namespace std; +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeSMDTriangleVertices::ComputeSMDTriangleVertices(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) { + if (narg != 3) + error->all(FLERR, "Illegal compute smd/triangle_vertices command"); + + peratom_flag = 1; + size_peratom_cols = 9; + + nmax = 0; + outputVector = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputeSMDTriangleVertices::~ComputeSMDTriangleVertices() { + memory->sfree(outputVector); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDTriangleVertices::init() { + + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style, "smd/triangle_vertices") == 0) + count++; + if (count > 1 && comm->me == 0) + error->warning(FLERR, "More than one compute smd/triangle_vertices"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDTriangleVertices::compute_peratom() { + + double **smd_data_9 = atom->smd_data_9; + tagint *mol = atom->molecule; + + invoked_peratom = update->ntimestep; + + // grow vector array if necessary + + if (atom->nlocal > nmax) { + memory->destroy(outputVector); + nmax = atom->nmax; + memory->create(outputVector, nmax, size_peratom_cols, "defgradVector"); + array_atom = outputVector; + } + + /* + * triangle vertices are stored using the smd_data_9 array ... + * this is a hack but ok for now as I do not have to create additional storage space + * all triangle particles have molecule id >= 65535 + */ + + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if ((mask[i] & groupbit) && (mol[i] >= 65535) ){ + outputVector[i][0] = smd_data_9[i][0]; + outputVector[i][1] = smd_data_9[i][1]; + outputVector[i][2] = smd_data_9[i][2]; + outputVector[i][3] = smd_data_9[i][3]; + outputVector[i][4] = smd_data_9[i][4]; + outputVector[i][5] = smd_data_9[i][5]; + outputVector[i][6] = smd_data_9[i][6]; + outputVector[i][7] = smd_data_9[i][7]; + outputVector[i][8] = smd_data_9[i][8]; + } else { + for (int j = 0; j < size_peratom_cols; j++) { + outputVector[i][j] = 0.0; + } + } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array + ------------------------------------------------------------------------- */ + +double ComputeSMDTriangleVertices::memory_usage() { + double bytes = size_peratom_cols * nmax * sizeof(double); + return bytes; +} diff --git a/src/USER-SMD/compute_smd_triangle_mesh_vertices.h b/src/USER-SMD/compute_smd_triangle_mesh_vertices.h new file mode 100644 index 0000000000..7514622714 --- /dev/null +++ b/src/USER-SMD/compute_smd_triangle_mesh_vertices.h @@ -0,0 +1,55 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(smd/triangle_vertices,ComputeSMDTriangleVertices) + +#else + +#ifndef LMP_COMPUTE_SMD_TRIANGLE_VERTICES_H +#define LMP_COMPUTE_SMD_TRIANGLE_VERTICES_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeSMDTriangleVertices : public Compute { + public: + ComputeSMDTriangleVertices(class LAMMPS *, int, char **); + ~ComputeSMDTriangleVertices(); + void init(); + void compute_peratom(); + double memory_usage(); + + private: + int nmax; + double **outputVector; +}; + +} + +#endif +#endif diff --git a/src/USER-SMD/compute_smd_ulsph_effm.cpp b/src/USER-SMD/compute_smd_ulsph_effm.cpp new file mode 100644 index 0000000000..313c259632 --- /dev/null +++ b/src/USER-SMD/compute_smd_ulsph_effm.cpp @@ -0,0 +1,115 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#include "string.h" +#include "compute_smd_ulsph_effm.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" +#include "pair.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeSMD_Ulsph_Effm::ComputeSMD_Ulsph_Effm(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) { + if (narg != 3) + error->all(FLERR, "Illegal compute smd/ulsph_effm command"); + if (atom->contact_radius_flag != 1) + error->all(FLERR, + "compute smd/ulsph_effm command requires atom_style with contact_radius (e.g. smd)"); + + peratom_flag = 1; + size_peratom_cols = 0; + + nmax = 0; + dt_vector = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputeSMD_Ulsph_Effm::~ComputeSMD_Ulsph_Effm() { + memory->sfree(dt_vector); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMD_Ulsph_Effm::init() { + + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style, "smd/ulsph_effm") == 0) + count++; + if (count > 1 && comm->me == 0) + error->warning(FLERR, "More than one compute smd/ulsph_effm"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMD_Ulsph_Effm::compute_peratom() { + invoked_peratom = update->ntimestep; + + // grow rhoVector array if necessary + + if (atom->nlocal > nmax) { + memory->sfree(dt_vector); + nmax = atom->nmax; + dt_vector = (double *) memory->smalloc(nmax * sizeof(double), + "atom:tlsph_dt_vector"); + vector_atom = dt_vector; + } + + int itmp = 0; + double *particle_dt = (double *) force->pair->extract("smd/ulsph/effective_modulus_ptr", + itmp); + if (particle_dt == NULL) { + error->all(FLERR, + "compute smd/ulsph_effm failed to access particle_dt array"); + } + + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + dt_vector[i] = particle_dt[i]; + } else { + dt_vector[i] = 0.0; + } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array + ------------------------------------------------------------------------- */ + +double ComputeSMD_Ulsph_Effm::memory_usage() { + double bytes = nmax * sizeof(double); + return bytes; +} diff --git a/src/USER-SMD/compute_smd_ulsph_effm.h b/src/USER-SMD/compute_smd_ulsph_effm.h new file mode 100644 index 0000000000..d4fb9180fe --- /dev/null +++ b/src/USER-SMD/compute_smd_ulsph_effm.h @@ -0,0 +1,55 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(smd/ulsph_effm,ComputeSMD_Ulsph_Effm) + +#else + +#ifndef LMP_COMPUTE_SMD_ULSPH_EFFM_H +#define LMP_COMPUTE_SMD_ULSPH_EFFM_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeSMD_Ulsph_Effm : public Compute { + public: + ComputeSMD_Ulsph_Effm(class LAMMPS *, int, char **); + ~ComputeSMD_Ulsph_Effm(); + void init(); + void compute_peratom(); + double memory_usage(); + + private: + int nmax; + double *dt_vector; +}; + +} + +#endif +#endif diff --git a/src/USER-SMD/compute_smd_ulsph_num_neighs.cpp b/src/USER-SMD/compute_smd_ulsph_num_neighs.cpp new file mode 100644 index 0000000000..c50db61bb1 --- /dev/null +++ b/src/USER-SMD/compute_smd_ulsph_num_neighs.cpp @@ -0,0 +1,107 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#include "string.h" +#include "compute_smd_ulsph_num_neighs.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" +#include "pair.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeSMDULSPHNumNeighs::ComputeSMDULSPHNumNeighs(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) { + if (narg != 3) + error->all(FLERR, "Illegal compute smd/ulsph_num_neighs command"); + + peratom_flag = 1; + size_peratom_cols = 0; + + nmax = 0; + numNeighsOutput = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputeSMDULSPHNumNeighs::~ComputeSMDULSPHNumNeighs() { + memory->destroy(numNeighsOutput); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDULSPHNumNeighs::init() { + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style, "smd/ulsph_num_neighs") == 0) + count++; + if (count > 1 && comm->me == 0) + error->warning(FLERR, "More than one compute smd/ulsph_num_neighs"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDULSPHNumNeighs::compute_peratom() { + invoked_peratom = update->ntimestep; + + if (atom->nlocal > nmax) { + memory->destroy(numNeighsOutput); + nmax = atom->nmax; + memory->create(numNeighsOutput, nmax, "ulsph/num_neighs:numNeighsRefConfigOutput"); + vector_atom = numNeighsOutput; + } + + int *mask = atom->mask; + int nlocal = atom->nlocal; + + int itmp = 0; + int *numNeighs = (int *) force->pair->extract("smd/ulsph/numNeighs_ptr", itmp); + if (numNeighs == NULL) { + error->all(FLERR, "compute smd/ulsph_num_neighs failed to access numNeighs array"); + } + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + numNeighsOutput[i] = numNeighs[i]; + } else { + numNeighsOutput[i] = 0.0; + } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array + ------------------------------------------------------------------------- */ + +double ComputeSMDULSPHNumNeighs::memory_usage() { + double bytes = nmax * sizeof(double); + return bytes; +} diff --git a/src/USER-SMD/compute_smd_ulsph_num_neighs.h b/src/USER-SMD/compute_smd_ulsph_num_neighs.h new file mode 100644 index 0000000000..c16d178666 --- /dev/null +++ b/src/USER-SMD/compute_smd_ulsph_num_neighs.h @@ -0,0 +1,69 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(smd/ulsph_num_neighs,ComputeSMDULSPHNumNeighs) + +#else + +#ifndef LMP_COMPUTE_SMD_ULSPH_NUM_NEIGHS_H +#define LMP_COMPUTE_SMD_ULSPH_NUM_NEIGHS_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeSMDULSPHNumNeighs : public Compute { + public: + ComputeSMDULSPHNumNeighs(class LAMMPS *, int, char **); + ~ComputeSMDULSPHNumNeighs(); + void init(); + void compute_peratom(); + double memory_usage(); + + private: + int nmax; + double *numNeighsOutput; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +W: More than one compute ke/atom + +It is not efficient to use compute ke/atom more than once. + +*/ diff --git a/src/USER-SMD/compute_smd_ulsph_strain.cpp b/src/USER-SMD/compute_smd_ulsph_strain.cpp new file mode 100644 index 0000000000..5cf4fa53fa --- /dev/null +++ b/src/USER-SMD/compute_smd_ulsph_strain.cpp @@ -0,0 +1,120 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#include "string.h" +#include "compute_smd_ulsph_strain.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" +#include "pair.h" +#include +#include +#include "stdlib.h" +#include "string.h" +#include +using namespace Eigen; +using namespace std; +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeSMDULSPHstrain::ComputeSMDULSPHstrain(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) { + if (narg != 3) + error->all(FLERR, "Illegal compute smd/tlsph_strain command"); + + peratom_flag = 1; + size_peratom_cols = 6; + + nmax = 0; + strainVector = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputeSMDULSPHstrain::~ComputeSMDULSPHstrain() { + memory->sfree(strainVector); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDULSPHstrain::init() { + + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style, "smd/tlsph_strain") == 0) + count++; + if (count > 1 && comm->me == 0) + error->warning(FLERR, "More than one compute smd/tlsph_strain"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDULSPHstrain::compute_peratom() { + double **atom_data9 = atom->smd_data_9; // ULSPH strain is stored in the first 6 entries of this data field + + invoked_peratom = update->ntimestep; + + // grow vector array if necessary + + if (atom->nlocal > nmax) { + memory->destroy(strainVector); + nmax = atom->nmax; + memory->create(strainVector, nmax, size_peratom_cols, "strainVector"); + array_atom = strainVector; + } + + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + + strainVector[i][0] = atom_data9[i][0]; + strainVector[i][1] = atom_data9[i][1]; + strainVector[i][2] = atom_data9[i][2]; + strainVector[i][3] = atom_data9[i][3]; + strainVector[i][4] = atom_data9[i][4]; + strainVector[i][5] = atom_data9[i][5]; + } else { + for (int j = 0; j < size_peratom_cols; j++) { + strainVector[i][j] = 0.0; + } + } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array + ------------------------------------------------------------------------- */ + +double ComputeSMDULSPHstrain::memory_usage() { + double bytes = size_peratom_cols * nmax * sizeof(double); + return bytes; +} diff --git a/src/USER-SMD/compute_smd_ulsph_strain.h b/src/USER-SMD/compute_smd_ulsph_strain.h new file mode 100644 index 0000000000..820b2450a8 --- /dev/null +++ b/src/USER-SMD/compute_smd_ulsph_strain.h @@ -0,0 +1,55 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(smd/ulsph_strain,ComputeSMDULSPHstrain) + +#else + +#ifndef LMP_COMPUTE_SMD_ULSPH_STRAIN_H +#define LMP_COMPUTE_SMD_ULSPH_STRAIN_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeSMDULSPHstrain : public Compute { + public: + ComputeSMDULSPHstrain(class LAMMPS *, int, char **); + ~ComputeSMDULSPHstrain(); + void init(); + void compute_peratom(); + double memory_usage(); + + private: + int nmax; + double **strainVector; +}; + +} + +#endif +#endif diff --git a/src/USER-SMD/compute_smd_ulsph_strain_rate.cpp b/src/USER-SMD/compute_smd_ulsph_strain_rate.cpp new file mode 100644 index 0000000000..542c87bc32 --- /dev/null +++ b/src/USER-SMD/compute_smd_ulsph_strain_rate.cpp @@ -0,0 +1,132 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#include "string.h" +#include "compute_smd_ulsph_strain_rate.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" +#include "pair.h" +#include +using namespace Eigen; +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeSMDULSPHStrainRate::ComputeSMDULSPHStrainRate(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) { + if (narg != 3) + error->all(FLERR, "Illegal compute smd/ulsph_strain_rate command"); + + peratom_flag = 1; + size_peratom_cols = 6; + + nmax = 0; + strain_rate_array = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputeSMDULSPHStrainRate::~ComputeSMDULSPHStrainRate() { + memory->sfree(strain_rate_array); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDULSPHStrainRate::init() { + + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style, "smd/ulsph_strain_rate") == 0) + count++; + if (count > 1 && comm->me == 0) + error->warning(FLERR, "More than one compute smd/ulsph_strain_rate"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDULSPHStrainRate::compute_peratom() { + invoked_peratom = update->ntimestep; + int *mask = atom->mask; + + // grow vector array if necessary + + if (atom->nlocal > nmax) { + memory->destroy(strain_rate_array); + nmax = atom->nmax; + memory->create(strain_rate_array, nmax, size_peratom_cols, "stresstensorVector"); + array_atom = strain_rate_array; + } + + int itmp = 0; + Matrix3d *L = (Matrix3d *) force->pair->extract("smd/ulsph/velocityGradient_ptr", itmp); + if (L == NULL) { + error->all(FLERR, + "compute smd/ulsph_strain_rate could not access any velocity gradients. Are the matching pair styles present?"); + } + int nlocal = atom->nlocal; + Matrix3d D; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + D = 0.5 * (L[i] + L[i].transpose()); + strain_rate_array[i][0] = D(0, 0); // xx + strain_rate_array[i][1] = D(1, 1); // yy + strain_rate_array[i][2] = D(2, 2); // zz + strain_rate_array[i][3] = D(0, 1); // xy + strain_rate_array[i][4] = D(0, 2); // xz + strain_rate_array[i][5] = D(1, 2); // yz + } else { + strain_rate_array[i][0] = 0.0; + strain_rate_array[i][1] = 0.0; + strain_rate_array[i][2] = 0.0; + strain_rate_array[i][3] = 0.0; + strain_rate_array[i][4] = 0.0; + strain_rate_array[i][5] = 0.0; + } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array + ------------------------------------------------------------------------- */ + +double ComputeSMDULSPHStrainRate::memory_usage() { + double bytes = size_peratom_cols * nmax * sizeof(double); + return bytes; +} + +/* + * deviator of a tensor + */ +Matrix3d ComputeSMDULSPHStrainRate::Deviator(Matrix3d M) { + Matrix3d eye; + eye.setIdentity(); + eye *= M.trace() / 3.0; + return M - eye; +} diff --git a/src/USER-SMD/compute_smd_ulsph_strain_rate.h b/src/USER-SMD/compute_smd_ulsph_strain_rate.h new file mode 100644 index 0000000000..b200e15722 --- /dev/null +++ b/src/USER-SMD/compute_smd_ulsph_strain_rate.h @@ -0,0 +1,58 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(smd/ulsph_strain_rate,ComputeSMDULSPHStrainRate) + +#else + +#ifndef LMP_COMPUTE_SMD_ULSPH_STRAIN_RATE_H +#define LMP_COMPUTE_SMD_ULSPH_STRAIN_RATE_H + +#include "compute.h" +#include +using namespace Eigen; + +namespace LAMMPS_NS { + +class ComputeSMDULSPHStrainRate : public Compute { + public: + ComputeSMDULSPHStrainRate(class LAMMPS *, int, char **); + ~ComputeSMDULSPHStrainRate(); + void init(); + void compute_peratom(); + double memory_usage(); + Matrix3d Deviator(Matrix3d); + + private: + int nmax; + double **strain_rate_array; +}; + +} + +#endif +#endif diff --git a/src/USER-SMD/compute_smd_ulsph_stress.cpp b/src/USER-SMD/compute_smd_ulsph_stress.cpp new file mode 100644 index 0000000000..26b323e7ee --- /dev/null +++ b/src/USER-SMD/compute_smd_ulsph_stress.cpp @@ -0,0 +1,133 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#include "string.h" +#include "compute_smd_ulsph_stress.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" +#include "pair.h" +#include +using namespace Eigen; +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeSMDULSPHStress::ComputeSMDULSPHStress(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) { + if (narg != 3) + error->all(FLERR, "Illegal compute smd/ulsph_stress command"); + + peratom_flag = 1; + size_peratom_cols = 7; + + nmax = 0; + stress_array = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputeSMDULSPHStress::~ComputeSMDULSPHStress() { + memory->sfree(stress_array); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDULSPHStress::init() { + + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style, "smd/ulsph_stress") == 0) + count++; + if (count > 1 && comm->me == 0) + error->warning(FLERR, "More than one compute smd/ulsph_stress"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDULSPHStress::compute_peratom() { + invoked_peratom = update->ntimestep; + int *mask = atom->mask; + Matrix3d stress_deviator; + double von_mises_stress; + + // grow vector array if necessary + + if (atom->nlocal > nmax) { + memory->destroy(stress_array); + nmax = atom->nmax; + memory->create(stress_array, nmax, size_peratom_cols, "stresstensorVector"); + array_atom = stress_array; + } + + int itmp = 0; + Matrix3d *T = (Matrix3d *) force->pair->extract("smd/ulsph/stressTensor_ptr", itmp); + if (T == NULL) { + error->all(FLERR, "compute smd/ulsph_stress could not access stress tensors. Are the matching pair styles present?"); + } + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + + if (mask[i] & groupbit) { + stress_deviator = Deviator(T[i]); + von_mises_stress = sqrt(3. / 2.) * stress_deviator.norm(); + stress_array[i][0] = T[i](0, 0); // xx + stress_array[i][1] = T[i](1, 1); // yy + stress_array[i][2] = T[i](2, 2); // zz + stress_array[i][3] = T[i](0, 1); // xy + stress_array[i][4] = T[i](0, 2); // xz + stress_array[i][5] = T[i](1, 2); // yz + stress_array[i][6] = von_mises_stress; + + } else { + for (int j = 0; j < size_peratom_cols; j++) { + stress_array[i][j] = 0.0; + } + } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array + ------------------------------------------------------------------------- */ + +double ComputeSMDULSPHStress::memory_usage() { + double bytes = size_peratom_cols * nmax * sizeof(double); + return bytes; +} + +/* + * deviator of a tensor + */ +Matrix3d ComputeSMDULSPHStress::Deviator(Matrix3d M) { + Matrix3d eye; + eye.setIdentity(); + eye *= M.trace() / 3.0; + return M - eye; +} diff --git a/src/USER-SMD/compute_smd_ulsph_stress.h b/src/USER-SMD/compute_smd_ulsph_stress.h new file mode 100644 index 0000000000..5b31a111a4 --- /dev/null +++ b/src/USER-SMD/compute_smd_ulsph_stress.h @@ -0,0 +1,58 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(smd/ulsph_stress, ComputeSMDULSPHStress) + +#else + +#ifndef LMP_COMPUTE_SMD_ULSPH_STRESS_H +#define LMP_COMPUTE_SMD_ULSPH_STRESS_H + +#include "compute.h" +#include +using namespace Eigen; + +namespace LAMMPS_NS { + +class ComputeSMDULSPHStress : public Compute { + public: + ComputeSMDULSPHStress(class LAMMPS *, int, char **); + ~ComputeSMDULSPHStress(); + void init(); + void compute_peratom(); + double memory_usage(); + Matrix3d Deviator(Matrix3d); + + private: + int nmax; + double **stress_array; +}; + +} + +#endif +#endif diff --git a/src/USER-SMD/compute_smd_vol.cpp b/src/USER-SMD/compute_smd_vol.cpp new file mode 100644 index 0000000000..1826e3d976 --- /dev/null +++ b/src/USER-SMD/compute_smd_vol.cpp @@ -0,0 +1,130 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#include "string.h" +#include "compute_smd_vol.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeSMDVol::ComputeSMDVol(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) { + if (narg != 3) + error->all(FLERR, "Illegal compute smd/volume command"); + if (atom->vfrac_flag != 1) + error->all(FLERR, "compute smd/volume command requires atom_style with density (e.g. smd)"); + + scalar_flag = 1; + peratom_flag = 1; + size_peratom_cols = 0; + + nmax = 0; + volVector = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputeSMDVol::~ComputeSMDVol() { + memory->sfree(volVector); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDVol::init() { + + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style, "smd/volume") == 0) + count++; + if (count > 1 && comm->me == 0) + error->warning(FLERR, "More than one compute smd/volume"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSMDVol::compute_peratom() { + invoked_peratom = update->ntimestep; + + // grow volVector array if necessary + + if (atom->nlocal > nmax) { + memory->sfree(volVector); + nmax = atom->nmax; + volVector = (double *) memory->smalloc(nmax * sizeof(double), "atom:volVector"); + vector_atom = volVector; + } + + double *vfrac = atom->vfrac; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + volVector[i] = vfrac[i]; + } else { + volVector[i] = 0.0; + } + } +} + +/* ---------------------------------------------------------------------- */ + +double ComputeSMDVol::compute_scalar() { + + invoked_scalar = update->ntimestep; + double *vfrac = atom->vfrac; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + double this_proc_sum_volumes = 0.0; + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + this_proc_sum_volumes += vfrac[i]; + } + } + + //printf("this_proc_sum_volumes = %g\n", this_proc_sum_volumes); + MPI_Allreduce(&this_proc_sum_volumes, &scalar, 1, MPI_DOUBLE, MPI_SUM, world); + //if (comm->me == 0) printf("global sum_volumes = %g\n", scalar); + + return scalar; + +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array + ------------------------------------------------------------------------- */ + +double ComputeSMDVol::memory_usage() { + double bytes = nmax * sizeof(double); + return bytes; +} diff --git a/src/USER-SMD/compute_smd_vol.h b/src/USER-SMD/compute_smd_vol.h new file mode 100644 index 0000000000..e946ed85ca --- /dev/null +++ b/src/USER-SMD/compute_smd_vol.h @@ -0,0 +1,56 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(smd/volume,ComputeSMDVol) + +#else + +#ifndef LMP_COMPUTE_SMD_VOL_H +#define LMP_COMPUTE_SMD_VOL_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeSMDVol : public Compute { + public: + ComputeSMDVol(class LAMMPS *, int, char **); + ~ComputeSMDVol(); + void init(); + void compute_peratom(); + double compute_scalar(); + double memory_usage(); + + private: + int nmax; + double *volVector; +}; + +} + +#endif +#endif diff --git a/src/USER-SMD/fix_smd_adjust_dt.cpp b/src/USER-SMD/fix_smd_adjust_dt.cpp new file mode 100644 index 0000000000..48d5835059 --- /dev/null +++ b/src/USER-SMD/fix_smd_adjust_dt.cpp @@ -0,0 +1,233 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#include "math.h" +#include "stdlib.h" +#include "string.h" +#include "fix_smd_adjust_dt.h" +#include "atom.h" +#include "update.h" +#include "integrate.h" +#include "domain.h" +#include "lattice.h" +#include "force.h" +#include "pair.h" +#include "modify.h" +#include "fix.h" +#include "output.h" +#include "dump.h" +#include "comm.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +#define BIG 1.0e20 + +/* ---------------------------------------------------------------------- */ + +FixSMDTlsphDtReset::FixSMDTlsphDtReset(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) { + if (narg != 4) + error->all(FLERR, "Illegal fix smd/adjust_dt command"); + + // set time_depend, else elapsed time accumulation can be messed up + + time_depend = 1; + scalar_flag = 1; + vector_flag = 1; + size_vector = 2; + global_freq = 1; + extscalar = 0; + extvector = 0; + restart_global = 1; // this fix stores global (i.e., not per-atom) info: elaspsed time + + safety_factor = atof(arg[3]); + + // initializations + t_elapsed = 0.0; +} + +/* ---------------------------------------------------------------------- */ + +int FixSMDTlsphDtReset::setmask() { + int mask = 0; + mask |= INITIAL_INTEGRATE; + mask |= END_OF_STEP; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixSMDTlsphDtReset::init() { + dt = update->dt; +} + +/* ---------------------------------------------------------------------- */ + +void FixSMDTlsphDtReset::setup(int vflag) { + end_of_step(); +} + +/* ---------------------------------------------------------------------- */ + +void FixSMDTlsphDtReset::initial_integrate(int vflag) { + + //printf("in adjust_dt: dt = %20.10f\n", update->dt); + + t_elapsed += update->dt; +} + +/* ---------------------------------------------------------------------- */ + +void FixSMDTlsphDtReset::end_of_step() { + double dtmin = BIG; + int itmp = 0; + + /* + * extract minimum CFL timestep from TLSPH and ULSPH pair styles + */ + + double *dtCFL_TLSPH = (double *) force->pair->extract("smd/tlsph/dtCFL_ptr", itmp); + double *dtCFL_ULSPH = (double *) force->pair->extract("smd/ulsph/dtCFL_ptr", itmp); + double *dt_TRI = (double *) force->pair->extract("smd/tri_surface/stable_time_increment_ptr", itmp); + double *dt_HERTZ = (double *) force->pair->extract("smd/hertz/stable_time_increment_ptr", itmp); + double *dt_PERI_IPMB = (double *) force->pair->extract("smd/peri_ipmb/stable_time_increment_ptr", itmp); + + if ((dtCFL_TLSPH == NULL) && (dtCFL_ULSPH == NULL) && (dt_TRI == NULL) && (dt_HERTZ == NULL) + && (dt_PERI_IPMB == NULL)) { + error->all(FLERR, "fix smd/adjust_dt failed to access a valid dtCFL"); + } + + if (dtCFL_TLSPH != NULL) { + dtmin = MIN(dtmin, *dtCFL_TLSPH); + } + + if (dtCFL_ULSPH != NULL) { + dtmin = MIN(dtmin, *dtCFL_ULSPH); + } + + if (dt_TRI != NULL) { + dtmin = MIN(dtmin, *dt_TRI); + } + + if (dt_HERTZ != NULL) { + dtmin = MIN(dtmin, *dt_HERTZ); + } + + if (dt_PERI_IPMB != NULL) { + dtmin = MIN(dtmin, *dt_PERI_IPMB); + } + +// double **v = atom->v; +// double **f = atom->f; +// double *rmass = atom->rmass; +// double *radius = atom->radius; +// int *mask = atom->mask; +// int nlocal = atom->nlocal; +// double dtv, dtf, dtsq; +// double vsq, fsq, massinv, xmax; +// double delx, dely, delz, delr; + +// for (int i = 0; i < nlocal; i++) { +// if (mask[i] & groupbit) { +// xmax = 0.005 * radius[i]; +// massinv = 1.0 / rmass[i]; +// vsq = v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2]; +// fsq = f[i][0] * f[i][0] + f[i][1] * f[i][1] + f[i][2] * f[i][2]; +// dtv = dtf = BIG; +// if (vsq > 0.0) +// dtv = xmax / sqrt(vsq); +// if (fsq > 0.0) +// dtf = sqrt(2.0 * xmax / (sqrt(fsq) * massinv)); +// dt = MIN(dtv, dtf); +// dtmin = MIN(dtmin, dt); +// dtsq = dt * dt; +// delx = dt * v[i][0] + 0.5 * dtsq * massinv * f[i][0]; +// dely = dt * v[i][1] + 0.5 * dtsq * massinv * f[i][1]; +// delz = dt * v[i][2] + 0.5 * dtsq * massinv * f[i][2]; +// delr = sqrt(delx * delx + dely * dely + delz * delz); +// if (delr > xmax) +// dt *= xmax / delr; +// dtmin = MIN(dtmin, dt); +// +//// xmax = 0.05 * radius[i]; +//// massinv = 1.0 / rmass[i]; +//// fsq = f[i][0] * f[i][0] + f[i][1] * f[i][1] + f[i][2] * f[i][2]; +//// dtf = BIG; +//// if (fsq > 0.0) +//// dtf = sqrt(2.0 * xmax / (sqrt(fsq) * massinv)); +//// dtmin = MIN(dtmin, dtf); +// } +// } + + dtmin *= safety_factor; // apply safety factor + MPI_Allreduce(&dtmin, &dt, 1, MPI_DOUBLE, MPI_MIN, world); + + if (update->ntimestep == 0) { + dt = 1.0e-16; + } + + //printf("dtmin is now: %f, dt is now%f\n", dtmin, dt); + + + update->dt = dt; + if (force->pair) + force->pair->reset_dt(); + for (int i = 0; i < modify->nfix; i++) + modify->fix[i]->reset_dt(); +} + +/* ---------------------------------------------------------------------- */ + +double FixSMDTlsphDtReset::compute_scalar() { + return t_elapsed; +} + +/* ---------------------------------------------------------------------- + pack entire state of Fix into one write + ------------------------------------------------------------------------- */ + +void FixSMDTlsphDtReset::write_restart(FILE *fp) { + int n = 0; + double list[1]; + list[n++] = t_elapsed; + + if (comm->me == 0) { + int size = n * sizeof(double); + fwrite(&size, sizeof(int), 1, fp); + fwrite(list, sizeof(double), n, fp); + } +} + +/* ---------------------------------------------------------------------- + use state info from restart file to restart the Fix + ------------------------------------------------------------------------- */ + +void FixSMDTlsphDtReset::restart(char *buf) { + int n = 0; + double *list = (double *) buf; + t_elapsed = list[n++]; +} + diff --git a/src/USER-SMD/fix_smd_adjust_dt.h b/src/USER-SMD/fix_smd_adjust_dt.h new file mode 100644 index 0000000000..3b96d76d76 --- /dev/null +++ b/src/USER-SMD/fix_smd_adjust_dt.h @@ -0,0 +1,80 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(smd/adjust_dt,FixSMDTlsphDtReset) + +#else + +#ifndef LMP_FIX_TLSPH_DT_RESET_H +#define LMP_FIX_TLSPH_DT_RESET_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixSMDTlsphDtReset: public Fix { +public: + FixSMDTlsphDtReset(class LAMMPS *, int, char **); + ~FixSMDTlsphDtReset() { + } + int setmask(); + void init(); + void setup(int); + void initial_integrate(int); + void end_of_step(); + double compute_scalar(); + void write_restart(FILE *); + void restart(char *); + +private: + double safety_factor; + double dt, t_elapsed; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + + E: Illegal ... command + + Self-explanatory. Check the input script syntax and compare to the + documentation for the command. You can use -echo screen as a + command-line option when running LAMMPS to see the offending line. + + E: Use of fix dt/reset with undefined lattice + + Must use lattice command with fix dt/reset command if units option is + set to lattice. + + W: Dump dcd/xtc timestamp may be wrong with fix dt/reset + + If the fix changes the timestep, the dump dcd file will not + reflect the change. + + */ diff --git a/src/USER-SMD/fix_smd_integrate_tlsph.cpp b/src/USER-SMD/fix_smd_integrate_tlsph.cpp new file mode 100644 index 0000000000..a26ffede0d --- /dev/null +++ b/src/USER-SMD/fix_smd_integrate_tlsph.cpp @@ -0,0 +1,254 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#include "stdio.h" +#include "stdlib.h" +#include "string.h" +#include "fix_smd_integrate_tlsph.h" +#include "atom.h" +#include "force.h" +#include "update.h" +#include "error.h" +#include "pair.h" +#include "neigh_list.h" +#include +#include "domain.h" +#include "neighbor.h" +#include "comm.h" +#include "modify.h" +#include "stdio.h" +#include + +using namespace Eigen; +using namespace LAMMPS_NS; +using namespace FixConst; +using namespace std; + +/* ---------------------------------------------------------------------- */ + +FixSMDIntegrateTlsph::FixSMDIntegrateTlsph(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) { + if (narg < 3) { + printf("narg=%d\n", narg); + error->all(FLERR, "Illegal fix smd/integrate_tlsph command"); + } + + xsphFlag = false; + vlimit = -1.0; + int iarg = 3; + + if (comm->me == 0) { + printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n"); + printf("fix smd/integrate_tlsph is active for group: %s \n", arg[1]); + } + + while (true) { + + if (iarg >= narg) { + break; + } + + if (strcmp(arg[iarg], "xsph") == 0) { + xsphFlag = true; + if (comm->me == 0) { + error->one(FLERR, "XSPH is currently not available"); + printf("... will use XSPH time integration\n"); + } + } else if (strcmp(arg[iarg], "limit_velocity") == 0) { + iarg++; + if (iarg == narg) { + error->all(FLERR, "expected number following limit_velocity"); + } + + vlimit = force->numeric(FLERR, arg[iarg]); + if (comm->me == 0) { + printf("... will limit velocities to <= %g\n", vlimit); + } + } else { + char msg[128]; + sprintf(msg, "Illegal keyword for smd/integrate_tlsph: %s\n", arg[iarg]); + error->all(FLERR, msg); + } + + iarg++; + } + + if (comm->me == 0) { + printf(">>========>>========>>========>>========>>========>>========>>========>>========\n"); + } + + time_integrate = 1; + + // set comm sizes needed by this fix + + atom->add_callback(0); + +} + +/* ---------------------------------------------------------------------- */ + +int FixSMDIntegrateTlsph::setmask() { + int mask = 0; + mask |= INITIAL_INTEGRATE; + mask |= FINAL_INTEGRATE; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixSMDIntegrateTlsph::init() { + dtv = update->dt; + dtf = 0.5 * update->dt * force->ftm2v; + vlimitsq = vlimit * vlimit; +} + +/* ---------------------------------------------------------------------- + ------------------------------------------------------------------------- */ + +void FixSMDIntegrateTlsph::initial_integrate(int vflag) { + double dtfm, vsq, scale; + + // update v and x of atoms in group + + double **x = atom->x; + double **v = atom->v; + double **vest = atom->vest; + double **f = atom->f; + double *rmass = atom->rmass; + int *mask = atom->mask; + int nlocal = atom->nlocal; + int itmp; + double vxsph_x, vxsph_y, vxsph_z; + if (igroup == atom->firstgroup) + nlocal = atom->nfirst; + + Vector3d *smoothVelDifference = (Vector3d *) force->pair->extract("smd/tlsph/smoothVel_ptr", itmp); + + if (xsphFlag) { + if (smoothVelDifference == NULL) { + error->one(FLERR, + "fix smd/integrate_tlsph failed to access smoothVel array. Check if a pair style exist which calculates this quantity."); + } + } + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + dtfm = dtf / rmass[i]; + + // 1st part of Velocity_Verlet: push velocties 1/2 time increment ahead + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + + if (vlimit > 0.0) { + vsq = v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2]; + if (vsq > vlimitsq) { + scale = sqrt(vlimitsq / vsq); + v[i][0] *= scale; + v[i][1] *= scale; + v[i][2] *= scale; + } + } + + if (xsphFlag) { + + // construct XSPH velocity + vxsph_x = v[i][0] + 0.5 * smoothVelDifference[i](0); + vxsph_y = v[i][1] + 0.5 * smoothVelDifference[i](1); + vxsph_z = v[i][2] + 0.5 * smoothVelDifference[i](2); + + vest[i][0] = vxsph_x + dtfm * f[i][0]; + vest[i][1] = vxsph_y + dtfm * f[i][1]; + vest[i][2] = vxsph_z + dtfm * f[i][2]; + + x[i][0] += dtv * vxsph_x; + x[i][1] += dtv * vxsph_y; + x[i][2] += dtv * vxsph_z; + } else { + + // extrapolate velocity from half- to full-step + vest[i][0] = v[i][0] + dtfm * f[i][0]; + vest[i][1] = v[i][1] + dtfm * f[i][1]; + vest[i][2] = v[i][2] + dtfm * f[i][2]; + + x[i][0] += dtv * v[i][0]; // 2nd part of Velocity-Verlet: push positions one full time increment ahead + x[i][1] += dtv * v[i][1]; + x[i][2] += dtv * v[i][2]; + } + } + } + +} + +/* ---------------------------------------------------------------------- */ + +void FixSMDIntegrateTlsph::final_integrate() { + double dtfm, vsq, scale; + +// update v of atoms in group + + double **v = atom->v; + double **f = atom->f; + double *e = atom->e; + double *de = atom->de; + double *rmass = atom->rmass; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) + nlocal = atom->nfirst; + int i; + + for (i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + dtfm = dtf / rmass[i]; + + v[i][0] += dtfm * f[i][0]; // 3rd part of Velocity-Verlet: push velocities another half time increment ahead + v[i][1] += dtfm * f[i][1]; // both positions and velocities are now defined at full time-steps. + v[i][2] += dtfm * f[i][2]; + + // limit velocity + if (vlimit > 0.0) { + vsq = v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2]; + if (vsq > vlimitsq) { + scale = sqrt(vlimitsq / vsq); + v[i][0] *= scale; + v[i][1] *= scale; + v[i][2] *= scale; + } + } + + e[i] += dtv * de[i]; + } + } +} + +/* ---------------------------------------------------------------------- */ + +void FixSMDIntegrateTlsph::reset_dt() { + dtv = update->dt; + dtf = 0.5 * update->dt * force->ftm2v; + vlimitsq = vlimit * vlimit; +} + +/* ---------------------------------------------------------------------- */ diff --git a/src/USER-SMD/fix_smd_integrate_tlsph.h b/src/USER-SMD/fix_smd_integrate_tlsph.h new file mode 100644 index 0000000000..7119f8d919 --- /dev/null +++ b/src/USER-SMD/fix_smd_integrate_tlsph.h @@ -0,0 +1,73 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(smd/integrate_tlsph,FixSMDIntegrateTlsph) + +#else + +#ifndef LMP_FIX_SMD_INTEGRATE_TLSPH_H +#define LMP_FIX_SMD_INTEGRATE_TLSPH_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixSMDIntegrateTlsph: public Fix { + friend class Neighbor; + friend class PairTlsph; +public: + FixSMDIntegrateTlsph(class LAMMPS *, int, char **); + virtual ~FixSMDIntegrateTlsph() { + } + int setmask(); + virtual void init(); + virtual void initial_integrate(int); + virtual void final_integrate(); + virtual void reset_dt(); + +protected: + double dtv, dtf, vlimit, vlimitsq; + int mass_require; + bool xsphFlag; + + class Pair *pair; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + + E: Illegal ... command + + Self-explanatory. Check the input script syntax and compare to the + documentation for the command. You can use -echo screen as a + command-line option when running LAMMPS to see the offending line. + + */ diff --git a/src/USER-SMD/fix_smd_integrate_ulsph.cpp b/src/USER-SMD/fix_smd_integrate_ulsph.cpp new file mode 100644 index 0000000000..91b974b400 --- /dev/null +++ b/src/USER-SMD/fix_smd_integrate_ulsph.cpp @@ -0,0 +1,325 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#include "stdio.h" +#include "string.h" +#include "fix_smd_integrate_ulsph.h" +#include "math.h" +#include "stdlib.h" +#include "string.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "update.h" +#include "integrate.h" +#include "respa.h" +#include "memory.h" +#include "error.h" +#include "pair.h" +#include "domain.h" +#include + +using namespace Eigen; +using namespace LAMMPS_NS; +using namespace FixConst; + +/* ---------------------------------------------------------------------- */ + +FixSMDIntegrateUlsph::FixSMDIntegrateUlsph(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) { + + if ((atom->e_flag != 1) || (atom->vfrac_flag != 1)) + error->all(FLERR, "fix smd/integrate_ulsph command requires atom_style with both energy and volume"); + + if (narg < 3) + error->all(FLERR, "Illegal number of arguments for fix smd/integrate_ulsph command"); + + adjust_radius_flag = false; + xsphFlag = false; + vlimit = -1.0; + int iarg = 3; + + if (comm->me == 0) { + printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n"); + printf("fix smd/integrate_ulsph is active for group: %s \n", arg[1]); + } + while (true) { + + if (iarg >= narg) { + break; + } + + if (strcmp(arg[iarg], "xsph") == 0) { + xsphFlag = true; + if (comm->me == 0) { + error->one(FLERR, "XSPH is currently not available"); + printf("... will use XSPH time integration\n"); + } + } else if (strcmp(arg[iarg], "adjust_radius") == 0) { + adjust_radius_flag = true; + + iarg++; + if (iarg == narg) { + error->all(FLERR, "expected three numbers following adjust_radius: factor, min, max"); + } + + adjust_radius_factor = force->numeric(FLERR, arg[iarg]); + + iarg++; + if (iarg == narg) { + error->all(FLERR, "expected three numbers following adjust_radius: factor, min, max"); + } + + min_nn = force->inumeric(FLERR, arg[iarg]); + + iarg++; + if (iarg == narg) { + error->all(FLERR, "expected three numbers following adjust_radius: factor, min, max"); + } + + max_nn = force->inumeric(FLERR, arg[iarg]); + + if (comm->me == 0) { + printf("... will adjust smoothing length dynamically with factor %g to achieve %d to %d neighbors per particle.\n ", + adjust_radius_factor, min_nn, max_nn); + } + + } else if (strcmp(arg[iarg], "limit_velocity") == 0) { + iarg++; + if (iarg == narg) { + error->all(FLERR, "expected number following limit_velocity"); + } + vlimit = force->numeric(FLERR, arg[iarg]); + + if (comm->me == 0) { + printf("... will limit velocities to <= %g\n", vlimit); + } + } else { + char msg[128]; + sprintf(msg, "Illegal keyword for smd/integrate_ulsph: %s\n", arg[iarg]); + error->all(FLERR, msg); + } + + iarg++; + + } + + if (comm->me == 0) { + printf(">>========>>========>>========>>========>>========>>========>>========>>========\n\n"); + } + + // set comm sizes needed by this fix + atom->add_callback(0); + + time_integrate = 1; +} + +/* ---------------------------------------------------------------------- */ + +int FixSMDIntegrateUlsph::setmask() { + int mask = 0; + mask |= INITIAL_INTEGRATE; + mask |= FINAL_INTEGRATE; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixSMDIntegrateUlsph::init() { + dtv = update->dt; + dtf = 0.5 * update->dt * force->ftm2v; + vlimitsq = vlimit * vlimit; +} + +/* ---------------------------------------------------------------------- + allow for both per-type and per-atom mass + ------------------------------------------------------------------------- */ + +void FixSMDIntegrateUlsph::initial_integrate(int vflag) { + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + double **vest = atom->vest; + double *rmass = atom->rmass; + + int *mask = atom->mask; + int nlocal = atom->nlocal; + int i, itmp; + double dtfm, vsq, scale; + double vxsph_x, vxsph_y, vxsph_z; + + //printf("initial_integrate at timestep %d\n", update->ntimestep); + + /* + * get smoothed velocities from ULSPH pair style + */ + + Vector3d *smoothVel = (Vector3d *) force->pair->extract("smd/ulsph/smoothVel_ptr", itmp); + + if (xsphFlag) { + if (smoothVel == NULL) { + error->one(FLERR, "fix smd/integrate_ulsph failed to access smoothVel array"); + } + } + + if (igroup == atom->firstgroup) + nlocal = atom->nfirst; + + for (i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + dtfm = dtf / rmass[i]; + + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + + if (vlimit > 0.0) { + vsq = v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2]; + if (vsq > vlimitsq) { + scale = sqrt(vlimitsq / vsq); + v[i][0] *= scale; + v[i][1] *= scale; + v[i][2] *= scale; + + vest[i][0] = v[i][0]; + vest[i][1] = v[i][1]; + vest[i][2] = v[i][2]; + } + } + + if (xsphFlag) { + + // construct XSPH velocity + vxsph_x = v[i][0] - 0.5 * smoothVel[i](0); + vxsph_y = v[i][1] - 0.5 * smoothVel[i](1); + vxsph_z = v[i][2] - 0.5 * smoothVel[i](2); + + vest[i][0] = vxsph_x + dtfm * f[i][0]; + vest[i][1] = vxsph_y + dtfm * f[i][1]; + vest[i][2] = vxsph_z + dtfm * f[i][2]; + + x[i][0] += dtv * vxsph_x; + x[i][1] += dtv * vxsph_y; + x[i][2] += dtv * vxsph_z; + + + + + } else { + + // extrapolate velocity from half- to full-step + vest[i][0] = v[i][0] + dtfm * f[i][0]; + vest[i][1] = v[i][1] + dtfm * f[i][1]; + vest[i][2] = v[i][2] + dtfm * f[i][2]; + + x[i][0] += dtv * v[i][0]; + x[i][1] += dtv * v[i][1]; + x[i][2] += dtv * v[i][2]; + } + } + } +} + +/* ---------------------------------------------------------------------- */ + +void FixSMDIntegrateUlsph::final_integrate() { + double **v = atom->v; + double **f = atom->f; + double *e = atom->e; + double *de = atom->de; + double *vfrac = atom->vfrac; + double *radius = atom->radius; + double *contact_radius = atom->contact_radius; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) + nlocal = atom->nfirst; + double dtfm, vsq, scale; + double *rmass = atom->rmass; + double vol_increment; + Matrix3d D; + + /* + * get current number of SPH neighbors from ULSPH pair style + */ + + int itmp; + int *nn = (int *) force->pair->extract("smd/ulsph/numNeighs_ptr", itmp); + if (nn == NULL) { + error->one(FLERR, "fix smd/integrate_ulsph failed to accesss num_neighs array"); + } + + Matrix3d *L = (Matrix3d *) force->pair->extract("smd/ulsph/velocityGradient_ptr", itmp); + if (L == NULL) { + error->one(FLERR, "fix smd/integrate_ulsph failed to accesss velocityGradient array"); + } + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + + dtfm = dtf / rmass[i]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + + if (vlimit > 0.0) { + vsq = v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2]; + if (vsq > vlimitsq) { + scale = sqrt(vlimitsq / vsq); + v[i][0] *= scale; + v[i][1] *= scale; + v[i][2] *= scale; + } + } + + e[i] += dtf * de[i]; + + if (adjust_radius_flag) { + if (nn[i] < min_nn) { + radius[i] *= adjust_radius_factor; + } else if (nn[i] > max_nn) { + radius[i] /= adjust_radius_factor; + } + radius[i] = MAX(radius[i], 1.25 * contact_radius[i]); + radius[i] = MIN(radius[i], 4.0 * contact_radius[i]); + + } + + D = 0.5 * (L[i] + L[i].transpose()); + vol_increment = vfrac[i] * update->dt * D.trace(); // Jacobian of deformation + vfrac[i] += vol_increment; + } + } +} + +/* ---------------------------------------------------------------------- */ + +void FixSMDIntegrateUlsph::reset_dt() { + dtv = update->dt; + dtf = 0.5 * update->dt * force->ftm2v; +} + diff --git a/src/USER-SMD/fix_smd_integrate_ulsph.h b/src/USER-SMD/fix_smd_integrate_ulsph.h new file mode 100644 index 0000000000..19ae31a59e --- /dev/null +++ b/src/USER-SMD/fix_smd_integrate_ulsph.h @@ -0,0 +1,64 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(smd/integrate_ulsph,FixSMDIntegrateUlsph) + +#else + +#ifndef LMP_FIX_SMD_INTEGRATE_ULSPH_H +#define LMP_FIX_SMD_INTEGRATE_ULSPH_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixSMDIntegrateUlsph : public Fix { + public: + FixSMDIntegrateUlsph(class LAMMPS *, int, char **); + int setmask(); + virtual void init(); + virtual void initial_integrate(int); + virtual void final_integrate(); + void reset_dt(); + + private: + class NeighList *list; + protected: + double dtv,dtf, vlimit, vlimitsq;; + int mass_require; + bool xsphFlag; + bool adjust_radius_flag; + double adjust_radius_factor; + int min_nn, max_nn; // number of SPH neighbors should lie within this interval + + class Pair *pair; +}; + +} + +#endif +#endif diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp new file mode 100644 index 0000000000..407eabf452 --- /dev/null +++ b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp @@ -0,0 +1,517 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#include "stdio.h" +#include "string.h" +#include "fix_smd_move_triangulated_surface.h" +#include "math.h" +#include "stdlib.h" +#include "string.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "update.h" +#include "integrate.h" +#include "respa.h" +#include "memory.h" +#include "error.h" +#include "pair.h" +#include "domain.h" +#include +#include "math_const.h" + +using namespace Eigen; +using namespace LAMMPS_NS; +using namespace FixConst; +using namespace MathConst; +using namespace std; + +/* ---------------------------------------------------------------------- */ + +FixSMDMoveTriSurf::FixSMDMoveTriSurf(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) { + + if (atom->smd_flag != 1) { + error->all(FLERR, "fix fix smd/move_tri_surf command requires atom_style smd"); + } + + if (narg < 3) + error->all(FLERR, "Illegal number of arguments for fix fix smd/move_tri_surf command"); + + rotateFlag = linearFlag = wiggleFlag = false; + wiggle_direction = 1.0; + wiggle_max_travel = 0.0; + + int iarg = 3; + + if (comm->me == 0) { + printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n"); + printf("fix fix smd/move_tri_surf is active for group: %s \n", arg[1]); + } + while (true) { + + if (iarg >= narg) { + break; + } + + if (strcmp(arg[iarg], "*LINEAR") == 0) { + linearFlag = true; + if (comm->me == 0) { + printf("... will move surface in a linear fashion\n"); + } + + iarg++; + if (iarg == narg) { + error->all(FLERR, "expected three floats for velocity following *LINEAR"); + } + vx = force->numeric(FLERR, arg[iarg]); + + iarg++; + if (iarg == narg) { + error->all(FLERR, "expected three floats for velocity following *LINEAR"); + } + vy = force->numeric(FLERR, arg[iarg]); + + iarg++; + if (iarg == narg) { + error->all(FLERR, "expected three floats for velocity following *LINEAR"); + } + vz = force->numeric(FLERR, arg[iarg]); + + } else if (strcmp(arg[iarg], "*WIGGLE") == 0) { + wiggleFlag = true; + if (comm->me == 0) { + printf("... will move surface in wiggle fashion\n"); + } + + iarg++; + if (iarg == narg) { + error->all(FLERR, "expected 4 floats following *WIGGLE : vx vy vz max_travel"); + } + vx = force->numeric(FLERR, arg[iarg]); + + iarg++; + if (iarg == narg) { + error->all(FLERR, "expected 4 floats following *WIGGLE : vx vy vz max_travel"); + } + vy = force->numeric(FLERR, arg[iarg]); + + iarg++; + if (iarg == narg) { + error->all(FLERR, "expected 4 floats following *WIGGLE : vx vy vz max_travel"); + } + vz = force->numeric(FLERR, arg[iarg]); + + iarg++; + if (iarg == narg) { + error->all(FLERR, "expected 4 floats following *WIGGLE : vx vy vz max_travel"); + } + wiggle_max_travel = force->numeric(FLERR, arg[iarg]); + + } else if (strcmp(arg[iarg], "*ROTATE") == 0) { + rotateFlag = true; + + iarg++; + if (iarg == narg) { + error->all(FLERR, "expected 7 floats following *ROTATE: origin, rotation axis, and rotation period"); + } + origin(0) = force->numeric(FLERR, arg[iarg]); + + iarg++; + if (iarg == narg) { + error->all(FLERR, "expected 7 floats following *ROTATE: origin, rotation axis, and rotation period"); + } + origin(1) = force->numeric(FLERR, arg[iarg]); + + iarg++; + if (iarg == narg) { + error->all(FLERR, "expected 7 floats following *ROTATE: origin, rotation axis, and rotation period"); + } + origin(2) = force->numeric(FLERR, arg[iarg]); + + iarg++; + if (iarg == narg) { + error->all(FLERR, "expected 7 floats following *ROTATE: origin, rotation axis, and rotation period"); + } + rotation_axis(0) = force->numeric(FLERR, arg[iarg]); + + iarg++; + if (iarg == narg) { + error->all(FLERR, "expected 7 floats following *ROTATE: origin, rotation axis, and rotation period"); + } + rotation_axis(1) = force->numeric(FLERR, arg[iarg]); + + iarg++; + if (iarg == narg) { + error->all(FLERR, "expected 7 floats following *ROTATE: origin, rotation axis, and rotation period"); + } + rotation_axis(2) = force->numeric(FLERR, arg[iarg]); + + iarg++; + if (iarg == narg) { + error->all(FLERR, "expected 7 floats following *ROTATE: origin, rotation axis, and rotation period"); + } + rotation_period = force->numeric(FLERR, arg[iarg]); + + /* + * construct rotation matrix + */ + + u_cross(0, 0) = 0.0; + u_cross(0, 1) = -rotation_axis(2); + u_cross(0, 2) = rotation_axis(1); + + u_cross(1, 0) = rotation_axis(2); + u_cross(1, 1) = 0.0; + u_cross(1, 2) = -rotation_axis(0); + + u_cross(2, 0) = -rotation_axis(1); + u_cross(2, 1) = rotation_axis(0); + u_cross(2, 2) = 0.0; + + uxu = rotation_axis * rotation_axis.transpose(); + + if (comm->me == 0) { + printf("will rotate with period %f\n", rotation_period); + } + + } else { + char msg[128]; + sprintf(msg, "Illegal keyword for fix smd/move_tri_surf: %s\n", arg[iarg]); + error->all(FLERR, msg); + } + + iarg++; + + } + + if (comm->me == 0) { + printf(">>========>>========>>========>>========>>========>>========>>========>>========\n\n"); + } + + // set comm sizes needed by this fix + comm_forward = 12; + + //atom->add_callback(0); + //atom->add_callback(1); + + time_integrate = 1; +} + +/* ---------------------------------------------------------------------- */ + +FixSMDMoveTriSurf::~FixSMDMoveTriSurf() +{ + // unregister callbacks to this fix from Atom class + //atom->delete_callback(id,0); + //atom->delete_callback(id,1); +} + +/* ---------------------------------------------------------------------- */ + +int FixSMDMoveTriSurf::setmask() { + int mask = 0; + mask |= INITIAL_INTEGRATE; + //mask |= PRE_EXCHANGE; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixSMDMoveTriSurf::init() { + dtv = update->dt; +} + +/* ---------------------------------------------------------------------- + ------------------------------------------------------------------------- */ + +void FixSMDMoveTriSurf::initial_integrate(int vflag) { + double **x = atom->x; + double **x0 = atom->x0; + double **v = atom->v; + double **vest = atom->vest; + double **smd_data_9 = atom->smd_data_9; + int *mol = atom->molecule; + + int *mask = atom->mask; + int nlocal = atom->nlocal; + double phi; + int i; + Matrix3d eye, Rot; + eye.setIdentity(); + + Vector3d v1, v2, v3, n, point, rotated_point, R, vel; + + if (igroup == atom->firstgroup) + nlocal = atom->nfirst; + + if (linearFlag) { // translate particles + for (i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + + v[i][0] = vx; + v[i][1] = vy; + v[i][2] = vz; + + vest[i][0] = vx; + vest[i][1] = vy; + vest[i][2] = vz; + + x[i][0] += dtv * vx; + x[i][1] += dtv * vy; + x[i][2] += dtv * vz; + + /* + * if this is a triangle, move the vertices as well + */ + + if (mol[i] >= 65535) { + smd_data_9[i][0] += dtv * vx; + smd_data_9[i][1] += dtv * vy; + smd_data_9[i][2] += dtv * vz; + + smd_data_9[i][3] += dtv * vx; + smd_data_9[i][4] += dtv * vy; + smd_data_9[i][5] += dtv * vz; + + smd_data_9[i][6] += dtv * vx; + smd_data_9[i][7] += dtv * vy; + smd_data_9[i][8] += dtv * vz; + } + + } + } + } + + if (wiggleFlag) { // wiggle particles forward and backward + + wiggle_travel += sqrt(vx * vx + vy * vy + vz * vz ) * dtv; + double wiggle_vx = wiggle_direction * vx; + double wiggle_vy = wiggle_direction * vy; + double wiggle_vz = wiggle_direction * vz; + + //printf("wiggle vz is %f, wiggle_max_travel is %f, dir=%f\n", wiggle_vz, wiggle_max_travel, wiggle_direction); + + for (i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + + v[i][0] = wiggle_vx; + v[i][1] = wiggle_vy; + v[i][2] = wiggle_vz; + + vest[i][0] = wiggle_vx; + vest[i][1] = wiggle_vy; + vest[i][2] = wiggle_vz; + + x[i][0] += dtv * wiggle_vx; + x[i][1] += dtv * wiggle_vy; + x[i][2] += dtv * wiggle_vz; + + /* + * if this is a triangle, move the vertices as well + */ + + if (mol[i] >= 65535) { + smd_data_9[i][0] += dtv * wiggle_vx; + smd_data_9[i][1] += dtv * wiggle_vy; + smd_data_9[i][2] += dtv * wiggle_vz; + + smd_data_9[i][3] += dtv * wiggle_vx; + smd_data_9[i][4] += dtv * wiggle_vy; + smd_data_9[i][5] += dtv * wiggle_vz; + + smd_data_9[i][6] += dtv * wiggle_vx; + smd_data_9[i][7] += dtv * wiggle_vy; + smd_data_9[i][8] += dtv * wiggle_vz; + } + + } + } + + if (wiggle_travel >= wiggle_max_travel) { + wiggle_direction *= -1.0; + wiggle_travel = 0.0; + } + } + + if (rotateFlag) { // rotate particles + Vector3d xnew, R_new, x_correct; + + /* + * rotation angle and matrix form of Rodrigues' rotation formula + */ + + phi = MY_2PI * dtv / rotation_period; + //printf("dt=%f, phi =%f, T=%f\n", dtv, phi, rotation_period); + Rot = cos(phi) * eye + sin(phi) * u_cross + (1.0 - cos(phi)) * uxu; + + for (i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + + /* + * generate vector R from origin to point which is to be rotated + */ + point << x[i][0], x[i][1], x[i][2]; + R = point - origin; + + /* + * rotate vector and shift away from origin + */ + rotated_point = Rot * R + origin; + + /* + * determine velocity + */ + vel = (rotated_point - point) / update->dt; + + /* + * assign new velocities and coordinates + */ + v[i][0] = vel(0); + v[i][1] = vel(1); + v[i][2] = vel(2); + + vest[i][0] = vel(0); + vest[i][1] = vel(1); + vest[i][2] = vel(2); + + x[i][0] = rotated_point(0); + x[i][1] = rotated_point(1); + x[i][2] = rotated_point(2); + + /* + * if this is a triangle, rotate the vertices as well + */ + + if (mol[i] >= 65535) { + + v1 << smd_data_9[i][0], smd_data_9[i][1], smd_data_9[i][2]; + R = v1 - origin; + rotated_point = Rot * R + origin; + vel = (rotated_point - v1) / update->dt; + smd_data_9[i][0] = rotated_point(0); + smd_data_9[i][1] = rotated_point(1); + smd_data_9[i][2] = rotated_point(2); + v1 = rotated_point; + + v2 << smd_data_9[i][3], smd_data_9[i][4], smd_data_9[i][5]; + R = v2 - origin; + rotated_point = Rot * R + origin; + vel = (rotated_point - v2) / update->dt; + smd_data_9[i][3] = rotated_point(0); + smd_data_9[i][4] = rotated_point(1); + smd_data_9[i][5] = rotated_point(2); + v2 = rotated_point; + + v3 << smd_data_9[i][6], smd_data_9[i][7], smd_data_9[i][8]; + R = v3 - origin; + rotated_point = Rot * R + origin; + vel = (rotated_point - v3) / update->dt; + smd_data_9[i][6] = rotated_point(0); + smd_data_9[i][7] = rotated_point(1); + smd_data_9[i][8] = rotated_point(2); + v3 = rotated_point; + + // recalculate triangle normal + n = (v2 - v1).cross(v2 - v3); + n /= n.norm(); + x0[i][0] = n(0); + x0[i][1] = n(1); + x0[i][2] = n(2); + + } + + } + } + } + + // we changed smd_data_9, x0. perform communication to ghosts + comm->forward_comm_fix(this); + +} + +/* ---------------------------------------------------------------------- */ + +void FixSMDMoveTriSurf::reset_dt() { + dtv = update->dt; +} + +/* ---------------------------------------------------------------------- */ + +int FixSMDMoveTriSurf::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) { + int i, j, m; + double **x0 = atom->x0; + double **smd_data_9 = atom->smd_data_9; + + //printf("in FixSMDIntegrateTlsph::pack_forward_comm\n"); + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x0[j][0]; + buf[m++] = x0[j][1]; + buf[m++] = x0[j][2]; + + buf[m++] = smd_data_9[j][0]; + buf[m++] = smd_data_9[j][1]; + buf[m++] = smd_data_9[j][2]; + buf[m++] = smd_data_9[j][3]; + buf[m++] = smd_data_9[j][4]; + buf[m++] = smd_data_9[j][5]; + buf[m++] = smd_data_9[j][6]; + buf[m++] = smd_data_9[j][7]; + buf[m++] = smd_data_9[j][8]; + + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void FixSMDMoveTriSurf::unpack_forward_comm(int n, int first, double *buf) { + int i, m, last; + double **x0 = atom->x0; + double **smd_data_9 = atom->smd_data_9; + + //printf("in FixSMDMoveTriSurf::unpack_forward_comm\n"); + m = 0; + last = first + n; + for (i = first; i < last; i++) { + x0[i][0] = buf[m++]; + x0[i][1] = buf[m++]; + x0[i][2] = buf[m++]; + + smd_data_9[i][0] = buf[m++]; + smd_data_9[i][1] = buf[m++]; + smd_data_9[i][2] = buf[m++]; + smd_data_9[i][3] = buf[m++]; + smd_data_9[i][4] = buf[m++]; + smd_data_9[i][5] = buf[m++]; + smd_data_9[i][6] = buf[m++]; + smd_data_9[i][7] = buf[m++]; + smd_data_9[i][8] = buf[m++]; + } +} diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.h b/src/USER-SMD/fix_smd_move_triangulated_surface.h new file mode 100644 index 0000000000..e6593ea8b0 --- /dev/null +++ b/src/USER-SMD/fix_smd_move_triangulated_surface.h @@ -0,0 +1,65 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(smd/move_tri_surf,FixSMDMoveTriSurf) + +#else + +#ifndef LMP_FIX_SMD_INTEGRATE_TRIANGULAR_SURFACE_H +#define LMP_FIX_SMD_INTEGRATE_TRIANGULAR_SURFACE_H + +#include "fix.h" +#include + +using namespace Eigen; + +namespace LAMMPS_NS { + +class FixSMDMoveTriSurf: public Fix { +public: + FixSMDMoveTriSurf(class LAMMPS *, int, char **); + ~FixSMDMoveTriSurf(); + int setmask(); + virtual void init(); + virtual void initial_integrate(int); + void reset_dt(); + int pack_forward_comm(int, int *, double *, int, int *); + void unpack_forward_comm(int, int, double *); + +protected: + double dtv; + bool linearFlag, wiggleFlag, rotateFlag; + double vx, vy, vz; + Vector3d rotation_axis, origin; + double rotation_period; + Matrix3d u_cross, uxu; + double wiggle_travel, wiggle_max_travel, wiggle_direction; +}; + +} + +#endif +#endif diff --git a/src/USER-SMD/fix_smd_setvel.cpp b/src/USER-SMD/fix_smd_setvel.cpp new file mode 100644 index 0000000000..dbf21670f9 --- /dev/null +++ b/src/USER-SMD/fix_smd_setvel.cpp @@ -0,0 +1,375 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + + 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. + ------------------------------------------------------------------------- */ + +#include "string.h" +#include "stdlib.h" +#include "fix_smd_setvel.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "domain.h" +#include "region.h" +#include "respa.h" +#include "input.h" +#include "variable.h" +#include "memory.h" +#include "error.h" +#include "force.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +enum { + NONE, CONSTANT, EQUAL, ATOM +}; + +/* ---------------------------------------------------------------------- */ + +FixSMDSetVel::FixSMDSetVel(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) { + if (narg < 6) + error->all(FLERR, "Illegal fix setvelocity command"); + + dynamic_group_allow = 1; + vector_flag = 1; + size_vector = 3; + global_freq = 1; + extvector = 1; + + xstr = ystr = zstr = NULL; + + if (strstr(arg[3], "v_") == arg[3]) { + int n = strlen(&arg[3][2]) + 1; + xstr = new char[n]; + strcpy(xstr, &arg[3][2]); + } else if (strcmp(arg[3], "NULL") == 0) { + xstyle = NONE; + } else { + xvalue = force->numeric(FLERR, arg[3]); + xstyle = CONSTANT; + } + if (strstr(arg[4], "v_") == arg[4]) { + int n = strlen(&arg[4][2]) + 1; + ystr = new char[n]; + strcpy(ystr, &arg[4][2]); + } else if (strcmp(arg[4], "NULL") == 0) { + ystyle = NONE; + } else { + yvalue = force->numeric(FLERR, arg[4]); + ystyle = CONSTANT; + } + if (strstr(arg[5], "v_") == arg[5]) { + int n = strlen(&arg[5][2]) + 1; + zstr = new char[n]; + strcpy(zstr, &arg[5][2]); + } else if (strcmp(arg[5], "NULL") == 0) { + zstyle = NONE; + } else { + zvalue = force->numeric(FLERR, arg[5]); + zstyle = CONSTANT; + } + + // optional args + + iregion = -1; + idregion = NULL; + + int iarg = 6; + while (iarg < narg) { + if (strcmp(arg[iarg], "region") == 0) { + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix setvelocity command"); + iregion = domain->find_region(arg[iarg + 1]); + if (iregion == -1) + error->all(FLERR, "Region ID for fix setvelocity does not exist"); + int n = strlen(arg[iarg + 1]) + 1; + idregion = new char[n]; + strcpy(idregion, arg[iarg + 1]); + iarg += 2; + } else + error->all(FLERR, "Illegal fix setvelocity command"); + } + + force_flag = 0; + foriginal[0] = foriginal[1] = foriginal[2] = 0.0; + + maxatom = atom->nmax; + memory->create(sforce, maxatom, 3, "setvelocity:sforce"); +} + +/* ---------------------------------------------------------------------- */ + +FixSMDSetVel::~FixSMDSetVel() { + delete[] xstr; + delete[] ystr; + delete[] zstr; + delete[] idregion; + memory->destroy(sforce); +} + +/* ---------------------------------------------------------------------- */ + +int FixSMDSetVel::setmask() { + int mask = 0; + //mask |= INITIAL_INTEGRATE; + mask |= POST_FORCE; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixSMDSetVel::init() { + // check variables + + if (xstr) { + xvar = input->variable->find(xstr); + if (xvar < 0) + error->all(FLERR, "Variable name for fix setvelocity does not exist"); + if (input->variable->equalstyle(xvar)) + xstyle = EQUAL; + else if (input->variable->atomstyle(xvar)) + xstyle = ATOM; + else + error->all(FLERR, "Variable for fix setvelocity is invalid style"); + } + if (ystr) { + yvar = input->variable->find(ystr); + if (yvar < 0) + error->all(FLERR, "Variable name for fix setvelocity does not exist"); + if (input->variable->equalstyle(yvar)) + ystyle = EQUAL; + else if (input->variable->atomstyle(yvar)) + ystyle = ATOM; + else + error->all(FLERR, "Variable for fix setvelocity is invalid style"); + } + if (zstr) { + zvar = input->variable->find(zstr); + if (zvar < 0) + error->all(FLERR, "Variable name for fix setvelocity does not exist"); + if (input->variable->equalstyle(zvar)) + zstyle = EQUAL; + else if (input->variable->atomstyle(zvar)) + zstyle = ATOM; + else + error->all(FLERR, "Variable for fix setvelocity is invalid style"); + } + + // set index and check validity of region + + if (iregion >= 0) { + iregion = domain->find_region(idregion); + if (iregion == -1) + error->all(FLERR, "Region ID for fix setvelocity does not exist"); + } + + if (xstyle == ATOM || ystyle == ATOM || zstyle == ATOM) + varflag = ATOM; + else if (xstyle == EQUAL || ystyle == EQUAL || zstyle == EQUAL) + varflag = EQUAL; + else + varflag = CONSTANT; + + if (strstr(update->integrate_style, "respa")) + nlevels_respa = ((Respa *) update->integrate)->nlevels; + + // cannot use non-zero forces for a minimization since no energy is integrated + // use fix addforce instead + + int flag = 0; + if (update->whichflag == 2) { + if (xstyle == EQUAL || xstyle == ATOM) + flag = 1; + if (ystyle == EQUAL || ystyle == ATOM) + flag = 1; + if (zstyle == EQUAL || zstyle == ATOM) + flag = 1; + if (xstyle == CONSTANT && xvalue != 0.0) + flag = 1; + if (ystyle == CONSTANT && yvalue != 0.0) + flag = 1; + if (zstyle == CONSTANT && zvalue != 0.0) + flag = 1; + } + if (flag) + error->all(FLERR, "Cannot use non-zero forces in an energy minimization"); +} + +/* ---------------------------------------------------------------------- */ + +void FixSMDSetVel::setup(int vflag) { + if (strstr(update->integrate_style, "verlet")) + post_force(vflag); + else + for (int ilevel = 0; ilevel < nlevels_respa; ilevel++) { + ((Respa *) update->integrate)->copy_flevel_f(ilevel); + post_force_respa(vflag, ilevel, 0); + ((Respa *) update->integrate)->copy_f_flevel(ilevel); + } +} + +/* ---------------------------------------------------------------------- */ + +void FixSMDSetVel::min_setup(int vflag) { + post_force(vflag); +} + +/* ---------------------------------------------------------------------- */ + +//void FixSMDSetVel::initial_integrate(int vflag) { +void FixSMDSetVel::post_force(int vflag) { + double **x = atom->x; + double **f = atom->f; + double **v = atom->v; + double **vest = atom->vest; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + // update region if necessary + + Region *region = NULL; + if (iregion >= 0) { + region = domain->regions[iregion]; + region->prematch(); + } + + // reallocate sforce array if necessary + + if (varflag == ATOM && nlocal > maxatom) { + maxatom = atom->nmax; + memory->destroy(sforce); + memory->create(sforce, maxatom, 3, "setvelocity:sforce"); + } + + foriginal[0] = foriginal[1] = foriginal[2] = 0.0; + force_flag = 0; + + if (varflag == CONSTANT) { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + if (region && !region->match(x[i][0], x[i][1], x[i][2])) + continue; + foriginal[0] += f[i][0]; + foriginal[1] += f[i][1]; + foriginal[2] += f[i][2]; + if (xstyle) { + v[i][0] = xvalue; + vest[i][0] = xvalue; + f[i][0] = 0.0; + } + if (ystyle) { + v[i][1] = yvalue; + vest[i][1] = yvalue; + f[i][1] = 0.0; + } + if (zstyle) { + v[i][2] = zvalue; + vest[i][2] = zvalue; + f[i][2] = 0.0; + } + } + + // variable force, wrap with clear/add + + } else { + + modify->clearstep_compute(); + + if (xstyle == EQUAL) + xvalue = input->variable->compute_equal(xvar); + else if (xstyle == ATOM) + input->variable->compute_atom(xvar, igroup, &sforce[0][0], 3, 0); + if (ystyle == EQUAL) + yvalue = input->variable->compute_equal(yvar); + else if (ystyle == ATOM) + input->variable->compute_atom(yvar, igroup, &sforce[0][1], 3, 0); + if (zstyle == EQUAL) + zvalue = input->variable->compute_equal(zvar); + else if (zstyle == ATOM) + input->variable->compute_atom(zvar, igroup, &sforce[0][2], 3, 0); + + modify->addstep_compute(update->ntimestep + 1); + + //printf("setting velocity at timestep %d\n", update->ntimestep); + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + if (region && !region->match(x[i][0], x[i][1], x[i][2])) + continue; + foriginal[0] += f[i][0]; + foriginal[1] += f[i][1]; + foriginal[2] += f[i][2]; + if (xstyle == ATOM) { + vest[i][0] = v[i][0] = sforce[i][0]; + f[i][0] = 0.0; + } else if (xstyle) { + vest[i][0] = v[i][0] = xvalue; + f[i][0] = 0.0; + } + + if (ystyle == ATOM) { + vest[i][1] = v[i][1] = sforce[i][1]; + f[i][1] = 0.0; + } else if (ystyle) { + vest[i][1] = v[i][1] = yvalue; + f[i][1] = 0.0; + } + + if (zstyle == ATOM) { + vest[i][2] = v[i][2] = sforce[i][2]; + f[i][2] = 0.0; + } else if (zstyle) { + vest[i][2] = v[i][2] = zvalue; + f[i][2] = 0.0; + } + + } + } +} + +/* ---------------------------------------------------------------------- + return components of total force on fix group before force was changed + ------------------------------------------------------------------------- */ + +double FixSMDSetVel::compute_vector(int n) { +// only sum across procs one time + + if (force_flag == 0) { + MPI_Allreduce(foriginal, foriginal_all, 3, MPI_DOUBLE, MPI_SUM, world); + force_flag = 1; + } + return foriginal_all[n]; +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array + ------------------------------------------------------------------------- */ + +double FixSMDSetVel::memory_usage() { + double bytes = 0.0; + if (varflag == ATOM) + bytes = atom->nmax * 3 * sizeof(double); + return bytes; +} diff --git a/src/USER-SMD/fix_smd_setvel.h b/src/USER-SMD/fix_smd_setvel.h new file mode 100644 index 0000000000..9e5fe642eb --- /dev/null +++ b/src/USER-SMD/fix_smd_setvel.h @@ -0,0 +1,95 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + +/* -*- c++ -*- ---------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(smd/setvelocity,FixSMDSetVel) + +#else + +#ifndef LMP_FIX_SMD_SET_VELOCITY_H +#define LMP_FIX_SMD_SET_VELOCITY_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixSMDSetVel : public Fix { + public: + FixSMDSetVel(class LAMMPS *, int, char **); + ~FixSMDSetVel(); + int setmask(); + void init(); + void setup(int); + void min_setup(int); + //void initial_integrate(int); + void post_force(int); + double compute_vector(int); + double memory_usage(); + + private: + double xvalue,yvalue,zvalue; + int varflag,iregion; + char *xstr,*ystr,*zstr; + char *idregion; + int xvar,yvar,zvar,xstyle,ystyle,zstyle; + double foriginal[3],foriginal_all[3]; + int force_flag; + int nlevels_respa; + + int maxatom; + double **sforce; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Region ID for fix setforce does not exist + +Self-explanatory. + +E: Variable name for fix setforce does not exist + +Self-explanatory. + +E: Variable for fix setforce is invalid style + +Only equal-style variables can be used. + +E: Cannot use non-zero forces in an energy minimization + +Fix setforce cannot be used in this manner. Use fix addforce +instead. + +*/ diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp new file mode 100644 index 0000000000..bbfd1ec22b --- /dev/null +++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp @@ -0,0 +1,613 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * This file is based on the FixShearHistory class. + * + * ----------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#include "lattice.h" +#include "mpi.h" +#include "string.h" +#include "stdio.h" +#include "fix_smd_tlsph_reference_configuration.h" +#include "atom.h" +#include "comm.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "force.h" +#include "pair.h" +#include "update.h" +#include "modify.h" +#include "memory.h" +#include "error.h" +#include "domain.h" +#include +#include "smd_kernels.h" +#include "smd_math.h" + +using namespace Eigen; +using namespace LAMMPS_NS; +using namespace FixConst; +using namespace SMD_Kernels; +using namespace std; +using namespace SMD_Math; +#define DELTA 16384 + +#define INSERT_PREDEFINED_CRACKS false + +/* ---------------------------------------------------------------------- */ + +FixSMD_TLSPH_ReferenceConfiguration::FixSMD_TLSPH_ReferenceConfiguration(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) { + + if (atom->map_style == 0) + error->all(FLERR, "Pair tlsph with partner list requires an atom map, see atom_modify"); + + maxpartner = 1; + npartner = NULL; + partner = NULL; + wfd_list = NULL; + wf_list = NULL; + energy_per_bond = NULL; + degradation_ij = NULL; + grow_arrays(atom->nmax); + atom->add_callback(0); + + // initialize npartner to 0 so neighbor list creation is OK the 1st time + int nlocal = atom->nlocal; + for (int i = 0; i < nlocal; i++) { + npartner[i] = 0; + } + + comm_forward = 14; + updateFlag = 1; +} + +/* ---------------------------------------------------------------------- */ + +FixSMD_TLSPH_ReferenceConfiguration::~FixSMD_TLSPH_ReferenceConfiguration() { + // unregister this fix so atom class doesn't invoke it any more + + atom->delete_callback(id, 0); +// delete locally stored arrays + + memory->destroy(npartner); + memory->destroy(partner); + memory->destroy(wfd_list); + memory->destroy(wf_list); + memory->destroy(degradation_ij); + memory->destroy(energy_per_bond); +} + +/* ---------------------------------------------------------------------- */ + +int FixSMD_TLSPH_ReferenceConfiguration::setmask() { + int mask = 0; + mask |= PRE_EXCHANGE; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixSMD_TLSPH_ReferenceConfiguration::init() { + if (atom->tag_enable == 0) + error->all(FLERR, "Pair style tlsph requires atoms have IDs"); +} + +/* ---------------------------------------------------------------------- */ + +void FixSMD_TLSPH_ReferenceConfiguration::pre_exchange() { + //return; + + //printf("in FixSMD_TLSPH_ReferenceConfiguration::pre_exchange()\n"); + double **defgrad = atom->smd_data_9; + double *radius = atom->radius; + double *rho = atom->rho; + double *vfrac = atom->vfrac; + double **x = atom->x; + double **x0 = atom->x0; + double *rmass = atom->rmass; + int nlocal = atom->nlocal; + int i, itmp; + int *mask = atom->mask; + if (igroup == atom->firstgroup) { + nlocal = atom->nfirst; + } + + int *updateFlag_ptr = (int *) force->pair->extract("smd/tlsph/updateFlag_ptr", itmp); + if (updateFlag_ptr == NULL) { + error->one(FLERR, + "fix FixSMD_TLSPH_ReferenceConfiguration failed to access updateFlag pointer. Check if a pair style exist which calculates this quantity."); + } + + int *nn = (int *) force->pair->extract("smd/tlsph/numNeighsRefConfig_ptr", itmp); + if (nn == NULL) { + error->all(FLERR, "FixSMDIntegrateTlsph::updateReferenceConfiguration() failed to access numNeighsRefConfig_ptr array"); + } + + // sum all update flag across processors + MPI_Allreduce(updateFlag_ptr, &updateFlag, 1, MPI_INT, MPI_MAX, world); + + if (updateFlag > 0) { + if (comm->me == 0) { + printf("**** updating ref config at step: %ld\n", update->ntimestep); + } + + for (i = 0; i < nlocal; i++) { + + if (mask[i] & groupbit) { + + // re-set x0 coordinates + x0[i][0] = x[i][0]; + x0[i][1] = x[i][1]; + x0[i][2] = x[i][2]; + + // re-set deformation gradient + defgrad[i][0] = 1.0; + defgrad[i][1] = 0.0; + defgrad[i][2] = 0.0; + defgrad[i][3] = 0.0; + defgrad[i][4] = 1.0; + defgrad[i][5] = 0.0; + defgrad[i][6] = 0.0; + defgrad[i][7] = 0.0; + defgrad[i][8] = 1.0; + /* + * Adjust particle volume as the reference configuration is changed. + * We safeguard against excessive deformations by limiting the adjustment range + * to the intervale J \in [0.9..1.1] + */ + vfrac[i] = rmass[i] / rho[i]; +// + if (nn[i] < 15) { + radius[i] *= 1.2; + } // else //{ + // radius[i] *= pow(J, 1.0 / domain->dimension); + //} + } + } + + // update of reference config could have changed x0, vfrac, radius + // communicate these quantities now to ghosts: x0, vfrac, radius + comm->forward_comm_fix(this); + + setup(0); + } +} + +/* ---------------------------------------------------------------------- + copy partner info from neighbor lists to atom arrays + so can be migrated or stored with atoms + ------------------------------------------------------------------------- */ + +void FixSMD_TLSPH_ReferenceConfiguration::setup(int vflag) { + int i, j, ii, jj, n, inum, jnum; + int *ilist, *jlist, *numneigh, **firstneigh; + int itype, jtype; + double r, h, wf, wfd; + Vector3d dx; + + if (updateFlag == 0) + return; + + int nlocal = atom->nlocal; + nmax = atom->nmax; + grow_arrays(nmax); + +// 1st loop over neighbor list +// calculate npartner for each owned atom +// nlocal_neigh = nlocal when neigh list was built, may be smaller than nlocal + + double **x0 = atom->x; + double *radius = atom->radius; + int *type = atom->type; + int *mask = atom->mask; + tagint *tag = atom->tag; + NeighList *list = pair->list; + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // zero npartner for all current atoms + for (i = 0; i < nlocal; i++) + npartner[i] = 0; + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + + if (INSERT_PREDEFINED_CRACKS) { + if (!crack_exclude(i, j)) + continue; + } + + dx(0) = x0[i][0] - x0[j][0]; + dx(1) = x0[i][1] - x0[j][1]; + dx(2) = x0[i][2] - x0[j][2]; + r = dx.norm(); + h = radius[i] + radius[j]; + + if (r <= h) { + npartner[i]++; + if (j < nlocal) { + npartner[j]++; + } + } + } + } + + maxpartner = 0; + for (i = 0; i < nlocal; i++) + maxpartner = MAX(maxpartner, npartner[i]); + int maxall; + MPI_Allreduce(&maxpartner, &maxall, 1, MPI_INT, MPI_MAX, world); + maxpartner = maxall; + + grow_arrays(nmax); + + for (i = 0; i < nlocal; i++) { + npartner[i] = 0; + for (jj = 0; jj < maxpartner; jj++) { + wfd_list[i][jj] = 0.0; + wf_list[i][jj] = 0.0; + degradation_ij[i][jj] = 0.0; + energy_per_bond[i][jj] = 0.0; + } + } + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + dx(0) = x0[i][0] - x0[j][0]; + dx(1) = x0[i][1] - x0[j][1]; + dx(2) = x0[i][2] - x0[j][2]; + r = dx.norm(); + jtype = type[j]; + h = radius[i] + radius[j]; + + if (INSERT_PREDEFINED_CRACKS) { + if (!crack_exclude(i, j)) + continue; + } + + if (r < h) { + spiky_kernel_and_derivative(h, r, domain->dimension, wf, wfd); + + partner[i][npartner[i]] = tag[j]; + wfd_list[i][npartner[i]] = wfd; + wf_list[i][npartner[i]] = wf; + npartner[i]++; + if (j < nlocal) { + partner[j][npartner[j]] = tag[i]; + wfd_list[j][npartner[j]] = wfd; + wf_list[j][npartner[j]] = wf; + npartner[j]++; + } + } + } + } + + // count number of particles for which this group is active + + // bond statistics + if (update->ntimestep > -1) { + n = 0; + int count = 0; + for (i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + n += npartner[i]; + count += 1; + } + } + int nall, countall; + MPI_Allreduce(&n, &nall, 1, MPI_INT, MPI_SUM, world); + MPI_Allreduce(&count, &countall, 1, MPI_INT, MPI_SUM, world); + + if (comm->me == 0) { + if (screen) { + printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n"); + fprintf(screen, "TLSPH neighbors:\n"); + fprintf(screen, " max # of neighbors for a single particle = %d\n", maxpartner); + fprintf(screen, " average # of neighbors/particle in group tlsph = %g\n", (double) nall / countall); + printf(">>========>>========>>========>>========>>========>>========>>========>>========\n\n"); + } + if (logfile) { + fprintf(logfile, "\nTLSPH neighbors:\n"); + fprintf(logfile, " max # of neighbors for a single particle = %d\n", maxpartner); + fprintf(logfile, " average # of neighbors/particle in group tlsph = %g\n", (double) nall / countall); + } + } + } + + updateFlag = 0; // set update flag to zero after the update + +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based arrays + ------------------------------------------------------------------------- */ + +double FixSMD_TLSPH_ReferenceConfiguration::memory_usage() { + int nmax = atom->nmax; + int bytes = nmax * sizeof(int); + bytes += nmax * maxpartner * sizeof(tagint); // partner array + bytes += nmax * maxpartner * sizeof(float); // wf_list + bytes += nmax * maxpartner * sizeof(float); // wfd_list + bytes += nmax * maxpartner * sizeof(float); // damage_per_interaction array + bytes += nmax * sizeof(int); // npartner array + return bytes; + +} + +/* ---------------------------------------------------------------------- + allocate local atom-based arrays + ------------------------------------------------------------------------- */ + +void FixSMD_TLSPH_ReferenceConfiguration::grow_arrays(int nmax) { + //printf("in FixSMD_TLSPH_ReferenceConfiguration::grow_arrays\n"); + memory->grow(npartner, nmax, "tlsph_refconfig_neigh:npartner"); + memory->grow(partner, nmax, maxpartner, "tlsph_refconfig_neigh:partner"); + memory->grow(wfd_list, nmax, maxpartner, "tlsph_refconfig_neigh:wfd"); + memory->grow(wf_list, nmax, maxpartner, "tlsph_refconfig_neigh:wf"); + memory->grow(degradation_ij, nmax, maxpartner, "tlsph_refconfig_neigh:degradation_ij"); + memory->grow(energy_per_bond, nmax, maxpartner, "tlsph_refconfig_neigh:damage_onset_strain"); +} + +/* ---------------------------------------------------------------------- + copy values within local atom-based arrays + ------------------------------------------------------------------------- */ + +void FixSMD_TLSPH_ReferenceConfiguration::copy_arrays(int i, int j, int delflag) { + npartner[j] = npartner[i]; + for (int m = 0; m < npartner[j]; m++) { + partner[j][m] = partner[i][m]; + wfd_list[j][m] = wfd_list[i][m]; + wf_list[j][m] = wf_list[i][m]; + degradation_ij[j][m] = degradation_ij[i][m]; + energy_per_bond[j][m] = energy_per_bond[i][m]; + } +} + +/* ---------------------------------------------------------------------- + pack values in local atom-based arrays for exchange with another proc + ------------------------------------------------------------------------- */ + +int FixSMD_TLSPH_ReferenceConfiguration::pack_exchange(int i, double *buf) { +// NOTE: how do I know comm buf is big enough if extreme # of touching neighs +// Comm::BUFEXTRA may need to be increased + +//printf("pack_exchange ...\n"); + + int m = 0; + buf[m++] = npartner[i]; + for (int n = 0; n < npartner[i]; n++) { + buf[m++] = partner[i][n]; + buf[m++] = wfd_list[i][n]; + buf[m++] = wf_list[i][n]; + buf[m++] = degradation_ij[i][n]; + buf[m++] = energy_per_bond[i][n]; + } + return m; + +} + +/* ---------------------------------------------------------------------- + unpack values in local atom-based arrays from exchange with another proc + ------------------------------------------------------------------------- */ + +int FixSMD_TLSPH_ReferenceConfiguration::unpack_exchange(int nlocal, double *buf) { + if (nlocal == nmax) { + //printf("nlocal=%d, nmax=%d\n", nlocal, nmax); + nmax = nmax / DELTA * DELTA; + nmax += DELTA; + grow_arrays(nmax); + + error->message(FLERR, + "in Fixtlsph_refconfigNeighGCG::unpack_exchange: local arrays too small for receiving partner information; growing arrays"); + } +//printf("nlocal=%d, nmax=%d\n", nlocal, nmax); + + int m = 0; + npartner[nlocal] = static_cast(buf[m++]); + for (int n = 0; n < npartner[nlocal]; n++) { + partner[nlocal][n] = static_cast(buf[m++]); + wfd_list[nlocal][n] = static_cast(buf[m++]); + wf_list[nlocal][n] = static_cast(buf[m++]); + degradation_ij[nlocal][n] = static_cast(buf[m++]); + energy_per_bond[nlocal][n] = static_cast(buf[m++]); + } + return m; +} + +/* ---------------------------------------------------------------------- + pack values in local atom-based arrays for restart file + ------------------------------------------------------------------------- */ + +int FixSMD_TLSPH_ReferenceConfiguration::pack_restart(int i, double *buf) { + int m = 0; + buf[m++] = 4 * npartner[i] + 2; + buf[m++] = npartner[i]; + for (int n = 0; n < npartner[i]; n++) { + buf[m++] = partner[i][n]; + buf[m++] = wfd_list[i][n]; + buf[m++] = wf_list[i][n]; + buf[m++] = degradation_ij[i][n]; + buf[m++] = energy_per_bond[i][n]; + } + return m; +} + +/* ---------------------------------------------------------------------- + unpack values from atom->extra array to restart the fix + ------------------------------------------------------------------------- */ + +void FixSMD_TLSPH_ReferenceConfiguration::unpack_restart(int nlocal, int nth) { +// ipage = NULL if being called from granular pair style init() + +// skip to Nth set of extra values + +// double **extra = atom->extra; +// +// int m = 0; +// for (int i = 0; i < nth; i++) +// m += static_cast(extra[nlocal][m]); +// m++; +// +// // allocate new chunks from ipage,dpage for incoming values +// +// npartner[nlocal] = static_cast(extra[nlocal][m++]); +// for (int n = 0; n < npartner[nlocal]; n++) { +// partner[nlocal][n] = static_cast(extra[nlocal][m++]); +// } +} + +/* ---------------------------------------------------------------------- + maxsize of any atom's restart data + ------------------------------------------------------------------------- */ + +int FixSMD_TLSPH_ReferenceConfiguration::maxsize_restart() { +// maxtouch_all = max # of touching partners across all procs + + int maxtouch_all; + MPI_Allreduce(&maxpartner, &maxtouch_all, 1, MPI_INT, MPI_MAX, world); + return 4 * maxtouch_all + 2; +} + +/* ---------------------------------------------------------------------- + size of atom nlocal's restart data + ------------------------------------------------------------------------- */ + +int FixSMD_TLSPH_ReferenceConfiguration::size_restart(int nlocal) { + return 4 * npartner[nlocal] + 2; +} + +/* ---------------------------------------------------------------------- */ + +int FixSMD_TLSPH_ReferenceConfiguration::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) { + int i, j, m; + double *radius = atom->radius; + double *vfrac = atom->vfrac; + double **x0 = atom->x0; + double **defgrad0 = atom->smd_data_9; + + //printf("FixSMD_TLSPH_ReferenceConfiguration:::pack_forward_comm\n"); + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x0[j][0]; + buf[m++] = x0[j][1]; + buf[m++] = x0[j][2]; + + buf[m++] = vfrac[j]; + buf[m++] = radius[j]; + + buf[m++] = defgrad0[i][0]; + buf[m++] = defgrad0[i][1]; + buf[m++] = defgrad0[i][2]; + buf[m++] = defgrad0[i][3]; + buf[m++] = defgrad0[i][4]; + buf[m++] = defgrad0[i][5]; + buf[m++] = defgrad0[i][6]; + buf[m++] = defgrad0[i][7]; + buf[m++] = defgrad0[i][8]; + + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void FixSMD_TLSPH_ReferenceConfiguration::unpack_forward_comm(int n, int first, double *buf) { + int i, m, last; + double *radius = atom->radius; + double *vfrac = atom->vfrac; + double **x0 = atom->x0; + double **defgrad0 = atom->smd_data_9; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + x0[i][0] = buf[m++]; + x0[i][1] = buf[m++]; + x0[i][2] = buf[m++]; + + vfrac[i] = buf[m++]; + radius[i] = buf[m++]; + + defgrad0[i][0] = buf[m++]; + defgrad0[i][1] = buf[m++]; + defgrad0[i][2] = buf[m++]; + defgrad0[i][3] = buf[m++]; + defgrad0[i][4] = buf[m++]; + defgrad0[i][5] = buf[m++]; + defgrad0[i][6] = buf[m++]; + defgrad0[i][7] = buf[m++]; + defgrad0[i][8] = buf[m++]; + } +} + +/* ---------------------------------------------------------------------- + routine for excluding bonds across a hardcoded slit crack + Note that everything is scaled by lattice constant l0 to avoid + numerical inaccuracies. + ------------------------------------------------------------------------- */ + +bool FixSMD_TLSPH_ReferenceConfiguration::crack_exclude(int i, int j) { + + double **x = atom->x; + double l0 = domain->lattice->xlattice; + + // line between pair of atoms i,j + double x1 = x[i][0] / l0; + double y1 = x[i][1] / l0; + + double x2 = x[j][0] / l0; + double y2 = x[j][1] / l0; + + // hardcoded crack line + double x3 = -0.1 / l0; + double y3 = ((int) 1.0 / l0) + 0.5; + //printf("y3 = %f\n", y3); + double x4 = 0.1 / l0 - 1.0 + 0.1; + double y4 = y3; + + bool retVal = DoLineSegmentsIntersect(x1, y1, x2, y2, x3, y3, x4, y4); + + return !retVal; + //return 1; +} + diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.h b/src/USER-SMD/fix_smd_tlsph_reference_configuration.h new file mode 100644 index 0000000000..ede06151ee --- /dev/null +++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.h @@ -0,0 +1,86 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * This file is based on the FixShearHistory class. + * + * ----------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + + +#ifdef FIX_CLASS + +FixStyle(SMD_TLSPH_NEIGHBORS,FixSMD_TLSPH_ReferenceConfiguration) + +#else + +#ifndef LMP_FIX_SMD_TLSPH_REFERENCE_H +#define LMP_FIX_SMD_TLSPH_REFERENCE_H + +#include "fix.h" +#include "my_page.h" + +namespace LAMMPS_NS { + +class FixSMD_TLSPH_ReferenceConfiguration: public Fix { + friend class Neighbor; + friend class PairTlsph; + +public: + FixSMD_TLSPH_ReferenceConfiguration(class LAMMPS *, int, char **); + ~FixSMD_TLSPH_ReferenceConfiguration(); + int setmask(); + void init(); + void setup(int); + void pre_exchange(); + int pack_forward_comm(int, int *, double *, int, int *); + void unpack_forward_comm(int, int, double *); + + double memory_usage(); + void grow_arrays(int); + void copy_arrays(int, int, int); + int pack_exchange(int, double *); + int unpack_exchange(int, double *); + int pack_restart(int, double *); + void unpack_restart(int, int); + int size_restart(int); + int maxsize_restart(); + + bool crack_exclude(int i, int j); + bool get_line_intersection(int i, int j); + +protected: + int updateFlag; // flag to update reference configuration + int nmax; + int maxpartner; + int *npartner; // # of touching partners of each atom + tagint **partner; // global atom IDs for the partners + float **wfd_list, **wf_list, **energy_per_bond; + float **degradation_ij; // per-pair interaction degradation status + + class Pair *pair; + +}; + +} + +#endif +#endif + diff --git a/src/USER-SMD/fix_smd_wall_surface.cpp b/src/USER-SMD/fix_smd_wall_surface.cpp new file mode 100644 index 0000000000..16bd1c7809 --- /dev/null +++ b/src/USER-SMD/fix_smd_wall_surface.cpp @@ -0,0 +1,507 @@ +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Mike Parks (SNL), Ezwanur Rahman, J.T. Foster (UTSA) + ------------------------------------------------------------------------- */ + +#include "math.h" +#include "fix_smd_wall_surface.h" +#include "atom.h" +#include "domain.h" +#include "force.h" +#include "comm.h" +#include "update.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "pair.h" +#include "lattice.h" +#include "memory.h" +#include "error.h" +#include +#include +#include +#include "atom_vec.h" + +using namespace LAMMPS_NS; +using namespace FixConst; +using namespace Eigen; +using namespace std; +#define DELTA 16384 +#define EPSILON 1.0e-6 +enum { + LAYOUT_UNIFORM, LAYOUT_NONUNIFORM, LAYOUT_TILED +}; +// several files + +/* ---------------------------------------------------------------------- */ + +FixSMDWallSurface::FixSMDWallSurface(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) { + + restart_global = 0; + restart_peratom = 0; + first = 1; + + //atom->add_callback(0); + //atom->add_callback(1); + + if (narg != 6) + error->all(FLERR, "Illegal number of arguments for fix smd/wall_surface"); + + filename.assign(arg[3]); + wall_particle_type = force->inumeric(FLERR, arg[4]); + wall_molecule_id = force->inumeric(FLERR, arg[5]); + if (wall_molecule_id < 65535) { + error->one(FLERR, "wall molcule id must be >= 65535\n"); + } + + if (comm->me == 0) { + printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n"); + printf("fix smd/wall_surface reads trianglulated surface from file: %s\n", filename.c_str()); + printf("fix smd/wall_surface has particle type %d \n", wall_particle_type); + printf("fix smd/wall_surface has molecule id %d \n", wall_molecule_id); + printf(">>========>>========>>========>>========>>========>>========>>========>>========\n"); + } +} + +/* ---------------------------------------------------------------------- */ + +FixSMDWallSurface::~FixSMDWallSurface() { + // unregister this fix so atom class doesn't invoke it any more + + //atom->delete_callback(id, 0); + //atom->delete_callback(id, 1); +} + +/* ---------------------------------------------------------------------- */ + +int FixSMDWallSurface::setmask() { + int mask = 0; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixSMDWallSurface::init() { + if (!first) + return; +} + +/* ---------------------------------------------------------------------- + For minimization: setup as with dynamics + ------------------------------------------------------------------------- */ + +void FixSMDWallSurface::min_setup(int vflag) { + setup(vflag); +} + +/* ---------------------------------------------------------------------- + create initial list of neighbor partners via call to neighbor->build() + must be done in setup (not init) since fix init comes before neigh init + ------------------------------------------------------------------------- */ + +void FixSMDWallSurface::setup(int vflag) { + + if (!first) + return; + first = 0; + + // set bounds for my proc + // if periodic and I am lo/hi proc, adjust bounds by EPSILON + // insures all data atoms will be owned even with round-off + + int triclinic = domain->triclinic; + + double epsilon[3]; + if (triclinic) + epsilon[0] = epsilon[1] = epsilon[2] = EPSILON; + else { + epsilon[0] = domain->prd[0] * EPSILON; + epsilon[1] = domain->prd[1] * EPSILON; + epsilon[2] = domain->prd[2] * EPSILON; + } + + if (triclinic == 0) { + sublo[0] = domain->sublo[0]; + subhi[0] = domain->subhi[0]; + sublo[1] = domain->sublo[1]; + subhi[1] = domain->subhi[1]; + sublo[2] = domain->sublo[2]; + subhi[2] = domain->subhi[2]; + } else { + sublo[0] = domain->sublo_lamda[0]; + subhi[0] = domain->subhi_lamda[0]; + sublo[1] = domain->sublo_lamda[1]; + subhi[1] = domain->subhi_lamda[1]; + sublo[2] = domain->sublo_lamda[2]; + subhi[2] = domain->subhi_lamda[2]; + } + + if (comm->layout != LAYOUT_TILED) { + if (domain->xperiodic) { + if (comm->myloc[0] == 0) + sublo[0] -= epsilon[0]; + if (comm->myloc[0] == comm->procgrid[0] - 1) + subhi[0] += epsilon[0]; + } + if (domain->yperiodic) { + if (comm->myloc[1] == 0) + sublo[1] -= epsilon[1]; + if (comm->myloc[1] == comm->procgrid[1] - 1) + subhi[1] += epsilon[1]; + } + if (domain->zperiodic) { + if (comm->myloc[2] == 0) + sublo[2] -= epsilon[2]; + if (comm->myloc[2] == comm->procgrid[2] - 1) + subhi[2] += epsilon[2]; + } + + } else { + if (domain->xperiodic) { + if (comm->mysplit[0][0] == 0.0) + sublo[0] -= epsilon[0]; + if (comm->mysplit[0][1] == 1.0) + subhi[0] += epsilon[0]; + } + if (domain->yperiodic) { + if (comm->mysplit[1][0] == 0.0) + sublo[1] -= epsilon[1]; + if (comm->mysplit[1][1] == 1.0) + subhi[1] += epsilon[1]; + } + if (domain->zperiodic) { + if (comm->mysplit[2][0] == 0.0) + sublo[2] -= epsilon[2]; + if (comm->mysplit[2][1] == 1.0) + subhi[2] += epsilon[2]; + } + } + + read_triangles(0); +} + +/* ---------------------------------------------------------------------- + function to determine number of values in a text line + ------------------------------------------------------------------------- */ + +int FixSMDWallSurface::count_words(const char *line) { + int n = strlen(line) + 1; + char *copy; + memory->create(copy, n, "atom:copy"); + strcpy(copy, line); + + char *ptr; + if ((ptr = strchr(copy, '#'))) + *ptr = '\0'; + + if (strtok(copy, " \t\n\r\f") == NULL) { + memory->destroy(copy); + return 0; + } + n = 1; + while (strtok(NULL, " \t\n\r\f")) + n++; + + memory->destroy(copy); + return n; +} + +/* ---------------------------------------------------------------------- + size of atom nlocal's restart data + ------------------------------------------------------------------------- */ + +void FixSMDWallSurface::read_triangles(int pass) { + + double coord[3]; + + int nlocal_previous = atom->nlocal; + int ilocal = nlocal_previous; + int m; + int me; + + bigint natoms_previous = atom->natoms; + Vector3d *vert; + vert = new Vector3d[3]; + Vector3d normal, center; + + FILE *fp = fopen(filename.c_str(), "r"); + if (fp == NULL) { + char str[128]; + sprintf(str, "Cannot open file %s", filename.c_str()); + error->one(FLERR, str); + } + + MPI_Comm_rank(world, &me); + if (me == 0) { + if (screen) { + if (pass == 0) { + printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n"); + fprintf(screen, " scanning triangle pairs ...\n"); + } else { + fprintf(screen, " reading triangle pairs ...\n"); + } + } + if (logfile) { + if (pass == 0) { + fprintf(logfile, " scanning triangle pairs ...\n"); + } else { + fprintf(logfile, " reading triangle pairs ...\n"); + } + } + } + + char str[128]; + char line[256]; + char *retpointer; + char **values; + int nwords; + + // read STL solid name + retpointer = fgets(line, sizeof(line), fp); + if (retpointer == NULL) { + sprintf(str, "error reading number of triangle pairs"); + error->one(FLERR, str); + } + + nwords = count_words(line); + if (nwords < 1) { + sprintf(str, "first line of file is incorrect"); + error->one(FLERR, str); + } + +// values = new char*[nwords]; +// values[0] = strtok(line, " \t\n\r\f"); +// if (values[0] == NULL) +// error->all(FLERR, "Incorrect atom format in data file"); +// for (m = 1; m < nwords; m++) { +// values[m] = strtok(NULL, " \t\n\r\f"); +// if (values[m] == NULL) +// error->all(FLERR, "Incorrect atom format in data file"); +// } +// delete[] values; +// +// if (comm->me == 0) { +// cout << "STL file contains solid body with name: " << values[1] << endl; +// } + + // iterate over STL facets util end of body is reached + + while (fgets(line, sizeof(line), fp)) { // read a line, should be the facet line + + // evaluate facet line + nwords = count_words(line); + if (nwords != 5) { + //sprintf(str, "found end solid line"); + //error->message(FLERR, str); + break; + } else { + // should be facet line + } + + values = new char*[nwords]; + values[0] = strtok(line, " \t\n\r\f"); + if (values[0] == NULL) + error->all(FLERR, "Incorrect atom format in data file"); + for (m = 1; m < nwords; m++) { + values[m] = strtok(NULL, " \t\n\r\f"); + if (values[m] == NULL) + error->all(FLERR, "Incorrect atom format in data file"); + } + + normal << force->numeric(FLERR, values[2]), force->numeric(FLERR, values[3]), force->numeric(FLERR, values[4]); + //cout << "normal is " << normal << endl; + + delete[] values; + + // read outer loop line + retpointer = fgets(line, sizeof(line), fp); + if (retpointer == NULL) { + sprintf(str, "error reading outer loop"); + error->one(FLERR, str); + } + + nwords = count_words(line); + if (nwords != 2) { + sprintf(str, "error reading outer loop"); + error->one(FLERR, str); + } + + // read vertex lines + + for (int k = 0; k < 3; k++) { + retpointer = fgets(line, sizeof(line), fp); + if (retpointer == NULL) { + sprintf(str, "error reading vertex line"); + error->one(FLERR, str); + } + + nwords = count_words(line); + if (nwords != 4) { + sprintf(str, "error reading vertex line"); + error->one(FLERR, str); + } + + values = new char*[nwords]; + values[0] = strtok(line, " \t\n\r\f"); + if (values[0] == NULL) + error->all(FLERR, "Incorrect vertex line"); + for (m = 1; m < nwords; m++) { + values[m] = strtok(NULL, " \t\n\r\f"); + if (values[m] == NULL) + error->all(FLERR, "Incorrect vertex line"); + } + + vert[k] << force->numeric(FLERR, values[1]), force->numeric(FLERR, values[2]), force->numeric(FLERR, values[3]); + //cout << "vertex is " << vert[k] << endl; + //printf("%s %s %s\n", values[1], values[2], values[3]); + delete[] values; + //exit(1); + + } + + // read end loop line + retpointer = fgets(line, sizeof(line), fp); + if (retpointer == NULL) { + sprintf(str, "error reading endloop"); + error->one(FLERR, str); + } + + nwords = count_words(line); + if (nwords != 1) { + sprintf(str, "error reading endloop"); + error->one(FLERR, str); + } + + // read end facet line + retpointer = fgets(line, sizeof(line), fp); + if (retpointer == NULL) { + sprintf(str, "error reading endfacet"); + error->one(FLERR, str); + } + + nwords = count_words(line); + if (nwords != 1) { + sprintf(str, "error reading endfacet"); + error->one(FLERR, str); + } + + // now we have a normal and three vertices ... proceed with adding triangle + + center = (vert[0] + vert[1] + vert[2]) / 3.0; + + // cout << "center is " << center << endl; + + double r1 = (center - vert[0]).norm(); + double r2 = (center - vert[1]).norm(); + double r3 = (center - vert[2]).norm(); + double r = MAX(r1, r2); + r = MAX(r, r3); + + /* + * if atom/molecule is in my subbox, create it + * ... use x0 to hold triangle normal. + * ... use smd_data_9 to hold the three vertices + * ... use x to hold triangle center + * ... radius is the mmaximal distance from triangle center to all vertices + */ + + // printf("coord: %f %f %f\n", coord[0], coord[1], coord[2]); + // printf("sublo: %f %f %f\n", sublo[0], sublo[1], sublo[2]); + // printf("subhi: %f %f %f\n", subhi[0], subhi[1], subhi[2]); + //printf("ilocal = %d\n", ilocal); + if (center(0) >= sublo[0] && center(0) < subhi[0] && center(1) >= sublo[1] && center(1) < subhi[1] && center(2) >= sublo[2] + && center(2) < subhi[2]) { + //printf("******* KERATIN nlocal=%d ***\n", nlocal); + coord[0] = center(0); + coord[1] = center(1); + coord[2] = center(2); + atom->avec->create_atom(wall_particle_type, coord); + + /* + * need to initialize pointers to atom vec arrays here, because they could have changed + * due to calling grow() in create_atoms() above; + */ + + int *mol = atom->molecule; + int *type = atom->type; + double *radius = atom->radius; + double *contact_radius = atom->contact_radius; + double **smd_data_9 = atom->smd_data_9; + double **x0 = atom->x0; + + radius[ilocal] = r; //ilocal; + contact_radius[ilocal] = r; //ilocal; + mol[ilocal] = wall_molecule_id; + type[ilocal] = wall_particle_type; + x0[ilocal][0] = normal(0); + x0[ilocal][1] = normal(1); + x0[ilocal][2] = normal(2); + smd_data_9[ilocal][0] = vert[0](0); + smd_data_9[ilocal][1] = vert[0](1); + smd_data_9[ilocal][2] = vert[0](2); + smd_data_9[ilocal][3] = vert[1](0); + smd_data_9[ilocal][4] = vert[1](1); + smd_data_9[ilocal][5] = vert[1](2); + smd_data_9[ilocal][6] = vert[2](0); + smd_data_9[ilocal][7] = vert[2](1); + smd_data_9[ilocal][8] = vert[2](2); + + ilocal++; + } + + } + +// set new total # of atoms and error check + + bigint nblocal = atom->nlocal; + MPI_Allreduce(&nblocal, &atom->natoms, 1, MPI_LMP_BIGINT, MPI_SUM, world); + if (atom->natoms < 0 || atom->natoms >= MAXBIGINT) + error->all(FLERR, "Too many total atoms"); + +// add IDs for newly created atoms +// check that atom IDs are valid + + if (atom->tag_enable) + atom->tag_extend(); + atom->tag_check(); + +// create global mapping of atoms +// zero nghost in case are adding new atoms to existing atoms + + if (atom->map_style) { + atom->nghost = 0; + atom->map_init(); + atom->map_set(); + } + +// print status + if (comm->me == 0) { + if (screen) { + printf("... fix smd/wall_surface finished reading triangulated surface\n"); + fprintf(screen, "fix smd/wall_surface created " BIGINT_FORMAT " atoms\n", atom->natoms - natoms_previous); + printf(">>========>>========>>========>>========>>========>>========>>========>>========\n"); + } + if (logfile) { + fprintf(logfile, "... fix smd/wall_surface finished reading triangulated surface\n"); + fprintf(logfile, "fix smd/wall_surface created " BIGINT_FORMAT " atoms\n", atom->natoms - natoms_previous); + fprintf(logfile, ">>========>>========>>========>>========>>========>>========>>========>>========\n"); + } + } + + delete[] vert; + fclose(fp); +} + diff --git a/src/USER-SMD/fix_smd_wall_surface.h b/src/USER-SMD/fix_smd_wall_surface.h new file mode 100644 index 0000000000..32fb934d63 --- /dev/null +++ b/src/USER-SMD/fix_smd_wall_surface.h @@ -0,0 +1,53 @@ +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(smd/wall_surface,FixSMDWallSurface) + +#else + +#ifndef LMP_FIX_SMD_WALL_SURFACE_H +#define LMP_FIX_SMD_WALL_SURFACE_H + +#include "fix.h" +#include +using namespace std; + +namespace LAMMPS_NS { + +class FixSMDWallSurface: public Fix { + +public: + FixSMDWallSurface(class LAMMPS *, int, char **); + virtual ~FixSMDWallSurface(); + int setmask(); + void init(); + void setup(int); + void min_setup(int); + + int count_words(const char *line); + void read_triangles(int pass); + +private: + int first; // flag for first time initialization + double sublo[3], subhi[3]; // epsilon-extended proc sub-box for adding atoms; + std::string filename; + int wall_particle_type; + int wall_molecule_id; +}; +} + +#endif +#endif + diff --git a/src/USER-SMD/pair_smd_hertz.cpp b/src/USER-SMD/pair_smd_hertz.cpp new file mode 100644 index 0000000000..b39ea946c0 --- /dev/null +++ b/src/USER-SMD/pair_smd_hertz.cpp @@ -0,0 +1,385 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Mike Parks (SNL) + ------------------------------------------------------------------------- */ + +#include "math.h" +#include "float.h" +#include "stdlib.h" +#include "string.h" +#include "pair_smd_hertz.h" +#include "atom.h" +#include "domain.h" +#include "force.h" +#include "update.h" +#include "modify.h" +#include "fix.h" +#include "comm.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +#define SQRT2 1.414213562e0 + +/* ---------------------------------------------------------------------- */ + +PairHertz::PairHertz(LAMMPS *lmp) : + Pair(lmp) { + + onerad_dynamic = onerad_frozen = maxrad_dynamic = maxrad_frozen = NULL; + bulkmodulus = NULL; + kn = NULL; + scale = 1.0; +} + +/* ---------------------------------------------------------------------- */ + +PairHertz::~PairHertz() { + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + memory->destroy(bulkmodulus); + memory->destroy(kn); + + delete[] onerad_dynamic; + delete[] onerad_frozen; + delete[] maxrad_dynamic; + delete[] maxrad_frozen; + } +} + +/* ---------------------------------------------------------------------- */ + +void PairHertz::compute(int eflag, int vflag) { + int i, j, ii, jj, inum, jnum, itype, jtype; + double xtmp, ytmp, ztmp, delx, dely, delz; + double rsq, r, evdwl, fpair; + int *ilist, *jlist, *numneigh, **firstneigh; + double rcut, r_geom, delta, ri, rj, dt_crit; + double *rmass = atom->rmass; + + evdwl = 0.0; + if (eflag || vflag) + ev_setup(eflag, vflag); + else + evflag = vflag_fdotr = 0; + + double **f = atom->f; + double **x = atom->x; + double **x0 = atom->x0; + int *type = atom->type; + int nlocal = atom->nlocal; + double *radius = atom->contact_radius; + double *sph_radius = atom->radius; + double rcutSq; + double delx0, dely0, delz0, rSq0, sphCut; + + int newton_pair = force->newton_pair; + int periodic = (domain->xperiodic || domain->yperiodic || domain->zperiodic); + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + stable_time_increment = 1.0e22; + + // loop over neighbors of my atoms + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + ri = scale * radius[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + jtype = type[j]; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + + rsq = delx * delx + dely * dely + delz * delz; + + rj = scale * radius[j]; + rcut = ri + rj; + rcutSq = rcut * rcut; + + if (rsq < rcutSq) { + + /* + * self contact option: + * if pair of particles was initially close enough to interact via a bulk continuum mechanism (e.g. SPH), exclude pair from contact forces. + * this approach should work well if no updates of the reference configuration are performed. + */ + + if (itype == jtype) { + delx0 = x0[j][0] - x0[i][0]; + dely0 = x0[j][1] - x0[i][1]; + delz0 = x0[j][2] - x0[i][2]; + if (periodic) { + domain->minimum_image(delx0, dely0, delz0); + } + rSq0 = delx0 * delx0 + dely0 * dely0 + delz0 * delz0; // initial distance + sphCut = sph_radius[i] + sph_radius[j]; + if (rSq0 < sphCut * sphCut) { + rcut = 0.5 * rcut; + rcutSq = rcut * rcut; + if (rsq > rcutSq) { + continue; + } + } + } + + r = sqrt(rsq); + //printf("hertz interaction, r=%f, cut=%f, h=%f\n", r, rcut, sqrt(rSq0)); + + // Hertzian short-range forces + delta = rcut - r; // overlap distance + r_geom = ri * rj / rcut; + //assuming poisson ratio = 1/4 for 3d + fpair = 1.066666667e0 * bulkmodulus[itype][jtype] * delta * sqrt(delta * r_geom); // units: N + evdwl = fpair * 0.4e0 * delta; // GCG 25 April: this expression conserves total energy + dt_crit = 3.14 * sqrt(0.5 * (rmass[i] + rmass[j]) / (fpair / delta)); + + stable_time_increment = MIN(stable_time_increment, dt_crit); + if (r > 2.0e-16) { + fpair /= r; // divide by r and multiply with non-normalized distance vector + } else { + fpair = 0.0; + } + + /* + * contact viscosity -- needs to be done, see GRANULAR package for normal & shear damping + * for now: no damping and thus no viscous energy deltaE + */ + + if (evflag) { + ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, delx, dely, delz); + } + + f[i][0] += delx * fpair; + f[i][1] += dely * fpair; + f[i][2] += delz * fpair; + + if (newton_pair || j < nlocal) { + f[j][0] -= delx * fpair; + f[j][1] -= dely * fpair; + f[j][2] -= delz * fpair; + } + + } + } + } + +// double stable_time_increment_all = 0.0; +// MPI_Allreduce(&stable_time_increment, &stable_time_increment_all, 1, MPI_DOUBLE, MPI_MIN, world); +// if (comm->me == 0) { +// printf("stable time step for pair smd/hertz is %f\n", stable_time_increment_all); +// } +} + +/* ---------------------------------------------------------------------- + allocate all arrays + ------------------------------------------------------------------------- */ + +void PairHertz::allocate() { + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag, n + 1, n + 1, "pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(bulkmodulus, n + 1, n + 1, "pair:kspring"); + memory->create(kn, n + 1, n + 1, "pair:kn"); + + memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); // always needs to be allocated, even with granular neighborlist + + onerad_dynamic = new double[n + 1]; + onerad_frozen = new double[n + 1]; + maxrad_dynamic = new double[n + 1]; + maxrad_frozen = new double[n + 1]; +} + +/* ---------------------------------------------------------------------- + global settings + ------------------------------------------------------------------------- */ + +void PairHertz::settings(int narg, char **arg) { + if (narg != 1) + error->all(FLERR, "Illegal number of args for pair_style hertz"); + + scale = force->numeric(FLERR, arg[0]); + if (comm->me == 0) { + printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n"); + printf("SMD/HERTZ CONTACT SETTINGS:\n"); + printf("... effective contact radius is scaled by %f\n", scale); + printf(">>========>>========>>========>>========>>========>>========>>========>>========\n"); + } + +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs + ------------------------------------------------------------------------- */ + +void PairHertz::coeff(int narg, char **arg) { + if (narg != 3) + error->all(FLERR, "Incorrect args for pair coefficients"); + if (!allocated) + allocate(); + + int ilo, ihi, jlo, jhi; + force->bounds(arg[0], atom->ntypes, ilo, ihi); + force->bounds(arg[1], atom->ntypes, jlo, jhi); + + double bulkmodulus_one = atof(arg[2]); + + // set short-range force constant + double kn_one = 0.0; + if (domain->dimension == 3) { + kn_one = (16. / 15.) * bulkmodulus_one; //assuming poisson ratio = 1/4 for 3d + } else { + kn_one = 0.251856195 * (2. / 3.) * bulkmodulus_one; //assuming poisson ratio = 1/3 for 2d + } + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo, i); j <= jhi; j++) { + bulkmodulus[i][j] = bulkmodulus_one; + kn[i][j] = kn_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) + error->all(FLERR, "Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i + ------------------------------------------------------------------------- */ + +double PairHertz::init_one(int i, int j) { + + if (!allocated) + allocate(); + + if (setflag[i][j] == 0) + error->all(FLERR, "All pair coeffs are not set"); + + bulkmodulus[j][i] = bulkmodulus[i][j]; + kn[j][i] = kn[i][j]; + + // cutoff = sum of max I,J radii for + // dynamic/dynamic & dynamic/frozen interactions, but not frozen/frozen + + double cutoff = maxrad_dynamic[i] + maxrad_dynamic[j]; + cutoff = MAX(cutoff, maxrad_frozen[i] + maxrad_dynamic[j]); + cutoff = MAX(cutoff, maxrad_dynamic[i] + maxrad_frozen[j]); + + if (comm->me == 0) { + printf("cutoff for pair smd/hertz = %f\n", cutoff); + } + return cutoff; +} + +/* ---------------------------------------------------------------------- + init specific to this pair style + ------------------------------------------------------------------------- */ + +void PairHertz::init_style() { + int i; + + // error checks + + if (!atom->contact_radius_flag) + error->all(FLERR, "Pair style smd/hertz requires atom style with contact_radius"); + + int irequest = neighbor->request(this); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->gran = 1; + + // set maxrad_dynamic and maxrad_frozen for each type + // include future Fix pour particles as dynamic + + for (i = 1; i <= atom->ntypes; i++) + onerad_dynamic[i] = onerad_frozen[i] = 0.0; + + double *radius = atom->radius; + int *type = atom->type; + int nlocal = atom->nlocal; + + for (i = 0; i < nlocal; i++) { + onerad_dynamic[type[i]] = MAX(onerad_dynamic[type[i]], radius[i]); + } + + MPI_Allreduce(&onerad_dynamic[1], &maxrad_dynamic[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world); + MPI_Allreduce(&onerad_frozen[1], &maxrad_frozen[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world); +} + +/* ---------------------------------------------------------------------- + neighbor callback to inform pair style of neighbor list to use + optional granular history list + ------------------------------------------------------------------------- */ + +void PairHertz::init_list(int id, NeighList *ptr) { + if (id == 0) + list = ptr; +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based arrays + ------------------------------------------------------------------------- */ + +double PairHertz::memory_usage() { + + return 0.0; +} + +void *PairHertz::extract(const char *str, int &i) { + //printf("in PairTriSurf::extract\n"); + if (strcmp(str, "smd/hertz/stable_time_increment_ptr") == 0) { + return (void *) &stable_time_increment; + } + + return NULL; + +} diff --git a/src/USER-SMD/pair_smd_hertz.h b/src/USER-SMD/pair_smd_hertz.h new file mode 100644 index 0000000000..8a207709ad --- /dev/null +++ b/src/USER-SMD/pair_smd_hertz.h @@ -0,0 +1,69 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(smd/hertz,PairHertz) + +#else + +#ifndef LMP_SMD_HERTZ_H +#define LMP_SMD_HERTZ_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairHertz : public Pair { + public: + PairHertz(class LAMMPS *); + virtual ~PairHertz(); + virtual void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + double init_one(int, int); + void init_style(); + void init_list(int, class NeighList *); + virtual double memory_usage(); + void *extract(const char *, int &); + + protected: + double **bulkmodulus; + double **kn; + + double *onerad_dynamic,*onerad_frozen; + double *maxrad_dynamic,*maxrad_frozen; + + double scale; + double stable_time_increment; // stable time step size + + void allocate(); +}; + +} + +#endif +#endif + diff --git a/src/USER-SMD/pair_smd_tlsph.cpp b/src/USER-SMD/pair_smd_tlsph.cpp new file mode 100644 index 0000000000..73adf2ed31 --- /dev/null +++ b/src/USER-SMD/pair_smd_tlsph.cpp @@ -0,0 +1,2165 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#include "group.h" +#include "math.h" +#include "float.h" +#include "stdlib.h" +#include "string.h" +#include "pair_smd_tlsph.h" +#include "fix_smd_tlsph_reference_configuration.h" +#include "atom.h" +#include "domain.h" +#include "force.h" +#include "update.h" +#include "modify.h" +#include "fix.h" +#include "comm.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "memory.h" +#include "error.h" +#include +#include +#include "math_special.h" +#include +#include "update.h" +#include +#include +#include "smd_material_models.h" +#include "smd_kernels.h" +#include "smd_math.h" +using namespace SMD_Kernels; +using namespace Eigen; +using namespace std; +using namespace LAMMPS_NS; +using namespace SMD_Math; + +#define JAUMANN false +#define DETF_MIN 0.2 // maximum compression deformation allow +#define DETF_MAX 2.0 // maximum tension deformation allowed +#define TLSPH_DEBUG 0 +#define PLASTIC_STRAIN_AVERAGE_WINDOW 100.0 + +/* ---------------------------------------------------------------------- */ + +PairTlsph::PairTlsph(LAMMPS *lmp) : + Pair(lmp) { + + onerad_dynamic = onerad_frozen = maxrad_dynamic = maxrad_frozen = NULL; + + failureModel = NULL; + strengthModel = eos = NULL; + + nmax = 0; // make sure no atom on this proc such that initial memory allocation is correct + Fdot = Fincr = K = PK1 = NULL; + R = FincrInv = W = D = NULL; + detF = NULL; + smoothVelDifference = NULL; + numNeighsRefConfig = NULL; + CauchyStress = NULL; + hourglass_error = NULL; + Lookup = NULL; + particle_dt = NULL; + + updateFlag = 0; + first = true; + dtCFL = 0.0; // initialize dtCFL so it is set to safe value if extracted on zero-th timestep + + comm_forward = 22; // this pair style communicates 20 doubles to ghost atoms : PK1 tensor + F tensor + shepardWeight + fix_tlsph_reference_configuration = NULL; + + cut_comm = MAX(neighbor->cutneighmax, comm->cutghostuser); // cutoff radius within which ghost atoms are communicated. +} + +/* ---------------------------------------------------------------------- */ + +PairTlsph::~PairTlsph() { + //printf("in PairTlsph::~PairTlsph()\n"); + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + memory->destroy(strengthModel); + memory->destroy(eos); + memory->destroy(Lookup); + + delete[] onerad_dynamic; + delete[] onerad_frozen; + delete[] maxrad_dynamic; + delete[] maxrad_frozen; + + delete[] Fdot; + delete[] Fincr; + delete[] K; + delete[] detF; + delete[] PK1; + delete[] smoothVelDifference; + delete[] R; + delete[] FincrInv; + delete[] W; + delete[] D; + delete[] numNeighsRefConfig; + delete[] CauchyStress; + delete[] hourglass_error; + delete[] particle_dt; + + delete[] failureModel; + } +} + +/* ---------------------------------------------------------------------- + * + * use half neighbor list to re-compute shape matrix + * + ---------------------------------------------------------------------- */ + +void PairTlsph::PreCompute() { + int *mol = atom->molecule; + double *vfrac = atom->vfrac; + double *radius = atom->radius; + double **x0 = atom->x0; + double **x = atom->x; + double **v = atom->vest; // extrapolated velocities corresponding to current positions + double **vint = atom->v; // Velocity-Verlet algorithm velocities + double *damage = atom->damage; + int *tag = atom->tag; + int *type = atom->type; + int nlocal = atom->nlocal; + int jnum, jj, i, j, itype, idim; + + tagint **partner = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->partner; + int *npartner = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->npartner; + float **wfd_list = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->wfd_list; + float **wf_list = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->wf_list; + float **degradation_ij = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->degradation_ij; + double r0, r0Sq, wf, wfd, h, irad, voli, volj, scale, shepardWeight; + Vector3d dx, dx0, dv, g; + Matrix3d Ktmp, Ftmp, Fdottmp, L, U, eye; + Vector3d vi, vj, vinti, vintj, xi, xj, x0i, x0j, dvint; + int periodic = (domain->xperiodic || domain->yperiodic || domain->zperiodic); + bool status; + Matrix3d F0; + + eye.setIdentity(); + + for (i = 0; i < nlocal; i++) { + + itype = type[i]; + if (setflag[itype][itype] == 1) { + + K[i].setZero(); + Fincr[i].setZero(); + Fdot[i].setZero(); + numNeighsRefConfig[i] = 0; + smoothVelDifference[i].setZero(); + hourglass_error[i] = 0.0; + + if (mol[i] < 0) { // valid SPH particle have mol > 0 + continue; + } + + // initialize aveage mass density + h = 2.0 * radius[i]; + r0 = 0.0; + spiky_kernel_and_derivative(h, r0, domain->dimension, wf, wfd); + shepardWeight = wf * voli; + + jnum = npartner[i]; + irad = radius[i]; + voli = vfrac[i]; + + // initialize Eigen data structures from LAMMPS data structures + for (idim = 0; idim < 3; idim++) { + xi(idim) = x[i][idim]; + x0i(idim) = x0[i][idim]; + vi(idim) = v[i][idim]; + vinti(idim) = vint[i][idim]; + } + + for (jj = 0; jj < jnum; jj++) { + + if (partner[i][jj] == 0) + continue; + j = atom->map(partner[i][jj]); + if (j < 0) { // // check if lost a partner without first breaking bond + partner[i][jj] = 0; + continue; + } + + if (mol[j] < 0) { // particle has failed. do not include it for computing any property + continue; + } + + if (mol[i] != mol[j]) { + continue; + } + + // initialize Eigen data structures from LAMMPS data structures + for (idim = 0; idim < 3; idim++) { + xj(idim) = x[j][idim]; + x0j(idim) = x0[j][idim]; + vj(idim) = v[j][idim]; + vintj(idim) = vint[j][idim]; + } + dx0 = x0j - x0i; + dx = xj - xi; + + if (periodic) + domain->minimum_image(dx0(0), dx0(1), dx0(2)); + + r0Sq = dx0.squaredNorm(); + h = irad + radius[j]; + + r0 = sqrt(r0Sq); + volj = vfrac[j]; + + // distance vectors in current and reference configuration, velocity difference + dv = vj - vi; + dvint = vintj - vinti; + + // scale the interaction according to the damage variable + scale = 1.0 - degradation_ij[i][jj]; + wf = wf_list[i][jj] * scale; + wfd = wfd_list[i][jj] * scale; + g = (wfd / r0) * dx0; + + /* build matrices */ + Ktmp = -g * dx0.transpose(); + Fdottmp = -dv * g.transpose(); + Ftmp = -(dx - dx0) * g.transpose(); + + K[i] += volj * Ktmp; + Fdot[i] += volj * Fdottmp; + Fincr[i] += volj * Ftmp; + shepardWeight += volj * wf; + smoothVelDifference[i] += volj * wf * dvint; + numNeighsRefConfig[i]++; + } // end loop over j + + // normalize average velocity field around an integration point + if (shepardWeight > 0.0) { + smoothVelDifference[i] /= shepardWeight; + } else { + smoothVelDifference[i].setZero(); + } + + pseudo_inverse_SVD(K[i]); + Fdot[i] *= K[i]; + Fincr[i] *= K[i]; + Fincr[i] += eye; + + if (JAUMANN) { + R[i].setIdentity(); // for Jaumann stress rate, we do not need a subsequent rotation back into the reference configuration + } else { + status = PolDec(Fincr[i], R[i], U, false); // polar decomposition of the deformation gradient, F = R * U + if (!status) { + error->message(FLERR, "Polar decomposition of deformation gradient failed.\n"); + mol[i] = -1; + } else { + Fincr[i] = R[i] * U; + } + } + + detF[i] = Fincr[i].determinant(); + FincrInv[i] = Fincr[i].inverse(); + + // velocity gradient + L = Fdot[i] * FincrInv[i]; + + // symmetric (D) and asymmetric (W) parts of L + D[i] = 0.5 * (L + L.transpose()); + W[i] = 0.5 * (L - L.transpose()); // spin tensor:: need this for Jaumann rate + + // unrotated rate-of-deformation tensor d, see right side of Pronto2d, eqn.(2.1.7) + // convention: unrotated frame is that one, where the true rotation of an integration point has been subtracted. + // stress in the unrotated frame of reference is denoted sigma (stress seen by an observer doing rigid body rotations along with the material) + // stress in the true frame of reference (a stationary observer) is denoted by T, "true stress" + D[i] = (R[i].transpose() * D[i] * R[i]).eval(); + + // limit strain rate + //double limit = 1.0e-3 * Lookup[SIGNAL_VELOCITY][itype] / radius[i]; + //D[i] = LimitEigenvalues(D[i], limit); + + /* + * make sure F stays within some limits + */ + + if ((detF[i] < DETF_MIN) || (detF[i] > DETF_MAX) || (numNeighsRefConfig[i] == 0)) { + printf("deleting particle [%d] because det(F)=%f is outside stable range %f -- %f \n", tag[i], + Fincr[i].determinant(), + DETF_MIN, DETF_MAX); + printf("nn = %d, damage=%f\n", numNeighsRefConfig[i], damage[i]); + cout << "Here is matrix F:" << endl << Fincr[i] << endl; + cout << "Here is matrix F-1:" << endl << FincrInv[i] << endl; + cout << "Here is matrix K-1:" << endl << K[i] << endl; + cout << "Here is matrix K:" << endl << K[i].inverse() << endl; + cout << "Here is det of K" << endl << (K[i].inverse()).determinant() << endl; + cout << "Here is matrix R:" << endl << R[i] << endl; + cout << "Here is det of R" << endl << R[i].determinant() << endl; + cout << "Here is matrix U:" << endl << U << endl; + mol[i] = -1; + //error->one(FLERR, ""); + } + + if (mol[i] < 0) { + D[i].setZero(); + Fdot[i].setZero(); + Fincr[i].setIdentity(); + smoothVelDifference[i].setZero(); + detF[i] = 1.0; + K[i].setIdentity(); + + vint[i][0] = 0.0; + vint[i][1] = 0.0; + vint[i][2] = 0.0; + } + } // end loop over i + } // end check setflag +} + +/* ---------------------------------------------------------------------- */ + +void PairTlsph::compute(int eflag, int vflag) { + + if (atom->nmax > nmax) { + nmax = atom->nmax; + delete[] Fdot; + Fdot = new Matrix3d[nmax]; // memory usage: 9 doubles + delete[] Fincr; + Fincr = new Matrix3d[nmax]; // memory usage: 9 doubles + delete[] K; + K = new Matrix3d[nmax]; // memory usage: 9 doubles + delete[] PK1; + PK1 = new Matrix3d[nmax]; // memory usage: 9 doubles; total 5*9=45 doubles + delete[] detF; + detF = new double[nmax]; // memory usage: 1 double; total 46 doubles + delete[] smoothVelDifference; + smoothVelDifference = new Vector3d[nmax]; // memory usage: 3 doubles; total 49 doubles + delete[] R; + R = new Matrix3d[nmax]; // memory usage: 9 doubles; total 67 doubles + delete[] FincrInv; + FincrInv = new Matrix3d[nmax]; // memory usage: 9 doubles; total 85 doubles + delete[] W; + W = new Matrix3d[nmax]; // memory usage: 9 doubles; total 94 doubles + delete[] D; + D = new Matrix3d[nmax]; // memory usage: 9 doubles; total 103 doubles + delete[] numNeighsRefConfig; + numNeighsRefConfig = new int[nmax]; // memory usage: 1 int; total 108 doubles + delete[] CauchyStress; + CauchyStress = new Matrix3d[nmax]; // memory usage: 9 doubles; total 118 doubles + delete[] hourglass_error; + hourglass_error = new double[nmax]; + delete[] particle_dt; + particle_dt = new double[nmax]; + } + + if (first) { // return on first call, because reference connectivity lists still needs to be built. Also zero quantities which are otherwise undefined. + first = false; + + for (int i = 0; i < atom->nlocal; i++) { + Fincr[i].setZero(); + detF[i] = 0.0; + smoothVelDifference[i].setZero(); + D[i].setZero(); + numNeighsRefConfig[i] = 0; + CauchyStress[i].setZero(); + hourglass_error[i] = 0.0; + particle_dt[i] = 0.0; + } + + return; + } + + /* + * calculate deformations and rate-of-deformations + */ + PairTlsph::PreCompute(); + + /* + * calculate stresses from constitutive models + */ + PairTlsph::AssembleStress(); + + /* + * QUANTITIES ABOVE HAVE ONLY BEEN CALCULATED FOR NLOCAL PARTICLES. + * NEED TO DO A FORWARD COMMUNICATION TO GHOST ATOMS NOW + */ + comm->forward_comm_pair(this); + + /* + * compute forces between particles + */ + updateFlag = 0; + ComputeForces(eflag, vflag); +} + +void PairTlsph::ComputeForces(int eflag, int vflag) { + int *mol = atom->molecule; + double **x = atom->x; + double **v = atom->vest; + double **x0 = atom->x0; + double **f = atom->f; + double *vfrac = atom->vfrac; + double *de = atom->de; + double *rmass = atom->rmass; + double *radius = atom->radius; + double *damage = atom->damage; + double *plastic_strain = atom->eff_plastic_strain; + int *type = atom->type; + int nlocal = atom->nlocal; + int i, j, jj, jnum, itype, idim; + double r, hg_mag, wf, wfd, h, r0, r0Sq, voli, volj; + double delVdotDelR, visc_magnitude, deltaE, mu_ij, hg_err, gamma_dot_dx, delta, scale; + double strain1d, strain1d_max, softening_strain, shepardWeight; + char str[128]; + Vector3d fi, fj, dx0, dx, dv, f_stress, f_hg, dxp_i, dxp_j, gamma, g, gamma_i, gamma_j, x0i, x0j; + Vector3d xi, xj, vi, vj, f_visc, sumForces, f_spring; + int periodic = (domain->xperiodic || domain->yperiodic || domain->zperiodic); + + tagint **partner = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->partner; + int *npartner = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->npartner; + float **wfd_list = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->wfd_list; + float **wf_list = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->wf_list; + float **degradation_ij = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->degradation_ij; + float **energy_per_bond = ((FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[ifix_tlsph])->energy_per_bond; + Matrix3d eye; + eye.setIdentity(); + + if (eflag || vflag) + ev_setup(eflag, vflag); + else + evflag = vflag_fdotr = 0; + + /* + * iterate over pairs of particles i, j and assign forces using PK1 stress tensor + */ + + //updateFlag = 0; + hMin = 1.0e22; + dtRelative = 1.0e22; + + for (i = 0; i < nlocal; i++) { + + if (mol[i] < 0) { + continue; // Particle i is not a valid SPH particle (anymore). Skip all interactions with this particle. + } + + itype = type[i]; + jnum = npartner[i]; + voli = vfrac[i]; + + // initialize aveage mass density + h = 2.0 * radius[i]; + r = 0.0; + spiky_kernel_and_derivative(h, r, domain->dimension, wf, wfd); + shepardWeight = wf * voli; + + for (idim = 0; idim < 3; idim++) { + x0i(idim) = x0[i][idim]; + xi(idim) = x[i][idim]; + vi(idim) = v[i][idim]; + } + + for (jj = 0; jj < jnum; jj++) { + if (partner[i][jj] == 0) + continue; + j = atom->map(partner[i][jj]); + if (j < 0) { // // check if lost a partner without first breaking bond + partner[i][jj] = 0; + continue; + } + + if (mol[j] < 0) { + continue; // Particle j is not a valid SPH particle (anymore). Skip all interactions with this particle. + } + + if (mol[i] != mol[j]) { + continue; + } + + if (type[j] != itype) { + sprintf(str, "particle pair is not of same type!"); + error->all(FLERR, str); + } + + for (idim = 0; idim < 3; idim++) { + x0j(idim) = x0[j][idim]; + xj(idim) = x[j][idim]; + vj(idim) = v[j][idim]; + } + + if (periodic) + domain->minimum_image(dx0(0), dx0(1), dx0(2)); + + // check that distance between i and j (in the reference config) is less than cutoff + dx0 = x0j - x0i; + r0Sq = dx0.squaredNorm(); + h = radius[i] + radius[j]; + hMin = MIN(hMin, h); + r0 = sqrt(r0Sq); + volj = vfrac[j]; + + // distance vectors in current and reference configuration, velocity difference + dx = xj - xi; + dv = vj - vi; + r = dx.norm(); // current distance + + // scale the interaction according to the damage variable + scale = 1.0 - degradation_ij[i][jj]; + wf = wf_list[i][jj] * scale; + wfd = wfd_list[i][jj] * scale; + + g = (wfd / r0) * dx0; // uncorrected kernel gradient + + /* + * force contribution -- note that the kernel gradient correction has been absorbed into PK1 + */ + + f_stress = -voli * volj * (PK1[i] + PK1[j]) * g; + + /* + * artificial viscosity + */ + delVdotDelR = dx.dot(dv) / (r + 0.1 * h); // project relative velocity onto unit particle distance vector [m/s] + LimitDoubleMagnitude(delVdotDelR, 0.01 * Lookup[SIGNAL_VELOCITY][itype]); + mu_ij = h * delVdotDelR / (r + 0.1 * h); // units: [m * m/s / m = m/s] + visc_magnitude = (-Lookup[VISCOSITY_Q1][itype] * Lookup[SIGNAL_VELOCITY][itype] * mu_ij + + Lookup[VISCOSITY_Q2][itype] * mu_ij * mu_ij) / Lookup[REFERENCE_DENSITY][itype]; // units: m^5/(s^2 kg)) + f_visc = rmass[i] * rmass[j] * visc_magnitude * wfd * dx / (r + 1.0e-2 * h); // units: kg^2 * m^5/(s^2 kg) * m^-4 = kg m / s^2 = N + + /* + * hourglass deviation of particles i and j + */ + + gamma = 0.5 * (Fincr[i] + Fincr[j]) * dx0 - dx; + hg_err = gamma.norm() / r0; + hourglass_error[i] += volj * wf * hg_err; + + /* SPH-like hourglass formulation */ + + if (MAX(plastic_strain[i], plastic_strain[j]) > 1.0e-3) { + /* + * viscous hourglass formulation for particles with plastic deformation + */ + delta = gamma.dot(dx); + if (delVdotDelR * delta < 0.0) { + hg_err = MAX(hg_err, 0.05); // limit hg_err to avoid numerical instabilities + hg_mag = -hg_err * Lookup[HOURGLASS_CONTROL_AMPLITUDE][itype] * Lookup[SIGNAL_VELOCITY][itype] * mu_ij + / Lookup[REFERENCE_DENSITY][itype]; // this has units of pressure + } else { + hg_mag = 0.0; + } + f_hg = rmass[i] * rmass[j] * hg_mag * wfd * dx / (r + 1.0e-2 * h); + + } else { + /* + * stiffness hourglass formulation for particle in the elastic regime + */ + + gamma_dot_dx = gamma.dot(dx); // project hourglass error vector onto pair distance vector + LimitDoubleMagnitude(gamma_dot_dx, 0.1 * r); // limit projected vector to avoid numerical instabilities + delta = 0.5 * gamma_dot_dx / (r + 0.1 * h); // delta has dimensions of [m] + hg_mag = Lookup[HOURGLASS_CONTROL_AMPLITUDE][itype] * delta / (r0Sq + 0.01 * h * h); // hg_mag has dimensions [m^(-1)] + hg_mag *= -voli * volj * wf * Lookup[YOUNGS_MODULUS][itype]; // hg_mag has dimensions [J*m^(-1)] = [N] + f_hg = (hg_mag / (r + 0.01 * h)) * dx; + } + + // scale hourglass force with damage + f_hg *= (1.0 - damage[i]) * (1.0 - damage[j]); + + // sum stress, viscous, and hourglass forces + sumForces = f_stress + f_visc + f_hg; // + f_spring; + + // energy rate -- project velocity onto force vector + deltaE = 0.5 * sumForces.dot(dv); + + // apply forces to pair of particles + f[i][0] += sumForces(0); + f[i][1] += sumForces(1); + f[i][2] += sumForces(2); + de[i] += deltaE; + + // tally atomistic stress tensor + if (evflag) { + ev_tally_xyz(i, j, nlocal, 0, 0.0, 0.0, sumForces(0), sumForces(1), sumForces(2), dx(0), dx(1), dx(2)); + } + + shepardWeight += wf * volj; + + // check if a particle has moved too much w.r.t another particle + if (r > r0) { + if (update_method == UPDATE_CONSTANT_THRESHOLD) { + if (r - r0 > update_threshold) { + updateFlag = 1; + } + } else if (update_method == UPDATE_PAIRWISE_RATIO) { + if ((r - r0) / h > update_threshold) { + updateFlag = 1; + } + } + } + + if (failureModel[itype].failure_max_pairwise_strain) { + + strain1d = (r - r0) / r0; + strain1d_max = Lookup[FAILURE_MAX_PAIRWISE_STRAIN_THRESHOLD][itype]; + softening_strain = 2.0 * strain1d_max; + + if (strain1d > strain1d_max) { + degradation_ij[i][jj] = (strain1d - strain1d_max) / softening_strain; + } else { + degradation_ij[i][jj] = 0.0; + } + + if (degradation_ij[i][jj] >= 1.0) { // delete interaction if fully damaged + partner[i][jj] = 0; + } + } + + if (failureModel[itype].failure_energy_release_rate) { + + // integration approach + energy_per_bond[i][jj] += update->dt * f_stress.dot(dv) / (voli * volj); + double Vic = (2.0 / 3.0) * h * h * h; // interaction volume for 2d plane strain + double critical_energy_per_bond = Lookup[CRITICAL_ENERGY_RELEASE_RATE][itype] / (2.0 * Vic); + + if (energy_per_bond[i][jj] > critical_energy_per_bond) { + //degradation_ij[i][jj] = 1.0; + partner[i][jj] = 0; + } + } + + if (failureModel[itype].integration_point_wise) { + + strain1d = (r - r0) / r0; + + if (strain1d > 0.0) { + + if ((damage[i] == 1.0) && (damage[j] == 1.0)) { + // check if damage_onset is already defined + if (energy_per_bond[i][jj] == 0.0) { // pair damage not defined yet + energy_per_bond[i][jj] = strain1d; + } else { // damage initiation strain already defined + strain1d_max = energy_per_bond[i][jj]; + softening_strain = 2.0 * strain1d_max; + + if (strain1d > strain1d_max) { + degradation_ij[i][jj] = (strain1d - strain1d_max) / softening_strain; + } else { + degradation_ij[i][jj] = 0.0; + } + } + } + + if (degradation_ij[i][jj] >= 1.0) { // delete interaction if fully damaged + partner[i][jj] = 0; + } + + } else { + degradation_ij[i][jj] = 0.0; + } // end failureModel[itype].integration_point_wise + + } + + } // end loop over jj neighbors of i + + if (shepardWeight != 0.0) { + hourglass_error[i] /= shepardWeight; + } + + } // end loop over i + + if (vflag_fdotr) + virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + assemble unrotated stress tensor using deviatoric and pressure components. + Convert to corotational Cauchy stress, then to PK1 stress and apply + shape matrix correction + ------------------------------------------------------------------------- */ +void PairTlsph::AssembleStress() { + int *mol = atom->molecule; + double *eff_plastic_strain = atom->eff_plastic_strain; + double *eff_plastic_strain_rate = atom->eff_plastic_strain_rate; + double **tlsph_stress = atom->smd_stress; + int *type = atom->type; + double *radius = atom->radius; + double *damage = atom->damage; + double *rmass = atom->rmass; + double *vfrac = atom->vfrac; + double *e = atom->e; + double pInitial, d_iso, pFinal, p_rate, plastic_strain_increment; + int i, itype; + int nlocal = atom->nlocal; + double dt = update->dt; + double M_eff, p_wave_speed, mass_specific_energy, vol_specific_energy, rho; + Matrix3d sigma_rate, eye, sigmaInitial, sigmaFinal, T, T_damaged, Jaumann_rate, sigma_rate_check; + Matrix3d d_dev, sigmaInitial_dev, sigmaFinal_dev, sigma_dev_rate, strain; + Vector3d x0i, xi, xp; + + eye.setIdentity(); + dtCFL = 1.0e22; + pFinal = 0.0; + + for (i = 0; i < nlocal; i++) { + particle_dt[i] = 0.0; + + itype = type[i]; + if (setflag[itype][itype] == 1) { + if (mol[i] > 0) { // only do the following if particle has not failed -- mol < 0 means particle has failed + + /* + * initial stress state: given by the unrotateted Cauchy stress. + * Assemble Eigen 3d matrix from stored stress state + */ + sigmaInitial(0, 0) = tlsph_stress[i][0]; + sigmaInitial(0, 1) = tlsph_stress[i][1]; + sigmaInitial(0, 2) = tlsph_stress[i][2]; + sigmaInitial(1, 1) = tlsph_stress[i][3]; + sigmaInitial(1, 2) = tlsph_stress[i][4]; + sigmaInitial(2, 2) = tlsph_stress[i][5]; + sigmaInitial(1, 0) = sigmaInitial(0, 1); + sigmaInitial(2, 0) = sigmaInitial(0, 2); + sigmaInitial(2, 1) = sigmaInitial(1, 2); + + //cout << "this is sigma initial" << endl << sigmaInitial << endl; + + pInitial = sigmaInitial.trace() / 3.0; // isotropic part of initial stress + sigmaInitial_dev = Deviator(sigmaInitial); + d_iso = D[i].trace(); // volumetric part of stretch rate + d_dev = Deviator(D[i]); // deviatoric part of stretch rate + strain = 0.5 * (Fincr[i].transpose() * Fincr[i] - eye); + mass_specific_energy = e[i] / rmass[i]; // energy per unit mass + rho = rmass[i] / (detF[i] * vfrac[i]); + vol_specific_energy = mass_specific_energy * rho; // energy per current volume + + /* + * pressure: compute pressure rate p_rate and final pressure pFinal + */ + + ComputePressure(i, rho, mass_specific_energy, vol_specific_energy, pInitial, d_iso, pFinal, p_rate); + + /* + * material strength + */ + + //cout << "this is the strain deviator rate" << endl << d_dev << endl; + ComputeStressDeviator(i, sigmaInitial_dev, d_dev, sigmaFinal_dev, sigma_dev_rate, plastic_strain_increment); + //cout << "this is the stress deviator rate" << endl << sigma_dev_rate << endl; + + // keep a rolling average of the plastic strain rate over the last 100 or so timesteps + eff_plastic_strain[i] += plastic_strain_increment; + + // compute a characteristic time over which to average the plastic strain + double tav = 1000 * radius[i] / (Lookup[SIGNAL_VELOCITY][itype]); + eff_plastic_strain_rate[i] -= eff_plastic_strain_rate[i] / tav; + eff_plastic_strain_rate[i] += (plastic_strain_increment / dt) / tav; + eff_plastic_strain_rate[i] = MAX(0.0, eff_plastic_strain_rate[i]); + + /* + * assemble total stress from pressure and deviatoric stress + */ + sigmaFinal = pFinal * eye + sigmaFinal_dev; // this is the stress that is kept + + if (JAUMANN) { + /* + * sigma is already the co-rotated Cauchy stress. + * The stress rate, however, needs to be made objective. + */ + + if (dt > 1.0e-16) { + sigma_rate = (1.0 / dt) * (sigmaFinal - sigmaInitial); + } else { + sigma_rate.setZero(); + } + + Jaumann_rate = sigma_rate + W[i] * sigmaInitial + sigmaInitial * W[i].transpose(); + sigmaFinal = sigmaInitial + dt * Jaumann_rate; + T = sigmaFinal; + } else { + /* + * sigma is the unrotated stress. + * need to do forward rotation of the unrotated stress sigma to the current configuration + */ + T = R[i] * sigmaFinal * R[i].transpose(); + } + + /* + * store unrotated stress in atom vector + * symmetry is exploited + */ + tlsph_stress[i][0] = sigmaFinal(0, 0); + tlsph_stress[i][1] = sigmaFinal(0, 1); + tlsph_stress[i][2] = sigmaFinal(0, 2); + tlsph_stress[i][3] = sigmaFinal(1, 1); + tlsph_stress[i][4] = sigmaFinal(1, 2); + tlsph_stress[i][5] = sigmaFinal(2, 2); + + /* + * Damage due to failure criteria. + */ + + if (failureModel[itype].integration_point_wise) { + ComputeDamage(i, strain, T, T_damaged); + //T = T_damaged; Do not do this, it is undefined as of now + } + + // store rotated, "true" Cauchy stress + CauchyStress[i] = T; + + /* + * We have the corotational Cauchy stress. + * Convert to PK1. Note that reference configuration used for computing the forces is linked via + * the incremental deformation gradient, not the full deformation gradient. + */ + PK1[i] = detF[i] * T * FincrInv[i].transpose(); + + /* + * pre-multiply stress tensor with shape matrix to save computation in force loop + */ + PK1[i] = PK1[i] * K[i]; + + /* + * compute stable time step according to Pronto 2d + */ + + Matrix3d deltaSigma; + deltaSigma = sigmaFinal - sigmaInitial; + p_rate = deltaSigma.trace() / (3.0 * dt + 1.0e-16); + sigma_dev_rate = Deviator(deltaSigma) / (dt + 1.0e-16); + + double K_eff, mu_eff; + effective_longitudinal_modulus(itype, dt, d_iso, p_rate, d_dev, sigma_dev_rate, damage[i], K_eff, mu_eff, M_eff); + p_wave_speed = sqrt(M_eff / rho); + + if (mol[i] < 0) { + error->one(FLERR, "this should not happen"); + } + + particle_dt[i] = 2.0 * radius[i] / p_wave_speed; + dtCFL = MIN(dtCFL, particle_dt[i]); + + } else { // end if mol > 0 + PK1[i].setZero(); + K[i].setIdentity(); + CauchyStress[i].setZero(); + sigma_rate.setZero(); + tlsph_stress[i][0] = 0.0; + tlsph_stress[i][1] = 0.0; + tlsph_stress[i][2] = 0.0; + tlsph_stress[i][3] = 0.0; + tlsph_stress[i][4] = 0.0; + tlsph_stress[i][5] = 0.0; + } // end if mol > 0 + } // end setflag + } // end for +} + +/* ---------------------------------------------------------------------- + allocate all arrays + ------------------------------------------------------------------------- */ + +void PairTlsph::allocate() { + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag, n + 1, n + 1, "pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(strengthModel, n + 1, "pair:strengthmodel"); + memory->create(eos, n + 1, "pair:eosmodel"); + failureModel = new failure_types[n + 1]; + memory->create(Lookup, MAX_KEY_VALUE, n + 1, "pair:LookupTable"); + + memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); // always needs to be allocated, even with granular neighborlist + + onerad_dynamic = new double[n + 1]; + onerad_frozen = new double[n + 1]; + maxrad_dynamic = new double[n + 1]; + maxrad_frozen = new double[n + 1]; + +} + +/* ---------------------------------------------------------------------- + global settings + ------------------------------------------------------------------------- */ + +void PairTlsph::settings(int narg, char **arg) { + + if (comm->me == 0) { + printf( + "\n>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========\n"); + printf("TLSPH settings\n"); + } + + /* + * default value for update_threshold for updates of reference configuration: + * The maximum relative displacement which is tracked by the construction of LAMMPS' neighborlists + * is the folowing. + */ + + cut_comm = MAX(neighbor->cutneighmax, comm->cutghostuser); // cutoff radius within which ghost atoms are communicated. + update_threshold = cut_comm; + update_method = UPDATE_NONE; + + int iarg = 0; + + while (true) { + + if (iarg >= narg) { + break; + } + + if (strcmp(arg[iarg], "*UPDATE_CONSTANT") == 0) { + iarg++; + if (iarg == narg) { + error->all(FLERR, "expected number following *UPDATE_CONSTANT keyword"); + } + + update_method = UPDATE_CONSTANT_THRESHOLD; + update_threshold = force->numeric(FLERR, arg[iarg]); + + } else if (strcmp(arg[iarg], "*UPDATE_PAIRWISE") == 0) { + iarg++; + if (iarg == narg) { + error->all(FLERR, "expected number following *UPDATE_PAIRWISE keyword"); + } + + update_method = UPDATE_PAIRWISE_RATIO; + update_threshold = force->numeric(FLERR, arg[iarg]); + + } else { + char msg[128]; + sprintf(msg, "Illegal keyword for smd/integrate_tlsph: %s\n", arg[iarg]); + error->all(FLERR, msg); + } + + iarg++; + } + + if ((update_threshold > cut_comm) && (update_method == UPDATE_CONSTANT_THRESHOLD)) { + if (comm->me == 0) { + printf("\n ***** WARNING ***\n"); + printf("requested reference configuration update threshold is %g length units\n", update_threshold); + printf("This value exceeds the maximum value %g beyond which TLSPH displacements can be tracked at current settings.\n", + cut_comm); + printf("Expect loss of neighbors!\n"); + } + } + + if (comm->me == 0) { + + if (update_method == UPDATE_CONSTANT_THRESHOLD) { + printf("... will update reference configuration if magnitude of relative displacement exceeds %g length units\n", + update_threshold); + } else if (update_method == UPDATE_PAIRWISE_RATIO) { + printf("... will update reference configuration if ratio pairwise distance / smoothing length exceeds %g\n", + update_threshold); + } else if (update_method == UPDATE_NONE) { + printf("... will never update reference configuration"); + } + printf( + ">>========>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========\n"); + + } + +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs + ------------------------------------------------------------------------- */ + +void PairTlsph::coeff(int narg, char **arg) { + int ioffset, iarg, iNextKwd, itype; + char str[128]; + std::string s, t; + + if (narg < 3) { + sprintf(str, "number of arguments for pair tlsph is too small!"); + error->all(FLERR, str); + } + if (!allocated) + allocate(); + + /* + * check that TLSPH parameters are given only in i,i form + */ + if (force->inumeric(FLERR, arg[0]) != force->inumeric(FLERR, arg[1])) { + sprintf(str, "TLSPH coefficients can only be specified between particles of same type!"); + error->all(FLERR, str); + } + itype = force->inumeric(FLERR, arg[0]); + +// set all eos, strength and failure models to inactive by default + eos[itype] = EOS_NONE; + strengthModel[itype] = STRENGTH_NONE; + + if (comm->me == 0) { + printf( + "\n>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========\n"); + printf("SMD / TLSPH PROPERTIES OF PARTICLE TYPE %d:\n", itype); + } + + /* + * read parameters which are common -- regardless of material / eos model + */ + + ioffset = 2; + if (strcmp(arg[ioffset], "*COMMON") != 0) { + sprintf(str, "common keyword missing!"); + error->all(FLERR, str); + } + + t = string("*"); + iNextKwd = -1; + for (iarg = ioffset + 1; iarg < narg; iarg++) { + s = string(arg[iarg]); + if (s.compare(0, t.length(), t) == 0) { + iNextKwd = iarg; + break; + } + } + +//printf("keyword following *COMMON is %s\n", arg[iNextKwd]); + + if (iNextKwd < 0) { + sprintf(str, "no *KEYWORD terminates *COMMON"); + error->all(FLERR, str); + } + + if (iNextKwd - ioffset != 7 + 1) { + sprintf(str, "expected 7 arguments following *COMMON but got %d\n", iNextKwd - ioffset - 1); + error->all(FLERR, str); + } + + Lookup[REFERENCE_DENSITY][itype] = force->numeric(FLERR, arg[ioffset + 1]); + Lookup[YOUNGS_MODULUS][itype] = force->numeric(FLERR, arg[ioffset + 2]); + Lookup[POISSON_RATIO][itype] = force->numeric(FLERR, arg[ioffset + 3]); + Lookup[VISCOSITY_Q1][itype] = force->numeric(FLERR, arg[ioffset + 4]); + Lookup[VISCOSITY_Q2][itype] = force->numeric(FLERR, arg[ioffset + 5]); + Lookup[HOURGLASS_CONTROL_AMPLITUDE][itype] = force->numeric(FLERR, arg[ioffset + 6]); + Lookup[HEAT_CAPACITY][itype] = force->numeric(FLERR, arg[ioffset + 7]); + + Lookup[LAME_LAMBDA][itype] = Lookup[YOUNGS_MODULUS][itype] * Lookup[POISSON_RATIO][itype] + / ((1.0 + Lookup[POISSON_RATIO][itype] * (1.0 - 2.0 * Lookup[POISSON_RATIO][itype]))); + Lookup[SHEAR_MODULUS][itype] = Lookup[YOUNGS_MODULUS][itype] / (2.0 * (1.0 + Lookup[POISSON_RATIO][itype])); + Lookup[M_MODULUS][itype] = Lookup[LAME_LAMBDA][itype] + 2.0 * Lookup[SHEAR_MODULUS][itype]; + Lookup[SIGNAL_VELOCITY][itype] = sqrt( + (Lookup[LAME_LAMBDA][itype] + 2.0 * Lookup[SHEAR_MODULUS][itype]) / Lookup[REFERENCE_DENSITY][itype]); + Lookup[BULK_MODULUS][itype] = Lookup[LAME_LAMBDA][itype] + 2.0 * Lookup[SHEAR_MODULUS][itype] / 3.0; + + if (comm->me == 0) { + printf("\n material unspecific properties for SMD/TLSPH definition of particle type %d:\n", itype); + printf("%60s : %g\n", "reference density", Lookup[REFERENCE_DENSITY][itype]); + printf("%60s : %g\n", "Young's modulus", Lookup[YOUNGS_MODULUS][itype]); + printf("%60s : %g\n", "Poisson ratio", Lookup[POISSON_RATIO][itype]); + printf("%60s : %g\n", "linear viscosity coefficient", Lookup[VISCOSITY_Q1][itype]); + printf("%60s : %g\n", "quadratic viscosity coefficient", Lookup[VISCOSITY_Q2][itype]); + printf("%60s : %g\n", "hourglass control coefficient", Lookup[HOURGLASS_CONTROL_AMPLITUDE][itype]); + printf("%60s : %g\n", "heat capacity [energy / (mass * temperature)]", Lookup[HEAT_CAPACITY][itype]); + printf("%60s : %g\n", "Lame constant lambda", Lookup[LAME_LAMBDA][itype]); + printf("%60s : %g\n", "shear modulus", Lookup[SHEAR_MODULUS][itype]); + printf("%60s : %g\n", "bulk modulus", Lookup[BULK_MODULUS][itype]); + printf("%60s : %g\n", "signal velocity", Lookup[SIGNAL_VELOCITY][itype]); + + } + + /* + * read following material cards + */ + +//printf("next kwd is %s\n", arg[iNextKwd]); + eos[itype] = EOS_NONE; + strengthModel[itype] = STRENGTH_NONE; + + while (true) { + if (strcmp(arg[iNextKwd], "*END") == 0) { + if (comm->me == 0) { + printf("found *END keyword"); + printf( + "\n>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========>>========\n\n"); + } + break; + } + + /* + * Linear Elasticity model based on deformation gradient + */ + ioffset = iNextKwd; + if (strcmp(arg[ioffset], "*LINEAR_DEFGRAD") == 0) { + strengthModel[itype] = LINEAR_DEFGRAD; + + if (comm->me == 0) { + printf("reading *LINEAR_DEFGRAD\n"); + } + + t = string("*"); + iNextKwd = -1; + for (iarg = ioffset + 1; iarg < narg; iarg++) { + s = string(arg[iarg]); + if (s.compare(0, t.length(), t) == 0) { + iNextKwd = iarg; + break; + } + } + + if (iNextKwd < 0) { + sprintf(str, "no *KEYWORD terminates *LINEAR_DEFGRAD"); + error->all(FLERR, str); + } + + if (iNextKwd - ioffset != 1) { + sprintf(str, "expected 0 arguments following *LINEAR_DEFGRAD but got %d\n", iNextKwd - ioffset - 1); + error->all(FLERR, str); + } + + if (comm->me == 0) { + printf("\n%60s\n", "Linear Elasticity model based on deformation gradient"); + } + } else if (strcmp(arg[ioffset], "*STRENGTH_LINEAR") == 0) { + + /* + * Linear Elasticity strength only model based on strain rate + */ + + strengthModel[itype] = STRENGTH_LINEAR; + if (comm->me == 0) { + printf("reading *STRENGTH_LINEAR\n"); + } + + t = string("*"); + iNextKwd = -1; + for (iarg = ioffset + 1; iarg < narg; iarg++) { + s = string(arg[iarg]); + if (s.compare(0, t.length(), t) == 0) { + iNextKwd = iarg; + break; + } + } + + if (iNextKwd < 0) { + sprintf(str, "no *KEYWORD terminates *STRENGTH_LINEAR"); + error->all(FLERR, str); + } + + if (iNextKwd - ioffset != 1) { + sprintf(str, "expected 0 arguments following *STRENGTH_LINEAR but got %d\n", iNextKwd - ioffset - 1); + error->all(FLERR, str); + } + + if (comm->me == 0) { + printf("%60s\n", "Linear Elasticity strength based on strain rate"); + } + } // end Linear Elasticity strength only model based on strain rate + + else if (strcmp(arg[ioffset], "*STRENGTH_LINEAR_PLASTIC") == 0) { + + /* + * Linear Elastic / perfectly plastic strength only model based on strain rate + */ + + strengthModel[itype] = STRENGTH_LINEAR_PLASTIC; + if (comm->me == 0) { + printf("reading *STRENGTH_LINEAR_PLASTIC\n"); + } + + t = string("*"); + iNextKwd = -1; + for (iarg = ioffset + 1; iarg < narg; iarg++) { + s = string(arg[iarg]); + if (s.compare(0, t.length(), t) == 0) { + iNextKwd = iarg; + break; + } + } + + if (iNextKwd < 0) { + sprintf(str, "no *KEYWORD terminates *STRENGTH_LINEAR_PLASTIC"); + error->all(FLERR, str); + } + + if (iNextKwd - ioffset != 2 + 1) { + sprintf(str, "expected 2 arguments following *STRENGTH_LINEAR_PLASTIC but got %d\n", iNextKwd - ioffset - 1); + error->all(FLERR, str); + } + + Lookup[YIELD_STRESS][itype] = force->numeric(FLERR, arg[ioffset + 1]); + Lookup[HARDENING_PARAMETER][itype] = force->numeric(FLERR, arg[ioffset + 2]); + + if (comm->me == 0) { + printf("%60s\n", "Linear elastic / perfectly plastic strength based on strain rate"); + printf("%60s : %g\n", "Young's modulus", Lookup[YOUNGS_MODULUS][itype]); + printf("%60s : %g\n", "Poisson ratio", Lookup[POISSON_RATIO][itype]); + printf("%60s : %g\n", "shear modulus", Lookup[SHEAR_MODULUS][itype]); + printf("%60s : %g\n", "constant yield stress", Lookup[YIELD_STRESS][itype]); + printf("%60s : %g\n", "constant hardening parameter", Lookup[HARDENING_PARAMETER][itype]); + } + } // end Linear Elastic / perfectly plastic strength only model based on strain rate + + else if (strcmp(arg[ioffset], "*JOHNSON_COOK") == 0) { + + /* + * JOHNSON - COOK + */ + + strengthModel[itype] = STRENGTH_JOHNSON_COOK; + if (comm->me == 0) { + printf("reading *JOHNSON_COOK\n"); + } + + t = string("*"); + iNextKwd = -1; + for (iarg = ioffset + 1; iarg < narg; iarg++) { + s = string(arg[iarg]); + if (s.compare(0, t.length(), t) == 0) { + iNextKwd = iarg; + break; + } + } + + if (iNextKwd < 0) { + sprintf(str, "no *KEYWORD terminates *JOHNSON_COOK"); + error->all(FLERR, str); + } + + if (iNextKwd - ioffset != 8 + 1) { + sprintf(str, "expected 8 arguments following *JOHNSON_COOK but got %d\n", iNextKwd - ioffset - 1); + error->all(FLERR, str); + } + + Lookup[JC_A][itype] = force->numeric(FLERR, arg[ioffset + 1]); + Lookup[JC_B][itype] = force->numeric(FLERR, arg[ioffset + 2]); + Lookup[JC_a][itype] = force->numeric(FLERR, arg[ioffset + 3]); + Lookup[JC_C][itype] = force->numeric(FLERR, arg[ioffset + 4]); + Lookup[JC_epdot0][itype] = force->numeric(FLERR, arg[ioffset + 5]); + Lookup[JC_T0][itype] = force->numeric(FLERR, arg[ioffset + 6]); + Lookup[JC_Tmelt][itype] = force->numeric(FLERR, arg[ioffset + 7]); + Lookup[JC_M][itype] = force->numeric(FLERR, arg[ioffset + 8]); + + if (comm->me == 0) { + printf("%60s\n", "Johnson Cook material strength model"); + printf("%60s : %g\n", "A: initial yield stress", Lookup[JC_A][itype]); + printf("%60s : %g\n", "B : proportionality factor for plastic strain dependency", Lookup[JC_B][itype]); + printf("%60s : %g\n", "a : exponent for plastic strain dependency", Lookup[JC_a][itype]); + printf("%60s : %g\n", "C : proportionality factor for logarithmic plastic strain rate dependency", + Lookup[JC_C][itype]); + printf("%60s : %g\n", "epdot0 : dimensionality factor for plastic strain rate dependency", + Lookup[JC_epdot0][itype]); + printf("%60s : %g\n", "T0 : reference (room) temperature", Lookup[JC_T0][itype]); + printf("%60s : %g\n", "Tmelt : melting temperature", Lookup[JC_Tmelt][itype]); + printf("%60s : %g\n", "M : exponent for temperature dependency", Lookup[JC_M][itype]); + } + + } else if (strcmp(arg[ioffset], "*EOS_NONE") == 0) { + + /* + * no eos + */ + + eos[itype] = EOS_NONE; + if (comm->me == 0) { + printf("reading *EOS_NONE\n"); + } + + t = string("*"); + iNextKwd = -1; + for (iarg = ioffset + 1; iarg < narg; iarg++) { + s = string(arg[iarg]); + if (s.compare(0, t.length(), t) == 0) { + iNextKwd = iarg; + break; + } + } + + if (iNextKwd < 0) { + sprintf(str, "no *KEYWORD terminates *EOS_NONE"); + error->all(FLERR, str); + } + + if (iNextKwd - ioffset != 1) { + sprintf(str, "expected 0 arguments following *EOS_NONE but got %d\n", iNextKwd - ioffset - 1); + error->all(FLERR, str); + } + + if (comm->me == 0) { + printf("\n%60s\n", "no EOS selected"); + } + + } else if (strcmp(arg[ioffset], "*EOS_LINEAR") == 0) { + + /* + * linear eos + */ + + eos[itype] = EOS_LINEAR; + if (comm->me == 0) { + printf("reading *EOS_LINEAR\n"); + } + + t = string("*"); + iNextKwd = -1; + for (iarg = ioffset + 1; iarg < narg; iarg++) { + s = string(arg[iarg]); + if (s.compare(0, t.length(), t) == 0) { + iNextKwd = iarg; + break; + } + } + + if (iNextKwd < 0) { + sprintf(str, "no *KEYWORD terminates *EOS_LINEAR"); + error->all(FLERR, str); + } + + if (iNextKwd - ioffset != 1) { + sprintf(str, "expected 0 arguments following *EOS_LINEAR but got %d\n", iNextKwd - ioffset - 1); + error->all(FLERR, str); + } + + if (comm->me == 0) { + printf("\n%60s\n", "linear EOS based on strain rate"); + printf("%60s : %g\n", "bulk modulus", Lookup[BULK_MODULUS][itype]); + } + } // end linear eos + else if (strcmp(arg[ioffset], "*EOS_SHOCK") == 0) { + + /* + * shock eos + */ + + eos[itype] = EOS_SHOCK; + if (comm->me == 0) { + printf("reading *EOS_SHOCK\n"); + } + + t = string("*"); + iNextKwd = -1; + for (iarg = ioffset + 1; iarg < narg; iarg++) { + s = string(arg[iarg]); + if (s.compare(0, t.length(), t) == 0) { + iNextKwd = iarg; + break; + } + } + + if (iNextKwd < 0) { + sprintf(str, "no *KEYWORD terminates *EOS_SHOCK"); + error->all(FLERR, str); + } + + if (iNextKwd - ioffset != 3 + 1) { + sprintf(str, "expected 3 arguments (c0, S, Gamma) following *EOS_SHOCK but got %d\n", iNextKwd - ioffset - 1); + error->all(FLERR, str); + } + + Lookup[EOS_SHOCK_C0][itype] = force->numeric(FLERR, arg[ioffset + 1]); + Lookup[EOS_SHOCK_S][itype] = force->numeric(FLERR, arg[ioffset + 2]); + Lookup[EOS_SHOCK_GAMMA][itype] = force->numeric(FLERR, arg[ioffset + 3]); + if (comm->me == 0) { + printf("\n%60s\n", "shock EOS based on strain rate"); + printf("%60s : %g\n", "reference speed of sound", Lookup[EOS_SHOCK_C0][itype]); + printf("%60s : %g\n", "Hugoniot parameter S", Lookup[EOS_SHOCK_S][itype]); + printf("%60s : %g\n", "Grueneisen Gamma", Lookup[EOS_SHOCK_GAMMA][itype]); + } + } // end shock eos + + else if (strcmp(arg[ioffset], "*EOS_POLYNOMIAL") == 0) { + /* + * polynomial eos + */ + + eos[itype] = EOS_POLYNOMIAL; + if (comm->me == 0) { + printf("reading *EOS_POLYNOMIAL\n"); + } + + t = string("*"); + iNextKwd = -1; + for (iarg = ioffset + 1; iarg < narg; iarg++) { + s = string(arg[iarg]); + if (s.compare(0, t.length(), t) == 0) { + iNextKwd = iarg; + break; + } + } + + if (iNextKwd < 0) { + sprintf(str, "no *KEYWORD terminates *EOS_POLYNOMIAL"); + error->all(FLERR, str); + } + + if (iNextKwd - ioffset != 7 + 1) { + sprintf(str, "expected 7 arguments following *EOS_POLYNOMIAL but got %d\n", iNextKwd - ioffset - 1); + error->all(FLERR, str); + } + + Lookup[EOS_POLYNOMIAL_C0][itype] = force->numeric(FLERR, arg[ioffset + 1]); + Lookup[EOS_POLYNOMIAL_C1][itype] = force->numeric(FLERR, arg[ioffset + 2]); + Lookup[EOS_POLYNOMIAL_C2][itype] = force->numeric(FLERR, arg[ioffset + 3]); + Lookup[EOS_POLYNOMIAL_C3][itype] = force->numeric(FLERR, arg[ioffset + 4]); + Lookup[EOS_POLYNOMIAL_C4][itype] = force->numeric(FLERR, arg[ioffset + 5]); + Lookup[EOS_POLYNOMIAL_C5][itype] = force->numeric(FLERR, arg[ioffset + 6]); + Lookup[EOS_POLYNOMIAL_C6][itype] = force->numeric(FLERR, arg[ioffset + 7]); + if (comm->me == 0) { + printf("\n%60s\n", "polynomial EOS based on strain rate"); + printf("%60s : %g\n", "parameter c0", Lookup[EOS_POLYNOMIAL_C0][itype]); + printf("%60s : %g\n", "parameter c1", Lookup[EOS_POLYNOMIAL_C1][itype]); + printf("%60s : %g\n", "parameter c2", Lookup[EOS_POLYNOMIAL_C2][itype]); + printf("%60s : %g\n", "parameter c3", Lookup[EOS_POLYNOMIAL_C3][itype]); + printf("%60s : %g\n", "parameter c4", Lookup[EOS_POLYNOMIAL_C4][itype]); + printf("%60s : %g\n", "parameter c5", Lookup[EOS_POLYNOMIAL_C5][itype]); + printf("%60s : %g\n", "parameter c6", Lookup[EOS_POLYNOMIAL_C6][itype]); + } + } // end polynomial eos + + else if (strcmp(arg[ioffset], "*FAILURE_MAX_PLASTIC_STRAIN") == 0) { + + /* + * maximum plastic strain failure criterion + */ + + if (comm->me == 0) { + printf("reading *FAILURE_MAX_PLASTIC_SRTRAIN\n"); + } + + t = string("*"); + iNextKwd = -1; + for (iarg = ioffset + 1; iarg < narg; iarg++) { + s = string(arg[iarg]); + if (s.compare(0, t.length(), t) == 0) { + iNextKwd = iarg; + break; + } + } + + if (iNextKwd < 0) { + sprintf(str, "no *KEYWORD terminates *FAILURE_MAX_PLASTIC_STRAIN"); + error->all(FLERR, str); + } + + if (iNextKwd - ioffset != 1 + 1) { + sprintf(str, "expected 1 arguments following *FAILURE_MAX_PLASTIC_STRAIN but got %d\n", iNextKwd - ioffset - 1); + error->all(FLERR, str); + } + + failureModel[itype].failure_max_plastic_strain = true; + failureModel[itype].integration_point_wise = true; + Lookup[FAILURE_MAX_PLASTIC_STRAIN_THRESHOLD][itype] = force->numeric(FLERR, arg[ioffset + 1]); + + if (comm->me == 0) { + printf("\n%60s\n", "maximum plastic strain failure criterion"); + printf("%60s : %g\n", "failure occurs when plastic strain reaches limit", + Lookup[FAILURE_MAX_PLASTIC_STRAIN_THRESHOLD][itype]); + } + } // end maximum plastic strain failure criterion + else if (strcmp(arg[ioffset], "*FAILURE_MAX_PAIRWISE_STRAIN") == 0) { + + /* + * failure criterion based on maximum strain between a pair of TLSPH particles. + */ + + if (comm->me == 0) { + printf("reading *FAILURE_MAX_PAIRWISE_STRAIN\n"); + } + + if (update_method != UPDATE_NONE) { + error->all(FLERR, "cannot use *FAILURE_MAX_PAIRWISE_STRAIN with updated Total-Lagrangian formalism"); + } + + t = string("*"); + iNextKwd = -1; + for (iarg = ioffset + 1; iarg < narg; iarg++) { + s = string(arg[iarg]); + if (s.compare(0, t.length(), t) == 0) { + iNextKwd = iarg; + break; + } + } + + if (iNextKwd < 0) { + sprintf(str, "no *KEYWORD terminates *FAILURE_MAX_PAIRWISE_STRAIN"); + error->all(FLERR, str); + } + + if (iNextKwd - ioffset != 1 + 1) { + sprintf(str, "expected 1 arguments following *FAILURE_MAX_PAIRWISE_STRAIN but got %d\n", iNextKwd - ioffset - 1); + error->all(FLERR, str); + } + + failureModel[itype].failure_max_pairwise_strain = true; + failureModel[itype].integration_point_wise = true; + Lookup[FAILURE_MAX_PAIRWISE_STRAIN_THRESHOLD][itype] = force->numeric(FLERR, arg[ioffset + 1]); + + if (comm->me == 0) { + printf("\n%60s\n", "maximum pairwise strain failure criterion"); + printf("%60s : %g\n", "failure occurs when pairwise strain reaches limit", + Lookup[FAILURE_MAX_PAIRWISE_STRAIN_THRESHOLD][itype]); + } + } // end pair based maximum strain failure criterion + else if (strcmp(arg[ioffset], "*FAILURE_MAX_PRINCIPAL_STRAIN") == 0) { + error->all(FLERR, "this failure model is currently unsupported"); + + /* + * maximum principal strain failure criterion + */ + if (comm->me == 0) { + printf("reading *FAILURE_MAX_PRINCIPAL_STRAIN\n"); + } + + t = string("*"); + iNextKwd = -1; + for (iarg = ioffset + 1; iarg < narg; iarg++) { + s = string(arg[iarg]); + if (s.compare(0, t.length(), t) == 0) { + iNextKwd = iarg; + break; + } + } + + if (iNextKwd < 0) { + sprintf(str, "no *KEYWORD terminates *FAILURE_MAX_PRINCIPAL_STRAIN"); + error->all(FLERR, str); + } + + if (iNextKwd - ioffset != 1 + 1) { + sprintf(str, "expected 1 arguments following *FAILURE_MAX_PRINCIPAL_STRAIN but got %d\n", iNextKwd - ioffset - 1); + error->all(FLERR, str); + } + + failureModel[itype].failure_max_principal_strain = true; + failureModel[itype].integration_point_wise = true; + Lookup[FAILURE_MAX_PRINCIPAL_STRAIN_THRESHOLD][itype] = force->numeric(FLERR, arg[ioffset + 1]); + + if (comm->me == 0) { + printf("\n%60s\n", "maximum principal strain failure criterion"); + printf("%60s : %g\n", "failure occurs when principal strain reaches limit", + Lookup[FAILURE_MAX_PRINCIPAL_STRAIN_THRESHOLD][itype]); + } + } // end maximum principal strain failure criterion + else if (strcmp(arg[ioffset], "*FAILURE_JOHNSON_COOK") == 0) { + error->all(FLERR, "this failure model is currently unsupported"); + if (comm->me == 0) { + printf("reading *FAILURE_JOHNSON_COOK\n"); + } + + t = string("*"); + iNextKwd = -1; + for (iarg = ioffset + 1; iarg < narg; iarg++) { + s = string(arg[iarg]); + if (s.compare(0, t.length(), t) == 0) { + iNextKwd = iarg; + break; + } + } + + if (iNextKwd < 0) { + sprintf(str, "no *KEYWORD terminates *FAILURE_JOHNSON_COOK"); + error->all(FLERR, str); + } + + if (iNextKwd - ioffset != 5 + 1) { + sprintf(str, "expected 5 arguments following *FAILURE_JOHNSON_COOK but got %d\n", iNextKwd - ioffset - 1); + error->all(FLERR, str); + } + + failureModel[itype].failure_johnson_cook = true; + failureModel[itype].integration_point_wise = true; + + Lookup[FAILURE_JC_D1][itype] = force->numeric(FLERR, arg[ioffset + 1]); + Lookup[FAILURE_JC_D2][itype] = force->numeric(FLERR, arg[ioffset + 2]); + Lookup[FAILURE_JC_D3][itype] = force->numeric(FLERR, arg[ioffset + 3]); + Lookup[FAILURE_JC_D4][itype] = force->numeric(FLERR, arg[ioffset + 4]); + Lookup[FAILURE_JC_EPDOT0][itype] = force->numeric(FLERR, arg[ioffset + 5]); + + if (comm->me == 0) { + printf("\n%60s\n", "Johnson-Cook failure criterion"); + printf("%60s : %g\n", "parameter d1", Lookup[FAILURE_JC_D1][itype]); + printf("%60s : %g\n", "parameter d2", Lookup[FAILURE_JC_D2][itype]); + printf("%60s : %g\n", "parameter d3", Lookup[FAILURE_JC_D3][itype]); + printf("%60s : %g\n", "parameter d4", Lookup[FAILURE_JC_D4][itype]); + printf("%60s : %g\n", "reference plastic strain rate", Lookup[FAILURE_JC_EPDOT0][itype]); + } + + } else if (strcmp(arg[ioffset], "*FAILURE_MAX_PRINCIPAL_STRESS") == 0) { + error->all(FLERR, "this failure model is currently unsupported"); + + /* + * maximum principal stress failure criterion + */ + + if (comm->me == 0) { + printf("reading *FAILURE_MAX_PRINCIPAL_STRESS\n"); + } + + t = string("*"); + iNextKwd = -1; + for (iarg = ioffset + 1; iarg < narg; iarg++) { + s = string(arg[iarg]); + if (s.compare(0, t.length(), t) == 0) { + iNextKwd = iarg; + break; + } + } + + if (iNextKwd < 0) { + sprintf(str, "no *KEYWORD terminates *FAILURE_MAX_PRINCIPAL_STRESS"); + error->all(FLERR, str); + } + + if (iNextKwd - ioffset != 1 + 1) { + sprintf(str, "expected 1 arguments following *FAILURE_MAX_PRINCIPAL_STRESS but got %d\n", iNextKwd - ioffset - 1); + error->all(FLERR, str); + } + + failureModel[itype].failure_max_principal_stress = true; + failureModel[itype].integration_point_wise = true; + Lookup[FAILURE_MAX_PRINCIPAL_STRESS_THRESHOLD][itype] = force->numeric(FLERR, arg[ioffset + 1]); + + if (comm->me == 0) { + printf("\n%60s\n", "maximum principal stress failure criterion"); + printf("%60s : %g\n", "failure occurs when principal stress reaches limit", + Lookup[FAILURE_MAX_PRINCIPAL_STRESS_THRESHOLD][itype]); + } + } // end maximum principal stress failure criterion + + else if (strcmp(arg[ioffset], "*FAILURE_ENERGY_RELEASE_RATE") == 0) { + if (comm->me == 0) { + printf("reading *FAILURE_ENERGY_RELEASE_RATE\n"); + } + + t = string("*"); + iNextKwd = -1; + for (iarg = ioffset + 1; iarg < narg; iarg++) { + s = string(arg[iarg]); + if (s.compare(0, t.length(), t) == 0) { + iNextKwd = iarg; + break; + } + } + + if (iNextKwd < 0) { + sprintf(str, "no *KEYWORD terminates *FAILURE_ENERGY_RELEASE_RATE"); + error->all(FLERR, str); + } + + if (iNextKwd - ioffset != 1 + 1) { + sprintf(str, "expected 1 arguments following *FAILURE_ENERGY_RELEASE_RATE but got %d\n", iNextKwd - ioffset - 1); + error->all(FLERR, str); + } + + failureModel[itype].failure_energy_release_rate = true; + Lookup[CRITICAL_ENERGY_RELEASE_RATE][itype] = force->numeric(FLERR, arg[ioffset + 1]); + + if (comm->me == 0) { + printf("\n%60s\n", "critical energy release rate failure criterion"); + printf("%60s : %g\n", "failure occurs when energy release rate reaches limit", + Lookup[CRITICAL_ENERGY_RELEASE_RATE][itype]); + } + } // end energy release rate failure criterion + + else { + sprintf(str, "unknown *KEYWORD: %s", arg[ioffset]); + error->all(FLERR, str); + } + + } + + setflag[itype][itype] = 1; + +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i + ------------------------------------------------------------------------- */ + +double PairTlsph::init_one(int i, int j) { + + if (!allocated) + allocate(); + + if (setflag[i][j] == 0) + error->all(FLERR, "All pair coeffs are not set"); + + if (force->newton == 1) + error->all(FLERR, "Pair style tlsph requires newton off"); + +// cutoff = sum of max I,J radii for +// dynamic/dynamic & dynamic/frozen interactions, but not frozen/frozen + + double cutoff = maxrad_dynamic[i] + maxrad_dynamic[j]; + cutoff = MAX(cutoff, maxrad_frozen[i] + maxrad_dynamic[j]); + cutoff = MAX(cutoff, maxrad_dynamic[i] + maxrad_frozen[j]); +//printf("cutoff for pair pair tlsph = %f\n", cutoff); + return cutoff; +} + +/* ---------------------------------------------------------------------- + init specific to this pair style + ------------------------------------------------------------------------- */ + +void PairTlsph::init_style() { + int i; + + if (force->newton_pair == 1) { + error->all(FLERR, "Pair style tlsph requires newton pair off"); + } + +// request a granular neighbor list + int irequest = neighbor->request(this); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->gran = 1; + +// set maxrad_dynamic and maxrad_frozen for each type +// include future Fix pour particles as dynamic + + for (i = 1; i <= atom->ntypes; i++) + onerad_dynamic[i] = onerad_frozen[i] = 0.0; + + double *radius = atom->radius; + int *type = atom->type; + int nlocal = atom->nlocal; + + for (i = 0; i < nlocal; i++) + onerad_dynamic[type[i]] = MAX(onerad_dynamic[type[i]], radius[i]); + + MPI_Allreduce(&onerad_dynamic[1], &maxrad_dynamic[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world); + MPI_Allreduce(&onerad_frozen[1], &maxrad_frozen[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world); + +// if first init, create Fix needed for storing reference configuration neighbors + + int igroup = group->find("tlsph"); + if (igroup == -1) + error->all(FLERR, "Pair style tlsph requires its particles to be part of a group named tlsph. This group does not exist."); + + if (fix_tlsph_reference_configuration == NULL) { + char **fixarg = new char*[3]; + fixarg[0] = (char *) "SMD_TLSPH_NEIGHBORS"; + fixarg[1] = (char *) "tlsph"; + fixarg[2] = (char *) "SMD_TLSPH_NEIGHBORS"; + modify->add_fix(3, fixarg); + delete[] fixarg; + fix_tlsph_reference_configuration = (FixSMD_TLSPH_ReferenceConfiguration *) modify->fix[modify->nfix - 1]; + fix_tlsph_reference_configuration->pair = this; + } + +// find associated SMD_TLSPH_NEIGHBORS fix that must exist +// could have changed locations in fix list since created + + ifix_tlsph = -1; + for (int i = 0; i < modify->nfix; i++) + if (strcmp(modify->fix[i]->style, "SMD_TLSPH_NEIGHBORS") == 0) + ifix_tlsph = i; + if (ifix_tlsph == -1) + error->all(FLERR, "Fix SMD_TLSPH_NEIGHBORS does not exist"); + +} + +/* ---------------------------------------------------------------------- + neighbor callback to inform pair style of neighbor list to use + optional granular history list + ------------------------------------------------------------------------- */ + +void PairTlsph::init_list(int id, NeighList *ptr) { + if (id == 0) + list = ptr; +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based arrays + ------------------------------------------------------------------------- */ + +double PairTlsph::memory_usage() { + + return 118 * nmax * sizeof(double); +} + +/* ---------------------------------------------------------------------- + extract method to provide access to this class' data structures + ------------------------------------------------------------------------- */ + +void *PairTlsph::extract(const char *str, int &i) { +//printf("in PairTlsph::extract\n"); + if (strcmp(str, "smd/tlsph/Fincr_ptr") == 0) { + return (void *) Fincr; + } else if (strcmp(str, "smd/tlsph/detF_ptr") == 0) { + return (void *) detF; + } else if (strcmp(str, "smd/tlsph/PK1_ptr") == 0) { + return (void *) PK1; + } else if (strcmp(str, "smd/tlsph/smoothVel_ptr") == 0) { + return (void *) smoothVelDifference; + } else if (strcmp(str, "smd/tlsph/numNeighsRefConfig_ptr") == 0) { + return (void *) numNeighsRefConfig; + } else if (strcmp(str, "smd/tlsph/stressTensor_ptr") == 0) { + return (void *) CauchyStress; + } else if (strcmp(str, "smd/tlsph/updateFlag_ptr") == 0) { + return (void *) &updateFlag; + } else if (strcmp(str, "smd/tlsph/strain_rate_ptr") == 0) { + return (void *) D; + } else if (strcmp(str, "smd/tlsph/hMin_ptr") == 0) { + return (void *) &hMin; + } else if (strcmp(str, "smd/tlsph/dtCFL_ptr") == 0) { + return (void *) &dtCFL; + } else if (strcmp(str, "smd/tlsph/dtRelative_ptr") == 0) { + return (void *) &dtRelative; + } else if (strcmp(str, "smd/tlsph/hourglass_error_ptr") == 0) { + return (void *) hourglass_error; + } else if (strcmp(str, "smd/tlsph/particle_dt_ptr") == 0) { + return (void *) particle_dt; + } else if (strcmp(str, "smd/tlsph/rotation_ptr") == 0) { + return (void *) R; + } + + return NULL; +} + +/* ---------------------------------------------------------------------- */ + +int PairTlsph::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) { + int i, j, m; + int *mol = atom->molecule; + double *damage = atom->damage; + double *eff_plastic_strain = atom->eff_plastic_strain; + double *eff_plastic_strain_rate = atom->eff_plastic_strain_rate; + +//printf("in PairTlsph::pack_forward_comm\n"); + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = PK1[j](0, 0); // PK1 is not symmetric + buf[m++] = PK1[j](0, 1); + buf[m++] = PK1[j](0, 2); + buf[m++] = PK1[j](1, 0); + buf[m++] = PK1[j](1, 1); + buf[m++] = PK1[j](1, 2); + buf[m++] = PK1[j](2, 0); + buf[m++] = PK1[j](2, 1); + buf[m++] = PK1[j](2, 2); // 9 + + buf[m++] = Fincr[j](0, 0); // Fincr is not symmetric + buf[m++] = Fincr[j](0, 1); + buf[m++] = Fincr[j](0, 2); + buf[m++] = Fincr[j](1, 0); + buf[m++] = Fincr[j](1, 1); + buf[m++] = Fincr[j](1, 2); + buf[m++] = Fincr[j](2, 0); + buf[m++] = Fincr[j](2, 1); + buf[m++] = Fincr[j](2, 2); // 9 + 9 = 18 + + buf[m++] = mol[j]; //19 + buf[m++] = damage[j]; //20 + buf[m++] = eff_plastic_strain[j]; //21 + buf[m++] = eff_plastic_strain_rate[j]; //22 + + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void PairTlsph::unpack_forward_comm(int n, int first, double *buf) { + int i, m, last; + int *mol = atom->molecule; + double *damage = atom->damage; + double *eff_plastic_strain = atom->eff_plastic_strain; + double *eff_plastic_strain_rate = atom->eff_plastic_strain_rate; + +//printf("in PairTlsph::unpack_forward_comm\n"); + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + + PK1[i](0, 0) = buf[m++]; // PK1 is not symmetric + PK1[i](0, 1) = buf[m++]; + PK1[i](0, 2) = buf[m++]; + PK1[i](1, 0) = buf[m++]; + PK1[i](1, 1) = buf[m++]; + PK1[i](1, 2) = buf[m++]; + PK1[i](2, 0) = buf[m++]; + PK1[i](2, 1) = buf[m++]; + PK1[i](2, 2) = buf[m++]; + + Fincr[i](0, 0) = buf[m++]; + Fincr[i](0, 1) = buf[m++]; + Fincr[i](0, 2) = buf[m++]; + Fincr[i](1, 0) = buf[m++]; + Fincr[i](1, 1) = buf[m++]; + Fincr[i](1, 2) = buf[m++]; + Fincr[i](2, 0) = buf[m++]; + Fincr[i](2, 1) = buf[m++]; + Fincr[i](2, 2) = buf[m++]; + + mol[i] = static_cast(buf[m++]); + damage[i] = buf[m++]; + eff_plastic_strain[i] = buf[m++]; //22 + eff_plastic_strain_rate[i] = buf[m++]; //23 + } +} + +/* ---------------------------------------------------------------------- + compute effective P-wave speed + determined by longitudinal modulus + ------------------------------------------------------------------------- */ + +void PairTlsph::effective_longitudinal_modulus(const int itype, const double dt, const double d_iso, const double p_rate, + const Matrix3d d_dev, const Matrix3d sigma_dev_rate, const double damage, double &K_eff, double &mu_eff, double &M_eff) { + double M0; // initial longitudinal modulus + double shear_rate_sq; + +// if (damage >= 0.5) { +// M_eff = Lookup[M_MODULUS][itype]; +// K_eff = Lookup[BULK_MODULUS][itype]; +// mu_eff = Lookup[SHEAR_MODULUS][itype]; +// return; +// } + + M0 = Lookup[M_MODULUS][itype]; + + if (dt * d_iso > 1.0e-6) { + K_eff = p_rate / d_iso; + if (K_eff < 0.0) { // it is possible for K_eff to become negative due to strain softening +// if (damage == 0.0) { +// error->one(FLERR, "computed a negative effective bulk modulus but particle is not damaged."); +// } + K_eff = Lookup[BULK_MODULUS][itype]; + } + } else { + K_eff = Lookup[BULK_MODULUS][itype]; + } + + if (domain->dimension == 3) { +// Calculate 2 mu by looking at ratio shear stress / shear strain. Use numerical softening to avoid divide-by-zero. + mu_eff = 0.5 + * (sigma_dev_rate(0, 1) / (d_dev(0, 1) + 1.0e-16) + sigma_dev_rate(0, 2) / (d_dev(0, 2) + 1.0e-16) + + sigma_dev_rate(1, 2) / (d_dev(1, 2) + 1.0e-16)); + +// Calculate magnitude of deviatoric strain rate. This is used for deciding if shear modulus should be computed from current rate or be taken as the initial value. + shear_rate_sq = d_dev(0, 1) * d_dev(0, 1) + d_dev(0, 2) * d_dev(0, 2) + d_dev(1, 2) * d_dev(1, 2); + } else { + mu_eff = 0.5 * (sigma_dev_rate(0, 1) / (d_dev(0, 1) + 1.0e-16)); + shear_rate_sq = d_dev(0, 1) * d_dev(0, 1); + } + + if (dt * dt * shear_rate_sq < 1.0e-8) { + mu_eff = Lookup[SHEAR_MODULUS][itype]; + } + + if (mu_eff < Lookup[SHEAR_MODULUS][itype]) { // it is possible for mu_eff to become negative due to strain softening +// if (damage == 0.0) { +// printf("mu_eff = %f, tau=%f, gamma=%f\n", mu_eff, sigma_dev_rate(0, 1), d_dev(0, 1)); +// error->message(FLERR, "computed a negative effective shear modulus but particle is not damaged."); +// } + mu_eff = Lookup[SHEAR_MODULUS][itype]; + } + +//mu_eff = Lookup[SHEAR_MODULUS][itype]; + + if (K_eff < 0.0) { + printf("K_eff = %f, p_rate=%f, vol_rate=%f\n", K_eff, p_rate, d_iso); + } + + if (mu_eff < 0.0) { + printf("mu_eff = %f, tau=%f, gamma=%f\n", mu_eff, sigma_dev_rate(0, 1), d_dev(0, 1)); + error->one(FLERR, ""); + } + + M_eff = (K_eff + 4.0 * mu_eff / 3.0); // effective dilational modulus, see Pronto 2d eqn 3.4.8 + + if (M_eff < M0) { // do not allow effective dilatational modulus to decrease beyond its initial value + M_eff = M0; + } +} + +/* ---------------------------------------------------------------------- + compute pressure. Called from AssembleStress(). + ------------------------------------------------------------------------- */ +void PairTlsph::ComputePressure(const int i, const double rho, const double mass_specific_energy, const double vol_specific_energy, + const double pInitial, const double d_iso, double &pFinal, double &p_rate) { + int *type = atom->type; + double dt = update->dt; + + int itype; + + itype = type[i]; + + switch (eos[itype]) { + case EOS_LINEAR: + LinearEOS(Lookup[BULK_MODULUS][itype], pInitial, d_iso, dt, pFinal, p_rate); + break; + case EOS_NONE: + pFinal = 0.0; + p_rate = 0.0; + break; + case EOS_SHOCK: +// rho, rho0, e, e0, c0, S, Gamma, pInitial, dt, &pFinal, &p_rate); + ShockEOS(rho, Lookup[REFERENCE_DENSITY][itype], mass_specific_energy, 0.0, Lookup[EOS_SHOCK_C0][itype], + Lookup[EOS_SHOCK_S][itype], Lookup[EOS_SHOCK_GAMMA][itype], pInitial, dt, pFinal, p_rate); + break; + case EOS_POLYNOMIAL: + polynomialEOS(rho, Lookup[REFERENCE_DENSITY][itype], vol_specific_energy, Lookup[EOS_POLYNOMIAL_C0][itype], + Lookup[EOS_POLYNOMIAL_C1][itype], Lookup[EOS_POLYNOMIAL_C2][itype], Lookup[EOS_POLYNOMIAL_C3][itype], + Lookup[EOS_POLYNOMIAL_C4][itype], Lookup[EOS_POLYNOMIAL_C5][itype], Lookup[EOS_POLYNOMIAL_C6][itype], pInitial, dt, + pFinal, p_rate); + + break; + default: + error->one(FLERR, "unknown EOS."); + break; + } +} + +/* ---------------------------------------------------------------------- + Compute stress deviator. Called from AssembleStress(). + ------------------------------------------------------------------------- */ +void PairTlsph::ComputeStressDeviator(const int i, const Matrix3d sigmaInitial_dev, const Matrix3d d_dev, Matrix3d &sigmaFinal_dev, + Matrix3d &sigma_dev_rate, double &plastic_strain_increment) { + double *eff_plastic_strain = atom->eff_plastic_strain; + double *eff_plastic_strain_rate = atom->eff_plastic_strain_rate; + int *type = atom->type; + double *rmass = atom->rmass; +//double *vfrac = atom->vfrac; + double *e = atom->e; + double dt = update->dt; + double yieldStress; + int itype; + + double mass_specific_energy = e[i] / rmass[i]; // energy per unit mass + plastic_strain_increment = 0.0; + itype = type[i]; + + switch (strengthModel[itype]) { + case STRENGTH_LINEAR: + + sigma_dev_rate = 2.0 * Lookup[SHEAR_MODULUS][itype] * d_dev; + sigmaFinal_dev = sigmaInitial_dev + dt * sigma_dev_rate; + + break; + case LINEAR_DEFGRAD: +//LinearStrengthDefgrad(Lookup[LAME_LAMBDA][itype], Lookup[SHEAR_MODULUS][itype], Fincr[i], &sigmaFinal_dev); +//eff_plastic_strain[i] = 0.0; +//p_rate = pInitial - sigmaFinal_dev.trace() / 3.0; +//sigma_dev_rate = sigmaInitial_dev - Deviator(sigmaFinal_dev); + error->one(FLERR, "LINEAR_DEFGRAD is only for debugging purposes and currently deactivated."); + R[i].setIdentity(); + break; + case STRENGTH_LINEAR_PLASTIC: + + yieldStress = Lookup[YIELD_STRESS][itype] + Lookup[HARDENING_PARAMETER][itype] * eff_plastic_strain[i]; + LinearPlasticStrength(Lookup[SHEAR_MODULUS][itype], yieldStress, sigmaInitial_dev, d_dev, dt, sigmaFinal_dev, + sigma_dev_rate, plastic_strain_increment); + break; + case STRENGTH_JOHNSON_COOK: + JohnsonCookStrength(Lookup[SHEAR_MODULUS][itype], Lookup[HEAT_CAPACITY][itype], mass_specific_energy, Lookup[JC_A][itype], + Lookup[JC_B][itype], Lookup[JC_a][itype], Lookup[JC_C][itype], Lookup[JC_epdot0][itype], Lookup[JC_T0][itype], + Lookup[JC_Tmelt][itype], Lookup[JC_M][itype], dt, eff_plastic_strain[i], eff_plastic_strain_rate[i], + sigmaInitial_dev, d_dev, sigmaFinal_dev, sigma_dev_rate, plastic_strain_increment); + break; + case STRENGTH_NONE: + sigmaFinal_dev.setZero(); + sigma_dev_rate.setZero(); + break; + default: + error->one(FLERR, "unknown strength model."); + break; + } + +} + +/* ---------------------------------------------------------------------- + Compute damage. Called from AssembleStress(). + ------------------------------------------------------------------------- */ +void PairTlsph::ComputeDamage(const int i, const Matrix3d strain, const Matrix3d stress, Matrix3d &stress_damaged) { + double *eff_plastic_strain = atom->eff_plastic_strain; + double *eff_plastic_strain_rate = atom->eff_plastic_strain_rate; + double *radius = atom->radius; + double *damage = atom->damage; + int *type = atom->type; + int itype = type[i]; + bool damage_flag = false; + double jc_failure_strain; +//double damage_gap, damage_rate; + Matrix3d eye, stress_deviator; + + eye.setIdentity(); + stress_deviator = Deviator(stress); + double pressure = -stress.trace() / 3.0; + + if (failureModel[itype].failure_max_principal_stress) { + error->one(FLERR, "not yet implemented"); + /* + * maximum stress failure criterion: + */ + damage_flag = IsotropicMaxStressDamage(stress, Lookup[FAILURE_MAX_PRINCIPAL_STRESS_THRESHOLD][itype]); + } else if (failureModel[itype].failure_max_principal_strain) { + error->one(FLERR, "not yet implemented"); + /* + * maximum strain failure criterion: + */ + damage_flag = IsotropicMaxStrainDamage(strain, Lookup[FAILURE_MAX_PRINCIPAL_STRAIN_THRESHOLD][itype]); + } else if (failureModel[itype].failure_max_plastic_strain) { + if (eff_plastic_strain[i] >= Lookup[FAILURE_MAX_PLASTIC_STRAIN_THRESHOLD][itype]) { + damage_flag = true; + damage[i] = 1.0; + //double damage_gap = 0.5 * Lookup[FAILURE_MAX_PLASTIC_STRAIN_THRESHOLD][itype]; + //damage[i] = (eff_plastic_strain[i] - Lookup[FAILURE_MAX_PLASTIC_STRAIN_THRESHOLD][itype]) / damage_gap; + } + } else if (failureModel[itype].failure_johnson_cook) { + + //cout << "this is stress deviator" << stress_deviator << endl; + + jc_failure_strain = JohnsonCookFailureStrain(pressure, stress_deviator, Lookup[FAILURE_JC_D1][itype], + Lookup[FAILURE_JC_D2][itype], Lookup[FAILURE_JC_D3][itype], Lookup[FAILURE_JC_D4][itype], + Lookup[FAILURE_JC_EPDOT0][itype], eff_plastic_strain_rate[i]); + + //cout << "plastic strain increment is " << plastic_strain_increment << " jc fs is " << jc_failure_strain << endl; + //printf("JC failure strain is: %f\n", jc_failure_strain); + + if (eff_plastic_strain[i] >= jc_failure_strain) { + damage_flag = true; + double damage_rate = Lookup[SIGNAL_VELOCITY][itype] / (100.0 * radius[i]); + damage[i] += damage_rate * update->dt; + //damage[i] = 1.0; + } + } + + /* + * Apply damage to integration point + */ + +// damage[i] = MIN(damage[i], 0.8); +// +// if (pressure > 0.0) { // compression: particle can carry compressive load but reduced shear +// stress_damaged = -pressure * eye + (1.0 - damage[i]) * Deviator(stress); +// } else { // tension: particle has reduced tensile and shear load bearing capability +// stress_damaged = (1.0 - damage[i]) * (-pressure * eye + Deviator(stress)); +// } + +} + diff --git a/src/USER-SMD/pair_smd_tlsph.h b/src/USER-SMD/pair_smd_tlsph.h new file mode 100644 index 0000000000..b02a1c585e --- /dev/null +++ b/src/USER-SMD/pair_smd_tlsph.h @@ -0,0 +1,229 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(smd/tlsph,PairTlsph) + +#else + +#ifndef LMP_TLSPH_NEW_H +#define LMP_TLSPH_NEW_H + +#include "pair.h" +#include +#include +#include +#include + +using namespace std; +using namespace Eigen; +namespace LAMMPS_NS { + +class PairTlsph: public Pair { +public: + + PairTlsph(class LAMMPS *); + virtual ~PairTlsph(); + virtual void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + double init_one(int, int); + void init_style(); + void init_list(int, class NeighList *); + void write_restart_settings(FILE *) { + } + void read_restart_settings(FILE *) { + } + virtual double memory_usage(); + void compute_shape_matrix(void); + void material_model(void); + void *extract(const char *, int &); + int pack_forward_comm(int, int *, double *, int, int *); + void unpack_forward_comm(int, int, double *); + void AssembleStress(); + + void PreCompute(); + void ComputeForces(int eflag, int vflag); + void effective_longitudinal_modulus(const int itype, const double dt, const double d_iso, const double p_rate, + const Matrix3d d_dev, const Matrix3d sigma_dev_rate, const double damage, double &K_eff, double &mu_eff, double &M_eff); + + void ComputePressure(const int i, const double rho, const double mass_specific_energy, const double vol_specific_energy, + const double pInitial, const double d_iso, double &pFinal, double &p_rate); + void ComputeStressDeviator(const int i, const Matrix3d sigmaInitial_dev, const Matrix3d d_dev, Matrix3d &sigmaFinal_dev, + Matrix3d &sigma_dev_rate, double &plastic_strain_increment); + void ComputeDamage(const int i, const Matrix3d strain, const Matrix3d sigmaFinal, Matrix3d &sigma_damaged); + + +protected: + void allocate(); + char *suffix; + + /* + * per-type arrays + */ + int *strengthModel, *eos; + double *onerad_dynamic, *onerad_frozen, *maxrad_dynamic, *maxrad_frozen; + + /* + * per atom arrays + */ + Matrix3d *K, *PK1, *Fdot, *Fincr; + Matrix3d *R; // rotation matrix + Matrix3d *FincrInv; + Matrix3d *D, *W; // strain rate and spin tensor + Vector3d *smoothVelDifference; + Matrix3d *CauchyStress; + double *detF, *particle_dt; + double *hourglass_error; + int *numNeighsRefConfig; + + int nmax; // max number of atoms on this proc + double hMin; // minimum kernel radius for two particles + double dtCFL; + double dtRelative; // relative velocity of two particles, divided by sound speed + int updateFlag; + double update_threshold; // updateFlage is set to one if the relative displacement of a pair exceeds update_threshold + double cut_comm; + + enum { + UPDATE_NONE = 5000, UPDATE_CONSTANT_THRESHOLD = 5001, UPDATE_PAIRWISE_RATIO = 5002, + }; + + enum { + LINEAR_DEFGRAD = 0, + STRENGTH_LINEAR = 1, + STRENGTH_LINEAR_PLASTIC = 2, + STRENGTH_JOHNSON_COOK = 3, + STRENGTH_NONE = 4, + EOS_LINEAR = 5, + EOS_SHOCK = 6, + EOS_POLYNOMIAL = 7, + EOS_NONE = 8, + REFERENCE_DENSITY = 9, + YOUNGS_MODULUS = 10, + POISSON_RATIO = 11, + HOURGLASS_CONTROL_AMPLITUDE = 12, + HEAT_CAPACITY = 13, + LAME_LAMBDA = 14, + SHEAR_MODULUS = 15, + M_MODULUS = 16, + SIGNAL_VELOCITY = 17, + BULK_MODULUS = 18, + VISCOSITY_Q1 = 19, + VISCOSITY_Q2 = 20, + YIELD_STRESS = 21, + FAILURE_MAX_PLASTIC_STRAIN_THRESHOLD = 22, + JC_A = 23, + JC_B = 24, + JC_a = 25, + JC_C = 26, + JC_epdot0 = 27, + JC_T0 = 28, + JC_Tmelt = 29, + JC_M = 30, + EOS_SHOCK_C0 = 31, + EOS_SHOCK_S = 32, + EOS_SHOCK_GAMMA = 33, + HARDENING_PARAMETER = 34, + FAILURE_MAX_PRINCIPAL_STRAIN_THRESHOLD = 35, + FAILURE_MAX_PRINCIPAL_STRESS_THRESHOLD = 36, + FAILURE_MAX_PAIRWISE_STRAIN_THRESHOLD = 37, + EOS_POLYNOMIAL_C0 = 38, + EOS_POLYNOMIAL_C1 = 39, + EOS_POLYNOMIAL_C2 = 40, + EOS_POLYNOMIAL_C3 = 41, + EOS_POLYNOMIAL_C4 = 42, + EOS_POLYNOMIAL_C5 = 43, + EOS_POLYNOMIAL_C6 = 44, + + FAILURE_JC_D1 = 45, + FAILURE_JC_D2 = 46, + FAILURE_JC_D3 = 47, + FAILURE_JC_D4 = 48, + FAILURE_JC_EPDOT0 = 49, + + CRITICAL_ENERGY_RELEASE_RATE = 50, + + MAX_KEY_VALUE = 51 + }; + + struct failure_types { // this is defined per type and determines which failure/damage model is active + bool failure_none; + bool failure_max_principal_strain; + bool failure_max_principal_stress; + bool failure_max_plastic_strain; + bool failure_johnson_cook; + bool failure_max_pairwise_strain; + bool integration_point_wise; // true if failure model applies to stress/strain state of integration point + bool failure_energy_release_rate; + + failure_types() { + failure_none = true; + failure_max_principal_strain = false; + failure_max_principal_stress = false; + failure_max_plastic_strain = false; + failure_johnson_cook = false; + failure_max_pairwise_strain = false; + integration_point_wise = false; + failure_energy_release_rate = false; + //printf("constructed failure type\n"); + } + }; + failure_types *failureModel; + + int ifix_tlsph; + int update_method; + + class FixSMD_TLSPH_ReferenceConfiguration *fix_tlsph_reference_configuration; + +private: + double **Lookup; // holds per-type material parameters for the quantities defined in enum statement above. + bool first; // if first is true, do not perform any computations, beacuse reference configuration is not ready yet. +}; + +} + +#endif +#endif + +/* + * materialCoeffs array for EOS parameters: + * 1: rho0 + * + * + * materialCoeffs array for strength parameters: + * + * Common + * 10: maximum strain threshold for damage model + * 11: maximum stress threshold for damage model + * + * Linear Plasticity model: + * 12: plastic yield stress + * + * + * Blei: rho = 11.34e-6, c0=2000, s=1.46, Gamma=2.77 + * Stahl 1403: rho = 7.86e-3, c=4569, s=1.49, Gamma=2.17 + */ + diff --git a/src/USER-SMD/pair_smd_triangulated_surface.cpp b/src/USER-SMD/pair_smd_triangulated_surface.cpp new file mode 100644 index 0000000000..9fc057e1db --- /dev/null +++ b/src/USER-SMD/pair_smd_triangulated_surface.cpp @@ -0,0 +1,846 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Mike Parks (SNL) + ------------------------------------------------------------------------- */ + +#include "math.h" +#include "float.h" +#include "stdlib.h" +#include "string.h" +#include "pair_smd_triangulated_surface.h" +#include "atom.h" +#include "domain.h" +#include "force.h" +#include "update.h" +#include "modify.h" +#include "fix.h" +#include "comm.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "memory.h" +#include "error.h" +#include +#include +#include + +using namespace std; +using namespace LAMMPS_NS; +using namespace Eigen; + +#define SQRT2 1.414213562e0 + +/* ---------------------------------------------------------------------- */ + +PairTriSurf::PairTriSurf(LAMMPS *lmp) : + Pair(lmp) { + + onerad_dynamic = onerad_frozen = maxrad_dynamic = maxrad_frozen = NULL; + bulkmodulus = NULL; + kn = NULL; + scale = 1.0; +} + +/* ---------------------------------------------------------------------- */ + +PairTriSurf::~PairTriSurf() { + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + memory->destroy(bulkmodulus); + memory->destroy(kn); + + delete[] onerad_dynamic; + delete[] onerad_frozen; + delete[] maxrad_dynamic; + delete[] maxrad_frozen; + } +} + +/* ---------------------------------------------------------------------- */ + +void PairTriSurf::compute(int eflag, int vflag) { + int i, j, ii, jj, inum, jnum, itype, jtype; + double rsq, r, evdwl, fpair; + int *ilist, *jlist, *numneigh, **firstneigh; + double rcut, r_geom, delta, r_tri, r_particle, touch_distance, dt_crit; + int tri, particle; + Vector3d normal, x1, x2, x3, x4, x13, x23, x43, w, cp, x4cp, vnew, v_old; + ; + Vector3d xi, x_center, dx; + Matrix2d C; + Vector2d w2d, rhs; + + evdwl = 0.0; + if (eflag || vflag) + ev_setup(eflag, vflag); + else + evflag = vflag_fdotr = 0; + + int *mol = atom->molecule; + double **f = atom->f; + double **smd_data_9 = atom->smd_data_9; + double **x = atom->x; + double **x0 = atom->x0; + double **v = atom->v; + double *rmass = atom->rmass; + int *type = atom->type; + int nlocal = atom->nlocal; + double *radius = atom->contact_radius; + double rcutSq; + Vector3d offset; + + int newton_pair = force->newton_pair; + int periodic = (domain->xperiodic || domain->yperiodic || domain->zperiodic); + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + int max_neighs = 0; + stable_time_increment = 1.0e22; + + // loop over neighbors of my atoms using a half neighbor list + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + max_neighs = MAX(max_neighs, jnum); + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + + j &= NEIGHMASK; + + jtype = type[j]; + + /* + * decide which one of i, j is triangle and which is particle + */ + if ((mol[i] < 65535) && (mol[j] >= 65535)) { + particle = i; + tri = j; + } else if ((mol[j] < 65535) && (mol[i] >= 65535)) { + particle = j; + tri = i; + } else { + error->one(FLERR, "unknown case"); + } + + //x_center << x[tri][0], x[tri][1], x[tri][2]; // center of triangle + x_center(0) = x[tri][0]; + x_center(1) = x[tri][1]; + x_center(2) = x[tri][2]; + //x4 << x[particle][0], x[particle][1], x[particle][2]; + x4(0) = x[particle][0]; + x4(1) = x[particle][1]; + x4(2) = x[particle][2]; + dx = x_center - x4; // + if (periodic) { + domain->minimum_image(dx(0), dx(1), dx(2)); + } + rsq = dx.squaredNorm(); + + r_tri = scale * radius[tri]; + r_particle = scale * radius[particle]; + rcut = r_tri + r_particle; + rcutSq = rcut * rcut; + + //printf("type i=%d, type j=%d, r=%f, ri=%f, rj=%f\n", itype, jtype, sqrt(rsq), ri, rj); + + if (rsq < rcutSq) { + + /* + * gather triangle information + */ + normal(0) = x0[tri][0]; + normal(1) = x0[tri][1]; + normal(2) = x0[tri][2]; + + /* + * distance check: is particle closer than its radius to the triangle plane? + */ + if (fabs(dx.dot(normal)) < radius[particle]) { + /* + * get other two triangle vertices + */ + x1(0) = smd_data_9[tri][0]; + x1(1) = smd_data_9[tri][1]; + x1(2) = smd_data_9[tri][2]; + x2(0) = smd_data_9[tri][3]; + x2(1) = smd_data_9[tri][4]; + x2(2) = smd_data_9[tri][5]; + x3(0) = smd_data_9[tri][6]; + x3(1) = smd_data_9[tri][7]; + x3(2) = smd_data_9[tri][8]; + + PointTriangleDistance(x4, x1, x2, x3, cp, r); + + /* + * distance to closest point + */ + x4cp = x4 - cp; + + /* + * flip normal to point in direction of x4cp + */ + + if (x4cp.dot(normal) < 0.0) { + normal *= -1.0; + } + + /* + * penalty force pushes particle away from triangle + */ + if (r < 1.0 * radius[particle]) { + + delta = radius[particle] - r; // overlap distance + r_geom = radius[particle]; + fpair = 1.066666667e0 * bulkmodulus[itype][jtype] * delta * sqrt(delta * r_geom); + dt_crit = 3.14 * sqrt(rmass[particle] / (fpair / delta)); + stable_time_increment = MIN(stable_time_increment, dt_crit); + + evdwl = r * fpair * 0.4e0 * delta; // GCG 25 April: this expression conserves total energy + + fpair /= (r + 1.0e-2 * radius[particle]); // divide by r + softening and multiply with non-normalized distance vector + + if (particle < nlocal) { + f[particle][0] += x4cp(0) * fpair; + f[particle][1] += x4cp(1) * fpair; + f[particle][2] += x4cp(2) * fpair; + } + + if (tri < nlocal) { + f[tri][0] -= x4cp(0) * fpair; + f[tri][1] -= x4cp(1) * fpair; + f[tri][2] -= x4cp(2) * fpair; + } + + if (evflag) { + ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, x4cp(0), x4cp(1), x4cp(2)); + } + + } + + /* + * if particle comes too close to triangle, reflect its velocity and explicitely move it away + */ + + touch_distance = 1.0 * radius[particle]; + if (r < touch_distance) { + + /* + * reflect velocity if it points toward triangle + */ + + normal = x4cp / r; + + //v_old << v[particle][0], v[particle][1], v[particle][2]; + v_old(0) = v[particle][0]; + v_old(1) = v[particle][1]; + v_old(2) = v[particle][2]; + if (v_old.dot(normal) < 0.0) { + //printf("flipping velocity\n"); + vnew = 1.0 * (-2.0 * v_old.dot(normal) * normal + v_old); + v[particle][0] = vnew(0); + v[particle][1] = vnew(1); + v[particle][2] = vnew(2); + } + + //printf("moving particle on top of triangle\n"); + x[particle][0] = cp(0) + touch_distance * normal(0); + x[particle][1] = cp(1) + touch_distance * normal(1); + x[particle][2] = cp(2) + touch_distance * normal(2); + } + + } + } + } + } + +// int max_neighs_all = 0; +// MPI_Allreduce(&max_neighs, &max_neighs_all, 1, MPI_INT, MPI_MAX, world); +// if (comm->me == 0) { +// printf("max. neighs in tri pair is %d\n", max_neighs_all); +// } +// +// double stable_time_increment_all = 0.0; +// MPI_Allreduce(&stable_time_increment, &stable_time_increment_all, 1, MPI_DOUBLE, MPI_MIN, world); +// if (comm->me == 0) { +// printf("stable time step tri pair is %f\n", stable_time_increment_all); +// } +} + +/* ---------------------------------------------------------------------- + allocate all arrays + ------------------------------------------------------------------------- */ + +void PairTriSurf::allocate() { + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag, n + 1, n + 1, "pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(bulkmodulus, n + 1, n + 1, "pair:kspring"); + memory->create(kn, n + 1, n + 1, "pair:kn"); + + memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); // always needs to be allocated, even with granular neighborlist + + onerad_dynamic = new double[n + 1]; + onerad_frozen = new double[n + 1]; + maxrad_dynamic = new double[n + 1]; + maxrad_frozen = new double[n + 1]; +} + +/* ---------------------------------------------------------------------- + global settings + ------------------------------------------------------------------------- */ + +void PairTriSurf::settings(int narg, char **arg) { + if (narg != 1) + error->all(FLERR, "Illegal number of args for pair_style smd/tri_surface"); + + scale = force->numeric(FLERR, arg[0]); + if (comm->me == 0) { + printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n"); + printf("SMD/TRI_SURFACE CONTACT SETTINGS:\n"); + printf("... effective contact radius is scaled by %f\n", scale); + printf(">>========>>========>>========>>========>>========>>========>>========>>========\n"); + } + +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs + ------------------------------------------------------------------------- */ + +void PairTriSurf::coeff(int narg, char **arg) { + if (narg != 3) + error->all(FLERR, "Incorrect args for pair coefficients"); + if (!allocated) + allocate(); + + int ilo, ihi, jlo, jhi; + force->bounds(arg[0], atom->ntypes, ilo, ihi); + force->bounds(arg[1], atom->ntypes, jlo, jhi); + + double bulkmodulus_one = atof(arg[2]); + + // set short-range force constant + double kn_one = 0.0; + if (domain->dimension == 3) { + kn_one = (16. / 15.) * bulkmodulus_one; //assuming poisson ratio = 1/4 for 3d + } else { + kn_one = 0.251856195 * (2. / 3.) * bulkmodulus_one; //assuming poisson ratio = 1/3 for 2d + } + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo, i); j <= jhi; j++) { + bulkmodulus[i][j] = bulkmodulus_one; + kn[i][j] = kn_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) + error->all(FLERR, "Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i + ------------------------------------------------------------------------- */ + +double PairTriSurf::init_one(int i, int j) { + + if (!allocated) + allocate(); + + if (setflag[i][j] == 0) + error->all(FLERR, "All pair coeffs are not set"); + + bulkmodulus[j][i] = bulkmodulus[i][j]; + kn[j][i] = kn[i][j]; + + // cutoff = sum of max I,J radii for + // dynamic/dynamic & dynamic/frozen interactions, but not frozen/frozen + + double cutoff = maxrad_dynamic[i] + maxrad_dynamic[j]; + cutoff = MAX(cutoff, maxrad_frozen[i] + maxrad_dynamic[j]); + cutoff = MAX(cutoff, maxrad_dynamic[i] + maxrad_frozen[j]); + + if (comm->me == 0) { + printf("cutoff for pair smd/smd/tri_surface = %f\n", cutoff); + } + return cutoff; +} + +/* ---------------------------------------------------------------------- + init specific to this pair style + ------------------------------------------------------------------------- */ + +void PairTriSurf::init_style() { + int i; + + // error checks + + if (!atom->contact_radius_flag) + error->all(FLERR, "Pair style smd/smd/tri_surface requires atom style with contact_radius"); + + // old: half list + int irequest = neighbor->request(this); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->gran = 1; + + // need a full neighbor list +// int irequest = neighbor->request(this); +// neighbor->requests[irequest]->half = 0; +// neighbor->requests[irequest]->full = 1; + + // set maxrad_dynamic and maxrad_frozen for each type + // include future Fix pour particles as dynamic + + for (i = 1; i <= atom->ntypes; i++) + onerad_dynamic[i] = onerad_frozen[i] = 0.0; + + double *radius = atom->radius; + int *type = atom->type; + int nlocal = atom->nlocal; + + for (i = 0; i < nlocal; i++) { + onerad_dynamic[type[i]] = MAX(onerad_dynamic[type[i]], radius[i]); + } + + MPI_Allreduce(&onerad_dynamic[1], &maxrad_dynamic[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world); + MPI_Allreduce(&onerad_frozen[1], &maxrad_frozen[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world); +} + +/* ---------------------------------------------------------------------- + neighbor callback to inform pair style of neighbor list to use + optional granular history list + ------------------------------------------------------------------------- */ + +void PairTriSurf::init_list(int id, NeighList *ptr) { + if (id == 0) + list = ptr; +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based arrays + ------------------------------------------------------------------------- */ + +double PairTriSurf::memory_usage() { + + return 0.0; +} + +/* + * distance between triangle and point + */ +/* + function [dist,PP0] = pointTriangleDistance(TRI,P) + % calculate distance between a point and a triangle in 3D + % SYNTAX + % dist = pointTriangleDistance(TRI,P) + % [dist,PP0] = pointTriangleDistance(TRI,P) + % + % DESCRIPTION + % Calculate the distance of a given point P from a triangle TRI. + % Point P is a row vector of the form 1x3. The triangle is a matrix + % formed by three rows of points TRI = [P1;P2;P3] each of size 1x3. + % dist = pointTriangleDistance(TRI,P) returns the distance of the point P + % to the triangle TRI. + % [dist,PP0] = pointTriangleDistance(TRI,P) additionally returns the + % closest point PP0 to P on the triangle TRI. + % + % Author: Gwendolyn Fischer + % Release: 1.0 + % Release date: 09/02/02 + % Release: 1.1 Fixed Bug because of normalization + % Release: 1.2 Fixed Bug because of typo in region 5 20101013 + % Release: 1.3 Fixed Bug because of typo in region 2 20101014 + + % Possible extention could be a version tailored not to return the distance + % and additionally the closest point, but instead return only the closest + % point. Could lead to a small speed gain. + + % Example: + % %% The Problem + % P0 = [0.5 -0.3 0.5]; + % + % P1 = [0 -1 0]; + % P2 = [1 0 0]; + % P3 = [0 0 0]; + % + % vertices = [P1; P2; P3]; + % faces = [1 2 3]; + % + % %% The Engine + % [dist,PP0] = pointTriangleDistance([P1;P2;P3],P0); + % + % %% Visualization + % [x,y,z] = sphere(20); + % x = dist*x+P0(1); + % y = dist*y+P0(2); + % z = dist*z+P0(3); + % + % figure + % hold all + % patch('Vertices',vertices,'Faces',faces,'FaceColor','r','FaceAlpha',0.8); + % plot3(P0(1),P0(2),P0(3),'b*'); + % plot3(PP0(1),PP0(2),PP0(3),'*g') + % surf(x,y,z,'FaceColor','b','FaceAlpha',0.3) + % view(3) + + % The algorithm is based on + % "David Eberly, 'Distance Between Point and Triangle in 3D', + % Geometric Tools, LLC, (1999)" + % http:\\www.geometrictools.com/Documentation/DistancePoint3Triangle3.pdf + % + % ^t + % \ | + % \reg2| + % \ | + % \ | + % \ | + % \| + % *P2 + % |\ +% | \ +% reg3 | \ reg1 + % | \ +% |reg0\ +% | \ +% | \ P1 + % -------*-------*------->s + % |P0 \ +% reg4 | reg5 \ reg6 + */ + +//void PairTriSurf::PointTriangleDistance(const Vector3d P, const Vector3d TRI1, const Vector3d TRI2, const Vector3d TRI3, +// Vector3d &CP, double &dist) { +// +// Vector3d B, E0, E1, D; +// double a, b, c, d, e, f; +// double det, s, t, sqrDistance, tmp0, tmp1, numer, denom, invDet; +// +// // rewrite triangle in normal form +// B = TRI1; +// E0 = TRI2 - B; +// E1 = TRI3 - B; +// +// D = B - P; +// a = E0.dot(E0); +// b = E0.dot(E1); +// c = E1.dot(E1); +// d = E0.dot(D); +// e = E1.dot(D); +// f = D.dot(D); +// +// det = a * c - b * b; +// //% do we have to use abs here? +// s = b * e - c * d; +// t = b * d - a * e; +// +// //% Terible tree of conditionals to determine in which region of the diagram +// //% shown above the projection of the point into the triangle-plane lies. +// if ((s + t) <= det) { +// if (s < 0) { +// if (t < 0) { +// // %region4 +// if (d < 0) { +// t = 0; +// if (-d >= a) { +// s = 1; +// sqrDistance = a + 2 * d + f; +// } else { +// s = -d / a; +// sqrDistance = d * s + f; +// } +// } else { +// s = 0; +// if (e >= 0) { +// t = 0; +// sqrDistance = f; +// } else { +// if (-e >= c) { +// t = 1; +// sqrDistance = c + 2 * e + f; +// } else { +// t = -e / c; +// sqrDistance = e * t + f; +// } +// } +// } +// // end % of region 4 +// } else { +// // % region 3 +// s = 0; +// if (e >= 0) { +// t = 0; +// sqrDistance = f; +// } else { +// if (-e >= c) { +// t = 1; +// sqrDistance = c + 2 * e + f; +// } else { +// t = -e / c; +// sqrDistance = e * t + f; +// } +// } +// } +// // end of region 3 +// } else { +// if (t < 0) { +// //% region 5 +// t = 0; +// if (d >= 0) { +// s = 0; +// sqrDistance = f; +// } else { +// if (-d >= a) { +// s = 1; +// sqrDistance = a + 2 * d + f; +// } else { +// s = -d / a; +// sqrDistance = d * s + f; +// } +// } +// } else { +// // region 0 +// invDet = 1 / det; +// s = s * invDet; +// t = t * invDet; +// sqrDistance = s * (a * s + b * t + 2 * d) + t * (b * s + c * t + 2 * e) + f; +// } +// } +// } else { +// if (s < 0) { +// // % region 2 +// tmp0 = b + d; +// tmp1 = c + e; +// if (tmp1 > tmp0) { //% minimum on edge s+t=1 +// numer = tmp1 - tmp0; +// denom = a - 2 * b + c; +// if (numer >= denom) { +// s = 1; +// t = 0; +// sqrDistance = a + 2 * d + f; +// } else { +// s = numer / denom; +// t = 1 - s; +// sqrDistance = s * (a * s + b * t + 2 * d) + t * (b * s + c * t + 2 * e) + f; +// } +// } else +// // % minimum on edge s=0 +// s = 0; +// if (tmp1 <= 0) { +// t = 1; +// sqrDistance = c + 2 * e + f; +// } else { +// if (e >= 0) { +// t = 0; +// sqrDistance = f; +// } else { +// t = -e / c; +// sqrDistance = e * t + f; +// } +// } +// } //end % of region 2 +// else { +// if (t < 0) { +// // %region6 +// tmp0 = b + e; +// tmp1 = a + d; +// if (tmp1 > tmp0) { +// numer = tmp1 - tmp0; +// denom = a - 2 * b + c; +// if (numer >= denom) { +// t = 1; +// s = 0; +// sqrDistance = c + 2 * e + f; +// } else { +// t = numer / denom; +// s = 1 - t; +// sqrDistance = s * (a * s + b * t + 2 * d) + t * (b * s + c * t + 2 * e) + f; +// } +// } else { +// t = 0; +// if (tmp1 <= 0) { +// s = 1; +// sqrDistance = a + 2 * d + f; +// } else { +// if (d >= 0) { +// s = 0; +// sqrDistance = f; +// } else { +// s = -d / a; +// sqrDistance = d * s + f; +// } +// } +// } // % end region 6 +// } else { +// //% region 1 +// numer = c + e - b - d; +// if (numer <= 0) { +// s = 0; +// t = 1; +// sqrDistance = c + 2 * e + f; +// } else { +// denom = a - 2 * b + c; +// if (numer >= denom) { +// s = 1; +// t = 0; +// sqrDistance = a + 2 * d + f; +// } else { +// s = numer / denom; +// t = 1 - s; +// sqrDistance = s * (a * s + b * t + 2 * d) + t * (b * s + c * t + 2 * e) + f; +// } +// } //% end of region 1 +// } +// } +// } +// +// // % account for numerical round-off error +// if (sqrDistance < 0) { +// sqrDistance = 0; +// } +// +// dist = sqrt(sqrDistance); +// +// // closest point +// CP = B + s * E0 + t * E1; +// +//} +/* + * % The algorithm is based on + % "David Eberly, 'Distance Between Point and Triangle in 3D', + % Geometric Tools, LLC, (1999)" + % http:\\www.geometrictools.com/Documentation/DistancePoint3Triangle3.pdf + */ + +void PairTriSurf::PointTriangleDistance(const Vector3d sourcePosition, const Vector3d TRI0, const Vector3d TRI1, + const Vector3d TRI2, Vector3d &CP, double &dist) { + + Vector3d edge0 = TRI1 - TRI0; + Vector3d edge1 = TRI2 - TRI0; + Vector3d v0 = TRI0 - sourcePosition; + + double a = edge0.dot(edge0); + double b = edge0.dot(edge1); + double c = edge1.dot(edge1); + double d = edge0.dot(v0); + double e = edge1.dot(v0); + + double det = a * c - b * b; + double s = b * e - c * d; + double t = b * d - a * e; + + if (s + t < det) { + if (s < 0.f) { + if (t < 0.f) { + if (d < 0.f) { + s = clamp(-d / a, 0.f, 1.f); + t = 0.f; + } else { + s = 0.f; + t = clamp(-e / c, 0.f, 1.f); + } + } else { + s = 0.f; + t = clamp(-e / c, 0.f, 1.f); + } + } else if (t < 0.f) { + s = clamp(-d / a, 0.f, 1.f); + t = 0.f; + } else { + float invDet = 1.f / det; + s *= invDet; + t *= invDet; + } + } else { + if (s < 0.f) { + float tmp0 = b + d; + float tmp1 = c + e; + if (tmp1 > tmp0) { + float numer = tmp1 - tmp0; + float denom = a - 2 * b + c; + s = clamp(numer / denom, 0.f, 1.f); + t = 1 - s; + } else { + t = clamp(-e / c, 0.f, 1.f); + s = 0.f; + } + } else if (t < 0.f) { + if (a + d > b + e) { + float numer = c + e - b - d; + float denom = a - 2 * b + c; + s = clamp(numer / denom, 0.f, 1.f); + t = 1 - s; + } else { + s = clamp(-e / c, 0.f, 1.f); + t = 0.f; + } + } else { + float numer = c + e - b - d; + float denom = a - 2 * b + c; + s = clamp(numer / denom, 0.f, 1.f); + t = 1.f - s; + } + } + + CP = TRI0 + s * edge0 + t * edge1; + dist = (CP - sourcePosition).norm(); + +} + +double PairTriSurf::clamp(const double a, const double min, const double max) { + if (a < min) { + return min; + } else if (a > max) { + return max; + } else { + return a; + } +} + +void *PairTriSurf::extract(const char *str, int &i) { + //printf("in PairTriSurf::extract\n"); + if (strcmp(str, "smd/tri_surface/stable_time_increment_ptr") == 0) { + return (void *) &stable_time_increment; + } + + return NULL; + +} diff --git a/src/USER-SMD/pair_smd_triangulated_surface.h b/src/USER-SMD/pair_smd_triangulated_surface.h new file mode 100644 index 0000000000..1cfd88f1fa --- /dev/null +++ b/src/USER-SMD/pair_smd_triangulated_surface.h @@ -0,0 +1,75 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(smd/tri_surface,PairTriSurf) + +#else + +#ifndef LMP_SMD_TRI_SURFACE_H +#define LMP_SMD_TRI_SURFACE_H + +#include "pair.h" +#include +using namespace Eigen; + + +namespace LAMMPS_NS { + +class PairTriSurf : public Pair { + public: + PairTriSurf(class LAMMPS *); + virtual ~PairTriSurf(); + virtual void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + double init_one(int, int); + void init_style(); + void init_list(int, class NeighList *); + virtual double memory_usage(); + void PointTriangleDistance(const Vector3d P, const Vector3d TRI1, const Vector3d TRI2, const Vector3d TRI3, + Vector3d &CP, double &dist); + double clamp(const double a, const double min, const double max); + void *extract(const char *, int &); + + protected: + double **bulkmodulus; + double **kn; + + double *onerad_dynamic,*onerad_frozen; + double *maxrad_dynamic,*maxrad_frozen; + + double scale; + double stable_time_increment; // stable time step size + + void allocate(); +}; + +} + +#endif +#endif + diff --git a/src/USER-SMD/pair_smd_ulsph.cpp b/src/USER-SMD/pair_smd_ulsph.cpp new file mode 100644 index 0000000000..92b6a6c0fd --- /dev/null +++ b/src/USER-SMD/pair_smd_ulsph.cpp @@ -0,0 +1,1655 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#include "math.h" +#include "float.h" +#include "stdlib.h" +#include "string.h" +#include "pair_smd_ulsph.h" +#include "atom.h" +#include "domain.h" +#include "force.h" +#include "update.h" +#include "modify.h" +#include "fix.h" +#include "comm.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "memory.h" +#include "error.h" +#include +#include +#include "smd_material_models.h" +#include "smd_math.h" +#include "smd_kernels.h" + +using namespace SMD_Kernels; +using namespace std; +using namespace LAMMPS_NS; +using namespace SMD_Math; + +#include +#include +using namespace Eigen; + +#define ARTIFICIAL_STRESS false +#define FORMAT1 "%60s : %g\n" +#define FORMAT2 "\n.............................. %s \n" + +PairULSPH::PairULSPH(LAMMPS *lmp) : + Pair(lmp) { + + // per-type arrays + Q1 = NULL; + eos = viscosity = strength = NULL; + c0_type = NULL; + c0 = NULL; + Lookup = NULL; + artificial_stress = NULL; + artificial_pressure = NULL; + + nmax = 0; // make sure no atom on this proc such that initial memory allocation is correct + stressTensor = L = K = NULL; + shepardWeight = NULL; + smoothVel = NULL; + numNeighs = NULL; + F = NULL; + rho = NULL; + effm = NULL; + + velocity_gradient_required = false; // turn off computation of velocity gradient by default + density_summation = velocity_gradient = false; + + comm_forward = 18; // this pair style communicates 18 doubles to ghost atoms + updateFlag = 0; +} + +/* ---------------------------------------------------------------------- */ + +PairULSPH::~PairULSPH() { + if (allocated) { + //printf("... deallocating\n"); + memory->destroy(Q1); + memory->destroy(rho0); + memory->destroy(eos); + memory->destroy(viscosity); + memory->destroy(strength); + memory->destroy(c0_type); + memory->destroy(Lookup); + memory->destroy(artificial_pressure); + memory->destroy(artificial_stress); + + delete[] onerad_dynamic; + delete[] onerad_frozen; + delete[] maxrad_dynamic; + delete[] maxrad_frozen; + + delete[] K; + delete[] shepardWeight; + delete[] c0; + delete[] smoothVel; + delete[] stressTensor; + delete[] L; + delete[] numNeighs; + delete[] F; + delete[] rho; + delete[] effm; + + } +} + +/* ---------------------------------------------------------------------- + * + * Re-compute mass density from scratch. + * Only used for plain fluid SPH with no physical viscosity models. + * + ---------------------------------------------------------------------- */ + +void PairULSPH::PreCompute_DensitySummation() { + double *radius = atom->radius; + double **x = atom->x; + double *rmass = atom->rmass; + int *type = atom->type; + int *ilist, *jlist, *numneigh; + int **firstneigh; + int nlocal = atom->nlocal; + int inum, jnum, ii, jj, i, itype, jtype, j; + double h, irad, hsq, rSq, wf; + Vector3d dx, xi, xj; + + // set up neighbor list variables + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // zero accumulators + for (i = 0; i < nlocal; i++) { + rho[i] = 0.0; + //shepardWeight[i] = 0.0; + } + + /* + * only recompute mass density if density summation is used. + * otherwise, change in mass density is time-integrated + */ + for (i = 0; i < nlocal; i++) { + itype = type[i]; + if (setflag[itype][itype] == 1) { + // initialize particle density with self-contribution. + h = 2.0 * radius[i]; + hsq = h * h; + Poly6Kernel(hsq, h, 0.0, domain->dimension, wf); + rho[i] = wf * rmass[i]; // / shepardWeight[i]; + //printf("SIC to rho is %f\n", rho[i]); + } + } + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + irad = radius[i]; + + xi << x[i][0], x[i][1], x[i][2]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + xj << x[j][0], x[j][1], x[j][2]; + dx = xj - xi; + rSq = dx.squaredNorm(); + h = irad + radius[j]; + hsq = h * h; + if (rSq < hsq) { + + jtype = type[j]; + Poly6Kernel(hsq, h, rSq, domain->dimension, wf); + + if (setflag[itype][itype] == 1) { + rho[i] += wf * rmass[j]; // / shepardWeight[i]; + } + + if (j < nlocal) { + if (setflag[jtype][jtype] == 1) { + rho[j] += wf * rmass[i]; // / shepardWeight[j]; + } + } + } // end if check distance + } // end loop over j + } // end loop over i +} + +/* ---------------------------------------------------------------------- + * + * Compute shape matrix for kernel gradient correction and velocity gradient. + * This is used if material strength or viscosity models are employed. + * + ---------------------------------------------------------------------- */ + +void PairULSPH::PreCompute() { + double **atom_data9 = atom->smd_data_9; + double *radius = atom->radius; + double **x = atom->x; + double **x0 = atom->x0; + double **v = atom->vest; + double *vfrac = atom->vfrac; + int *type = atom->type; + int *ilist, *jlist, *numneigh; + int **firstneigh; + int nlocal = atom->nlocal; + int inum, jnum, ii, jj, i, itype, jtype, j, idim; + double wfd, h, irad, r, rSq, wf, ivol, jvol; + Vector3d dx, dv, g, du; + Matrix3d Ktmp, Ltmp, Ftmp, K3di, D; + Vector3d xi, xj, vi, vj, x0i, x0j, dx0; + Matrix2d K2di, K2d; + + // zero accumulators + for (i = 0; i < nlocal; i++) { + itype = type[i]; + if (setflag[itype][itype]) { + if (gradient_correction_flag) { + K[i].setZero(); + } else { + K[i].setIdentity(); + } + L[i].setZero(); + F[i].setZero(); + } + } + + // set up neighbor list variables + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + irad = radius[i]; + ivol = vfrac[i]; + + // initialize Eigen data structures from LAMMPS data structures + for (idim = 0; idim < 3; idim++) { + x0i(idim) = x0[i][idim]; + xi(idim) = x[i][idim]; + vi(idim) = v[i][idim]; + } + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + for (idim = 0; idim < 3; idim++) { + x0j(idim) = x0[j][idim]; + xj(idim) = x[j][idim]; + vj(idim) = v[j][idim]; + } + + dx = xj - xi; + + rSq = dx.squaredNorm(); + h = irad + radius[j]; + if (rSq < h * h) { + + r = sqrt(rSq); + jtype = type[j]; + jvol = vfrac[j]; + + // distance vectors in current and reference configuration, velocity difference + dv = vj - vi; + dx0 = x0j - x0i; + + // kernel and derivative + spiky_kernel_and_derivative(h, r, domain->dimension, wf, wfd); + //barbara_kernel_and_derivative(h, r, domain->dimension, wf, wfd); + + // uncorrected kernel gradient + g = (wfd / r) * dx; + + /* build correction matrix for kernel derivatives */ + if (gradient_correction_flag) { + Ktmp = -g * dx.transpose(); + K[i] += jvol * Ktmp; + } + + // velocity gradient L + Ltmp = -dv * g.transpose(); + L[i] += jvol * Ltmp; + + // deformation gradient F in Eulerian frame + du = dx - dx0; + Ftmp = dv * g.transpose(); + F[i] += jvol * Ftmp; + + if (j < nlocal) { + + if (gradient_correction_flag) { + K[j] += ivol * Ktmp; + } + + L[j] += ivol * Ltmp; + F[j] += ivol * Ftmp; + } + } // end if check distance + } // end loop over j + } // end loop over i + + /* + * invert shape matrix and compute corrected quantities + */ + + for (i = 0; i < nlocal; i++) { + itype = type[i]; + if (setflag[itype][itype]) { + if (gradient_correction_flag) { + pseudo_inverse_SVD(K[i]); + K[i] = LimitEigenvalues(K[i], 2.0); + L[i] *= K[i]; + F[i] *= K[i]; + } // end if (gradient_correction[itype]) { + + /* + * accumulate strain increments + * we abuse the atom array "atom_data_9" for this purpose, which was originally designed to hold the deformation gradient. + */ + D = update->dt * 0.5 * (L[i] + L[i].transpose()); + atom_data9[i][0] += D(0, 0); // xx + atom_data9[i][1] += D(1, 1); // yy + atom_data9[i][2] += D(2, 2); // zz + atom_data9[i][3] += D(0, 1); // xy + atom_data9[i][4] += D(0, 2); // xz + atom_data9[i][5] += D(1, 2); // yz + + } // end if (setflag[itype][itype]) + } // end loop over i = 0 to nlocal + +} + +/* ---------------------------------------------------------------------- */ + +void PairULSPH::compute(int eflag, int vflag) { + double **x = atom->x; + double **v = atom->vest; + double **vint = atom->v; // Velocity-Verlet algorithm velocities + double **f = atom->f; + double *vfrac = atom->vfrac; + double *de = atom->de; + double *rmass = atom->rmass; + double *radius = atom->radius; + double *contact_radius = atom->contact_radius; + double **atom_data9 = atom->smd_data_9; + + int *type = atom->type; + int nlocal = atom->nlocal; + int i, j, ii, jj, jnum, itype, jtype, iDim, inum; + double r, wf, wfd, h, rSq, ivol, jvol; + double mu_ij, c_ij, rho_ij; + double delVdotDelR, visc_magnitude, deltaE; + int *ilist, *jlist, *numneigh; + int **firstneigh; + Vector3d fi, fj, dx, dv, f_stress, g, vinti, vintj, dvint; + Vector3d xi, xj, vi, vj, f_visc, sumForces, f_stress_new; + Vector3d gamma, f_hg, dx0, du_est, du; + double r_ref, weight, p; + //int periodic = (domain->xperiodic || domain->yperiodic || domain->zperiodic); + + double ini_dist; + Matrix3d S, D, V, eye; + eye.setIdentity(); + int k; + SelfAdjointEigenSolver < Matrix3d > es; + + if (eflag || vflag) + ev_setup(eflag, vflag); + else + evflag = vflag_fdotr = 0; + + if (atom->nmax > nmax) { +//printf("... allocating in compute with nmax = %d\n", atom->nmax); + nmax = atom->nmax; + delete[] K; + K = new Matrix3d[nmax]; + delete[] shepardWeight; + shepardWeight = new double[nmax]; + delete[] c0; + c0 = new double[nmax]; + delete[] smoothVel; + smoothVel = new Vector3d[nmax]; + delete[] stressTensor; + stressTensor = new Matrix3d[nmax]; + delete[] L; + L = new Matrix3d[nmax]; + delete[] numNeighs; + numNeighs = new int[nmax]; + delete[] F; + F = new Matrix3d[nmax]; + delete[] rho; + rho = new double[nmax]; + delete[] effm; + effm = new double[nmax]; + } + +// zero accumulators + for (i = 0; i < nlocal; i++) { + shepardWeight[i] = 0.0; + smoothVel[i].setZero(); + numNeighs[i] = 0; + + h = 2.0 * radius[i]; + r = 0.0; + spiky_kernel_and_derivative(h, r, domain->dimension, wf, wfd); + } + + /* + * if this is the very first step, zero the array which holds the accumulated strain + */ + if (update->ntimestep == 0) { + for (i = 0; i < nlocal; i++) { + itype = type[i]; + if (setflag[itype][itype]) { + for (j = 0; j < 9; j++) { + atom_data9[i][j] = 0.0; + } + } + } + } + + if (density_summation) { + //printf("dens summ\n"); + PreCompute_DensitySummation(); + + for (i = 0; i < nlocal; i++) { //compute volumes from rho + itype = type[i]; + if (setflag[itype][itype]) { + vfrac[i] = rmass[i] / rho[i]; + } + } + + } + + if (velocity_gradient) { + PairULSPH::PreCompute(); // get velocity gradient and kernel gradient correction + } + + PairULSPH::AssembleStressTensor(); + + /* + * QUANTITIES ABOVE HAVE ONLY BEEN CALCULATED FOR NLOCAL PARTICLES. + * NEED TO DO A FORWARD COMMUNICATION TO GHOST ATOMS NOW + */ + comm->forward_comm_pair(this); + + updateFlag = 0; + + /* + * iterate over pairs of particles i, j and assign forces using pre-computed pressure + */ + +// set up neighbor list variables + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + ivol = vfrac[i]; + + // initialize Eigen data structures from LAMMPS data structures + for (iDim = 0; iDim < 3; iDim++) { + xi(iDim) = x[i][iDim]; + vi(iDim) = v[i][iDim]; + vinti(iDim) = vint[i][iDim]; + } + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + xj(0) = x[j][0]; + xj(1) = x[j][1]; + xj(2) = x[j][2]; + + dx = xj - xi; + rSq = dx.squaredNorm(); + h = radius[i] + radius[j]; + if (rSq < h * h) { + + // initialize Eigen data structures from LAMMPS data structures + for (iDim = 0; iDim < 3; iDim++) { + vj(iDim) = v[j][iDim]; + vintj(iDim) = vint[j][iDim]; + } + + r = sqrt(rSq); + jtype = type[j]; + jvol = vfrac[j]; + + // distance vectors in current and reference configuration, velocity difference + dv = vj - vi; + dvint = vintj - vinti; + + // kernel and derivative + spiky_kernel_and_derivative(h, r, domain->dimension, wf, wfd); + //barbara_kernel_and_derivative(h, r, domain->dimension, wf, wfd); + + // uncorrected kernel gradient + g = (wfd / r) * dx; + + delVdotDelR = dx.dot(dv) / (r + 0.1 * h); // project relative velocity onto unit particle distance vector [m/s] + + S = stressTensor[i] + stressTensor[j]; + + if (artificial_pressure[itype][jtype] > 0.0) { + p = S.trace(); + if (p > 0.0) { // we are in tension + r_ref = contact_radius[i] + contact_radius[j]; + weight = Kernel_Cubic_Spline(r, h) / Kernel_Cubic_Spline(r_ref, h); + weight = pow(weight, 4.0); + S -= artificial_pressure[itype][jtype] * weight * p * eye; + } + } + + /* + * artificial stress to control tensile instability + * Only works if particles are uniformly spaced initially. + */ + if (artificial_stress[itype][jtype] > 0.0) { + ini_dist = contact_radius[i] + contact_radius[j]; + weight = Kernel_Cubic_Spline(r, h) / Kernel_Cubic_Spline(ini_dist, h); + weight = pow(weight, 4.0); + + es.compute(S); + D = es.eigenvalues().asDiagonal(); + for (k = 0; k < 3; k++) { + if (D(k, k) > 0.0) { + D(k, k) -= weight * artificial_stress[itype][jtype] * D(k, k); + } + } + V = es.eigenvectors(); + S = V * D * V.inverse(); + } + + // compute forces + f_stress = -ivol * jvol * S * g; // DO NOT TOUCH SIGN + + /* + * artificial viscosity -- alpha is dimensionless + * MonaghanBalsara form of the artificial viscosity + */ + + c_ij = 0.5 * (c0[i] + c0[j]); + LimitDoubleMagnitude(delVdotDelR, 1.1 * c_ij); + + mu_ij = h * delVdotDelR / (r + 0.1 * h); // units: [m * m/s / m = m/s] + rho_ij = 0.5 * (rmass[i] / ivol + rmass[j] / jvol); + visc_magnitude = 0.5 * (Q1[itype] + Q1[jtype]) * c_ij * mu_ij / rho_ij; + f_visc = -rmass[i] * rmass[j] * visc_magnitude * g; + + if ((Lookup[HOURGLASS_CONTROL_AMPLITUDE][itype] > 0.0) && (Lookup[HOURGLASS_CONTROL_AMPLITUDE][jtype] > 0.0)) { + f_hg = ComputeHourglassForce(i, itype, j, jtype, dv, dx, g, c_ij, mu_ij, rho_ij); + + } else { + f_hg.setZero(); + } + + sumForces = f_stress + f_visc + f_hg; + + // energy rate -- project velocity onto force vector + deltaE = sumForces.dot(dv); + + // apply forces to pair of particles + f[i][0] += sumForces(0); + f[i][1] += sumForces(1); + f[i][2] += sumForces(2); + de[i] += deltaE; + + // accumulate smooth velocities + shepardWeight[i] += jvol * wf; + smoothVel[i] += jvol * wf * dvint; + numNeighs[i] += 1; + + if (j < nlocal) { + f[j][0] -= sumForces(0); + f[j][1] -= sumForces(1); + f[j][2] -= sumForces(2); + de[j] += deltaE; + + shepardWeight[j] += ivol * wf; + smoothVel[j] -= ivol * wf * dvint; + numNeighs[j] += 1; + } + + // tally atomistic stress tensor + if (evflag) { + ev_tally_xyz(i, j, nlocal, 0, 0.0, 0.0, sumForces(0), sumForces(1), sumForces(2), dx(0), dx(1), dx(2)); + } + } + + } + } + + for (i = 0; i < nlocal; i++) { + itype = type[i]; + if (setflag[itype][itype] == 1) { + if (shepardWeight[i] != 0.0) { + smoothVel[i] /= shepardWeight[i]; + } else { + smoothVel[i].setZero(); + } + } // end check if particle is SPH-type + } // end loop over i = 0 to nlocal + + if (vflag_fdotr) + virial_fdotr_compute(); + +} + +/* ---------------------------------------------------------------------- + Assemble total stress tensor with pressure, material sterength, and + viscosity contributions. + ------------------------------------------------------------------------- */ +void PairULSPH::AssembleStressTensor() { + double *radius = atom->radius; + double *vfrac = atom->vfrac; + double *rmass = atom->rmass; + double *eff_plastic_strain = atom->eff_plastic_strain; + double **tlsph_stress = atom->smd_stress; + double *e = atom->e; + int *type = atom->type; + double pFinal; + int i, itype; + int nlocal = atom->nlocal; + Matrix3d D, Ddev, W, V, sigma_diag; + Matrix3d eye, stressRate, StressRateDevJaumann; + Matrix3d sigmaInitial_dev, d_dev, sigmaFinal_dev, stressRateDev, oldStressDeviator, newStressDeviator; + double plastic_strain_increment, yieldStress; + double dt = update->dt; + double vol, newPressure; + double G_eff = 0.0; // effective shear modulus + double K_eff; // effective bulk modulus + double M, p_wave_speed; + double rho, effectiveViscosity; + Matrix3d deltaStressDev; + + dtCFL = 1.0e22; + eye.setIdentity(); + + for (i = 0; i < nlocal; i++) { + itype = type[i]; + if (setflag[itype][itype] == 1) { + newStressDeviator.setZero(); + newPressure = 0.0; + stressTensor[i].setZero(); + vol = vfrac[i]; + rho = rmass[i] / vfrac[i]; + effectiveViscosity = 0.0; + K_eff = 0.0; + G_eff = 0.0; + + //printf("rho = %f\n", rho); + + switch (eos[itype]) { + default: + error->one(FLERR, "unknown EOS."); + break; + case NONE: + pFinal = 0.0; + c0[i] = 1.0; + break; + case EOS_TAIT: + TaitEOS_density(Lookup[EOS_TAIT_EXPONENT][itype], Lookup[REFERENCE_SOUNDSPEED][itype], + Lookup[REFERENCE_DENSITY][itype], rho, newPressure, c0[i]); + //printf("new pressure =%f\n", newPressure); + + break; + case EOS_PERFECT_GAS: + PerfectGasEOS(Lookup[EOS_PERFECT_GAS_GAMMA][itype], vol, rmass[i], e[i], newPressure, c0[i]); + break; + case EOS_LINEAR: + newPressure = Lookup[BULK_MODULUS][itype] * (rho / Lookup[REFERENCE_DENSITY][itype] - 1.0); + //printf("p=%f, rho0=%f, rho=%f\n", newPressure, Lookup[REFERENCE_DENSITY][itype], rho); + c0[i] = Lookup[REFERENCE_SOUNDSPEED][itype]; + break; + } + + K_eff = c0[i] * c0[i] * rho; // effective bulk modulus + + /* + * ******************************* STRENGTH MODELS ************************************************ + */ + + if (strength[itype] != NONE) { + /* + * initial stress state: given by the unrotateted Cauchy stress. + * Assemble Eigen 3d matrix from stored stress state + */ + oldStressDeviator(0, 0) = tlsph_stress[i][0]; + oldStressDeviator(0, 1) = tlsph_stress[i][1]; + oldStressDeviator(0, 2) = tlsph_stress[i][2]; + oldStressDeviator(1, 1) = tlsph_stress[i][3]; + oldStressDeviator(1, 2) = tlsph_stress[i][4]; + oldStressDeviator(2, 2) = tlsph_stress[i][5]; + oldStressDeviator(1, 0) = oldStressDeviator(0, 1); + oldStressDeviator(2, 0) = oldStressDeviator(0, 2); + oldStressDeviator(2, 1) = oldStressDeviator(1, 2); + + D = 0.5 * (L[i] + L[i].transpose()); + W = 0.5 * (L[i] - L[i].transpose()); // spin tensor:: need this for Jaumann rate + d_dev = Deviator(D); + + switch (strength[itype]) { + default: + error->one(FLERR, "unknown strength model."); + break; + case STRENGTH_LINEAR: + + // here in a version with pressure part +// stressRateDev = Lookup[BULK_MODULUS][itype] * d_iso * eye + 2.0 * Lookup[SHEAR_MODULUS][itype] * d_dev; +// c0[i] = Lookup[REFERENCE_SOUNDSPEED][itype]; +// newPressure = 0.0; + + // here only stress deviator + stressRateDev = 2.0 * Lookup[SHEAR_MODULUS][itype] * d_dev; + //cout << "stress rate deviator is " << endl << stressRateDev << endl; + break; + + case STRENGTH_LINEAR_PLASTIC: + yieldStress = Lookup[YIELD_STRENGTH][itype] + Lookup[HARDENING_PARAMETER][itype] * eff_plastic_strain[i]; + LinearPlasticStrength(Lookup[SHEAR_MODULUS][itype], yieldStress, oldStressDeviator, d_dev, dt, + newStressDeviator, stressRateDev, plastic_strain_increment); + eff_plastic_strain[i] += plastic_strain_increment; + + break; + } + + //double m = effective_longitudinal_modulus(itype, dt, d_iso, p_rate, d_dev, stressRate_dev, damage); + + StressRateDevJaumann = stressRateDev - W * oldStressDeviator + oldStressDeviator * W; + newStressDeviator = oldStressDeviator + dt * StressRateDevJaumann; + + tlsph_stress[i][0] = newStressDeviator(0, 0); + tlsph_stress[i][1] = newStressDeviator(0, 1); + tlsph_stress[i][2] = newStressDeviator(0, 2); + tlsph_stress[i][3] = newStressDeviator(1, 1); + tlsph_stress[i][4] = newStressDeviator(1, 2); + tlsph_stress[i][5] = newStressDeviator(2, 2); + + // estimate effective shear modulus for time step stability + deltaStressDev = oldStressDeviator - newStressDeviator; + G_eff = effective_shear_modulus(d_dev, deltaStressDev, dt, itype); + + } // end if (strength[itype] != NONE) + + if (viscosity[itype] != NONE) { + D = 0.5 * (L[i] + L[i].transpose()); + d_dev = Deviator(D); + + switch (viscosity[itype]) { + default: + error->one(FLERR, "unknown viscosity model."); + break; + case VISCOSITY_NEWTON: + effectiveViscosity = Lookup[VISCOSITY_MU][itype]; +// double shear_rate = 2.0 +// * sqrt(d_dev(0, 1) * d_dev(0, 1) + d_dev(0, 2) * d_dev(0, 2) + d_dev(1, 2) * d_dev(1, 2)); // 3d + //cout << "shear rate: " << shear_rate << endl; + //effectiveViscosity = PA6_270C(shear_rate); + //if (effectiveViscosity > 178.062e-6) { + // printf("effective visc is %f\n", effectiveViscosity); + //} + newStressDeviator = 2.0 * effectiveViscosity * d_dev; // newton original + //cout << "this is Ddev " << endl << d_dev << endl << endl; + break; + } + } // end if (viscosity[itype] != NONE) + + /* + * assemble stress Tensor from pressure and deviatoric parts + */ + + stressTensor[i] = -newPressure * eye + newStressDeviator; + + /* + * stable timestep based on speed-of-sound + */ + + M = K_eff + 4.0 * G_eff / 3.0; + p_wave_speed = sqrt(M / rho); + effm[i] = G_eff; + dtCFL = MIN(2 * radius[i] / p_wave_speed, dtCFL); + + /* + * stable timestep based on viscosity + */ + if (viscosity[itype] != NONE) { + dtCFL = MIN(4 * radius[i] * radius[i] * rho / effectiveViscosity, dtCFL); + } + + /* + * kernel gradient correction + */ + if (gradient_correction_flag) { + stressTensor[i] *= K[i]; + } + } + // end if (setflag[itype][itype] == 1) + } // end loop over nlocal + +//printf("stable timestep = %g\n", 0.1 * hMin * MaxBulkVelocity); +} + +/* ---------------------------------------------------------------------- + allocate all arrays + ------------------------------------------------------------------------- */ + +void PairULSPH::allocate() { + + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag, n + 1, n + 1, "pair:setflag"); + + memory->create(Q1, n + 1, "pair:Q1"); + memory->create(rho0, n + 1, "pair:Q2"); + memory->create(c0_type, n + 1, "pair:c0_type"); + memory->create(eos, n + 1, "pair:eosmodel"); + memory->create(viscosity, n + 1, "pair:viscositymodel"); + memory->create(strength, n + 1, "pair:strengthmodel"); + + memory->create(Lookup, MAX_KEY_VALUE, n + 1, "pair:LookupTable"); + + memory->create(artificial_pressure, n + 1, n + 1, "pair:artificial_pressure"); + memory->create(artificial_stress, n + 1, n + 1, "pair:artificial_stress"); + memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); // always needs to be allocated, even with granular neighborlist + + /* + * initialize arrays to default values + */ + + for (int i = 1; i <= n; i++) { + for (int j = i; j <= n; j++) { + artificial_pressure[i][j] = 0.0; + artificial_stress[i][j] = 0.0; + setflag[i][j] = 0; + } + } + + onerad_dynamic = new double[n + 1]; + onerad_frozen = new double[n + 1]; + maxrad_dynamic = new double[n + 1]; + maxrad_frozen = new double[n + 1]; + +} + +/* ---------------------------------------------------------------------- + global settings + ------------------------------------------------------------------------- */ + +void PairULSPH::settings(int narg, char **arg) { + if (narg != 3) { + printf("narg = %d\n", narg); + error->all(FLERR, "Illegal number of arguments for pair_style ulsph"); + } + + if (comm->me == 0) { + printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n"); + printf("... SMD / ULSPH PROPERTIES\n\n"); + } + + if (strcmp(arg[0], "*DENSITY_SUMMATION") == 0) { + density_summation = true; + density_continuity = false; + if (comm->me == 0) + printf("... density summation active\n"); + } else if (strcmp(arg[0], "*DENSITY_CONTINUITY") == 0) { + density_continuity = true; + density_summation = false; + if (comm->me == 0) + printf("... density continuity active\n"); + } else { + error->all(FLERR, + "Illegal settings keyword for first keyword of pair style ulsph. Must be either *DENSITY_SUMMATION or *DENSITY_CONTINUITY"); + } + + if (strcmp(arg[1], "*VELOCITY_GRADIENT") == 0) { + velocity_gradient = true; + if (comm->me == 0) + printf("... computation of velocity gradients active\n"); + } else if (strcmp(arg[1], "*NO_VELOCITY_GRADIENT") == 0) { + velocity_gradient = false; + if (comm->me == 0) + printf("... computation of velocity gradients NOT active\n"); + } else { + error->all(FLERR, + "Illegal settings keyword for first keyword of pair style ulsph. Must be either *VELOCITY_GRADIENT or *NO_VELOCITY_GRADIENT"); + } + + if (strcmp(arg[2], "*GRADIENT_CORRECTION") == 0) { + gradient_correction_flag = true; + if (comm->me == 0) + printf("... first order correction of kernel gradients is active\n"); + } else if (strcmp(arg[2], "*NO_GRADIENT_CORRECTION") == 0) { + gradient_correction_flag = false; + if (comm->me == 0) + printf("... first order correction of kernel gradients is NOT active\n"); + } else { + error->all(FLERR, "Illegal settings keyword for pair style ulsph"); + } + +// error check + //if ((gradient_correction_flag == true) && (density_summation)) { + // error->all(FLERR, "Cannot use *DENSITY_SUMMATION in combination with *YES_GRADIENT_CORRECTION"); + //} + + if (comm->me == 0) + printf(">>========>>========>>========>>========>>========>>========>>========>>========\n"); + +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs + ------------------------------------------------------------------------- */ + +void PairULSPH::coeff(int narg, char **arg) { + int ioffset, iarg, iNextKwd, itype, jtype; + char str[128]; + std::string s, t; + + if (narg < 3) { + sprintf(str, "number of arguments for pair ulsph is too small!"); + error->all(FLERR, str); + } + if (!allocated) + allocate(); + + /* + * if parameters are give in i,i form, i.e., no a cross interaction, set material parameters + */ + + if (force->inumeric(FLERR, arg[0]) == force->inumeric(FLERR, arg[1])) { + + itype = force->inumeric(FLERR, arg[0]); + eos[itype] = viscosity[itype] = strength[itype] = NONE; + + if (comm->me == 0) { + printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n"); + printf("...SMD / ULSPH PROPERTIES OF PARTICLE TYPE %d\n\n", itype); + } + + /* + * read parameters which are common -- regardless of material / eos model + */ + + ioffset = 2; + if (strcmp(arg[ioffset], "*COMMON") != 0) { + sprintf(str, "common keyword missing!"); + error->all(FLERR, str); + } else { + } + + t = string("*"); + iNextKwd = -1; + for (iarg = ioffset + 1; iarg < narg; iarg++) { + s = string(arg[iarg]); + if (s.compare(0, t.length(), t) == 0) { + iNextKwd = iarg; + break; + } + } + + //printf("keyword following *COMMON is %s\n", arg[iNextKwd]); + + if (iNextKwd < 0) { + sprintf(str, "no *KEYWORD terminates *COMMON"); + error->all(FLERR, str); + } + + if (iNextKwd - ioffset != 5 + 1) { + sprintf(str, "expected 5 arguments following *COMMON but got %d\n", iNextKwd - ioffset - 1); + error->all(FLERR, str); + } + + Lookup[REFERENCE_DENSITY][itype] = force->numeric(FLERR, arg[ioffset + 1]); + Lookup[REFERENCE_SOUNDSPEED][itype] = force->numeric(FLERR, arg[ioffset + 2]); + Q1[itype] = force->numeric(FLERR, arg[ioffset + 3]); + Lookup[HEAT_CAPACITY][itype] = force->numeric(FLERR, arg[ioffset + 4]); + Lookup[HOURGLASS_CONTROL_AMPLITUDE][itype] = force->numeric(FLERR, arg[ioffset + 5]); + + Lookup[BULK_MODULUS][itype] = Lookup[REFERENCE_SOUNDSPEED][itype] * Lookup[REFERENCE_SOUNDSPEED][itype] + * Lookup[REFERENCE_DENSITY][itype]; + + if (comm->me == 0) { + printf("material unspecific properties for SMD/ULSPH definition of particle type %d:\n", itype); + printf(FORMAT1, "reference density", Lookup[REFERENCE_DENSITY][itype]); + printf(FORMAT1, "reference speed of sound", Lookup[REFERENCE_SOUNDSPEED][itype]); + printf(FORMAT1, "linear viscosity coefficient", Q1[itype]); + printf(FORMAT1, "heat capacity [energy / (mass * temperature)]", Lookup[HEAT_CAPACITY][itype]); + printf(FORMAT1, "bulk modulus", Lookup[BULK_MODULUS][itype]); + printf(FORMAT1, "hourglass control amplitude", Lookup[HOURGLASS_CONTROL_AMPLITUDE][itype]); + } + + /* + * read following material cards + */ + +// if (comm->me == 0) { +// printf("next kwd is %s\n", arg[iNextKwd]); +// } + while (true) { + if (strcmp(arg[iNextKwd], "*END") == 0) { +// if (comm->me == 0) { +// sprintf(str, "found *END"); +// error->message(FLERR, str); +// } + break; + } + + ioffset = iNextKwd; + if (strcmp(arg[ioffset], "*EOS_TAIT") == 0) { + + /* + * Tait EOS + */ + + eos[itype] = EOS_TAIT; + //printf("reading *EOS_TAIT\n"); + + t = string("*"); + iNextKwd = -1; + for (iarg = ioffset + 1; iarg < narg; iarg++) { + s = string(arg[iarg]); + if (s.compare(0, t.length(), t) == 0) { + iNextKwd = iarg; + break; + } + } + + if (iNextKwd < 0) { + sprintf(str, "no *KEYWORD terminates *EOS_TAIT"); + error->all(FLERR, str); + } + + if (iNextKwd - ioffset != 1 + 1) { + sprintf(str, "expected 1 arguments following *EOS_TAIT but got %d\n", iNextKwd - ioffset - 1); + error->all(FLERR, str); + } + + Lookup[EOS_TAIT_EXPONENT][itype] = force->numeric(FLERR, arg[ioffset + 1]); + + if (comm->me == 0) { + printf(FORMAT2, "Tait EOS"); + printf(FORMAT1, "Exponent", Lookup[EOS_TAIT_EXPONENT][itype]); + } + } // end Tait EOS + + else if (strcmp(arg[ioffset], "*EOS_PERFECT_GAS") == 0) { + + /* + * Perfect Gas EOS + */ + + eos[itype] = EOS_PERFECT_GAS; + //printf("reading *EOS_PERFECT_GAS\n"); + + t = string("*"); + iNextKwd = -1; + for (iarg = ioffset + 1; iarg < narg; iarg++) { + s = string(arg[iarg]); + if (s.compare(0, t.length(), t) == 0) { + iNextKwd = iarg; + break; + } + } + + if (iNextKwd < 0) { + sprintf(str, "no *KEYWORD terminates *EOS_PERFECT_GAS"); + error->all(FLERR, str); + } + + if (iNextKwd - ioffset != 1 + 1) { + sprintf(str, "expected 1 arguments following *EOS_PERFECT_GAS but got %d\n", iNextKwd - ioffset - 1); + error->all(FLERR, str); + } + + Lookup[EOS_PERFECT_GAS_GAMMA][itype] = force->numeric(FLERR, arg[ioffset + 1]); + + if (comm->me == 0) { + printf(FORMAT2, "Perfect Gas EOS"); + printf(FORMAT1, "Heat Capacity Ratio Gamma", Lookup[EOS_PERFECT_GAS_GAMMA][itype]); + } + } // end Perfect Gas EOS + else if (strcmp(arg[ioffset], "*EOS_LINEAR") == 0) { + + /* + * Linear EOS + */ + + eos[itype] = EOS_LINEAR; + + t = string("*"); + iNextKwd = -1; + for (iarg = ioffset + 1; iarg < narg; iarg++) { + s = string(arg[iarg]); + if (s.compare(0, t.length(), t) == 0) { + iNextKwd = iarg; + break; + } + } + + if (iNextKwd < 0) { + sprintf(str, "no *KEYWORD terminates *EOS_LINEAR"); + error->all(FLERR, str); + } + + if (iNextKwd - ioffset != 0 + 1) { + sprintf(str, "expected 0 arguments following *EOS_LINEAR but got %d\n", iNextKwd - ioffset - 1); + error->all(FLERR, str); + } + + if (comm->me == 0) { + printf(FORMAT2, "Linear EOS"); + printf(FORMAT1, "Bulk modulus", Lookup[BULK_MODULUS][itype]); + } + } // end Linear EOS + else if (strcmp(arg[ioffset], "*STRENGTH_LINEAR_PLASTIC") == 0) { + + if (velocity_gradient != true) { + error->all(FLERR, "A strength model was requested but *VELOCITY_GRADIENT is not set"); + } + + /* + * linear elastic / ideal plastic material model with strength + */ + + strength[itype] = STRENGTH_LINEAR_PLASTIC; + velocity_gradient_required = true; + //printf("reading *LINEAR_PLASTIC\n"); + + t = string("*"); + iNextKwd = -1; + for (iarg = ioffset + 1; iarg < narg; iarg++) { + s = string(arg[iarg]); + if (s.compare(0, t.length(), t) == 0) { + iNextKwd = iarg; + break; + } + } + + if (iNextKwd < 0) { + sprintf(str, "no *KEYWORD terminates *STRENGTH_LINEAR_PLASTIC"); + error->all(FLERR, str); + } + + if (iNextKwd - ioffset != 3 + 1) { + sprintf(str, "expected 3 arguments following *STRENGTH_LINEAR_PLASTIC but got %d\n", iNextKwd - ioffset - 1); + error->all(FLERR, str); + } + + Lookup[SHEAR_MODULUS][itype] = force->numeric(FLERR, arg[ioffset + 1]); + Lookup[YIELD_STRENGTH][itype] = force->numeric(FLERR, arg[ioffset + 2]); + Lookup[HARDENING_PARAMETER][itype] = force->numeric(FLERR, arg[ioffset + 3]); + + if (comm->me == 0) { + printf(FORMAT2, "linear elastic / ideal plastic material mode"); + printf(FORMAT1, "yield_strength", Lookup[YIELD_STRENGTH][itype]); + printf(FORMAT1, "constant hardening parameter", Lookup[HARDENING_PARAMETER][itype]); + printf(FORMAT1, "shear modulus", Lookup[SHEAR_MODULUS][itype]); + } + } // end *STRENGTH_LINEAR_PLASTIC + else if (strcmp(arg[ioffset], "*STRENGTH_LINEAR") == 0) { + + if (velocity_gradient != true) { + error->all(FLERR, "A strength model was requested but *VELOCITY_GRADIENT is not set"); + } + + /* + * linear elastic / ideal plastic material model with strength + */ + + strength[itype] = STRENGTH_LINEAR; + t = string("*"); + iNextKwd = -1; + for (iarg = ioffset + 1; iarg < narg; iarg++) { + s = string(arg[iarg]); + if (s.compare(0, t.length(), t) == 0) { + iNextKwd = iarg; + break; + } + } + + if (iNextKwd < 0) { + sprintf(str, "no *KEYWORD terminates *STRENGTH_LINEAR"); + error->all(FLERR, str); + } + + if (iNextKwd - ioffset != 1 + 1) { + sprintf(str, "expected 1 arguments following *STRENGTH_LINEAR but got %d\n", iNextKwd - ioffset - 1); + error->all(FLERR, str); + } + + Lookup[SHEAR_MODULUS][itype] = force->numeric(FLERR, arg[ioffset + 1]); + + if (comm->me == 0) { + printf(FORMAT2, "linear elastic strength model"); + printf(FORMAT1, "shear modulus", Lookup[SHEAR_MODULUS][itype]); + } + } // end *STRENGTH_LINEAR + else if (strcmp(arg[ioffset], "*VISCOSITY_NEWTON") == 0) { + + if (velocity_gradient != true) { + error->all(FLERR, "A viscosity model was requested but *VELOCITY_GRADIENT is not set"); + } + + /* + * linear elastic / ideal plastic material model with strength + */ + + viscosity[itype] = VISCOSITY_NEWTON; + t = string("*"); + iNextKwd = -1; + for (iarg = ioffset + 1; iarg < narg; iarg++) { + s = string(arg[iarg]); + if (s.compare(0, t.length(), t) == 0) { + iNextKwd = iarg; + break; + } + } + + if (iNextKwd < 0) { + sprintf(str, "no *KEYWORD terminates *VISCOSITY_NEWTON"); + error->all(FLERR, str); + } + + if (iNextKwd - ioffset != 1 + 1) { + sprintf(str, "expected 1 arguments following *VISCOSITY_NEWTON but got %d\n", iNextKwd - ioffset - 1); + error->all(FLERR, str); + } + + Lookup[VISCOSITY_MU][itype] = force->numeric(FLERR, arg[ioffset + 1]); + + if (comm->me == 0) { + printf(FORMAT2, "Newton viscosity model"); + printf(FORMAT1, "viscosity mu", Lookup[VISCOSITY_MU][itype]); + } + } // end *STRENGTH_VISCOSITY_NEWTON + + else if (strcmp(arg[ioffset], "*ARTIFICIAL_PRESSURE") == 0) { + + /* + * use Monaghan's artificial pressure to prevent particle clumping + */ + + t = string("*"); + iNextKwd = -1; + for (iarg = ioffset + 1; iarg < narg; iarg++) { + s = string(arg[iarg]); + if (s.compare(0, t.length(), t) == 0) { + iNextKwd = iarg; + break; + } + } + + if (iNextKwd < 0) { + sprintf(str, "no *KEYWORD terminates *ARTIFICIAL_PRESSURE"); + error->all(FLERR, str); + } + + if (iNextKwd - ioffset != 1 + 1) { + sprintf(str, "expected 1 arguments following *ARTIFICIAL_PRESSURE but got %d\n", iNextKwd - ioffset - 1); + error->all(FLERR, str); + } + + artificial_pressure[itype][itype] = force->numeric(FLERR, arg[ioffset + 1]); + + if (comm->me == 0) { + printf(FORMAT2, "Artificial Pressure is enabled."); + printf(FORMAT1, "Artificial Pressure amplitude", artificial_pressure[itype][itype]); + } + } // end *ARTIFICIAL_PRESSURE + + else if (strcmp(arg[ioffset], "*ARTIFICIAL_STRESS") == 0) { + + /* + * use Monaghan's artificial stress to prevent particle clumping + */ + + t = string("*"); + iNextKwd = -1; + for (iarg = ioffset + 1; iarg < narg; iarg++) { + s = string(arg[iarg]); + if (s.compare(0, t.length(), t) == 0) { + iNextKwd = iarg; + break; + } + } + + if (iNextKwd < 0) { + sprintf(str, "no *KEYWORD terminates *ARTIFICIAL_STRESS"); + error->all(FLERR, str); + } + + if (iNextKwd - ioffset != 1 + 1) { + sprintf(str, "expected 1 arguments following *ARTIFICIAL_STRESS but got %d\n", iNextKwd - ioffset - 1); + error->all(FLERR, str); + } + + artificial_stress[itype][itype] = force->numeric(FLERR, arg[ioffset + 1]); + + if (comm->me == 0) { + printf(FORMAT2, "Artificial Stress is enabled."); + printf(FORMAT1, "Artificial Stress amplitude", artificial_stress[itype][itype]); + } + } // end *ARTIFICIAL_STRESS + + else { + sprintf(str, "unknown *KEYWORD: %s", arg[ioffset]); + error->all(FLERR, str); + } + + } + + /* + * copy data which is looked up in inner pairwise loops from slow maps to fast arrays + */ + + rho0[itype] = Lookup[REFERENCE_DENSITY][itype]; + c0_type[itype] = Lookup[REFERENCE_SOUNDSPEED][itype]; + setflag[itype][itype] = 1; + + /* + * error checks + */ + + if ((viscosity[itype] != NONE) && (strength[itype] != NONE)) { + sprintf(str, "cannot have both a strength and viscosity model for particle type %d", itype); + error->all(FLERR, str); + } + + if (eos[itype] == NONE) { + sprintf(str, "must specify an EOS for particle type %d", itype); + error->all(FLERR, str); + } + + } else { + /* + * we are reading a cross-interaction line for particle types i, j + */ + + itype = force->inumeric(FLERR, arg[0]); + jtype = force->inumeric(FLERR, arg[1]); + + if (strcmp(arg[2], "*CROSS") != 0) { + sprintf(str, "ulsph cross interaction between particle type %d and %d requested, however, *CROSS keyword is missing", + itype, jtype); + error->all(FLERR, str); + } + + if (setflag[itype][itype] != 1) { + sprintf(str, + "ulsph cross interaction between particle type %d and %d requested, however, properties of type %d have not yet been specified", + itype, jtype, itype); + error->all(FLERR, str); + } + + if (setflag[jtype][jtype] != 1) { + sprintf(str, + "ulsph cross interaction between particle type %d and %d requested, however, properties of type %d have not yet been specified", + itype, jtype, jtype); + error->all(FLERR, str); + } + + setflag[itype][jtype] = 1; + setflag[jtype][itype] = 1; + + if ((artificial_pressure[itype][itype] > 0.0) && (artificial_pressure[jtype][jtype] > 0.0)) { + artificial_pressure[itype][jtype] = 0.5 * (artificial_pressure[itype][itype] + artificial_pressure[jtype][jtype]); + artificial_pressure[jtype][itype] = artificial_pressure[itype][jtype]; + } else { + artificial_pressure[itype][jtype] = artificial_pressure[jtype][itype] = 0.0; + } + + if ((artificial_stress[itype][itype] > 0.0) && (artificial_stress[jtype][jtype] > 0.0)) { + artificial_stress[itype][jtype] = 0.5 * (artificial_stress[itype][itype] + artificial_stress[jtype][jtype]); + artificial_stress[jtype][itype] = artificial_stress[itype][jtype]; + } else { + artificial_stress[itype][jtype] = artificial_stress[jtype][itype] = 0.0; + } + + if (comm->me == 0) { + printf(">>========>>========>>========>>========>>========>>========>>========>>========\n"); + } + + } +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i + ------------------------------------------------------------------------- */ + +double PairULSPH::init_one(int i, int j) { + + if (!allocated) + allocate(); + + if (setflag[i][j] == 0) + error->all(FLERR, "All pair coeffs are not set"); + +// cutoff = sum of max I,J radii for +// dynamic/dynamic & dynamic/frozen interactions, but not frozen/frozen + + double cutoff = maxrad_dynamic[i] + maxrad_dynamic[j]; + cutoff = MAX(cutoff, maxrad_frozen[i] + maxrad_dynamic[j]); + cutoff = MAX(cutoff, maxrad_dynamic[i] + maxrad_frozen[j]); +//printf("cutoff for pair sph/fluid = %f\n", cutoff); + return cutoff; +} + +/* ---------------------------------------------------------------------- + init specific to this pair style + ------------------------------------------------------------------------- */ + +void PairULSPH::init_style() { + int i; + +//printf(" in init style\n"); +// request a granular neighbor list + int irequest = neighbor->request(this); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->gran = 1; + +// set maxrad_dynamic and maxrad_frozen for each type +// include future Fix pour particles as dynamic + + for (i = 1; i <= atom->ntypes; i++) + onerad_dynamic[i] = onerad_frozen[i] = 0.0; + + double *radius = atom->radius; + int *type = atom->type; + int nlocal = atom->nlocal; + + for (i = 0; i < nlocal; i++) + onerad_dynamic[type[i]] = MAX(onerad_dynamic[type[i]], radius[i]); + + MPI_Allreduce(&onerad_dynamic[1], &maxrad_dynamic[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world); + MPI_Allreduce(&onerad_frozen[1], &maxrad_frozen[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world); + +} + +/* ---------------------------------------------------------------------- + neighbor callback to inform pair style of neighbor list to use + optional granular history list + ------------------------------------------------------------------------- */ + +void PairULSPH::init_list(int id, NeighList *ptr) { + if (id == 0) + list = ptr; +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based arrays + ------------------------------------------------------------------------- */ + +double PairULSPH::memory_usage() { + +//printf("in memory usage\n"); + + return 11 * nmax * sizeof(double); + +} + +/* ---------------------------------------------------------------------- */ + +int PairULSPH::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) { + double *vfrac = atom->vfrac; + double *eff_plastic_strain = atom->eff_plastic_strain; + int i, j, m; + +//printf("packing comm\n"); + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = vfrac[j]; + buf[m++] = c0[j]; //2 + + buf[m++] = stressTensor[j](0, 0); // pack symmetric stress tensor + buf[m++] = stressTensor[j](1, 1); + buf[m++] = stressTensor[j](2, 2); + buf[m++] = stressTensor[j](0, 1); + buf[m++] = stressTensor[j](0, 2); + buf[m++] = stressTensor[j](1, 2); // 2 + 6 = 8 + + buf[m++] = F[j](0, 0); // F is not symmetric + buf[m++] = F[j](0, 1); + buf[m++] = F[j](0, 2); + buf[m++] = F[j](1, 0); + buf[m++] = F[j](1, 1); + buf[m++] = F[j](1, 2); + buf[m++] = F[j](2, 0); + buf[m++] = F[j](2, 1); + buf[m++] = F[j](2, 2); // 8 + 9 = 17 + + buf[m++] = eff_plastic_strain[j]; // 18 + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void PairULSPH::unpack_forward_comm(int n, int first, double *buf) { + double *vfrac = atom->vfrac; + double *eff_plastic_strain = atom->eff_plastic_strain; + int i, m, last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + vfrac[i] = buf[m++]; + c0[i] = buf[m++]; // 2 + + stressTensor[i](0, 0) = buf[m++]; + stressTensor[i](1, 1) = buf[m++]; + stressTensor[i](2, 2) = buf[m++]; + stressTensor[i](0, 1) = buf[m++]; + stressTensor[i](0, 2) = buf[m++]; + stressTensor[i](1, 2) = buf[m++]; // 2 + 6 = 8 + stressTensor[i](1, 0) = stressTensor[i](0, 1); + stressTensor[i](2, 0) = stressTensor[i](0, 2); + stressTensor[i](2, 1) = stressTensor[i](1, 2); + + F[i](0, 0) = buf[m++]; + F[i](0, 1) = buf[m++]; + F[i](0, 2) = buf[m++]; + F[i](1, 0) = buf[m++]; + F[i](1, 1) = buf[m++]; + F[i](1, 2) = buf[m++]; + F[i](2, 0) = buf[m++]; + F[i](2, 1) = buf[m++]; + F[i](2, 2) = buf[m++]; // 8 + 9 = 17 + + eff_plastic_strain[i] = buf[m++]; // 18 + } +} + +/* + * EXTRACT + */ + +void *PairULSPH::extract(const char *str, int &i) { +//printf("in extract\n"); + if (strcmp(str, "smd/ulsph/smoothVel_ptr") == 0) { + return (void *) smoothVel; + } else if (strcmp(str, "smd/ulsph/stressTensor_ptr") == 0) { + return (void *) stressTensor; + } else if (strcmp(str, "smd/ulsph/velocityGradient_ptr") == 0) { + return (void *) L; + } else if (strcmp(str, "smd/ulsph/numNeighs_ptr") == 0) { + return (void *) numNeighs; + } else if (strcmp(str, "smd/ulsph/dtCFL_ptr") == 0) { +//printf("dtcfl = %f\n", dtCFL); + return (void *) &dtCFL; + } else if (strcmp(str, "smd/ulsph/updateFlag_ptr") == 0) { + return (void *) &updateFlag; + } else if (strcmp(str, "smd/ulsph/effective_modulus_ptr") == 0) { + return (void *) effm; + } else if (strcmp(str, "smd/ulsph/shape_matrix_ptr") == 0) { + return (void *) K; + } + + return NULL; +} + +/* ---------------------------------------------------------------------- + compute effective shear modulus by dividing rate of deviatoric stress with rate of shear deformation + ------------------------------------------------------------------------- */ + +double PairULSPH::effective_shear_modulus(const Matrix3d d_dev, const Matrix3d deltaStressDev, const double dt, const int itype) { + double G_eff; // effective shear modulus, see Pronto 2d eq. 3.4.7 + double deltaStressDevSum, shearRateSq, strain_increment; + + if (domain->dimension == 3) { + deltaStressDevSum = deltaStressDev(0, 1) * deltaStressDev(0, 1) + deltaStressDev(0, 2) * deltaStressDev(0, 2) + + deltaStressDev(1, 2) * deltaStressDev(1, 2); + shearRateSq = d_dev(0, 1) * d_dev(0, 1) + d_dev(0, 2) * d_dev(0, 2) + d_dev(1, 2) * d_dev(1, 2); + } else { + deltaStressDevSum = deltaStressDev(0, 1) * deltaStressDev(0, 1); + shearRateSq = d_dev(0, 1) * d_dev(0, 1); + } + + strain_increment = dt * dt * shearRateSq; + + if (strain_increment > 1.0e-12) { + G_eff = 0.5 * sqrt(deltaStressDevSum / strain_increment); + } else { + if (strength[itype] != NONE) { + G_eff = Lookup[SHEAR_MODULUS][itype]; + } else { + G_eff = 0.0; + } + } + + return G_eff; + +} + +/* ---------------------------------------------------------------------- + hourglass force for updated Lagrangian SPH + input: particles indices i, j, particle types ityep, jtype + ------------------------------------------------------------------------- */ + +Vector3d PairULSPH::ComputeHourglassForce(const int i, const int itype, const int j, const int jtype, const Vector3d dv, + const Vector3d xij, const Vector3d g, const double c_ij, const double mu_ij, const double rho_ij) { + + double *rmass = atom->rmass; + Vector3d dv_est, f_hg; + double visc_magnitude; + + dv_est = -0.5 * (F[i] + F[j]) * xij; + double hurz = dv_est.dot(dv) / (dv_est.norm() * dv.norm() + 1.0e-16); + if (hurz < 0.0) { + + visc_magnitude = 0.5 * (Q1[itype] + Q1[jtype]) * c_ij * mu_ij / rho_ij; + f_hg = -rmass[i] * rmass[j] * visc_magnitude * g; +// printf(" f_hg = %f %f %f\n", f_hg(0), f_hg(1), f_hg(2)); +// printf("\nnegative\n"); +// printf(" dv_est = %f %f %f\n", dv_est(0), dv_est(1), dv_est(2)); +// printf(" dv = %f %f %f\n", dv(0), dv(1), dv(2)); + } else { + f_hg.setZero(); + } + + return f_hg; + +} diff --git a/src/USER-SMD/pair_smd_ulsph.h b/src/USER-SMD/pair_smd_ulsph.h new file mode 100644 index 0000000000..81919afdb0 --- /dev/null +++ b/src/USER-SMD/pair_smd_ulsph.h @@ -0,0 +1,140 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(smd/ulsph,PairULSPH) + +#else + +#ifndef LMP_ULSPH_H +#define LMP_ULSPH_H + +#include "pair.h" +#include +#include +#include + +using namespace Eigen; +using namespace std; +namespace LAMMPS_NS { + +class PairULSPH: public Pair { +public: + PairULSPH(class LAMMPS *); + virtual ~PairULSPH(); + virtual void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + double init_one(int, int); + void init_style(); + void init_list(int, class NeighList *); + virtual double memory_usage(); + int pack_forward_comm(int, int *, double *, int, int *); + void unpack_forward_comm(int, int, double *); + void AssembleStressTensor(); + void *extract(const char *, int &); + void PreCompute(); + void PreCompute_DensitySummation(); + double effective_shear_modulus(const Matrix3d d_dev, const Matrix3d deltaStressDev, const double dt, const int itype); + + Vector3d ComputeHourglassForce(const int i, const int itype, const int j, const int jtype, const Vector3d dv, + const Vector3d xij, const Vector3d g, const double c_ij, const double mu_ij, const double rho_ij); + +protected: + + double *c0_type; // reference speed of sound defined per particle type + double *rho0; // reference mass density per type + double *Q1; // linear artificial viscosity coeff + int *eos, *viscosity, *strength; // eos and strength material models + double **artificial_pressure; // true/false: use Monaghan's artificial pressure correction? + double **artificial_stress; // artificial stress amplitude + + double *onerad_dynamic, *onerad_frozen; + double *maxrad_dynamic, *maxrad_frozen; + + void allocate(); + + int nmax; // max number of atoms on this proc + int *numNeighs; + Matrix3d *K; + double *shepardWeight, *c0, *rho; + Vector3d *smoothVel; + Matrix3d *stressTensor, *L, *F; + + double dtCFL; + +private: + + // enumerate EOSs. MUST BE IN THE RANGE [1000, 2000) + enum { + EOS_LINEAR = 1000, EOS_PERFECT_GAS = 1001, EOS_TAIT = 1002, + }; + + // enumerate physical viscosity models. MUST BE IN THE RANGE [2000, 3000) + enum { + VISCOSITY_NEWTON = 2000 + }; + + // enumerate strength models. MUST BE IN THE RANGE [3000, 4000) + enum { + STRENGTH_LINEAR = 3000, STRENGTH_LINEAR_PLASTIC = 3001 + }; + + // enumerate some quantitities and associate these with integer values such that they can be used for lookup in an array structure + enum { + NONE = 0, + BULK_MODULUS = 1, + HOURGLASS_CONTROL_AMPLITUDE = 2, + EOS_TAIT_EXPONENT = 3, + REFERENCE_SOUNDSPEED = 4, + REFERENCE_DENSITY = 5, + EOS_PERFECT_GAS_GAMMA = 6, + SHEAR_MODULUS = 7, + YIELD_STRENGTH = 8, + YOUNGS_MODULUS = 9, + POISSON_RATIO = 10, + LAME_LAMBDA = 11, + HEAT_CAPACITY = 12, + M_MODULUS = 13, + HARDENING_PARAMETER = 14, + VISCOSITY_MU = 15, + MAX_KEY_VALUE = 16 + }; + double **Lookup; // holds per-type material parameters for the quantities defined in enum statement above. + + bool velocity_gradient_required; + int updateFlag; // indicates if any relative particle pair movement is significant compared to smoothing length + + + bool density_summation, density_continuity, velocity_gradient, gradient_correction_flag; + double *effm; + +}; + +} + +#endif +#endif + diff --git a/src/USER-SMD/smd_kernels.h b/src/USER-SMD/smd_kernels.h new file mode 100644 index 0000000000..ba40699fc7 --- /dev/null +++ b/src/USER-SMD/smd_kernels.h @@ -0,0 +1,146 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + +#ifndef SMD_KERNEL_FUNCTIONS_H_ +#define SMD_KERNEL_FUNCTIONS_H_ + +namespace SMD_Kernels { +static inline double Kernel_Wendland_Quintic_NotNormalized(const double r, const double h) { + if (r < h) { + double q = 2.0 * r / h; + return pow(1.0 - 0.5 * q, 4) * (2.0 * q + 1.0); + } else { + return 0.0; + } +} + +static inline double Kernel_Cubic_Spline(const double r, const double h) { + double q = 2.0 * r / h; + if (q > 2.0) { + return 0.0; + } else if ((q <= 2.0) && (q > 1.0)) { + return pow(2.0 - q, 3.0) / 6.0; + } else if ((q >= 0.0) && (q <= 1.0)) { + return 2. / 3. - q * q + 0.5 * q * q * q; + } else { + return 0.0; + } +} + +static inline double Kernel_Barbara(const double r, const double h) { + double arg = (1.570796327 * (r + h)) / h; + double hsq = h * h; + //wf = (1.680351548 * (cos(arg) + 1.)) / hsq; + return -2.639490040 * sin(arg) / (hsq * h); +} + +static inline void spiky_kernel_and_derivative(const double h, const double r, const int dimension, double &wf, double &wfd) { + + /* + * Spiky kernel + */ + + if (r > h) { + printf("r=%f > h=%f in Spiky kernel\n", r, h); + wf = wfd = 0.0; + return; + } + + double hr = h - r; // [m] + if (dimension == 2) { + double n = 0.3141592654e0 * h * h * h * h * h; // [m^5] + wfd = -3.0e0 * hr * hr / n; // [m*m/m^5] = [1/m^3] ==> correct for dW/dr in 2D + wf = -0.333333333333e0 * hr * wfd; // [m/m^3] ==> [1/m^2] correct for W in 2D + } else { + wfd = -14.0323944878e0 * hr * hr / (h * h * h * h * h * h); // [1/m^4] ==> correct for dW/dr in 3D + wf = -0.333333333333e0 * hr * wfd; // [m/m^4] ==> [1/m^3] correct for W in 3D + } + + // alternative formulation +// double hr = h - r; +// +// /* +// * Spiky kernel +// */ +// +// if (domain->dimension == 2) { +// double h5 = h * h * h * h * h; +// wf = 3.183098861e0 * hr * hr * hr / h5; +// wfd = -9.549296583 * hr * hr / h5; +// +// } else { +// double h6 = h * h * h * h * h * h; +// wf = 4.774648292 * hr * hr * hr / h6; +// wfd = -14.32394487 * hr * hr / h6; +// } +// } + +} + +static inline void barbara_kernel_and_derivative(const double h, const double r, const int dimension, double &wf, double &wfd) { + + /* + * Barbara kernel + */ + + double arg = (1.570796327 * (r + h)) / h; + double hsq = h * h; + + if (r > h) { + printf("r = %f > h = %f in barbara kernel function\n", r, h); + exit(1); + //wf = wfd = 0.0; + //return; + } + + if (dimension == 2) { + wf = (1.680351548 * (cos(arg) + 1.)) / hsq; + wfd = -2.639490040 * sin(arg) / (hsq * h); + } else { + wf = 2.051578323 * (cos(arg) + 1.) / (hsq * h); + wfd = -3.222611694 * sin(arg) / (hsq * hsq); + } +} + +/* + * compute a normalized smoothing kernel only + */ +static inline void Poly6Kernel(const double hsq, const double h, const double rsq, const int dimension, double &wf) { + + double tmp = hsq - rsq; + if (dimension == 2) { + wf = tmp * tmp * tmp / (0.7853981635e0 * hsq * hsq * hsq * hsq); + } else { + wf = tmp * tmp * tmp / (0.6382918409e0 * hsq * hsq * hsq * hsq * h); + } +} + +/* + * M4 Prime Kernel + */ + +static inline void M4PrimeKernel(const double s, double &wf) { + if (s < 1.0) { + //wf = 1.0 - 2.5 * s * s + (3./2.) * s * s * s; + wf = 1.0 - s * s *(2.5 -1.5 *s); + } else if (s < 2.0) { + //wf = 0.5 * (1.0 - s) * ((2.0 - s) * (2.0 - s)); + wf = 2.0 + (-4.0 + (2.5 - 0.5 * s)*s)*s; + } else { + wf = 0.0; + } +} + +} + + + +#endif /* SMD_KERNEL_FUNCTIONS_H_ */ diff --git a/src/USER-SMD/smd_material_models.cpp b/src/USER-SMD/smd_material_models.cpp new file mode 100644 index 0000000000..fd06d4c3bb --- /dev/null +++ b/src/USER-SMD/smd_material_models.cpp @@ -0,0 +1,476 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + 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. + ------------------------------------------------------------------------- */ +#include +#include "math_special.h" +#include "stdio.h" + +#include +#include +#include + +using namespace LAMMPS_NS::MathSpecial; +using namespace std; +using namespace Eigen; + +#define MIN(A,B) ((A) < (B) ? (A) : (B)) +#define MAX(A,B) ((A) > (B) ? (A) : (B)) + +/* ---------------------------------------------------------------------- + linear EOS for use with linear elasticity + input: initial pressure pInitial, isotropic part of the strain rate d, time-step dt + output: final pressure pFinal, pressure rate p_rate + ------------------------------------------------------------------------- */ +void LinearEOS(double lambda, double pInitial, double d, double dt, double &pFinal, double &p_rate) { + + /* + * pressure rate + */ + p_rate = lambda * d; + + pFinal = pInitial + dt * p_rate; // increment pressure using pressure rate + //cout << "hurz" << endl; + +} + +/* ---------------------------------------------------------------------- + shock EOS + input: + current density rho + reference density rho0 + current energy density e + reference energy density e0 + reference speed of sound c0 + shock Hugoniot parameter S + Grueneisen parameter Gamma + initial pressure pInitial + time step dt + + output: + pressure rate p_rate + final pressure pFinal + + ------------------------------------------------------------------------- */ +void ShockEOS(double rho, double rho0, double e, double e0, double c0, double S, double Gamma, double pInitial, double dt, + double &pFinal, double &p_rate) { + + double mu = rho / rho0 - 1.0; + double pH = rho0 * square(c0) * mu * (1.0 + mu) / square(1.0 - (S - 1.0) * mu); + + pFinal = (pH + rho * Gamma * (e - e0)); + + //printf("shock EOS: rho = %g, rho0 = %g, Gamma=%f, c0=%f, S=%f, e=%f, e0=%f\n", rho, rho0, Gamma, c0, S, e, e0); + //printf("pFinal = %f\n", pFinal); + p_rate = (pFinal - pInitial) / dt; + +} + +/* ---------------------------------------------------------------------- + polynomial EOS + input: + current density rho + reference density rho0 + coefficients 0 .. 6 + initial pressure pInitial + time step dt + + output: + pressure rate p_rate + final pressure pFinal + + ------------------------------------------------------------------------- */ +void polynomialEOS(double rho, double rho0, double e, double C0, double C1, double C2, double C3, double C4, double C5, double C6, + double pInitial, double dt, double &pFinal, double &p_rate) { + + double mu = rho / rho0 - 1.0; + + if (mu > 0.0) { + pFinal = C0 + C1 * mu + C2 * mu * mu + C3 * mu * mu * mu; // + (C4 + C5 * mu + C6 * mu * mu) * e; + } else { + pFinal = C0 + C1 * mu + C3 * mu * mu * mu; // + (C4 + C5 * mu) * e; + } + pFinal = -pFinal; // we want the mean stress, not the pressure. + + + //printf("pFinal = %f\n", pFinal); + p_rate = (pFinal - pInitial) / dt; + +} + +/* ---------------------------------------------------------------------- + Tait EOS based on current density vs. reference density. + + input: (1) reference sound speed + (2) equilibrium mass density + (3) current mass density + + output:(1) pressure + (2) current speed of sound + ------------------------------------------------------------------------- */ +void TaitEOS_density(const double exponent, const double c0_reference, const double rho_reference, const double rho_current, + double &pressure, double &sound_speed) { + + double B = rho_reference * c0_reference * c0_reference / exponent; + double tmp = pow(rho_current / rho_reference, exponent); + pressure = B * (tmp - 1.0); + double bulk_modulus = B * tmp * exponent; // computed as rho * d(pressure)/d(rho) + sound_speed = sqrt(bulk_modulus / rho_current); + +// if (fabs(pressure) > 0.01) { +// printf("tmp = %f, press=%f, K=%f\n", tmp, pressure, bulk_modulus); +// } + +} + +/* ---------------------------------------------------------------------- + perfect gas EOS + input: gamma -- adiabatic index (ratio of specific heats) + J -- determinant of deformation gradient + volume0 -- reference configuration volume of particle + energy -- energy of particle + pInitial -- initial pressure of the particle + d -- isotropic part of the strain rate tensor, + dt -- time-step size + + output: final pressure pFinal, pressure rate p_rate + ------------------------------------------------------------------------- */ +void PerfectGasEOS(const double gamma, const double vol, const double mass, const double energy, double &pFinal, double &c0) { + + /* + * perfect gas EOS is p = (gamma - 1) rho e + */ + + if (energy > 0.0) { + + pFinal = (1.0 - gamma) * energy / vol; +//printf("gamma = %f, vol%f, e=%g ==> p=%g\n", gamma, vol, energy, *pFinal__/1.0e-9); + + c0 = sqrt((gamma - 1.0) * energy / mass); + + } else { + pFinal = c0 = 0.0; + } + +} + +/* ---------------------------------------------------------------------- + linear strength model for use with linear elasticity + input: lambda, mu : Lame parameters + input: sigmaInitial_dev, d_dev: initial stress deviator, deviatoric part of the strain rate tensor + input: dt: time-step + output: sigmaFinal_dev, sigmaFinal_dev_rate__: final stress deviator and its rate. + ------------------------------------------------------------------------- */ +void LinearStrength(const double mu, const Matrix3d sigmaInitial_dev, const Matrix3d d_dev, const double dt, + Matrix3d &sigmaFinal_dev__, Matrix3d &sigma_dev_rate__) { + + /* + * deviatoric rate of unrotated stress + */ + sigma_dev_rate__ = 2.0 * mu * d_dev; + + /* + * elastic update to the deviatoric stress + */ + sigmaFinal_dev__ = sigmaInitial_dev + dt * sigma_dev_rate__; +} + +/* ---------------------------------------------------------------------- + linear strength model for use with linear elasticity + input: lambda, mu : Lame parameters + input: F: deformation gradient + output: total stress tensor, deviator + pressure + ------------------------------------------------------------------------- */ +//void PairTlsph::LinearStrengthDefgrad(double lambda, double mu, Matrix3d F, Matrix3d *T) { +// Matrix3d E, PK2, eye, sigma, S, tau; +// +// eye.setIdentity(); +// +// E = 0.5 * (F * F.transpose() - eye); // strain measure E = 0.5 * (B - I) = 0.5 * (F * F^T - I) +// tau = lambda * E.trace() * eye + 2.0 * mu * E; // Kirchhoff stress, work conjugate to above strain +// sigma = tau / F.determinant(); // convert Kirchhoff stress to Cauchy stress +// +////printf("l=%f, mu=%f, sigma xy = %f\n", lambda, mu, sigma(0,1)); +// +//// E = 0.5 * (F.transpose() * F - eye); // Green-Lagrange Strain E = 0.5 * (C - I) +//// S = lambda * E.trace() * eye + 2.0 * mu * Deviator(E); // PK2 stress +//// tau = F * S * F.transpose(); // convert PK2 to Kirchhoff stress +//// sigma = tau / F.determinant(); +// +// //*T = sigma; +// +// /* +// * neo-hookean model due to Bonet +// */ +//// lambda = mu = 100.0; +//// // left Cauchy-Green Tensor, b = F.F^T +// double J = F.determinant(); +// double logJ = log(J); +// Matrix3d b; +// b = F * F.transpose(); +// +// sigma = (mu / J) * (b - eye) + (lambda / J) * logJ * eye; +// *T = sigma; +//} +/* ---------------------------------------------------------------------- + linear strength model for use with linear elasticity + input: lambda, mu : Lame parameters + input: sigmaInitial_dev, d_dev: initial stress deviator, deviatoric part of the strain rate tensor + input: dt: time-step + output: sigmaFinal_dev, sigmaFinal_dev_rate__: final stress deviator and its rate. + ------------------------------------------------------------------------- */ +void LinearPlasticStrength(const double G, const double yieldStress, const Matrix3d sigmaInitial_dev, const Matrix3d d_dev, + const double dt, Matrix3d &sigmaFinal_dev__, Matrix3d &sigma_dev_rate__, double &plastic_strain_increment) { + + Matrix3d sigmaTrial_dev, dev_rate; + double J2; + + /* + * deviatoric rate of unrotated stress + */ + dev_rate = 2.0 * G * d_dev; + + /* + * perform a trial elastic update to the deviatoric stress + */ + sigmaTrial_dev = sigmaInitial_dev + dt * dev_rate; // increment stress deviator using deviatoric rate + + /* + * check yield condition + */ + J2 = sqrt(3. / 2.) * sigmaTrial_dev.norm(); + + if (J2 < yieldStress) { + /* + * no yielding has occured. + * final deviatoric stress is trial deviatoric stress + */ + sigma_dev_rate__ = dev_rate; + sigmaFinal_dev__ = sigmaTrial_dev; + plastic_strain_increment = 0.0; + //printf("no yield\n"); + + } else { + //printf("yiedl\n"); + /* + * yielding has occured + */ + plastic_strain_increment = (J2 - yieldStress) / (3.0 * G); + + /* + * new deviatoric stress: + * obtain by scaling the trial stress deviator + */ + sigmaFinal_dev__ = (yieldStress / J2) * sigmaTrial_dev; + + /* + * new deviatoric stress rate + */ + sigma_dev_rate__ = sigmaFinal_dev__ - sigmaInitial_dev; + //printf("yielding has occured.\n"); + } +} + +/* ---------------------------------------------------------------------- + Johnson Cook Material Strength model + input: + G : shear modulus + cp : heat capacity + espec : energy / mass + A : initial yield stress under quasi-static / room temperature conditions + B : proportionality factor for plastic strain dependency + a : exponent for plastic strain dpendency + C : proportionality factor for logarithmic plastic strain rate dependency + epdot0 : dimensionality factor for plastic strain rate dependency + T : current temperature + T0 : reference (room) temperature + Tmelt : melting temperature + input: sigmaInitial_dev, d_dev: initial stress deviator, deviatoric part of the strain rate tensor + input: dt: time-step + output: sigmaFinal_dev, sigmaFinal_dev_rate__: final stress deviator and its rate. + ------------------------------------------------------------------------- */ +void JohnsonCookStrength(const double G, const double cp, const double espec, const double A, const double B, const double a, + const double C, const double epdot0, const double T0, const double Tmelt, const double M, const double dt, const double ep, + const double epdot, const Matrix3d sigmaInitial_dev, const Matrix3d d_dev, Matrix3d &sigmaFinal_dev__, + Matrix3d &sigma_dev_rate__, double &plastic_strain_increment) { + + Matrix3d sigmaTrial_dev, dev_rate; + double J2, yieldStress; + + double deltaT = espec / cp; + double TH = deltaT / (Tmelt - T0); + TH = MAX(TH, 0.0); + double epdot_ratio = epdot / epdot0; + epdot_ratio = MAX(epdot_ratio, 1.0); + //printf("current temperature delta is %f, TH=%f\n", deltaT, TH); + + yieldStress = (A + B * pow(ep, a)) * (1.0 + C * log(epdot_ratio)); // * (1.0 - pow(TH, M)); + + /* + * deviatoric rate of unrotated stress + */ + dev_rate = 2.0 * G * d_dev; + + /* + * perform a trial elastic update to the deviatoric stress + */ + sigmaTrial_dev = sigmaInitial_dev + dt * dev_rate; // increment stress deviator using deviatoric rate + + /* + * check yield condition + */ + J2 = sqrt(3. / 2.) * sigmaTrial_dev.norm(); + + if (J2 < yieldStress) { + /* + * no yielding has occured. + * final deviatoric stress is trial deviatoric stress + */ + sigma_dev_rate__ = dev_rate; + sigmaFinal_dev__ = sigmaTrial_dev; + plastic_strain_increment = 0.0; + //printf("no yield\n"); + + } else { + //printf("yiedl\n"); + /* + * yielding has occured + */ + plastic_strain_increment = (J2 - yieldStress) / (3.0 * G); + + /* + * new deviatoric stress: + * obtain by scaling the trial stress deviator + */ + sigmaFinal_dev__ = (yieldStress / J2) * sigmaTrial_dev; + + /* + * new deviatoric stress rate + */ + sigma_dev_rate__ = sigmaFinal_dev__ - sigmaInitial_dev; + //printf("yielding has occured.\n"); + } +} + +/* ---------------------------------------------------------------------- + isotropic maximum strain damage model + input: + current strain + maximum value of allowed principal strain + + output: + return value is true if any eigenvalue of the current strain exceeds the allowed principal strain + + ------------------------------------------------------------------------- */ + +bool IsotropicMaxStrainDamage(const Matrix3d E, const double maxStrain) { + + /* + * compute Eigenvalues of strain matrix + */ + SelfAdjointEigenSolver < Matrix3d > es; + es.compute(E); // compute eigenvalue and eigenvectors of strain + + double max_eigenvalue = es.eigenvalues().maxCoeff(); + + if (max_eigenvalue > maxStrain) { + return true; + } else { + return false; + } +} + +/* ---------------------------------------------------------------------- + isotropic maximum stress damage model + input: + current stress + maximum value of allowed principal stress + + output: + return value is true if any eigenvalue of the current stress exceeds the allowed principal stress + + ------------------------------------------------------------------------- */ + +bool IsotropicMaxStressDamage(const Matrix3d S, const double maxStress) { + + /* + * compute Eigenvalues of strain matrix + */ + SelfAdjointEigenSolver < Matrix3d > es; + es.compute(S); // compute eigenvalue and eigenvectors of strain + + double max_eigenvalue = es.eigenvalues().maxCoeff(); + + if (max_eigenvalue > maxStress) { + return true; + } else { + return false; + } +} + +/* ---------------------------------------------------------------------- + Johnson-Cook failure model + input: + + + output: + + + ------------------------------------------------------------------------- */ + +double JohnsonCookFailureStrain(const double p, const Matrix3d Sdev, const double d1, const double d2, const double d3, + const double d4, const double epdot0, const double epdot) { + + + + double vm = sqrt(3. / 2.) * Sdev.norm(); // von-Mises equivalent stress + if (vm < 0.0) { + cout << "this is sdev " << endl << Sdev << endl; + printf("vm=%f < 0.0, surely must be an error\n", vm); + exit(1); + } + + // determine stress triaxiality + double triax = p / (vm + 0.01 * fabs(p)); // have softening in denominator to avoid divison by zero + if (triax < 0.0) { + triax = 0.0; + } else if (triax > 3.0) { + triax = 3.0; + } + + // Johnson-Cook failure strain, dependence on stress triaxiality + double jc_failure_strain = d1 + d2 * exp(d3 * triax); + + // include strain rate dependency if parameter d4 is defined and current plastic strain rate exceeds reference strain rate + if (d4 > 0.0) { // + if (epdot > epdot0) { + double epdot_ratio = epdot / epdot0; + jc_failure_strain *= (1.0 + d4 * log(epdot_ratio)); + //printf("epsdot=%f, epsdot0=%f, factor = %f\n", epdot, epdot0, (1.0 + d4 * log(epdot_ratio))); + //exit(1); + + } + } + + return jc_failure_strain; + +} diff --git a/src/USER-SMD/smd_material_models.h b/src/USER-SMD/smd_material_models.h new file mode 100644 index 0000000000..858c5bbbdf --- /dev/null +++ b/src/USER-SMD/smd_material_models.h @@ -0,0 +1,65 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + 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 SMD_MATERIAL_MODELS_H_ +#define SMD_MATERIAL_MODELS_H_ + +using namespace Eigen; + +/* + * EOS models + */ +void LinearEOS(double lambda, double pInitial, double d, double dt, double &pFinal, double &p_rate); +void ShockEOS(double rho, double rho0, double e, double e0, double c0, double S, double Gamma, double pInitial, double dt, + double &pFinal, double &p_rate); +void polynomialEOS(double rho, double rho0, double e, double C0, double C1, double C2, double C3, double C4, double C5, double C6, + double pInitial, double dt, double &pFinal, double &p_rate); +void TaitEOS_density(const double exponent, const double c0_reference, const double rho_reference, const double rho_current, + double &pressure, double &sound_speed); +void PerfectGasEOS(const double gamma, const double vol, const double mass, const double energy, double &pFinal__, double &c0); + +/* + * Material strength models + */ +void LinearStrength(const double mu, const Matrix3d sigmaInitial_dev, const Matrix3d d_dev, const double dt, + Matrix3d &sigmaFinal_dev__, Matrix3d &sigma_dev_rate__); +void LinearPlasticStrength(const double G, const double yieldStress, const Matrix3d sigmaInitial_dev, const Matrix3d d_dev, + const double dt, Matrix3d &sigmaFinal_dev__, Matrix3d &sigma_dev_rate__, double &plastic_strain_increment); +void JohnsonCookStrength(const double G, const double cp, const double espec, const double A, const double B, const double a, + const double C, const double epdot0, const double T0, const double Tmelt, const double M, const double dt, const double ep, + const double epdot, const Matrix3d sigmaInitial_dev, const Matrix3d d_dev, Matrix3d &sigmaFinal_dev__, + Matrix3d &sigma_dev_rate__, double &plastic_strain_increment); + +/* + * Damage models + */ + +bool IsotropicMaxStrainDamage(const Matrix3d E, const double maxStrain); +bool IsotropicMaxStressDamage(const Matrix3d E, const double maxStrain); +double JohnsonCookFailureStrain(const double p, const Matrix3d Sdev, const double d1, const double d2, const double d3, + const double d4, const double epdot0, const double epdot); + + + +#endif /* SMD_MATERIAL_MODELS_H_ */ diff --git a/src/USER-SMD/smd_math.h b/src/USER-SMD/smd_math.h new file mode 100644 index 0000000000..5352cfccf9 --- /dev/null +++ b/src/USER-SMD/smd_math.h @@ -0,0 +1,287 @@ +/* ---------------------------------------------------------------------- + * + * *** Smooth Mach Dynamics *** + * + * This file is part of the USER-SMD package for LAMMPS. + * Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de + * Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI, + * Eckerstrasse 4, D-79104 Freiburg i.Br, Germany. + * + * ----------------------------------------------------------------------- */ + +//test +#ifndef SMD_MATH_H_ +#define SMD_MATH_H_ + +#include +#include +using namespace Eigen; +using namespace std; + +namespace SMD_Math { +static inline void LimitDoubleMagnitude(double &x, const double limit) { + /* + * if |x| exceeds limit, set x to limit with the sign of x + */ + if (fabs(x) > limit) { // limit delVdotDelR to a fraction of speed of sound + x = limit * copysign(1, x); + } +} + +/* + * deviator of a tensor + */ +static inline Matrix3d Deviator(const Matrix3d M) { + Matrix3d eye; + eye.setIdentity(); + eye *= M.trace() / 3.0; + return M - eye; +} + +/* + * Polar Decomposition M = R * T + * where R is a rotation and T a pure translation/stretch matrix. + * + * The decomposition is achieved using SVD, i.e. M = U S V^T, + * where U = R V and S is diagonal. + * + * + * For any physically admissible deformation gradient, the determinant of R must equal +1. + * However, scenerios can arise, where the particles interpenetrate and cause inversion, leading to a determinant of R equal to -1. + * In this case, the inversion direction is heuristically identified with the eigenvector of the smallest entry of S, which should work for most cases. + * The sign of this corresponding eigenvalue is flipped, the original matrix M is recomputed using the flipped S, and the rotation and translation matrices are + * obtained again from an SVD. The rotation should proper now, i.e., det(R) = +1. + */ + +static inline bool PolDec(Matrix3d M, Matrix3d &R, Matrix3d &T, bool scaleF) { + + JacobiSVD svd(M, ComputeFullU | ComputeFullV); // SVD(A) = U S V* + Vector3d S_eigenvalues = svd.singularValues(); + Matrix3d S = svd.singularValues().asDiagonal(); + Matrix3d U = svd.matrixU(); + Matrix3d V = svd.matrixV(); + Matrix3d eye; + eye.setIdentity(); + + // now do polar decomposition into M = R * T, where R is rotation + // and T is translation matrix + R = U * V.transpose(); + T = V * S * V.transpose(); + + if (R.determinant() < 0.0) { // this is an improper rotation + // identify the smallest entry in S and flip its sign + int imin; + S_eigenvalues.minCoeff(&imin); + S(imin, imin) *= -1.0; + + R = M * V * S.inverse() * V.transpose(); // recompute R using flipped stretch eigenvalues + } + + /* + * scale S to avoid small principal strains + */ + + if (scaleF) { + double min = 0.3; // 0.3^2 = 0.09, should suffice for most problems + double max = 2.0; + for (int i = 0; i < 3; i++) { + if (S(i, i) < min) { + S(i, i) = min; + } else if (S(i, i) > max) { + S(i, i) = max; + } + } + T = V * S * V.transpose(); + } + + if (R.determinant() > 0.0) { + return true; + } else { + return false; + } +} + +/* + * Pseudo-inverse via SVD + */ + +static inline void pseudo_inverse_SVD(Matrix3d &M) { + + //JacobiSVD < Matrix3d > svd(M, ComputeFullU | ComputeFullV); + JacobiSVD svd(M, ComputeFullU); // one Eigevector base is sufficient because matrix is square and symmetric + + Vector3d singularValuesInv; + Vector3d singularValues = svd.singularValues(); + +//cout << "Here is the matrix V:" << endl << V * singularValues.asDiagonal() * U << endl; +//cout << "Its singular values are:" << endl << singularValues << endl; + + double pinvtoler = 1.0e-16; // 2d machining example goes unstable if this value is increased (1.0e-16). + for (int row = 0; row < 3; row++) { + if (singularValues(row) > pinvtoler) { + singularValuesInv(row) = 1.0 / singularValues(row); + } else { + singularValuesInv(row) = 0.0; + } + } + + M = svd.matrixU() * singularValuesInv.asDiagonal() * svd.matrixU().transpose(); + +// JacobiSVD < Matrix3d > svd(M, ComputeFullU | ComputeFullV); +// +// Vector3d singularValuesInv; +// Vector3d singularValues = svd.singularValues(); +// +// //cout << "Here is the matrix V:" << endl << V * singularValues.asDiagonal() * U << endl; +// //cout << "Its singular values are:" << endl << singularValues << endl; +// +// double pinvtoler = 1.0e-16; // 2d machining example goes unstable if this value is increased (1.0e-16). +// for (int row = 0; row < 3; row++) { +// if (singularValues(row) > pinvtoler) { +// singularValuesInv(row) = 1.0 / singularValues(row); +// } else { +// singularValuesInv(row) = 0.0; +// } +// } +// +// M = svd.matrixU() * singularValuesInv.asDiagonal() * svd.matrixV().transpose(); + +} + +/* + * test if two matrices are equal + */ +static inline double TestMatricesEqual(Matrix3d A, Matrix3d B, double eps) { + Matrix3d diff; + diff = A - B; + double norm = diff.norm(); + if (norm > eps) { + printf("Matrices A and B are not equal! The L2-norm difference is: %g\n", norm); + cout << "Here is matrix A:" << endl << A << endl; + cout << "Here is matrix B:" << endl << B << endl; + } + return norm; +} + +/* ---------------------------------------------------------------------- + Limit eigenvalues of a matrix to upper and lower bounds. + ------------------------------------------------------------------------- */ + +static inline Matrix3d LimitEigenvalues(Matrix3d S, double limitEigenvalue) { + + /* + * compute Eigenvalues of matrix S + */ + SelfAdjointEigenSolver < Matrix3d > es; + es.compute(S); + + double max_eigenvalue = es.eigenvalues().maxCoeff(); + double min_eigenvalue = es.eigenvalues().minCoeff(); + double amax_eigenvalue = fabs(max_eigenvalue); + double amin_eigenvalue = fabs(min_eigenvalue); + + if ((amax_eigenvalue > limitEigenvalue) || (amin_eigenvalue > limitEigenvalue)) { + if (amax_eigenvalue > amin_eigenvalue) { // need to scale with max_eigenvalue + double scale = amax_eigenvalue / limitEigenvalue; + Matrix3d V = es.eigenvectors(); + Matrix3d S_diag = V.inverse() * S * V; // diagonalized input matrix + S_diag /= scale; + Matrix3d S_scaled = V * S_diag * V.inverse(); // undiagonalize matrix + return S_scaled; + } else { // need to scale using min_eigenvalue + double scale = amin_eigenvalue / limitEigenvalue; + Matrix3d V = es.eigenvectors(); + Matrix3d S_diag = V.inverse() * S * V; // diagonalized input matrix + S_diag /= scale; + Matrix3d S_scaled = V * S_diag * V.inverse(); // undiagonalize matrix + return S_scaled; + } + } else { // limiting does not apply + return S; + } +} + +static inline bool LimitMinMaxEigenvalues(Matrix3d &S, double min, double max) { + + /* + * compute Eigenvalues of matrix S + */ + SelfAdjointEigenSolver < Matrix3d > es; + es.compute(S); + + if ((es.eigenvalues().maxCoeff() > max) || (es.eigenvalues().minCoeff() < min)) { + Matrix3d S_diag = es.eigenvalues().asDiagonal(); + Matrix3d V = es.eigenvectors(); + for (int i = 0; i < 3; i++) { + if (S_diag(i, i) < min) { + //printf("limiting eigenvalue %f --> %f\n", S_diag(i, i), min); + //printf("these are the eigenvalues of U: %f %f %f\n", es.eigenvalues()(0), es.eigenvalues()(1), es.eigenvalues()(2)); + S_diag(i, i) = min; + } else if (S_diag(i, i) > max) { + //printf("limiting eigenvalue %f --> %f\n", S_diag(i, i), max); + S_diag(i, i) = max; + } + } + S = V * S_diag * V.inverse(); // undiagonalize matrix + return true; + } else { + return false; + } +} + +static inline void reconstruct_rank_deficient_shape_matrix(Matrix3d &K) { + + JacobiSVD svd(K, ComputeFullU | ComputeFullV); + Vector3d singularValues = svd.singularValues(); + + for (int i = 0; i < 3; i++) { + if (singularValues(i) < 1.0e-8) { + singularValues(i) = 1.0; + } + } + +// int imin; +// double minev = singularValues.minCoeff(&imin); +// +// printf("min eigenvalue=%f has index %d\n", minev, imin); +// Vector3d singularVec = U.col(0).cross(U.col(1)); +// cout << "the eigenvalues are " << endl << singularValues << endl; +// cout << "the singular vector is " << endl << singularVec << endl; +// +// // reconstruct original K +// +// singularValues(2) = 1.0; + + K = svd.matrixU() * singularValues.asDiagonal() * svd.matrixV().transpose(); + //cout << "the reconstructed K is " << endl << K << endl; + //exit(1); +} + +/* ---------------------------------------------------------------------- + helper functions for crack_exclude + ------------------------------------------------------------------------- */ +static inline bool IsOnSegment(double xi, double yi, double xj, double yj, double xk, double yk) { + return (xi <= xk || xj <= xk) && (xk <= xi || xk <= xj) && (yi <= yk || yj <= yk) && (yk <= yi || yk <= yj); +} + +static inline char ComputeDirection(double xi, double yi, double xj, double yj, double xk, double yk) { + double a = (xk - xi) * (yj - yi); + double b = (xj - xi) * (yk - yi); + return a < b ? -1.0 : a > b ? 1.0 : 0; +} + +/** Do line segments (x1, y1)--(x2, y2) and (x3, y3)--(x4, y4) intersect? */ +static inline bool DoLineSegmentsIntersect(double x1, double y1, double x2, double y2, double x3, double y3, double x4, double y4) { + char d1 = ComputeDirection(x3, y3, x4, y4, x1, y1); + char d2 = ComputeDirection(x3, y3, x4, y4, x2, y2); + char d3 = ComputeDirection(x1, y1, x2, y2, x3, y3); + char d4 = ComputeDirection(x1, y1, x2, y2, x4, y4); + return (((d1 > 0 && d2 < 0) || (d1 < 0 && d2 > 0)) && ((d3 > 0 && d4 < 0) || (d3 < 0 && d4 > 0))) + || (d1 == 0 && IsOnSegment(x3, y3, x4, y4, x1, y1)) || (d2 == 0 && IsOnSegment(x3, y3, x4, y4, x2, y2)) + || (d3 == 0 && IsOnSegment(x1, y1, x2, y2, x3, y3)) || (d4 == 0 && IsOnSegment(x1, y1, x2, y2, x4, y4)); +} + +} + +#endif /* SMD_MATH_H_ */ + diff --git a/src/atom.cpp b/src/atom.cpp index 8171a8c654..fc7641f9ba 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -94,6 +94,17 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp) rho = drho = e = de = cv = NULL; vest = NULL; + // USER-SMD + + contact_radius = NULL; + smd_data_9 = NULL; + smd_stress = NULL; + eff_plastic_strain = NULL; + eff_plastic_strain_rate = NULL; + damage = NULL; + + // molecular info + bond_per_atom = extra_bond_per_atom = 0; num_bond = NULL; bond_type = NULL; @@ -148,6 +159,17 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp) rho_flag = e_flag = cv_flag = vest_flag = 0; + // USER-SMD + + smd_flag = 0; + contact_radius_flag = 0; + smd_data_9_flag = 0; + smd_stress_flag = 0; + x0_flag = 0; + eff_plastic_strain_flag = 0; + eff_plastic_strain_rate_flag = 0; + damage_flag = 0; + // Peridynamic scale factor pdscale = 1.0; @@ -245,6 +267,13 @@ Atom::~Atom() memory->destroy(cv); memory->destroy(vest); + memory->destroy(contact_radius); + memory->destroy(smd_data_9); + memory->destroy(smd_stress); + memory->destroy(eff_plastic_strain); + memory->destroy(eff_plastic_strain_rate); + memory->destroy(damage); + memory->destroy(nspecial); memory->destroy(special); @@ -2010,6 +2039,15 @@ void *Atom::extract(char *name) if (strcmp(name,"cv") == 0) return (void *) cv; if (strcmp(name,"vest") == 0) return (void *) vest; + if (strcmp(name, "contact_radius") == 0) return (void *) contact_radius; + if (strcmp(name, "smd_data_9") == 0) return (void *) smd_data_9; + if (strcmp(name, "smd_stress") == 0) return (void *) smd_stress; + if (strcmp(name, "eff_plastic_strain") == 0) + return (void *) eff_plastic_strain; + if (strcmp(name, "eff_plastic_strain_rate") == 0) + return (void *) eff_plastic_strain_rate; + if (strcmp(name, "damage") == 0) return (void *) damage; + return NULL; } diff --git a/src/atom.h b/src/atom.h index afd07b1bd2..1583dada7e 100644 --- a/src/atom.h +++ b/src/atom.h @@ -76,6 +76,17 @@ class Atom : protected Pointers { double *rho,*drho,*e,*de,*cv; double **vest; + // USER-SMD package + + double *contact_radius; + double **smd_data_9; + double **smd_stress; + double *eff_plastic_strain; + double *eff_plastic_strain_rate; + double *damage; + + // molecular info + int **nspecial; // 0,1,2 = cummulative # of 1-2,1-3,1-4 neighs tagint **special; // IDs of 1-2,1-3,1-4 neighs of each atom int maxspecial; // special[nlocal][maxspecial] @@ -123,6 +134,17 @@ class Atom : protected Pointers { int cs_flag,csforce_flag,vforce_flag,ervelforce_flag,etag_flag; int rho_flag,e_flag,cv_flag,vest_flag; + // USER-SMD package + + int smd_flag; + int contact_radius_flag; + int smd_data_9_flag; + int smd_stress_flag; + int x0_flag; + int eff_plastic_strain_flag; + int eff_plastic_strain_rate_flag; + int damage_flag; + // Peridynamics scale factor, used by dump cfg double pdscale; diff --git a/src/set.cpp b/src/set.cpp index 5f3af82122..737568a085 100644 --- a/src/set.cpp +++ b/src/set.cpp @@ -43,7 +43,7 @@ enum{ATOM_SELECT,MOL_SELECT,TYPE_SELECT,GROUP_SELECT,REGION_SELECT}; enum{TYPE,TYPE_FRACTION,MOLECULE,X,Y,Z,CHARGE,MASS,SHAPE,LENGTH,TRI, DIPOLE,DIPOLE_RANDOM,QUAT,QUAT_RANDOM,THETA,ANGMOM, DIAMETER,DENSITY,VOLUME,IMAGE,BOND,ANGLE,DIHEDRAL,IMPROPER, - MESO_E,MESO_CV,MESO_RHO,INAME,DNAME}; + MESO_E,MESO_CV,MESO_RHO,SMD_MASS_DENSITY,SMD_CONTACT_RADIUS,INAME,DNAME}; #define BIG INT_MAX @@ -384,6 +384,24 @@ void Set::command(int narg, char **arg) set(MESO_RHO); iarg += 2; + } else if (strcmp(arg[iarg],"smd_mass_density") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal set command"); + if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1); + else dvalue = force->numeric(FLERR,arg[iarg+1]); + if (!atom->smd_flag) + error->all(FLERR,"Cannot set smd_mass_density for this atom style"); + set(SMD_MASS_DENSITY); + iarg += 2; + + } else if (strcmp(arg[iarg],"smd_contact_radius") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal set command"); + if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1); + else dvalue = force->numeric(FLERR,arg[iarg+1]); + if (!atom->smd_flag) + error->all(FLERR,"Cannot set smd_contact_radius for this atom style"); + set(SMD_CONTACT_RADIUS); + iarg += 2; + } else if (strstr(arg[iarg],"i_") == arg[iarg]) { if (iarg+2 > narg) error->all(FLERR,"Illegal set command"); if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1); @@ -571,6 +589,10 @@ void Set::set(int keyword) else if (keyword == MESO_E) atom->e[i] = dvalue; else if (keyword == MESO_CV) atom->cv[i] = dvalue; else if (keyword == MESO_RHO) atom->rho[i] = dvalue; + else if (keyword == SMD_MASS_DENSITY) { // set mass from volume and supplied mass density + atom->rmass[i] = atom->vfrac[i] * dvalue; + } + else if (keyword == SMD_CONTACT_RADIUS) atom->contact_radius[i] = dvalue; // set shape of ellipsoidal particle diff --git a/src/version.h b/src/version.h index 3b49c05ebb..4eec9db081 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "28 Jul 2015" +#define LAMMPS_VERSION "4 Aug 2015" diff --git a/tools/moltemplate/common/graphene.lt b/tools/moltemplate/common/graphene.lt index 1410cac9bb..c54a380f62 100644 --- a/tools/moltemplate/common/graphene.lt +++ b/tools/moltemplate/common/graphene.lt @@ -25,6 +25,9 @@ Graphene { group Cgraphene type @atom:C } write_once("In Init") { + # -- Default styles (used in this file for graphene carbon) -- + units real + atom_style full #(full enables you to to add other molecules later) pair_style hybrid lj/cut/coul/long 10.0 } } # Graphene diff --git a/tools/moltemplate/common/spce.lt b/tools/moltemplate/common/spce.lt index f1a1376a5e..1f0f0f61b5 100644 --- a/tools/moltemplate/common/spce.lt +++ b/tools/moltemplate/common/spce.lt @@ -27,10 +27,10 @@ SPCE { } write_once("In Settings") { - bond_coeff @bond:OH harmonic 1000.0 1.0 - angle_coeff @angle:HOH harmonic 1000.0 109.47 + bond_coeff @bond:OH harmonic 600.0 1.0 + angle_coeff @angle:HOH harmonic 75.0 109.47 pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 - pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058 + pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 0.0 group spce type @atom:O @atom:H fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH # (Remember to "unfix" fShakeSPCE during minimization.) diff --git a/tools/moltemplate/common/watmw.lt b/tools/moltemplate/common/watmw.lt index c7aaecebbc..f4eedc4049 100644 --- a/tools/moltemplate/common/watmw.lt +++ b/tools/moltemplate/common/watmw.lt @@ -7,6 +7,29 @@ # in liquid water (as well as hexagonal ice, type II ice, and # low-density super-cooled liquid/amorphous water phases). +#### +# +# NOTE: THIS FILE IS INTENDED FOR SIMULATIONS OF PURE WATER ONLY. +# IF YOU HAVE OTHER ATOMS IN YOUR SYSTEM (BESIDES WATER), +# YOU MUST REPLACE THIS LINE: +# +# pair_coeff * * sw system.in.sw mW +# +# WITH THIS LINE: +# +# pair_coeff * * sw system.in.sw mW NULL NULL NULL +# +# ...IN THE FILE BELOW. +# +# (Note:The number of "NULL" entries in the list should match the +# number of other atom types defined somewhere in your simulation. +# In the "3bodyWater+hydrocarbons_MW+TraPPE" example, there are 3 +# types of carbon defined in "trappe1998.lt", so "NULL" appears 3 times. +#### + + + + WatMW { write("Data Atoms") { $atom:mW $mol:. @atom:mW 0.0 0.0 0.0 0.0 @@ -30,7 +53,7 @@ WatMW { # --Now indicate which atom type(s) are simulated using the "sw" pair style # -- In this case only one of the atom types is used (the mW water "atom"). - pair_coeff * * sw system.in.sw mW NULL NULL NULL + pair_coeff * * sw system.in.sw mW # SEE COMMENT ABOVE # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so # -- the atoms are identified by order in the list, not by name. (The "mW" diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/benzene/README_run.sh b/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/benzene/README_run.sh index 8b01ab92d7..9f923a6c7e 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/benzene/README_run.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/benzene/README_run.sh @@ -12,12 +12,12 @@ # If not, carry out the instructions in "README_setup.sh". # # -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, +# If "lmp_mpi" is the name of the command you use to invoke lammps, # then you would run lammps on these files this way: -lmp_linux -i run.in.npt # minimization and simulation at constant pressure -lmp_linux -i run.in.nvt # minimization and simulation at constant volume +lmp_mpi -i run.in.npt # minimization and simulation at constant pressure +lmp_mpi -i run.in.nvt # minimization and simulation at constant volume #(Note: The constant volume simulation lacks pressure equilibration. These are # completely separate simulations. The results of the constant pressure @@ -34,6 +34,6 @@ lmp_linux -i run.in.nvt # minimization and simulation at constant volume # If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.npt -#mpirun -np 4 lmp_linux -i run.in.nvt +#mpirun -np 4 lmp_mpi -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.nvt # (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/benzene/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/benzene/README_setup.sh index d085370b38..510ae9b400 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/benzene/README_setup.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/benzene/README_setup.sh @@ -19,11 +19,14 @@ cd moltemplate_files # Optional: # The "./output_ttree/" directory is full of temporary files generated by # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - - # Optional: - # Delete the "oplsaa.lt" file: - rm -f oplsaa.lt - + #rm -rf output_ttree/ cd ../ + + +# Optional: +# Note: The system.data and system.in.settings files contain extra information +# for atoms defined in GAFF which you are not using in this simulation. This +# is harmless, but if you to delete this information from your +# system.in.settings and system.in.data files, follow the instructions in +# this script: "optional_cleanup/README_remove_irrelevant_info.sh" diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/benzene/optional_cleanup/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/benzene/optional_cleanup/README_remove_irrelevant_info.sh index d4494c4507..3251991775 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/benzene/optional_cleanup/README_remove_irrelevant_info.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/benzene/optional_cleanup/README_remove_irrelevant_info.sh @@ -13,15 +13,22 @@ # However if you want to eliminate this junk from these files # For now, we can strip this out using ltemplify.py to build a new .lt file. # + # NOTE: If you decide to use this script, it was meant to be run it from + # the parent directory (../) (If you run it from somewhere else, be sure to + # modify the "PATH_TO_DATA_FILE" and "PATH_TO_OUTPUT_TTREE" variables below.) + # # I suggest you do this in a temporary_directory + PATH_TO_DATA_FILE="." + + pushd "$PATH_TO_DATA_FILE" + mkdir new_lt_file cd new_lt_file/ # now run ltemplify.py ltemplify.py ../system.in.init ../system.in.settings ../system.data > system.lt - rm -rf ../system.data ../system.in* # these old lammps files no longer needed # This creates a new .LT file named "system.lt" in the local directory. @@ -31,10 +38,13 @@ # "moltemplate_files/output_ttree/Data Boundary" # then you can copy that information from this file into system.lt + PATH_TO_OUTPUT_TTREE="../moltemplate_files/output_ttree" + echo "write_once(\"Data Boundary\") {" >> system.lt - cat "../moltemplate_files/output_ttree/Data Boundary" >> system.lt + cat "$PATH_TO_OUTPUT_TTREE/Data Boundary" >> system.lt echo "}" >> system.lt echo "" >> system.lt + # Now, run moltemplate on this new .LT file. moltemplate.sh system.lt # This will create: "system.data" "system.in.init" "system.in.settings." @@ -43,10 +53,11 @@ # be ready to run in LAMMPS. # Now copy the system.data and system.in.* files to the place where - # you plan to run moltemplate + # you plan to run LAMMPS mv -f system.data system.in.* ../ cd ../ # Now delete all of the temporary files we generated rm -rf new_lt_file/ + popd diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/README_run.sh b/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/README_run.sh index 8b01ab92d7..9f923a6c7e 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/README_run.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/README_run.sh @@ -12,12 +12,12 @@ # If not, carry out the instructions in "README_setup.sh". # # -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, +# If "lmp_mpi" is the name of the command you use to invoke lammps, # then you would run lammps on these files this way: -lmp_linux -i run.in.npt # minimization and simulation at constant pressure -lmp_linux -i run.in.nvt # minimization and simulation at constant volume +lmp_mpi -i run.in.npt # minimization and simulation at constant pressure +lmp_mpi -i run.in.nvt # minimization and simulation at constant volume #(Note: The constant volume simulation lacks pressure equilibration. These are # completely separate simulations. The results of the constant pressure @@ -34,6 +34,6 @@ lmp_linux -i run.in.nvt # minimization and simulation at constant volume # If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.npt -#mpirun -np 4 lmp_linux -i run.in.nvt +#mpirun -np 4 lmp_mpi -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.nvt # (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/README_setup.sh index 3d00e27e90..510ae9b400 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/README_setup.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/README_setup.sh @@ -3,8 +3,9 @@ # and set it to the "common" subdirectory of your moltemplate distribution. # (See the "Installation" section in the moltemplate manual.) -# Create LAMMPS input files this way: + +# Create LAMMPS input files this way: cd moltemplate_files # run moltemplate @@ -12,25 +13,20 @@ cd moltemplate_files moltemplate.sh system.lt # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). + # Move them to the directory where you plan to run LAMMPS (in this case "../") mv -f system.data system.in* ../ # Optional: # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away + # moltemplate. They can be useful for debugging, but are usually thrown away. #rm -rf output_ttree/ cd ../ - - - # Optional: # Note: The system.data and system.in.settings files contain extra information # for atoms defined in GAFF which you are not using in this simulation. This # is harmless, but if you to delete this information from your # system.in.settings and system.in.data files, follow the instructions in # this script: "optional_cleanup/README_remove_irrelevant_info.sh" - diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/optional_cleanup/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/optional_cleanup/README_remove_irrelevant_info.sh index d4494c4507..3251991775 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/optional_cleanup/README_remove_irrelevant_info.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/ethylene+benzene/optional_cleanup/README_remove_irrelevant_info.sh @@ -13,15 +13,22 @@ # However if you want to eliminate this junk from these files # For now, we can strip this out using ltemplify.py to build a new .lt file. # + # NOTE: If you decide to use this script, it was meant to be run it from + # the parent directory (../) (If you run it from somewhere else, be sure to + # modify the "PATH_TO_DATA_FILE" and "PATH_TO_OUTPUT_TTREE" variables below.) + # # I suggest you do this in a temporary_directory + PATH_TO_DATA_FILE="." + + pushd "$PATH_TO_DATA_FILE" + mkdir new_lt_file cd new_lt_file/ # now run ltemplify.py ltemplify.py ../system.in.init ../system.in.settings ../system.data > system.lt - rm -rf ../system.data ../system.in* # these old lammps files no longer needed # This creates a new .LT file named "system.lt" in the local directory. @@ -31,10 +38,13 @@ # "moltemplate_files/output_ttree/Data Boundary" # then you can copy that information from this file into system.lt + PATH_TO_OUTPUT_TTREE="../moltemplate_files/output_ttree" + echo "write_once(\"Data Boundary\") {" >> system.lt - cat "../moltemplate_files/output_ttree/Data Boundary" >> system.lt + cat "$PATH_TO_OUTPUT_TTREE/Data Boundary" >> system.lt echo "}" >> system.lt echo "" >> system.lt + # Now, run moltemplate on this new .LT file. moltemplate.sh system.lt # This will create: "system.data" "system.in.init" "system.in.settings." @@ -43,10 +53,11 @@ # be ready to run in LAMMPS. # Now copy the system.data and system.in.* files to the place where - # you plan to run moltemplate + # you plan to run LAMMPS mv -f system.data system.in.* ../ cd ../ # Now delete all of the temporary files we generated rm -rf new_lt_file/ + popd diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/hexadecane/README_run.sh b/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/hexadecane/README_run.sh index 8b01ab92d7..9f923a6c7e 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/hexadecane/README_run.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/hexadecane/README_run.sh @@ -12,12 +12,12 @@ # If not, carry out the instructions in "README_setup.sh". # # -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, +# If "lmp_mpi" is the name of the command you use to invoke lammps, # then you would run lammps on these files this way: -lmp_linux -i run.in.npt # minimization and simulation at constant pressure -lmp_linux -i run.in.nvt # minimization and simulation at constant volume +lmp_mpi -i run.in.npt # minimization and simulation at constant pressure +lmp_mpi -i run.in.nvt # minimization and simulation at constant volume #(Note: The constant volume simulation lacks pressure equilibration. These are # completely separate simulations. The results of the constant pressure @@ -34,6 +34,6 @@ lmp_linux -i run.in.nvt # minimization and simulation at constant volume # If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.npt -#mpirun -np 4 lmp_linux -i run.in.nvt +#mpirun -np 4 lmp_mpi -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.nvt # (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/hexadecane/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/hexadecane/README_setup.sh index 3d00e27e90..510ae9b400 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/hexadecane/README_setup.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/hexadecane/README_setup.sh @@ -3,8 +3,9 @@ # and set it to the "common" subdirectory of your moltemplate distribution. # (See the "Installation" section in the moltemplate manual.) -# Create LAMMPS input files this way: + +# Create LAMMPS input files this way: cd moltemplate_files # run moltemplate @@ -12,25 +13,20 @@ cd moltemplate_files moltemplate.sh system.lt # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). + # Move them to the directory where you plan to run LAMMPS (in this case "../") mv -f system.data system.in* ../ # Optional: # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away + # moltemplate. They can be useful for debugging, but are usually thrown away. #rm -rf output_ttree/ cd ../ - - - # Optional: # Note: The system.data and system.in.settings files contain extra information # for atoms defined in GAFF which you are not using in this simulation. This # is harmless, but if you to delete this information from your # system.in.settings and system.in.data files, follow the instructions in # this script: "optional_cleanup/README_remove_irrelevant_info.sh" - diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/hexadecane/optional_cleanup/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/hexadecane/optional_cleanup/README_remove_irrelevant_info.sh index d4494c4507..3251991775 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/hexadecane/optional_cleanup/README_remove_irrelevant_info.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/hexadecane/optional_cleanup/README_remove_irrelevant_info.sh @@ -13,15 +13,22 @@ # However if you want to eliminate this junk from these files # For now, we can strip this out using ltemplify.py to build a new .lt file. # + # NOTE: If you decide to use this script, it was meant to be run it from + # the parent directory (../) (If you run it from somewhere else, be sure to + # modify the "PATH_TO_DATA_FILE" and "PATH_TO_OUTPUT_TTREE" variables below.) + # # I suggest you do this in a temporary_directory + PATH_TO_DATA_FILE="." + + pushd "$PATH_TO_DATA_FILE" + mkdir new_lt_file cd new_lt_file/ # now run ltemplify.py ltemplify.py ../system.in.init ../system.in.settings ../system.data > system.lt - rm -rf ../system.data ../system.in* # these old lammps files no longer needed # This creates a new .LT file named "system.lt" in the local directory. @@ -31,10 +38,13 @@ # "moltemplate_files/output_ttree/Data Boundary" # then you can copy that information from this file into system.lt + PATH_TO_OUTPUT_TTREE="../moltemplate_files/output_ttree" + echo "write_once(\"Data Boundary\") {" >> system.lt - cat "../moltemplate_files/output_ttree/Data Boundary" >> system.lt + cat "$PATH_TO_OUTPUT_TTREE/Data Boundary" >> system.lt echo "}" >> system.lt echo "" >> system.lt + # Now, run moltemplate on this new .LT file. moltemplate.sh system.lt # This will create: "system.data" "system.in.init" "system.in.settings." @@ -43,10 +53,11 @@ # be ready to run in LAMMPS. # Now copy the system.data and system.in.* files to the place where - # you plan to run moltemplate + # you plan to run LAMMPS mv -f system.data system.in.* ../ cd ../ # Now delete all of the temporary files we generated rm -rf new_lt_file/ + popd diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/README_run.sh b/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/README_run.sh index 8b01ab92d7..9f923a6c7e 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/README_run.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/README_run.sh @@ -12,12 +12,12 @@ # If not, carry out the instructions in "README_setup.sh". # # -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, +# If "lmp_mpi" is the name of the command you use to invoke lammps, # then you would run lammps on these files this way: -lmp_linux -i run.in.npt # minimization and simulation at constant pressure -lmp_linux -i run.in.nvt # minimization and simulation at constant volume +lmp_mpi -i run.in.npt # minimization and simulation at constant pressure +lmp_mpi -i run.in.nvt # minimization and simulation at constant volume #(Note: The constant volume simulation lacks pressure equilibration. These are # completely separate simulations. The results of the constant pressure @@ -34,6 +34,6 @@ lmp_linux -i run.in.nvt # minimization and simulation at constant volume # If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.npt -#mpirun -np 4 lmp_linux -i run.in.nvt +#mpirun -np 4 lmp_mpi -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.nvt # (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/README_setup.sh index ef5e35b672..510ae9b400 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/README_setup.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/README_setup.sh @@ -3,8 +3,9 @@ # and set it to the "common" subdirectory of your moltemplate distribution. # (See the "Installation" section in the moltemplate manual.) -# Create LAMMPS input files this way: + +# Create LAMMPS input files this way: cd moltemplate_files # run moltemplate @@ -12,8 +13,7 @@ cd moltemplate_files moltemplate.sh system.lt # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). + # Move them to the directory where you plan to run LAMMPS (in this case "../") mv -f system.data system.in* ../ # Optional: @@ -24,9 +24,6 @@ cd moltemplate_files cd ../ - - - # Optional: # Note: The system.data and system.in.settings files contain extra information # for atoms defined in GAFF which you are not using in this simulation. This diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/optional_cleanup/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/optional_cleanup/README_remove_irrelevant_info.sh index d4494c4507..3251991775 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/optional_cleanup/README_remove_irrelevant_info.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_AMBER/waterTIP3P+isobutane/optional_cleanup/README_remove_irrelevant_info.sh @@ -13,15 +13,22 @@ # However if you want to eliminate this junk from these files # For now, we can strip this out using ltemplify.py to build a new .lt file. # + # NOTE: If you decide to use this script, it was meant to be run it from + # the parent directory (../) (If you run it from somewhere else, be sure to + # modify the "PATH_TO_DATA_FILE" and "PATH_TO_OUTPUT_TTREE" variables below.) + # # I suggest you do this in a temporary_directory + PATH_TO_DATA_FILE="." + + pushd "$PATH_TO_DATA_FILE" + mkdir new_lt_file cd new_lt_file/ # now run ltemplify.py ltemplify.py ../system.in.init ../system.in.settings ../system.data > system.lt - rm -rf ../system.data ../system.in* # these old lammps files no longer needed # This creates a new .LT file named "system.lt" in the local directory. @@ -31,10 +38,13 @@ # "moltemplate_files/output_ttree/Data Boundary" # then you can copy that information from this file into system.lt + PATH_TO_OUTPUT_TTREE="../moltemplate_files/output_ttree" + echo "write_once(\"Data Boundary\") {" >> system.lt - cat "../moltemplate_files/output_ttree/Data Boundary" >> system.lt + cat "$PATH_TO_OUTPUT_TTREE/Data Boundary" >> system.lt echo "}" >> system.lt echo "" >> system.lt + # Now, run moltemplate on this new .LT file. moltemplate.sh system.lt # This will create: "system.data" "system.in.init" "system.in.settings." @@ -43,10 +53,11 @@ # be ready to run in LAMMPS. # Now copy the system.data and system.in.* files to the place where - # you plan to run moltemplate + # you plan to run LAMMPS mv -f system.data system.in.* ../ cd ../ # Now delete all of the temporary files we generated rm -rf new_lt_file/ + popd diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/README.TXT b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/README.TXT index 599c6f85c7..dfbbda86df 100644 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/README.TXT +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/README.TXT @@ -5,8 +5,7 @@ in a vacuum at room temperature using the OPLSAA force field. NOTE: This particular file contains instructions for how to build molecules using the OPLSAA force-field. However, moltemplate is not limited to OPLSAA. Moltemplate allows users to access any of the force-field - styles available in LAMMPS (including custom, user-defined force-fields - implemented by editing the LAMMPS source code). + styles available in LAMMPS (including custom, user-defined force-fields). -------- INSTRUCTIONS FOR USING OPLSAA WITH YOUR OWN MOLECULES: -------- @@ -51,9 +50,8 @@ To do this, type "make yes-user-misc" before compiling LAMMPS. 6) Run LAMMPS in this order: -lmp_g++ -i run.in.min -lmp_g++ -i run.in.npt -lmp_g++ -i run.in.nvt +lmp_g++ -i run.in.min # minimize the energy (to avoid atom overlap) before... +lmp_g++ -i run.in.nvt # running the simulation at constant temperature (Replace "lmp_g++" with the name of the LAMMPS executable you are using.) diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/README_run.sh b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/README_run.sh index 8b01ab92d7..9f923a6c7e 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/README_run.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/README_run.sh @@ -12,12 +12,12 @@ # If not, carry out the instructions in "README_setup.sh". # # -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, +# If "lmp_mpi" is the name of the command you use to invoke lammps, # then you would run lammps on these files this way: -lmp_linux -i run.in.npt # minimization and simulation at constant pressure -lmp_linux -i run.in.nvt # minimization and simulation at constant volume +lmp_mpi -i run.in.npt # minimization and simulation at constant pressure +lmp_mpi -i run.in.nvt # minimization and simulation at constant volume #(Note: The constant volume simulation lacks pressure equilibration. These are # completely separate simulations. The results of the constant pressure @@ -34,6 +34,6 @@ lmp_linux -i run.in.nvt # minimization and simulation at constant volume # If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.npt -#mpirun -np 4 lmp_linux -i run.in.nvt +#mpirun -np 4 lmp_mpi -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.nvt # (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/README_setup.sh index d80df900ef..2c3c217135 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/README_setup.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/README_setup.sh @@ -10,7 +10,7 @@ cd moltemplate_files # Create the "oplsaa.lt" file which moltemplate will need cd oplsaa_lt_generator/ - ./oplsaa_moltemplate.py oplsaa_subset.prm + oplsaa_moltemplate.py oplsaa_subset.prm mv -f oplsaa.lt .. cd .. diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/README.TXT b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/README.TXT index 06779d847d..dedba938bc 100644 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/README.TXT +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/README.TXT @@ -16,7 +16,7 @@ so that it only contains atom types you plan to have in your simulation (see below for details). Then run the opls_moltemplate.py script this way: -python oplsaa_moltemplate.py oplsaa_subset.prm +oplsaa_moltemplate.py oplsaa_subset.prm This will create a file named "oplsaa.lt" diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py deleted file mode 100755 index 32980aab1f..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py +++ /dev/null @@ -1,408 +0,0 @@ -#! /usr/bin/env python -# -# The purpose of this script is to create a moltemplate lt file for the oplsaa. -# forcefield. This will assist researchers in building complex simulations using -# this OPLS-UA and the OPLS-AA forcefields. - -__author__="Jason Lambert" -# (some additional corrections by Miguel Gonzalez and Andrew Jewett) -__version__="0.18" - -import sys -import os -from operator import itemgetter - -g_program_name = __file__.split('/')[-1] - -# To do that, first make a copy of the \"oplsaa.prm\" file -# (which can be downloaded from the TINKER web site). -# The lines in this file beginning with the word \"atoms\" should -# define the atoms which you plan to put in your simulation. All other -# lines beginning with the word \"atoms\" should be deleted. -# (Leave the other sections of this file alone.) -#""") - - - -#input data from file containing opls aa force field parameters. -try: - f=open(sys.argv[1],"r") -except: - sys.stderr.write("Error: \n" - " You need to specify a file name as an input argument:\n" - " python oplsaa_moltemplate.py \n" - " (or the file name is specified incorrectly)\n") - sys.exit() - - -sys.stderr.write(g_program_name+", version "+__version__+"\n" - "Reading parameter file...\n") - - -#output lt file -g=open("oplsaa.lt","w") - - - -lines = f.readlines() - - - -# Ignore/Comment out lines before the "## Atom Type Definitions ##" section. - -for i in range(0, len(lines)): - if (lines[i].find("## Atom Type Definitions ##") != -1): - break - else: - lines[i] = '# ' + lines[i] - - -# As of late 2014, there appear to be 906 atom types, but we don't assume this. -# First try to infer out how many atom types there were in the original -# oplsaa.prm file, or at least find an upper bound on the atom-type numbers. -# (Keep track of the maximum value of the first column in the "atom" section.) -max_atomType = 0 -num_atomTypes = 0 -for line in lines: - # skip over text after a # comment character - ic = line.find('#') - if ic != -1: - line = (line[:ic]).strip() - else: - line = line.strip() - # now look for lines beginning with the word "atom" - tokens = line.split() - if ((len(tokens)>2) and (tokens[0] == "atom")): - num_atomTypes += 1 - if (int(tokens[1]) > max_atomType): - max_atomType = int(tokens[1]) - -if num_atomTypes > 25: - sys.stderr.write("\n" - "(Note: If your computer freezes while running "+g_program_name+",\n" - " it could be because you forgot to edit the .prm file.\n" - " The original \"oplsaa.prm\" file distributed with TINKER has over 900 atom\n" - " types. If you run "+g_program_name+" on this file, it may freeze or\n" - " crash. Instead, run "+g_program_name+" on a SUBSET of the OPLS atoms\n" - " relevant to your problem. To do that, delete the lines from the .prm\n" - " file beginning with \"atom\" which you do not need.)\n\n") - -#temporary storage file -h=open("temp.txt","w+") -atom_lookup={} #this dictionary contains all the atom ffid's as a key and the number of atoms with that key -#atom=[[10000,10000] for i in range(906)] <- don't assume there are 906 atoms -atom=[[-10000,-10000] for i in range(0,max_atomType+1)] -#charge_by_type={} # lookup charge by atom type -#vdw_by_type={} # lookup epsilon & sigma paramters by atom type -charge_by_type=[0.0 for i in range(0,max_atomType+1)] # lookup charge by atom -vdw_by_type=[(0.0,0.0) for i in range(0,max_atomType+1)] # lookup epsilon & sigma - - - -#atom is declared this way so for sorting purposes. -#atom contains the following data upon allocation -#atom[][0]=atom_id( Important for partial charges and non_bonded interactions) -#atom[][1]=atom_ffid( Important for stretches, bending, torsions and impropers) -#atom[][2]=atom_mass -#atom[][3]=partial charge -#atom[][4]=non_bonding sigma -#atom[][5]=non_bonding epsilon -#atom[][6]=atom comment -bond=[] -#bond contains the following data -#bond[0]=atom 1 ffid -#bond[1]=atom 2 ffid -#bond[2]=bond spring constant(OPLS-aa compatible) -#bond[3]=equilibrium bond distance(Angstrom) -angle=[] -#angle contains the following data -#angle[0]=atom 1 ffid -#angle[1]=atom 2 ffid -#angle[2]=atom 3 ffid -#angle[3]=spring constant -#angle[4]=equilibrium angle (degrees) -dihedral=[] -#dihedral contains the following data -#dihedral[0]=atom 1 ffid -#dihedral[1]=atom 2 ffid -#dihedral[2]=atom 3 ffid -#dihedral[3]=atom 4 ffid -#dihedral[4]=v1 -#dihedral[5]=v2 -#dihedral[6]=v3 -#dihedral[7]=v4 -improper=[] -#improper[0]=atom 1 ffid -#improper[1]=atom 2 ffid(central atom) -#improper[2]=atom 3 ffid -#improper[3]=atom 4 ffid -#improper[4]=spring coefficient -#improper[5]=equilibrium angle - - -#This section gets all the parameters from the force field file -for line in lines: - - # skip over text after a # comment character - ic = line.find('#') - if ic != -1: - line = (line[:ic]).strip() - else: - line = line.strip() - - if line.find("atom") == 0: - line=line.split() - atom[int(line[1])-1]=[int(line[1]),int(line[2]),float(line[-2]), - 0.0,0.0,0.0," ".join(line[3:-2])] - elif line.find("vdw") == 0: - line=line.split() - #vdw_temp.append([float(line[1]),float(line[2]),float(line[3])]) - if (int(line[1]) <= max_atomType): - vdw_by_type[int(line[1])] = (float(line[2]),float(line[3])) - elif line.find("bond") == 0: - line=line.split() - bond.append([int(line[1]),int(line[2]),float(line[3]),float(line[4])]) - elif line.find("angle") == 0: - line=line.split() - angle.append([int(line[1]),int(line[2]),int(line[3]), - float(line[4]),float(line[5])]) - elif line.find("torsion") == 0: - line=line.split() - dihedral.append([int(line[1]),int(line[2]),int(line[3]),int(line[4]), - float(line[5]),float(line[8]), float(line[11]), 0.0]) - elif line.find("charge") == 0: - line=line.split() - #charge_temp.append([int(line[1]),float(line[2])]) - if (int(line[1]) <= max_atomType): - charge_by_type[int(line[1])] = float(line[2]) - elif line.find("imptors") == 0: - line=line.split() - improper.append([int(line[1]), int(line[2]), - int(line[3]), int(line[4]), float(line[5]), float(line[6])]) - -if len(atom) > 600: - sys.stderr.write("WARNING: The number of atom types in your file exceeds 600\n" - " (You were supposed to edit out the atoms you don't need.\n" - " Not doing this may crash your computer.)\n" - "\n" - " Proceed? (Y/N): ") - reply = sys.stdin.readline() - if find(reply.strip().lower(), 'y') != 0: - exit(0) - -#adding the charge and Lennard Jones parameters to -#to each atom type. -#----------------------------------------------# -for i in range(0,len(atom)): - atom_type_num = atom[i][0] - #q = charge_by_type.get(atomTypeNum) - #if q: - # atom[i][3] = q - if atom_type_num != -10000: - q = charge_by_type[atom_type_num] - atom[i][3] = q - -for i in range(0,len(atom)): - atom_type_num = atom[i][0] - #vdw_params = vdw_by_type.get(atomTypeNum) - #if vdw_params: - # atom[i][4] = vdw_params[0] - # atom[i][5] = vdw_params[1] - if atom_type_num != -10000: - vdw_params = vdw_by_type[atom_type_num] - atom[i][4] = vdw_params[0] - atom[i][5] = vdw_params[1] - -del(charge_by_type) -del(vdw_by_type) - -#----------------------------------------------------------# -#begin writing content to lt file -g.write("OPLSAA {\n\n" ) - -#write out the atom masses -#----------------------------------------------------------# -g.write(" write_once(\"Data Masses\"){\n")#checked with gaff -for i,x in enumerate(atom): - if x[0] != -10000: - g.write(" @atom:{} {} #{} partial charge={}\n".format( - x[0],x[2],x[6],x[3])) -g.write(" } #(end of atom masses)\n\n") -#----------------------------------------------------------# - - -#write out the pair coefficients -#----------------------------------------------------------# -g.write(" write_once(\"In Settings\"){\n")#checked with gaff -for i,x in enumerate(atom): - if x[0] != -10000: - g.write(" pair_coeff @atom:{0} @atom:{0} lj/cut/coul/long {1} {2}\n".format(x[0],x[5],x[4])) -g.write(" } #(end of pair coeffs)\n\n") - -g.write(" write_once(\"In Charges\"){\n")#checked with gaff -for i,x in enumerate(atom): - if x[0] != -10000: - g.write(" set type @atom:{0} charge {1}\n".format(x[0],x[3])) -g.write(" } #(end of atom charges)\n\n") - -#-----------------------------------------------------------# - -# This part of the code creates a lookup dictionary -# that allows you to find every type of atom by its -# force field id. force field id is the id number -# relevant to bonds, angles, dihedrals, and impropers. -# This greatly increases the speed of angle, bond, dihedral -# and improper assignment. -#------------------------------------------------------------# -atom=sorted(atom,key=itemgetter(1)) -atom_ffid=0 -for x in atom: - if x[1]==atom_ffid: - atom_lookup[x[1]].append(x[0]) - elif x[1]>atom_ffid: - atom_lookup[x[1]]=[x[0]] - atom_ffid=x[1] -atom_lookup[0]=["*"] -#-------------------------------------------------------------# - - -#writing out the bond coefficients and bond parameters# -#-------------------------------------------------------------# -g.write(" write_once(\"In Settings\") {\n") -index1=0 -for x in bond: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - #g.write(" bond_coeff @bond:{}-{} harmonic {} {}\n".format(y,z,x[2]/2,x[3])) - # Miguel Gonzales corrected this line to: - g.write(" bond_coeff @bond:{}-{} harmonic {} {}\n".format(y,z,x[2],x[3])) - h.write(" @bond:{0}-{1} @atom:{0} @atom:{1}\n".format(y,z)) -g.write(" } #(end of bond_coeffs)\n\n") -h.seek(0,0) -g.write(" write_once(\"Data Bonds By Type\") {\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of bonds by type)\n\n") -del(bond) -h.close() -#-----------------------------------------------------------# -h=open("temp.txt","w+") - -#writing out angle coefficients and angles by type.---------# -#-----------------------------------------------------------# -g.write(" write_once(\"Data Angles By Type\"){\n") -for x in angle: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - for u in atom_lookup.get(x[2],[]): - #print(y,z,u,x) - #h.write(" angle_coeff @angle:{}-{}-{} harmonic {} {}\n".format(y,z,u,x[3]/2.0,x[4])) - # Miguel Gonzales corrected this line: - h.write(" angle_coeff @angle:{}-{}-{} harmonic {} {}\n".format(y,z,u,x[3],x[4])) - g.write(" @angle:{0}-{1}-{2} @atom:{0} @atom:{1} @atom:{2}\n".format(y,z,u)) - - -g.write(" } #(end of angles by type)\n\n") -h.seek(0,0) -g.write(" write_once(\"In Settings\" ){\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of angle_coeffs)\n\n") -del(angle) -h.close() -#----------------------------------------------------------# - -#writing dihedrals by type and dihedral coefficients-------# -h=h=open("temp.txt","w+") -g.write(" write_once(\"Data Dihedrals By Type\") {\n") -#print(atom_lookup) -for x in dihedral: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - for u in atom_lookup.get(x[2],[]): - for v in atom_lookup.get(x[3],[]): - if x[0]!=0 and x[3]!=0: - g.write(" @dihedral:{0}-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( - y,z,u,v)) - h.write(" dihedral_coeff @dihedral:{}-{}-{}-{} opls {} {} {} {}\n".format( - y,z,u,v,x[4],x[5],x[6],x[7])) - elif x[0]==0 and x[3]!=0: - g.write(" @dihedral:0-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( - y,z,u,v)) - h.write(" dihedral_coeff @dihedral:0-{}-{}-{} opls {} {} {} {}\n".format( - z,u,v,x[4],x[5],x[6],x[7])) - elif x[0]==0 and x[3]==0: - g.write(" @dihedral:0-{1}-{2}-0 @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( - y,z,u,v)) - #h.write(" dihedral_coeff @dihedral:0-{}-{}-0 harmonic {} {} {} {}\n".format( - h.write(" dihedral_coeff @dihedral:0-{}-{}-0 opls {} {} {} {}\n".format( - z,u,x[4],x[5],x[6],x[7])) - -del(dihedral) -g.write(" } #(end of Dihedrals by type)\n\n") -h.seek(0,0) -g.write(" write_once(\"In Settings\") {\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of dihedral_coeffs)\n\n") -h.close() -#-----------------------------------------------------------------------# - -#----writing out improper coefficients and impropers by type------------# -h=open("temp.txt","w+") -g.write(" write_once(\"Data Impropers By Type (opls_imp.py)\") {\n") -for x in improper: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - for u in atom_lookup.get(x[2],[]): - for v in atom_lookup.get(x[3],[]): - # Notation: let I,J,K,L denote the atom types ("biotypes") - # listed in the order they appear in the "oplsaa.prm" file. - # (I think J and L are represented by "u" and "v" in the code here.) - # It looks like the "oplsaa.prm" file distributed with tinker - # treats the third atom ("K") as the central atom. - # After checking the code, it appears that the improper angle is - # calculated as the angle between the I,J,K and the J,K,L planes - if x[0]==0 and x[1]==0 and x[3]==0: - g.write(" @improper:0-0-{2}-0 @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v)) - h.write(" improper_coeff @improper:0-0-{2}-0 harmonic {4} {5} \n".format(y,z,u,v,x[4]/2,180)) - else: - g.write(" @improper:0-0-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v)) - h.write(" improper_coeff @improper:0-0-{2}-{3} harmonic {4} {5} \n".format(y,z,u,v,x[4]/2,180)) - - -g.write(" } #(end of impropers by type)\n\n") -h.seek(0,0) -g.write(" write_once(\"In Settings\") {\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of improp_coeffs)\n\n") -#-----------------------------------------------------------------------# - -#This section writes out the input parameters required for an opls-aa simulation -# lammps. -g.write(" write_once(\"In Init\") {\n") -g.write(" units real\n") -g.write(" atom_style full\n") -g.write(" bond_style hybrid harmonic\n") -g.write(" angle_style hybrid harmonic\n") -g.write(" dihedral_style hybrid opls\n") -g.write(" improper_style hybrid harmonic\n") -#g.write(" pair_style hybrid lj/cut/coul/cut 10.0 10.0\n") -g.write(" pair_style hybrid lj/cut/coul/long 10.0 10.0\n") -g.write(" pair_modify mix geometric\n") -g.write(" special_bonds lj/coul 0.0 0.0 0.5\n") -g.write(" kspace_style pppm 0.0001\n") -g.write(" } #end of init parameters\n\n") -g.write("} # OPLSAA\n") -f.close() -g.close() -h.close() -os.remove("temp.txt") - - -sys.stderr.write("...finished.\n") - - - - diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm index ea7a9ade76..1260acdbd3 100644 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm @@ -9,9 +9,14 @@ # # When building your own molecules, you should download this file, and delete # only the lines from the "atoms" section which you don't need. (But leave the -# rest of that file alone.) Rename the resulting file "oplsaa_subset.prm" +# rest of that file alone. I deleted other sections of this file here in order +# to reduce the file size, but this is not necessary.) +# +# Rename the resulting file "oplsaa_subset.prm" +# # Then you can create an oplsaa.lt file (which moltemplate.sh needs) this way: -# python oplsaa_moltemplate.py oplsaa_subset.prm +# oplsaa_moltemplate.py oplsaa_subset.prm +# # Then copy the newly created "oplsa.lt" file to the directory where you # plan to run moltemplate, and run moltemplate: # moltemplate system.lt diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/run.in.min b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/run.in.min index fc85e4c464..5d0bcffd8e 100644 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/run.in.min +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/alkane_chain_single/run.in.min @@ -2,8 +2,6 @@ # # You must use moltemplate.sh to create 3 files: # system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) # # ------------------------------- Initialization Section -------------------- @@ -25,8 +23,7 @@ include "system.in.charges" # Note: The minimization step is not necessary in this example. However # in general, it's always a good idea to minimize the system beforehand. -# (The "fShakeSPCE" fix was defined in system.in.settings. -# It is incompatible with "minimize", so we disable it first.) + thermo 50 dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz minimize 1.0e-4 1.0e-6 100000 400000 diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/README_run.sh b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/README_run.sh index 8b01ab92d7..9f923a6c7e 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/README_run.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/README_run.sh @@ -12,12 +12,12 @@ # If not, carry out the instructions in "README_setup.sh". # # -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, +# If "lmp_mpi" is the name of the command you use to invoke lammps, # then you would run lammps on these files this way: -lmp_linux -i run.in.npt # minimization and simulation at constant pressure -lmp_linux -i run.in.nvt # minimization and simulation at constant volume +lmp_mpi -i run.in.npt # minimization and simulation at constant pressure +lmp_mpi -i run.in.nvt # minimization and simulation at constant volume #(Note: The constant volume simulation lacks pressure equilibration. These are # completely separate simulations. The results of the constant pressure @@ -34,6 +34,6 @@ lmp_linux -i run.in.nvt # minimization and simulation at constant volume # If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.npt -#mpirun -np 4 lmp_linux -i run.in.nvt +#mpirun -np 4 lmp_mpi -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.nvt # (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/README_setup.sh index b3180b7e0e..2e4ecb9acc 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/README_setup.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/README_setup.sh @@ -10,7 +10,7 @@ cd moltemplate_files # Create the "oplsaa.lt" file which moltemplate will need cd oplsaa_lt_generator/ - ./oplsaa_moltemplate.py oplsaa_subset.prm + oplsaa_moltemplate.py oplsaa_subset.prm mv -f oplsaa.lt .. cd .. diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/README.TXT b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/README.TXT index b3063ce87b..6da3456025 100644 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/README.TXT +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/README.TXT @@ -15,7 +15,7 @@ so that it only contains atom types you plan to have in your simulation (see below for details). Then run the opls_moltemplate.py script this way: -python oplsaa_moltemplate.py oplsaa_subset.prm +oplsaa_moltemplate.py oplsaa_subset.prm This will create a file named "oplsaa.lt" diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py deleted file mode 100755 index 32980aab1f..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py +++ /dev/null @@ -1,408 +0,0 @@ -#! /usr/bin/env python -# -# The purpose of this script is to create a moltemplate lt file for the oplsaa. -# forcefield. This will assist researchers in building complex simulations using -# this OPLS-UA and the OPLS-AA forcefields. - -__author__="Jason Lambert" -# (some additional corrections by Miguel Gonzalez and Andrew Jewett) -__version__="0.18" - -import sys -import os -from operator import itemgetter - -g_program_name = __file__.split('/')[-1] - -# To do that, first make a copy of the \"oplsaa.prm\" file -# (which can be downloaded from the TINKER web site). -# The lines in this file beginning with the word \"atoms\" should -# define the atoms which you plan to put in your simulation. All other -# lines beginning with the word \"atoms\" should be deleted. -# (Leave the other sections of this file alone.) -#""") - - - -#input data from file containing opls aa force field parameters. -try: - f=open(sys.argv[1],"r") -except: - sys.stderr.write("Error: \n" - " You need to specify a file name as an input argument:\n" - " python oplsaa_moltemplate.py \n" - " (or the file name is specified incorrectly)\n") - sys.exit() - - -sys.stderr.write(g_program_name+", version "+__version__+"\n" - "Reading parameter file...\n") - - -#output lt file -g=open("oplsaa.lt","w") - - - -lines = f.readlines() - - - -# Ignore/Comment out lines before the "## Atom Type Definitions ##" section. - -for i in range(0, len(lines)): - if (lines[i].find("## Atom Type Definitions ##") != -1): - break - else: - lines[i] = '# ' + lines[i] - - -# As of late 2014, there appear to be 906 atom types, but we don't assume this. -# First try to infer out how many atom types there were in the original -# oplsaa.prm file, or at least find an upper bound on the atom-type numbers. -# (Keep track of the maximum value of the first column in the "atom" section.) -max_atomType = 0 -num_atomTypes = 0 -for line in lines: - # skip over text after a # comment character - ic = line.find('#') - if ic != -1: - line = (line[:ic]).strip() - else: - line = line.strip() - # now look for lines beginning with the word "atom" - tokens = line.split() - if ((len(tokens)>2) and (tokens[0] == "atom")): - num_atomTypes += 1 - if (int(tokens[1]) > max_atomType): - max_atomType = int(tokens[1]) - -if num_atomTypes > 25: - sys.stderr.write("\n" - "(Note: If your computer freezes while running "+g_program_name+",\n" - " it could be because you forgot to edit the .prm file.\n" - " The original \"oplsaa.prm\" file distributed with TINKER has over 900 atom\n" - " types. If you run "+g_program_name+" on this file, it may freeze or\n" - " crash. Instead, run "+g_program_name+" on a SUBSET of the OPLS atoms\n" - " relevant to your problem. To do that, delete the lines from the .prm\n" - " file beginning with \"atom\" which you do not need.)\n\n") - -#temporary storage file -h=open("temp.txt","w+") -atom_lookup={} #this dictionary contains all the atom ffid's as a key and the number of atoms with that key -#atom=[[10000,10000] for i in range(906)] <- don't assume there are 906 atoms -atom=[[-10000,-10000] for i in range(0,max_atomType+1)] -#charge_by_type={} # lookup charge by atom type -#vdw_by_type={} # lookup epsilon & sigma paramters by atom type -charge_by_type=[0.0 for i in range(0,max_atomType+1)] # lookup charge by atom -vdw_by_type=[(0.0,0.0) for i in range(0,max_atomType+1)] # lookup epsilon & sigma - - - -#atom is declared this way so for sorting purposes. -#atom contains the following data upon allocation -#atom[][0]=atom_id( Important for partial charges and non_bonded interactions) -#atom[][1]=atom_ffid( Important for stretches, bending, torsions and impropers) -#atom[][2]=atom_mass -#atom[][3]=partial charge -#atom[][4]=non_bonding sigma -#atom[][5]=non_bonding epsilon -#atom[][6]=atom comment -bond=[] -#bond contains the following data -#bond[0]=atom 1 ffid -#bond[1]=atom 2 ffid -#bond[2]=bond spring constant(OPLS-aa compatible) -#bond[3]=equilibrium bond distance(Angstrom) -angle=[] -#angle contains the following data -#angle[0]=atom 1 ffid -#angle[1]=atom 2 ffid -#angle[2]=atom 3 ffid -#angle[3]=spring constant -#angle[4]=equilibrium angle (degrees) -dihedral=[] -#dihedral contains the following data -#dihedral[0]=atom 1 ffid -#dihedral[1]=atom 2 ffid -#dihedral[2]=atom 3 ffid -#dihedral[3]=atom 4 ffid -#dihedral[4]=v1 -#dihedral[5]=v2 -#dihedral[6]=v3 -#dihedral[7]=v4 -improper=[] -#improper[0]=atom 1 ffid -#improper[1]=atom 2 ffid(central atom) -#improper[2]=atom 3 ffid -#improper[3]=atom 4 ffid -#improper[4]=spring coefficient -#improper[5]=equilibrium angle - - -#This section gets all the parameters from the force field file -for line in lines: - - # skip over text after a # comment character - ic = line.find('#') - if ic != -1: - line = (line[:ic]).strip() - else: - line = line.strip() - - if line.find("atom") == 0: - line=line.split() - atom[int(line[1])-1]=[int(line[1]),int(line[2]),float(line[-2]), - 0.0,0.0,0.0," ".join(line[3:-2])] - elif line.find("vdw") == 0: - line=line.split() - #vdw_temp.append([float(line[1]),float(line[2]),float(line[3])]) - if (int(line[1]) <= max_atomType): - vdw_by_type[int(line[1])] = (float(line[2]),float(line[3])) - elif line.find("bond") == 0: - line=line.split() - bond.append([int(line[1]),int(line[2]),float(line[3]),float(line[4])]) - elif line.find("angle") == 0: - line=line.split() - angle.append([int(line[1]),int(line[2]),int(line[3]), - float(line[4]),float(line[5])]) - elif line.find("torsion") == 0: - line=line.split() - dihedral.append([int(line[1]),int(line[2]),int(line[3]),int(line[4]), - float(line[5]),float(line[8]), float(line[11]), 0.0]) - elif line.find("charge") == 0: - line=line.split() - #charge_temp.append([int(line[1]),float(line[2])]) - if (int(line[1]) <= max_atomType): - charge_by_type[int(line[1])] = float(line[2]) - elif line.find("imptors") == 0: - line=line.split() - improper.append([int(line[1]), int(line[2]), - int(line[3]), int(line[4]), float(line[5]), float(line[6])]) - -if len(atom) > 600: - sys.stderr.write("WARNING: The number of atom types in your file exceeds 600\n" - " (You were supposed to edit out the atoms you don't need.\n" - " Not doing this may crash your computer.)\n" - "\n" - " Proceed? (Y/N): ") - reply = sys.stdin.readline() - if find(reply.strip().lower(), 'y') != 0: - exit(0) - -#adding the charge and Lennard Jones parameters to -#to each atom type. -#----------------------------------------------# -for i in range(0,len(atom)): - atom_type_num = atom[i][0] - #q = charge_by_type.get(atomTypeNum) - #if q: - # atom[i][3] = q - if atom_type_num != -10000: - q = charge_by_type[atom_type_num] - atom[i][3] = q - -for i in range(0,len(atom)): - atom_type_num = atom[i][0] - #vdw_params = vdw_by_type.get(atomTypeNum) - #if vdw_params: - # atom[i][4] = vdw_params[0] - # atom[i][5] = vdw_params[1] - if atom_type_num != -10000: - vdw_params = vdw_by_type[atom_type_num] - atom[i][4] = vdw_params[0] - atom[i][5] = vdw_params[1] - -del(charge_by_type) -del(vdw_by_type) - -#----------------------------------------------------------# -#begin writing content to lt file -g.write("OPLSAA {\n\n" ) - -#write out the atom masses -#----------------------------------------------------------# -g.write(" write_once(\"Data Masses\"){\n")#checked with gaff -for i,x in enumerate(atom): - if x[0] != -10000: - g.write(" @atom:{} {} #{} partial charge={}\n".format( - x[0],x[2],x[6],x[3])) -g.write(" } #(end of atom masses)\n\n") -#----------------------------------------------------------# - - -#write out the pair coefficients -#----------------------------------------------------------# -g.write(" write_once(\"In Settings\"){\n")#checked with gaff -for i,x in enumerate(atom): - if x[0] != -10000: - g.write(" pair_coeff @atom:{0} @atom:{0} lj/cut/coul/long {1} {2}\n".format(x[0],x[5],x[4])) -g.write(" } #(end of pair coeffs)\n\n") - -g.write(" write_once(\"In Charges\"){\n")#checked with gaff -for i,x in enumerate(atom): - if x[0] != -10000: - g.write(" set type @atom:{0} charge {1}\n".format(x[0],x[3])) -g.write(" } #(end of atom charges)\n\n") - -#-----------------------------------------------------------# - -# This part of the code creates a lookup dictionary -# that allows you to find every type of atom by its -# force field id. force field id is the id number -# relevant to bonds, angles, dihedrals, and impropers. -# This greatly increases the speed of angle, bond, dihedral -# and improper assignment. -#------------------------------------------------------------# -atom=sorted(atom,key=itemgetter(1)) -atom_ffid=0 -for x in atom: - if x[1]==atom_ffid: - atom_lookup[x[1]].append(x[0]) - elif x[1]>atom_ffid: - atom_lookup[x[1]]=[x[0]] - atom_ffid=x[1] -atom_lookup[0]=["*"] -#-------------------------------------------------------------# - - -#writing out the bond coefficients and bond parameters# -#-------------------------------------------------------------# -g.write(" write_once(\"In Settings\") {\n") -index1=0 -for x in bond: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - #g.write(" bond_coeff @bond:{}-{} harmonic {} {}\n".format(y,z,x[2]/2,x[3])) - # Miguel Gonzales corrected this line to: - g.write(" bond_coeff @bond:{}-{} harmonic {} {}\n".format(y,z,x[2],x[3])) - h.write(" @bond:{0}-{1} @atom:{0} @atom:{1}\n".format(y,z)) -g.write(" } #(end of bond_coeffs)\n\n") -h.seek(0,0) -g.write(" write_once(\"Data Bonds By Type\") {\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of bonds by type)\n\n") -del(bond) -h.close() -#-----------------------------------------------------------# -h=open("temp.txt","w+") - -#writing out angle coefficients and angles by type.---------# -#-----------------------------------------------------------# -g.write(" write_once(\"Data Angles By Type\"){\n") -for x in angle: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - for u in atom_lookup.get(x[2],[]): - #print(y,z,u,x) - #h.write(" angle_coeff @angle:{}-{}-{} harmonic {} {}\n".format(y,z,u,x[3]/2.0,x[4])) - # Miguel Gonzales corrected this line: - h.write(" angle_coeff @angle:{}-{}-{} harmonic {} {}\n".format(y,z,u,x[3],x[4])) - g.write(" @angle:{0}-{1}-{2} @atom:{0} @atom:{1} @atom:{2}\n".format(y,z,u)) - - -g.write(" } #(end of angles by type)\n\n") -h.seek(0,0) -g.write(" write_once(\"In Settings\" ){\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of angle_coeffs)\n\n") -del(angle) -h.close() -#----------------------------------------------------------# - -#writing dihedrals by type and dihedral coefficients-------# -h=h=open("temp.txt","w+") -g.write(" write_once(\"Data Dihedrals By Type\") {\n") -#print(atom_lookup) -for x in dihedral: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - for u in atom_lookup.get(x[2],[]): - for v in atom_lookup.get(x[3],[]): - if x[0]!=0 and x[3]!=0: - g.write(" @dihedral:{0}-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( - y,z,u,v)) - h.write(" dihedral_coeff @dihedral:{}-{}-{}-{} opls {} {} {} {}\n".format( - y,z,u,v,x[4],x[5],x[6],x[7])) - elif x[0]==0 and x[3]!=0: - g.write(" @dihedral:0-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( - y,z,u,v)) - h.write(" dihedral_coeff @dihedral:0-{}-{}-{} opls {} {} {} {}\n".format( - z,u,v,x[4],x[5],x[6],x[7])) - elif x[0]==0 and x[3]==0: - g.write(" @dihedral:0-{1}-{2}-0 @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( - y,z,u,v)) - #h.write(" dihedral_coeff @dihedral:0-{}-{}-0 harmonic {} {} {} {}\n".format( - h.write(" dihedral_coeff @dihedral:0-{}-{}-0 opls {} {} {} {}\n".format( - z,u,x[4],x[5],x[6],x[7])) - -del(dihedral) -g.write(" } #(end of Dihedrals by type)\n\n") -h.seek(0,0) -g.write(" write_once(\"In Settings\") {\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of dihedral_coeffs)\n\n") -h.close() -#-----------------------------------------------------------------------# - -#----writing out improper coefficients and impropers by type------------# -h=open("temp.txt","w+") -g.write(" write_once(\"Data Impropers By Type (opls_imp.py)\") {\n") -for x in improper: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - for u in atom_lookup.get(x[2],[]): - for v in atom_lookup.get(x[3],[]): - # Notation: let I,J,K,L denote the atom types ("biotypes") - # listed in the order they appear in the "oplsaa.prm" file. - # (I think J and L are represented by "u" and "v" in the code here.) - # It looks like the "oplsaa.prm" file distributed with tinker - # treats the third atom ("K") as the central atom. - # After checking the code, it appears that the improper angle is - # calculated as the angle between the I,J,K and the J,K,L planes - if x[0]==0 and x[1]==0 and x[3]==0: - g.write(" @improper:0-0-{2}-0 @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v)) - h.write(" improper_coeff @improper:0-0-{2}-0 harmonic {4} {5} \n".format(y,z,u,v,x[4]/2,180)) - else: - g.write(" @improper:0-0-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v)) - h.write(" improper_coeff @improper:0-0-{2}-{3} harmonic {4} {5} \n".format(y,z,u,v,x[4]/2,180)) - - -g.write(" } #(end of impropers by type)\n\n") -h.seek(0,0) -g.write(" write_once(\"In Settings\") {\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of improp_coeffs)\n\n") -#-----------------------------------------------------------------------# - -#This section writes out the input parameters required for an opls-aa simulation -# lammps. -g.write(" write_once(\"In Init\") {\n") -g.write(" units real\n") -g.write(" atom_style full\n") -g.write(" bond_style hybrid harmonic\n") -g.write(" angle_style hybrid harmonic\n") -g.write(" dihedral_style hybrid opls\n") -g.write(" improper_style hybrid harmonic\n") -#g.write(" pair_style hybrid lj/cut/coul/cut 10.0 10.0\n") -g.write(" pair_style hybrid lj/cut/coul/long 10.0 10.0\n") -g.write(" pair_modify mix geometric\n") -g.write(" special_bonds lj/coul 0.0 0.0 0.5\n") -g.write(" kspace_style pppm 0.0001\n") -g.write(" } #end of init parameters\n\n") -g.write("} # OPLSAA\n") -f.close() -g.close() -h.close() -os.remove("temp.txt") - - -sys.stderr.write("...finished.\n") - - - - diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm index f226e55959..c802793ada 100644 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm @@ -2,6 +2,8 @@ # http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm # In this version, all of the lines beginning with "atom" have been deleted # except for the atom types we will be using in this simulation +# (I also deleted some other lines from that file data to reduce the file size, +# but doing that is not necessary.) # # If you use this file, please also cite the software this file comes from: # diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_run.sh b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_run.sh index 8b01ab92d7..9f923a6c7e 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_run.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_run.sh @@ -12,12 +12,12 @@ # If not, carry out the instructions in "README_setup.sh". # # -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, +# If "lmp_mpi" is the name of the command you use to invoke lammps, # then you would run lammps on these files this way: -lmp_linux -i run.in.npt # minimization and simulation at constant pressure -lmp_linux -i run.in.nvt # minimization and simulation at constant volume +lmp_mpi -i run.in.npt # minimization and simulation at constant pressure +lmp_mpi -i run.in.nvt # minimization and simulation at constant volume #(Note: The constant volume simulation lacks pressure equilibration. These are # completely separate simulations. The results of the constant pressure @@ -34,6 +34,6 @@ lmp_linux -i run.in.nvt # minimization and simulation at constant volume # If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.npt -#mpirun -np 4 lmp_linux -i run.in.nvt +#mpirun -np 4 lmp_mpi -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.nvt # (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_setup.sh index 33645bfc8c..0cf5ae7950 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_setup.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_setup.sh @@ -19,7 +19,7 @@ cd moltemplate_files # Create the "oplsaa.lt" file which moltemplate will need cd oplsaa_lt_generator/ - ./oplsaa_moltemplate.py oplsaa_subset.prm + oplsaa_moltemplate.py oplsaa_subset.prm mv -f oplsaa.lt .. cd .. diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/README.TXT b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/README.TXT index b3063ce87b..6da3456025 100644 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/README.TXT +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/README.TXT @@ -15,7 +15,7 @@ so that it only contains atom types you plan to have in your simulation (see below for details). Then run the opls_moltemplate.py script this way: -python oplsaa_moltemplate.py oplsaa_subset.prm +oplsaa_moltemplate.py oplsaa_subset.prm This will create a file named "oplsaa.lt" diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py deleted file mode 100755 index 32980aab1f..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py +++ /dev/null @@ -1,408 +0,0 @@ -#! /usr/bin/env python -# -# The purpose of this script is to create a moltemplate lt file for the oplsaa. -# forcefield. This will assist researchers in building complex simulations using -# this OPLS-UA and the OPLS-AA forcefields. - -__author__="Jason Lambert" -# (some additional corrections by Miguel Gonzalez and Andrew Jewett) -__version__="0.18" - -import sys -import os -from operator import itemgetter - -g_program_name = __file__.split('/')[-1] - -# To do that, first make a copy of the \"oplsaa.prm\" file -# (which can be downloaded from the TINKER web site). -# The lines in this file beginning with the word \"atoms\" should -# define the atoms which you plan to put in your simulation. All other -# lines beginning with the word \"atoms\" should be deleted. -# (Leave the other sections of this file alone.) -#""") - - - -#input data from file containing opls aa force field parameters. -try: - f=open(sys.argv[1],"r") -except: - sys.stderr.write("Error: \n" - " You need to specify a file name as an input argument:\n" - " python oplsaa_moltemplate.py \n" - " (or the file name is specified incorrectly)\n") - sys.exit() - - -sys.stderr.write(g_program_name+", version "+__version__+"\n" - "Reading parameter file...\n") - - -#output lt file -g=open("oplsaa.lt","w") - - - -lines = f.readlines() - - - -# Ignore/Comment out lines before the "## Atom Type Definitions ##" section. - -for i in range(0, len(lines)): - if (lines[i].find("## Atom Type Definitions ##") != -1): - break - else: - lines[i] = '# ' + lines[i] - - -# As of late 2014, there appear to be 906 atom types, but we don't assume this. -# First try to infer out how many atom types there were in the original -# oplsaa.prm file, or at least find an upper bound on the atom-type numbers. -# (Keep track of the maximum value of the first column in the "atom" section.) -max_atomType = 0 -num_atomTypes = 0 -for line in lines: - # skip over text after a # comment character - ic = line.find('#') - if ic != -1: - line = (line[:ic]).strip() - else: - line = line.strip() - # now look for lines beginning with the word "atom" - tokens = line.split() - if ((len(tokens)>2) and (tokens[0] == "atom")): - num_atomTypes += 1 - if (int(tokens[1]) > max_atomType): - max_atomType = int(tokens[1]) - -if num_atomTypes > 25: - sys.stderr.write("\n" - "(Note: If your computer freezes while running "+g_program_name+",\n" - " it could be because you forgot to edit the .prm file.\n" - " The original \"oplsaa.prm\" file distributed with TINKER has over 900 atom\n" - " types. If you run "+g_program_name+" on this file, it may freeze or\n" - " crash. Instead, run "+g_program_name+" on a SUBSET of the OPLS atoms\n" - " relevant to your problem. To do that, delete the lines from the .prm\n" - " file beginning with \"atom\" which you do not need.)\n\n") - -#temporary storage file -h=open("temp.txt","w+") -atom_lookup={} #this dictionary contains all the atom ffid's as a key and the number of atoms with that key -#atom=[[10000,10000] for i in range(906)] <- don't assume there are 906 atoms -atom=[[-10000,-10000] for i in range(0,max_atomType+1)] -#charge_by_type={} # lookup charge by atom type -#vdw_by_type={} # lookup epsilon & sigma paramters by atom type -charge_by_type=[0.0 for i in range(0,max_atomType+1)] # lookup charge by atom -vdw_by_type=[(0.0,0.0) for i in range(0,max_atomType+1)] # lookup epsilon & sigma - - - -#atom is declared this way so for sorting purposes. -#atom contains the following data upon allocation -#atom[][0]=atom_id( Important for partial charges and non_bonded interactions) -#atom[][1]=atom_ffid( Important for stretches, bending, torsions and impropers) -#atom[][2]=atom_mass -#atom[][3]=partial charge -#atom[][4]=non_bonding sigma -#atom[][5]=non_bonding epsilon -#atom[][6]=atom comment -bond=[] -#bond contains the following data -#bond[0]=atom 1 ffid -#bond[1]=atom 2 ffid -#bond[2]=bond spring constant(OPLS-aa compatible) -#bond[3]=equilibrium bond distance(Angstrom) -angle=[] -#angle contains the following data -#angle[0]=atom 1 ffid -#angle[1]=atom 2 ffid -#angle[2]=atom 3 ffid -#angle[3]=spring constant -#angle[4]=equilibrium angle (degrees) -dihedral=[] -#dihedral contains the following data -#dihedral[0]=atom 1 ffid -#dihedral[1]=atom 2 ffid -#dihedral[2]=atom 3 ffid -#dihedral[3]=atom 4 ffid -#dihedral[4]=v1 -#dihedral[5]=v2 -#dihedral[6]=v3 -#dihedral[7]=v4 -improper=[] -#improper[0]=atom 1 ffid -#improper[1]=atom 2 ffid(central atom) -#improper[2]=atom 3 ffid -#improper[3]=atom 4 ffid -#improper[4]=spring coefficient -#improper[5]=equilibrium angle - - -#This section gets all the parameters from the force field file -for line in lines: - - # skip over text after a # comment character - ic = line.find('#') - if ic != -1: - line = (line[:ic]).strip() - else: - line = line.strip() - - if line.find("atom") == 0: - line=line.split() - atom[int(line[1])-1]=[int(line[1]),int(line[2]),float(line[-2]), - 0.0,0.0,0.0," ".join(line[3:-2])] - elif line.find("vdw") == 0: - line=line.split() - #vdw_temp.append([float(line[1]),float(line[2]),float(line[3])]) - if (int(line[1]) <= max_atomType): - vdw_by_type[int(line[1])] = (float(line[2]),float(line[3])) - elif line.find("bond") == 0: - line=line.split() - bond.append([int(line[1]),int(line[2]),float(line[3]),float(line[4])]) - elif line.find("angle") == 0: - line=line.split() - angle.append([int(line[1]),int(line[2]),int(line[3]), - float(line[4]),float(line[5])]) - elif line.find("torsion") == 0: - line=line.split() - dihedral.append([int(line[1]),int(line[2]),int(line[3]),int(line[4]), - float(line[5]),float(line[8]), float(line[11]), 0.0]) - elif line.find("charge") == 0: - line=line.split() - #charge_temp.append([int(line[1]),float(line[2])]) - if (int(line[1]) <= max_atomType): - charge_by_type[int(line[1])] = float(line[2]) - elif line.find("imptors") == 0: - line=line.split() - improper.append([int(line[1]), int(line[2]), - int(line[3]), int(line[4]), float(line[5]), float(line[6])]) - -if len(atom) > 600: - sys.stderr.write("WARNING: The number of atom types in your file exceeds 600\n" - " (You were supposed to edit out the atoms you don't need.\n" - " Not doing this may crash your computer.)\n" - "\n" - " Proceed? (Y/N): ") - reply = sys.stdin.readline() - if find(reply.strip().lower(), 'y') != 0: - exit(0) - -#adding the charge and Lennard Jones parameters to -#to each atom type. -#----------------------------------------------# -for i in range(0,len(atom)): - atom_type_num = atom[i][0] - #q = charge_by_type.get(atomTypeNum) - #if q: - # atom[i][3] = q - if atom_type_num != -10000: - q = charge_by_type[atom_type_num] - atom[i][3] = q - -for i in range(0,len(atom)): - atom_type_num = atom[i][0] - #vdw_params = vdw_by_type.get(atomTypeNum) - #if vdw_params: - # atom[i][4] = vdw_params[0] - # atom[i][5] = vdw_params[1] - if atom_type_num != -10000: - vdw_params = vdw_by_type[atom_type_num] - atom[i][4] = vdw_params[0] - atom[i][5] = vdw_params[1] - -del(charge_by_type) -del(vdw_by_type) - -#----------------------------------------------------------# -#begin writing content to lt file -g.write("OPLSAA {\n\n" ) - -#write out the atom masses -#----------------------------------------------------------# -g.write(" write_once(\"Data Masses\"){\n")#checked with gaff -for i,x in enumerate(atom): - if x[0] != -10000: - g.write(" @atom:{} {} #{} partial charge={}\n".format( - x[0],x[2],x[6],x[3])) -g.write(" } #(end of atom masses)\n\n") -#----------------------------------------------------------# - - -#write out the pair coefficients -#----------------------------------------------------------# -g.write(" write_once(\"In Settings\"){\n")#checked with gaff -for i,x in enumerate(atom): - if x[0] != -10000: - g.write(" pair_coeff @atom:{0} @atom:{0} lj/cut/coul/long {1} {2}\n".format(x[0],x[5],x[4])) -g.write(" } #(end of pair coeffs)\n\n") - -g.write(" write_once(\"In Charges\"){\n")#checked with gaff -for i,x in enumerate(atom): - if x[0] != -10000: - g.write(" set type @atom:{0} charge {1}\n".format(x[0],x[3])) -g.write(" } #(end of atom charges)\n\n") - -#-----------------------------------------------------------# - -# This part of the code creates a lookup dictionary -# that allows you to find every type of atom by its -# force field id. force field id is the id number -# relevant to bonds, angles, dihedrals, and impropers. -# This greatly increases the speed of angle, bond, dihedral -# and improper assignment. -#------------------------------------------------------------# -atom=sorted(atom,key=itemgetter(1)) -atom_ffid=0 -for x in atom: - if x[1]==atom_ffid: - atom_lookup[x[1]].append(x[0]) - elif x[1]>atom_ffid: - atom_lookup[x[1]]=[x[0]] - atom_ffid=x[1] -atom_lookup[0]=["*"] -#-------------------------------------------------------------# - - -#writing out the bond coefficients and bond parameters# -#-------------------------------------------------------------# -g.write(" write_once(\"In Settings\") {\n") -index1=0 -for x in bond: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - #g.write(" bond_coeff @bond:{}-{} harmonic {} {}\n".format(y,z,x[2]/2,x[3])) - # Miguel Gonzales corrected this line to: - g.write(" bond_coeff @bond:{}-{} harmonic {} {}\n".format(y,z,x[2],x[3])) - h.write(" @bond:{0}-{1} @atom:{0} @atom:{1}\n".format(y,z)) -g.write(" } #(end of bond_coeffs)\n\n") -h.seek(0,0) -g.write(" write_once(\"Data Bonds By Type\") {\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of bonds by type)\n\n") -del(bond) -h.close() -#-----------------------------------------------------------# -h=open("temp.txt","w+") - -#writing out angle coefficients and angles by type.---------# -#-----------------------------------------------------------# -g.write(" write_once(\"Data Angles By Type\"){\n") -for x in angle: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - for u in atom_lookup.get(x[2],[]): - #print(y,z,u,x) - #h.write(" angle_coeff @angle:{}-{}-{} harmonic {} {}\n".format(y,z,u,x[3]/2.0,x[4])) - # Miguel Gonzales corrected this line: - h.write(" angle_coeff @angle:{}-{}-{} harmonic {} {}\n".format(y,z,u,x[3],x[4])) - g.write(" @angle:{0}-{1}-{2} @atom:{0} @atom:{1} @atom:{2}\n".format(y,z,u)) - - -g.write(" } #(end of angles by type)\n\n") -h.seek(0,0) -g.write(" write_once(\"In Settings\" ){\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of angle_coeffs)\n\n") -del(angle) -h.close() -#----------------------------------------------------------# - -#writing dihedrals by type and dihedral coefficients-------# -h=h=open("temp.txt","w+") -g.write(" write_once(\"Data Dihedrals By Type\") {\n") -#print(atom_lookup) -for x in dihedral: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - for u in atom_lookup.get(x[2],[]): - for v in atom_lookup.get(x[3],[]): - if x[0]!=0 and x[3]!=0: - g.write(" @dihedral:{0}-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( - y,z,u,v)) - h.write(" dihedral_coeff @dihedral:{}-{}-{}-{} opls {} {} {} {}\n".format( - y,z,u,v,x[4],x[5],x[6],x[7])) - elif x[0]==0 and x[3]!=0: - g.write(" @dihedral:0-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( - y,z,u,v)) - h.write(" dihedral_coeff @dihedral:0-{}-{}-{} opls {} {} {} {}\n".format( - z,u,v,x[4],x[5],x[6],x[7])) - elif x[0]==0 and x[3]==0: - g.write(" @dihedral:0-{1}-{2}-0 @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( - y,z,u,v)) - #h.write(" dihedral_coeff @dihedral:0-{}-{}-0 harmonic {} {} {} {}\n".format( - h.write(" dihedral_coeff @dihedral:0-{}-{}-0 opls {} {} {} {}\n".format( - z,u,x[4],x[5],x[6],x[7])) - -del(dihedral) -g.write(" } #(end of Dihedrals by type)\n\n") -h.seek(0,0) -g.write(" write_once(\"In Settings\") {\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of dihedral_coeffs)\n\n") -h.close() -#-----------------------------------------------------------------------# - -#----writing out improper coefficients and impropers by type------------# -h=open("temp.txt","w+") -g.write(" write_once(\"Data Impropers By Type (opls_imp.py)\") {\n") -for x in improper: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - for u in atom_lookup.get(x[2],[]): - for v in atom_lookup.get(x[3],[]): - # Notation: let I,J,K,L denote the atom types ("biotypes") - # listed in the order they appear in the "oplsaa.prm" file. - # (I think J and L are represented by "u" and "v" in the code here.) - # It looks like the "oplsaa.prm" file distributed with tinker - # treats the third atom ("K") as the central atom. - # After checking the code, it appears that the improper angle is - # calculated as the angle between the I,J,K and the J,K,L planes - if x[0]==0 and x[1]==0 and x[3]==0: - g.write(" @improper:0-0-{2}-0 @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v)) - h.write(" improper_coeff @improper:0-0-{2}-0 harmonic {4} {5} \n".format(y,z,u,v,x[4]/2,180)) - else: - g.write(" @improper:0-0-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v)) - h.write(" improper_coeff @improper:0-0-{2}-{3} harmonic {4} {5} \n".format(y,z,u,v,x[4]/2,180)) - - -g.write(" } #(end of impropers by type)\n\n") -h.seek(0,0) -g.write(" write_once(\"In Settings\") {\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of improp_coeffs)\n\n") -#-----------------------------------------------------------------------# - -#This section writes out the input parameters required for an opls-aa simulation -# lammps. -g.write(" write_once(\"In Init\") {\n") -g.write(" units real\n") -g.write(" atom_style full\n") -g.write(" bond_style hybrid harmonic\n") -g.write(" angle_style hybrid harmonic\n") -g.write(" dihedral_style hybrid opls\n") -g.write(" improper_style hybrid harmonic\n") -#g.write(" pair_style hybrid lj/cut/coul/cut 10.0 10.0\n") -g.write(" pair_style hybrid lj/cut/coul/long 10.0 10.0\n") -g.write(" pair_modify mix geometric\n") -g.write(" special_bonds lj/coul 0.0 0.0 0.5\n") -g.write(" kspace_style pppm 0.0001\n") -g.write(" } #end of init parameters\n\n") -g.write("} # OPLSAA\n") -f.close() -g.close() -h.close() -os.remove("temp.txt") - - -sys.stderr.write("...finished.\n") - - - - diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm index f226e55959..c802793ada 100644 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm @@ -2,6 +2,8 @@ # http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm # In this version, all of the lines beginning with "atom" have been deleted # except for the atom types we will be using in this simulation +# (I also deleted some other lines from that file data to reduce the file size, +# but doing that is not necessary.) # # If you use this file, please also cite the software this file comes from: # diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/system.xyz b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/system.xyz new file mode 100644 index 0000000000..d64a95504d --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/system.xyz @@ -0,0 +1,12002 @@ + 12000 + Built with Packmol + C1 22.651014 24.498564 11.614060 + C2 22.571262 24.140589 10.326266 + H11 23.515857 24.451603 12.160727 + H12 21.853441 24.847475 12.153636 + H21 23.368835 23.791678 9.786690 + H22 21.706418 24.187550 9.779599 + C1 21.435403 10.177603 61.812264 + C2 20.874880 11.369561 61.571491 + H11 22.444012 10.040471 61.925867 + H12 20.899589 9.309329 61.901752 + 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75.916639 28.008916 28.212103 + H21 75.024835 25.754133 27.691885 + H31 72.790129 25.081442 28.530001 + H41 71.447656 26.662930 29.889005 + H51 72.339460 28.917713 30.409223 + H61 74.573738 29.591009 29.570436 + C1 23.719511 40.242223 11.064073 + C2 24.323332 39.218357 10.324513 + C3 25.335655 39.521658 9.406308 + C4 25.744157 40.848827 9.227662 + C5 25.139708 41.872519 9.966464 + C6 24.127385 41.569218 10.884669 + H11 22.938485 40.008276 11.771944 + H21 24.008701 38.194316 10.462678 + H31 25.802050 38.731565 8.836602 + H41 26.524555 41.082600 8.519033 + H51 25.454339 42.896560 9.828299 + H61 23.661618 42.359485 11.455133 + C1 75.550908 48.414066 3.044270 + C2 76.727555 47.725722 3.362917 + C3 77.624638 48.265909 4.292074 + C4 77.345073 49.494439 4.902584 + C5 76.169063 50.183007 4.583199 + C6 75.271980 49.642821 3.654042 + H11 74.859260 47.997575 2.327352 + H21 76.943080 46.777595 2.892445 + H31 78.531811 47.734271 4.538520 + H41 78.037358 49.911154 5.618765 + H51 75.953538 51.131135 5.053671 + H61 74.364171 50.174233 3.408334 + C1 2.118900 68.274556 65.655093 + C2 3.301933 67.768490 65.103566 + C3 3.293418 66.535948 64.439745 + C4 2.101870 65.809472 64.327451 + C5 0.919318 66.315115 64.879746 + C6 0.927833 67.547657 65.543567 + H11 2.125618 69.224984 66.167397 + H21 4.221174 68.329149 65.189587 + H31 4.205941 66.146179 64.013461 + H41 2.095633 64.858621 63.815915 + H51 0.000077 65.754457 64.793726 + H61 0.014829 67.937850 65.969083 + C1 75.899323 69.201341 7.124091 + C2 75.601985 69.394991 8.478322 + C3 75.378498 68.291644 9.310529 + C4 75.452350 66.994647 8.788506 + C5 75.748711 66.801204 7.434296 + C6 75.972197 67.904552 6.602089 + H11 76.071293 70.052361 6.482214 + H21 75.545580 70.395556 8.881346 + H31 75.150124 68.441189 10.355430 + H41 75.279403 66.143834 9.430403 + H51 75.805115 65.800639 7.031271 + H61 76.201549 67.754799 5.557167 + C1 51.945333 67.492308 17.935227 + C2 51.765445 67.428284 19.322091 + C3 51.774692 68.602730 20.083986 + C4 51.963825 69.841199 19.459016 + C5 52.144613 69.904985 18.072516 + C6 52.135366 68.730539 17.310622 + H11 51.938581 66.586436 17.347719 + H21 51.618901 66.472922 19.804324 + H31 51.634899 68.553239 21.153726 + H41 51.971477 70.746833 20.046888 + H51 52.291157 70.860347 17.590283 + H61 52.274259 68.780267 16.240516 + C1 63.199160 29.800629 49.859610 + C2 63.888360 29.106168 50.860900 + C3 65.287511 29.136626 50.897500 + C4 65.997463 29.861545 49.932810 + C5 65.308297 30.555058 48.931199 + C6 63.909146 30.524600 48.894600 + H11 62.120069 29.776776 49.831209 + H21 63.340742 28.547349 51.605598 + H31 65.818984 28.601660 51.670600 + H41 67.076588 29.884451 49.960890 + H51 65.855915 31.113878 48.186501 + H61 63.377639 31.060513 48.121821 + C1 36.483801 75.804887 14.595253 + C2 35.278751 76.374641 14.167369 + C3 34.928335 76.335689 12.812532 + C4 35.782970 75.726983 11.885579 + C5 36.988214 75.158206 12.313380 + C6 37.338630 75.197158 13.668217 + H11 36.754185 75.835308 15.640136 + H21 34.619002 76.843754 14.882494 + H31 33.998203 76.774380 12.482774 + H41 35.512780 75.697539 10.840613 + H51 37.647963 74.689093 11.598254 + H61 38.268569 74.757489 13.998058 + C1 70.698397 43.827631 66.227920 + C2 71.014925 45.120813 66.660752 + C3 72.331057 45.436591 67.018481 + C4 73.330662 44.459189 66.943379 + C5 73.013872 43.166027 66.511512 + C6 71.697739 42.850248 66.153783 + H11 69.683226 43.584045 65.952407 + H21 70.243948 45.875160 66.718158 + H31 72.575252 46.434525 67.351400 + H41 74.345571 44.702794 67.219857 + H51 73.784849 42.411679 66.454106 + H61 71.453807 41.852296 65.819899 + C1 57.208831 27.297751 7.825242 + C2 57.530329 25.950944 8.031642 + C3 56.546531 24.965961 7.883850 + C4 55.241236 25.327786 7.529658 + C5 54.919705 26.674470 7.324250 + C6 55.903502 27.659453 7.472042 + H11 57.967545 28.057411 7.939627 + H21 58.537480 25.671584 8.304306 + H31 56.794968 23.926941 8.042129 + H41 54.482489 24.568003 7.416265 + H51 53.912554 26.953831 7.051586 + H61 55.655099 28.698596 7.312771 + C1 44.040163 74.312204 76.314010 + C2 42.819789 74.390229 76.995516 + C3 42.452239 75.577945 77.639045 + C4 43.305064 76.687635 77.601067 + C5 44.525613 76.609188 76.920451 + C6 44.893163 75.421472 76.276922 + H11 44.323754 73.396016 75.818036 + H21 42.161445 73.534372 77.024381 + H31 41.510305 75.638276 78.163884 + H41 43.021648 77.603401 78.097931 + H51 45.183957 77.465045 76.891586 + H61 45.834922 75.361563 75.751194 + C1 21.348389 54.169732 52.154683 + C2 21.701005 52.880255 52.570331 + C3 23.050659 52.525957 52.683456 + C4 24.047697 53.461135 52.380933 + C5 23.695007 54.750048 51.964462 + C6 22.345353 55.104346 51.851337 + H11 20.307440 54.442800 52.067079 + H21 20.931893 52.158840 52.804358 + H31 23.322495 51.531474 53.005087 + H41 25.088572 53.187503 52.467714 + H51 24.464119 55.471463 51.730435 + H61 22.073591 56.099393 51.530529 + C1 26.197950 69.277423 8.235662 + C2 27.259753 69.918617 7.586590 + C3 28.327724 69.167228 7.081869 + C4 28.333892 67.774644 7.226220 + C5 27.272677 67.133782 7.876030 + C6 26.204706 67.885171 8.380751 + H11 25.374490 69.857033 8.625253 + H21 27.254836 70.992943 7.474602 + H31 29.146266 69.661944 6.580290 + H41 29.157939 67.195366 6.837367 + H51 27.277594 66.059456 7.988018 + H61 25.385575 67.390124 8.881593 + C1 67.455021 39.524735 72.123171 + C2 68.519078 40.144181 71.456897 + C3 69.110328 39.521178 70.351374 + C4 68.637522 38.278730 69.912124 + C5 67.574272 37.659067 70.578947 + C6 66.983022 38.282069 71.684470 + H11 66.999317 40.005102 72.976046 + H21 68.883558 41.103027 71.795289 + H31 69.930512 39.999658 69.836890 + H41 69.094033 37.798145 69.059798 + H51 67.209793 36.700220 70.240555 + H61 66.162031 37.803807 72.198405 + C1 4.772877 61.080316 30.441400 + C2 5.330659 61.713812 29.324524 + C3 5.046592 63.060692 29.069354 + C4 4.204744 63.774076 29.931060 + C5 3.646374 63.140317 31.047172 + C6 3.930440 61.793437 31.302342 + H11 4.991693 60.041417 30.637927 + H21 5.980663 61.163728 28.659961 + H31 5.477780 63.549507 28.208264 + H41 3.985340 64.812711 29.733769 + H51 2.996370 63.690401 31.711735 + H61 3.499841 61.304886 32.164196 + C1 76.374200 27.099629 38.604675 + C2 77.400333 26.149561 38.670050 + C3 77.533476 25.340145 39.804514 + C4 76.640487 25.480795 40.873603 + C5 75.615163 26.431378 40.808507 + C6 75.482020 27.240795 39.674043 + H11 76.271807 27.724133 37.729847 + H21 78.088983 26.040509 37.845059 + H31 78.324519 24.606588 39.854351 + H41 76.743689 24.856807 41.748710 + H51 74.926514 26.540431 41.633498 + H61 74.690168 27.973836 39.623927 + C1 47.762159 7.110335 60.494537 + C2 48.347009 5.929705 60.967733 + C3 48.816273 4.969746 60.063212 + C4 48.700688 5.190416 58.685493 + C5 48.115067 6.370450 58.212521 + C6 47.645802 7.330409 59.117043 + H11 47.399902 7.850494 61.192211 + H21 48.436811 5.759592 62.030625 + H31 49.268333 4.059474 60.428429 + H41 49.062174 4.449662 57.988044 + H51 48.025265 6.540563 57.149630 + H61 47.194514 8.241277 58.751601 + C1 23.350138 77.181586 56.994509 + C2 23.602396 78.262954 57.847071 + C3 24.637143 79.159069 57.553528 + C4 25.419632 78.973817 56.407423 + C5 25.167923 77.892067 55.555604 + C6 24.133176 76.995952 55.849147 + H11 22.552320 76.490266 57.221172 + H21 22.998387 78.406357 58.731010 + H31 24.830952 79.993792 58.210804 + H41 26.217999 79.664755 56.181503 + H51 25.771932 77.748664 54.671665 + H61 23.938818 76.161611 55.191128 + C1 61.748925 34.659583 28.793291 + C2 62.183774 34.457279 30.108521 + C3 61.303398 34.666471 31.176729 + C4 59.988173 35.077966 30.929707 + C5 59.553810 35.281110 29.614718 + C6 60.434185 35.071918 28.546510 + H11 62.428086 34.498602 27.969495 + H21 63.198272 34.139213 30.299225 + H31 61.638735 34.509385 32.191229 + H41 59.309497 35.239787 31.753744 + H51 58.539311 35.599177 29.424014 + H61 60.098363 35.228164 27.531769 + C1 20.424924 22.860619 14.405888 + C2 19.964320 21.541982 14.311586 + C3 20.787183 20.482828 14.712808 + C4 22.070651 20.742310 15.208332 + C5 22.531401 22.060691 15.301678 + C6 21.708538 23.119845 14.900456 + H11 19.790381 23.677427 14.096059 + H21 18.973906 21.341673 13.929881 + H31 20.431312 19.465711 14.640932 + H41 22.705340 19.925247 15.517205 + H51 23.521815 22.261000 15.683383 + H61 22.064263 24.137217 14.973288 diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/run.in.npt b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/run.in.npt index 527599ba88..1066f810d7 100644 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/run.in.npt +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/ethylene+benzene_PACKMOL/run.in.npt @@ -53,6 +53,6 @@ fix fxnpt all npt temp 300.0 300.0 100.0 iso 50.0 50.0 1000.0 drag 1 thermo 100 #thermo_modify flush yes -run 100000 +run 200000 write_data system_after_npt.data diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/README_run.sh b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/README_run.sh index 8b01ab92d7..9f923a6c7e 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/README_run.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/README_run.sh @@ -12,12 +12,12 @@ # If not, carry out the instructions in "README_setup.sh". # # -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, +# If "lmp_mpi" is the name of the command you use to invoke lammps, # then you would run lammps on these files this way: -lmp_linux -i run.in.npt # minimization and simulation at constant pressure -lmp_linux -i run.in.nvt # minimization and simulation at constant volume +lmp_mpi -i run.in.npt # minimization and simulation at constant pressure +lmp_mpi -i run.in.nvt # minimization and simulation at constant volume #(Note: The constant volume simulation lacks pressure equilibration. These are # completely separate simulations. The results of the constant pressure @@ -34,6 +34,6 @@ lmp_linux -i run.in.nvt # minimization and simulation at constant volume # If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.npt -#mpirun -np 4 lmp_linux -i run.in.nvt +#mpirun -np 4 lmp_mpi -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.nvt # (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/README_setup.sh index b3180b7e0e..2e4ecb9acc 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/README_setup.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/README_setup.sh @@ -10,7 +10,7 @@ cd moltemplate_files # Create the "oplsaa.lt" file which moltemplate will need cd oplsaa_lt_generator/ - ./oplsaa_moltemplate.py oplsaa_subset.prm + oplsaa_moltemplate.py oplsaa_subset.prm mv -f oplsaa.lt .. cd .. diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator/README.TXT b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator/README.TXT index a3e8a6a84c..5b6e32d845 100644 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator/README.TXT +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator/README.TXT @@ -15,7 +15,7 @@ so that it only contains atom types you plan to have in your simulation (see below for details). Then run the opls_moltemplate.py script this way: -python oplsaa_moltemplate.py oplsaa_subset.prm +oplsaa_moltemplate.py oplsaa_subset.prm This will create a file named "oplsaa.lt" diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py deleted file mode 100755 index 32980aab1f..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py +++ /dev/null @@ -1,408 +0,0 @@ -#! /usr/bin/env python -# -# The purpose of this script is to create a moltemplate lt file for the oplsaa. -# forcefield. This will assist researchers in building complex simulations using -# this OPLS-UA and the OPLS-AA forcefields. - -__author__="Jason Lambert" -# (some additional corrections by Miguel Gonzalez and Andrew Jewett) -__version__="0.18" - -import sys -import os -from operator import itemgetter - -g_program_name = __file__.split('/')[-1] - -# To do that, first make a copy of the \"oplsaa.prm\" file -# (which can be downloaded from the TINKER web site). -# The lines in this file beginning with the word \"atoms\" should -# define the atoms which you plan to put in your simulation. All other -# lines beginning with the word \"atoms\" should be deleted. -# (Leave the other sections of this file alone.) -#""") - - - -#input data from file containing opls aa force field parameters. -try: - f=open(sys.argv[1],"r") -except: - sys.stderr.write("Error: \n" - " You need to specify a file name as an input argument:\n" - " python oplsaa_moltemplate.py \n" - " (or the file name is specified incorrectly)\n") - sys.exit() - - -sys.stderr.write(g_program_name+", version "+__version__+"\n" - "Reading parameter file...\n") - - -#output lt file -g=open("oplsaa.lt","w") - - - -lines = f.readlines() - - - -# Ignore/Comment out lines before the "## Atom Type Definitions ##" section. - -for i in range(0, len(lines)): - if (lines[i].find("## Atom Type Definitions ##") != -1): - break - else: - lines[i] = '# ' + lines[i] - - -# As of late 2014, there appear to be 906 atom types, but we don't assume this. -# First try to infer out how many atom types there were in the original -# oplsaa.prm file, or at least find an upper bound on the atom-type numbers. -# (Keep track of the maximum value of the first column in the "atom" section.) -max_atomType = 0 -num_atomTypes = 0 -for line in lines: - # skip over text after a # comment character - ic = line.find('#') - if ic != -1: - line = (line[:ic]).strip() - else: - line = line.strip() - # now look for lines beginning with the word "atom" - tokens = line.split() - if ((len(tokens)>2) and (tokens[0] == "atom")): - num_atomTypes += 1 - if (int(tokens[1]) > max_atomType): - max_atomType = int(tokens[1]) - -if num_atomTypes > 25: - sys.stderr.write("\n" - "(Note: If your computer freezes while running "+g_program_name+",\n" - " it could be because you forgot to edit the .prm file.\n" - " The original \"oplsaa.prm\" file distributed with TINKER has over 900 atom\n" - " types. If you run "+g_program_name+" on this file, it may freeze or\n" - " crash. Instead, run "+g_program_name+" on a SUBSET of the OPLS atoms\n" - " relevant to your problem. To do that, delete the lines from the .prm\n" - " file beginning with \"atom\" which you do not need.)\n\n") - -#temporary storage file -h=open("temp.txt","w+") -atom_lookup={} #this dictionary contains all the atom ffid's as a key and the number of atoms with that key -#atom=[[10000,10000] for i in range(906)] <- don't assume there are 906 atoms -atom=[[-10000,-10000] for i in range(0,max_atomType+1)] -#charge_by_type={} # lookup charge by atom type -#vdw_by_type={} # lookup epsilon & sigma paramters by atom type -charge_by_type=[0.0 for i in range(0,max_atomType+1)] # lookup charge by atom -vdw_by_type=[(0.0,0.0) for i in range(0,max_atomType+1)] # lookup epsilon & sigma - - - -#atom is declared this way so for sorting purposes. -#atom contains the following data upon allocation -#atom[][0]=atom_id( Important for partial charges and non_bonded interactions) -#atom[][1]=atom_ffid( Important for stretches, bending, torsions and impropers) -#atom[][2]=atom_mass -#atom[][3]=partial charge -#atom[][4]=non_bonding sigma -#atom[][5]=non_bonding epsilon -#atom[][6]=atom comment -bond=[] -#bond contains the following data -#bond[0]=atom 1 ffid -#bond[1]=atom 2 ffid -#bond[2]=bond spring constant(OPLS-aa compatible) -#bond[3]=equilibrium bond distance(Angstrom) -angle=[] -#angle contains the following data -#angle[0]=atom 1 ffid -#angle[1]=atom 2 ffid -#angle[2]=atom 3 ffid -#angle[3]=spring constant -#angle[4]=equilibrium angle (degrees) -dihedral=[] -#dihedral contains the following data -#dihedral[0]=atom 1 ffid -#dihedral[1]=atom 2 ffid -#dihedral[2]=atom 3 ffid -#dihedral[3]=atom 4 ffid -#dihedral[4]=v1 -#dihedral[5]=v2 -#dihedral[6]=v3 -#dihedral[7]=v4 -improper=[] -#improper[0]=atom 1 ffid -#improper[1]=atom 2 ffid(central atom) -#improper[2]=atom 3 ffid -#improper[3]=atom 4 ffid -#improper[4]=spring coefficient -#improper[5]=equilibrium angle - - -#This section gets all the parameters from the force field file -for line in lines: - - # skip over text after a # comment character - ic = line.find('#') - if ic != -1: - line = (line[:ic]).strip() - else: - line = line.strip() - - if line.find("atom") == 0: - line=line.split() - atom[int(line[1])-1]=[int(line[1]),int(line[2]),float(line[-2]), - 0.0,0.0,0.0," ".join(line[3:-2])] - elif line.find("vdw") == 0: - line=line.split() - #vdw_temp.append([float(line[1]),float(line[2]),float(line[3])]) - if (int(line[1]) <= max_atomType): - vdw_by_type[int(line[1])] = (float(line[2]),float(line[3])) - elif line.find("bond") == 0: - line=line.split() - bond.append([int(line[1]),int(line[2]),float(line[3]),float(line[4])]) - elif line.find("angle") == 0: - line=line.split() - angle.append([int(line[1]),int(line[2]),int(line[3]), - float(line[4]),float(line[5])]) - elif line.find("torsion") == 0: - line=line.split() - dihedral.append([int(line[1]),int(line[2]),int(line[3]),int(line[4]), - float(line[5]),float(line[8]), float(line[11]), 0.0]) - elif line.find("charge") == 0: - line=line.split() - #charge_temp.append([int(line[1]),float(line[2])]) - if (int(line[1]) <= max_atomType): - charge_by_type[int(line[1])] = float(line[2]) - elif line.find("imptors") == 0: - line=line.split() - improper.append([int(line[1]), int(line[2]), - int(line[3]), int(line[4]), float(line[5]), float(line[6])]) - -if len(atom) > 600: - sys.stderr.write("WARNING: The number of atom types in your file exceeds 600\n" - " (You were supposed to edit out the atoms you don't need.\n" - " Not doing this may crash your computer.)\n" - "\n" - " Proceed? (Y/N): ") - reply = sys.stdin.readline() - if find(reply.strip().lower(), 'y') != 0: - exit(0) - -#adding the charge and Lennard Jones parameters to -#to each atom type. -#----------------------------------------------# -for i in range(0,len(atom)): - atom_type_num = atom[i][0] - #q = charge_by_type.get(atomTypeNum) - #if q: - # atom[i][3] = q - if atom_type_num != -10000: - q = charge_by_type[atom_type_num] - atom[i][3] = q - -for i in range(0,len(atom)): - atom_type_num = atom[i][0] - #vdw_params = vdw_by_type.get(atomTypeNum) - #if vdw_params: - # atom[i][4] = vdw_params[0] - # atom[i][5] = vdw_params[1] - if atom_type_num != -10000: - vdw_params = vdw_by_type[atom_type_num] - atom[i][4] = vdw_params[0] - atom[i][5] = vdw_params[1] - -del(charge_by_type) -del(vdw_by_type) - -#----------------------------------------------------------# -#begin writing content to lt file -g.write("OPLSAA {\n\n" ) - -#write out the atom masses -#----------------------------------------------------------# -g.write(" write_once(\"Data Masses\"){\n")#checked with gaff -for i,x in enumerate(atom): - if x[0] != -10000: - g.write(" @atom:{} {} #{} partial charge={}\n".format( - x[0],x[2],x[6],x[3])) -g.write(" } #(end of atom masses)\n\n") -#----------------------------------------------------------# - - -#write out the pair coefficients -#----------------------------------------------------------# -g.write(" write_once(\"In Settings\"){\n")#checked with gaff -for i,x in enumerate(atom): - if x[0] != -10000: - g.write(" pair_coeff @atom:{0} @atom:{0} lj/cut/coul/long {1} {2}\n".format(x[0],x[5],x[4])) -g.write(" } #(end of pair coeffs)\n\n") - -g.write(" write_once(\"In Charges\"){\n")#checked with gaff -for i,x in enumerate(atom): - if x[0] != -10000: - g.write(" set type @atom:{0} charge {1}\n".format(x[0],x[3])) -g.write(" } #(end of atom charges)\n\n") - -#-----------------------------------------------------------# - -# This part of the code creates a lookup dictionary -# that allows you to find every type of atom by its -# force field id. force field id is the id number -# relevant to bonds, angles, dihedrals, and impropers. -# This greatly increases the speed of angle, bond, dihedral -# and improper assignment. -#------------------------------------------------------------# -atom=sorted(atom,key=itemgetter(1)) -atom_ffid=0 -for x in atom: - if x[1]==atom_ffid: - atom_lookup[x[1]].append(x[0]) - elif x[1]>atom_ffid: - atom_lookup[x[1]]=[x[0]] - atom_ffid=x[1] -atom_lookup[0]=["*"] -#-------------------------------------------------------------# - - -#writing out the bond coefficients and bond parameters# -#-------------------------------------------------------------# -g.write(" write_once(\"In Settings\") {\n") -index1=0 -for x in bond: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - #g.write(" bond_coeff @bond:{}-{} harmonic {} {}\n".format(y,z,x[2]/2,x[3])) - # Miguel Gonzales corrected this line to: - g.write(" bond_coeff @bond:{}-{} harmonic {} {}\n".format(y,z,x[2],x[3])) - h.write(" @bond:{0}-{1} @atom:{0} @atom:{1}\n".format(y,z)) -g.write(" } #(end of bond_coeffs)\n\n") -h.seek(0,0) -g.write(" write_once(\"Data Bonds By Type\") {\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of bonds by type)\n\n") -del(bond) -h.close() -#-----------------------------------------------------------# -h=open("temp.txt","w+") - -#writing out angle coefficients and angles by type.---------# -#-----------------------------------------------------------# -g.write(" write_once(\"Data Angles By Type\"){\n") -for x in angle: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - for u in atom_lookup.get(x[2],[]): - #print(y,z,u,x) - #h.write(" angle_coeff @angle:{}-{}-{} harmonic {} {}\n".format(y,z,u,x[3]/2.0,x[4])) - # Miguel Gonzales corrected this line: - h.write(" angle_coeff @angle:{}-{}-{} harmonic {} {}\n".format(y,z,u,x[3],x[4])) - g.write(" @angle:{0}-{1}-{2} @atom:{0} @atom:{1} @atom:{2}\n".format(y,z,u)) - - -g.write(" } #(end of angles by type)\n\n") -h.seek(0,0) -g.write(" write_once(\"In Settings\" ){\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of angle_coeffs)\n\n") -del(angle) -h.close() -#----------------------------------------------------------# - -#writing dihedrals by type and dihedral coefficients-------# -h=h=open("temp.txt","w+") -g.write(" write_once(\"Data Dihedrals By Type\") {\n") -#print(atom_lookup) -for x in dihedral: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - for u in atom_lookup.get(x[2],[]): - for v in atom_lookup.get(x[3],[]): - if x[0]!=0 and x[3]!=0: - g.write(" @dihedral:{0}-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( - y,z,u,v)) - h.write(" dihedral_coeff @dihedral:{}-{}-{}-{} opls {} {} {} {}\n".format( - y,z,u,v,x[4],x[5],x[6],x[7])) - elif x[0]==0 and x[3]!=0: - g.write(" @dihedral:0-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( - y,z,u,v)) - h.write(" dihedral_coeff @dihedral:0-{}-{}-{} opls {} {} {} {}\n".format( - z,u,v,x[4],x[5],x[6],x[7])) - elif x[0]==0 and x[3]==0: - g.write(" @dihedral:0-{1}-{2}-0 @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( - y,z,u,v)) - #h.write(" dihedral_coeff @dihedral:0-{}-{}-0 harmonic {} {} {} {}\n".format( - h.write(" dihedral_coeff @dihedral:0-{}-{}-0 opls {} {} {} {}\n".format( - z,u,x[4],x[5],x[6],x[7])) - -del(dihedral) -g.write(" } #(end of Dihedrals by type)\n\n") -h.seek(0,0) -g.write(" write_once(\"In Settings\") {\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of dihedral_coeffs)\n\n") -h.close() -#-----------------------------------------------------------------------# - -#----writing out improper coefficients and impropers by type------------# -h=open("temp.txt","w+") -g.write(" write_once(\"Data Impropers By Type (opls_imp.py)\") {\n") -for x in improper: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - for u in atom_lookup.get(x[2],[]): - for v in atom_lookup.get(x[3],[]): - # Notation: let I,J,K,L denote the atom types ("biotypes") - # listed in the order they appear in the "oplsaa.prm" file. - # (I think J and L are represented by "u" and "v" in the code here.) - # It looks like the "oplsaa.prm" file distributed with tinker - # treats the third atom ("K") as the central atom. - # After checking the code, it appears that the improper angle is - # calculated as the angle between the I,J,K and the J,K,L planes - if x[0]==0 and x[1]==0 and x[3]==0: - g.write(" @improper:0-0-{2}-0 @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v)) - h.write(" improper_coeff @improper:0-0-{2}-0 harmonic {4} {5} \n".format(y,z,u,v,x[4]/2,180)) - else: - g.write(" @improper:0-0-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v)) - h.write(" improper_coeff @improper:0-0-{2}-{3} harmonic {4} {5} \n".format(y,z,u,v,x[4]/2,180)) - - -g.write(" } #(end of impropers by type)\n\n") -h.seek(0,0) -g.write(" write_once(\"In Settings\") {\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of improp_coeffs)\n\n") -#-----------------------------------------------------------------------# - -#This section writes out the input parameters required for an opls-aa simulation -# lammps. -g.write(" write_once(\"In Init\") {\n") -g.write(" units real\n") -g.write(" atom_style full\n") -g.write(" bond_style hybrid harmonic\n") -g.write(" angle_style hybrid harmonic\n") -g.write(" dihedral_style hybrid opls\n") -g.write(" improper_style hybrid harmonic\n") -#g.write(" pair_style hybrid lj/cut/coul/cut 10.0 10.0\n") -g.write(" pair_style hybrid lj/cut/coul/long 10.0 10.0\n") -g.write(" pair_modify mix geometric\n") -g.write(" special_bonds lj/coul 0.0 0.0 0.5\n") -g.write(" kspace_style pppm 0.0001\n") -g.write(" } #end of init parameters\n\n") -g.write("} # OPLSAA\n") -f.close() -g.close() -h.close() -os.remove("temp.txt") - - -sys.stderr.write("...finished.\n") - - - - diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm index ea7a9ade76..1260acdbd3 100644 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm @@ -9,9 +9,14 @@ # # When building your own molecules, you should download this file, and delete # only the lines from the "atoms" section which you don't need. (But leave the -# rest of that file alone.) Rename the resulting file "oplsaa_subset.prm" +# rest of that file alone. I deleted other sections of this file here in order +# to reduce the file size, but this is not necessary.) +# +# Rename the resulting file "oplsaa_subset.prm" +# # Then you can create an oplsaa.lt file (which moltemplate.sh needs) this way: -# python oplsaa_moltemplate.py oplsaa_subset.prm +# oplsaa_moltemplate.py oplsaa_subset.prm +# # Then copy the newly created "oplsa.lt" file to the directory where you # plan to run moltemplate, and run moltemplate: # moltemplate system.lt diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/run.in.npt b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/run.in.npt index 4b79b54478..1b1a28fabc 100644 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/run.in.npt +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/run.in.npt @@ -16,6 +16,7 @@ read_data system.data # ------------------------------- Settings Section -------------------------- include system.in.settings +include system.in.charges # ------------------------------- Run Section ------------------------------- diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/run.in.nvt index 0bb7699896..38815745c5 100644 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/run.in.nvt +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane/run.in.nvt @@ -26,6 +26,7 @@ read_data system_after_eq3_npt.data # ------------------------------- Settings Section -------------------------- include system.in.settings +include system.in.charges # ------------------------------- Run Section ------------------------------- diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/README_run.sh b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/README_run.sh index 8b01ab92d7..9f923a6c7e 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/README_run.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/README_run.sh @@ -12,12 +12,12 @@ # If not, carry out the instructions in "README_setup.sh". # # -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, +# If "lmp_mpi" is the name of the command you use to invoke lammps, # then you would run lammps on these files this way: -lmp_linux -i run.in.npt # minimization and simulation at constant pressure -lmp_linux -i run.in.nvt # minimization and simulation at constant volume +lmp_mpi -i run.in.npt # minimization and simulation at constant pressure +lmp_mpi -i run.in.nvt # minimization and simulation at constant volume #(Note: The constant volume simulation lacks pressure equilibration. These are # completely separate simulations. The results of the constant pressure @@ -34,6 +34,6 @@ lmp_linux -i run.in.nvt # minimization and simulation at constant volume # If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.npt -#mpirun -np 4 lmp_linux -i run.in.nvt +#mpirun -np 4 lmp_mpi -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.nvt # (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/README_setup.sh index d80df900ef..2c3c217135 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/README_setup.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/README_setup.sh @@ -10,7 +10,7 @@ cd moltemplate_files # Create the "oplsaa.lt" file which moltemplate will need cd oplsaa_lt_generator/ - ./oplsaa_moltemplate.py oplsaa_subset.prm + oplsaa_moltemplate.py oplsaa_subset.prm mv -f oplsaa.lt .. cd .. diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/README.TXT b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/README.TXT index 00fd871b00..3336341da8 100644 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/README.TXT +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/README.TXT @@ -16,7 +16,7 @@ so that it only contains atom types you plan to have in your simulation (see below for details). Then run the opls_moltemplate.py script this way: -python oplsaa_moltemplate.py oplsaa_subset.prm +oplsaa_moltemplate.py oplsaa_subset.prm This will create a file named "oplsaa.lt" diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py deleted file mode 100755 index 32980aab1f..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py +++ /dev/null @@ -1,408 +0,0 @@ -#! /usr/bin/env python -# -# The purpose of this script is to create a moltemplate lt file for the oplsaa. -# forcefield. This will assist researchers in building complex simulations using -# this OPLS-UA and the OPLS-AA forcefields. - -__author__="Jason Lambert" -# (some additional corrections by Miguel Gonzalez and Andrew Jewett) -__version__="0.18" - -import sys -import os -from operator import itemgetter - -g_program_name = __file__.split('/')[-1] - -# To do that, first make a copy of the \"oplsaa.prm\" file -# (which can be downloaded from the TINKER web site). -# The lines in this file beginning with the word \"atoms\" should -# define the atoms which you plan to put in your simulation. All other -# lines beginning with the word \"atoms\" should be deleted. -# (Leave the other sections of this file alone.) -#""") - - - -#input data from file containing opls aa force field parameters. -try: - f=open(sys.argv[1],"r") -except: - sys.stderr.write("Error: \n" - " You need to specify a file name as an input argument:\n" - " python oplsaa_moltemplate.py \n" - " (or the file name is specified incorrectly)\n") - sys.exit() - - -sys.stderr.write(g_program_name+", version "+__version__+"\n" - "Reading parameter file...\n") - - -#output lt file -g=open("oplsaa.lt","w") - - - -lines = f.readlines() - - - -# Ignore/Comment out lines before the "## Atom Type Definitions ##" section. - -for i in range(0, len(lines)): - if (lines[i].find("## Atom Type Definitions ##") != -1): - break - else: - lines[i] = '# ' + lines[i] - - -# As of late 2014, there appear to be 906 atom types, but we don't assume this. -# First try to infer out how many atom types there were in the original -# oplsaa.prm file, or at least find an upper bound on the atom-type numbers. -# (Keep track of the maximum value of the first column in the "atom" section.) -max_atomType = 0 -num_atomTypes = 0 -for line in lines: - # skip over text after a # comment character - ic = line.find('#') - if ic != -1: - line = (line[:ic]).strip() - else: - line = line.strip() - # now look for lines beginning with the word "atom" - tokens = line.split() - if ((len(tokens)>2) and (tokens[0] == "atom")): - num_atomTypes += 1 - if (int(tokens[1]) > max_atomType): - max_atomType = int(tokens[1]) - -if num_atomTypes > 25: - sys.stderr.write("\n" - "(Note: If your computer freezes while running "+g_program_name+",\n" - " it could be because you forgot to edit the .prm file.\n" - " The original \"oplsaa.prm\" file distributed with TINKER has over 900 atom\n" - " types. If you run "+g_program_name+" on this file, it may freeze or\n" - " crash. Instead, run "+g_program_name+" on a SUBSET of the OPLS atoms\n" - " relevant to your problem. To do that, delete the lines from the .prm\n" - " file beginning with \"atom\" which you do not need.)\n\n") - -#temporary storage file -h=open("temp.txt","w+") -atom_lookup={} #this dictionary contains all the atom ffid's as a key and the number of atoms with that key -#atom=[[10000,10000] for i in range(906)] <- don't assume there are 906 atoms -atom=[[-10000,-10000] for i in range(0,max_atomType+1)] -#charge_by_type={} # lookup charge by atom type -#vdw_by_type={} # lookup epsilon & sigma paramters by atom type -charge_by_type=[0.0 for i in range(0,max_atomType+1)] # lookup charge by atom -vdw_by_type=[(0.0,0.0) for i in range(0,max_atomType+1)] # lookup epsilon & sigma - - - -#atom is declared this way so for sorting purposes. -#atom contains the following data upon allocation -#atom[][0]=atom_id( Important for partial charges and non_bonded interactions) -#atom[][1]=atom_ffid( Important for stretches, bending, torsions and impropers) -#atom[][2]=atom_mass -#atom[][3]=partial charge -#atom[][4]=non_bonding sigma -#atom[][5]=non_bonding epsilon -#atom[][6]=atom comment -bond=[] -#bond contains the following data -#bond[0]=atom 1 ffid -#bond[1]=atom 2 ffid -#bond[2]=bond spring constant(OPLS-aa compatible) -#bond[3]=equilibrium bond distance(Angstrom) -angle=[] -#angle contains the following data -#angle[0]=atom 1 ffid -#angle[1]=atom 2 ffid -#angle[2]=atom 3 ffid -#angle[3]=spring constant -#angle[4]=equilibrium angle (degrees) -dihedral=[] -#dihedral contains the following data -#dihedral[0]=atom 1 ffid -#dihedral[1]=atom 2 ffid -#dihedral[2]=atom 3 ffid -#dihedral[3]=atom 4 ffid -#dihedral[4]=v1 -#dihedral[5]=v2 -#dihedral[6]=v3 -#dihedral[7]=v4 -improper=[] -#improper[0]=atom 1 ffid -#improper[1]=atom 2 ffid(central atom) -#improper[2]=atom 3 ffid -#improper[3]=atom 4 ffid -#improper[4]=spring coefficient -#improper[5]=equilibrium angle - - -#This section gets all the parameters from the force field file -for line in lines: - - # skip over text after a # comment character - ic = line.find('#') - if ic != -1: - line = (line[:ic]).strip() - else: - line = line.strip() - - if line.find("atom") == 0: - line=line.split() - atom[int(line[1])-1]=[int(line[1]),int(line[2]),float(line[-2]), - 0.0,0.0,0.0," ".join(line[3:-2])] - elif line.find("vdw") == 0: - line=line.split() - #vdw_temp.append([float(line[1]),float(line[2]),float(line[3])]) - if (int(line[1]) <= max_atomType): - vdw_by_type[int(line[1])] = (float(line[2]),float(line[3])) - elif line.find("bond") == 0: - line=line.split() - bond.append([int(line[1]),int(line[2]),float(line[3]),float(line[4])]) - elif line.find("angle") == 0: - line=line.split() - angle.append([int(line[1]),int(line[2]),int(line[3]), - float(line[4]),float(line[5])]) - elif line.find("torsion") == 0: - line=line.split() - dihedral.append([int(line[1]),int(line[2]),int(line[3]),int(line[4]), - float(line[5]),float(line[8]), float(line[11]), 0.0]) - elif line.find("charge") == 0: - line=line.split() - #charge_temp.append([int(line[1]),float(line[2])]) - if (int(line[1]) <= max_atomType): - charge_by_type[int(line[1])] = float(line[2]) - elif line.find("imptors") == 0: - line=line.split() - improper.append([int(line[1]), int(line[2]), - int(line[3]), int(line[4]), float(line[5]), float(line[6])]) - -if len(atom) > 600: - sys.stderr.write("WARNING: The number of atom types in your file exceeds 600\n" - " (You were supposed to edit out the atoms you don't need.\n" - " Not doing this may crash your computer.)\n" - "\n" - " Proceed? (Y/N): ") - reply = sys.stdin.readline() - if find(reply.strip().lower(), 'y') != 0: - exit(0) - -#adding the charge and Lennard Jones parameters to -#to each atom type. -#----------------------------------------------# -for i in range(0,len(atom)): - atom_type_num = atom[i][0] - #q = charge_by_type.get(atomTypeNum) - #if q: - # atom[i][3] = q - if atom_type_num != -10000: - q = charge_by_type[atom_type_num] - atom[i][3] = q - -for i in range(0,len(atom)): - atom_type_num = atom[i][0] - #vdw_params = vdw_by_type.get(atomTypeNum) - #if vdw_params: - # atom[i][4] = vdw_params[0] - # atom[i][5] = vdw_params[1] - if atom_type_num != -10000: - vdw_params = vdw_by_type[atom_type_num] - atom[i][4] = vdw_params[0] - atom[i][5] = vdw_params[1] - -del(charge_by_type) -del(vdw_by_type) - -#----------------------------------------------------------# -#begin writing content to lt file -g.write("OPLSAA {\n\n" ) - -#write out the atom masses -#----------------------------------------------------------# -g.write(" write_once(\"Data Masses\"){\n")#checked with gaff -for i,x in enumerate(atom): - if x[0] != -10000: - g.write(" @atom:{} {} #{} partial charge={}\n".format( - x[0],x[2],x[6],x[3])) -g.write(" } #(end of atom masses)\n\n") -#----------------------------------------------------------# - - -#write out the pair coefficients -#----------------------------------------------------------# -g.write(" write_once(\"In Settings\"){\n")#checked with gaff -for i,x in enumerate(atom): - if x[0] != -10000: - g.write(" pair_coeff @atom:{0} @atom:{0} lj/cut/coul/long {1} {2}\n".format(x[0],x[5],x[4])) -g.write(" } #(end of pair coeffs)\n\n") - -g.write(" write_once(\"In Charges\"){\n")#checked with gaff -for i,x in enumerate(atom): - if x[0] != -10000: - g.write(" set type @atom:{0} charge {1}\n".format(x[0],x[3])) -g.write(" } #(end of atom charges)\n\n") - -#-----------------------------------------------------------# - -# This part of the code creates a lookup dictionary -# that allows you to find every type of atom by its -# force field id. force field id is the id number -# relevant to bonds, angles, dihedrals, and impropers. -# This greatly increases the speed of angle, bond, dihedral -# and improper assignment. -#------------------------------------------------------------# -atom=sorted(atom,key=itemgetter(1)) -atom_ffid=0 -for x in atom: - if x[1]==atom_ffid: - atom_lookup[x[1]].append(x[0]) - elif x[1]>atom_ffid: - atom_lookup[x[1]]=[x[0]] - atom_ffid=x[1] -atom_lookup[0]=["*"] -#-------------------------------------------------------------# - - -#writing out the bond coefficients and bond parameters# -#-------------------------------------------------------------# -g.write(" write_once(\"In Settings\") {\n") -index1=0 -for x in bond: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - #g.write(" bond_coeff @bond:{}-{} harmonic {} {}\n".format(y,z,x[2]/2,x[3])) - # Miguel Gonzales corrected this line to: - g.write(" bond_coeff @bond:{}-{} harmonic {} {}\n".format(y,z,x[2],x[3])) - h.write(" @bond:{0}-{1} @atom:{0} @atom:{1}\n".format(y,z)) -g.write(" } #(end of bond_coeffs)\n\n") -h.seek(0,0) -g.write(" write_once(\"Data Bonds By Type\") {\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of bonds by type)\n\n") -del(bond) -h.close() -#-----------------------------------------------------------# -h=open("temp.txt","w+") - -#writing out angle coefficients and angles by type.---------# -#-----------------------------------------------------------# -g.write(" write_once(\"Data Angles By Type\"){\n") -for x in angle: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - for u in atom_lookup.get(x[2],[]): - #print(y,z,u,x) - #h.write(" angle_coeff @angle:{}-{}-{} harmonic {} {}\n".format(y,z,u,x[3]/2.0,x[4])) - # Miguel Gonzales corrected this line: - h.write(" angle_coeff @angle:{}-{}-{} harmonic {} {}\n".format(y,z,u,x[3],x[4])) - g.write(" @angle:{0}-{1}-{2} @atom:{0} @atom:{1} @atom:{2}\n".format(y,z,u)) - - -g.write(" } #(end of angles by type)\n\n") -h.seek(0,0) -g.write(" write_once(\"In Settings\" ){\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of angle_coeffs)\n\n") -del(angle) -h.close() -#----------------------------------------------------------# - -#writing dihedrals by type and dihedral coefficients-------# -h=h=open("temp.txt","w+") -g.write(" write_once(\"Data Dihedrals By Type\") {\n") -#print(atom_lookup) -for x in dihedral: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - for u in atom_lookup.get(x[2],[]): - for v in atom_lookup.get(x[3],[]): - if x[0]!=0 and x[3]!=0: - g.write(" @dihedral:{0}-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( - y,z,u,v)) - h.write(" dihedral_coeff @dihedral:{}-{}-{}-{} opls {} {} {} {}\n".format( - y,z,u,v,x[4],x[5],x[6],x[7])) - elif x[0]==0 and x[3]!=0: - g.write(" @dihedral:0-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( - y,z,u,v)) - h.write(" dihedral_coeff @dihedral:0-{}-{}-{} opls {} {} {} {}\n".format( - z,u,v,x[4],x[5],x[6],x[7])) - elif x[0]==0 and x[3]==0: - g.write(" @dihedral:0-{1}-{2}-0 @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( - y,z,u,v)) - #h.write(" dihedral_coeff @dihedral:0-{}-{}-0 harmonic {} {} {} {}\n".format( - h.write(" dihedral_coeff @dihedral:0-{}-{}-0 opls {} {} {} {}\n".format( - z,u,x[4],x[5],x[6],x[7])) - -del(dihedral) -g.write(" } #(end of Dihedrals by type)\n\n") -h.seek(0,0) -g.write(" write_once(\"In Settings\") {\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of dihedral_coeffs)\n\n") -h.close() -#-----------------------------------------------------------------------# - -#----writing out improper coefficients and impropers by type------------# -h=open("temp.txt","w+") -g.write(" write_once(\"Data Impropers By Type (opls_imp.py)\") {\n") -for x in improper: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - for u in atom_lookup.get(x[2],[]): - for v in atom_lookup.get(x[3],[]): - # Notation: let I,J,K,L denote the atom types ("biotypes") - # listed in the order they appear in the "oplsaa.prm" file. - # (I think J and L are represented by "u" and "v" in the code here.) - # It looks like the "oplsaa.prm" file distributed with tinker - # treats the third atom ("K") as the central atom. - # After checking the code, it appears that the improper angle is - # calculated as the angle between the I,J,K and the J,K,L planes - if x[0]==0 and x[1]==0 and x[3]==0: - g.write(" @improper:0-0-{2}-0 @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v)) - h.write(" improper_coeff @improper:0-0-{2}-0 harmonic {4} {5} \n".format(y,z,u,v,x[4]/2,180)) - else: - g.write(" @improper:0-0-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v)) - h.write(" improper_coeff @improper:0-0-{2}-{3} harmonic {4} {5} \n".format(y,z,u,v,x[4]/2,180)) - - -g.write(" } #(end of impropers by type)\n\n") -h.seek(0,0) -g.write(" write_once(\"In Settings\") {\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of improp_coeffs)\n\n") -#-----------------------------------------------------------------------# - -#This section writes out the input parameters required for an opls-aa simulation -# lammps. -g.write(" write_once(\"In Init\") {\n") -g.write(" units real\n") -g.write(" atom_style full\n") -g.write(" bond_style hybrid harmonic\n") -g.write(" angle_style hybrid harmonic\n") -g.write(" dihedral_style hybrid opls\n") -g.write(" improper_style hybrid harmonic\n") -#g.write(" pair_style hybrid lj/cut/coul/cut 10.0 10.0\n") -g.write(" pair_style hybrid lj/cut/coul/long 10.0 10.0\n") -g.write(" pair_modify mix geometric\n") -g.write(" special_bonds lj/coul 0.0 0.0 0.5\n") -g.write(" kspace_style pppm 0.0001\n") -g.write(" } #end of init parameters\n\n") -g.write("} # OPLSAA\n") -f.close() -g.close() -h.close() -os.remove("temp.txt") - - -sys.stderr.write("...finished.\n") - - - - diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm index 074940eb2b..5f982059b3 100644 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/methane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm @@ -2,6 +2,8 @@ # http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm # In this version, all of the lines beginning with "atom" have been deleted # except for the atom types we will be using in this simulation +# (I also deleted some other lines from that file data to reduce the file size, +# but doing that is not necessary.) # # If you use this file, please also cite the software this file comes from: # @@ -71,14 +73,6 @@ explicit hydrogen atoms. atom 83 13 CT "Methane CH4" 6 12.011 4 atom 85 46 HC "Alkane H-C" 1 1.008 1 -# NOTE: You can use the OPLSAA force field to look up water parameters as well. -# In that case, you could do this by uncommenting these next two lines: -# atom 76 42 OW "SPC Water O" 8 15.999 2 -# atom 77 43 HW "SPC Water H" 1 1.008 1 -# (...You will have to modify the "spce.lt" file accordingly.) - - - ################################ ## ## ## Van der Waals Parameters ## @@ -86,912 +80,8 @@ atom 85 46 HC "Alkane H-C" 1 1.008 1 ################################ -vdw 1 2.9400 0.0610 -vdw 2 3.9050 0.1180 -vdw 3 3.7500 0.1050 -vdw 4 2.9600 0.2100 -vdw 5 3.0000 0.1700 -vdw 6 3.9100 0.1600 -vdw 7 0.0000 0.0000 -vdw 8 3.7300 0.2940 -vdw 9 3.7750 0.2070 -vdw 10 3.9050 0.1750 -vdw 11 3.9100 0.1600 -vdw 12 3.9600 0.1450 -vdw 13 3.9050 0.1180 -vdw 14 3.8500 0.1400 -vdw 15 3.8500 0.0800 -vdw 16 3.8000 0.1150 -vdw 17 3.7500 0.1100 -vdw 18 3.8000 0.0500 -vdw 19 3.7500 0.1050 -vdw 20 3.0700 0.1700 -vdw 21 0.0000 0.0000 -vdw 22 3.7750 0.2070 -vdw 23 3.9050 0.1180 -vdw 24 3.7000 0.2500 -vdw 25 3.5500 0.2500 -vdw 26 3.5500 0.2500 -vdw 27 3.5500 0.2500 -vdw 28 0.0000 0.0000 -vdw 29 0.0000 0.0000 -vdw 30 3.7750 0.2070 -vdw 31 3.9050 0.1180 -vdw 32 3.8000 0.1700 -vdw 33 3.8000 0.1180 -vdw 34 3.8000 0.1700 -vdw 35 3.8000 0.1180 -vdw 36 3.2000 0.1700 -vdw 37 3.6500 0.1500 -vdw 38 3.7750 0.2070 -vdw 39 3.8500 0.0800 -vdw 40 3.8000 0.0500 -vdw 41 3.0000 0.1700 -vdw 42 3.8000 0.1700 -vdw 43 3.8000 0.1180 -vdw 44 3.8000 0.1180 -vdw 45 3.4000 0.3000 -vdw 46 3.8000 0.0800 -vdw 47 3.4700 0.3000 -vdw 48 3.8000 0.0500 -vdw 49 3.4700 0.2660 -vdw 50 3.5600 0.3950 -vdw 51 2.9300 0.2800 -vdw 52 3.8100 0.1600 -vdw 53 2.9600 0.2100 -vdw 54 3.2500 0.1700 -vdw 55 3.8000 0.1150 -vdw 56 3.8000 0.1700 -vdw 57 0.0000 0.0000 -vdw 58 2.5560 0.0200 -vdw 59 2.7800 0.0690 -vdw 60 3.4010 0.2339 -vdw 61 3.6240 0.3170 -vdw 62 3.9350 0.4330 -vdw 63 3.15061 0.1521 -vdw 64 0.0000 0.0000 -vdw 65 3.15365 0.1550 -vdw 66 0.0000 0.0000 -vdw 67 0.0000 0.0000 -vdw 68 3.1760 0.1500 -vdw 69 0.0000 0.0000 -vdw 70 3.2700 0.1000 -vdw 71 0.0000 0.0000 -vdw 72 0.0000 0.0000 -vdw 73 3.1200 0.1600 -vdw 74 0.0000 0.0000 -vdw 75 0.0000 0.0000 -vdw 76 3.16557 0.1554 -vdw 77 0.0000 0.0000 -vdw 78 3.4200 0.1700 -vdw 79 0.0000 0.0000 -vdw 80 3.5000 0.0660 -vdw 81 3.5000 0.0660 -vdw 82 3.5000 0.0660 vdw 83 3.5000 0.0660 -vdw 84 3.5000 0.0660 vdw 85 2.5000 0.0300 -vdw 86 3.5500 0.0760 -vdw 87 3.5500 0.0760 -vdw 88 3.5500 0.0760 -vdw 89 2.4200 0.0300 -vdw 90 3.5500 0.0700 -vdw 91 2.4200 0.0300 -vdw 92 3.5500 0.0700 -vdw 93 3.5000 0.0660 -vdw 94 3.5000 0.0660 -vdw 95 3.5500 0.0760 -vdw 96 3.1200 0.1700 -vdw 97 0.0000 0.0000 -vdw 98 2.5000 0.0300 -vdw 99 3.5000 0.0660 -vdw 100 3.5000 0.0660 -vdw 101 3.5000 0.0660 -vdw 102 3.5000 0.0660 -vdw 103 3.2500 0.0620 -vdw 104 3.0700 0.1700 -vdw 105 0.0000 0.0000 -vdw 106 2.9400 0.0610 -vdw 107 2.5000 0.0300 -vdw 108 3.5500 0.0700 -vdw 109 3.0700 0.1700 -vdw 110 0.0000 0.0000 -vdw 111 3.0700 0.1700 -vdw 112 0.0000 0.0000 -vdw 113 3.0700 0.1700 -vdw 114 0.0000 0.0000 -vdw 115 3.5000 0.0660 -vdw 116 3.5000 0.0660 -vdw 117 3.5000 0.0660 -vdw 118 2.5000 0.0300 -vdw 119 2.9000 0.1400 -vdw 120 3.5500 0.0760 -vdw 121 2.9000 0.1400 -vdw 122 2.9000 0.1400 -vdw 123 3.5000 0.0660 -vdw 124 3.5000 0.0660 -vdw 125 3.5000 0.0660 -vdw 126 3.5000 0.0660 -vdw 127 2.5000 0.0300 -vdw 128 2.9000 0.1400 -vdw 129 3.0700 0.1700 -vdw 130 0.0000 0.0000 -vdw 131 3.5000 0.0660 -vdw 132 2.5000 0.0300 -vdw 133 3.5000 0.0660 -vdw 134 2.5000 0.0300 -vdw 135 3.5000 0.0660 -vdw 136 2.5000 0.0300 -vdw 137 3.5000 0.0660 -vdw 138 2.5000 0.0300 -vdw 139 3.5000 0.0660 -vdw 140 3.5000 0.0660 -vdw 141 3.5500 0.0700 -vdw 142 3.5500 0.2500 -vdw 143 3.7000 0.2500 -vdw 144 3.5500 0.2500 -vdw 145 3.5500 0.2500 -vdw 146 0.0000 0.0000 -vdw 147 0.0000 0.0000 -vdw 148 3.5000 0.0660 -vdw 149 3.5000 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0.0700 -vdw 845 3.7500 0.1050 -vdw 846 2.9600 0.2100 -vdw 847 3.2500 0.1700 -vdw 848 3.5000 0.0660 -vdw 849 3.5000 0.0660 -vdw 850 3.5000 0.0660 -vdw 851 3.5000 0.0660 -vdw 852 2.4200 0.0150 -vdw 853 3.7500 0.1050 -vdw 854 2.9600 0.2100 -vdw 855 2.4200 0.0150 -vdw 856 3.5000 0.0660 -vdw 857 3.5000 0.0660 -vdw 858 3.5000 0.0660 -vdw 859 3.5000 0.0660 -vdw 860 3.5000 0.0660 -vdw 861 3.5000 0.0660 -vdw 862 3.5000 0.0660 -vdw 863 3.5000 0.0660 -vdw 864 3.5000 0.0660 -vdw 865 3.5000 0.0660 -vdw 866 4.0000 0.1000 -vdw 867 4.0000 0.1000 -vdw 868 4.0000 0.1000 -vdw 869 4.0000 0.1000 -vdw 870 2.5000 0.0300 -vdw 871 3.5000 0.0660 -vdw 872 3.5000 0.0660 -vdw 873 3.5000 0.0660 -vdw 874 3.5000 0.0660 -vdw 875 3.0800 0.7200 -vdw 876 4.1800 0.11779 -vdw 877 4.5100 0.0900 -vdw 878 5.1500 0.0700 -vdw 879 2.7000 0.018279 -vdw 880 3.3500 0.002772 -vdw 881 4.0600 0.000328 -vdw 882 4.3200 0.000171 -vdw 883 4.8200 0.000081 -vdw 884 2.9100 0.875044 -vdw 885 3.4700 0.449657 -vdw 886 3.8200 0.118226 -vdw 887 4.1800 0.047096 -vdw 888 3.5000 0.0660 -vdw 889 3.5000 0.0660 -vdw 890 3.5000 0.0660 -vdw 891 3.5000 0.0660 -vdw 892 2.5000 0.0300 -vdw 893 3.2500 0.1700 -vdw 894 3.5500 0.0700 -vdw 895 3.2500 0.1700 -vdw 896 3.5500 0.0700 -vdw 897 3.5500 0.0760 -vdw 898 3.5500 0.0760 -vdw 899 2.4200 0.0300 -vdw 900 3.3000 0.0860 -vdw 901 3.3000 0.0860 -vdw 902 3.3000 0.0860 -vdw 903 3.3000 0.0860 -vdw 904 3.3000 0.0860 -vdw 905 2.9600 0.2100 -vdw 906 3.5000 0.0660 ################################## @@ -1001,385 +91,7 @@ vdw 906 3.5000 0.0660 ################################## -bond 1 2 367.00 1.3800 -bond 1 3 420.00 1.3570 -bond 1 13 367.00 1.3600 -bond 1 19 450.00 1.2790 -bond 1 25 300.00 0.3000 -bond 1 47 420.00 1.3400 -bond 1 48 420.00 1.3540 -bond 1 82 420.00 1.3540 -bond 1 83 420.00 1.3540 -bond 1 84 420.00 1.3540 -bond 1 87 420.00 1.3540 -bond 1 88 420.00 1.3540 -bond 1 108 461.00 1.5700 -bond 2 2 260.00 1.5260 -bond 2 3 317.00 1.5220 -bond 2 5 386.00 1.4250 -bond 2 6 260.00 1.5260 -bond 2 10 260.00 1.5260 -bond 2 11 317.00 1.5000 -bond 2 12 317.00 1.5100 -bond 2 13 260.00 1.5260 -bond 2 14 317.00 1.5000 -bond 2 15 222.00 1.8100 -bond 2 16 222.00 1.8100 -bond 2 20 320.00 1.4250 -bond 2 24 337.00 1.4490 -bond 2 44 382.00 1.4480 -bond 2 48 317.00 1.5100 -bond 2 51 260.00 1.5260 -bond 2 53 367.00 1.4710 -bond 2 55 337.00 1.4630 -bond 2 80 317.00 1.4950 -bond 3 3 350.00 1.5100 -bond 3 4 570.00 1.2290 -bond 3 5 450.00 1.3640 -bond 3 6 317.00 1.5220 -bond 3 10 317.00 1.5220 -bond 3 12 469.00 1.4000 -bond 3 13 317.00 1.5220 -bond 3 19 400.00 1.4440 -bond 3 20 214.00 1.3270 -bond 3 21 300.00 1.7900 -bond 3 24 490.00 1.3350 -bond 3 44 317.00 1.5220 -bond 3 46 340.00 1.0900 -bond 3 47 410.00 1.4440 -bond 3 48 400.00 1.4900 -bond 3 50 385.00 1.4600 -bond 3 52 656.00 1.2500 -bond 3 56 457.00 1.3580 -bond 3 57 418.00 1.3880 -bond 3 60 447.00 1.4190 -bond 3 65 300.00 1.9800 -bond 3 84 400.00 1.4900 -bond 3 86 385.00 1.4600 -bond 3 105 424.00 1.3830 -bond 3 107 490.00 1.3350 -bond 4 25 553.00 0.3000 -bond 4 64 525.00 1.4800 -bond 4 89 570.00 1.2290 -bond 4 110 700.00 1.1710 -bond 5 6 386.00 1.4250 -bond 5 7 553.00 0.9450 -bond 5 10 386.00 1.4250 -bond 5 13 320.00 1.4100 -bond 5 20 250.00 1.4700 -bond 5 24 400.00 1.3800 -bond 5 25 340.00 0.3000 -bond 5 44 320.00 1.4500 -bond 5 47 450.00 1.3700 -bond 5 48 450.00 1.3640 -bond 5 51 320.00 1.3800 -bond 5 64 230.00 1.6100 -bond 5 79 450.00 1.6700 -bond 5 106 94.00 1.8000 -bond 5 108 374.00 1.6400 -bond 6 6 260.00 1.5260 -bond 6 10 260.00 1.5260 -bond 6 11 317.00 1.5000 -bond 6 13 260.00 1.5260 -bond 6 14 317.00 1.5000 -bond 6 15 222.00 1.8100 -bond 6 16 222.00 1.8100 -bond 6 20 320.00 1.4250 -bond 6 24 337.00 1.4490 -bond 6 44 382.00 1.4480 -bond 6 47 317.00 1.5100 -bond 6 51 260.00 1.5260 -bond 6 53 367.00 1.4710 -bond 6 55 337.00 1.4630 -bond 6 79 222.00 1.8100 -bond 6 105 337.00 1.4750 -bond 7 20 553.00 0.9450 -bond 7 25 340.00 0.1000 -bond 9 9 530.00 1.3400 -bond 9 11 530.00 1.3400 -bond 9 14 530.00 1.3400 -bond 10 10 260.00 1.5260 -bond 10 11 317.00 1.5000 -bond 10 14 317.00 1.5000 -bond 10 20 320.00 1.4250 -bond 10 24 337.00 1.4490 -bond 10 44 382.00 1.4480 -bond 10 105 337.00 1.4750 -bond 11 11 530.00 1.3400 -bond 11 13 317.00 1.5000 -bond 11 14 530.00 1.3400 -bond 11 79 222.00 1.7600 -bond 12 12 469.00 1.4000 -bond 12 48 469.00 1.4000 -bond 12 60 469.00 1.4000 -bond 12 81 469.00 1.4000 -bond 13 13 268.00 1.5290 -bond 13 14 317.00 1.5000 -bond 13 15 222.00 1.8100 -bond 13 16 222.00 1.8100 -bond 13 18 390.00 1.4300 -bond 13 19 390.00 1.4700 -bond 13 20 320.00 1.4100 -bond 13 21 245.00 1.7810 -bond 13 22 340.00 1.7900 -bond 13 24 337.00 1.4490 -bond 13 25 340.00 0.3000 -bond 13 44 382.00 1.4480 bond 13 46 340.00 1.0900 -bond 13 47 317.00 1.5100 -bond 13 48 317.00 1.5100 -bond 13 50 317.00 1.5100 -bond 13 51 268.00 1.5290 -bond 13 53 367.00 1.4710 -bond 13 55 337.00 1.4630 -bond 13 56 337.00 1.4490 -bond 13 57 337.00 1.4750 -bond 13 60 317.00 1.5100 -bond 13 64 212.00 1.8430 -bond 13 65 245.00 1.9450 -bond 13 66 200.00 2.1900 -bond 13 79 340.00 1.7700 -bond 13 80 317.00 1.4950 -bond 13 83 317.00 1.5040 -bond 13 84 317.00 1.5040 -bond 13 85 317.00 1.5040 -bond 13 87 317.00 1.4950 -bond 13 90 337.00 1.4490 -bond 13 91 280.00 1.5100 -bond 13 95 532.80 1.4600 -bond 13 101 382.00 1.4480 -bond 13 102 375.00 1.4900 -bond 13 104 212.00 1.8200 -bond 13 105 337.00 1.4750 -bond 13 107 337.00 1.4490 -bond 13 108 187.00 1.8600 -bond 13 109 317.00 1.5100 -bond 14 14 530.00 1.3400 -bond 15 17 274.00 1.3360 -bond 15 48 250.00 1.7400 -bond 16 16 166.00 2.0380 -bond 16 19 300.00 1.6850 -bond 16 24 250.00 1.7300 -bond 16 25 340.00 0.5000 -bond 16 47 250.00 1.7600 -bond 16 48 250.00 1.7600 -bond 16 61 250.00 1.7300 -bond 16 82 250.00 1.7600 -bond 16 84 250.00 1.7400 -bond 16 91 222.00 1.8100 -bond 16 108 144.00 2.1500 -bond 17 25 340.00 0.1000 -bond 18 18 550.00 1.1200 -bond 18 19 650.00 1.1570 -bond 18 48 400.00 1.4100 -bond 18 56 550.00 1.2400 -bond 19 19 1150.00 1.2100 -bond 19 21 330.00 1.6370 -bond 19 46 420.00 1.0800 -bond 19 47 400.00 1.4260 -bond 19 48 400.00 1.4510 -bond 19 50 400.00 1.4260 -bond 19 65 330.00 1.7840 -bond 19 88 400.00 1.4510 -bond 19 91 400.00 1.4510 -bond 20 20 250.00 1.4700 -bond 20 21 200.00 1.6900 -bond 20 24 320.00 1.4500 -bond 20 25 340.00 0.3000 -bond 20 44 320.00 1.4500 -bond 20 47 450.00 1.3700 -bond 20 48 450.00 1.3640 -bond 20 51 320.00 1.3800 -bond 20 60 340.00 1.3600 -bond 20 61 462.00 1.3990 -bond 20 64 230.00 1.6100 -bond 20 82 462.00 1.3570 -bond 20 84 340.00 1.3600 -bond 20 108 374.00 1.6400 -bond 21 25 300.00 0.3000 -bond 21 47 300.00 1.7250 -bond 21 48 300.00 1.7250 -bond 21 82 300.00 1.7250 -bond 21 83 300.00 1.7250 -bond 21 84 300.00 1.7250 -bond 21 87 300.00 1.7250 -bond 21 88 300.00 1.7250 -bond 21 108 223.00 2.0200 -bond 22 23 700.00 1.5300 -bond 22 25 340.00 0.5000 -bond 23 25 340.00 0.3000 -bond 23 79 700.00 1.4400 -bond 24 25 367.00 0.3000 -bond 24 45 434.00 1.0100 -bond 24 48 427.00 1.3810 -bond 24 59 427.00 1.3810 -bond 24 79 434.00 1.6700 -bond 24 84 427.00 1.3810 -bond 24 88 427.00 1.3810 -bond 24 91 337.00 1.4490 -bond 24 103 500.00 1.2700 -bond 24 106 40.00 2.0500 -bond 25 25 340.00 0.3000 -bond 25 44 340.00 0.3000 -bond 25 45 340.00 0.1000 -bond 25 46 340.00 0.3000 -bond 25 47 340.00 0.3000 -bond 25 48 367.00 0.3000 -bond 25 49 340.00 0.3000 -bond 25 53 340.00 0.3000 -bond 25 56 367.00 0.3000 -bond 25 61 367.00 0.3000 -bond 25 65 300.00 0.3000 -bond 25 103 340.00 0.1000 -bond 31 32 600.00 0.9572 -bond 31 33 900.00 0.1500 -bond 31 106 40.00 2.0500 -bond 34 35 529.60 0.9572 -bond 36 37 600.00 0.9572 -bond 36 38 900.00 0.1750 -bond 39 40 600.00 0.9572 -bond 39 41 900.00 0.7000 -bond 42 43 600.00 1.0000 -bond 44 44 350.00 1.4450 -bond 44 45 434.00 1.0100 -bond 44 48 481.00 1.3400 -bond 44 79 340.00 1.7700 -bond 44 91 382.00 1.4480 -bond 44 108 266.00 1.7400 -bond 45 53 434.00 1.0100 -bond 45 55 434.00 1.0100 -bond 45 56 434.00 1.0100 -bond 45 57 434.00 1.0100 -bond 45 101 434.00 1.0100 -bond 45 105 434.00 1.0100 -bond 45 108 166.00 1.4800 -bond 46 47 340.00 1.0800 -bond 46 50 340.00 1.0800 -bond 46 51 340.00 1.0900 -bond 46 80 340.00 1.0800 -bond 46 91 340.00 1.0880 -bond 46 95 532.80 1.0840 -bond 46 108 166.00 1.4800 -bond 46 109 340.00 1.0800 -bond 47 47 549.00 1.3400 -bond 47 48 427.00 1.4330 -bond 47 50 549.00 1.3400 -bond 47 57 448.00 1.3650 -bond 47 58 367.00 1.0800 -bond 47 65 300.00 1.9000 -bond 47 66 250.00 2.0800 -bond 47 86 385.00 1.4600 -bond 47 91 317.00 1.5100 -bond 47 105 448.00 1.3650 -bond 47 110 700.00 1.3050 -bond 48 48 469.00 1.4000 -bond 48 49 367.00 1.0800 -bond 48 50 427.00 1.4330 -bond 48 53 400.00 1.4500 -bond 48 55 481.00 1.3400 -bond 48 56 483.00 1.3390 -bond 48 57 427.00 1.3810 -bond 48 60 469.00 1.4040 -bond 48 61 414.00 1.3910 -bond 48 64 220.00 1.7800 -bond 48 65 300.00 1.8700 -bond 48 66 250.00 2.0800 -bond 48 79 340.00 1.7700 -bond 48 81 469.00 1.4000 -bond 48 84 546.00 1.3670 -bond 48 86 469.00 1.4000 -bond 48 88 469.00 1.4210 -bond 48 91 317.00 1.4900 -bond 48 101 382.00 1.3850 -bond 48 102 400.00 1.4600 -bond 48 109 427.00 1.4330 -bond 49 59 367.00 1.0800 -bond 49 62 340.00 1.0800 -bond 49 82 367.00 1.0800 -bond 49 83 367.00 1.0800 -bond 49 84 367.00 1.0800 -bond 49 85 367.00 1.0800 -bond 49 87 367.00 1.0800 -bond 49 88 367.00 1.0800 -bond 50 50 385.00 1.4600 -bond 50 56 457.00 1.2900 -bond 50 84 549.00 1.3650 -bond 50 109 385.00 1.4600 -bond 51 105 337.00 1.4750 -bond 52 64 525.00 1.4800 -bond 53 54 434.00 1.0100 -bond 54 55 434.00 1.0100 -bond 55 59 481.00 1.3400 -bond 55 82 481.00 1.3400 -bond 56 56 500.00 1.3200 -bond 56 59 502.00 1.3240 -bond 56 60 461.00 1.3540 -bond 56 82 461.00 1.3540 -bond 56 86 483.00 1.3390 -bond 56 103 550.00 1.2100 -bond 56 109 457.00 1.2900 -bond 57 60 436.00 1.3740 -bond 57 61 400.00 1.3490 -bond 57 62 440.00 1.3710 -bond 57 81 428.00 1.3800 -bond 57 82 477.00 1.3430 -bond 57 84 427.00 1.3810 -bond 57 85 427.00 1.3810 -bond 57 86 385.00 1.4400 -bond 58 83 367.00 1.0800 -bond 58 84 367.00 1.0800 -bond 59 63 367.00 1.0800 -bond 60 60 520.00 1.3700 -bond 60 61 414.00 1.3910 -bond 60 80 388.00 1.4590 -bond 60 81 447.00 1.4190 -bond 60 87 469.00 1.4240 -bond 60 105 436.00 1.3740 -bond 61 61 400.00 1.2800 -bond 61 62 529.00 1.3040 -bond 61 82 488.00 1.3350 -bond 61 83 410.00 1.3940 -bond 61 84 410.00 1.3940 -bond 61 88 410.00 1.3200 -bond 62 63 367.00 1.0800 -bond 62 105 440.00 1.3710 -bond 63 82 367.00 1.0800 -bond 64 108 108.00 2.2500 -bond 65 82 300.00 1.8700 -bond 65 83 300.00 1.8700 -bond 65 84 300.00 1.8700 -bond 65 87 300.00 1.8700 -bond 65 88 300.00 1.8700 -bond 65 108 151.00 2.1900 -bond 66 82 250.00 2.0800 -bond 66 83 250.00 2.0800 -bond 66 84 250.00 2.0800 -bond 66 87 250.00 2.0800 -bond 66 88 250.00 2.0800 -bond 66 108 108.00 2.4400 -bond 77 78 500.00 1.8000 -bond 80 84 546.00 1.3520 -bond 82 86 385.00 1.4600 -bond 82 87 520.00 1.3700 -bond 83 84 520.00 1.3700 -bond 83 86 385.00 1.4600 -bond 84 84 512.00 1.3750 -bond 84 86 385.00 1.4600 -bond 84 87 546.00 1.3670 -bond 84 88 520.00 1.3700 -bond 85 85 520.00 1.3700 -bond 86 86 385.00 1.4600 -bond 86 87 385.00 1.4600 -bond 86 88 385.00 1.4600 -bond 87 87 469.00 1.4240 -bond 87 88 469.00 1.4240 -bond 89 90 490.00 1.3350 -bond 89 91 317.00 1.5220 -bond 90 91 337.00 1.4490 -bond 91 91 260.00 1.5200 -bond 102 103 550.00 1.2250 -bond 108 108 94.00 2.3200 -bond 109 109 549.00 1.3450 ################################ @@ -1389,2040 +101,7 @@ bond 109 109 549.00 1.3450 ################################ -angle 25 1 25 33.00 109.47 -angle 1 2 2 50.00 109.50 -angle 2 2 2 63.00 112.40 -angle 2 2 3 63.00 112.40 -angle 2 2 5 80.00 109.50 -angle 2 2 6 63.00 112.40 -angle 6 2 6 63.00 112.40 -angle 5 2 6 80.00 109.50 -angle 2 2 10 63.00 112.40 -angle 3 2 10 63.00 112.40 -angle 6 2 10 63.00 112.40 -angle 10 2 10 63.00 112.40 -angle 5 2 10 80.00 109.50 -angle 10 2 12 63.00 114.00 -angle 6 2 13 63.00 112.40 -angle 10 2 15 50.00 108.60 -angle 2 2 16 50.00 114.70 -angle 10 2 16 50.00 114.70 -angle 2 2 20 80.00 109.50 -angle 6 2 20 80.00 109.50 -angle 10 2 20 80.00 109.50 -angle 3 2 24 80.00 110.30 -angle 2 2 24 80.00 111.20 -angle 2 2 44 56.20 109.47 -angle 6 2 44 56.20 109.47 -angle 10 2 44 56.20 109.47 -angle 13 2 44 56.20 109.47 -angle 3 2 44 80.00 111.20 -angle 2 2 48 63.00 112.40 -angle 10 2 48 63.00 114.00 -angle 2 2 51 63.00 112.40 -angle 6 2 51 63.00 112.40 -angle 2 2 53 80.00 111.20 -angle 2 2 55 80.00 111.20 -angle 10 2 80 63.00 115.60 -angle 2 3 4 80.00 120.40 -angle 1 3 4 80.00 121.00 -angle 3 3 4 80.00 121.40 -angle 4 3 4 80.00 126.00 -angle 4 3 5 80.00 121.00 -angle 4 3 6 80.00 120.40 -angle 5 3 10 70.00 115.00 -angle 4 3 10 80.00 120.40 -angle 5 3 12 70.00 120.00 -angle 12 3 12 85.00 120.00 -angle 5 3 13 70.00 108.00 -angle 13 3 13 70.00 116.00 -angle 1 3 13 80.00 111.00 -angle 3 3 13 80.00 117.20 -angle 4 3 13 80.00 120.40 -angle 10 3 20 81.00 111.40 -angle 13 3 20 81.00 111.40 -angle 4 3 20 83.00 123.40 -angle 13 3 21 75.00 109.00 -angle 4 3 21 75.00 119.00 -angle 24 3 24 70.00 114.20 -angle 2 3 24 70.00 116.60 -angle 3 3 24 70.00 116.60 -angle 6 3 24 70.00 116.60 -angle 10 3 24 70.00 116.60 -angle 13 3 24 70.00 116.60 -angle 4 3 24 80.00 122.90 -angle 20 3 24 81.00 111.40 -angle 13 3 44 70.00 116.00 -angle 4 3 44 80.00 120.40 -angle 13 3 46 35.00 115.00 -angle 46 3 46 35.00 115.00 -angle 4 3 46 35.00 123.00 -angle 24 3 46 40.00 114.00 -angle 5 3 46 40.00 115.00 -angle 20 3 46 40.00 115.00 -angle 24 3 47 70.00 115.50 -angle 4 3 47 80.00 125.30 -angle 46 3 48 35.00 115.00 -angle 24 3 48 70.00 115.50 -angle 13 3 48 70.00 116.00 -angle 5 3 48 70.00 120.00 -angle 4 3 48 80.00 120.40 -angle 20 3 48 81.00 111.40 -angle 48 3 48 85.00 120.00 -angle 13 3 50 70.00 116.00 -angle 46 3 50 80.00 116.00 -angle 4 3 50 80.00 124.00 -angle 10 3 52 65.00 117.00 -angle 2 3 52 70.00 117.00 -angle 6 3 52 70.00 117.00 -angle 13 3 52 70.00 117.00 -angle 48 3 52 70.00 117.00 -angle 4 3 52 80.00 126.00 -angle 52 3 52 80.00 126.00 -angle 46 3 56 35.00 116.00 -angle 46 3 56 35.00 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103.00 -angle 13 79 82 62.00 102.00 -angle 46 80 60 35.00 126.80 -angle 2 80 60 70.00 128.60 -angle 13 80 60 70.00 128.60 -angle 46 80 84 35.00 126.80 -angle 2 80 84 70.00 125.00 -angle 13 80 84 70.00 125.00 -angle 60 80 84 85.00 106.40 -angle 12 81 57 70.00 132.80 -angle 48 81 57 70.00 132.80 -angle 57 81 60 70.00 104.40 -angle 12 81 60 85.00 122.70 -angle 48 81 60 85.00 122.70 -angle 13 82 16 70.00 125.00 -angle 16 82 24 70.00 125.00 -angle 16 82 44 70.00 120.20 -angle 20 82 49 35.00 117.00 -angle 16 82 49 35.00 125.00 -angle 49 82 57 35.00 120.00 -angle 57 82 57 70.00 120.00 -angle 13 82 57 70.00 125.00 -angle 48 82 57 70.00 125.00 -angle 56 82 57 70.00 126.20 -angle 49 82 61 35.00 120.00 -angle 16 82 61 70.00 113.60 -angle 16 82 61 70.00 115.00 -angle 20 82 61 70.00 115.00 -angle 57 82 61 70.00 120.00 -angle 13 82 61 70.00 125.00 -angle 44 82 61 70.00 126.10 -angle 24 82 61 70.00 126.20 -angle 57 82 79 70.00 120.00 -angle 61 82 79 70.00 120.00 -angle 20 82 86 70.00 122.00 -angle 61 82 86 70.00 130.00 -angle 57 82 87 70.00 106.20 -angle 56 82 87 70.00 127.70 -angle 49 83 61 35.00 120.00 -angle 48 83 61 70.00 111.00 -angle 13 83 61 70.00 124.50 -angle 49 83 84 35.00 128.20 -angle 61 83 84 70.00 111.00 -angle 13 83 84 70.00 130.70 -angle 13 84 16 70.00 125.00 -angle 13 84 20 70.00 121.60 -angle 16 84 24 70.00 125.00 -angle 20 84 49 35.00 113.40 -angle 16 84 49 35.00 125.00 -angle 48 84 49 35.00 130.70 -angle 49 84 50 35.00 130.70 -angle 20 84 50 70.00 110.00 -angle 49 84 57 35.00 121.60 -angle 13 84 57 70.00 121.60 -angle 48 84 57 70.00 121.60 -angle 3 84 57 85.00 120.00 -angle 57 84 58 35.00 120.00 -angle 13 84 61 70.00 118.90 -angle 49 84 80 35.00 120.00 -angle 57 84 80 70.00 108.70 -angle 49 84 83 35.00 130.70 -angle 57 84 83 70.00 106.30 -angle 20 84 83 70.00 108.00 -angle 16 84 83 70.00 111.00 -angle 13 84 83 70.00 130.70 -angle 13 84 84 70.00 120.00 -angle 57 84 84 70.00 120.00 -angle 61 84 84 70.00 120.00 -angle 20 84 86 70.00 121.60 -angle 57 84 86 70.00 121.60 -angle 49 84 87 35.00 132.10 -angle 57 84 87 70.00 107.70 -angle 20 84 87 70.00 110.60 -angle 16 84 87 70.00 111.00 -angle 61 84 87 70.00 111.90 -angle 13 84 87 70.00 132.10 -angle 48 84 87 70.00 132.10 -angle 86 84 87 70.00 132.10 -angle 3 84 87 85.00 120.00 -angle 49 85 57 35.00 120.00 -angle 13 85 57 70.00 121.60 -angle 49 85 85 35.00 130.70 -angle 57 85 85 70.00 106.30 -angle 13 85 85 70.00 130.70 -angle 48 86 48 63.00 120.00 -angle 48 86 56 70.00 124.00 -angle 48 86 82 63.00 120.00 -angle 48 86 83 63.00 120.00 -angle 48 86 84 63.00 120.00 -angle 48 86 86 63.00 120.00 -angle 56 86 86 70.00 124.00 -angle 48 86 87 63.00 120.00 -angle 48 86 88 63.00 120.00 -angle 49 87 60 35.00 120.00 -angle 46 87 60 35.00 126.80 -angle 13 87 60 70.00 128.60 -angle 49 87 84 35.00 125.70 -angle 46 87 84 35.00 126.80 -angle 84 87 84 70.00 103.80 -angle 82 87 84 70.00 110.40 -angle 2 87 84 70.00 125.00 -angle 13 87 84 70.00 125.00 -angle 3 87 84 70.00 130.00 -angle 60 87 84 85.00 106.40 -angle 84 87 86 70.00 125.70 -angle 49 87 87 35.00 127.50 -angle 60 87 87 70.00 107.30 -angle 84 87 87 70.00 107.30 -angle 86 87 87 70.00 127.50 -angle 84 87 88 70.00 103.80 -angle 48 88 49 35.00 128.60 -angle 49 88 61 35.00 118.90 -angle 13 88 61 70.00 118.90 -angle 19 88 61 70.00 118.90 -angle 61 88 87 70.00 111.90 -angle 4 89 90 80.00 134.00 -angle 90 89 91 70.00 91.00 -angle 4 89 91 80.00 134.00 -angle 13 90 89 55.00 127.00 -angle 89 90 91 50.00 94.00 -angle 13 90 91 50.00 126.00 -angle 24 91 46 35.00 108.00 -angle 13 91 46 35.00 114.30 -angle 44 91 46 35.00 114.30 -angle 46 91 46 35.00 114.30 -angle 16 91 46 37.50 108.00 -angle 46 91 47 35.00 109.50 -angle 46 91 89 37.50 110.00 -angle 24 91 89 70.00 117.00 -angle 46 91 90 35.00 111.00 -angle 16 91 90 55.00 109.00 -angle 91 91 91 30.00 79.20 -angle 13 91 91 37.50 117.20 -angle 44 91 91 37.50 117.20 -angle 46 91 91 37.50 117.20 -angle 24 91 91 37.50 126.00 -angle 16 91 91 55.00 128.00 -angle 89 91 91 63.00 85.00 -angle 47 91 91 63.00 114.00 -angle 90 91 91 80.00 89.00 -angle 13 95 13 172.80 120.00 -angle 13 95 46 144.00 120.00 -angle 13 101 45 35.00 109.50 -angle 45 101 45 43.60 106.40 -angle 45 101 48 50.00 112.50 -angle 13 101 48 50.00 120.50 -angle 13 102 103 80.00 117.50 -angle 48 102 103 80.00 117.50 -angle 103 102 103 80.00 125.00 -angle 25 103 25 10.00 109.50 -angle 25 103 102 10.00 109.50 -angle 13 104 13 45.00 109.50 -angle 3 105 10 70.00 117.60 -angle 3 105 13 70.00 117.60 -angle 3 105 45 35.00 119.20 -angle 45 105 47 35.00 119.20 -angle 13 105 47 70.00 121.20 -angle 3 105 47 70.00 121.60 -angle 3 105 51 70.00 117.60 -angle 47 105 51 70.00 121.20 -angle 45 105 60 30.00 125.80 -angle 6 105 60 70.00 125.80 -angle 10 105 60 70.00 125.80 -angle 13 105 60 70.00 125.80 -angle 51 105 60 70.00 125.80 -angle 45 105 62 30.00 128.80 -angle 60 105 62 70.00 105.40 -angle 6 105 62 70.00 128.80 -angle 10 105 62 70.00 128.80 -angle 13 105 62 70.00 128.80 -angle 51 105 62 70.00 128.80 -angle 4 106 24 20.00 109.50 -angle 24 106 24 20.00 109.50 -angle 13 107 13 50.00 118.00 -angle 3 107 13 50.00 121.90 -angle 1 108 13 35.00 110.50 -angle 13 108 13 60.00 110.00 -angle 13 108 20 60.00 100.00 -angle 20 108 20 60.00 110.00 -angle 13 108 21 35.00 110.50 -angle 45 108 45 35.00 109.50 -angle 13 108 45 35.00 110.50 -angle 46 108 46 35.00 109.50 -angle 13 108 46 35.00 110.50 -angle 13 108 65 35.00 110.50 -angle 13 108 66 35.00 110.50 -angle 13 108 108 50.00 112.00 -angle 46 109 48 35.00 123.30 -angle 46 109 50 35.00 120.00 -angle 13 109 50 70.00 124.00 -angle 46 109 109 35.00 120.00 -angle 13 109 109 70.00 124.00 -angle 50 109 109 70.00 124.00 -angle 48 109 109 85.00 117.00 -angle 4 110 47 160.00 180.00 -angle 47 110 47 160.00 180.00 - - - ################################ - ## ## - ## Urey-Bradley Parameters ## - ## ## - ################################ - - -ureybrad 35 34 35 38.25 1.5537 - - - ##################################### - ## ## - ## Improper Torsional Parameters ## - ## ## - ##################################### - - -imptors 0 0 3 4 21.000 180.0 2 -imptors 0 0 3 52 21.000 180.0 2 -imptors 0 0 24 0 5.000 180.0 2 -imptors 0 0 47 0 30.000 180.0 2 -imptors 0 0 48 0 5.000 180.0 2 - - - ############################ - ## ## - ## Torsional Parameters ## - ## ## - ############################ - - - ################################################################### - ## ## - ## Alternative Torsional Parameter Values for Use with OPLS-AA ## - ## ## - ## For some torsions, OPLS-AA has multiple possible parameter ## - ## values; the list below shows functional groups for which ## - ## these alternate (commented) values should be preferred; the ## - ## values are in the same order as in the full parameter list ## - ## ## - ## 4 3 3 36 generic (default) ## - ## 4 3 3 36 dicarbonyls ## - ## 36 3 3 36 hydrocarbon (default) ## - ## 36 3 3 36 dicarbonyls ## - ## 13 3 5 7 carboxylic acid (default) ## - ## 13 3 5 7 1,2-diacid monoanion ## - ## 4 3 13 13 peptide (default) ## - ## 4 3 13 13 propanamide ## - ## 4 3 13 13 carboxylic acid ## - ## 4 3 13 13 dicarboxylic acid ## - ## 4 3 13 13 aldyhyde, ketone, acyl halide ## - ## 4 3 13 13 1,2-diacid monoanion ## - ## 5 3 13 13 carboxylic acid (default) ## - ## 5 3 13 13 dicarboxylic acid ## - ## 35 3 13 13 peptide psi' (default) ## - ## 35 3 13 13 propanamide ## - ## 35 3 13 13 beta-3-peptide, last psi ## - ## 4 3 29 13 esters (default) ## - ## 4 3 29 13 benzoic esters ## - ## 7 5 13 13 alcohols (default) ## - ## 7 5 13 13 trifluoroethanol ## - ## 7 5 13 13 hexopyranoses ## - ## 7 5 13 36 alcohols (default) ## - ## 7 5 13 36 axial cyclohexanol ## - ## 7 5 13 36 trifluoroethanol ## - ## 0 13 13 13 alcohols, ethers (default) ## - ## 0 13 13 13 hexopyranoses ## - ## 3 13 13 3 dicarboxylic acid (default) ## - ## 3 13 13 3 1,2-diacid monoanion ## - ## 3 13 13 13 butanamide (default) ## - ## 3 13 13 13 carboxylate ion ## - ## 3 13 13 13 aldyhyde, ketone, acyl halide ## - ## 3 13 13 36 all carbonyls (default) ## - ## 3 13 13 36 dicarboxylic acid ## - ## 3 13 13 36 aldehyde, ketone, acyl halide ## - ## 5 13 13 5 diols only (default) ## - ## 5 13 13 5 triols only ## - ## 5 13 13 5 hexopyranoses ## - ## 13 13 13 13 hydrocarbon (default) ## - ## 13 13 13 13 perfluoroalkane ## - ## 13 13 13 35 peptide chi-1 (default) ## - ## 13 13 13 35 N-propylformamide ## - ## 36 13 13 69 generic (default) ## - ## 36 13 13 69 sulfone ## - ## 13 13 33 13 amine (default) ## - ## 13 13 33 13 exocyclic amine ## - ## 13 13 33 13 exocyclic 1,4-diamine ## - ## 13 13 33 34 amine (default) ## - ## 13 13 33 34 azetidine, 4-ring ## - ## 13 13 33 34 pyrrolidine, 5-ring ## - ## 13 13 33 34 cyclic amine ## - ## 13 13 33 34 cyclic 1,4-diamine ## - ## 13 13 35 3 peptide phi' (default) ## - ## 13 13 35 3 N-ethylformamide ## - ## 13 13 35 3 beta-3-peptide, first theta tors ## - ## 13 13 35 13 proline, CD-N-CA-CB (default) ## - ## 13 13 35 13 proline, CG-CD-N-CA ## - ## 36 13 35 3 peptide phi'' (default) ## - ## 36 13 35 3 N-methylformamide ## - ## 13 13 47 0 imidazole, indole, purine (default) ## - ## 13 13 47 0 nucleoside chi ## - ## 13 13 47 52 nucleoside (default) ## - ## 13 13 47 52 imidazole, indole, purine ## - ## 29 13 47 0 imidazole, indole, purine (default) ## - ## 29 13 47 0 nucleoside chi ## - ## 29 13 95 52 nucleoside (default) ## - ## 29 13 95 52 imidazole, indole, purine ## - ## 13 13 97 13 generic (default) ## - ## 13 13 97 13 generic ## - ## 17 15 38 0 aromatic thiol (default) ## - ## 17 15 38 0 aromatic thiol, N-C-S-H ## - ## 13 29 54 42 phosphonates (default) ## - ## 13 29 54 42 dimethyl phosphate ## - ## 34 35 72 16 diaryl amine (default) ## - ## 34 35 72 16 aniline-like ## - ## 34 35 72 29 diaryl amine (default) ## - ## 34 35 72 29 aniline-like ## - ## 13 40 40 37 diene (default) ## - ## 13 40 40 37 2-methyl-1,3-butadiene ## - ## 0 46 72 0 generic (default) ## - ## 0 46 72 0 generic ## - ## 0 47 72 0 generic (default) ## - ## 0 47 72 0 generic ## - ## 0 47 74 0 generic (default) ## - ## 0 47 74 0 generic ## - ## 0 47 74 0 generic ## - ## 0 51 72 0 generic (default) ## - ## 0 51 72 0 HA-CR-NB-?? or N?-CR-NB-?? ## - ## 0 72 77 0 generic (default) ## - ## 0 72 77 0 biphenyl-like, N-C-C-C ## - ## ## - ################################################################### - - -torsion 0 2 2 2 -2.500 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 0 2 2 6 -2.500 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 1 2 2 2 -2.000 0.0 1 0.700 180.0 2 3.000 0.0 3 -torsion 1 2 2 6 -2.000 0.0 1 0.700 180.0 2 3.000 0.0 3 -torsion 2 2 2 2 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 2 2 2 6 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 2 2 2 10 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 2 2 2 13 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 2 2 2 65 -2.000 0.0 1 0.500 180.0 2 3.250 0.0 3 -torsion 6 2 2 6 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 6 2 2 65 -2.000 0.0 1 0.500 180.0 2 3.250 0.0 3 -torsion 10 2 2 10 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 2 2 5 7 0.300 0.0 1 0.000 180.0 2 1.300 0.0 3 -torsion 6 2 5 7 0.300 0.0 1 0.000 180.0 2 1.300 0.0 3 -torsion 10 2 5 7 0.300 0.0 1 0.000 180.0 2 1.300 0.0 3 -torsion 0 2 10 2 -2.500 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 2 2 10 2 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 2 2 13 2 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 6 2 20 2 -7.400 0.0 1 3.000 180.0 2 1.800 0.0 3 -torsion 6 2 20 6 -8.400 0.0 1 3.000 180.0 2 1.800 0.0 3 -torsion 4 3 3 4 1.600 0.0 1 3.200 180.0 2 0.000 0.0 3 -torsion 4 3 3 13 0.000 0.0 1 0.500 180.0 2 0.000 0.0 3 -torsion 4 3 3 24 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 4 3 3 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -#torsion 4 3 3 36 0.000 0.0 1 0.200 180.0 2 0.000 0.0 3 -torsion 13 3 3 13 0.700 0.0 1 -1.500 180.0 2 0.000 0.0 3 -torsion 13 3 3 24 -0.500 0.0 1 0.200 180.0 2 0.000 0.0 3 -torsion 13 3 3 46 0.800 0.0 1 -0.760 180.0 2 0.000 0.0 3 -torsion 24 3 3 46 -0.900 0.0 1 0.300 180.0 2 0.000 0.0 3 -torsion 46 3 3 46 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -#torsion 36 3 3 36 0.800 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 3 3 5 7 3.000 0.0 1 5.500 180.0 2 0.000 0.0 3 -torsion 4 3 5 7 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 13 3 5 7 1.500 0.0 1 5.500 180.0 2 0.000 0.0 3 -#torsion 13 3 5 7 3.200 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 24 3 5 7 -2.000 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 46 3 5 7 1.500 0.0 1 5.500 180.0 2 0.000 0.0 3 -torsion 48 3 5 7 4.000 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 1 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 1 3 13 46 0.000 0.0 1 0.000 180.0 2 0.360 0.0 3 -torsion 3 3 13 46 0.000 0.0 1 0.000 180.0 2 0.085 0.0 3 -torsion 4 3 13 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 4 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -#torsion 4 3 13 13 0.000 0.0 1 1.166 180.0 2 0.000 0.0 3 -#torsion 4 3 13 13 0.000 0.0 1 0.546 180.0 2 0.000 0.0 3 -#torsion 4 3 13 13 -0.750 0.0 1 -0.550 180.0 2 -0.250 0.0 3 -#torsion 4 3 13 13 -0.277 0.0 1 1.228 180.0 2 -0.694 0.0 3 -#torsion 4 3 13 13 -1.000 0.0 1 -1.900 180.0 2 -0.900 0.0 3 -torsion 4 3 13 21 -0.650 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 4 3 13 44 0.000 0.0 1 0.820 180.0 2 0.000 0.0 3 -torsion 4 3 13 24 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 4 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 4 3 13 48 0.000 0.0 1 0.546 180.0 2 0.000 0.0 3 -torsion 5 3 13 13 0.000 0.0 1 1.412 180.0 2 0.000 0.0 3 -#torsion 5 3 13 13 1.000 0.0 1 0.546 180.0 2 0.450 0.0 3 -torsion 5 3 13 44 5.260 0.0 1 0.820 180.0 2 0.000 0.0 3 -torsion 5 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 13 3 13 13 1.454 0.0 1 -0.144 180.0 2 -0.775 0.0 3 -torsion 13 3 13 46 0.000 0.0 1 0.000 180.0 2 0.275 0.0 3 -torsion 20 3 13 13 0.000 0.0 1 0.000 180.0 2 -0.553 0.0 3 -torsion 20 3 13 46 0.000 0.0 1 0.000 180.0 2 0.132 0.0 3 -torsion 21 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 21 3 13 46 0.000 0.0 1 0.000 180.0 2 0.360 0.0 3 -torsion 24 3 13 13 1.173 0.0 1 0.189 180.0 2 -1.200 0.0 3 -#torsion 35 3 13 13 3.250 0.0 1 -0.402 180.0 2 -0.136 0.0 3 -#torsion 35 3 13 13 3.260 0.0 1 0.440 180.0 2 0.600 0.0 3 -torsion 24 3 13 21 0.650 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 24 3 13 24 1.816 0.0 1 1.222 180.0 2 1.581 0.0 3 -torsion 24 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 46 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 46 3 13 46 0.000 0.0 1 0.000 180.0 2 0.360 0.0 3 -torsion 48 3 13 46 0.000 0.0 1 0.000 180.0 2 0.275 0.0 3 -torsion 52 3 13 13 0.000 0.0 1 0.820 180.0 2 0.000 0.0 3 -torsion 52 3 13 44 0.000 0.0 1 0.820 180.0 2 0.000 0.0 3 -torsion 52 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 65 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 65 3 13 46 0.000 0.0 1 0.000 180.0 2 0.360 0.0 3 -torsion 107 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 4 3 20 13 0.000 0.0 1 5.124 180.0 2 0.000 0.0 3 -#torsion 4 3 29 13 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 4 3 20 48 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 13 3 20 13 4.669 0.0 1 5.124 180.0 2 0.000 0.0 3 -torsion 13 3 20 48 1.500 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 24 3 20 13 -2.000 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 46 3 20 13 4.669 0.0 1 5.124 180.0 2 0.000 0.0 3 -torsion 48 3 20 13 4.000 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 3 3 24 13 0.400 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 3 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 4 3 24 5 0.000 0.0 1 6.603 180.0 2 0.000 0.0 3 -torsion 4 3 24 13 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 4 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 4 3 24 47 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 4 3 24 48 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 4 3 24 91 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 5 3 24 13 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 5 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 13 3 24 5 4.542 0.0 1 6.603 180.0 2 1.045 0.0 3 -torsion 13 3 24 13 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 13 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 13 3 24 48 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 20 3 24 13 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 20 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 24 3 24 3 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 24 3 24 13 4.600 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 24 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 46 3 24 13 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 46 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 47 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 48 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 48 3 24 48 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 48 3 24 84 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 48 3 24 87 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 84 3 24 48 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 84 3 24 84 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 84 3 24 87 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 87 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 87 3 24 48 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 87 3 24 84 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 87 3 24 87 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 0 3 47 13 0.900 0.0 1 0.230 180.0 2 -0.505 0.0 3 -torsion 4 3 47 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 4 3 47 47 2.500 0.0 1 6.000 180.0 2 0.000 0.0 3 -torsion 5 3 47 47 3.200 0.0 1 -3.000 180.0 2 0.000 0.0 3 -torsion 24 3 47 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 24 3 47 47 2.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 107 3 47 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 107 3 47 47 2.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 4 3 48 48 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3 -torsion 5 3 48 48 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3 -torsion 13 3 48 48 0.000 0.0 1 0.200 180.0 2 0.000 0.0 3 -torsion 20 3 48 48 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3 -torsion 24 3 48 48 0.000 0.0 1 1.100 180.0 2 0.000 0.0 3 -torsion 46 3 48 48 0.000 0.0 1 0.200 180.0 2 0.000 0.0 3 -torsion 0 3 50 13 0.900 0.0 1 0.230 180.0 2 -0.505 0.0 3 -torsion 4 3 50 47 2.500 0.0 1 6.000 180.0 2 0.000 0.0 3 -torsion 5 3 50 47 3.200 0.0 1 -3.000 180.0 2 0.000 0.0 3 -torsion 13 3 50 47 0.800 0.0 1 -3.000 180.0 2 0.000 0.0 3 -torsion 13 3 56 0 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 13 3 56 13 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 46 3 56 0 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 46 3 56 45 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 0 3 60 0 0.000 0.0 1 7.000 180.0 2 0.000 0.0 3 -torsion 4 3 60 0 0.000 0.0 1 7.000 180.0 2 0.000 0.0 3 -torsion 4 3 82 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 4 3 82 57 2.000 0.0 1 1.000 180.0 2 0.000 0.0 3 -torsion 4 3 82 61 0.000 0.0 1 1.000 180.0 2 0.000 0.0 3 -torsion 82 3 82 57 -2.000 0.0 1 1.000 180.0 2 0.000 0.0 3 -torsion 82 3 82 61 0.000 0.0 1 1.000 180.0 2 0.000 0.0 3 -torsion 4 3 84 20 -0.750 0.0 1 1.500 180.0 2 0.000 0.0 3 -torsion 4 3 84 87 0.750 0.0 1 1.500 180.0 2 0.000 0.0 3 -torsion 84 3 84 20 0.000 0.0 1 1.500 180.0 2 0.000 0.0 3 -torsion 84 3 84 87 0.000 0.0 1 1.500 180.0 2 0.000 0.0 3 -torsion 48 3 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 0 3 87 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 4 3 87 84 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3 -torsion 4 3 87 87 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3 -torsion 24 3 87 84 0.000 0.0 1 1.100 180.0 2 0.000 0.0 3 -torsion 24 3 87 87 0.000 0.0 1 1.100 180.0 2 0.000 0.0 3 -torsion 4 3 107 13 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 13 3 107 13 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 4 3 109 109 2.500 0.0 1 6.000 180.0 2 0.000 0.0 3 -torsion 5 3 109 109 3.200 0.0 1 -3.000 180.0 2 0.000 0.0 3 -torsion 0 4 106 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 7 5 10 2 0.300 0.0 1 0.000 180.0 2 0.500 0.0 3 -torsion 7 5 10 6 0.300 0.0 1 0.000 180.0 2 0.500 0.0 3 -torsion 7 5 13 2 0.000 0.0 1 0.000 180.0 2 0.200 0.0 3 -torsion 7 5 13 6 0.000 0.0 1 0.000 180.0 2 0.200 0.0 3 -torsion 7 5 13 13 -0.356 0.0 1 -0.174 180.0 2 0.492 0.0 3 -#torsion 7 5 13 13 4.478 0.0 1 -2.175 180.0 2 0.000 0.0 3 -#torsion 7 5 13 13 2.674 0.0 1 -2.883 180.0 2 1.026 0.0 3 -torsion 7 5 13 46 0.000 0.0 1 0.000 180.0 2 0.352 0.0 3 -#torsion 7 5 13 36 -2.589 0.0 1 -1.123 180.0 2 0.270 0.0 3 -#torsion 7 5 13 36 0.000 0.0 1 0.000 180.0 2 0.476 0.0 3 -torsion 7 5 13 47 -0.900 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 7 5 13 48 -0.900 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 7 5 13 50 -0.900 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 7 5 44 13 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -torsion 7 5 44 45 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -torsion 7 5 24 3 5.519 0.0 1 -6.700 180.0 2 0.581 0.0 3 -torsion 7 5 24 45 2.722 0.0 1 -5.154 180.0 2 0.000 0.0 3 -torsion 7 5 47 47 0.000 0.0 1 1.682 180.0 2 0.000 0.0 3 -torsion 7 5 48 48 0.000 0.0 1 1.682 180.0 2 0.000 0.0 3 -torsion 7 5 51 20 -1.257 0.0 1 -1.806 180.0 2 0.003 0.0 3 -torsion 7 5 56 3 3.000 0.0 1 3.000 180.0 2 0.000 0.0 3 -torsion 7 5 64 4 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 7 5 64 5 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 7 5 79 13 -0.750 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 7 5 79 23 0.750 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 7 5 79 48 2.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 0 13 13 3 -4.344 0.0 1 -1.714 180.0 2 0.000 0.0 3 -torsion 0 13 13 13 1.711 0.0 1 -0.500 180.0 2 0.663 0.0 3 -#torsion 0 13 13 13 -1.336 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 0 13 13 24 1.428 0.0 1 0.086 180.0 2 0.029 0.0 3 -torsion 1 13 13 1 -2.500 0.0 1 0.000 180.0 2 0.250 0.0 3 -torsion 1 13 13 5 0.000 0.0 1 0.000 180.0 2 0.540 0.0 3 -torsion 1 13 13 13 0.300 0.0 1 -0.400 180.0 2 0.400 0.0 3 -torsion 1 13 13 46 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 -torsion 3 13 13 3 -0.550 0.0 1 0.000 180.0 2 1.000 0.0 3 -#torsion 3 13 13 3 0.800 0.0 1 0.000 180.0 2 0.900 0.0 3 -torsion 3 13 13 5 -6.180 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 3 13 13 13 -2.060 0.0 1 -0.313 180.0 2 0.315 0.0 3 -#torsion 3 13 13 13 -3.185 0.0 1 -0.825 180.0 2 0.493 0.0 3 -#torsion 3 13 13 13 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3 -torsion 3 13 13 15 -4.344 0.0 1 -1.714 180.0 2 0.000 0.0 3 -torsion 3 13 13 16 -4.344 0.0 1 -1.714 180.0 2 0.000 0.0 3 -torsion 3 13 13 24 -9.000 0.0 1 2.000 180.0 2 0.800 0.0 3 -torsion 3 13 13 46 0.000 0.0 1 0.000 180.0 2 -0.100 0.0 3 -#torsion 3 13 13 36 0.000 0.0 1 0.000 180.0 2 0.074 0.0 3 -#torsion 3 13 13 36 0.000 0.0 1 0.000 180.0 2 -0.076 0.0 3 -torsion 3 13 13 48 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3 -torsion 3 13 13 80 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3 -torsion 5 13 13 5 9.508 0.0 1 0.000 180.0 2 0.000 0.0 3 -#torsion 5 13 13 5 12.234 0.0 1 0.000 180.0 2 0.000 0.0 3 -#torsion 5 13 13 5 9.066 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 5 13 13 13 -1.552 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 5 13 13 20 4.319 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 5 13 13 44 8.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 5 13 13 24 6.280 0.0 1 -1.467 180.0 2 2.030 0.0 3 -torsion 5 13 13 46 0.000 0.0 1 0.000 180.0 2 0.468 0.0 3 -torsion 13 13 13 13 1.300 0.0 1 -0.050 180.0 2 0.200 0.0 3 -#torsion 13 13 13 13 6.622 0. 1 0.948 180. 2 -1.388 0. 3 -2.118 180. 4 -torsion 13 13 13 15 1.262 0.0 1 -0.198 180.0 2 0.465 0.0 3 -torsion 13 13 13 16 2.619 0.0 1 -0.620 180.0 2 0.258 0.0 3 -torsion 13 13 13 19 0.000 0.0 1 -0.650 180.0 2 0.000 0.0 3 -torsion 13 13 13 21 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 -torsion 13 13 13 44 2.392 0.0 1 -0.674 180.0 2 0.550 0.0 3 -torsion 13 13 13 24 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3 -#torsion 13 13 13 35 1.964 0.0 1 0.000 180.0 2 0.659 0.0 3 -torsion 13 13 13 46 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -torsion 13 13 13 51 1.300 0.0 1 -0.050 180.0 2 0.200 0.0 3 -torsion 13 13 13 53 2.732 0.0 1 -0.229 180.0 2 0.485 0.0 3 -torsion 13 13 13 65 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 -torsion 13 13 13 66 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 -torsion 13 13 13 79 1.262 0.0 1 -0.198 180.0 2 0.465 0.0 3 -torsion 13 13 13 107 1.964 0.0 1 0.000 180.0 2 0.659 0.0 3 -torsion 13 13 13 108 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 15 13 13 46 0.000 0.0 1 0.000 180.0 2 0.452 0.0 3 -torsion 16 13 13 46 0.000 0.0 1 0.000 180.0 2 0.452 0.0 3 -torsion 19 13 13 46 0.000 0.0 1 0.000 180.0 2 0.366 0.0 3 -torsion 20 13 13 20 -0.550 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 20 13 13 46 0.000 0.0 1 0.000 180.0 2 0.468 0.0 3 -torsion 21 13 13 21 -0.250 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 21 13 13 44 2.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 21 13 13 46 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 -torsion 44 13 13 44 11.035 0.0 1 -0.968 180.0 2 0.270 0.0 3 -torsion 44 13 13 46 -1.013 0.0 1 -0.709 180.0 2 0.473 0.0 3 -torsion 44 13 13 48 -0.800 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 24 13 13 46 0.000 0.0 1 0.000 180.0 2 0.464 0.0 3 -torsion 24 13 13 48 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3 -torsion 24 13 13 80 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3 -torsion 46 13 13 46 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -torsion 46 13 13 47 0.000 0.0 1 0.000 180.0 2 0.366 0.0 3 -torsion 46 13 13 48 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 -torsion 46 13 13 51 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -torsion 46 13 13 53 0.000 0.0 1 0.000 180.0 2 0.384 0.0 3 -torsion 46 13 13 55 0.000 0.0 1 0.000 180.0 2 -0.582 0.0 3 -torsion 46 13 13 59 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 -torsion 46 13 13 62 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 -torsion 46 13 13 65 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 -torsion 46 13 13 66 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 -torsion 46 13 13 79 0.000 0.0 1 0.000 180.0 2 0.452 0.0 3 -#torsion 36 13 13 69 0.000 0.0 1 0.000 180.0 2 0.350 0.0 3 -torsion 46 13 13 80 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 -torsion 46 13 13 82 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 -torsion 46 13 13 83 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 -torsion 46 13 13 84 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 -torsion 46 13 13 87 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 -torsion 46 13 13 88 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 -torsion 46 13 13 102 0.000 0.0 1 0.000 180.0 2 -0.225 0.0 3 -torsion 46 13 13 104 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -torsion 46 13 13 107 0.000 0.0 1 0.000 180.0 2 0.464 0.0 3 -torsion 46 13 13 108 0.000 0.0 1 0.000 180.0 2 0.450 0.0 3 -torsion 46 13 13 109 0.000 0.0 1 0.000 180.0 2 0.366 0.0 3 -torsion 48 13 13 53 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 108 13 13 108 5.200 0.0 1 -0.500 180.0 2 0.000 0.0 3 -torsion 13 13 15 17 -0.759 0.0 1 -0.282 180.0 2 0.680 0.0 3 -torsion 46 13 15 17 0.000 0.0 1 0.000 180.0 2 0.480 0.0 3 -torsion 13 13 16 13 0.925 0.0 1 -0.576 180.0 2 0.677 0.0 3 -torsion 13 13 16 16 1.941 0.0 1 -0.836 180.0 2 0.935 0.0 3 -torsion 46 13 16 13 0.000 0.0 1 0.000 180.0 2 0.647 0.0 3 -torsion 46 13 16 16 0.000 0.0 1 0.000 180.0 2 0.558 0.0 3 -torsion 46 13 16 48 0.000 0.0 1 0.000 180.0 2 0.647 0.0 3 -torsion 0 13 18 19 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 46 13 18 19 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 0 13 19 18 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 0 13 19 19 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 13 13 19 19 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 46 13 19 19 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 0 13 20 13 -0.521 0.0 1 -2.018 180.0 2 1.996 0.0 3 -torsion 56 13 20 13 -0.500 0.0 1 -1.500 180.0 2 1.000 0.0 3 -torsion 57 13 20 13 -0.500 0.0 1 -1.500 180.0 2 1.000 0.0 3 -torsion 13 13 20 3 -1.220 0.0 1 -0.126 180.0 2 0.422 0.0 3 -torsion 13 13 20 13 0.650 0.0 1 -0.250 180.0 2 0.670 0.0 3 -torsion 13 13 20 64 -1.420 0.0 1 -0.620 180.0 2 0.100 0.0 3 -torsion 46 13 20 0 0.000 0.0 1 0.000 180.0 2 0.760 0.0 3 -torsion 46 13 20 3 0.000 0.0 1 0.000 180.0 2 0.198 0.0 3 -torsion 46 13 20 47 0.000 0.0 1 0.000 180.0 2 0.760 0.0 3 -torsion 46 13 20 48 0.000 0.0 1 0.000 180.0 2 0.760 0.0 3 -torsion 46 13 20 51 0.000 0.0 1 0.000 180.0 2 0.760 0.0 3 -torsion 46 13 20 64 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -torsion 13 13 44 13 0.416 0.0 1 -0.128 180.0 2 0.695 0.0 3 -#torsion 13 13 33 13 1.536 0.0 1 -0.128 180.0 2 0.695 0.0 3 -#torsion 13 13 33 13 1.464 0.0 1 -0.128 180.0 2 0.695 0.0 3 -torsion 13 13 44 45 -0.190 0.0 1 -0.417 180.0 2 0.418 0.0 3 -#torsion 13 13 33 34 0.000 0.0 1 4.000 180.0 2 0.000 0.0 3 -#torsion 13 13 33 34 0.200 0.0 1 -0.417 180.0 2 0.418 0.0 3 -#torsion 13 13 33 34 0.819 0.0 1 -0.417 180.0 2 0.418 0.0 3 -#torsion 13 13 33 34 1.522 0.0 1 -0.417 180.0 2 0.418 0.0 3 -torsion 46 13 44 13 0.000 0.0 1 0.000 180.0 2 0.560 0.0 3 -torsion 46 13 44 45 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 -torsion 46 13 44 48 0.000 0.0 1 0.000 180.0 2 0.560 0.0 3 -torsion 0 13 24 45 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 3 13 24 3 -2.365 0.0 1 0.912 180.0 2 -0.850 0.0 3 -torsion 3 13 24 13 -1.737 0.0 1 1.251 180.0 2 -3.501 0.0 3 -torsion 3 13 24 45 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 13 13 24 3 0.000 0.0 1 0.462 180.0 2 0.000 0.0 3 -#torsion 13 13 35 3 -1.396 0.0 1 -0.427 180.0 2 0.000 0.0 3 -#torsion 13 13 35 3 1.130 0.0 1 -1.420 180.0 2 0.440 0.0 3 -torsion 13 13 24 13 4.753 0.0 1 -0.734 180.0 2 0.000 0.0 3 -#torsion 13 13 35 13 2.859 0.0 1 2.058 180.0 2 -11.266 0.0 3 -torsion 13 13 24 45 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1 2.170 180.0 2 0.000 0.0 3 -torsion 0 24 88 0 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 3 24 91 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 3 24 91 89 -1.396 0.0 1 -0.427 180.0 2 0.000 0.0 3 -torsion 3 24 91 91 -1.396 0.0 1 -0.427 180.0 2 0.000 0.0 3 -torsion 45 24 91 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 45 24 91 89 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 45 24 91 91 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 0 24 106 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 47 46 47 13 0.000 0.0 1 -8.000 180.0 2 0.000 0.0 3 -torsion 47 46 47 46 0.000 0.0 1 -8.000 180.0 2 0.000 0.0 3 -torsion 0 47 47 0 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 0 47 47 19 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 3 47 47 24 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 3 47 47 46 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 5 47 47 13 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 5 47 47 46 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 13 47 47 13 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 13 47 47 19 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 13 47 47 20 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 13 47 47 46 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 19 47 47 46 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 20 47 47 46 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 21 47 47 21 -1.600 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 21 47 47 46 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 46 47 47 46 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 46 47 47 48 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 13 47 48 48 0.205 0.0 1 -0.531 180.0 2 0.000 0.0 3 -torsion 46 47 48 48 0.000 0.0 1 0.000 180.0 2 -0.372 0.0 3 -torsion 46 47 48 56 0.000 0.0 1 0.000 180.0 2 -0.372 0.0 3 -torsion 47 47 48 48 1.241 0.0 1 3.353 180.0 2 -0.286 0.0 3 -torsion 13 47 50 13 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 13 47 50 46 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 13 47 50 48 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 13 47 50 50 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 13 47 50 109 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 24 47 50 3 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 46 47 50 13 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 46 47 50 46 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 46 47 50 48 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 46 47 50 50 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 46 47 50 109 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 0 47 84 0 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 0 47 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 3 47 86 86 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 49 47 86 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 49 47 86 24 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 0 47 87 0 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 0 47 88 0 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 13 47 110 47 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 46 47 110 47 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 0 48 48 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 0 48 48 13 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 0 48 48 48 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 0 48 48 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 1 48 48 48 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 1 48 48 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 13 48 48 13 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 13 48 48 48 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 13 48 48 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 13 48 48 50 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 21 48 48 48 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 21 48 48 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 44 48 48 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 47 48 48 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 48 48 48 48 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 48 48 48 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 48 48 48 50 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 48 48 48 55 0.0 0. 1 1.62 180. 2 0.0 0. 3 -0.44 180. 4 -torsion 48 48 48 60 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 48 48 48 65 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 48 48 48 66 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 48 48 48 86 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 48 48 48 109 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 49 48 48 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 49 48 48 50 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 49 48 48 60 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 49 48 48 65 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 49 48 48 66 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 49 48 48 86 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 49 48 48 109 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 56 48 48 86 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 48 48 50 46 0.000 0.0 1 0.000 180.0 2 -0.372 0.0 3 -torsion 48 48 50 47 1.241 0.0 1 3.353 180.0 2 -0.286 0.0 3 -torsion 56 48 50 46 0.000 0.0 1 0.000 180.0 2 -0.372 0.0 3 -torsion 56 48 50 47 1.241 0.0 1 3.353 180.0 2 -0.286 0.0 3 -torsion 48 48 53 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 48 48 53 54 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 0 48 55 45 0.000 0.0 1 2.030 180.0 2 0.000 0.0 3 -torsion 48 48 55 45 0.000 0.0 1 3.900 180.0 2 0.000 0.0 3 -torsion 55 48 55 13 0.000 0.0 1 7.936 180.0 2 0.000 0.0 3 -torsion 55 48 55 45 0.000 0.0 1 3.900 180.0 2 0.000 0.0 3 -torsion 60 48 55 45 0.000 0.0 1 2.030 180.0 2 0.000 0.0 3 -torsion 0 48 56 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 48 48 56 48 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 49 48 56 48 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 0 48 60 0 0.000 0.0 1 7.000 180.0 2 0.000 0.0 3 -torsion 0 48 79 23 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 48 48 79 13 0.000 0.0 1 -0.900 180.0 2 0.000 0.0 3 -torsion 48 48 79 24 1.656 0.0 1 -0.768 180.0 2 -0.117 0.0 3 -torsion 48 48 86 48 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 48 48 86 56 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 48 48 86 86 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 49 48 86 48 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 49 48 86 56 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 49 48 86 86 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 56 48 86 48 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 56 48 86 86 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 49 48 88 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 56 48 101 13 0.000 0.0 1 3.651 180.0 2 0.000 0.0 3 -torsion 48 48 102 103 0.000 0.0 1 1.150 180.0 2 0.000 0.0 3 -torsion 48 48 109 13 0.205 0.0 1 -0.531 180.0 2 0.000 0.0 3 -torsion 48 48 109 46 0.000 0.0 1 0.000 180.0 2 -0.372 0.0 3 -torsion 48 48 109 109 1.241 0.0 1 3.353 180.0 2 -0.286 0.0 3 -torsion 0 50 50 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 3 50 50 3 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 13 50 50 13 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -torsion 13 50 50 46 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -torsion 13 50 50 47 0.000 0.0 1 0.000 180.0 2 -0.372 0.0 3 -#torsion 13 40 40 37 0.900 0.0 1 0.230 180.0 2 -0.505 0.0 3 -torsion 46 50 50 46 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -torsion 46 50 50 47 0.000 0.0 1 0.000 180.0 2 -0.372 0.0 3 -torsion 47 50 50 47 1.423 0.0 1 4.055 180.0 2 0.858 0.0 3 -torsion 13 50 109 13 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -torsion 13 50 109 109 0.000 0.0 1 0.000 180.0 2 -0.372 0.0 3 -torsion 46 50 109 13 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -torsion 46 50 109 46 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -torsion 46 50 109 109 0.000 0.0 1 0.000 180.0 2 -0.372 0.0 3 -torsion 47 50 109 13 0.000 0.0 1 0.000 180.0 2 -0.372 0.0 3 -torsion 47 50 109 46 0.000 0.0 1 0.000 180.0 2 -0.372 0.0 3 -torsion 47 50 109 109 1.423 0.0 1 4.055 180.0 2 0.858 0.0 3 -torsion 13 53 82 61 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3 -torsion 48 53 82 61 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3 -torsion 45 55 59 0 0.000 0.0 1 2.030 180.0 2 0.000 0.0 3 -torsion 13 56 56 13 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 13 56 56 48 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 48 56 56 48 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 0 56 59 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 0 56 59 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 0 56 60 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 0 56 62 0 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 -torsion 0 56 82 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -#torsion 0 46 72 0 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 -torsion 48 56 86 48 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 48 56 86 86 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 0 57 60 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 45 57 60 0 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 0 57 61 0 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 -torsion 0 57 62 0 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 -torsion 0 57 81 0 0.000 0.0 1 3.050 180.0 2 0.000 0.0 3 -torsion 0 57 82 0 0.000 0.0 1 4.650 180.0 2 0.000 0.0 3 -#torsion 0 47 72 0 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 -torsion 0 57 82 49 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 -torsion 45 57 82 0 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 0 57 84 0 0.000 0.0 1 2.800 180.0 2 0.000 0.0 3 -#torsion 0 47 74 0 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 -#torsion 0 47 74 0 0.000 0.0 1 3.000 180.0 2 0.000 0.0 3 -torsion 45 57 84 0 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 61 57 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 84 57 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 0 60 60 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 0 60 61 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 0 60 80 0 0.000 0.0 1 3.350 180.0 2 0.000 0.0 3 -torsion 0 60 81 0 0.000 0.0 1 6.000 180.0 2 0.000 0.0 3 -torsion 0 60 87 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 48 60 87 84 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 60 60 87 84 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 0 61 61 0 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 -torsion 0 61 62 0 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 -torsion 0 61 82 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -#torsion 0 51 72 0 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 -torsion 0 61 82 49 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 -torsion 83 61 82 16 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 88 61 82 16 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 88 61 82 20 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 0 61 83 0 0.000 0.0 1 4.800 180.0 2 0.000 0.0 3 -torsion 82 61 83 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 82 61 83 84 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 0 61 84 0 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 -torsion 0 61 88 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 82 61 88 84 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 0 80 84 0 0.000 0.0 1 13.050 180.0 2 0.000 0.0 3 -torsion 0 82 84 0 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 16 82 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 20 82 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 57 82 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 61 82 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 0 82 87 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -#torsion 0 72 77 0 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 0 83 84 0 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3 -torsion 0 83 84 49 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3 -torsion 49 83 84 0 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3 -torsion 49 83 84 16 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3 -torsion 49 83 84 49 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3 -torsion 61 83 84 16 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 61 83 84 20 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 61 83 84 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 0 83 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 61 83 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 61 83 87 0 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 84 83 87 0 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 0 84 84 0 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3 -torsion 0 84 84 49 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3 -torsion 16 84 84 49 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3 -torsion 49 84 84 49 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3 -torsion 0 84 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 16 84 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 20 84 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 57 84 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 0 84 87 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 0 84 87 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 49 84 87 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 0 84 88 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 16 84 88 49 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3 -torsion 16 84 88 61 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 20 84 88 61 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 49 84 88 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 49 84 88 61 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 48 86 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 48 86 86 56 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 48 86 87 0 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 48 86 88 0 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 48 86 88 61 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 56 86 88 0 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 0 87 87 20 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 0 87 87 57 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 0 87 87 87 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 49 87 87 49 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 4 89 90 13 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 4 89 90 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 4 89 90 48 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 4 89 90 91 0.000 0.0 1 20.000 180.0 2 0.000 0.0 3 -torsion 91 89 90 13 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 91 89 90 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 91 89 90 48 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 91 89 90 91 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 0 89 91 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 4 89 91 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 4 89 91 91 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 90 89 91 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 90 89 91 91 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 0 90 91 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 0 90 91 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 0 90 91 91 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 0 91 91 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 0 91 91 24 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 13 91 91 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 13 91 91 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 46 91 91 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 46 91 91 91 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 91 91 91 91 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 0 109 109 0 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 13 109 109 13 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 13 109 109 46 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 13 109 109 48 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 13 109 109 50 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 13 109 109 109 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 46 109 109 46 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 46 109 109 48 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 46 109 109 50 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 46 109 109 109 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 48 109 109 48 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 48 109 109 50 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 48 109 109 109 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 50 109 109 50 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 50 109 109 109 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 109 109 109 109 1.423 0.0 1 4.055 180.0 2 0.858 0.0 3 - - - ################################################################ - ## ## - ## Additional Torsional Parameter Values Used with OPLS-AA ## - ## ## - ## The torsions listed below were added to official OPLS-AA ## - ## to complete the set needed for proteins; the values were ## - ## obtained by analogy from the closest OPLS-AA torsions; ## - ## most of the added values are for HIP or N-terminal AAs; ## - ## ## - ################################################################ - - -torsion 24 3 13 53 1.816 0.0 1 1.222 180.0 2 1.581 0.0 3 -torsion 52 3 13 24 0.000 0.0 1 0.820 180.0 2 0.000 0.0 3 -torsion 3 13 13 53 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 3 13 13 83 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3 -torsion 3 13 13 84 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3 -torsion 3 13 13 85 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3 -torsion 5 13 13 53 6.280 0.0 1 -1.467 180.0 2 2.030 0.0 3 -torsion 15 13 13 53 1.428 0.0 1 0.086 180.0 2 0.029 0.0 3 -torsion 16 13 13 53 1.428 0.0 1 0.086 180.0 2 0.029 0.0 3 -torsion 13 13 13 55 2.732 0.0 1 -0.229 180.0 2 0.485 0.0 3 -torsion 24 13 13 83 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3 -torsion 53 13 13 83 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 24 13 13 84 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3 -torsion 53 13 13 84 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 24 13 13 85 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3 -torsion 46 13 13 85 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 -torsion 53 13 13 85 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 3 13 53 13 1.438 0.0 1 -0.124 180.0 2 0.264 0.0 3 -torsion 3 13 53 54 0.000 0.0 1 0.000 180.0 2 0.347 0.0 3 -torsion 13 13 53 54 0.000 0.0 1 0.000 180.0 2 0.347 0.0 3 -torsion 46 13 55 54 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 13 13 85 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 13 13 85 57 1.700 0.0 1 -0.600 180.0 2 0.000 0.0 3 -torsion 46 13 85 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 55 48 55 54 0.000 0.0 1 3.900 180.0 2 0.000 0.0 3 -torsion 0 48 81 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 0 57 85 0 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 0 85 85 0 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3 - - - ################################################################ - ## ## - ## Additional Torsional Parameter Values Used with OPLS-AA ## - ## ## - ## The torsions listed below were added to official OPLS-AA ## - ## to complete the values needed for selected organics ## - ## ## - ################################################################ - - -torsion 13 13 13 20 1.300 0.0 1 -0.050 180.0 2 0.200 0.0 3 -torsion 13 13 13 47 1.300 0.0 1 -0.050 180.0 2 0.200 0.0 3 ######################################## @@ -3432,1705 +111,5 @@ torsion 13 13 13 47 1.300 0.0 1 -0.050 180.0 2 0.200 0.0 3 ######################################## -charge 1 -0.2200 -charge 2 0.2200 -charge 3 0.5500 -charge 4 -0.5000 -charge 5 -0.5800 -charge 6 0.0800 -charge 7 0.4500 -charge 8 0.0000 -charge 9 0.0000 -charge 10 0.0000 -charge 11 0.0000 -charge 12 0.0000 -charge 13 0.0000 -charge 14 0.0000 -charge 15 0.0000 -charge 16 0.0000 -charge 17 0.0000 -charge 18 0.0000 -charge 19 0.0000 -charge 20 -0.7000 -charge 21 0.4350 -charge 22 0.2650 -charge 23 0.2650 -charge 24 -0.4700 -charge 25 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0.1000 -charge 133 0.2650 -charge 134 0.1000 -charge 135 0.3000 -charge 136 0.1000 -charge 137 0.3650 -charge 138 0.1000 -charge 139 0.4000 -charge 140 0.4650 -charge 141 0.0850 -charge 142 -0.3350 -charge 143 -0.4700 -charge 144 -0.4350 -charge 145 -0.2175 -charge 146 0.1550 -charge 147 0.2350 -charge 148 0.0600 -charge 149 0.1200 -charge 150 0.1800 -charge 151 0.0375 -charge 152 0.0975 -charge 153 0.1575 -charge 154 0.2175 -charge 155 0.0375 -charge 156 0.0975 -charge 157 0.1575 -charge 158 0.2175 -charge 159 0.0000 -charge 160 0.2000 -charge 161 0.2600 -charge 162 0.3200 -charge 163 -0.0550 -charge 164 -0.3200 -charge 165 0.0800 -charge 166 0.1400 -charge 167 0.2000 -charge 168 -0.1200 -charge 169 0.0050 -charge 170 0.1025 -charge 171 0.1400 -charge 172 0.2000 -charge 173 0.7000 -charge 174 0.5650 -charge 175 0.5850 -charge 176 0.6150 -charge 177 0.5000 -charge 178 -0.5000 -charge 179 -0.7600 -charge 180 -0.5000 -charge 181 -0.1400 -charge 182 0.3800 -charge 183 0.3000 -charge 184 0.0200 -charge 185 -0.1100 -charge 186 0.0800 -charge 187 -0.0500 -charge 188 0.0100 -charge 189 0.1420 -charge 190 -0.3900 -charge 191 -0.5420 -charge 192 0.3330 -charge 193 -0.4900 -charge 194 0.4200 -charge 195 -0.4200 -charge 196 0.3700 -charge 197 0.0600 -charge 198 -0.1200 -charge 199 -0.0600 -charge 200 0.0000 -charge 201 0.0600 -charge 202 0.0350 -charge 203 0.3950 -charge 204 -0.4300 -charge 205 0.1800 -charge 206 -0.1800 -charge 207 -0.3850 -charge 208 0.0850 -charge 209 0.5200 -charge 210 -0.4400 -charge 211 -0.5300 -charge 212 0.4500 -charge 213 0.7000 -charge 214 -0.8000 -charge 215 -0.2800 -charge 216 -0.2200 -charge 217 -0.1600 -charge 218 -0.1000 -charge 219 0.4500 -charge 220 -0.4500 -charge 221 0.0000 -charge 222 0.4700 -charge 223 -0.4700 -charge 224 0.0600 -charge 225 0.0400 -charge 226 -0.0200 -charge 227 0.1000 -charge 228 -0.0900 -charge 229 -0.4000 -charge 230 -0.3000 -charge 231 0.0000 -charge 232 0.3500 -charge 233 0.3300 -charge 234 0.1300 -charge 235 0.1900 -charge 236 0.2500 -charge 237 0.3100 -charge 238 0.2300 -charge 239 0.1700 -charge 240 0.1100 -charge 241 0.0900 -charge 242 0.1500 -charge 243 -0.8000 -charge 244 0.4600 -charge 245 0.6400 -charge 246 -0.7000 -charge 247 0.4400 -charge 248 0.2000 -charge 249 -0.1100 -charge 250 0.1900 -charge 251 -0.0500 -charge 252 -0.2000 -charge 253 0.3100 -charge 254 -0.4600 -charge 255 0.3600 -charge 256 -0.8500 -charge 257 0.3700 -charge 258 -0.1500 -charge 259 0.1000 -charge 260 -0.0400 -charge 261 0.1000 -charge 262 -0.6000 -charge 263 0.5000 -charge 264 -0.5100 -charge 265 0.4500 -charge 266 -0.0700 -charge 267 0.0800 -charge 268 0.4100 -charge 269 -0.4000 -charge 270 0.3600 -charge 271 -0.4200 -charge 272 0.1000 -charge 273 0.1000 -charge 274 -0.1400 -charge 275 0.0800 -charge 276 -0.5600 -charge 277 0.5500 -charge 278 -0.5400 -charge 279 0.4600 -charge 280 -0.0600 -charge 281 0.1000 -charge 282 0.3800 -charge 283 -0.4800 -charge 284 -0.7900 -charge 285 0.3850 -charge 286 0.3550 -charge 287 0.1000 -charge 288 0.1000 -charge 289 -0.5300 -charge 290 0.2200 -charge 291 -0.5500 -charge 292 0.3800 -charge 293 0.1500 -charge 294 0.4400 -charge 295 -0.4900 -charge 296 0.2000 -charge 297 -0.5000 -charge 298 0.2000 -charge 299 -0.8100 -charge 300 0.3850 -charge 301 0.3550 -charge 302 0.2000 -charge 303 0.3500 -charge 304 -0.5600 -charge 305 0.4600 -charge 306 -0.5100 -charge 307 0.3400 -charge 308 0.1200 -charge 309 0.5200 -charge 310 0.3800 -charge 311 -0.8000 -charge 312 0.4000 -charge 313 -0.5100 -charge 314 -0.0100 -charge 315 0.1200 -charge 316 -0.0100 -charge 317 0.1400 -charge 318 -0.0100 -charge 319 0.1300 -charge 320 -0.6400 -charge 321 0.6500 -charge 322 -0.7400 -charge 323 0.6600 -charge 324 -0.0600 -charge 325 0.1000 -charge 326 0.4900 -charge 327 -0.3000 -charge 328 0.4800 -charge 329 -0.8100 -charge 330 0.4600 -charge 331 0.4300 -charge 332 0.1400 -charge 333 0.1400 -charge 334 0.0100 -charge 335 0.1600 -charge 336 0.7800 -charge 337 -0.6600 -charge 338 -0.4300 -charge 339 0.2000 -charge 340 0.1800 -charge 341 -0.0600 -charge 342 0.1200 -charge 343 -1.0000 -charge 344 -1.0000 -charge 345 -1.0000 -charge 346 -1.0000 -charge 347 1.0000 -charge 348 1.0000 -charge 349 1.0000 -charge 350 1.0000 -charge 351 1.0000 -charge 352 1.0000 -charge 353 2.0000 -charge 354 2.0000 -charge 355 2.0000 -charge 356 2.0000 -charge 357 -0.4000 -charge 358 0.1000 -charge 359 -0.9000 -charge 360 -0.2000 -charge 361 0.0600 -charge 362 -0.9800 -charge 363 -1.0700 -charge 364 0.1900 -charge 365 0.5100 -charge 366 -0.8200 -charge 367 -0.3000 -charge 368 0.0700 -charge 369 -1.3100 -charge 370 0.4000 -charge 371 -0.4000 -charge 372 0.0800 -charge 373 0.0000 -charge 374 0.0700 -charge 375 -0.9800 -charge 376 -1.3000 -charge 377 0.3000 -charge 378 2.5000 -charge 379 -0.2500 -charge 380 -0.8650 -charge 381 1.6200 -charge 382 -0.9200 -charge 383 -0.6000 -charge 384 0.3000 -charge 385 -0.0300 -charge 386 1.9200 -charge 387 -1.1200 -charge 388 -0.7000 -charge 389 0.4400 -charge 390 -0.1000 -charge 391 1.6200 -charge 392 -0.9700 -charge 393 -0.6300 -charge 394 0.2800 -charge 395 -0.0200 -charge 396 -0.5100 -charge 397 0.0800 -charge 398 -0.1400 -charge 399 0.3200 -charge 400 0.0200 -charge 401 -0.0400 -charge 402 -0.4700 -charge 403 0.1200 -charge 404 0.1400 -charge 405 0.2400 -charge 406 0.5100 -charge 407 -0.4300 -charge 408 -0.3300 -charge 409 0.1600 -charge 410 0.0300 -charge 411 0.6350 -charge 412 0.6250 -charge 413 0.1350 -charge 414 -0.2150 -charge 415 1.4800 -charge 416 -0.6800 -charge 417 -0.5400 -charge 418 0.1800 -charge 419 -1.0000 -charge 420 0.4400 -charge 421 -0.8000 -charge 422 0.4100 -charge 423 0.1800 -charge 424 0.0300 -charge 425 0.3900 -charge 426 -0.0600 -charge 427 -0.1800 -charge 428 0.0600 -charge 429 0.0000 -charge 430 0.0300 -charge 431 0.1900 -charge 432 0.2200 -charge 433 0.2500 -charge 434 1.3740 -charge 435 -0.6870 -charge 436 0.2450 -charge 437 0.1300 -charge 438 -0.4200 -charge 439 -0.0350 -charge 440 0.0250 -charge 441 0.0750 -charge 442 -0.0550 -charge 443 0.1300 -charge 444 -0.5700 -charge 445 0.4200 -charge 446 -0.0050 -charge 447 0.2950 -charge 448 -0.0150 -charge 449 0.0150 -charge 450 0.3850 -charge 451 0.2150 -charge 452 -0.4900 -charge 453 -0.5400 -charge 454 0.4600 -charge 455 -0.1150 -charge 456 0.0550 -charge 457 0.1150 -charge 458 -0.0300 -charge 459 0.0850 -charge 460 0.0000 -charge 461 -0.6780 -charge 462 0.4730 -charge 463 -0.4470 -charge 464 0.2270 -charge 465 0.0120 -charge 466 0.1550 -charge 467 0.0650 -charge 468 -0.4680 -charge 469 0.1920 -charge 470 0.0420 -charge 471 -0.8390 -charge 472 0.8740 -charge 473 0.6530 -charge 474 -0.6890 -charge 475 -0.0320 -charge 476 0.0110 -charge 477 0.1970 -charge 478 -0.3310 -charge 479 0.3780 -charge 480 -0.1600 -charge 481 -0.0090 -charge 482 0.1220 -charge 483 -0.2390 -charge 484 -0.1630 -charge 485 -0.1490 -charge 486 0.3170 -charge 487 0.1550 -charge 488 0.1180 -charge 489 -0.0590 -charge 490 -0.4910 -charge 491 0.2460 -charge 492 -0.3200 -charge 493 -0.0340 -charge 494 0.3010 -charge 495 0.0720 -charge 496 0.1500 -charge 497 0.1350 -charge 498 -0.2570 -charge 499 0.2750 -charge 500 -0.5630 -charge 501 0.1850 -charge 502 -0.2860 -charge 503 0.3060 -charge 504 0.0780 -charge 505 0.0750 -charge 506 0.1870 -charge 507 -0.1900 -charge 508 -0.0190 -charge 509 -0.1540 -charge 510 0.1420 -charge 511 0.1260 -charge 512 -0.2570 -charge 513 0.5110 -charge 514 -0.5900 -charge 515 0.1690 -charge 516 -0.1480 -charge 517 0.0430 -charge 518 0.0910 -charge 519 0.1810 -charge 520 -0.1220 -charge 521 -0.4130 -charge 522 0.4050 -charge 523 -0.4550 -charge 524 0.2500 -charge 525 0.0530 -charge 526 0.1840 -charge 527 0.0980 -charge 528 -0.5000 -charge 529 0.0010 -charge 530 -0.3900 -charge 531 -0.2700 -charge 532 -0.1270 -charge 533 -0.1080 -charge 534 -0.2580 -charge 535 0.2200 -charge 536 0.2250 -charge 537 0.3760 -charge 538 0.1470 -charge 539 0.1720 -charge 540 0.1550 -charge 541 0.1070 -charge 542 0.1100 -charge 543 0.1400 -charge 544 -0.6940 -charge 545 0.4250 -charge 546 -0.3590 -charge 547 -0.0080 -charge 548 -0.1970 -charge 549 -0.1120 -charge 550 -0.0700 -charge 551 -0.3070 -charge 552 0.5630 -charge 553 -0.0510 -charge 554 0.0280 -charge 555 0.1460 -charge 556 0.1190 -charge 557 0.1330 -charge 558 0.1130 -charge 559 0.1140 -charge 560 0.1570 -charge 561 -0.7600 -charge 562 0.6790 -charge 563 -0.7880 -charge 564 0.7360 -charge 565 0.0380 -charge 566 0.3430 -charge 567 -0.6420 -charge 568 0.4520 -charge 569 -0.6820 -charge 570 0.0240 -charge 571 0.1010 -charge 572 0.0860 -charge 573 0.4130 -charge 574 -0.0300 -charge 575 0.2420 -charge 576 -0.5150 -charge 577 0.2280 -charge 578 -0.2990 -charge 579 0.1010 -charge 580 0.0680 -charge 581 0.2050 -charge 582 -0.9510 -charge 583 0.9650 -charge 584 -0.0140 -charge 585 0.1300 -charge 586 0.0520 -charge 587 -0.5990 -charge 588 0.3920 -charge 589 -0.3480 -charge 590 0.0200 -charge 591 -0.0420 -charge 592 0.3470 -charge 593 -0.1960 -charge 594 0.0320 -charge 595 0.1460 -charge 596 0.1080 -charge 597 0.1400 -charge 598 0.1220 -charge 599 0.1660 -charge 600 -0.5800 -charge 601 0.1730 -charge 602 -0.3950 -charge 603 -0.1990 -charge 604 0.1180 -charge 605 0.0930 -charge 606 0.2080 -charge 607 0.0980 -charge 608 -0.1390 -charge 609 -0.0790 -charge 610 0.0990 -charge 611 -0.1680 -charge 612 -0.1080 -charge 613 -0.1890 -charge 614 -0.1290 -charge 615 -0.1690 -charge 616 -0.1090 -charge 617 -0.1380 -charge 618 -0.0780 -charge 619 -0.0250 -charge 620 0.0350 -charge 621 -0.0380 -charge 622 0.0220 -charge 623 -0.3340 -charge 624 0.2550 -charge 625 0.5230 -charge 626 0.5000 -charge 627 -0.1400 -charge 628 0.2275 -charge 629 0.1400 -charge 630 -0.0080 -charge 631 0.5880 -charge 632 -0.1030 -charge 633 -0.3320 -charge 634 0.0400 -charge 635 0.3420 -charge 636 -0.0500 -charge 637 -0.2050 -charge 638 3.0000 -charge 639 4.0000 -charge 640 3.0000 -charge 641 0.6190 -charge 642 -0.3950 -charge 643 0.1740 -charge 644 3.0000 -charge 645 3.0000 -charge 646 3.0000 -charge 647 3.0000 -charge 648 3.0000 -charge 649 -0.3440 -charge 650 -0.6280 -charge 651 0.2000 -charge 652 -0.1200 -charge 653 -0.0600 -charge 654 0.0000 -charge 655 -0.2300 -charge 656 0.0300 -charge 657 -0.0990 -charge 658 0.0990 -charge 659 0.2200 -charge 660 -0.2200 -charge 661 0.1300 -charge 662 -0.1300 -charge 663 -0.2200 -charge 664 0.2200 -charge 665 0.1500 -charge 666 0.4500 -charge 667 -0.2000 -charge 668 0.2000 -charge 669 -0.2000 -charge 670 0.2000 -charge 671 -0.2000 -charge 672 0.1000 -charge 673 -0.1000 -charge 674 0.0550 -charge 675 -0.2200 -charge 676 0.0650 -charge 677 0.0130 -charge 678 -0.1060 -charge 679 -0.0900 -charge 680 -0.1190 -charge 681 0.1410 -charge 682 0.1290 -charge 683 0.8270 -charge 684 -0.8850 -charge 685 0.4260 -charge 686 0.4650 -charge 687 0.1190 -charge 688 -0.0200 -charge 689 0.0400 -charge 690 -0.6200 -charge 691 -0.7850 -charge 692 -0.7850 -charge 693 0.5500 -charge 694 -0.5600 -charge 695 0.4600 -charge 696 -0.0800 -charge 697 -0.0200 -charge 698 0.0400 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0.1030 -charge 803 0.0970 -charge 804 0.2000 -charge 805 -0.2000 -charge 806 -0.0060 -charge 807 0.1030 -charge 808 0.0970 -charge 809 0.2000 -charge 810 -0.0800 -charge 811 -0.0800 -charge 812 -0.0800 -charge 813 0.1000 -charge 814 -0.2500 -charge 815 0.6000 -charge 816 -0.1500 -charge 817 -0.0250 -charge 818 -0.0450 -charge 819 0.1450 -charge 820 0.8880 -charge 821 1.0030 -charge 822 -0.6580 -charge 823 -0.6340 -charge 824 0.4110 -charge 825 -0.4420 -charge 826 0.4350 -charge 827 0.2250 -charge 828 0.2550 -charge 829 -0.0340 -charge 830 0.0030 -charge 831 0.3000 -charge 832 -0.0400 -charge 833 -0.0575 -charge 834 2.0000 -charge 835 -0.0700 -charge 836 0.0300 -charge 837 0.1300 -charge 838 -0.1300 -charge 839 0.1000 -charge 840 -0.6850 -charge 841 0.1550 -charge 842 -0.1000 -charge 843 -0.4270 -charge 844 0.2180 -charge 845 0.6000 -charge 846 -0.6000 -charge 847 -0.3600 -charge 848 0.0000 -charge 849 0.0600 -charge 850 0.1200 -charge 851 0.1800 -charge 852 0.0600 -charge 853 0.5700 -charge 854 -0.5700 -charge 855 0.0000 -charge 856 0.0200 -charge 857 -0.0400 -charge 858 0.0000 -charge 859 0.0600 -charge 860 -0.0700 -charge 861 -0.1400 -charge 862 0.1700 -charge 863 0.1100 -charge 864 0.1500 -charge 865 0.1700 -charge 866 1.0000 -charge 867 0.8500 -charge 868 0.7000 -charge 869 0.5500 -charge 870 -0.1000 -charge 871 -0.4300 -charge 872 -0.3700 -charge 873 -0.3100 -charge 874 -0.2500 -charge 875 -1.0000 -charge 876 -1.0000 -charge 877 -1.0000 -charge 878 -1.0000 -charge 879 1.0000 -charge 880 1.0000 -charge 881 1.0000 -charge 882 1.0000 -charge 883 1.0000 -charge 884 2.0000 -charge 885 2.0000 -charge 886 2.0000 -charge 887 2.0000 -charge 888 -0.0500 -charge 889 0.0500 -charge 890 0.1500 -charge 891 0.2500 -charge 892 0.1000 -charge 893 0.1150 -charge 894 0.1350 -charge 895 0.0150 -charge 896 0.1550 -charge 897 0.0000 -charge 898 -0.1150 -charge 899 0.1500 -charge 900 -0.2500 -charge 901 -0.1000 -charge 902 0.0500 -charge 903 -0.1000 -charge 904 0.2000 -charge 905 -0.2500 -charge 906 0.0880 - - - ######################################## - ## ## - ## Biopolymer Atom Type Conversions ## - ## ## - ######################################## - - -biotype 1 N "Glycine" 180 -biotype 2 CA "Glycine" 165 -biotype 3 C "Glycine" 177 -biotype 4 HN "Glycine" 183 -biotype 5 O "Glycine" 178 -biotype 6 HA "Glycine" 85 -biotype 7 N "Alanine" 180 -biotype 8 CA "Alanine" 166 -biotype 9 C "Alanine" 177 -biotype 10 HN "Alanine" 183 -biotype 11 O "Alanine" 178 -biotype 12 HA "Alanine" 85 -biotype 13 CB "Alanine" 80 -biotype 14 HB "Alanine" 85 -biotype 15 N "Valine" 180 -biotype 16 CA "Valine" 166 -biotype 17 C "Valine" 177 -biotype 18 HN "Valine" 183 -biotype 19 O "Valine" 178 -biotype 20 HA "Valine" 85 -biotype 21 CB "Valine" 82 -biotype 22 HB "Valine" 85 -biotype 23 CG1 "Valine" 80 -biotype 24 HG1 "Valine" 85 -biotype 25 CG2 "Valine" 80 -biotype 26 HG2 "Valine" 85 -biotype 27 N "Leucine" 180 -biotype 28 CA "Leucine" 166 -biotype 29 C "Leucine" 177 -biotype 30 HN "Leucine" 183 -biotype 31 O "Leucine" 178 -biotype 32 HA "Leucine" 85 -biotype 33 CB "Leucine" 81 -biotype 34 HB "Leucine" 85 -biotype 35 CG "Leucine" 82 -biotype 36 HG "Leucine" 85 -biotype 37 CD1 "Leucine" 80 -biotype 38 HD1 "Leucine" 85 -biotype 39 CD2 "Leucine" 80 -biotype 40 HD2 "Leucine" 85 -biotype 41 N "Isoleucine" 180 -biotype 42 CA "Isoleucine" 166 -biotype 43 C "Isoleucine" 177 -biotype 44 HN "Isoleucine" 183 -biotype 45 O "Isoleucine" 178 -biotype 46 HA "Isoleucine" 85 -biotype 47 CB "Isoleucine" 82 -biotype 48 HB "Isoleucine" 85 -biotype 49 CG1 "Isoleucine" 80 -biotype 50 HG1 "Isoleucine" 85 -biotype 51 CG2 "Isoleucine" 81 -biotype 52 HG2 "Isoleucine" 85 -biotype 53 CD "Isoleucine" 80 -biotype 54 HD "Isoleucine" 85 -biotype 55 N "Serine" 180 -biotype 56 CA "Serine" 166 -biotype 57 C "Serine" 177 -biotype 58 HN "Serine" 183 -biotype 59 O "Serine" 178 -biotype 60 HA "Serine" 85 -biotype 61 CB "Serine" 99 -biotype 62 HB "Serine" 85 -biotype 63 OG "Serine" 96 -biotype 64 HG "Serine" 97 -biotype 65 N "Threonine" 180 -biotype 66 CA "Threonine" 166 -biotype 67 C "Threonine" 177 -biotype 68 HN "Threonine" 183 -biotype 69 O "Threonine" 178 -biotype 70 HA "Threonine" 85 -biotype 71 CB "Threonine" 100 -biotype 72 HB "Threonine" 85 -biotype 73 OG1 "Threonine" 96 -biotype 74 HG1 "Threonine" 97 -biotype 75 CG2 "Threonine" 80 -biotype 76 HG2 "Threonine" 85 -biotype 77 N "Cysteine (SH)" 180 -biotype 78 CA "Cysteine (SH)" 166 -biotype 79 C "Cysteine (SH)" 177 -biotype 80 HN "Cysteine (SH)" 183 -biotype 81 O "Cysteine (SH)" 178 -biotype 82 HA "Cysteine (SH)" 85 -biotype 83 CB "Cysteine (SH)" 148 -biotype 84 HB "Cysteine (SH)" 85 -biotype 85 SG "Cysteine (SH)" 142 -biotype 86 HG "Cysteine (SH)" 146 -biotype 87 N "Cystine (SS)" 180 -biotype 88 CA "Cystine (SS)" 166 -biotype 89 C "Cystine (SS)" 177 -biotype 90 HN "Cystine (SS)" 183 -biotype 91 O "Cystine (SS)" 178 -biotype 92 HA "Cystine (SS)" 85 -biotype 93 CB "Cystine (SS)" 156 -biotype 94 HB "Cystine (SS)" 85 -biotype 95 SG "Cystine (SS)" 145 -biotype 96 N "Cysteine (S-)" -1 -biotype 97 CA "Cysteine (S-)" -1 -biotype 98 C "Cysteine (S-)" -1 -biotype 99 HN "Cysteine (S-)" -1 -biotype 100 O "Cysteine (S-)" -1 -biotype 101 HA "Cysteine (S-)" -1 -biotype 102 CB "Cysteine (S-)" -1 -biotype 103 HB "Cysteine (S-)" -1 -biotype 104 SG "Cysteine (S-)" -1 -biotype 105 N "Proline" 181 -biotype 106 CA "Proline" 188 -biotype 107 C "Proline" 177 -biotype 108 O "Proline" 178 -biotype 109 HA "Proline" 85 -biotype 110 CB "Proline" 81 -biotype 111 HB "Proline" 85 -biotype 112 CG "Proline" 81 -biotype 113 HG "Proline" 85 -biotype 114 CD "Proline" 187 -biotype 115 HD "Proline" 85 -biotype 116 N "Phenylalanine" 180 -biotype 117 CA "Phenylalanine" 166 -biotype 118 C "Phenylalanine" 177 -biotype 119 HN "Phenylalanine" 183 -biotype 120 O "Phenylalanine" 178 -biotype 121 HA "Phenylalanine" 85 -biotype 122 CB "Phenylalanine" 94 -biotype 123 HB "Phenylalanine" 85 -biotype 124 CG "Phenylalanine" 90 -biotype 125 CD "Phenylalanine" 90 -biotype 126 HD "Phenylalanine" 91 -biotype 127 CE "Phenylalanine" 90 -biotype 128 HE "Phenylalanine" 91 -biotype 129 CZ "Phenylalanine" 90 -biotype 130 HZ "Phenylalanine" 91 -biotype 131 N "Tyrosine" 180 -biotype 132 CA "Tyrosine" 166 -biotype 133 C "Tyrosine" 177 -biotype 134 HN "Tyrosine" 183 -biotype 135 O "Tyrosine" 178 -biotype 136 HA "Tyrosine" 85 -biotype 137 CB "Tyrosine" 94 -biotype 138 HB "Tyrosine" 85 -biotype 139 CG "Tyrosine" 90 -biotype 140 CD "Tyrosine" 90 -biotype 141 HD "Tyrosine" 91 -biotype 142 CE "Tyrosine" 90 -biotype 143 HE "Tyrosine" 91 -biotype 144 CZ "Tyrosine" 108 -biotype 145 OH "Tyrosine" 109 -biotype 146 HH "Tyrosine" 110 -biotype 147 N "Tyrosine (O-)" -1 -biotype 148 CA "Tyrosine (O-)" -1 -biotype 149 C "Tyrosine (O-)" -1 -biotype 150 HN "Tyrosine (O-)" -1 -biotype 151 O "Tyrosine (O-)" -1 -biotype 152 HA "Tyrosine (O-)" -1 -biotype 153 CB "Tyrosine (O-)" -1 -biotype 154 HB "Tyrosine (O-)" -1 -biotype 155 CG "Tyrosine (O-)" -1 -biotype 156 CD "Tyrosine (O-)" -1 -biotype 157 HD "Tyrosine (O-)" -1 -biotype 158 CE "Tyrosine (O-)" -1 -biotype 159 HE "Tyrosine (O-)" -1 -biotype 160 CZ "Tyrosine (O-)" -1 -biotype 161 OH "Tyrosine (O-)" -1 -biotype 162 N "Tryptophan" 180 -biotype 163 CA "Tryptophan" 166 -biotype 164 C "Tryptophan" 177 -biotype 165 HN "Tryptophan" 183 -biotype 166 O "Tryptophan" 178 -biotype 167 HA "Tryptophan" 85 -biotype 168 CB "Tryptophan" 81 -biotype 169 HB "Tryptophan" 85 -biotype 170 CG "Tryptophan" 441 -biotype 171 CD1 "Tryptophan" 455 -biotype 172 HD1 "Tryptophan" 91 -biotype 173 CD2 "Tryptophan" 442 -biotype 174 NE1 "Tryptophan" 444 -biotype 175 HE1 "Tryptophan" 445 -biotype 176 CE2 "Tryptophan" 443 -biotype 177 CE3 "Tryptophan" 90 -biotype 178 HE3 "Tryptophan" 91 -biotype 179 CZ2 "Tryptophan" 90 -biotype 180 HZ2 "Tryptophan" 91 -biotype 181 CZ3 "Tryptophan" 90 -biotype 182 HZ3 "Tryptophan" 91 -biotype 183 CH2 "Tryptophan" 90 -biotype 184 HH2 "Tryptophan" 91 -biotype 185 N "Histidine (+)" 180 -biotype 186 CA "Histidine (+)" 166 -biotype 187 C "Histidine (+)" 177 -biotype 188 HN "Histidine (+)" 183 -biotype 189 O "Histidine (+)" 178 -biotype 190 HA "Histidine (+)" 85 -biotype 191 CB "Histidine (+)" 446 -biotype 192 HB "Histidine (+)" 85 -biotype 193 CG "Histidine (+)" 451 -biotype 194 ND1 "Histidine (+)" 453 -biotype 195 HD1 "Histidine (+)" 454 -biotype 196 CD2 "Histidine (+)" 451 -biotype 197 HD2 "Histidine (+)" 91 -biotype 198 CE1 "Histidine (+)" 450 -biotype 199 HE1 "Histidine (+)" 91 -biotype 200 NE2 "Histidine (+)" 453 -biotype 201 HE2 "Histidine (+)" 454 -biotype 202 N "Histidine (HD)" 180 -biotype 203 CA "Histidine (HD)" 166 -biotype 204 C "Histidine (HD)" 177 -biotype 205 HN "Histidine (HD)" 183 -biotype 206 O "Histidine (HD)" 178 -biotype 207 HA "Histidine (HD)" 85 -biotype 208 CB "Histidine (HD)" 446 -biotype 209 HB "Histidine (HD)" 85 -biotype 210 CG "Histidine (HD)" 449 -biotype 211 ND1 "Histidine (HD)" 444 -biotype 212 HD1 "Histidine (HD)" 445 -biotype 213 CD2 "Histidine (HD)" 448 -biotype 214 HD2 "Histidine (HD)" 91 -biotype 215 CE1 "Histidine (HD)" 447 -biotype 216 HE1 "Histidine (HD)" 91 -biotype 217 NE2 "Histidine (HD)" 452 -biotype 218 N "Histidine (HE)" 180 -biotype 219 CA "Histidine (HE)" 166 -biotype 220 C "Histidine (HE)" 177 -biotype 221 HN "Histidine (HE)" 183 -biotype 222 O "Histidine (HE)" 178 -biotype 223 HA "Histidine (HE)" 85 -biotype 224 CB "Histidine (HE)" 446 -biotype 225 HB "Histidine (HE)" 85 -biotype 226 CG "Histidine (HE)" 448 -biotype 227 ND1 "Histidine (HE)" 452 -biotype 228 CD2 "Histidine (HE)" 449 -biotype 229 HD2 "Histidine (HE)" 91 -biotype 230 CE1 "Histidine (HE)" 447 -biotype 231 HE1 "Histidine (HE)" 91 -biotype 232 NE2 "Histidine (HE)" 444 -biotype 233 HE2 "Histidine (HE)" 445 -biotype 234 N "Aspartic Acid" 180 -biotype 235 CA "Aspartic Acid" 166 -biotype 236 C "Aspartic Acid" 177 -biotype 237 HN "Aspartic Acid" 183 -biotype 238 O "Aspartic Acid" 178 -biotype 239 HA "Aspartic Acid" 85 -biotype 240 CB "Aspartic Acid" 216 -biotype 241 HB "Aspartic Acid" 85 -biotype 242 CG "Aspartic Acid" 213 -biotype 243 OD "Aspartic Acid" 214 -biotype 244 N "Aspartic Acid (COOH)" -1 -biotype 245 CA "Aspartic Acid (COOH)" -1 -biotype 246 C "Aspartic Acid (COOH)" -1 -biotype 247 HN "Aspartic Acid (COOH)" -1 -biotype 248 O "Aspartic Acid (COOH)" -1 -biotype 249 HA "Aspartic Acid (COOH)" -1 -biotype 250 CB "Aspartic Acid (COOH)" -1 -biotype 251 HB "Aspartic Acid (COOH)" -1 -biotype 252 CG "Aspartic Acid (COOH)" -1 -biotype 253 OD1 "Aspartic Acid (COOH)" -1 -biotype 254 OD2 "Aspartic Acid (COOH)" -1 -biotype 255 HD2 "Aspartic Acid (COOH)" -1 -biotype 256 N "Asparagine" 180 -biotype 257 CA "Asparagine" 166 -biotype 258 C "Asparagine" 177 -biotype 259 HN "Asparagine" 183 -biotype 260 O "Asparagine" 178 -biotype 261 HA "Asparagine" 85 -biotype 262 CB "Asparagine" 81 -biotype 263 HB "Asparagine" 85 -biotype 264 CG "Asparagine" 177 -biotype 265 OD1 "Asparagine" 178 -biotype 266 ND2 "Asparagine" 179 -biotype 267 HD2 "Asparagine" 182 -biotype 268 N "Glutamic Acid" 180 -biotype 269 CA "Glutamic Acid" 166 -biotype 270 C "Glutamic Acid" 177 -biotype 271 HN "Glutamic Acid" 183 -biotype 272 O "Glutamic Acid" 178 -biotype 273 HA "Glutamic Acid" 85 -biotype 274 CB "Glutamic Acid" 81 -biotype 275 HB "Glutamic Acid" 85 -biotype 276 CG "Glutamic Acid" 216 -biotype 277 HG "Glutamic Acid" 85 -biotype 278 CD "Glutamic Acid" 213 -biotype 279 OE "Glutamic Acid" 214 -biotype 280 N "Glutamic Acid (COOH)" -1 -biotype 281 CA "Glutamic Acid (COOH)" -1 -biotype 282 C "Glutamic Acid (COOH)" -1 -biotype 283 HN "Glutamic Acid (COOH)" -1 -biotype 284 O "Glutamic Acid (COOH)" -1 -biotype 285 HA "Glutamic Acid (COOH)" -1 -biotype 286 CB "Glutamic Acid (COOH)" -1 -biotype 287 HB "Glutamic Acid (COOH)" -1 -biotype 288 CG "Glutamic Acid (COOH)" -1 -biotype 289 HG "Glutamic Acid (COOH)" -1 -biotype 290 CD "Glutamic Acid (COOH)" -1 -biotype 291 OE1 "Glutamic Acid (COOH)" -1 -biotype 292 OE2 "Glutamic Acid (COOH)" -1 -biotype 293 HE2 "Glutamic Acid (COOH)" -1 -biotype 294 N "Glutamine" 180 -biotype 295 CA "Glutamine" 166 -biotype 296 C "Glutamine" 177 -biotype 297 HN "Glutamine" 183 -biotype 298 O "Glutamine" 178 -biotype 299 HA "Glutamine" 85 -biotype 300 CB "Glutamine" 81 -biotype 301 HB "Glutamine" 85 -biotype 302 CG "Glutamine" 81 -biotype 303 HG "Glutamine" 85 -biotype 304 CD "Glutamine" 177 -biotype 305 OE1 "Glutamine" 178 -biotype 306 NE2 "Glutamine" 179 -biotype 307 HE2 "Glutamine" 182 -biotype 308 N "Methionine" 180 -biotype 309 CA "Methionine" 166 -biotype 310 C "Methionine" 177 -biotype 311 HN "Methionine" 183 -biotype 312 O "Methionine" 178 -biotype 313 HA "Methionine" 85 -biotype 314 CB "Methionine" 81 -biotype 315 HB "Methionine" 85 -biotype 316 CG "Methionine" 152 -biotype 317 HG "Methionine" 85 -biotype 318 SD "Methionine" 144 -biotype 319 CE "Methionine" 151 -biotype 320 HE "Methionine" 85 -biotype 321 N "Lysine" 180 -biotype 322 CA "Lysine" 166 -biotype 323 C "Lysine" 177 -biotype 324 HN "Lysine" 183 -biotype 325 O "Lysine" 178 -biotype 326 HA "Lysine" 85 -biotype 327 CB "Lysine" 81 -biotype 328 HB "Lysine" 85 -biotype 329 CG "Lysine" 81 -biotype 330 HG "Lysine" 85 -biotype 331 CD "Lysine" 81 -biotype 332 HD "Lysine" 85 -biotype 333 CE "Lysine" 235 -biotype 334 HE "Lysine" 85 -biotype 335 NZ "Lysine" 230 -biotype 336 HZ "Lysine" 233 -biotype 337 N "Lysine (NH2)" -1 -biotype 338 CA "Lysine (NH2)" -1 -biotype 339 C "Lysine (NH2)" -1 -biotype 340 HN "Lysine (NH2)" -1 -biotype 341 O "Lysine (NH2)" -1 -biotype 342 HA "Lysine (NH2)" -1 -biotype 343 CB "Lysine (NH2)" -1 -biotype 344 HB "Lysine (NH2)" -1 -biotype 345 CG "Lysine (NH2)" -1 -biotype 346 HG "Lysine (NH2)" -1 -biotype 347 CD "Lysine (NH2)" -1 -biotype 348 HD "Lysine (NH2)" -1 -biotype 349 CE "Lysine (NH2)" -1 -biotype 350 HE "Lysine (NH2)" -1 -biotype 351 NZ "Lysine (NH2)" -1 -biotype 352 HZ "Lysine (NH2)" -1 -biotype 353 N "Arginine" 180 -biotype 354 CA "Arginine" 166 -biotype 355 C "Arginine" 177 -biotype 356 HN "Arginine" 183 -biotype 357 O "Arginine" 178 -biotype 358 HA "Arginine" 85 -biotype 359 CB "Arginine" 81 -biotype 360 HB "Arginine" 85 -biotype 361 CG "Arginine" 251 -biotype 362 HG "Arginine" 85 -biotype 363 CD "Arginine" 250 -biotype 364 HD "Arginine" 85 -biotype 365 NE "Arginine" 246 -biotype 366 HE "Arginine" 247 -biotype 367 CZ "Arginine" 245 -biotype 368 NH "Arginine" 243 -biotype 369 HH "Arginine" 244 -biotype 370 N "Ornithine" 180 -biotype 371 CA "Ornithine" 166 -biotype 372 C "Ornithine" 177 -biotype 373 HN "Ornithine" 183 -biotype 374 O "Ornithine" 178 -biotype 375 HA "Ornithine" 85 -biotype 376 CB "Ornithine" 81 -biotype 377 HB "Ornithine" 85 -biotype 378 CG "Ornithine" 81 -biotype 379 HG "Ornithine" 85 -biotype 380 CD "Ornithine" 235 -biotype 381 HD "Ornithine" 85 -biotype 382 NE "Ornithine" 230 -biotype 383 HE "Ornithine" 233 -biotype 384 N "MethylAlanine (AIB)" 180 -biotype 385 CA "MethylAlanine (AIB)" 167 -biotype 386 C "MethylAlanine (AIB)" 177 -biotype 387 HN "MethylAlanine (AIB)" 183 -biotype 388 O "MethylAlanine (AIB)" 178 -biotype 389 CB "MethylAlanine (AIB)" 80 -biotype 390 HB "MethylAlanine (AIB)" 85 -biotype 391 N "Pyroglutamic Acid" 180 -biotype 392 CA "Pyroglutamic Acid" 166 -biotype 393 C "Pyroglutamic Acid" 177 -biotype 394 HN "Pyroglutamic Acid" 183 -biotype 395 O "Pyroglutamic Acid" 178 -biotype 396 HA "Pyroglutamic Acid" 85 -biotype 397 CB "Pyroglutamic Acid" 81 -biotype 398 HB "Pyroglutamic Acid" 85 -biotype 399 CG "Pyroglutamic Acid" 216 -biotype 400 HG "Pyroglutamic Acid" 85 -biotype 401 CD "Pyroglutamic Acid" 177 -biotype 402 OE "Pyroglutamic Acid" 178 -biotype 403 N "N-Terminal GLY" 230 -biotype 404 CA "N-Terminal GLY" 235 -biotype 405 C "N-Terminal GLY" 177 -biotype 406 HN "N-Terminal GLY" 233 -biotype 407 O "N-Terminal GLY" 178 -biotype 408 HA "N-Terminal GLY" 85 -biotype 409 N "N-Terminal ALA" 230 -biotype 410 CA "N-Terminal ALA" 236 -biotype 411 C "N-Terminal ALA" 177 -biotype 412 HN "N-Terminal ALA" 233 -biotype 413 O "N-Terminal ALA" 178 -biotype 414 HA "N-Terminal ALA" 85 -biotype 415 N "N-Terminal VAL" 230 -biotype 416 CA "N-Terminal VAL" 236 -biotype 417 C "N-Terminal VAL" 177 -biotype 418 HN "N-Terminal VAL" 233 -biotype 419 O "N-Terminal VAL" 178 -biotype 420 HA "N-Terminal VAL" 85 -biotype 421 N "N-Terminal LEU" 230 -biotype 422 CA "N-Terminal LEU" 236 -biotype 423 C "N-Terminal LEU" 177 -biotype 424 HN "N-Terminal LEU" 233 -biotype 425 O "N-Terminal LEU" 178 -biotype 426 HA "N-Terminal LEU" 85 -biotype 427 N "N-Terminal ILE" 230 -biotype 428 CA "N-Terminal ILE" 236 -biotype 429 C "N-Terminal ILE" 177 -biotype 430 HN "N-Terminal ILE" 233 -biotype 431 O "N-Terminal ILE" 178 -biotype 432 HA "N-Terminal ILE" 85 -biotype 433 N "N-Terminal SER" 230 -biotype 434 CA "N-Terminal SER" 236 -biotype 435 C "N-Terminal SER" 177 -biotype 436 HN "N-Terminal SER" 233 -biotype 437 O "N-Terminal SER" 178 -biotype 438 HA "N-Terminal SER" 85 -biotype 439 N "N-Terminal THR" 230 -biotype 440 CA "N-Terminal THR" 236 -biotype 441 C "N-Terminal THR" 177 -biotype 442 HN "N-Terminal THR" 233 -biotype 443 O "N-Terminal THR" 178 -biotype 444 HA "N-Terminal THR" 85 -biotype 445 N "N-Terminal CYS (SH)" 230 -biotype 446 CA "N-Terminal CYS (SH)" 236 -biotype 447 C "N-Terminal CYS (SH)" 177 -biotype 448 HN "N-Terminal CYS (SH)" 233 -biotype 449 O "N-Terminal CYS (SH)" 178 -biotype 450 HA "N-Terminal CYS (SH)" 85 -biotype 451 N "N-Terminal CYX (SS)" 230 -biotype 452 CA "N-Terminal CYX (SS)" 236 -biotype 453 C "N-Terminal CYX (SS)" 177 -biotype 454 HN "N-Terminal CYX (SS)" 233 -biotype 455 O "N-Terminal CYX (SS)" 178 -biotype 456 HA "N-Terminal CYX (SS)" 85 -biotype 457 N "N-Terminal CYD (S-)" -1 -biotype 458 CA "N-Terminal CYD (S-)" -1 -biotype 459 C "N-Terminal CYD (S-)" -1 -biotype 460 HN "N-Terminal CYD (S-)" -1 -biotype 461 O "N-Terminal CYD (S-)" -1 -biotype 462 HA "N-Terminal CYD (S-)" -1 -biotype 463 N "N-Terminal PRO" 252 -biotype 464 CA "N-Terminal PRO" 238 -biotype 465 C "N-Terminal PRO" 177 -biotype 466 HN "N-Terminal PRO" 253 -biotype 467 O "N-Terminal PRO" 178 -biotype 468 HA "N-Terminal PRO" 85 -biotype 469 CD "N-Terminal PRO" 239 -biotype 470 HD "N-Terminal PRO" 85 -biotype 471 N "N-Terminal PHE" 230 -biotype 472 CA "N-Terminal PHE" 236 -biotype 473 C "N-Terminal PHE" 177 -biotype 474 HN "N-Terminal PHE" 233 -biotype 475 O "N-Terminal PHE" 178 -biotype 476 HA "N-Terminal PHE" 85 -biotype 477 N "N-Terminal TYR" 230 -biotype 478 CA "N-Terminal TYR" 236 -biotype 479 C "N-Terminal TYR" 177 -biotype 480 HN "N-Terminal TYR" 233 -biotype 481 O "N-Terminal TYR" 178 -biotype 482 HA "N-Terminal TYR" 85 -biotype 483 N "N-Terminal TYD (O-)" -1 -biotype 484 CA "N-Terminal TYD (O-)" -1 -biotype 485 C "N-Terminal TYD (O-)" -1 -biotype 486 HN "N-Terminal TYD (O-)" -1 -biotype 487 O "N-Terminal TYD (O-)" -1 -biotype 488 HA "N-Terminal TYD (O-)" -1 -biotype 489 N "N-Terminal TRP" 230 -biotype 490 CA "N-Terminal TRP" 236 -biotype 491 C "N-Terminal TRP" 177 -biotype 492 HN "N-Terminal TRP" 233 -biotype 493 O "N-Terminal TRP" 178 -biotype 494 HA "N-Terminal TRP" 85 -biotype 495 N "N-Terminal HIS (+)" 230 -biotype 496 CA "N-Terminal HIS (+)" 236 -biotype 497 C "N-Terminal HIS (+)" 177 -biotype 498 HN "N-Terminal HIS (+)" 233 -biotype 499 O "N-Terminal HIS (+)" 178 -biotype 500 HA "N-Terminal HIS (+)" 85 -biotype 501 N "N-Terminal HIS (HD)" 230 -biotype 502 CA "N-Terminal HIS (HD)" 236 -biotype 503 C "N-Terminal HIS (HD)" 177 -biotype 504 HN "N-Terminal HIS (HD)" 233 -biotype 505 O "N-Terminal HIS (HD)" 178 -biotype 506 HA "N-Terminal HIS (HD)" 85 -biotype 507 N "N-Terminal HIS (HE)" 230 -biotype 508 CA "N-Terminal HIS (HE)" 236 -biotype 509 C "N-Terminal HIS (HE)" 177 -biotype 510 HN "N-Terminal HIS (HE)" 233 -biotype 511 O "N-Terminal HIS (HE)" 178 -biotype 512 HA "N-Terminal HIS (HE)" 85 -biotype 513 N "N-Terminal ASP" 230 -biotype 514 CA "N-Terminal ASP" 236 -biotype 515 C "N-Terminal ASP" 177 -biotype 516 HN "N-Terminal ASP" 233 -biotype 517 O "N-Terminal ASP" 178 -biotype 518 HA "N-Terminal ASP" 85 -biotype 519 N "N-Terminal ASH (COOH)" -1 -biotype 520 CA "N-Terminal ASH (COOH)" -1 -biotype 521 C "N-Terminal ASH (COOH)" -1 -biotype 522 HN "N-Terminal ASH (COOH)" -1 -biotype 523 O "N-Terminal ASH (COOH)" -1 -biotype 524 HA "N-Terminal ASH (COOH)" -1 -biotype 525 N "N-Terminal ASN" 230 -biotype 526 CA "N-Terminal ASN" 236 -biotype 527 C "N-Terminal ASN" 177 -biotype 528 HN "N-Terminal ASN" 233 -biotype 529 O "N-Terminal ASN" 178 -biotype 530 HA "N-Terminal ASN" 85 -biotype 531 N "N-Terminal GLU" 230 -biotype 532 CA "N-Terminal GLU" 236 -biotype 533 C "N-Terminal GLU" 177 -biotype 534 HN "N-Terminal GLU" 233 -biotype 535 O "N-Terminal GLU" 178 -biotype 536 HA "N-Terminal GLU" 85 -biotype 537 N "N-Terminal GLH (COOH)" -1 -biotype 538 CA "N-Terminal GLH (COOH)" -1 -biotype 539 C "N-Terminal GLH (COOH)" -1 -biotype 540 HN "N-Terminal GLH (COOH)" -1 -biotype 541 O "N-Terminal GLH (COOH)" -1 -biotype 542 HA "N-Terminal GLH (COOH)" -1 -biotype 543 N "N-Terminal GLN" 230 -biotype 544 CA "N-Terminal GLN" 236 -biotype 545 C "N-Terminal GLN" 177 -biotype 546 HN "N-Terminal GLN" 233 -biotype 547 O "N-Terminal GLN" 178 -biotype 548 HA "N-Terminal GLN" 85 -biotype 549 N "N-Terminal MET" 230 -biotype 550 CA "N-Terminal MET" 236 -biotype 551 C "N-Terminal MET" 177 -biotype 552 HN "N-Terminal MET" 233 -biotype 553 O "N-Terminal MET" 178 -biotype 554 HA "N-Terminal MET" 85 -biotype 555 N "N-Terminal LYS" 230 -biotype 556 CA "N-Terminal LYS" 236 -biotype 557 C "N-Terminal LYS" 177 -biotype 558 HN "N-Terminal LYS" 233 -biotype 559 O "N-Terminal LYS" 178 -biotype 560 HA "N-Terminal LYS" 85 -biotype 561 N "N-Terminal LYD (NH2)" -1 -biotype 562 CA "N-Terminal LYD (NH2)" -1 -biotype 563 C "N-Terminal LYD (NH2)" -1 -biotype 564 HN "N-Terminal LYD (NH2)" -1 -biotype 565 O "N-Terminal LYD (NH2)" -1 -biotype 566 HA "N-Terminal LYD (NH2)" -1 -biotype 567 N "N-Terminal ARG" 230 -biotype 568 CA "N-Terminal ARG" 236 -biotype 569 C "N-Terminal ARG" 177 -biotype 570 HN "N-Terminal ARG" 233 -biotype 571 O "N-Terminal ARG" 178 -biotype 572 HA "N-Terminal ARG" 85 -biotype 573 N "N-Terminal ORN" 230 -biotype 574 CA "N-Terminal ORN" 236 -biotype 575 C "N-Terminal ORN" 177 -biotype 576 HN "N-Terminal ORN" 233 -biotype 577 O "N-Terminal ORN" 178 -biotype 578 HA "N-Terminal ORN" 85 -biotype 579 N "N-Terminal AIB" 230 -biotype 580 CA "N-Terminal AIB" 237 -biotype 581 C "N-Terminal AIB" 177 -biotype 582 HN "N-Terminal AIB" 233 -biotype 583 O "N-Terminal AIB" 178 -biotype 584 N "C-Terminal GLY" 180 -biotype 585 CA "C-Terminal GLY" 226 -biotype 586 C "C-Terminal GLY" 213 -biotype 587 HN "C-Terminal GLY" 183 -biotype 588 OXT "C-Terminal GLY" 214 -biotype 589 HA "C-Terminal GLY" 85 -biotype 590 N "C-Terminal ALA" 180 -biotype 591 CA "C-Terminal ALA" 225 -biotype 592 C "C-Terminal ALA" 213 -biotype 593 HN "C-Terminal ALA" 183 -biotype 594 OXT "C-Terminal ALA" 214 -biotype 595 HA "C-Terminal ALA" 85 -biotype 596 N "C-Terminal VAL" 180 -biotype 597 CA "C-Terminal VAL" 225 -biotype 598 C "C-Terminal VAL" 213 -biotype 599 HN "C-Terminal VAL" 183 -biotype 600 OXT "C-Terminal VAL" 214 -biotype 601 HA "C-Terminal VAL" 85 -biotype 602 N "C-Terminal LEU" 180 -biotype 603 CA "C-Terminal LEU" 225 -biotype 604 C "C-Terminal LEU" 213 -biotype 605 HN "C-Terminal LEU" 183 -biotype 606 OXT "C-Terminal LEU" 214 -biotype 607 HA "C-Terminal LEU" 85 -biotype 608 N "C-Terminal ILE" 180 -biotype 609 CA "C-Terminal ILE" 225 -biotype 610 C "C-Terminal ILE" 213 -biotype 611 HN "C-Terminal ILE" 183 -biotype 612 OXT "C-Terminal ILE" 214 -biotype 613 HA "C-Terminal ILE" 85 -biotype 614 N "C-Terminal SER" 180 -biotype 615 CA "C-Terminal SER" 225 -biotype 616 C "C-Terminal SER" 213 -biotype 617 HN "C-Terminal SER" 183 -biotype 618 OXT "C-Terminal SER" 214 -biotype 619 HA "C-Terminal SER" 85 -biotype 620 N "C-Terminal THR" 180 -biotype 621 CA "C-Terminal THR" 225 -biotype 622 C "C-Terminal THR" 213 -biotype 623 HN "C-Terminal THR" 183 -biotype 624 OXT "C-Terminal THR" 214 -biotype 625 HA "C-Terminal THR" 85 -biotype 626 N "C-Terminal CYS (SH)" 180 -biotype 627 CA "C-Terminal CYS (SH)" 225 -biotype 628 C "C-Terminal CYS (SH)" 213 -biotype 629 HN "C-Terminal CYS (SH)" 183 -biotype 630 OXT "C-Terminal CYS (SH)" 214 -biotype 631 HA "C-Terminal CYS (SH)" 85 -biotype 632 N "C-Terminal CYX (SS)" 180 -biotype 633 CA "C-Terminal CYX (SS)" 225 -biotype 634 C "C-Terminal CYX (SS)" 213 -biotype 635 HN "C-Terminal CYX (SS)" 183 -biotype 636 OXT "C-Terminal CYX (SS)" 214 -biotype 637 HA "C-Terminal CYX (SS)" 85 -biotype 638 N "C-Terminal CYD (S-)" -1 -biotype 639 CA "C-Terminal CYD (S-)" -1 -biotype 640 C "C-Terminal CYD (S-)" -1 -biotype 641 HN "C-Terminal CYD (S-)" -1 -biotype 642 OXT "C-Terminal CYD (S-)" -1 -biotype 643 HA "C-Terminal CYD (S-)" -1 -biotype 644 N "C-Terminal PRO" 181 -biotype 645 CA "C-Terminal PRO" 228 -biotype 646 C "C-Terminal PRO" 213 -biotype 647 OXT "C-Terminal PRO" 214 -biotype 648 HA "C-Terminal PRO" 85 -biotype 649 N "C-Terminal PHE" 180 -biotype 650 CA "C-Terminal PHE" 225 -biotype 651 C "C-Terminal PHE" 213 -biotype 652 HN "C-Terminal PHE" 183 -biotype 653 OXT "C-Terminal PHE" 214 -biotype 654 HA "C-Terminal PHE" 85 -biotype 655 N "C-Terminal TYR" 180 -biotype 656 CA "C-Terminal TYR" 225 -biotype 657 C "C-Terminal TYR" 213 -biotype 658 HN "C-Terminal TYR" 183 -biotype 659 OXT "C-Terminal TYR" 214 -biotype 660 HA "C-Terminal TYR" 85 -biotype 661 N "C-Terminal TYD (O-)" -1 -biotype 662 CA "C-Terminal TYD (O-)" -1 -biotype 663 C "C-Terminal TYD (O-)" -1 -biotype 664 HN "C-Terminal TYD (O-)" -1 -biotype 665 OXT "C-Terminal TYD (O-)" -1 -biotype 666 HA "C-Terminal TYD (O-)" -1 -biotype 667 N "C-Terminal TRP" 180 -biotype 668 CA "C-Terminal TRP" 225 -biotype 669 C "C-Terminal TRP" 213 -biotype 670 HN "C-Terminal TRP" 183 -biotype 671 OXT "C-Terminal TRP" 214 -biotype 672 HA "C-Terminal TRP" 85 -biotype 673 N "C-Terminal HIS (+)" 180 -biotype 674 CA "C-Terminal HIS (+)" 225 -biotype 675 C "C-Terminal HIS (+)" 213 -biotype 676 HN "C-Terminal HIS (+)" 183 -biotype 677 OXT "C-Terminal HIS (+)" 214 -biotype 678 HA "C-Terminal HIS (+)" 85 -biotype 679 N "C-Terminal HIS (HD)" 180 -biotype 680 CA "C-Terminal HIS (HD)" 225 -biotype 681 C "C-Terminal HIS (HD)" 213 -biotype 682 HN "C-Terminal HIS (HD)" 183 -biotype 683 OXT "C-Terminal HIS (HD)" 214 -biotype 684 HA "C-Terminal HIS (HD)" 85 -biotype 685 N "C-Terminal HIS (HE)" 180 -biotype 686 CA "C-Terminal HIS (HE)" 225 -biotype 687 C "C-Terminal HIS (HE)" 213 -biotype 688 HN "C-Terminal HIS (HE)" 183 -biotype 689 OXT "C-Terminal HIS (HE)" 214 -biotype 690 HA "C-Terminal HIS (HE)" 85 -biotype 691 N "C-Terminal ASP" 180 -biotype 692 CA "C-Terminal ASP" 225 -biotype 693 C "C-Terminal ASP" 213 -biotype 694 HN "C-Terminal ASP" 183 -biotype 695 OXT "C-Terminal ASP" 214 -biotype 696 HA "C-Terminal ASP" 85 -biotype 697 N "C-Terminal ASH (COOH)" -1 -biotype 698 CA "C-Terminal ASH (COOH)" -1 -biotype 699 C "C-Terminal ASH (COOH)" -1 -biotype 700 HN "C-Terminal ASH (COOH)" -1 -biotype 701 OXT "C-Terminal ASH (COOH)" -1 -biotype 702 HA "C-Terminal ASH (COOH)" -1 -biotype 703 N "C-Terminal ASN" 180 -biotype 704 CA "C-Terminal ASN" 225 -biotype 705 C "C-Terminal ASN" 213 -biotype 706 HN "C-Terminal ASN" 183 -biotype 707 OXT "C-Terminal ASN" 214 -biotype 708 HA "C-Terminal ASN" 85 -biotype 709 N "C-Terminal GLU" 180 -biotype 710 CA "C-Terminal GLU" 225 -biotype 711 C "C-Terminal GLU" 213 -biotype 712 HN "C-Terminal GLU" 183 -biotype 713 OXT "C-Terminal GLU" 214 -biotype 714 HA "C-Terminal GLU" 85 -biotype 715 N "C-Terminal GLH (COOH)" -1 -biotype 716 CA "C-Terminal GLH (COOH)" -1 -biotype 717 C "C-Terminal GLH (COOH)" -1 -biotype 718 HN "C-Terminal GLH (COOH)" -1 -biotype 719 OXT "C-Terminal GLH (COOH)" -1 -biotype 720 HA "C-Terminal GLH (COOH)" -1 -biotype 721 N "C-Terminal GLN" 180 -biotype 722 CA "C-Terminal GLN" 225 -biotype 723 C "C-Terminal GLN" 213 -biotype 724 HN "C-Terminal GLN" 183 -biotype 725 OXT "C-Terminal GLN" 214 -biotype 726 HA "C-Terminal GLN" 85 -biotype 727 N "C-Terminal MET" 180 -biotype 728 CA "C-Terminal MET" 225 -biotype 729 C "C-Terminal MET" 213 -biotype 730 HN "C-Terminal MET" 183 -biotype 731 OXT "C-Terminal MET" 214 -biotype 732 HA "C-Terminal MET" 85 -biotype 733 N "C-Terminal LYS" 180 -biotype 734 CA "C-Terminal LYS" 225 -biotype 735 C "C-Terminal LYS" 213 -biotype 736 HN "C-Terminal LYS" 183 -biotype 737 OXT "C-Terminal LYS" 214 -biotype 738 HA "C-Terminal LYS" 85 -biotype 739 N "C-Terminal LYD (NH2)" -1 -biotype 740 CA "C-Terminal LYD (NH2)" -1 -biotype 741 C "C-Terminal LYD (NH2)" -1 -biotype 742 HN "C-Terminal LYD (NH2)" -1 -biotype 743 OXT "C-Terminal LYD (NH2)" -1 -biotype 744 HA "C-Terminal LYD (NH2)" -1 -biotype 745 N "C-Terminal ARG" 180 -biotype 746 CA "C-Terminal ARG" 225 -biotype 747 C "C-Terminal ARG" 213 -biotype 748 HN "C-Terminal ARG" 183 -biotype 749 OXT "C-Terminal ARG" 214 -biotype 750 HA "C-Terminal ARG" 85 -biotype 751 N "C-Terminal ORN" 180 -biotype 752 CA "C-Terminal ORN" 225 -biotype 753 C "C-Terminal ORN" 213 -biotype 754 HN "C-Terminal ORN" 183 -biotype 755 OXT "C-Terminal ORN" 214 -biotype 756 HA "C-Terminal ORN" 85 -biotype 757 N "C-Terminal AIB" 180 -biotype 758 CA "C-Terminal AIB" 227 -biotype 759 C "C-Terminal AIB" 213 -biotype 760 HN "C-Terminal AIB" 183 -biotype 761 OXT "C-Terminal AIB" 214 -biotype 762 N "Deprotonated N-Terminus" -1 -biotype 763 H "Deprotonated N-Terminus" -1 -biotype 764 C "Formyl N-Terminus" 177 -biotype 765 H "Formyl N-Terminus" 221 -biotype 766 O "Formyl N-Terminus" 178 -biotype 767 CH3 "Acetyl N-Terminus" 80 -biotype 768 H "Acetyl N-Terminus" 85 -biotype 769 C "Acetyl N-Terminus" 177 -biotype 770 O "Acetyl N-Terminus" 178 -biotype 771 C "Protonated C-Terminus" -1 -biotype 772 O "Protonated C-Terminus" -1 -biotype 773 OH "Protonated C-Terminus" -1 -biotype 774 HO "Protonated C-Terminus" -1 -biotype 775 N "Amide C-Terminus" 179 -biotype 776 HN "Amide C-Terminus" 182 -biotype 777 N "N-MeAmide C-Terminus" 180 -biotype 778 HN "N-MeAmide C-Terminus" 183 -biotype 779 CH3 "N-MeAmide C-Terminus" 184 -biotype 780 H "N-MeAmide C-Terminus" 85 -biotype 2001 O "Water" 63 -biotype 2002 H "Water" 64 -biotype 2003 NA "Sodium Ion" -1 -biotype 2004 K "Potassium Ion" -1 -biotype 2005 MG "Magnesium Ion" -1 -biotype 2006 CA "Calcium Ion" -1 -biotype 2007 CL "Chloride Ion" -1 diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/README_run.sh b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/README_run.sh index 8b01ab92d7..9f923a6c7e 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/README_run.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/README_run.sh @@ -12,12 +12,12 @@ # If not, carry out the instructions in "README_setup.sh". # # -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, +# If "lmp_mpi" is the name of the command you use to invoke lammps, # then you would run lammps on these files this way: -lmp_linux -i run.in.npt # minimization and simulation at constant pressure -lmp_linux -i run.in.nvt # minimization and simulation at constant volume +lmp_mpi -i run.in.npt # minimization and simulation at constant pressure +lmp_mpi -i run.in.nvt # minimization and simulation at constant volume #(Note: The constant volume simulation lacks pressure equilibration. These are # completely separate simulations. The results of the constant pressure @@ -34,6 +34,6 @@ lmp_linux -i run.in.nvt # minimization and simulation at constant volume # If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.npt -#mpirun -np 4 lmp_linux -i run.in.nvt +#mpirun -np 4 lmp_mpi -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.nvt # (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/README_setup.sh index d80df900ef..2c3c217135 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/README_setup.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/README_setup.sh @@ -10,7 +10,7 @@ cd moltemplate_files # Create the "oplsaa.lt" file which moltemplate will need cd oplsaa_lt_generator/ - ./oplsaa_moltemplate.py oplsaa_subset.prm + oplsaa_moltemplate.py oplsaa_subset.prm mv -f oplsaa.lt .. cd .. diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/README.TXT b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/README.TXT index c49ef8a6ad..0bc46d88c8 100644 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/README.TXT +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/README.TXT @@ -19,7 +19,7 @@ so that it only contains atom types you plan to have in your simulation (see below for details). Then run the opls_moltemplate.py script this way: -python oplsaa_moltemplate.py oplsaa_subset.prm +oplsaa_moltemplate.py oplsaa_subset.prm This will create a file named "oplsaa.lt" diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py deleted file mode 100755 index 32980aab1f..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py +++ /dev/null @@ -1,408 +0,0 @@ -#! /usr/bin/env python -# -# The purpose of this script is to create a moltemplate lt file for the oplsaa. -# forcefield. This will assist researchers in building complex simulations using -# this OPLS-UA and the OPLS-AA forcefields. - -__author__="Jason Lambert" -# (some additional corrections by Miguel Gonzalez and Andrew Jewett) -__version__="0.18" - -import sys -import os -from operator import itemgetter - -g_program_name = __file__.split('/')[-1] - -# To do that, first make a copy of the \"oplsaa.prm\" file -# (which can be downloaded from the TINKER web site). -# The lines in this file beginning with the word \"atoms\" should -# define the atoms which you plan to put in your simulation. All other -# lines beginning with the word \"atoms\" should be deleted. -# (Leave the other sections of this file alone.) -#""") - - - -#input data from file containing opls aa force field parameters. -try: - f=open(sys.argv[1],"r") -except: - sys.stderr.write("Error: \n" - " You need to specify a file name as an input argument:\n" - " python oplsaa_moltemplate.py \n" - " (or the file name is specified incorrectly)\n") - sys.exit() - - -sys.stderr.write(g_program_name+", version "+__version__+"\n" - "Reading parameter file...\n") - - -#output lt file -g=open("oplsaa.lt","w") - - - -lines = f.readlines() - - - -# Ignore/Comment out lines before the "## Atom Type Definitions ##" section. - -for i in range(0, len(lines)): - if (lines[i].find("## Atom Type Definitions ##") != -1): - break - else: - lines[i] = '# ' + lines[i] - - -# As of late 2014, there appear to be 906 atom types, but we don't assume this. -# First try to infer out how many atom types there were in the original -# oplsaa.prm file, or at least find an upper bound on the atom-type numbers. -# (Keep track of the maximum value of the first column in the "atom" section.) -max_atomType = 0 -num_atomTypes = 0 -for line in lines: - # skip over text after a # comment character - ic = line.find('#') - if ic != -1: - line = (line[:ic]).strip() - else: - line = line.strip() - # now look for lines beginning with the word "atom" - tokens = line.split() - if ((len(tokens)>2) and (tokens[0] == "atom")): - num_atomTypes += 1 - if (int(tokens[1]) > max_atomType): - max_atomType = int(tokens[1]) - -if num_atomTypes > 25: - sys.stderr.write("\n" - "(Note: If your computer freezes while running "+g_program_name+",\n" - " it could be because you forgot to edit the .prm file.\n" - " The original \"oplsaa.prm\" file distributed with TINKER has over 900 atom\n" - " types. If you run "+g_program_name+" on this file, it may freeze or\n" - " crash. Instead, run "+g_program_name+" on a SUBSET of the OPLS atoms\n" - " relevant to your problem. To do that, delete the lines from the .prm\n" - " file beginning with \"atom\" which you do not need.)\n\n") - -#temporary storage file -h=open("temp.txt","w+") -atom_lookup={} #this dictionary contains all the atom ffid's as a key and the number of atoms with that key -#atom=[[10000,10000] for i in range(906)] <- don't assume there are 906 atoms -atom=[[-10000,-10000] for i in range(0,max_atomType+1)] -#charge_by_type={} # lookup charge by atom type -#vdw_by_type={} # lookup epsilon & sigma paramters by atom type -charge_by_type=[0.0 for i in range(0,max_atomType+1)] # lookup charge by atom -vdw_by_type=[(0.0,0.0) for i in range(0,max_atomType+1)] # lookup epsilon & sigma - - - -#atom is declared this way so for sorting purposes. -#atom contains the following data upon allocation -#atom[][0]=atom_id( Important for partial charges and non_bonded interactions) -#atom[][1]=atom_ffid( Important for stretches, bending, torsions and impropers) -#atom[][2]=atom_mass -#atom[][3]=partial charge -#atom[][4]=non_bonding sigma -#atom[][5]=non_bonding epsilon -#atom[][6]=atom comment -bond=[] -#bond contains the following data -#bond[0]=atom 1 ffid -#bond[1]=atom 2 ffid -#bond[2]=bond spring constant(OPLS-aa compatible) -#bond[3]=equilibrium bond distance(Angstrom) -angle=[] -#angle contains the following data -#angle[0]=atom 1 ffid -#angle[1]=atom 2 ffid -#angle[2]=atom 3 ffid -#angle[3]=spring constant -#angle[4]=equilibrium angle (degrees) -dihedral=[] -#dihedral contains the following data -#dihedral[0]=atom 1 ffid -#dihedral[1]=atom 2 ffid -#dihedral[2]=atom 3 ffid -#dihedral[3]=atom 4 ffid -#dihedral[4]=v1 -#dihedral[5]=v2 -#dihedral[6]=v3 -#dihedral[7]=v4 -improper=[] -#improper[0]=atom 1 ffid -#improper[1]=atom 2 ffid(central atom) -#improper[2]=atom 3 ffid -#improper[3]=atom 4 ffid -#improper[4]=spring coefficient -#improper[5]=equilibrium angle - - -#This section gets all the parameters from the force field file -for line in lines: - - # skip over text after a # comment character - ic = line.find('#') - if ic != -1: - line = (line[:ic]).strip() - else: - line = line.strip() - - if line.find("atom") == 0: - line=line.split() - atom[int(line[1])-1]=[int(line[1]),int(line[2]),float(line[-2]), - 0.0,0.0,0.0," ".join(line[3:-2])] - elif line.find("vdw") == 0: - line=line.split() - #vdw_temp.append([float(line[1]),float(line[2]),float(line[3])]) - if (int(line[1]) <= max_atomType): - vdw_by_type[int(line[1])] = (float(line[2]),float(line[3])) - elif line.find("bond") == 0: - line=line.split() - bond.append([int(line[1]),int(line[2]),float(line[3]),float(line[4])]) - elif line.find("angle") == 0: - line=line.split() - angle.append([int(line[1]),int(line[2]),int(line[3]), - float(line[4]),float(line[5])]) - elif line.find("torsion") == 0: - line=line.split() - dihedral.append([int(line[1]),int(line[2]),int(line[3]),int(line[4]), - float(line[5]),float(line[8]), float(line[11]), 0.0]) - elif line.find("charge") == 0: - line=line.split() - #charge_temp.append([int(line[1]),float(line[2])]) - if (int(line[1]) <= max_atomType): - charge_by_type[int(line[1])] = float(line[2]) - elif line.find("imptors") == 0: - line=line.split() - improper.append([int(line[1]), int(line[2]), - int(line[3]), int(line[4]), float(line[5]), float(line[6])]) - -if len(atom) > 600: - sys.stderr.write("WARNING: The number of atom types in your file exceeds 600\n" - " (You were supposed to edit out the atoms you don't need.\n" - " Not doing this may crash your computer.)\n" - "\n" - " Proceed? (Y/N): ") - reply = sys.stdin.readline() - if find(reply.strip().lower(), 'y') != 0: - exit(0) - -#adding the charge and Lennard Jones parameters to -#to each atom type. -#----------------------------------------------# -for i in range(0,len(atom)): - atom_type_num = atom[i][0] - #q = charge_by_type.get(atomTypeNum) - #if q: - # atom[i][3] = q - if atom_type_num != -10000: - q = charge_by_type[atom_type_num] - atom[i][3] = q - -for i in range(0,len(atom)): - atom_type_num = atom[i][0] - #vdw_params = vdw_by_type.get(atomTypeNum) - #if vdw_params: - # atom[i][4] = vdw_params[0] - # atom[i][5] = vdw_params[1] - if atom_type_num != -10000: - vdw_params = vdw_by_type[atom_type_num] - atom[i][4] = vdw_params[0] - atom[i][5] = vdw_params[1] - -del(charge_by_type) -del(vdw_by_type) - -#----------------------------------------------------------# -#begin writing content to lt file -g.write("OPLSAA {\n\n" ) - -#write out the atom masses -#----------------------------------------------------------# -g.write(" write_once(\"Data Masses\"){\n")#checked with gaff -for i,x in enumerate(atom): - if x[0] != -10000: - g.write(" @atom:{} {} #{} partial charge={}\n".format( - x[0],x[2],x[6],x[3])) -g.write(" } #(end of atom masses)\n\n") -#----------------------------------------------------------# - - -#write out the pair coefficients -#----------------------------------------------------------# -g.write(" write_once(\"In Settings\"){\n")#checked with gaff -for i,x in enumerate(atom): - if x[0] != -10000: - g.write(" pair_coeff @atom:{0} @atom:{0} lj/cut/coul/long {1} {2}\n".format(x[0],x[5],x[4])) -g.write(" } #(end of pair coeffs)\n\n") - -g.write(" write_once(\"In Charges\"){\n")#checked with gaff -for i,x in enumerate(atom): - if x[0] != -10000: - g.write(" set type @atom:{0} charge {1}\n".format(x[0],x[3])) -g.write(" } #(end of atom charges)\n\n") - -#-----------------------------------------------------------# - -# This part of the code creates a lookup dictionary -# that allows you to find every type of atom by its -# force field id. force field id is the id number -# relevant to bonds, angles, dihedrals, and impropers. -# This greatly increases the speed of angle, bond, dihedral -# and improper assignment. -#------------------------------------------------------------# -atom=sorted(atom,key=itemgetter(1)) -atom_ffid=0 -for x in atom: - if x[1]==atom_ffid: - atom_lookup[x[1]].append(x[0]) - elif x[1]>atom_ffid: - atom_lookup[x[1]]=[x[0]] - atom_ffid=x[1] -atom_lookup[0]=["*"] -#-------------------------------------------------------------# - - -#writing out the bond coefficients and bond parameters# -#-------------------------------------------------------------# -g.write(" write_once(\"In Settings\") {\n") -index1=0 -for x in bond: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - #g.write(" bond_coeff @bond:{}-{} harmonic {} {}\n".format(y,z,x[2]/2,x[3])) - # Miguel Gonzales corrected this line to: - g.write(" bond_coeff @bond:{}-{} harmonic {} {}\n".format(y,z,x[2],x[3])) - h.write(" @bond:{0}-{1} @atom:{0} @atom:{1}\n".format(y,z)) -g.write(" } #(end of bond_coeffs)\n\n") -h.seek(0,0) -g.write(" write_once(\"Data Bonds By Type\") {\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of bonds by type)\n\n") -del(bond) -h.close() -#-----------------------------------------------------------# -h=open("temp.txt","w+") - -#writing out angle coefficients and angles by type.---------# -#-----------------------------------------------------------# -g.write(" write_once(\"Data Angles By Type\"){\n") -for x in angle: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - for u in atom_lookup.get(x[2],[]): - #print(y,z,u,x) - #h.write(" angle_coeff @angle:{}-{}-{} harmonic {} {}\n".format(y,z,u,x[3]/2.0,x[4])) - # Miguel Gonzales corrected this line: - h.write(" angle_coeff @angle:{}-{}-{} harmonic {} {}\n".format(y,z,u,x[3],x[4])) - g.write(" @angle:{0}-{1}-{2} @atom:{0} @atom:{1} @atom:{2}\n".format(y,z,u)) - - -g.write(" } #(end of angles by type)\n\n") -h.seek(0,0) -g.write(" write_once(\"In Settings\" ){\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of angle_coeffs)\n\n") -del(angle) -h.close() -#----------------------------------------------------------# - -#writing dihedrals by type and dihedral coefficients-------# -h=h=open("temp.txt","w+") -g.write(" write_once(\"Data Dihedrals By Type\") {\n") -#print(atom_lookup) -for x in dihedral: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - for u in atom_lookup.get(x[2],[]): - for v in atom_lookup.get(x[3],[]): - if x[0]!=0 and x[3]!=0: - g.write(" @dihedral:{0}-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( - y,z,u,v)) - h.write(" dihedral_coeff @dihedral:{}-{}-{}-{} opls {} {} {} {}\n".format( - y,z,u,v,x[4],x[5],x[6],x[7])) - elif x[0]==0 and x[3]!=0: - g.write(" @dihedral:0-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( - y,z,u,v)) - h.write(" dihedral_coeff @dihedral:0-{}-{}-{} opls {} {} {} {}\n".format( - z,u,v,x[4],x[5],x[6],x[7])) - elif x[0]==0 and x[3]==0: - g.write(" @dihedral:0-{1}-{2}-0 @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( - y,z,u,v)) - #h.write(" dihedral_coeff @dihedral:0-{}-{}-0 harmonic {} {} {} {}\n".format( - h.write(" dihedral_coeff @dihedral:0-{}-{}-0 opls {} {} {} {}\n".format( - z,u,x[4],x[5],x[6],x[7])) - -del(dihedral) -g.write(" } #(end of Dihedrals by type)\n\n") -h.seek(0,0) -g.write(" write_once(\"In Settings\") {\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of dihedral_coeffs)\n\n") -h.close() -#-----------------------------------------------------------------------# - -#----writing out improper coefficients and impropers by type------------# -h=open("temp.txt","w+") -g.write(" write_once(\"Data Impropers By Type (opls_imp.py)\") {\n") -for x in improper: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - for u in atom_lookup.get(x[2],[]): - for v in atom_lookup.get(x[3],[]): - # Notation: let I,J,K,L denote the atom types ("biotypes") - # listed in the order they appear in the "oplsaa.prm" file. - # (I think J and L are represented by "u" and "v" in the code here.) - # It looks like the "oplsaa.prm" file distributed with tinker - # treats the third atom ("K") as the central atom. - # After checking the code, it appears that the improper angle is - # calculated as the angle between the I,J,K and the J,K,L planes - if x[0]==0 and x[1]==0 and x[3]==0: - g.write(" @improper:0-0-{2}-0 @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v)) - h.write(" improper_coeff @improper:0-0-{2}-0 harmonic {4} {5} \n".format(y,z,u,v,x[4]/2,180)) - else: - g.write(" @improper:0-0-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v)) - h.write(" improper_coeff @improper:0-0-{2}-{3} harmonic {4} {5} \n".format(y,z,u,v,x[4]/2,180)) - - -g.write(" } #(end of impropers by type)\n\n") -h.seek(0,0) -g.write(" write_once(\"In Settings\") {\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of improp_coeffs)\n\n") -#-----------------------------------------------------------------------# - -#This section writes out the input parameters required for an opls-aa simulation -# lammps. -g.write(" write_once(\"In Init\") {\n") -g.write(" units real\n") -g.write(" atom_style full\n") -g.write(" bond_style hybrid harmonic\n") -g.write(" angle_style hybrid harmonic\n") -g.write(" dihedral_style hybrid opls\n") -g.write(" improper_style hybrid harmonic\n") -#g.write(" pair_style hybrid lj/cut/coul/cut 10.0 10.0\n") -g.write(" pair_style hybrid lj/cut/coul/long 10.0 10.0\n") -g.write(" pair_modify mix geometric\n") -g.write(" special_bonds lj/coul 0.0 0.0 0.5\n") -g.write(" kspace_style pppm 0.0001\n") -g.write(" } #end of init parameters\n\n") -g.write("} # OPLSAA\n") -f.close() -g.close() -h.close() -os.remove("temp.txt") - - -sys.stderr.write("...finished.\n") - - - - diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm index 074940eb2b..fee34956bc 100644 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm @@ -1,7 +1,9 @@ # This is a modified version of the file "oplsaa.prm" distributed with TINKER # http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm # In this version, all of the lines beginning with "atom" have been deleted -# except for the atom types we will be using in this simulation +# except for the atom types we will be using in this simulation. +# (I also deleted some other lines from that file data to reduce the file size, +# but doing that is not necessary.) # # If you use this file, please also cite the software this file comes from: # @@ -71,11 +73,10 @@ explicit hydrogen atoms. atom 83 13 CT "Methane CH4" 6 12.011 4 atom 85 46 HC "Alkane H-C" 1 1.008 1 -# NOTE: You can use the OPLSAA force field to look up water parameters as well. +# NOTE: You can use the OPLSAA force field to look up SPC water parameters as # In that case, you could do this by uncommenting these next two lines: # atom 76 42 OW "SPC Water O" 8 15.999 2 # atom 77 43 HW "SPC Water H" 1 1.008 1 -# (...You will have to modify the "spce.lt" file accordingly.) @@ -86,912 +87,8 @@ atom 85 46 HC "Alkane H-C" 1 1.008 1 ################################ -vdw 1 2.9400 0.0610 -vdw 2 3.9050 0.1180 -vdw 3 3.7500 0.1050 -vdw 4 2.9600 0.2100 -vdw 5 3.0000 0.1700 -vdw 6 3.9100 0.1600 -vdw 7 0.0000 0.0000 -vdw 8 3.7300 0.2940 -vdw 9 3.7750 0.2070 -vdw 10 3.9050 0.1750 -vdw 11 3.9100 0.1600 -vdw 12 3.9600 0.1450 -vdw 13 3.9050 0.1180 -vdw 14 3.8500 0.1400 -vdw 15 3.8500 0.0800 -vdw 16 3.8000 0.1150 -vdw 17 3.7500 0.1100 -vdw 18 3.8000 0.0500 -vdw 19 3.7500 0.1050 -vdw 20 3.0700 0.1700 -vdw 21 0.0000 0.0000 -vdw 22 3.7750 0.2070 -vdw 23 3.9050 0.1180 -vdw 24 3.7000 0.2500 -vdw 25 3.5500 0.2500 -vdw 26 3.5500 0.2500 -vdw 27 3.5500 0.2500 -vdw 28 0.0000 0.0000 -vdw 29 0.0000 0.0000 -vdw 30 3.7750 0.2070 -vdw 31 3.9050 0.1180 -vdw 32 3.8000 0.1700 -vdw 33 3.8000 0.1180 -vdw 34 3.8000 0.1700 -vdw 35 3.8000 0.1180 -vdw 36 3.2000 0.1700 -vdw 37 3.6500 0.1500 -vdw 38 3.7750 0.2070 -vdw 39 3.8500 0.0800 -vdw 40 3.8000 0.0500 -vdw 41 3.0000 0.1700 -vdw 42 3.8000 0.1700 -vdw 43 3.8000 0.1180 -vdw 44 3.8000 0.1180 -vdw 45 3.4000 0.3000 -vdw 46 3.8000 0.0800 -vdw 47 3.4700 0.3000 -vdw 48 3.8000 0.0500 -vdw 49 3.4700 0.2660 -vdw 50 3.5600 0.3950 -vdw 51 2.9300 0.2800 -vdw 52 3.8100 0.1600 -vdw 53 2.9600 0.2100 -vdw 54 3.2500 0.1700 -vdw 55 3.8000 0.1150 -vdw 56 3.8000 0.1700 -vdw 57 0.0000 0.0000 -vdw 58 2.5560 0.0200 -vdw 59 2.7800 0.0690 -vdw 60 3.4010 0.2339 -vdw 61 3.6240 0.3170 -vdw 62 3.9350 0.4330 -vdw 63 3.15061 0.1521 -vdw 64 0.0000 0.0000 -vdw 65 3.15365 0.1550 -vdw 66 0.0000 0.0000 -vdw 67 0.0000 0.0000 -vdw 68 3.1760 0.1500 -vdw 69 0.0000 0.0000 -vdw 70 3.2700 0.1000 -vdw 71 0.0000 0.0000 -vdw 72 0.0000 0.0000 -vdw 73 3.1200 0.1600 -vdw 74 0.0000 0.0000 -vdw 75 0.0000 0.0000 -vdw 76 3.16557 0.1554 -vdw 77 0.0000 0.0000 -vdw 78 3.4200 0.1700 -vdw 79 0.0000 0.0000 -vdw 80 3.5000 0.0660 -vdw 81 3.5000 0.0660 -vdw 82 3.5000 0.0660 vdw 83 3.5000 0.0660 -vdw 84 3.5000 0.0660 vdw 85 2.5000 0.0300 -vdw 86 3.5500 0.0760 -vdw 87 3.5500 0.0760 -vdw 88 3.5500 0.0760 -vdw 89 2.4200 0.0300 -vdw 90 3.5500 0.0700 -vdw 91 2.4200 0.0300 -vdw 92 3.5500 0.0700 -vdw 93 3.5000 0.0660 -vdw 94 3.5000 0.0660 -vdw 95 3.5500 0.0760 -vdw 96 3.1200 0.1700 -vdw 97 0.0000 0.0000 -vdw 98 2.5000 0.0300 -vdw 99 3.5000 0.0660 -vdw 100 3.5000 0.0660 -vdw 101 3.5000 0.0660 -vdw 102 3.5000 0.0660 -vdw 103 3.2500 0.0620 -vdw 104 3.0700 0.1700 -vdw 105 0.0000 0.0000 -vdw 106 2.9400 0.0610 -vdw 107 2.5000 0.0300 -vdw 108 3.5500 0.0700 -vdw 109 3.0700 0.1700 -vdw 110 0.0000 0.0000 -vdw 111 3.0700 0.1700 -vdw 112 0.0000 0.0000 -vdw 113 3.0700 0.1700 -vdw 114 0.0000 0.0000 -vdw 115 3.5000 0.0660 -vdw 116 3.5000 0.0660 -vdw 117 3.5000 0.0660 -vdw 118 2.5000 0.0300 -vdw 119 2.9000 0.1400 -vdw 120 3.5500 0.0760 -vdw 121 2.9000 0.1400 -vdw 122 2.9000 0.1400 -vdw 123 3.5000 0.0660 -vdw 124 3.5000 0.0660 -vdw 125 3.5000 0.0660 -vdw 126 3.5000 0.0660 -vdw 127 2.5000 0.0300 -vdw 128 2.9000 0.1400 -vdw 129 3.0700 0.1700 -vdw 130 0.0000 0.0000 -vdw 131 3.5000 0.0660 -vdw 132 2.5000 0.0300 -vdw 133 3.5000 0.0660 -vdw 134 2.5000 0.0300 -vdw 135 3.5000 0.0660 -vdw 136 2.5000 0.0300 -vdw 137 3.5000 0.0660 -vdw 138 2.5000 0.0300 -vdw 139 3.5000 0.0660 -vdw 140 3.5000 0.0660 -vdw 141 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836 3.5000 0.0660 -vdw 837 3.5000 0.0660 -vdw 838 3.7500 0.6000 -vdw 839 2.5000 0.0300 -vdw 840 3.2500 0.1700 -vdw 841 3.5500 0.0700 -vdw 842 3.5500 0.0700 -vdw 843 3.2500 0.1700 -vdw 844 3.5500 0.0700 -vdw 845 3.7500 0.1050 -vdw 846 2.9600 0.2100 -vdw 847 3.2500 0.1700 -vdw 848 3.5000 0.0660 -vdw 849 3.5000 0.0660 -vdw 850 3.5000 0.0660 -vdw 851 3.5000 0.0660 -vdw 852 2.4200 0.0150 -vdw 853 3.7500 0.1050 -vdw 854 2.9600 0.2100 -vdw 855 2.4200 0.0150 -vdw 856 3.5000 0.0660 -vdw 857 3.5000 0.0660 -vdw 858 3.5000 0.0660 -vdw 859 3.5000 0.0660 -vdw 860 3.5000 0.0660 -vdw 861 3.5000 0.0660 -vdw 862 3.5000 0.0660 -vdw 863 3.5000 0.0660 -vdw 864 3.5000 0.0660 -vdw 865 3.5000 0.0660 -vdw 866 4.0000 0.1000 -vdw 867 4.0000 0.1000 -vdw 868 4.0000 0.1000 -vdw 869 4.0000 0.1000 -vdw 870 2.5000 0.0300 -vdw 871 3.5000 0.0660 -vdw 872 3.5000 0.0660 -vdw 873 3.5000 0.0660 -vdw 874 3.5000 0.0660 -vdw 875 3.0800 0.7200 -vdw 876 4.1800 0.11779 -vdw 877 4.5100 0.0900 -vdw 878 5.1500 0.0700 -vdw 879 2.7000 0.018279 -vdw 880 3.3500 0.002772 -vdw 881 4.0600 0.000328 -vdw 882 4.3200 0.000171 -vdw 883 4.8200 0.000081 -vdw 884 2.9100 0.875044 -vdw 885 3.4700 0.449657 -vdw 886 3.8200 0.118226 -vdw 887 4.1800 0.047096 -vdw 888 3.5000 0.0660 -vdw 889 3.5000 0.0660 -vdw 890 3.5000 0.0660 -vdw 891 3.5000 0.0660 -vdw 892 2.5000 0.0300 -vdw 893 3.2500 0.1700 -vdw 894 3.5500 0.0700 -vdw 895 3.2500 0.1700 -vdw 896 3.5500 0.0700 -vdw 897 3.5500 0.0760 -vdw 898 3.5500 0.0760 -vdw 899 2.4200 0.0300 -vdw 900 3.3000 0.0860 -vdw 901 3.3000 0.0860 -vdw 902 3.3000 0.0860 -vdw 903 3.3000 0.0860 -vdw 904 3.3000 0.0860 -vdw 905 2.9600 0.2100 -vdw 906 3.5000 0.0660 ################################## @@ -1001,385 +98,8 @@ vdw 906 3.5000 0.0660 ################################## -bond 1 2 367.00 1.3800 -bond 1 3 420.00 1.3570 -bond 1 13 367.00 1.3600 -bond 1 19 450.00 1.2790 -bond 1 25 300.00 0.3000 -bond 1 47 420.00 1.3400 -bond 1 48 420.00 1.3540 -bond 1 82 420.00 1.3540 -bond 1 83 420.00 1.3540 -bond 1 84 420.00 1.3540 -bond 1 87 420.00 1.3540 -bond 1 88 420.00 1.3540 -bond 1 108 461.00 1.5700 -bond 2 2 260.00 1.5260 -bond 2 3 317.00 1.5220 -bond 2 5 386.00 1.4250 -bond 2 6 260.00 1.5260 -bond 2 10 260.00 1.5260 -bond 2 11 317.00 1.5000 -bond 2 12 317.00 1.5100 -bond 2 13 260.00 1.5260 -bond 2 14 317.00 1.5000 -bond 2 15 222.00 1.8100 -bond 2 16 222.00 1.8100 -bond 2 20 320.00 1.4250 -bond 2 24 337.00 1.4490 -bond 2 44 382.00 1.4480 -bond 2 48 317.00 1.5100 -bond 2 51 260.00 1.5260 -bond 2 53 367.00 1.4710 -bond 2 55 337.00 1.4630 -bond 2 80 317.00 1.4950 -bond 3 3 350.00 1.5100 -bond 3 4 570.00 1.2290 -bond 3 5 450.00 1.3640 -bond 3 6 317.00 1.5220 -bond 3 10 317.00 1.5220 -bond 3 12 469.00 1.4000 -bond 3 13 317.00 1.5220 -bond 3 19 400.00 1.4440 -bond 3 20 214.00 1.3270 -bond 3 21 300.00 1.7900 -bond 3 24 490.00 1.3350 -bond 3 44 317.00 1.5220 -bond 3 46 340.00 1.0900 -bond 3 47 410.00 1.4440 -bond 3 48 400.00 1.4900 -bond 3 50 385.00 1.4600 -bond 3 52 656.00 1.2500 -bond 3 56 457.00 1.3580 -bond 3 57 418.00 1.3880 -bond 3 60 447.00 1.4190 -bond 3 65 300.00 1.9800 -bond 3 84 400.00 1.4900 -bond 3 86 385.00 1.4600 -bond 3 105 424.00 1.3830 -bond 3 107 490.00 1.3350 -bond 4 25 553.00 0.3000 -bond 4 64 525.00 1.4800 -bond 4 89 570.00 1.2290 -bond 4 110 700.00 1.1710 -bond 5 6 386.00 1.4250 -bond 5 7 553.00 0.9450 -bond 5 10 386.00 1.4250 -bond 5 13 320.00 1.4100 -bond 5 20 250.00 1.4700 -bond 5 24 400.00 1.3800 -bond 5 25 340.00 0.3000 -bond 5 44 320.00 1.4500 -bond 5 47 450.00 1.3700 -bond 5 48 450.00 1.3640 -bond 5 51 320.00 1.3800 -bond 5 64 230.00 1.6100 -bond 5 79 450.00 1.6700 -bond 5 106 94.00 1.8000 -bond 5 108 374.00 1.6400 -bond 6 6 260.00 1.5260 -bond 6 10 260.00 1.5260 -bond 6 11 317.00 1.5000 -bond 6 13 260.00 1.5260 -bond 6 14 317.00 1.5000 -bond 6 15 222.00 1.8100 -bond 6 16 222.00 1.8100 -bond 6 20 320.00 1.4250 -bond 6 24 337.00 1.4490 -bond 6 44 382.00 1.4480 -bond 6 47 317.00 1.5100 -bond 6 51 260.00 1.5260 -bond 6 53 367.00 1.4710 -bond 6 55 337.00 1.4630 -bond 6 79 222.00 1.8100 -bond 6 105 337.00 1.4750 -bond 7 20 553.00 0.9450 -bond 7 25 340.00 0.1000 -bond 9 9 530.00 1.3400 -bond 9 11 530.00 1.3400 -bond 9 14 530.00 1.3400 -bond 10 10 260.00 1.5260 -bond 10 11 317.00 1.5000 -bond 10 14 317.00 1.5000 -bond 10 20 320.00 1.4250 -bond 10 24 337.00 1.4490 -bond 10 44 382.00 1.4480 -bond 10 105 337.00 1.4750 -bond 11 11 530.00 1.3400 -bond 11 13 317.00 1.5000 -bond 11 14 530.00 1.3400 -bond 11 79 222.00 1.7600 -bond 12 12 469.00 1.4000 -bond 12 48 469.00 1.4000 -bond 12 60 469.00 1.4000 -bond 12 81 469.00 1.4000 -bond 13 13 268.00 1.5290 -bond 13 14 317.00 1.5000 -bond 13 15 222.00 1.8100 -bond 13 16 222.00 1.8100 -bond 13 18 390.00 1.4300 -bond 13 19 390.00 1.4700 -bond 13 20 320.00 1.4100 -bond 13 21 245.00 1.7810 -bond 13 22 340.00 1.7900 -bond 13 24 337.00 1.4490 -bond 13 25 340.00 0.3000 -bond 13 44 382.00 1.4480 bond 13 46 340.00 1.0900 -bond 13 47 317.00 1.5100 -bond 13 48 317.00 1.5100 -bond 13 50 317.00 1.5100 -bond 13 51 268.00 1.5290 -bond 13 53 367.00 1.4710 -bond 13 55 337.00 1.4630 -bond 13 56 337.00 1.4490 -bond 13 57 337.00 1.4750 -bond 13 60 317.00 1.5100 -bond 13 64 212.00 1.8430 -bond 13 65 245.00 1.9450 -bond 13 66 200.00 2.1900 -bond 13 79 340.00 1.7700 -bond 13 80 317.00 1.4950 -bond 13 83 317.00 1.5040 -bond 13 84 317.00 1.5040 -bond 13 85 317.00 1.5040 -bond 13 87 317.00 1.4950 -bond 13 90 337.00 1.4490 -bond 13 91 280.00 1.5100 -bond 13 95 532.80 1.4600 -bond 13 101 382.00 1.4480 -bond 13 102 375.00 1.4900 -bond 13 104 212.00 1.8200 -bond 13 105 337.00 1.4750 -bond 13 107 337.00 1.4490 -bond 13 108 187.00 1.8600 -bond 13 109 317.00 1.5100 -bond 14 14 530.00 1.3400 -bond 15 17 274.00 1.3360 -bond 15 48 250.00 1.7400 -bond 16 16 166.00 2.0380 -bond 16 19 300.00 1.6850 -bond 16 24 250.00 1.7300 -bond 16 25 340.00 0.5000 -bond 16 47 250.00 1.7600 -bond 16 48 250.00 1.7600 -bond 16 61 250.00 1.7300 -bond 16 82 250.00 1.7600 -bond 16 84 250.00 1.7400 -bond 16 91 222.00 1.8100 -bond 16 108 144.00 2.1500 -bond 17 25 340.00 0.1000 -bond 18 18 550.00 1.1200 -bond 18 19 650.00 1.1570 -bond 18 48 400.00 1.4100 -bond 18 56 550.00 1.2400 -bond 19 19 1150.00 1.2100 -bond 19 21 330.00 1.6370 -bond 19 46 420.00 1.0800 -bond 19 47 400.00 1.4260 -bond 19 48 400.00 1.4510 -bond 19 50 400.00 1.4260 -bond 19 65 330.00 1.7840 -bond 19 88 400.00 1.4510 -bond 19 91 400.00 1.4510 -bond 20 20 250.00 1.4700 -bond 20 21 200.00 1.6900 -bond 20 24 320.00 1.4500 -bond 20 25 340.00 0.3000 -bond 20 44 320.00 1.4500 -bond 20 47 450.00 1.3700 -bond 20 48 450.00 1.3640 -bond 20 51 320.00 1.3800 -bond 20 60 340.00 1.3600 -bond 20 61 462.00 1.3990 -bond 20 64 230.00 1.6100 -bond 20 82 462.00 1.3570 -bond 20 84 340.00 1.3600 -bond 20 108 374.00 1.6400 -bond 21 25 300.00 0.3000 -bond 21 47 300.00 1.7250 -bond 21 48 300.00 1.7250 -bond 21 82 300.00 1.7250 -bond 21 83 300.00 1.7250 -bond 21 84 300.00 1.7250 -bond 21 87 300.00 1.7250 -bond 21 88 300.00 1.7250 -bond 21 108 223.00 2.0200 -bond 22 23 700.00 1.5300 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382.00 1.4480 -bond 44 108 266.00 1.7400 -bond 45 53 434.00 1.0100 -bond 45 55 434.00 1.0100 -bond 45 56 434.00 1.0100 -bond 45 57 434.00 1.0100 -bond 45 101 434.00 1.0100 -bond 45 105 434.00 1.0100 -bond 45 108 166.00 1.4800 -bond 46 47 340.00 1.0800 -bond 46 50 340.00 1.0800 -bond 46 51 340.00 1.0900 -bond 46 80 340.00 1.0800 -bond 46 91 340.00 1.0880 -bond 46 95 532.80 1.0840 -bond 46 108 166.00 1.4800 -bond 46 109 340.00 1.0800 -bond 47 47 549.00 1.3400 -bond 47 48 427.00 1.4330 -bond 47 50 549.00 1.3400 -bond 47 57 448.00 1.3650 -bond 47 58 367.00 1.0800 -bond 47 65 300.00 1.9000 -bond 47 66 250.00 2.0800 -bond 47 86 385.00 1.4600 -bond 47 91 317.00 1.5100 -bond 47 105 448.00 1.3650 -bond 47 110 700.00 1.3050 -bond 48 48 469.00 1.4000 -bond 48 49 367.00 1.0800 -bond 48 50 427.00 1.4330 -bond 48 53 400.00 1.4500 -bond 48 55 481.00 1.3400 -bond 48 56 483.00 1.3390 -bond 48 57 427.00 1.3810 -bond 48 60 469.00 1.4040 -bond 48 61 414.00 1.3910 -bond 48 64 220.00 1.7800 -bond 48 65 300.00 1.8700 -bond 48 66 250.00 2.0800 -bond 48 79 340.00 1.7700 -bond 48 81 469.00 1.4000 -bond 48 84 546.00 1.3670 -bond 48 86 469.00 1.4000 -bond 48 88 469.00 1.4210 -bond 48 91 317.00 1.4900 -bond 48 101 382.00 1.3850 -bond 48 102 400.00 1.4600 -bond 48 109 427.00 1.4330 -bond 49 59 367.00 1.0800 -bond 49 62 340.00 1.0800 -bond 49 82 367.00 1.0800 -bond 49 83 367.00 1.0800 -bond 49 84 367.00 1.0800 -bond 49 85 367.00 1.0800 -bond 49 87 367.00 1.0800 -bond 49 88 367.00 1.0800 -bond 50 50 385.00 1.4600 -bond 50 56 457.00 1.2900 -bond 50 84 549.00 1.3650 -bond 50 109 385.00 1.4600 -bond 51 105 337.00 1.4750 -bond 52 64 525.00 1.4800 -bond 53 54 434.00 1.0100 -bond 54 55 434.00 1.0100 -bond 55 59 481.00 1.3400 -bond 55 82 481.00 1.3400 -bond 56 56 500.00 1.3200 -bond 56 59 502.00 1.3240 -bond 56 60 461.00 1.3540 -bond 56 82 461.00 1.3540 -bond 56 86 483.00 1.3390 -bond 56 103 550.00 1.2100 -bond 56 109 457.00 1.2900 -bond 57 60 436.00 1.3740 -bond 57 61 400.00 1.3490 -bond 57 62 440.00 1.3710 -bond 57 81 428.00 1.3800 -bond 57 82 477.00 1.3430 -bond 57 84 427.00 1.3810 -bond 57 85 427.00 1.3810 -bond 57 86 385.00 1.4400 -bond 58 83 367.00 1.0800 -bond 58 84 367.00 1.0800 -bond 59 63 367.00 1.0800 -bond 60 60 520.00 1.3700 -bond 60 61 414.00 1.3910 -bond 60 80 388.00 1.4590 -bond 60 81 447.00 1.4190 -bond 60 87 469.00 1.4240 -bond 60 105 436.00 1.3740 -bond 61 61 400.00 1.2800 -bond 61 62 529.00 1.3040 -bond 61 82 488.00 1.3350 -bond 61 83 410.00 1.3940 -bond 61 84 410.00 1.3940 -bond 61 88 410.00 1.3200 -bond 62 63 367.00 1.0800 -bond 62 105 440.00 1.3710 -bond 63 82 367.00 1.0800 -bond 64 108 108.00 2.2500 -bond 65 82 300.00 1.8700 -bond 65 83 300.00 1.8700 -bond 65 84 300.00 1.8700 -bond 65 87 300.00 1.8700 -bond 65 88 300.00 1.8700 -bond 65 108 151.00 2.1900 -bond 66 82 250.00 2.0800 -bond 66 83 250.00 2.0800 -bond 66 84 250.00 2.0800 -bond 66 87 250.00 2.0800 -bond 66 88 250.00 2.0800 -bond 66 108 108.00 2.4400 -bond 77 78 500.00 1.8000 -bond 80 84 546.00 1.3520 -bond 82 86 385.00 1.4600 -bond 82 87 520.00 1.3700 -bond 83 84 520.00 1.3700 -bond 83 86 385.00 1.4600 -bond 84 84 512.00 1.3750 -bond 84 86 385.00 1.4600 -bond 84 87 546.00 1.3670 -bond 84 88 520.00 1.3700 -bond 85 85 520.00 1.3700 -bond 86 86 385.00 1.4600 -bond 86 87 385.00 1.4600 -bond 86 88 385.00 1.4600 -bond 87 87 469.00 1.4240 -bond 87 88 469.00 1.4240 -bond 89 90 490.00 1.3350 -bond 89 91 317.00 1.5220 -bond 90 91 337.00 1.4490 -bond 91 91 260.00 1.5200 -bond 102 103 550.00 1.2250 -bond 108 108 94.00 2.3200 -bond 109 109 549.00 1.3450 ################################ @@ -1389,2040 +109,8 @@ bond 109 109 549.00 1.3450 ################################ -angle 25 1 25 33.00 109.47 -angle 1 2 2 50.00 109.50 -angle 2 2 2 63.00 112.40 -angle 2 2 3 63.00 112.40 -angle 2 2 5 80.00 109.50 -angle 2 2 6 63.00 112.40 -angle 6 2 6 63.00 112.40 -angle 5 2 6 80.00 109.50 -angle 2 2 10 63.00 112.40 -angle 3 2 10 63.00 112.40 -angle 6 2 10 63.00 112.40 -angle 10 2 10 63.00 112.40 -angle 5 2 10 80.00 109.50 -angle 10 2 12 63.00 114.00 -angle 6 2 13 63.00 112.40 -angle 10 2 15 50.00 108.60 -angle 2 2 16 50.00 114.70 -angle 10 2 16 50.00 114.70 -angle 2 2 20 80.00 109.50 -angle 6 2 20 80.00 109.50 -angle 10 2 20 80.00 109.50 -angle 3 2 24 80.00 110.30 -angle 2 2 24 80.00 111.20 -angle 2 2 44 56.20 109.47 -angle 6 2 44 56.20 109.47 -angle 10 2 44 56.20 109.47 -angle 13 2 44 56.20 109.47 -angle 3 2 44 80.00 111.20 -angle 2 2 48 63.00 112.40 -angle 10 2 48 63.00 114.00 -angle 2 2 51 63.00 112.40 -angle 6 2 51 63.00 112.40 -angle 2 2 53 80.00 111.20 -angle 2 2 55 80.00 111.20 -angle 10 2 80 63.00 115.60 -angle 2 3 4 80.00 120.40 -angle 1 3 4 80.00 121.00 -angle 3 3 4 80.00 121.40 -angle 4 3 4 80.00 126.00 -angle 4 3 5 80.00 121.00 -angle 4 3 6 80.00 120.40 -angle 5 3 10 70.00 115.00 -angle 4 3 10 80.00 120.40 -angle 5 3 12 70.00 120.00 -angle 12 3 12 85.00 120.00 -angle 5 3 13 70.00 108.00 -angle 13 3 13 70.00 116.00 -angle 1 3 13 80.00 111.00 -angle 3 3 13 80.00 117.20 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107.00 -angle 13 79 44 62.00 102.00 -angle 23 79 44 74.00 108.90 -angle 13 79 48 62.00 102.00 -angle 23 79 48 74.00 107.20 -angle 5 79 48 75.00 96.40 -angle 24 79 48 100.00 103.00 -angle 13 79 82 62.00 102.00 -angle 46 80 60 35.00 126.80 -angle 2 80 60 70.00 128.60 -angle 13 80 60 70.00 128.60 -angle 46 80 84 35.00 126.80 -angle 2 80 84 70.00 125.00 -angle 13 80 84 70.00 125.00 -angle 60 80 84 85.00 106.40 -angle 12 81 57 70.00 132.80 -angle 48 81 57 70.00 132.80 -angle 57 81 60 70.00 104.40 -angle 12 81 60 85.00 122.70 -angle 48 81 60 85.00 122.70 -angle 13 82 16 70.00 125.00 -angle 16 82 24 70.00 125.00 -angle 16 82 44 70.00 120.20 -angle 20 82 49 35.00 117.00 -angle 16 82 49 35.00 125.00 -angle 49 82 57 35.00 120.00 -angle 57 82 57 70.00 120.00 -angle 13 82 57 70.00 125.00 -angle 48 82 57 70.00 125.00 -angle 56 82 57 70.00 126.20 -angle 49 82 61 35.00 120.00 -angle 16 82 61 70.00 113.60 -angle 16 82 61 70.00 115.00 -angle 20 82 61 70.00 115.00 -angle 57 82 61 70.00 120.00 -angle 13 82 61 70.00 125.00 -angle 44 82 61 70.00 126.10 -angle 24 82 61 70.00 126.20 -angle 57 82 79 70.00 120.00 -angle 61 82 79 70.00 120.00 -angle 20 82 86 70.00 122.00 -angle 61 82 86 70.00 130.00 -angle 57 82 87 70.00 106.20 -angle 56 82 87 70.00 127.70 -angle 49 83 61 35.00 120.00 -angle 48 83 61 70.00 111.00 -angle 13 83 61 70.00 124.50 -angle 49 83 84 35.00 128.20 -angle 61 83 84 70.00 111.00 -angle 13 83 84 70.00 130.70 -angle 13 84 16 70.00 125.00 -angle 13 84 20 70.00 121.60 -angle 16 84 24 70.00 125.00 -angle 20 84 49 35.00 113.40 -angle 16 84 49 35.00 125.00 -angle 48 84 49 35.00 130.70 -angle 49 84 50 35.00 130.70 -angle 20 84 50 70.00 110.00 -angle 49 84 57 35.00 121.60 -angle 13 84 57 70.00 121.60 -angle 48 84 57 70.00 121.60 -angle 3 84 57 85.00 120.00 -angle 57 84 58 35.00 120.00 -angle 13 84 61 70.00 118.90 -angle 49 84 80 35.00 120.00 -angle 57 84 80 70.00 108.70 -angle 49 84 83 35.00 130.70 -angle 57 84 83 70.00 106.30 -angle 20 84 83 70.00 108.00 -angle 16 84 83 70.00 111.00 -angle 13 84 83 70.00 130.70 -angle 13 84 84 70.00 120.00 -angle 57 84 84 70.00 120.00 -angle 61 84 84 70.00 120.00 -angle 20 84 86 70.00 121.60 -angle 57 84 86 70.00 121.60 -angle 49 84 87 35.00 132.10 -angle 57 84 87 70.00 107.70 -angle 20 84 87 70.00 110.60 -angle 16 84 87 70.00 111.00 -angle 61 84 87 70.00 111.90 -angle 13 84 87 70.00 132.10 -angle 48 84 87 70.00 132.10 -angle 86 84 87 70.00 132.10 -angle 3 84 87 85.00 120.00 -angle 49 85 57 35.00 120.00 -angle 13 85 57 70.00 121.60 -angle 49 85 85 35.00 130.70 -angle 57 85 85 70.00 106.30 -angle 13 85 85 70.00 130.70 -angle 48 86 48 63.00 120.00 -angle 48 86 56 70.00 124.00 -angle 48 86 82 63.00 120.00 -angle 48 86 83 63.00 120.00 -angle 48 86 84 63.00 120.00 -angle 48 86 86 63.00 120.00 -angle 56 86 86 70.00 124.00 -angle 48 86 87 63.00 120.00 -angle 48 86 88 63.00 120.00 -angle 49 87 60 35.00 120.00 -angle 46 87 60 35.00 126.80 -angle 13 87 60 70.00 128.60 -angle 49 87 84 35.00 125.70 -angle 46 87 84 35.00 126.80 -angle 84 87 84 70.00 103.80 -angle 82 87 84 70.00 110.40 -angle 2 87 84 70.00 125.00 -angle 13 87 84 70.00 125.00 -angle 3 87 84 70.00 130.00 -angle 60 87 84 85.00 106.40 -angle 84 87 86 70.00 125.70 -angle 49 87 87 35.00 127.50 -angle 60 87 87 70.00 107.30 -angle 84 87 87 70.00 107.30 -angle 86 87 87 70.00 127.50 -angle 84 87 88 70.00 103.80 -angle 48 88 49 35.00 128.60 -angle 49 88 61 35.00 118.90 -angle 13 88 61 70.00 118.90 -angle 19 88 61 70.00 118.90 -angle 61 88 87 70.00 111.90 -angle 4 89 90 80.00 134.00 -angle 90 89 91 70.00 91.00 -angle 4 89 91 80.00 134.00 -angle 13 90 89 55.00 127.00 -angle 89 90 91 50.00 94.00 -angle 13 90 91 50.00 126.00 -angle 24 91 46 35.00 108.00 -angle 13 91 46 35.00 114.30 -angle 44 91 46 35.00 114.30 -angle 46 91 46 35.00 114.30 -angle 16 91 46 37.50 108.00 -angle 46 91 47 35.00 109.50 -angle 46 91 89 37.50 110.00 -angle 24 91 89 70.00 117.00 -angle 46 91 90 35.00 111.00 -angle 16 91 90 55.00 109.00 -angle 91 91 91 30.00 79.20 -angle 13 91 91 37.50 117.20 -angle 44 91 91 37.50 117.20 -angle 46 91 91 37.50 117.20 -angle 24 91 91 37.50 126.00 -angle 16 91 91 55.00 128.00 -angle 89 91 91 63.00 85.00 -angle 47 91 91 63.00 114.00 -angle 90 91 91 80.00 89.00 -angle 13 95 13 172.80 120.00 -angle 13 95 46 144.00 120.00 -angle 13 101 45 35.00 109.50 -angle 45 101 45 43.60 106.40 -angle 45 101 48 50.00 112.50 -angle 13 101 48 50.00 120.50 -angle 13 102 103 80.00 117.50 -angle 48 102 103 80.00 117.50 -angle 103 102 103 80.00 125.00 -angle 25 103 25 10.00 109.50 -angle 25 103 102 10.00 109.50 -angle 13 104 13 45.00 109.50 -angle 3 105 10 70.00 117.60 -angle 3 105 13 70.00 117.60 -angle 3 105 45 35.00 119.20 -angle 45 105 47 35.00 119.20 -angle 13 105 47 70.00 121.20 -angle 3 105 47 70.00 121.60 -angle 3 105 51 70.00 117.60 -angle 47 105 51 70.00 121.20 -angle 45 105 60 30.00 125.80 -angle 6 105 60 70.00 125.80 -angle 10 105 60 70.00 125.80 -angle 13 105 60 70.00 125.80 -angle 51 105 60 70.00 125.80 -angle 45 105 62 30.00 128.80 -angle 60 105 62 70.00 105.40 -angle 6 105 62 70.00 128.80 -angle 10 105 62 70.00 128.80 -angle 13 105 62 70.00 128.80 -angle 51 105 62 70.00 128.80 -angle 4 106 24 20.00 109.50 -angle 24 106 24 20.00 109.50 -angle 13 107 13 50.00 118.00 -angle 3 107 13 50.00 121.90 -angle 1 108 13 35.00 110.50 -angle 13 108 13 60.00 110.00 -angle 13 108 20 60.00 100.00 -angle 20 108 20 60.00 110.00 -angle 13 108 21 35.00 110.50 -angle 45 108 45 35.00 109.50 -angle 13 108 45 35.00 110.50 -angle 46 108 46 35.00 109.50 -angle 13 108 46 35.00 110.50 -angle 13 108 65 35.00 110.50 -angle 13 108 66 35.00 110.50 -angle 13 108 108 50.00 112.00 -angle 46 109 48 35.00 123.30 -angle 46 109 50 35.00 120.00 -angle 13 109 50 70.00 124.00 -angle 46 109 109 35.00 120.00 -angle 13 109 109 70.00 124.00 -angle 50 109 109 70.00 124.00 -angle 48 109 109 85.00 117.00 -angle 4 110 47 160.00 180.00 -angle 47 110 47 160.00 180.00 - - - ################################ - ## ## - ## Urey-Bradley Parameters ## - ## ## - ################################ - - -ureybrad 35 34 35 38.25 1.5537 - - - ##################################### - ## ## - ## Improper Torsional Parameters ## - ## ## - ##################################### - - -imptors 0 0 3 4 21.000 180.0 2 -imptors 0 0 3 52 21.000 180.0 2 -imptors 0 0 24 0 5.000 180.0 2 -imptors 0 0 47 0 30.000 180.0 2 -imptors 0 0 48 0 5.000 180.0 2 - - - ############################ - ## ## - ## Torsional Parameters ## - ## ## - ############################ - - - ################################################################### - ## ## - ## Alternative Torsional Parameter Values for Use with OPLS-AA ## - ## ## - ## For some torsions, OPLS-AA has multiple possible parameter ## - ## values; the list below shows functional groups for which ## - ## these alternate (commented) values should be preferred; the ## - ## values are in the same order as in the full parameter list ## - ## ## - ## 4 3 3 36 generic (default) ## - ## 4 3 3 36 dicarbonyls ## - ## 36 3 3 36 hydrocarbon (default) ## - ## 36 3 3 36 dicarbonyls ## - ## 13 3 5 7 carboxylic acid (default) ## - ## 13 3 5 7 1,2-diacid monoanion ## - ## 4 3 13 13 peptide (default) ## - ## 4 3 13 13 propanamide ## - ## 4 3 13 13 carboxylic acid ## - ## 4 3 13 13 dicarboxylic acid ## - ## 4 3 13 13 aldyhyde, ketone, acyl halide ## - ## 4 3 13 13 1,2-diacid monoanion ## - ## 5 3 13 13 carboxylic acid (default) ## - ## 5 3 13 13 dicarboxylic acid ## - ## 35 3 13 13 peptide psi' (default) ## - ## 35 3 13 13 propanamide ## - ## 35 3 13 13 beta-3-peptide, last psi ## - ## 4 3 29 13 esters (default) ## - ## 4 3 29 13 benzoic esters ## - ## 7 5 13 13 alcohols (default) ## - ## 7 5 13 13 trifluoroethanol ## - ## 7 5 13 13 hexopyranoses ## - ## 7 5 13 36 alcohols (default) ## - ## 7 5 13 36 axial cyclohexanol ## - ## 7 5 13 36 trifluoroethanol ## - ## 0 13 13 13 alcohols, ethers (default) ## - ## 0 13 13 13 hexopyranoses ## - ## 3 13 13 3 dicarboxylic acid (default) ## - ## 3 13 13 3 1,2-diacid monoanion ## - ## 3 13 13 13 butanamide (default) ## - ## 3 13 13 13 carboxylate ion ## - ## 3 13 13 13 aldyhyde, ketone, acyl halide ## - ## 3 13 13 36 all carbonyls (default) ## - ## 3 13 13 36 dicarboxylic acid ## - ## 3 13 13 36 aldehyde, ketone, acyl halide ## - ## 5 13 13 5 diols only (default) ## - ## 5 13 13 5 triols only ## - ## 5 13 13 5 hexopyranoses ## - ## 13 13 13 13 hydrocarbon (default) ## - ## 13 13 13 13 perfluoroalkane ## - ## 13 13 13 35 peptide chi-1 (default) ## - ## 13 13 13 35 N-propylformamide ## - ## 36 13 13 69 generic (default) ## - ## 36 13 13 69 sulfone ## - ## 13 13 33 13 amine (default) ## - ## 13 13 33 13 exocyclic amine ## - ## 13 13 33 13 exocyclic 1,4-diamine ## - ## 13 13 33 34 amine (default) ## - ## 13 13 33 34 azetidine, 4-ring ## - ## 13 13 33 34 pyrrolidine, 5-ring ## - ## 13 13 33 34 cyclic amine ## - ## 13 13 33 34 cyclic 1,4-diamine ## - ## 13 13 35 3 peptide phi' (default) ## - ## 13 13 35 3 N-ethylformamide ## - ## 13 13 35 3 beta-3-peptide, first theta tors ## - ## 13 13 35 13 proline, CD-N-CA-CB (default) ## - ## 13 13 35 13 proline, CG-CD-N-CA ## - ## 36 13 35 3 peptide phi'' (default) ## - ## 36 13 35 3 N-methylformamide ## - ## 13 13 47 0 imidazole, indole, purine (default) ## - ## 13 13 47 0 nucleoside chi ## - ## 13 13 47 52 nucleoside (default) ## - ## 13 13 47 52 imidazole, indole, purine ## - ## 29 13 47 0 imidazole, indole, purine (default) ## - ## 29 13 47 0 nucleoside chi ## - ## 29 13 95 52 nucleoside (default) ## - ## 29 13 95 52 imidazole, indole, purine ## - ## 13 13 97 13 generic (default) ## - ## 13 13 97 13 generic ## - ## 17 15 38 0 aromatic thiol (default) ## - ## 17 15 38 0 aromatic thiol, N-C-S-H ## - ## 13 29 54 42 phosphonates (default) ## - ## 13 29 54 42 dimethyl phosphate ## - ## 34 35 72 16 diaryl amine (default) ## - ## 34 35 72 16 aniline-like ## - ## 34 35 72 29 diaryl amine (default) ## - ## 34 35 72 29 aniline-like ## - ## 13 40 40 37 diene (default) ## - ## 13 40 40 37 2-methyl-1,3-butadiene ## - ## 0 46 72 0 generic (default) ## - ## 0 46 72 0 generic ## - ## 0 47 72 0 generic (default) ## - ## 0 47 72 0 generic ## - ## 0 47 74 0 generic (default) ## - ## 0 47 74 0 generic ## - ## 0 47 74 0 generic ## - ## 0 51 72 0 generic (default) ## - ## 0 51 72 0 HA-CR-NB-?? or N?-CR-NB-?? ## - ## 0 72 77 0 generic (default) ## - ## 0 72 77 0 biphenyl-like, N-C-C-C ## - ## ## - ################################################################### - - -torsion 0 2 2 2 -2.500 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 0 2 2 6 -2.500 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 1 2 2 2 -2.000 0.0 1 0.700 180.0 2 3.000 0.0 3 -torsion 1 2 2 6 -2.000 0.0 1 0.700 180.0 2 3.000 0.0 3 -torsion 2 2 2 2 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 2 2 2 6 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 2 2 2 10 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 2 2 2 13 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 2 2 2 65 -2.000 0.0 1 0.500 180.0 2 3.250 0.0 3 -torsion 6 2 2 6 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 6 2 2 65 -2.000 0.0 1 0.500 180.0 2 3.250 0.0 3 -torsion 10 2 2 10 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 2 2 5 7 0.300 0.0 1 0.000 180.0 2 1.300 0.0 3 -torsion 6 2 5 7 0.300 0.0 1 0.000 180.0 2 1.300 0.0 3 -torsion 10 2 5 7 0.300 0.0 1 0.000 180.0 2 1.300 0.0 3 -torsion 0 2 10 2 -2.500 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 2 2 10 2 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 2 2 13 2 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 6 2 20 2 -7.400 0.0 1 3.000 180.0 2 1.800 0.0 3 -torsion 6 2 20 6 -8.400 0.0 1 3.000 180.0 2 1.800 0.0 3 -torsion 4 3 3 4 1.600 0.0 1 3.200 180.0 2 0.000 0.0 3 -torsion 4 3 3 13 0.000 0.0 1 0.500 180.0 2 0.000 0.0 3 -torsion 4 3 3 24 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 4 3 3 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -#torsion 4 3 3 36 0.000 0.0 1 0.200 180.0 2 0.000 0.0 3 -torsion 13 3 3 13 0.700 0.0 1 -1.500 180.0 2 0.000 0.0 3 -torsion 13 3 3 24 -0.500 0.0 1 0.200 180.0 2 0.000 0.0 3 -torsion 13 3 3 46 0.800 0.0 1 -0.760 180.0 2 0.000 0.0 3 -torsion 24 3 3 46 -0.900 0.0 1 0.300 180.0 2 0.000 0.0 3 -torsion 46 3 3 46 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -#torsion 36 3 3 36 0.800 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 3 3 5 7 3.000 0.0 1 5.500 180.0 2 0.000 0.0 3 -torsion 4 3 5 7 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 13 3 5 7 1.500 0.0 1 5.500 180.0 2 0.000 0.0 3 -#torsion 13 3 5 7 3.200 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 24 3 5 7 -2.000 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 46 3 5 7 1.500 0.0 1 5.500 180.0 2 0.000 0.0 3 -torsion 48 3 5 7 4.000 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 1 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 1 3 13 46 0.000 0.0 1 0.000 180.0 2 0.360 0.0 3 -torsion 3 3 13 46 0.000 0.0 1 0.000 180.0 2 0.085 0.0 3 -torsion 4 3 13 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 4 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -#torsion 4 3 13 13 0.000 0.0 1 1.166 180.0 2 0.000 0.0 3 -#torsion 4 3 13 13 0.000 0.0 1 0.546 180.0 2 0.000 0.0 3 -#torsion 4 3 13 13 -0.750 0.0 1 -0.550 180.0 2 -0.250 0.0 3 -#torsion 4 3 13 13 -0.277 0.0 1 1.228 180.0 2 -0.694 0.0 3 -#torsion 4 3 13 13 -1.000 0.0 1 -1.900 180.0 2 -0.900 0.0 3 -torsion 4 3 13 21 -0.650 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 4 3 13 44 0.000 0.0 1 0.820 180.0 2 0.000 0.0 3 -torsion 4 3 13 24 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 4 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 4 3 13 48 0.000 0.0 1 0.546 180.0 2 0.000 0.0 3 -torsion 5 3 13 13 0.000 0.0 1 1.412 180.0 2 0.000 0.0 3 -#torsion 5 3 13 13 1.000 0.0 1 0.546 180.0 2 0.450 0.0 3 -torsion 5 3 13 44 5.260 0.0 1 0.820 180.0 2 0.000 0.0 3 -torsion 5 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 13 3 13 13 1.454 0.0 1 -0.144 180.0 2 -0.775 0.0 3 -torsion 13 3 13 46 0.000 0.0 1 0.000 180.0 2 0.275 0.0 3 -torsion 20 3 13 13 0.000 0.0 1 0.000 180.0 2 -0.553 0.0 3 -torsion 20 3 13 46 0.000 0.0 1 0.000 180.0 2 0.132 0.0 3 -torsion 21 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 21 3 13 46 0.000 0.0 1 0.000 180.0 2 0.360 0.0 3 -torsion 24 3 13 13 1.173 0.0 1 0.189 180.0 2 -1.200 0.0 3 -#torsion 35 3 13 13 3.250 0.0 1 -0.402 180.0 2 -0.136 0.0 3 -#torsion 35 3 13 13 3.260 0.0 1 0.440 180.0 2 0.600 0.0 3 -torsion 24 3 13 21 0.650 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 24 3 13 24 1.816 0.0 1 1.222 180.0 2 1.581 0.0 3 -torsion 24 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 46 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 46 3 13 46 0.000 0.0 1 0.000 180.0 2 0.360 0.0 3 -torsion 48 3 13 46 0.000 0.0 1 0.000 180.0 2 0.275 0.0 3 -torsion 52 3 13 13 0.000 0.0 1 0.820 180.0 2 0.000 0.0 3 -torsion 52 3 13 44 0.000 0.0 1 0.820 180.0 2 0.000 0.0 3 -torsion 52 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 65 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 65 3 13 46 0.000 0.0 1 0.000 180.0 2 0.360 0.0 3 -torsion 107 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 4 3 20 13 0.000 0.0 1 5.124 180.0 2 0.000 0.0 3 -#torsion 4 3 29 13 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 4 3 20 48 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 13 3 20 13 4.669 0.0 1 5.124 180.0 2 0.000 0.0 3 -torsion 13 3 20 48 1.500 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 24 3 20 13 -2.000 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 46 3 20 13 4.669 0.0 1 5.124 180.0 2 0.000 0.0 3 -torsion 48 3 20 13 4.000 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 3 3 24 13 0.400 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 3 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 4 3 24 5 0.000 0.0 1 6.603 180.0 2 0.000 0.0 3 -torsion 4 3 24 13 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 4 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 4 3 24 47 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 4 3 24 48 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 4 3 24 91 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 5 3 24 13 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 5 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 13 3 24 5 4.542 0.0 1 6.603 180.0 2 1.045 0.0 3 -torsion 13 3 24 13 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 13 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 13 3 24 48 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 20 3 24 13 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 20 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 24 3 24 3 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 24 3 24 13 4.600 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 24 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 46 3 24 13 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 46 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 47 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 48 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 48 3 24 48 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 48 3 24 84 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 48 3 24 87 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 84 3 24 48 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 84 3 24 84 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 84 3 24 87 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 87 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 87 3 24 48 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 87 3 24 84 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 87 3 24 87 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 0 3 47 13 0.900 0.0 1 0.230 180.0 2 -0.505 0.0 3 -torsion 4 3 47 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 4 3 47 47 2.500 0.0 1 6.000 180.0 2 0.000 0.0 3 -torsion 5 3 47 47 3.200 0.0 1 -3.000 180.0 2 0.000 0.0 3 -torsion 24 3 47 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 24 3 47 47 2.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 107 3 47 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 107 3 47 47 2.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 4 3 48 48 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3 -torsion 5 3 48 48 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3 -torsion 13 3 48 48 0.000 0.0 1 0.200 180.0 2 0.000 0.0 3 -torsion 20 3 48 48 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3 -torsion 24 3 48 48 0.000 0.0 1 1.100 180.0 2 0.000 0.0 3 -torsion 46 3 48 48 0.000 0.0 1 0.200 180.0 2 0.000 0.0 3 -torsion 0 3 50 13 0.900 0.0 1 0.230 180.0 2 -0.505 0.0 3 -torsion 4 3 50 47 2.500 0.0 1 6.000 180.0 2 0.000 0.0 3 -torsion 5 3 50 47 3.200 0.0 1 -3.000 180.0 2 0.000 0.0 3 -torsion 13 3 50 47 0.800 0.0 1 -3.000 180.0 2 0.000 0.0 3 -torsion 13 3 56 0 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 13 3 56 13 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 46 3 56 0 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 46 3 56 45 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 0 3 60 0 0.000 0.0 1 7.000 180.0 2 0.000 0.0 3 -torsion 4 3 60 0 0.000 0.0 1 7.000 180.0 2 0.000 0.0 3 -torsion 4 3 82 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 4 3 82 57 2.000 0.0 1 1.000 180.0 2 0.000 0.0 3 -torsion 4 3 82 61 0.000 0.0 1 1.000 180.0 2 0.000 0.0 3 -torsion 82 3 82 57 -2.000 0.0 1 1.000 180.0 2 0.000 0.0 3 -torsion 82 3 82 61 0.000 0.0 1 1.000 180.0 2 0.000 0.0 3 -torsion 4 3 84 20 -0.750 0.0 1 1.500 180.0 2 0.000 0.0 3 -torsion 4 3 84 87 0.750 0.0 1 1.500 180.0 2 0.000 0.0 3 -torsion 84 3 84 20 0.000 0.0 1 1.500 180.0 2 0.000 0.0 3 -torsion 84 3 84 87 0.000 0.0 1 1.500 180.0 2 0.000 0.0 3 -torsion 48 3 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 0 3 87 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 4 3 87 84 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3 -torsion 4 3 87 87 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3 -torsion 24 3 87 84 0.000 0.0 1 1.100 180.0 2 0.000 0.0 3 -torsion 24 3 87 87 0.000 0.0 1 1.100 180.0 2 0.000 0.0 3 -torsion 4 3 107 13 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 13 3 107 13 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 4 3 109 109 2.500 0.0 1 6.000 180.0 2 0.000 0.0 3 -torsion 5 3 109 109 3.200 0.0 1 -3.000 180.0 2 0.000 0.0 3 -torsion 0 4 106 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 7 5 10 2 0.300 0.0 1 0.000 180.0 2 0.500 0.0 3 -torsion 7 5 10 6 0.300 0.0 1 0.000 180.0 2 0.500 0.0 3 -torsion 7 5 13 2 0.000 0.0 1 0.000 180.0 2 0.200 0.0 3 -torsion 7 5 13 6 0.000 0.0 1 0.000 180.0 2 0.200 0.0 3 -torsion 7 5 13 13 -0.356 0.0 1 -0.174 180.0 2 0.492 0.0 3 -#torsion 7 5 13 13 4.478 0.0 1 -2.175 180.0 2 0.000 0.0 3 -#torsion 7 5 13 13 2.674 0.0 1 -2.883 180.0 2 1.026 0.0 3 -torsion 7 5 13 46 0.000 0.0 1 0.000 180.0 2 0.352 0.0 3 -#torsion 7 5 13 36 -2.589 0.0 1 -1.123 180.0 2 0.270 0.0 3 -#torsion 7 5 13 36 0.000 0.0 1 0.000 180.0 2 0.476 0.0 3 -torsion 7 5 13 47 -0.900 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 7 5 13 48 -0.900 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 7 5 13 50 -0.900 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 7 5 44 13 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -torsion 7 5 44 45 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -torsion 7 5 24 3 5.519 0.0 1 -6.700 180.0 2 0.581 0.0 3 -torsion 7 5 24 45 2.722 0.0 1 -5.154 180.0 2 0.000 0.0 3 -torsion 7 5 47 47 0.000 0.0 1 1.682 180.0 2 0.000 0.0 3 -torsion 7 5 48 48 0.000 0.0 1 1.682 180.0 2 0.000 0.0 3 -torsion 7 5 51 20 -1.257 0.0 1 -1.806 180.0 2 0.003 0.0 3 -torsion 7 5 56 3 3.000 0.0 1 3.000 180.0 2 0.000 0.0 3 -torsion 7 5 64 4 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 7 5 64 5 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 7 5 79 13 -0.750 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 7 5 79 23 0.750 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 7 5 79 48 2.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 0 13 13 3 -4.344 0.0 1 -1.714 180.0 2 0.000 0.0 3 -torsion 0 13 13 13 1.711 0.0 1 -0.500 180.0 2 0.663 0.0 3 -#torsion 0 13 13 13 -1.336 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 0 13 13 24 1.428 0.0 1 0.086 180.0 2 0.029 0.0 3 -torsion 1 13 13 1 -2.500 0.0 1 0.000 180.0 2 0.250 0.0 3 -torsion 1 13 13 5 0.000 0.0 1 0.000 180.0 2 0.540 0.0 3 -torsion 1 13 13 13 0.300 0.0 1 -0.400 180.0 2 0.400 0.0 3 -torsion 1 13 13 46 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 -torsion 3 13 13 3 -0.550 0.0 1 0.000 180.0 2 1.000 0.0 3 -#torsion 3 13 13 3 0.800 0.0 1 0.000 180.0 2 0.900 0.0 3 -torsion 3 13 13 5 -6.180 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 3 13 13 13 -2.060 0.0 1 -0.313 180.0 2 0.315 0.0 3 -#torsion 3 13 13 13 -3.185 0.0 1 -0.825 180.0 2 0.493 0.0 3 -#torsion 3 13 13 13 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3 -torsion 3 13 13 15 -4.344 0.0 1 -1.714 180.0 2 0.000 0.0 3 -torsion 3 13 13 16 -4.344 0.0 1 -1.714 180.0 2 0.000 0.0 3 -torsion 3 13 13 24 -9.000 0.0 1 2.000 180.0 2 0.800 0.0 3 -torsion 3 13 13 46 0.000 0.0 1 0.000 180.0 2 -0.100 0.0 3 -#torsion 3 13 13 36 0.000 0.0 1 0.000 180.0 2 0.074 0.0 3 -#torsion 3 13 13 36 0.000 0.0 1 0.000 180.0 2 -0.076 0.0 3 -torsion 3 13 13 48 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3 -torsion 3 13 13 80 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3 -torsion 5 13 13 5 9.508 0.0 1 0.000 180.0 2 0.000 0.0 3 -#torsion 5 13 13 5 12.234 0.0 1 0.000 180.0 2 0.000 0.0 3 -#torsion 5 13 13 5 9.066 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 5 13 13 13 -1.552 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 5 13 13 20 4.319 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 5 13 13 44 8.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 5 13 13 24 6.280 0.0 1 -1.467 180.0 2 2.030 0.0 3 -torsion 5 13 13 46 0.000 0.0 1 0.000 180.0 2 0.468 0.0 3 -torsion 13 13 13 13 1.300 0.0 1 -0.050 180.0 2 0.200 0.0 3 -#torsion 13 13 13 13 6.622 0. 1 0.948 180. 2 -1.388 0. 3 -2.118 180. 4 -torsion 13 13 13 15 1.262 0.0 1 -0.198 180.0 2 0.465 0.0 3 -torsion 13 13 13 16 2.619 0.0 1 -0.620 180.0 2 0.258 0.0 3 -torsion 13 13 13 19 0.000 0.0 1 -0.650 180.0 2 0.000 0.0 3 -torsion 13 13 13 21 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 -torsion 13 13 13 44 2.392 0.0 1 -0.674 180.0 2 0.550 0.0 3 -torsion 13 13 13 24 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3 -#torsion 13 13 13 35 1.964 0.0 1 0.000 180.0 2 0.659 0.0 3 -torsion 13 13 13 46 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -torsion 13 13 13 51 1.300 0.0 1 -0.050 180.0 2 0.200 0.0 3 -torsion 13 13 13 53 2.732 0.0 1 -0.229 180.0 2 0.485 0.0 3 -torsion 13 13 13 65 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 -torsion 13 13 13 66 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 -torsion 13 13 13 79 1.262 0.0 1 -0.198 180.0 2 0.465 0.0 3 -torsion 13 13 13 107 1.964 0.0 1 0.000 180.0 2 0.659 0.0 3 -torsion 13 13 13 108 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 15 13 13 46 0.000 0.0 1 0.000 180.0 2 0.452 0.0 3 -torsion 16 13 13 46 0.000 0.0 1 0.000 180.0 2 0.452 0.0 3 -torsion 19 13 13 46 0.000 0.0 1 0.000 180.0 2 0.366 0.0 3 -torsion 20 13 13 20 -0.550 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 20 13 13 46 0.000 0.0 1 0.000 180.0 2 0.468 0.0 3 -torsion 21 13 13 21 -0.250 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 21 13 13 44 2.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 21 13 13 46 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 -torsion 44 13 13 44 11.035 0.0 1 -0.968 180.0 2 0.270 0.0 3 -torsion 44 13 13 46 -1.013 0.0 1 -0.709 180.0 2 0.473 0.0 3 -torsion 44 13 13 48 -0.800 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 24 13 13 46 0.000 0.0 1 0.000 180.0 2 0.464 0.0 3 -torsion 24 13 13 48 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3 -torsion 24 13 13 80 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3 -torsion 46 13 13 46 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -torsion 46 13 13 47 0.000 0.0 1 0.000 180.0 2 0.366 0.0 3 -torsion 46 13 13 48 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 -torsion 46 13 13 51 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -torsion 46 13 13 53 0.000 0.0 1 0.000 180.0 2 0.384 0.0 3 -torsion 46 13 13 55 0.000 0.0 1 0.000 180.0 2 -0.582 0.0 3 -torsion 46 13 13 59 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 -torsion 46 13 13 62 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 -torsion 46 13 13 65 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 -torsion 46 13 13 66 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 -torsion 46 13 13 79 0.000 0.0 1 0.000 180.0 2 0.452 0.0 3 -#torsion 36 13 13 69 0.000 0.0 1 0.000 180.0 2 0.350 0.0 3 -torsion 46 13 13 80 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 -torsion 46 13 13 82 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 -torsion 46 13 13 83 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 -torsion 46 13 13 84 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 -torsion 46 13 13 87 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 -torsion 46 13 13 88 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 -torsion 46 13 13 102 0.000 0.0 1 0.000 180.0 2 -0.225 0.0 3 -torsion 46 13 13 104 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -torsion 46 13 13 107 0.000 0.0 1 0.000 180.0 2 0.464 0.0 3 -torsion 46 13 13 108 0.000 0.0 1 0.000 180.0 2 0.450 0.0 3 -torsion 46 13 13 109 0.000 0.0 1 0.000 180.0 2 0.366 0.0 3 -torsion 48 13 13 53 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 108 13 13 108 5.200 0.0 1 -0.500 180.0 2 0.000 0.0 3 -torsion 13 13 15 17 -0.759 0.0 1 -0.282 180.0 2 0.680 0.0 3 -torsion 46 13 15 17 0.000 0.0 1 0.000 180.0 2 0.480 0.0 3 -torsion 13 13 16 13 0.925 0.0 1 -0.576 180.0 2 0.677 0.0 3 -torsion 13 13 16 16 1.941 0.0 1 -0.836 180.0 2 0.935 0.0 3 -torsion 46 13 16 13 0.000 0.0 1 0.000 180.0 2 0.647 0.0 3 -torsion 46 13 16 16 0.000 0.0 1 0.000 180.0 2 0.558 0.0 3 -torsion 46 13 16 48 0.000 0.0 1 0.000 180.0 2 0.647 0.0 3 -torsion 0 13 18 19 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 46 13 18 19 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 0 13 19 18 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 0 13 19 19 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 13 13 19 19 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 46 13 19 19 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 0 13 20 13 -0.521 0.0 1 -2.018 180.0 2 1.996 0.0 3 -torsion 56 13 20 13 -0.500 0.0 1 -1.500 180.0 2 1.000 0.0 3 -torsion 57 13 20 13 -0.500 0.0 1 -1.500 180.0 2 1.000 0.0 3 -torsion 13 13 20 3 -1.220 0.0 1 -0.126 180.0 2 0.422 0.0 3 -torsion 13 13 20 13 0.650 0.0 1 -0.250 180.0 2 0.670 0.0 3 -torsion 13 13 20 64 -1.420 0.0 1 -0.620 180.0 2 0.100 0.0 3 -torsion 46 13 20 0 0.000 0.0 1 0.000 180.0 2 0.760 0.0 3 -torsion 46 13 20 3 0.000 0.0 1 0.000 180.0 2 0.198 0.0 3 -torsion 46 13 20 47 0.000 0.0 1 0.000 180.0 2 0.760 0.0 3 -torsion 46 13 20 48 0.000 0.0 1 0.000 180.0 2 0.760 0.0 3 -torsion 46 13 20 51 0.000 0.0 1 0.000 180.0 2 0.760 0.0 3 -torsion 46 13 20 64 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -torsion 13 13 44 13 0.416 0.0 1 -0.128 180.0 2 0.695 0.0 3 -#torsion 13 13 33 13 1.536 0.0 1 -0.128 180.0 2 0.695 0.0 3 -#torsion 13 13 33 13 1.464 0.0 1 -0.128 180.0 2 0.695 0.0 3 -torsion 13 13 44 45 -0.190 0.0 1 -0.417 180.0 2 0.418 0.0 3 -#torsion 13 13 33 34 0.000 0.0 1 4.000 180.0 2 0.000 0.0 3 -#torsion 13 13 33 34 0.200 0.0 1 -0.417 180.0 2 0.418 0.0 3 -#torsion 13 13 33 34 0.819 0.0 1 -0.417 180.0 2 0.418 0.0 3 -#torsion 13 13 33 34 1.522 0.0 1 -0.417 180.0 2 0.418 0.0 3 -torsion 46 13 44 13 0.000 0.0 1 0.000 180.0 2 0.560 0.0 3 -torsion 46 13 44 45 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 -torsion 46 13 44 48 0.000 0.0 1 0.000 180.0 2 0.560 0.0 3 -torsion 0 13 24 45 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 3 13 24 3 -2.365 0.0 1 0.912 180.0 2 -0.850 0.0 3 -torsion 3 13 24 13 -1.737 0.0 1 1.251 180.0 2 -3.501 0.0 3 -torsion 3 13 24 45 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 13 13 24 3 0.000 0.0 1 0.462 180.0 2 0.000 0.0 3 -#torsion 13 13 35 3 -1.396 0.0 1 -0.427 180.0 2 0.000 0.0 3 -#torsion 13 13 35 3 1.130 0.0 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################################################################ - ## ## - ## Additional Torsional Parameter Values Used with OPLS-AA ## - ## ## - ## The torsions listed below were added to official OPLS-AA ## - ## to complete the set needed for proteins; the values were ## - ## obtained by analogy from the closest OPLS-AA torsions; ## - ## most of the added values are for HIP or N-terminal AAs; ## - ## ## - ################################################################ - - -torsion 24 3 13 53 1.816 0.0 1 1.222 180.0 2 1.581 0.0 3 -torsion 52 3 13 24 0.000 0.0 1 0.820 180.0 2 0.000 0.0 3 -torsion 3 13 13 53 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 3 13 13 83 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3 -torsion 3 13 13 84 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3 -torsion 3 13 13 85 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3 -torsion 5 13 13 53 6.280 0.0 1 -1.467 180.0 2 2.030 0.0 3 -torsion 15 13 13 53 1.428 0.0 1 0.086 180.0 2 0.029 0.0 3 -torsion 16 13 13 53 1.428 0.0 1 0.086 180.0 2 0.029 0.0 3 -torsion 13 13 13 55 2.732 0.0 1 -0.229 180.0 2 0.485 0.0 3 -torsion 24 13 13 83 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3 -torsion 53 13 13 83 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 24 13 13 84 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3 -torsion 53 13 13 84 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 24 13 13 85 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3 -torsion 46 13 13 85 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 -torsion 53 13 13 85 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 3 13 53 13 1.438 0.0 1 -0.124 180.0 2 0.264 0.0 3 -torsion 3 13 53 54 0.000 0.0 1 0.000 180.0 2 0.347 0.0 3 -torsion 13 13 53 54 0.000 0.0 1 0.000 180.0 2 0.347 0.0 3 -torsion 46 13 55 54 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 13 13 85 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 13 13 85 57 1.700 0.0 1 -0.600 180.0 2 0.000 0.0 3 -torsion 46 13 85 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 55 48 55 54 0.000 0.0 1 3.900 180.0 2 0.000 0.0 3 -torsion 0 48 81 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 0 57 85 0 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 0 85 85 0 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3 - - - ################################################################ - ## ## - ## Additional Torsional Parameter Values Used with OPLS-AA ## - ## ## - ## The torsions listed below were added to official OPLS-AA ## - ## to complete the values needed for selected organics ## - ## ## - ################################################################ - - -torsion 13 13 13 20 1.300 0.0 1 -0.050 180.0 2 0.200 0.0 3 -torsion 13 13 13 47 1.300 0.0 1 -0.050 180.0 2 0.200 0.0 3 ######################################## @@ -3432,1705 +120,7 @@ torsion 13 13 13 47 1.300 0.0 1 -0.050 180.0 2 0.200 0.0 3 ######################################## -charge 1 -0.2200 -charge 2 0.2200 -charge 3 0.5500 -charge 4 -0.5000 -charge 5 -0.5800 -charge 6 0.0800 -charge 7 0.4500 -charge 8 0.0000 -charge 9 0.0000 -charge 10 0.0000 -charge 11 0.0000 -charge 12 0.0000 -charge 13 0.0000 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-0.5600 -charge 277 0.5500 -charge 278 -0.5400 -charge 279 0.4600 -charge 280 -0.0600 -charge 281 0.1000 -charge 282 0.3800 -charge 283 -0.4800 -charge 284 -0.7900 -charge 285 0.3850 -charge 286 0.3550 -charge 287 0.1000 -charge 288 0.1000 -charge 289 -0.5300 -charge 290 0.2200 -charge 291 -0.5500 -charge 292 0.3800 -charge 293 0.1500 -charge 294 0.4400 -charge 295 -0.4900 -charge 296 0.2000 -charge 297 -0.5000 -charge 298 0.2000 -charge 299 -0.8100 -charge 300 0.3850 -charge 301 0.3550 -charge 302 0.2000 -charge 303 0.3500 -charge 304 -0.5600 -charge 305 0.4600 -charge 306 -0.5100 -charge 307 0.3400 -charge 308 0.1200 -charge 309 0.5200 -charge 310 0.3800 -charge 311 -0.8000 -charge 312 0.4000 -charge 313 -0.5100 -charge 314 -0.0100 -charge 315 0.1200 -charge 316 -0.0100 -charge 317 0.1400 -charge 318 -0.0100 -charge 319 0.1300 -charge 320 -0.6400 -charge 321 0.6500 -charge 322 -0.7400 -charge 323 0.6600 -charge 324 -0.0600 -charge 325 0.1000 -charge 326 0.4900 -charge 327 -0.3000 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-0.2500 -charge 380 -0.8650 -charge 381 1.6200 -charge 382 -0.9200 -charge 383 -0.6000 -charge 384 0.3000 -charge 385 -0.0300 -charge 386 1.9200 -charge 387 -1.1200 -charge 388 -0.7000 -charge 389 0.4400 -charge 390 -0.1000 -charge 391 1.6200 -charge 392 -0.9700 -charge 393 -0.6300 -charge 394 0.2800 -charge 395 -0.0200 -charge 396 -0.5100 -charge 397 0.0800 -charge 398 -0.1400 -charge 399 0.3200 -charge 400 0.0200 -charge 401 -0.0400 -charge 402 -0.4700 -charge 403 0.1200 -charge 404 0.1400 -charge 405 0.2400 -charge 406 0.5100 -charge 407 -0.4300 -charge 408 -0.3300 -charge 409 0.1600 -charge 410 0.0300 -charge 411 0.6350 -charge 412 0.6250 -charge 413 0.1350 -charge 414 -0.2150 -charge 415 1.4800 -charge 416 -0.6800 -charge 417 -0.5400 -charge 418 0.1800 -charge 419 -1.0000 -charge 420 0.4400 -charge 421 -0.8000 -charge 422 0.4100 -charge 423 0.1800 -charge 424 0.0300 -charge 425 0.3900 -charge 426 -0.0600 -charge 427 -0.1800 -charge 428 0.0600 -charge 429 0.0000 -charge 430 0.0300 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843 -0.4270 -charge 844 0.2180 -charge 845 0.6000 -charge 846 -0.6000 -charge 847 -0.3600 -charge 848 0.0000 -charge 849 0.0600 -charge 850 0.1200 -charge 851 0.1800 -charge 852 0.0600 -charge 853 0.5700 -charge 854 -0.5700 -charge 855 0.0000 -charge 856 0.0200 -charge 857 -0.0400 -charge 858 0.0000 -charge 859 0.0600 -charge 860 -0.0700 -charge 861 -0.1400 -charge 862 0.1700 -charge 863 0.1100 -charge 864 0.1500 -charge 865 0.1700 -charge 866 1.0000 -charge 867 0.8500 -charge 868 0.7000 -charge 869 0.5500 -charge 870 -0.1000 -charge 871 -0.4300 -charge 872 -0.3700 -charge 873 -0.3100 -charge 874 -0.2500 -charge 875 -1.0000 -charge 876 -1.0000 -charge 877 -1.0000 -charge 878 -1.0000 -charge 879 1.0000 -charge 880 1.0000 -charge 881 1.0000 -charge 882 1.0000 -charge 883 1.0000 -charge 884 2.0000 -charge 885 2.0000 -charge 886 2.0000 -charge 887 2.0000 -charge 888 -0.0500 -charge 889 0.0500 -charge 890 0.1500 -charge 891 0.2500 -charge 892 0.1000 -charge 893 0.1150 -charge 894 0.1350 -charge 895 0.0150 -charge 896 0.1550 -charge 897 0.0000 -charge 898 -0.1150 -charge 899 0.1500 -charge 900 -0.2500 -charge 901 -0.1000 -charge 902 0.0500 -charge 903 -0.1000 -charge 904 0.2000 -charge 905 -0.2500 -charge 906 0.0880 - - - ######################################## - ## ## - ## Biopolymer Atom Type Conversions ## - ## ## - ######################################## - - -biotype 1 N "Glycine" 180 -biotype 2 CA "Glycine" 165 -biotype 3 C "Glycine" 177 -biotype 4 HN "Glycine" 183 -biotype 5 O "Glycine" 178 -biotype 6 HA "Glycine" 85 -biotype 7 N "Alanine" 180 -biotype 8 CA "Alanine" 166 -biotype 9 C "Alanine" 177 -biotype 10 HN "Alanine" 183 -biotype 11 O "Alanine" 178 -biotype 12 HA "Alanine" 85 -biotype 13 CB "Alanine" 80 -biotype 14 HB "Alanine" 85 -biotype 15 N "Valine" 180 -biotype 16 CA "Valine" 166 -biotype 17 C "Valine" 177 -biotype 18 HN "Valine" 183 -biotype 19 O "Valine" 178 -biotype 20 HA "Valine" 85 -biotype 21 CB "Valine" 82 -biotype 22 HB "Valine" 85 -biotype 23 CG1 "Valine" 80 -biotype 24 HG1 "Valine" 85 -biotype 25 CG2 "Valine" 80 -biotype 26 HG2 "Valine" 85 -biotype 27 N "Leucine" 180 -biotype 28 CA "Leucine" 166 -biotype 29 C "Leucine" 177 -biotype 30 HN "Leucine" 183 -biotype 31 O "Leucine" 178 -biotype 32 HA "Leucine" 85 -biotype 33 CB "Leucine" 81 -biotype 34 HB "Leucine" 85 -biotype 35 CG "Leucine" 82 -biotype 36 HG "Leucine" 85 -biotype 37 CD1 "Leucine" 80 -biotype 38 HD1 "Leucine" 85 -biotype 39 CD2 "Leucine" 80 -biotype 40 HD2 "Leucine" 85 -biotype 41 N "Isoleucine" 180 -biotype 42 CA "Isoleucine" 166 -biotype 43 C "Isoleucine" 177 -biotype 44 HN "Isoleucine" 183 -biotype 45 O "Isoleucine" 178 -biotype 46 HA "Isoleucine" 85 -biotype 47 CB "Isoleucine" 82 -biotype 48 HB "Isoleucine" 85 -biotype 49 CG1 "Isoleucine" 80 -biotype 50 HG1 "Isoleucine" 85 -biotype 51 CG2 "Isoleucine" 81 -biotype 52 HG2 "Isoleucine" 85 -biotype 53 CD "Isoleucine" 80 -biotype 54 HD "Isoleucine" 85 -biotype 55 N "Serine" 180 -biotype 56 CA "Serine" 166 -biotype 57 C "Serine" 177 -biotype 58 HN "Serine" 183 -biotype 59 O "Serine" 178 -biotype 60 HA "Serine" 85 -biotype 61 CB "Serine" 99 -biotype 62 HB "Serine" 85 -biotype 63 OG "Serine" 96 -biotype 64 HG "Serine" 97 -biotype 65 N "Threonine" 180 -biotype 66 CA "Threonine" 166 -biotype 67 C "Threonine" 177 -biotype 68 HN "Threonine" 183 -biotype 69 O "Threonine" 178 -biotype 70 HA "Threonine" 85 -biotype 71 CB "Threonine" 100 -biotype 72 HB "Threonine" 85 -biotype 73 OG1 "Threonine" 96 -biotype 74 HG1 "Threonine" 97 -biotype 75 CG2 "Threonine" 80 -biotype 76 HG2 "Threonine" 85 -biotype 77 N "Cysteine (SH)" 180 -biotype 78 CA "Cysteine (SH)" 166 -biotype 79 C "Cysteine (SH)" 177 -biotype 80 HN "Cysteine (SH)" 183 -biotype 81 O "Cysteine (SH)" 178 -biotype 82 HA "Cysteine (SH)" 85 -biotype 83 CB "Cysteine (SH)" 148 -biotype 84 HB "Cysteine (SH)" 85 -biotype 85 SG "Cysteine (SH)" 142 -biotype 86 HG "Cysteine (SH)" 146 -biotype 87 N "Cystine (SS)" 180 -biotype 88 CA "Cystine (SS)" 166 -biotype 89 C "Cystine (SS)" 177 -biotype 90 HN "Cystine (SS)" 183 -biotype 91 O "Cystine (SS)" 178 -biotype 92 HA "Cystine (SS)" 85 -biotype 93 CB "Cystine (SS)" 156 -biotype 94 HB "Cystine (SS)" 85 -biotype 95 SG "Cystine (SS)" 145 -biotype 96 N "Cysteine (S-)" -1 -biotype 97 CA "Cysteine (S-)" -1 -biotype 98 C "Cysteine (S-)" -1 -biotype 99 HN "Cysteine (S-)" -1 -biotype 100 O "Cysteine (S-)" -1 -biotype 101 HA "Cysteine (S-)" -1 -biotype 102 CB "Cysteine (S-)" -1 -biotype 103 HB "Cysteine (S-)" -1 -biotype 104 SG "Cysteine (S-)" -1 -biotype 105 N "Proline" 181 -biotype 106 CA "Proline" 188 -biotype 107 C "Proline" 177 -biotype 108 O "Proline" 178 -biotype 109 HA "Proline" 85 -biotype 110 CB "Proline" 81 -biotype 111 HB "Proline" 85 -biotype 112 CG "Proline" 81 -biotype 113 HG "Proline" 85 -biotype 114 CD "Proline" 187 -biotype 115 HD "Proline" 85 -biotype 116 N "Phenylalanine" 180 -biotype 117 CA "Phenylalanine" 166 -biotype 118 C "Phenylalanine" 177 -biotype 119 HN "Phenylalanine" 183 -biotype 120 O "Phenylalanine" 178 -biotype 121 HA "Phenylalanine" 85 -biotype 122 CB "Phenylalanine" 94 -biotype 123 HB "Phenylalanine" 85 -biotype 124 CG "Phenylalanine" 90 -biotype 125 CD "Phenylalanine" 90 -biotype 126 HD "Phenylalanine" 91 -biotype 127 CE "Phenylalanine" 90 -biotype 128 HE "Phenylalanine" 91 -biotype 129 CZ "Phenylalanine" 90 -biotype 130 HZ "Phenylalanine" 91 -biotype 131 N "Tyrosine" 180 -biotype 132 CA "Tyrosine" 166 -biotype 133 C "Tyrosine" 177 -biotype 134 HN "Tyrosine" 183 -biotype 135 O "Tyrosine" 178 -biotype 136 HA "Tyrosine" 85 -biotype 137 CB "Tyrosine" 94 -biotype 138 HB "Tyrosine" 85 -biotype 139 CG "Tyrosine" 90 -biotype 140 CD "Tyrosine" 90 -biotype 141 HD "Tyrosine" 91 -biotype 142 CE "Tyrosine" 90 -biotype 143 HE "Tyrosine" 91 -biotype 144 CZ "Tyrosine" 108 -biotype 145 OH "Tyrosine" 109 -biotype 146 HH "Tyrosine" 110 -biotype 147 N "Tyrosine (O-)" -1 -biotype 148 CA "Tyrosine (O-)" -1 -biotype 149 C "Tyrosine (O-)" -1 -biotype 150 HN "Tyrosine (O-)" -1 -biotype 151 O "Tyrosine (O-)" -1 -biotype 152 HA "Tyrosine (O-)" -1 -biotype 153 CB "Tyrosine (O-)" -1 -biotype 154 HB "Tyrosine (O-)" -1 -biotype 155 CG "Tyrosine (O-)" -1 -biotype 156 CD "Tyrosine (O-)" -1 -biotype 157 HD "Tyrosine (O-)" -1 -biotype 158 CE "Tyrosine (O-)" -1 -biotype 159 HE "Tyrosine (O-)" -1 -biotype 160 CZ "Tyrosine (O-)" -1 -biotype 161 OH "Tyrosine (O-)" -1 -biotype 162 N "Tryptophan" 180 -biotype 163 CA "Tryptophan" 166 -biotype 164 C "Tryptophan" 177 -biotype 165 HN "Tryptophan" 183 -biotype 166 O "Tryptophan" 178 -biotype 167 HA "Tryptophan" 85 -biotype 168 CB "Tryptophan" 81 -biotype 169 HB "Tryptophan" 85 -biotype 170 CG "Tryptophan" 441 -biotype 171 CD1 "Tryptophan" 455 -biotype 172 HD1 "Tryptophan" 91 -biotype 173 CD2 "Tryptophan" 442 -biotype 174 NE1 "Tryptophan" 444 -biotype 175 HE1 "Tryptophan" 445 -biotype 176 CE2 "Tryptophan" 443 -biotype 177 CE3 "Tryptophan" 90 -biotype 178 HE3 "Tryptophan" 91 -biotype 179 CZ2 "Tryptophan" 90 -biotype 180 HZ2 "Tryptophan" 91 -biotype 181 CZ3 "Tryptophan" 90 -biotype 182 HZ3 "Tryptophan" 91 -biotype 183 CH2 "Tryptophan" 90 -biotype 184 HH2 "Tryptophan" 91 -biotype 185 N "Histidine (+)" 180 -biotype 186 CA "Histidine (+)" 166 -biotype 187 C "Histidine (+)" 177 -biotype 188 HN "Histidine (+)" 183 -biotype 189 O "Histidine (+)" 178 -biotype 190 HA "Histidine (+)" 85 -biotype 191 CB "Histidine (+)" 446 -biotype 192 HB "Histidine (+)" 85 -biotype 193 CG "Histidine (+)" 451 -biotype 194 ND1 "Histidine (+)" 453 -biotype 195 HD1 "Histidine (+)" 454 -biotype 196 CD2 "Histidine (+)" 451 -biotype 197 HD2 "Histidine (+)" 91 -biotype 198 CE1 "Histidine (+)" 450 -biotype 199 HE1 "Histidine (+)" 91 -biotype 200 NE2 "Histidine (+)" 453 -biotype 201 HE2 "Histidine (+)" 454 -biotype 202 N "Histidine (HD)" 180 -biotype 203 CA "Histidine (HD)" 166 -biotype 204 C "Histidine (HD)" 177 -biotype 205 HN "Histidine (HD)" 183 -biotype 206 O "Histidine (HD)" 178 -biotype 207 HA "Histidine (HD)" 85 -biotype 208 CB "Histidine (HD)" 446 -biotype 209 HB "Histidine (HD)" 85 -biotype 210 CG "Histidine (HD)" 449 -biotype 211 ND1 "Histidine (HD)" 444 -biotype 212 HD1 "Histidine (HD)" 445 -biotype 213 CD2 "Histidine (HD)" 448 -biotype 214 HD2 "Histidine (HD)" 91 -biotype 215 CE1 "Histidine (HD)" 447 -biotype 216 HE1 "Histidine (HD)" 91 -biotype 217 NE2 "Histidine (HD)" 452 -biotype 218 N "Histidine (HE)" 180 -biotype 219 CA "Histidine (HE)" 166 -biotype 220 C "Histidine (HE)" 177 -biotype 221 HN "Histidine (HE)" 183 -biotype 222 O "Histidine (HE)" 178 -biotype 223 HA "Histidine (HE)" 85 -biotype 224 CB "Histidine (HE)" 446 -biotype 225 HB "Histidine (HE)" 85 -biotype 226 CG "Histidine (HE)" 448 -biotype 227 ND1 "Histidine (HE)" 452 -biotype 228 CD2 "Histidine (HE)" 449 -biotype 229 HD2 "Histidine (HE)" 91 -biotype 230 CE1 "Histidine (HE)" 447 -biotype 231 HE1 "Histidine (HE)" 91 -biotype 232 NE2 "Histidine (HE)" 444 -biotype 233 HE2 "Histidine (HE)" 445 -biotype 234 N "Aspartic Acid" 180 -biotype 235 CA "Aspartic Acid" 166 -biotype 236 C "Aspartic Acid" 177 -biotype 237 HN "Aspartic Acid" 183 -biotype 238 O "Aspartic Acid" 178 -biotype 239 HA "Aspartic Acid" 85 -biotype 240 CB "Aspartic Acid" 216 -biotype 241 HB "Aspartic Acid" 85 -biotype 242 CG "Aspartic Acid" 213 -biotype 243 OD "Aspartic Acid" 214 -biotype 244 N "Aspartic Acid (COOH)" -1 -biotype 245 CA "Aspartic Acid (COOH)" -1 -biotype 246 C "Aspartic Acid (COOH)" -1 -biotype 247 HN "Aspartic Acid (COOH)" -1 -biotype 248 O "Aspartic Acid (COOH)" -1 -biotype 249 HA "Aspartic Acid (COOH)" -1 -biotype 250 CB "Aspartic Acid (COOH)" -1 -biotype 251 HB "Aspartic Acid (COOH)" -1 -biotype 252 CG "Aspartic Acid (COOH)" -1 -biotype 253 OD1 "Aspartic Acid (COOH)" -1 -biotype 254 OD2 "Aspartic Acid (COOH)" -1 -biotype 255 HD2 "Aspartic Acid (COOH)" -1 -biotype 256 N "Asparagine" 180 -biotype 257 CA "Asparagine" 166 -biotype 258 C "Asparagine" 177 -biotype 259 HN "Asparagine" 183 -biotype 260 O "Asparagine" 178 -biotype 261 HA "Asparagine" 85 -biotype 262 CB "Asparagine" 81 -biotype 263 HB "Asparagine" 85 -biotype 264 CG "Asparagine" 177 -biotype 265 OD1 "Asparagine" 178 -biotype 266 ND2 "Asparagine" 179 -biotype 267 HD2 "Asparagine" 182 -biotype 268 N "Glutamic Acid" 180 -biotype 269 CA "Glutamic Acid" 166 -biotype 270 C "Glutamic Acid" 177 -biotype 271 HN "Glutamic Acid" 183 -biotype 272 O "Glutamic Acid" 178 -biotype 273 HA "Glutamic Acid" 85 -biotype 274 CB "Glutamic Acid" 81 -biotype 275 HB "Glutamic Acid" 85 -biotype 276 CG "Glutamic Acid" 216 -biotype 277 HG "Glutamic Acid" 85 -biotype 278 CD "Glutamic Acid" 213 -biotype 279 OE "Glutamic Acid" 214 -biotype 280 N "Glutamic Acid (COOH)" -1 -biotype 281 CA "Glutamic Acid (COOH)" -1 -biotype 282 C "Glutamic Acid (COOH)" -1 -biotype 283 HN "Glutamic Acid (COOH)" -1 -biotype 284 O "Glutamic Acid (COOH)" -1 -biotype 285 HA "Glutamic Acid (COOH)" -1 -biotype 286 CB "Glutamic Acid (COOH)" -1 -biotype 287 HB "Glutamic Acid (COOH)" -1 -biotype 288 CG "Glutamic Acid (COOH)" -1 -biotype 289 HG "Glutamic Acid (COOH)" -1 -biotype 290 CD "Glutamic Acid (COOH)" -1 -biotype 291 OE1 "Glutamic Acid (COOH)" -1 -biotype 292 OE2 "Glutamic Acid (COOH)" -1 -biotype 293 HE2 "Glutamic Acid (COOH)" -1 -biotype 294 N "Glutamine" 180 -biotype 295 CA "Glutamine" 166 -biotype 296 C "Glutamine" 177 -biotype 297 HN "Glutamine" 183 -biotype 298 O "Glutamine" 178 -biotype 299 HA "Glutamine" 85 -biotype 300 CB "Glutamine" 81 -biotype 301 HB "Glutamine" 85 -biotype 302 CG "Glutamine" 81 -biotype 303 HG "Glutamine" 85 -biotype 304 CD "Glutamine" 177 -biotype 305 OE1 "Glutamine" 178 -biotype 306 NE2 "Glutamine" 179 -biotype 307 HE2 "Glutamine" 182 -biotype 308 N "Methionine" 180 -biotype 309 CA "Methionine" 166 -biotype 310 C "Methionine" 177 -biotype 311 HN "Methionine" 183 -biotype 312 O "Methionine" 178 -biotype 313 HA "Methionine" 85 -biotype 314 CB "Methionine" 81 -biotype 315 HB "Methionine" 85 -biotype 316 CG "Methionine" 152 -biotype 317 HG "Methionine" 85 -biotype 318 SD "Methionine" 144 -biotype 319 CE "Methionine" 151 -biotype 320 HE "Methionine" 85 -biotype 321 N "Lysine" 180 -biotype 322 CA "Lysine" 166 -biotype 323 C "Lysine" 177 -biotype 324 HN "Lysine" 183 -biotype 325 O "Lysine" 178 -biotype 326 HA "Lysine" 85 -biotype 327 CB "Lysine" 81 -biotype 328 HB "Lysine" 85 -biotype 329 CG "Lysine" 81 -biotype 330 HG "Lysine" 85 -biotype 331 CD "Lysine" 81 -biotype 332 HD "Lysine" 85 -biotype 333 CE "Lysine" 235 -biotype 334 HE "Lysine" 85 -biotype 335 NZ "Lysine" 230 -biotype 336 HZ "Lysine" 233 -biotype 337 N "Lysine (NH2)" -1 -biotype 338 CA "Lysine (NH2)" -1 -biotype 339 C "Lysine (NH2)" -1 -biotype 340 HN "Lysine (NH2)" -1 -biotype 341 O "Lysine (NH2)" -1 -biotype 342 HA "Lysine (NH2)" -1 -biotype 343 CB "Lysine (NH2)" -1 -biotype 344 HB "Lysine (NH2)" -1 -biotype 345 CG "Lysine (NH2)" -1 -biotype 346 HG "Lysine (NH2)" -1 -biotype 347 CD "Lysine (NH2)" -1 -biotype 348 HD "Lysine (NH2)" -1 -biotype 349 CE "Lysine (NH2)" -1 -biotype 350 HE "Lysine (NH2)" -1 -biotype 351 NZ "Lysine (NH2)" -1 -biotype 352 HZ "Lysine (NH2)" -1 -biotype 353 N "Arginine" 180 -biotype 354 CA "Arginine" 166 -biotype 355 C "Arginine" 177 -biotype 356 HN "Arginine" 183 -biotype 357 O "Arginine" 178 -biotype 358 HA "Arginine" 85 -biotype 359 CB "Arginine" 81 -biotype 360 HB "Arginine" 85 -biotype 361 CG "Arginine" 251 -biotype 362 HG "Arginine" 85 -biotype 363 CD "Arginine" 250 -biotype 364 HD "Arginine" 85 -biotype 365 NE "Arginine" 246 -biotype 366 HE "Arginine" 247 -biotype 367 CZ "Arginine" 245 -biotype 368 NH "Arginine" 243 -biotype 369 HH "Arginine" 244 -biotype 370 N "Ornithine" 180 -biotype 371 CA "Ornithine" 166 -biotype 372 C "Ornithine" 177 -biotype 373 HN "Ornithine" 183 -biotype 374 O "Ornithine" 178 -biotype 375 HA "Ornithine" 85 -biotype 376 CB "Ornithine" 81 -biotype 377 HB "Ornithine" 85 -biotype 378 CG "Ornithine" 81 -biotype 379 HG "Ornithine" 85 -biotype 380 CD "Ornithine" 235 -biotype 381 HD "Ornithine" 85 -biotype 382 NE "Ornithine" 230 -biotype 383 HE "Ornithine" 233 -biotype 384 N "MethylAlanine (AIB)" 180 -biotype 385 CA "MethylAlanine (AIB)" 167 -biotype 386 C "MethylAlanine (AIB)" 177 -biotype 387 HN "MethylAlanine (AIB)" 183 -biotype 388 O "MethylAlanine (AIB)" 178 -biotype 389 CB "MethylAlanine (AIB)" 80 -biotype 390 HB "MethylAlanine (AIB)" 85 -biotype 391 N "Pyroglutamic Acid" 180 -biotype 392 CA "Pyroglutamic Acid" 166 -biotype 393 C "Pyroglutamic Acid" 177 -biotype 394 HN "Pyroglutamic Acid" 183 -biotype 395 O "Pyroglutamic Acid" 178 -biotype 396 HA "Pyroglutamic Acid" 85 -biotype 397 CB "Pyroglutamic Acid" 81 -biotype 398 HB "Pyroglutamic Acid" 85 -biotype 399 CG "Pyroglutamic Acid" 216 -biotype 400 HG "Pyroglutamic Acid" 85 -biotype 401 CD "Pyroglutamic Acid" 177 -biotype 402 OE "Pyroglutamic Acid" 178 -biotype 403 N "N-Terminal GLY" 230 -biotype 404 CA "N-Terminal GLY" 235 -biotype 405 C "N-Terminal GLY" 177 -biotype 406 HN "N-Terminal GLY" 233 -biotype 407 O "N-Terminal GLY" 178 -biotype 408 HA "N-Terminal GLY" 85 -biotype 409 N "N-Terminal ALA" 230 -biotype 410 CA "N-Terminal ALA" 236 -biotype 411 C "N-Terminal ALA" 177 -biotype 412 HN "N-Terminal ALA" 233 -biotype 413 O "N-Terminal ALA" 178 -biotype 414 HA "N-Terminal ALA" 85 -biotype 415 N "N-Terminal VAL" 230 -biotype 416 CA "N-Terminal VAL" 236 -biotype 417 C "N-Terminal VAL" 177 -biotype 418 HN "N-Terminal VAL" 233 -biotype 419 O "N-Terminal VAL" 178 -biotype 420 HA "N-Terminal VAL" 85 -biotype 421 N "N-Terminal LEU" 230 -biotype 422 CA "N-Terminal LEU" 236 -biotype 423 C "N-Terminal LEU" 177 -biotype 424 HN "N-Terminal LEU" 233 -biotype 425 O "N-Terminal LEU" 178 -biotype 426 HA "N-Terminal LEU" 85 -biotype 427 N "N-Terminal ILE" 230 -biotype 428 CA "N-Terminal ILE" 236 -biotype 429 C "N-Terminal ILE" 177 -biotype 430 HN "N-Terminal ILE" 233 -biotype 431 O "N-Terminal ILE" 178 -biotype 432 HA "N-Terminal ILE" 85 -biotype 433 N "N-Terminal SER" 230 -biotype 434 CA "N-Terminal SER" 236 -biotype 435 C "N-Terminal SER" 177 -biotype 436 HN "N-Terminal SER" 233 -biotype 437 O "N-Terminal SER" 178 -biotype 438 HA "N-Terminal SER" 85 -biotype 439 N "N-Terminal THR" 230 -biotype 440 CA "N-Terminal THR" 236 -biotype 441 C "N-Terminal THR" 177 -biotype 442 HN "N-Terminal THR" 233 -biotype 443 O "N-Terminal THR" 178 -biotype 444 HA "N-Terminal THR" 85 -biotype 445 N "N-Terminal CYS (SH)" 230 -biotype 446 CA "N-Terminal CYS (SH)" 236 -biotype 447 C "N-Terminal CYS (SH)" 177 -biotype 448 HN "N-Terminal CYS (SH)" 233 -biotype 449 O "N-Terminal CYS (SH)" 178 -biotype 450 HA "N-Terminal CYS (SH)" 85 -biotype 451 N "N-Terminal CYX (SS)" 230 -biotype 452 CA "N-Terminal CYX (SS)" 236 -biotype 453 C "N-Terminal CYX (SS)" 177 -biotype 454 HN "N-Terminal CYX (SS)" 233 -biotype 455 O "N-Terminal CYX (SS)" 178 -biotype 456 HA "N-Terminal CYX (SS)" 85 -biotype 457 N "N-Terminal CYD (S-)" -1 -biotype 458 CA "N-Terminal CYD (S-)" -1 -biotype 459 C "N-Terminal CYD (S-)" -1 -biotype 460 HN "N-Terminal CYD (S-)" -1 -biotype 461 O "N-Terminal CYD (S-)" -1 -biotype 462 HA "N-Terminal CYD (S-)" -1 -biotype 463 N "N-Terminal PRO" 252 -biotype 464 CA "N-Terminal PRO" 238 -biotype 465 C "N-Terminal PRO" 177 -biotype 466 HN "N-Terminal PRO" 253 -biotype 467 O "N-Terminal PRO" 178 -biotype 468 HA "N-Terminal PRO" 85 -biotype 469 CD "N-Terminal PRO" 239 -biotype 470 HD "N-Terminal PRO" 85 -biotype 471 N "N-Terminal PHE" 230 -biotype 472 CA "N-Terminal PHE" 236 -biotype 473 C "N-Terminal PHE" 177 -biotype 474 HN "N-Terminal PHE" 233 -biotype 475 O "N-Terminal PHE" 178 -biotype 476 HA "N-Terminal PHE" 85 -biotype 477 N "N-Terminal TYR" 230 -biotype 478 CA "N-Terminal TYR" 236 -biotype 479 C "N-Terminal TYR" 177 -biotype 480 HN "N-Terminal TYR" 233 -biotype 481 O "N-Terminal TYR" 178 -biotype 482 HA "N-Terminal TYR" 85 -biotype 483 N "N-Terminal TYD (O-)" -1 -biotype 484 CA "N-Terminal TYD (O-)" -1 -biotype 485 C "N-Terminal TYD (O-)" -1 -biotype 486 HN "N-Terminal TYD (O-)" -1 -biotype 487 O "N-Terminal TYD (O-)" -1 -biotype 488 HA "N-Terminal TYD (O-)" -1 -biotype 489 N "N-Terminal TRP" 230 -biotype 490 CA "N-Terminal TRP" 236 -biotype 491 C "N-Terminal TRP" 177 -biotype 492 HN "N-Terminal TRP" 233 -biotype 493 O "N-Terminal TRP" 178 -biotype 494 HA "N-Terminal TRP" 85 -biotype 495 N "N-Terminal HIS (+)" 230 -biotype 496 CA "N-Terminal HIS (+)" 236 -biotype 497 C "N-Terminal HIS (+)" 177 -biotype 498 HN "N-Terminal HIS (+)" 233 -biotype 499 O "N-Terminal HIS (+)" 178 -biotype 500 HA "N-Terminal HIS (+)" 85 -biotype 501 N "N-Terminal HIS (HD)" 230 -biotype 502 CA "N-Terminal HIS (HD)" 236 -biotype 503 C "N-Terminal HIS (HD)" 177 -biotype 504 HN "N-Terminal HIS (HD)" 233 -biotype 505 O "N-Terminal HIS (HD)" 178 -biotype 506 HA "N-Terminal HIS (HD)" 85 -biotype 507 N "N-Terminal HIS (HE)" 230 -biotype 508 CA "N-Terminal HIS (HE)" 236 -biotype 509 C "N-Terminal HIS (HE)" 177 -biotype 510 HN "N-Terminal HIS (HE)" 233 -biotype 511 O "N-Terminal HIS (HE)" 178 -biotype 512 HA "N-Terminal HIS (HE)" 85 -biotype 513 N "N-Terminal ASP" 230 -biotype 514 CA "N-Terminal ASP" 236 -biotype 515 C "N-Terminal ASP" 177 -biotype 516 HN "N-Terminal ASP" 233 -biotype 517 O "N-Terminal ASP" 178 -biotype 518 HA "N-Terminal ASP" 85 -biotype 519 N "N-Terminal ASH (COOH)" -1 -biotype 520 CA "N-Terminal ASH (COOH)" -1 -biotype 521 C "N-Terminal ASH (COOH)" -1 -biotype 522 HN "N-Terminal ASH (COOH)" -1 -biotype 523 O "N-Terminal ASH (COOH)" -1 -biotype 524 HA "N-Terminal ASH (COOH)" -1 -biotype 525 N "N-Terminal ASN" 230 -biotype 526 CA "N-Terminal ASN" 236 -biotype 527 C "N-Terminal ASN" 177 -biotype 528 HN "N-Terminal ASN" 233 -biotype 529 O "N-Terminal ASN" 178 -biotype 530 HA "N-Terminal ASN" 85 -biotype 531 N "N-Terminal GLU" 230 -biotype 532 CA "N-Terminal GLU" 236 -biotype 533 C "N-Terminal GLU" 177 -biotype 534 HN "N-Terminal GLU" 233 -biotype 535 O "N-Terminal GLU" 178 -biotype 536 HA "N-Terminal GLU" 85 -biotype 537 N "N-Terminal GLH (COOH)" -1 -biotype 538 CA "N-Terminal GLH (COOH)" -1 -biotype 539 C "N-Terminal GLH (COOH)" -1 -biotype 540 HN "N-Terminal GLH (COOH)" -1 -biotype 541 O "N-Terminal GLH (COOH)" -1 -biotype 542 HA "N-Terminal GLH (COOH)" -1 -biotype 543 N "N-Terminal GLN" 230 -biotype 544 CA "N-Terminal GLN" 236 -biotype 545 C "N-Terminal GLN" 177 -biotype 546 HN "N-Terminal GLN" 233 -biotype 547 O "N-Terminal GLN" 178 -biotype 548 HA "N-Terminal GLN" 85 -biotype 549 N "N-Terminal MET" 230 -biotype 550 CA "N-Terminal MET" 236 -biotype 551 C "N-Terminal MET" 177 -biotype 552 HN "N-Terminal MET" 233 -biotype 553 O "N-Terminal MET" 178 -biotype 554 HA "N-Terminal MET" 85 -biotype 555 N "N-Terminal LYS" 230 -biotype 556 CA "N-Terminal LYS" 236 -biotype 557 C "N-Terminal LYS" 177 -biotype 558 HN "N-Terminal LYS" 233 -biotype 559 O "N-Terminal LYS" 178 -biotype 560 HA "N-Terminal LYS" 85 -biotype 561 N "N-Terminal LYD (NH2)" -1 -biotype 562 CA "N-Terminal LYD (NH2)" -1 -biotype 563 C "N-Terminal LYD (NH2)" -1 -biotype 564 HN "N-Terminal LYD (NH2)" -1 -biotype 565 O "N-Terminal LYD (NH2)" -1 -biotype 566 HA "N-Terminal LYD (NH2)" -1 -biotype 567 N "N-Terminal ARG" 230 -biotype 568 CA "N-Terminal ARG" 236 -biotype 569 C "N-Terminal ARG" 177 -biotype 570 HN "N-Terminal ARG" 233 -biotype 571 O "N-Terminal ARG" 178 -biotype 572 HA "N-Terminal ARG" 85 -biotype 573 N "N-Terminal ORN" 230 -biotype 574 CA "N-Terminal ORN" 236 -biotype 575 C "N-Terminal ORN" 177 -biotype 576 HN "N-Terminal ORN" 233 -biotype 577 O "N-Terminal ORN" 178 -biotype 578 HA "N-Terminal ORN" 85 -biotype 579 N "N-Terminal AIB" 230 -biotype 580 CA "N-Terminal AIB" 237 -biotype 581 C "N-Terminal AIB" 177 -biotype 582 HN "N-Terminal AIB" 233 -biotype 583 O "N-Terminal AIB" 178 -biotype 584 N "C-Terminal GLY" 180 -biotype 585 CA "C-Terminal GLY" 226 -biotype 586 C "C-Terminal GLY" 213 -biotype 587 HN "C-Terminal GLY" 183 -biotype 588 OXT "C-Terminal GLY" 214 -biotype 589 HA "C-Terminal GLY" 85 -biotype 590 N "C-Terminal ALA" 180 -biotype 591 CA "C-Terminal ALA" 225 -biotype 592 C "C-Terminal ALA" 213 -biotype 593 HN "C-Terminal ALA" 183 -biotype 594 OXT "C-Terminal ALA" 214 -biotype 595 HA "C-Terminal ALA" 85 -biotype 596 N "C-Terminal VAL" 180 -biotype 597 CA "C-Terminal VAL" 225 -biotype 598 C "C-Terminal VAL" 213 -biotype 599 HN "C-Terminal VAL" 183 -biotype 600 OXT "C-Terminal VAL" 214 -biotype 601 HA "C-Terminal VAL" 85 -biotype 602 N "C-Terminal LEU" 180 -biotype 603 CA "C-Terminal LEU" 225 -biotype 604 C "C-Terminal LEU" 213 -biotype 605 HN "C-Terminal LEU" 183 -biotype 606 OXT "C-Terminal LEU" 214 -biotype 607 HA "C-Terminal LEU" 85 -biotype 608 N "C-Terminal ILE" 180 -biotype 609 CA "C-Terminal ILE" 225 -biotype 610 C "C-Terminal ILE" 213 -biotype 611 HN "C-Terminal ILE" 183 -biotype 612 OXT "C-Terminal ILE" 214 -biotype 613 HA "C-Terminal ILE" 85 -biotype 614 N "C-Terminal SER" 180 -biotype 615 CA "C-Terminal SER" 225 -biotype 616 C "C-Terminal SER" 213 -biotype 617 HN "C-Terminal SER" 183 -biotype 618 OXT "C-Terminal SER" 214 -biotype 619 HA "C-Terminal SER" 85 -biotype 620 N "C-Terminal THR" 180 -biotype 621 CA "C-Terminal THR" 225 -biotype 622 C "C-Terminal THR" 213 -biotype 623 HN "C-Terminal THR" 183 -biotype 624 OXT "C-Terminal THR" 214 -biotype 625 HA "C-Terminal THR" 85 -biotype 626 N "C-Terminal CYS (SH)" 180 -biotype 627 CA "C-Terminal CYS (SH)" 225 -biotype 628 C "C-Terminal CYS (SH)" 213 -biotype 629 HN "C-Terminal CYS (SH)" 183 -biotype 630 OXT "C-Terminal CYS (SH)" 214 -biotype 631 HA "C-Terminal CYS (SH)" 85 -biotype 632 N "C-Terminal CYX (SS)" 180 -biotype 633 CA "C-Terminal CYX (SS)" 225 -biotype 634 C "C-Terminal CYX (SS)" 213 -biotype 635 HN "C-Terminal CYX (SS)" 183 -biotype 636 OXT "C-Terminal CYX (SS)" 214 -biotype 637 HA "C-Terminal CYX (SS)" 85 -biotype 638 N "C-Terminal CYD (S-)" -1 -biotype 639 CA "C-Terminal CYD (S-)" -1 -biotype 640 C "C-Terminal CYD (S-)" -1 -biotype 641 HN "C-Terminal CYD (S-)" -1 -biotype 642 OXT "C-Terminal CYD (S-)" -1 -biotype 643 HA "C-Terminal CYD (S-)" -1 -biotype 644 N "C-Terminal PRO" 181 -biotype 645 CA "C-Terminal PRO" 228 -biotype 646 C "C-Terminal PRO" 213 -biotype 647 OXT "C-Terminal PRO" 214 -biotype 648 HA "C-Terminal PRO" 85 -biotype 649 N "C-Terminal PHE" 180 -biotype 650 CA "C-Terminal PHE" 225 -biotype 651 C "C-Terminal PHE" 213 -biotype 652 HN "C-Terminal PHE" 183 -biotype 653 OXT "C-Terminal PHE" 214 -biotype 654 HA "C-Terminal PHE" 85 -biotype 655 N "C-Terminal TYR" 180 -biotype 656 CA "C-Terminal TYR" 225 -biotype 657 C "C-Terminal TYR" 213 -biotype 658 HN "C-Terminal TYR" 183 -biotype 659 OXT "C-Terminal TYR" 214 -biotype 660 HA "C-Terminal TYR" 85 -biotype 661 N "C-Terminal TYD (O-)" -1 -biotype 662 CA "C-Terminal TYD (O-)" -1 -biotype 663 C "C-Terminal TYD (O-)" -1 -biotype 664 HN "C-Terminal TYD (O-)" -1 -biotype 665 OXT "C-Terminal TYD (O-)" -1 -biotype 666 HA "C-Terminal TYD (O-)" -1 -biotype 667 N "C-Terminal TRP" 180 -biotype 668 CA "C-Terminal TRP" 225 -biotype 669 C "C-Terminal TRP" 213 -biotype 670 HN "C-Terminal TRP" 183 -biotype 671 OXT "C-Terminal TRP" 214 -biotype 672 HA "C-Terminal TRP" 85 -biotype 673 N "C-Terminal HIS (+)" 180 -biotype 674 CA "C-Terminal HIS (+)" 225 -biotype 675 C "C-Terminal HIS (+)" 213 -biotype 676 HN "C-Terminal HIS (+)" 183 -biotype 677 OXT "C-Terminal HIS (+)" 214 -biotype 678 HA "C-Terminal HIS (+)" 85 -biotype 679 N "C-Terminal HIS (HD)" 180 -biotype 680 CA "C-Terminal HIS (HD)" 225 -biotype 681 C "C-Terminal HIS (HD)" 213 -biotype 682 HN "C-Terminal HIS (HD)" 183 -biotype 683 OXT "C-Terminal HIS (HD)" 214 -biotype 684 HA "C-Terminal HIS (HD)" 85 -biotype 685 N "C-Terminal HIS (HE)" 180 -biotype 686 CA "C-Terminal HIS (HE)" 225 -biotype 687 C "C-Terminal HIS (HE)" 213 -biotype 688 HN "C-Terminal HIS (HE)" 183 -biotype 689 OXT "C-Terminal HIS (HE)" 214 -biotype 690 HA "C-Terminal HIS (HE)" 85 -biotype 691 N "C-Terminal ASP" 180 -biotype 692 CA "C-Terminal ASP" 225 -biotype 693 C "C-Terminal ASP" 213 -biotype 694 HN "C-Terminal ASP" 183 -biotype 695 OXT "C-Terminal ASP" 214 -biotype 696 HA "C-Terminal ASP" 85 -biotype 697 N "C-Terminal ASH (COOH)" -1 -biotype 698 CA "C-Terminal ASH (COOH)" -1 -biotype 699 C "C-Terminal ASH (COOH)" -1 -biotype 700 HN "C-Terminal ASH (COOH)" -1 -biotype 701 OXT "C-Terminal ASH (COOH)" -1 -biotype 702 HA "C-Terminal ASH (COOH)" -1 -biotype 703 N "C-Terminal ASN" 180 -biotype 704 CA "C-Terminal ASN" 225 -biotype 705 C "C-Terminal ASN" 213 -biotype 706 HN "C-Terminal ASN" 183 -biotype 707 OXT "C-Terminal ASN" 214 -biotype 708 HA "C-Terminal ASN" 85 -biotype 709 N "C-Terminal GLU" 180 -biotype 710 CA "C-Terminal GLU" 225 -biotype 711 C "C-Terminal GLU" 213 -biotype 712 HN "C-Terminal GLU" 183 -biotype 713 OXT "C-Terminal GLU" 214 -biotype 714 HA "C-Terminal GLU" 85 -biotype 715 N "C-Terminal GLH (COOH)" -1 -biotype 716 CA "C-Terminal GLH (COOH)" -1 -biotype 717 C "C-Terminal GLH (COOH)" -1 -biotype 718 HN "C-Terminal GLH (COOH)" -1 -biotype 719 OXT "C-Terminal GLH (COOH)" -1 -biotype 720 HA "C-Terminal GLH (COOH)" -1 -biotype 721 N "C-Terminal GLN" 180 -biotype 722 CA "C-Terminal GLN" 225 -biotype 723 C "C-Terminal GLN" 213 -biotype 724 HN "C-Terminal GLN" 183 -biotype 725 OXT "C-Terminal GLN" 214 -biotype 726 HA "C-Terminal GLN" 85 -biotype 727 N "C-Terminal MET" 180 -biotype 728 CA "C-Terminal MET" 225 -biotype 729 C "C-Terminal MET" 213 -biotype 730 HN "C-Terminal MET" 183 -biotype 731 OXT "C-Terminal MET" 214 -biotype 732 HA "C-Terminal MET" 85 -biotype 733 N "C-Terminal LYS" 180 -biotype 734 CA "C-Terminal LYS" 225 -biotype 735 C "C-Terminal LYS" 213 -biotype 736 HN "C-Terminal LYS" 183 -biotype 737 OXT "C-Terminal LYS" 214 -biotype 738 HA "C-Terminal LYS" 85 -biotype 739 N "C-Terminal LYD (NH2)" -1 -biotype 740 CA "C-Terminal LYD (NH2)" -1 -biotype 741 C "C-Terminal LYD (NH2)" -1 -biotype 742 HN "C-Terminal LYD (NH2)" -1 -biotype 743 OXT "C-Terminal LYD (NH2)" -1 -biotype 744 HA "C-Terminal LYD (NH2)" -1 -biotype 745 N "C-Terminal ARG" 180 -biotype 746 CA "C-Terminal ARG" 225 -biotype 747 C "C-Terminal ARG" 213 -biotype 748 HN "C-Terminal ARG" 183 -biotype 749 OXT "C-Terminal ARG" 214 -biotype 750 HA "C-Terminal ARG" 85 -biotype 751 N "C-Terminal ORN" 180 -biotype 752 CA "C-Terminal ORN" 225 -biotype 753 C "C-Terminal ORN" 213 -biotype 754 HN "C-Terminal ORN" 183 -biotype 755 OXT "C-Terminal ORN" 214 -biotype 756 HA "C-Terminal ORN" 85 -biotype 757 N "C-Terminal AIB" 180 -biotype 758 CA "C-Terminal AIB" 227 -biotype 759 C "C-Terminal AIB" 213 -biotype 760 HN "C-Terminal AIB" 183 -biotype 761 OXT "C-Terminal AIB" 214 -biotype 762 N "Deprotonated N-Terminus" -1 -biotype 763 H "Deprotonated N-Terminus" -1 -biotype 764 C "Formyl N-Terminus" 177 -biotype 765 H "Formyl N-Terminus" 221 -biotype 766 O "Formyl N-Terminus" 178 -biotype 767 CH3 "Acetyl N-Terminus" 80 -biotype 768 H "Acetyl N-Terminus" 85 -biotype 769 C "Acetyl N-Terminus" 177 -biotype 770 O "Acetyl N-Terminus" 178 -biotype 771 C "Protonated C-Terminus" -1 -biotype 772 O "Protonated C-Terminus" -1 -biotype 773 OH "Protonated C-Terminus" -1 -biotype 774 HO "Protonated C-Terminus" -1 -biotype 775 N "Amide C-Terminus" 179 -biotype 776 HN "Amide C-Terminus" 182 -biotype 777 N "N-MeAmide C-Terminus" 180 -biotype 778 HN "N-MeAmide C-Terminus" 183 -biotype 779 CH3 "N-MeAmide C-Terminus" 184 -biotype 780 H "N-MeAmide C-Terminus" 85 -biotype 2001 O "Water" 63 -biotype 2002 H "Water" 64 -biotype 2003 NA "Sodium Ion" -1 -biotype 2004 K "Potassium Ion" -1 -biotype 2005 MG "Magnesium Ion" -1 -biotype 2006 CA "Calcium Ion" -1 -biotype 2007 CL "Chloride Ion" -1 diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/spce.lt index 38596e7de3..fdf6172a4b 100644 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/spce.lt +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/spce.lt @@ -1,14 +1,3 @@ -# NOTE: THIS IS A SLIGHTLY ALTERED VERSION OF THE "spce.lt" FILE. -# This version uses "pair_style hybrid lj/cut/coul/long" to make it -# easier to combine with molecules using the OPLSAA force field. -# Otherwise, it is the same as the "common/spce.lt" file. -# -# (Note: Alternately, you can add this at the end of your "system.lt" file: -# write("In Init") { -# pair_style hybrid lj/cut/coul/long 10 lj/charmm/coul/long 9 10 10" -# } # ...but I decided it was simpler to use only one pair_style.) -# -# # file "spce.lt" # # H1 H2 @@ -38,10 +27,10 @@ SPCE { } write_once("In Settings") { - bond_coeff @bond:OH harmonic 1000.0 1.0 - angle_coeff @angle:HOH harmonic 1000.0 109.47 - pair_coeff @atom:O @atom:O lj/cut/coul/long 0.1553 3.166 - pair_coeff @atom:H @atom:H lj/cut/coul/long 0.0 2.058 + bond_coeff @bond:OH harmonic 600.0 1.0 + angle_coeff @angle:HOH harmonic 75.0 109.47 + pair_coeff @atom:O @atom:O lj/cut/coul/long 0.1553 3.166 + pair_coeff @atom:H @atom:H lj/cut/coul/long 0.0 0.0 group spce type @atom:O @atom:H fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH # (Remember to "unfix" fShakeSPCE during minimization.) @@ -52,11 +41,11 @@ SPCE { units real atom_style full # (Hybrid force fields were not necessary but are used for portability.) - pair_style hybrid lj/cut/coul/long 10.0 + pair_style hybrid lj/cut/coul/long 10.0 10.0 bond_style hybrid harmonic angle_style hybrid harmonic kspace_style pppm 0.0001 - pair_modify shift yes + #pair_modify mix arithmetic # LEAVE THIS UNSPECIFIED! } } # end of definition of "SPCE" water molecule type diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/README_run.sh b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/README_run.sh index 2fc88303d5..bf0ed33712 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/README_run.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/README_run.sh @@ -12,15 +12,15 @@ # If not, carry out the instructions in "README_setup.sh". # # -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, +# If "lmp_mpi" is the name of the command you use to invoke lammps, # then you would run lammps on these files this way: -lmp_linux -i run.in.npt # minimization and simulation at constant pressure -lmp_linux -i run.in.nvt # simulation at constant volume +lmp_mpi -i run.in.npt # minimization and simulation at constant pressure +lmp_mpi -i run.in.nvt # simulation at constant volume # If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.npt -#mpirun -np 4 lmp_linux -i run.in.nvt +#mpirun -np 4 lmp_mpi -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.nvt # (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/README_setup.sh index d80df900ef..2c3c217135 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/README_setup.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/README_setup.sh @@ -10,7 +10,7 @@ cd moltemplate_files # Create the "oplsaa.lt" file which moltemplate will need cd oplsaa_lt_generator/ - ./oplsaa_moltemplate.py oplsaa_subset.prm + oplsaa_moltemplate.py oplsaa_subset.prm mv -f oplsaa.lt .. cd .. diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/README.TXT b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/README.TXT index c49ef8a6ad..8ae373d713 100644 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/README.TXT +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/README.TXT @@ -19,7 +19,7 @@ so that it only contains atom types you plan to have in your simulation (see below for details). Then run the opls_moltemplate.py script this way: -python oplsaa_moltemplate.py oplsaa_subset.prm +oplsaa_moltemplate.py oplsaa_subset.prm This will create a file named "oplsaa.lt" @@ -39,10 +39,12 @@ other lines (beginning with the word "atom") must be deleted or commented out. (Leave the rest of the file alone.) For example: -If you were working with methane, you would delete every line +If you were working with methane and SPC water, you would delete every line beginning with the word "atom", except for these two lines: +atom 76 42 OW "SPC Water O" 8 15.999 2 +atom 77 43 HW "SPC Water H" 1 1.008 1 atom 83 13 CT "Methane CH4" 6 12.011 4 atom 85 46 HC "Alkane H-C" 1 1.008 1 @@ -78,8 +80,10 @@ By default, the OPLSAA force-field assigns atom charge according to atom type. When you run moltemplate, it will create a file named "system.in.charges", containing commands like: -set type 2 charge -0.42 -set type 3 charge 0.21 +set type 1 charge -0.82 +set type 2 charge 0.41 +set type 3 charge -0.42 +set type 4 charge 0.21 (This assumes your main moltemplate file is named "system.lt". If it was named something else, eg "polymer.lt", then the file created by moltemplate diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py deleted file mode 100755 index 32980aab1f..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py +++ /dev/null @@ -1,408 +0,0 @@ -#! /usr/bin/env python -# -# The purpose of this script is to create a moltemplate lt file for the oplsaa. -# forcefield. This will assist researchers in building complex simulations using -# this OPLS-UA and the OPLS-AA forcefields. - -__author__="Jason Lambert" -# (some additional corrections by Miguel Gonzalez and Andrew Jewett) -__version__="0.18" - -import sys -import os -from operator import itemgetter - -g_program_name = __file__.split('/')[-1] - -# To do that, first make a copy of the \"oplsaa.prm\" file -# (which can be downloaded from the TINKER web site). -# The lines in this file beginning with the word \"atoms\" should -# define the atoms which you plan to put in your simulation. All other -# lines beginning with the word \"atoms\" should be deleted. -# (Leave the other sections of this file alone.) -#""") - - - -#input data from file containing opls aa force field parameters. -try: - f=open(sys.argv[1],"r") -except: - sys.stderr.write("Error: \n" - " You need to specify a file name as an input argument:\n" - " python oplsaa_moltemplate.py \n" - " (or the file name is specified incorrectly)\n") - sys.exit() - - -sys.stderr.write(g_program_name+", version "+__version__+"\n" - "Reading parameter file...\n") - - -#output lt file -g=open("oplsaa.lt","w") - - - -lines = f.readlines() - - - -# Ignore/Comment out lines before the "## Atom Type Definitions ##" section. - -for i in range(0, len(lines)): - if (lines[i].find("## Atom Type Definitions ##") != -1): - break - else: - lines[i] = '# ' + lines[i] - - -# As of late 2014, there appear to be 906 atom types, but we don't assume this. -# First try to infer out how many atom types there were in the original -# oplsaa.prm file, or at least find an upper bound on the atom-type numbers. -# (Keep track of the maximum value of the first column in the "atom" section.) -max_atomType = 0 -num_atomTypes = 0 -for line in lines: - # skip over text after a # comment character - ic = line.find('#') - if ic != -1: - line = (line[:ic]).strip() - else: - line = line.strip() - # now look for lines beginning with the word "atom" - tokens = line.split() - if ((len(tokens)>2) and (tokens[0] == "atom")): - num_atomTypes += 1 - if (int(tokens[1]) > max_atomType): - max_atomType = int(tokens[1]) - -if num_atomTypes > 25: - sys.stderr.write("\n" - "(Note: If your computer freezes while running "+g_program_name+",\n" - " it could be because you forgot to edit the .prm file.\n" - " The original \"oplsaa.prm\" file distributed with TINKER has over 900 atom\n" - " types. If you run "+g_program_name+" on this file, it may freeze or\n" - " crash. Instead, run "+g_program_name+" on a SUBSET of the OPLS atoms\n" - " relevant to your problem. To do that, delete the lines from the .prm\n" - " file beginning with \"atom\" which you do not need.)\n\n") - -#temporary storage file -h=open("temp.txt","w+") -atom_lookup={} #this dictionary contains all the atom ffid's as a key and the number of atoms with that key -#atom=[[10000,10000] for i in range(906)] <- don't assume there are 906 atoms -atom=[[-10000,-10000] for i in range(0,max_atomType+1)] -#charge_by_type={} # lookup charge by atom type -#vdw_by_type={} # lookup epsilon & sigma paramters by atom type -charge_by_type=[0.0 for i in range(0,max_atomType+1)] # lookup charge by atom -vdw_by_type=[(0.0,0.0) for i in range(0,max_atomType+1)] # lookup epsilon & sigma - - - -#atom is declared this way so for sorting purposes. -#atom contains the following data upon allocation -#atom[][0]=atom_id( Important for partial charges and non_bonded interactions) -#atom[][1]=atom_ffid( Important for stretches, bending, torsions and impropers) -#atom[][2]=atom_mass -#atom[][3]=partial charge -#atom[][4]=non_bonding sigma -#atom[][5]=non_bonding epsilon -#atom[][6]=atom comment -bond=[] -#bond contains the following data -#bond[0]=atom 1 ffid -#bond[1]=atom 2 ffid -#bond[2]=bond spring constant(OPLS-aa compatible) -#bond[3]=equilibrium bond distance(Angstrom) -angle=[] -#angle contains the following data -#angle[0]=atom 1 ffid -#angle[1]=atom 2 ffid -#angle[2]=atom 3 ffid -#angle[3]=spring constant -#angle[4]=equilibrium angle (degrees) -dihedral=[] -#dihedral contains the following data -#dihedral[0]=atom 1 ffid -#dihedral[1]=atom 2 ffid -#dihedral[2]=atom 3 ffid -#dihedral[3]=atom 4 ffid -#dihedral[4]=v1 -#dihedral[5]=v2 -#dihedral[6]=v3 -#dihedral[7]=v4 -improper=[] -#improper[0]=atom 1 ffid -#improper[1]=atom 2 ffid(central atom) -#improper[2]=atom 3 ffid -#improper[3]=atom 4 ffid -#improper[4]=spring coefficient -#improper[5]=equilibrium angle - - -#This section gets all the parameters from the force field file -for line in lines: - - # skip over text after a # comment character - ic = line.find('#') - if ic != -1: - line = (line[:ic]).strip() - else: - line = line.strip() - - if line.find("atom") == 0: - line=line.split() - atom[int(line[1])-1]=[int(line[1]),int(line[2]),float(line[-2]), - 0.0,0.0,0.0," ".join(line[3:-2])] - elif line.find("vdw") == 0: - line=line.split() - #vdw_temp.append([float(line[1]),float(line[2]),float(line[3])]) - if (int(line[1]) <= max_atomType): - vdw_by_type[int(line[1])] = (float(line[2]),float(line[3])) - elif line.find("bond") == 0: - line=line.split() - bond.append([int(line[1]),int(line[2]),float(line[3]),float(line[4])]) - elif line.find("angle") == 0: - line=line.split() - angle.append([int(line[1]),int(line[2]),int(line[3]), - float(line[4]),float(line[5])]) - elif line.find("torsion") == 0: - line=line.split() - dihedral.append([int(line[1]),int(line[2]),int(line[3]),int(line[4]), - float(line[5]),float(line[8]), float(line[11]), 0.0]) - elif line.find("charge") == 0: - line=line.split() - #charge_temp.append([int(line[1]),float(line[2])]) - if (int(line[1]) <= max_atomType): - charge_by_type[int(line[1])] = float(line[2]) - elif line.find("imptors") == 0: - line=line.split() - improper.append([int(line[1]), int(line[2]), - int(line[3]), int(line[4]), float(line[5]), float(line[6])]) - -if len(atom) > 600: - sys.stderr.write("WARNING: The number of atom types in your file exceeds 600\n" - " (You were supposed to edit out the atoms you don't need.\n" - " Not doing this may crash your computer.)\n" - "\n" - " Proceed? (Y/N): ") - reply = sys.stdin.readline() - if find(reply.strip().lower(), 'y') != 0: - exit(0) - -#adding the charge and Lennard Jones parameters to -#to each atom type. -#----------------------------------------------# -for i in range(0,len(atom)): - atom_type_num = atom[i][0] - #q = charge_by_type.get(atomTypeNum) - #if q: - # atom[i][3] = q - if atom_type_num != -10000: - q = charge_by_type[atom_type_num] - atom[i][3] = q - -for i in range(0,len(atom)): - atom_type_num = atom[i][0] - #vdw_params = vdw_by_type.get(atomTypeNum) - #if vdw_params: - # atom[i][4] = vdw_params[0] - # atom[i][5] = vdw_params[1] - if atom_type_num != -10000: - vdw_params = vdw_by_type[atom_type_num] - atom[i][4] = vdw_params[0] - atom[i][5] = vdw_params[1] - -del(charge_by_type) -del(vdw_by_type) - -#----------------------------------------------------------# -#begin writing content to lt file -g.write("OPLSAA {\n\n" ) - -#write out the atom masses -#----------------------------------------------------------# -g.write(" write_once(\"Data Masses\"){\n")#checked with gaff -for i,x in enumerate(atom): - if x[0] != -10000: - g.write(" @atom:{} {} #{} partial charge={}\n".format( - x[0],x[2],x[6],x[3])) -g.write(" } #(end of atom masses)\n\n") -#----------------------------------------------------------# - - -#write out the pair coefficients -#----------------------------------------------------------# -g.write(" write_once(\"In Settings\"){\n")#checked with gaff -for i,x in enumerate(atom): - if x[0] != -10000: - g.write(" pair_coeff @atom:{0} @atom:{0} lj/cut/coul/long {1} {2}\n".format(x[0],x[5],x[4])) -g.write(" } #(end of pair coeffs)\n\n") - -g.write(" write_once(\"In Charges\"){\n")#checked with gaff -for i,x in enumerate(atom): - if x[0] != -10000: - g.write(" set type @atom:{0} charge {1}\n".format(x[0],x[3])) -g.write(" } #(end of atom charges)\n\n") - -#-----------------------------------------------------------# - -# This part of the code creates a lookup dictionary -# that allows you to find every type of atom by its -# force field id. force field id is the id number -# relevant to bonds, angles, dihedrals, and impropers. -# This greatly increases the speed of angle, bond, dihedral -# and improper assignment. -#------------------------------------------------------------# -atom=sorted(atom,key=itemgetter(1)) -atom_ffid=0 -for x in atom: - if x[1]==atom_ffid: - atom_lookup[x[1]].append(x[0]) - elif x[1]>atom_ffid: - atom_lookup[x[1]]=[x[0]] - atom_ffid=x[1] -atom_lookup[0]=["*"] -#-------------------------------------------------------------# - - -#writing out the bond coefficients and bond parameters# -#-------------------------------------------------------------# -g.write(" write_once(\"In Settings\") {\n") -index1=0 -for x in bond: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - #g.write(" bond_coeff @bond:{}-{} harmonic {} {}\n".format(y,z,x[2]/2,x[3])) - # Miguel Gonzales corrected this line to: - g.write(" bond_coeff @bond:{}-{} harmonic {} {}\n".format(y,z,x[2],x[3])) - h.write(" @bond:{0}-{1} @atom:{0} @atom:{1}\n".format(y,z)) -g.write(" } #(end of bond_coeffs)\n\n") -h.seek(0,0) -g.write(" write_once(\"Data Bonds By Type\") {\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of bonds by type)\n\n") -del(bond) -h.close() -#-----------------------------------------------------------# -h=open("temp.txt","w+") - -#writing out angle coefficients and angles by type.---------# -#-----------------------------------------------------------# -g.write(" write_once(\"Data Angles By Type\"){\n") -for x in angle: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - for u in atom_lookup.get(x[2],[]): - #print(y,z,u,x) - #h.write(" angle_coeff @angle:{}-{}-{} harmonic {} {}\n".format(y,z,u,x[3]/2.0,x[4])) - # Miguel Gonzales corrected this line: - h.write(" angle_coeff @angle:{}-{}-{} harmonic {} {}\n".format(y,z,u,x[3],x[4])) - g.write(" @angle:{0}-{1}-{2} @atom:{0} @atom:{1} @atom:{2}\n".format(y,z,u)) - - -g.write(" } #(end of angles by type)\n\n") -h.seek(0,0) -g.write(" write_once(\"In Settings\" ){\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of angle_coeffs)\n\n") -del(angle) -h.close() -#----------------------------------------------------------# - -#writing dihedrals by type and dihedral coefficients-------# -h=h=open("temp.txt","w+") -g.write(" write_once(\"Data Dihedrals By Type\") {\n") -#print(atom_lookup) -for x in dihedral: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - for u in atom_lookup.get(x[2],[]): - for v in atom_lookup.get(x[3],[]): - if x[0]!=0 and x[3]!=0: - g.write(" @dihedral:{0}-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( - y,z,u,v)) - h.write(" dihedral_coeff @dihedral:{}-{}-{}-{} opls {} {} {} {}\n".format( - y,z,u,v,x[4],x[5],x[6],x[7])) - elif x[0]==0 and x[3]!=0: - g.write(" @dihedral:0-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( - y,z,u,v)) - h.write(" dihedral_coeff @dihedral:0-{}-{}-{} opls {} {} {} {}\n".format( - z,u,v,x[4],x[5],x[6],x[7])) - elif x[0]==0 and x[3]==0: - g.write(" @dihedral:0-{1}-{2}-0 @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( - y,z,u,v)) - #h.write(" dihedral_coeff @dihedral:0-{}-{}-0 harmonic {} {} {} {}\n".format( - h.write(" dihedral_coeff @dihedral:0-{}-{}-0 opls {} {} {} {}\n".format( - z,u,x[4],x[5],x[6],x[7])) - -del(dihedral) -g.write(" } #(end of Dihedrals by type)\n\n") -h.seek(0,0) -g.write(" write_once(\"In Settings\") {\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of dihedral_coeffs)\n\n") -h.close() -#-----------------------------------------------------------------------# - -#----writing out improper coefficients and impropers by type------------# -h=open("temp.txt","w+") -g.write(" write_once(\"Data Impropers By Type (opls_imp.py)\") {\n") -for x in improper: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - for u in atom_lookup.get(x[2],[]): - for v in atom_lookup.get(x[3],[]): - # Notation: let I,J,K,L denote the atom types ("biotypes") - # listed in the order they appear in the "oplsaa.prm" file. - # (I think J and L are represented by "u" and "v" in the code here.) - # It looks like the "oplsaa.prm" file distributed with tinker - # treats the third atom ("K") as the central atom. - # After checking the code, it appears that the improper angle is - # calculated as the angle between the I,J,K and the J,K,L planes - if x[0]==0 and x[1]==0 and x[3]==0: - g.write(" @improper:0-0-{2}-0 @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v)) - h.write(" improper_coeff @improper:0-0-{2}-0 harmonic {4} {5} \n".format(y,z,u,v,x[4]/2,180)) - else: - g.write(" @improper:0-0-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v)) - h.write(" improper_coeff @improper:0-0-{2}-{3} harmonic {4} {5} \n".format(y,z,u,v,x[4]/2,180)) - - -g.write(" } #(end of impropers by type)\n\n") -h.seek(0,0) -g.write(" write_once(\"In Settings\") {\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of improp_coeffs)\n\n") -#-----------------------------------------------------------------------# - -#This section writes out the input parameters required for an opls-aa simulation -# lammps. -g.write(" write_once(\"In Init\") {\n") -g.write(" units real\n") -g.write(" atom_style full\n") -g.write(" bond_style hybrid harmonic\n") -g.write(" angle_style hybrid harmonic\n") -g.write(" dihedral_style hybrid opls\n") -g.write(" improper_style hybrid harmonic\n") -#g.write(" pair_style hybrid lj/cut/coul/cut 10.0 10.0\n") -g.write(" pair_style hybrid lj/cut/coul/long 10.0 10.0\n") -g.write(" pair_modify mix geometric\n") -g.write(" special_bonds lj/coul 0.0 0.0 0.5\n") -g.write(" kspace_style pppm 0.0001\n") -g.write(" } #end of init parameters\n\n") -g.write("} # OPLSAA\n") -f.close() -g.close() -h.close() -os.remove("temp.txt") - - -sys.stderr.write("...finished.\n") - - - - diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm index 923aacac00..60bf1d855e 100644 --- a/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm +++ b/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.prm @@ -1,7 +1,9 @@ # This is a modified version of the file "oplsaa.prm" distributed with TINKER # http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm # In this version, all of the lines beginning with "atom" have been deleted -# except for the atom types we will be using in this simulation +# except for the atom types we will be using in this simulation. +# (That's all you need to do, but in this version, I also deleted +# everything else we don't need to reduce the file size.) # # If you use this file, please also cite the software this file comes from: # @@ -75,912 +77,8 @@ atom 77 43 HW "SPC Water H" 1 1.008 1 ################################ -vdw 1 2.9400 0.0610 -vdw 2 3.9050 0.1180 -vdw 3 3.7500 0.1050 -vdw 4 2.9600 0.2100 -vdw 5 3.0000 0.1700 -vdw 6 3.9100 0.1600 -vdw 7 0.0000 0.0000 -vdw 8 3.7300 0.2940 -vdw 9 3.7750 0.2070 -vdw 10 3.9050 0.1750 -vdw 11 3.9100 0.1600 -vdw 12 3.9600 0.1450 -vdw 13 3.9050 0.1180 -vdw 14 3.8500 0.1400 -vdw 15 3.8500 0.0800 -vdw 16 3.8000 0.1150 -vdw 17 3.7500 0.1100 -vdw 18 3.8000 0.0500 -vdw 19 3.7500 0.1050 -vdw 20 3.0700 0.1700 -vdw 21 0.0000 0.0000 -vdw 22 3.7750 0.2070 -vdw 23 3.9050 0.1180 -vdw 24 3.7000 0.2500 -vdw 25 3.5500 0.2500 -vdw 26 3.5500 0.2500 -vdw 27 3.5500 0.2500 -vdw 28 0.0000 0.0000 -vdw 29 0.0000 0.0000 -vdw 30 3.7750 0.2070 -vdw 31 3.9050 0.1180 -vdw 32 3.8000 0.1700 -vdw 33 3.8000 0.1180 -vdw 34 3.8000 0.1700 -vdw 35 3.8000 0.1180 -vdw 36 3.2000 0.1700 -vdw 37 3.6500 0.1500 -vdw 38 3.7750 0.2070 -vdw 39 3.8500 0.0800 -vdw 40 3.8000 0.0500 -vdw 41 3.0000 0.1700 -vdw 42 3.8000 0.1700 -vdw 43 3.8000 0.1180 -vdw 44 3.8000 0.1180 -vdw 45 3.4000 0.3000 -vdw 46 3.8000 0.0800 -vdw 47 3.4700 0.3000 -vdw 48 3.8000 0.0500 -vdw 49 3.4700 0.2660 -vdw 50 3.5600 0.3950 -vdw 51 2.9300 0.2800 -vdw 52 3.8100 0.1600 -vdw 53 2.9600 0.2100 -vdw 54 3.2500 0.1700 -vdw 55 3.8000 0.1150 -vdw 56 3.8000 0.1700 -vdw 57 0.0000 0.0000 -vdw 58 2.5560 0.0200 -vdw 59 2.7800 0.0690 -vdw 60 3.4010 0.2339 -vdw 61 3.6240 0.3170 -vdw 62 3.9350 0.4330 -vdw 63 3.15061 0.1521 -vdw 64 0.0000 0.0000 -vdw 65 3.15365 0.1550 -vdw 66 0.0000 0.0000 -vdw 67 0.0000 0.0000 -vdw 68 3.1760 0.1500 -vdw 69 0.0000 0.0000 -vdw 70 3.2700 0.1000 -vdw 71 0.0000 0.0000 -vdw 72 0.0000 0.0000 -vdw 73 3.1200 0.1600 -vdw 74 0.0000 0.0000 -vdw 75 0.0000 0.0000 vdw 76 3.16557 0.1554 vdw 77 0.0000 0.0000 -vdw 78 3.4200 0.1700 -vdw 79 0.0000 0.0000 -vdw 80 3.5000 0.0660 -vdw 81 3.5000 0.0660 -vdw 82 3.5000 0.0660 -vdw 83 3.5000 0.0660 -vdw 84 3.5000 0.0660 -vdw 85 2.5000 0.0300 -vdw 86 3.5500 0.0760 -vdw 87 3.5500 0.0760 -vdw 88 3.5500 0.0760 -vdw 89 2.4200 0.0300 -vdw 90 3.5500 0.0700 -vdw 91 2.4200 0.0300 -vdw 92 3.5500 0.0700 -vdw 93 3.5000 0.0660 -vdw 94 3.5000 0.0660 -vdw 95 3.5500 0.0760 -vdw 96 3.1200 0.1700 -vdw 97 0.0000 0.0000 -vdw 98 2.5000 0.0300 -vdw 99 3.5000 0.0660 -vdw 100 3.5000 0.0660 -vdw 101 3.5000 0.0660 -vdw 102 3.5000 0.0660 -vdw 103 3.2500 0.0620 -vdw 104 3.0700 0.1700 -vdw 105 0.0000 0.0000 -vdw 106 2.9400 0.0610 -vdw 107 2.5000 0.0300 -vdw 108 3.5500 0.0700 -vdw 109 3.0700 0.1700 -vdw 110 0.0000 0.0000 -vdw 111 3.0700 0.1700 -vdw 112 0.0000 0.0000 -vdw 113 3.0700 0.1700 -vdw 114 0.0000 0.0000 -vdw 115 3.5000 0.0660 -vdw 116 3.5000 0.0660 -vdw 117 3.5000 0.0660 -vdw 118 2.5000 0.0300 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0.0700 -vdw 814 2.9000 0.1400 -vdw 815 3.5000 0.0660 -vdw 816 2.9000 0.0600 -vdw 817 3.2500 0.1700 -vdw 818 3.5500 0.0700 -vdw 819 3.5000 0.0660 -vdw 820 3.7500 0.1050 -vdw 821 3.7500 0.1050 -vdw 822 2.9600 0.2100 -vdw 823 3.2500 0.1700 -vdw 824 0.0000 0.0000 -vdw 825 3.1200 0.1700 -vdw 826 0.0000 0.0000 -vdw 827 3.5000 0.0660 -vdw 828 3.5000 0.0660 -vdw 829 3.5500 0.0700 -vdw 830 3.5500 0.0700 -vdw 831 3.5500 0.0700 -vdw 832 3.5500 0.0700 -vdw 833 3.5500 0.0700 -vdw 834 1.9600 0.0125 -vdw 835 3.5000 0.0660 -vdw 836 3.5000 0.0660 -vdw 837 3.5000 0.0660 -vdw 838 3.7500 0.6000 -vdw 839 2.5000 0.0300 -vdw 840 3.2500 0.1700 -vdw 841 3.5500 0.0700 -vdw 842 3.5500 0.0700 -vdw 843 3.2500 0.1700 -vdw 844 3.5500 0.0700 -vdw 845 3.7500 0.1050 -vdw 846 2.9600 0.2100 -vdw 847 3.2500 0.1700 -vdw 848 3.5000 0.0660 -vdw 849 3.5000 0.0660 -vdw 850 3.5000 0.0660 -vdw 851 3.5000 0.0660 -vdw 852 2.4200 0.0150 -vdw 853 3.7500 0.1050 -vdw 854 2.9600 0.2100 -vdw 855 2.4200 0.0150 -vdw 856 3.5000 0.0660 -vdw 857 3.5000 0.0660 -vdw 858 3.5000 0.0660 -vdw 859 3.5000 0.0660 -vdw 860 3.5000 0.0660 -vdw 861 3.5000 0.0660 -vdw 862 3.5000 0.0660 -vdw 863 3.5000 0.0660 -vdw 864 3.5000 0.0660 -vdw 865 3.5000 0.0660 -vdw 866 4.0000 0.1000 -vdw 867 4.0000 0.1000 -vdw 868 4.0000 0.1000 -vdw 869 4.0000 0.1000 -vdw 870 2.5000 0.0300 -vdw 871 3.5000 0.0660 -vdw 872 3.5000 0.0660 -vdw 873 3.5000 0.0660 -vdw 874 3.5000 0.0660 -vdw 875 3.0800 0.7200 -vdw 876 4.1800 0.11779 -vdw 877 4.5100 0.0900 -vdw 878 5.1500 0.0700 -vdw 879 2.7000 0.018279 -vdw 880 3.3500 0.002772 -vdw 881 4.0600 0.000328 -vdw 882 4.3200 0.000171 -vdw 883 4.8200 0.000081 -vdw 884 2.9100 0.875044 -vdw 885 3.4700 0.449657 -vdw 886 3.8200 0.118226 -vdw 887 4.1800 0.047096 -vdw 888 3.5000 0.0660 -vdw 889 3.5000 0.0660 -vdw 890 3.5000 0.0660 -vdw 891 3.5000 0.0660 -vdw 892 2.5000 0.0300 -vdw 893 3.2500 0.1700 -vdw 894 3.5500 0.0700 -vdw 895 3.2500 0.1700 -vdw 896 3.5500 0.0700 -vdw 897 3.5500 0.0760 -vdw 898 3.5500 0.0760 -vdw 899 2.4200 0.0300 -vdw 900 3.3000 0.0860 -vdw 901 3.3000 0.0860 -vdw 902 3.3000 0.0860 -vdw 903 3.3000 0.0860 -vdw 904 3.3000 0.0860 -vdw 905 2.9600 0.2100 -vdw 906 3.5000 0.0660 ################################## @@ -990,385 +88,7 @@ vdw 906 3.5000 0.0660 ################################## -bond 1 2 367.00 1.3800 -bond 1 3 420.00 1.3570 -bond 1 13 367.00 1.3600 -bond 1 19 450.00 1.2790 -bond 1 25 300.00 0.3000 -bond 1 47 420.00 1.3400 -bond 1 48 420.00 1.3540 -bond 1 82 420.00 1.3540 -bond 1 83 420.00 1.3540 -bond 1 84 420.00 1.3540 -bond 1 87 420.00 1.3540 -bond 1 88 420.00 1.3540 -bond 1 108 461.00 1.5700 -bond 2 2 260.00 1.5260 -bond 2 3 317.00 1.5220 -bond 2 5 386.00 1.4250 -bond 2 6 260.00 1.5260 -bond 2 10 260.00 1.5260 -bond 2 11 317.00 1.5000 -bond 2 12 317.00 1.5100 -bond 2 13 260.00 1.5260 -bond 2 14 317.00 1.5000 -bond 2 15 222.00 1.8100 -bond 2 16 222.00 1.8100 -bond 2 20 320.00 1.4250 -bond 2 24 337.00 1.4490 -bond 2 44 382.00 1.4480 -bond 2 48 317.00 1.5100 -bond 2 51 260.00 1.5260 -bond 2 53 367.00 1.4710 -bond 2 55 337.00 1.4630 -bond 2 80 317.00 1.4950 -bond 3 3 350.00 1.5100 -bond 3 4 570.00 1.2290 -bond 3 5 450.00 1.3640 -bond 3 6 317.00 1.5220 -bond 3 10 317.00 1.5220 -bond 3 12 469.00 1.4000 -bond 3 13 317.00 1.5220 -bond 3 19 400.00 1.4440 -bond 3 20 214.00 1.3270 -bond 3 21 300.00 1.7900 -bond 3 24 490.00 1.3350 -bond 3 44 317.00 1.5220 -bond 3 46 340.00 1.0900 -bond 3 47 410.00 1.4440 -bond 3 48 400.00 1.4900 -bond 3 50 385.00 1.4600 -bond 3 52 656.00 1.2500 -bond 3 56 457.00 1.3580 -bond 3 57 418.00 1.3880 -bond 3 60 447.00 1.4190 -bond 3 65 300.00 1.9800 -bond 3 84 400.00 1.4900 -bond 3 86 385.00 1.4600 -bond 3 105 424.00 1.3830 -bond 3 107 490.00 1.3350 -bond 4 25 553.00 0.3000 -bond 4 64 525.00 1.4800 -bond 4 89 570.00 1.2290 -bond 4 110 700.00 1.1710 -bond 5 6 386.00 1.4250 -bond 5 7 553.00 0.9450 -bond 5 10 386.00 1.4250 -bond 5 13 320.00 1.4100 -bond 5 20 250.00 1.4700 -bond 5 24 400.00 1.3800 -bond 5 25 340.00 0.3000 -bond 5 44 320.00 1.4500 -bond 5 47 450.00 1.3700 -bond 5 48 450.00 1.3640 -bond 5 51 320.00 1.3800 -bond 5 64 230.00 1.6100 -bond 5 79 450.00 1.6700 -bond 5 106 94.00 1.8000 -bond 5 108 374.00 1.6400 -bond 6 6 260.00 1.5260 -bond 6 10 260.00 1.5260 -bond 6 11 317.00 1.5000 -bond 6 13 260.00 1.5260 -bond 6 14 317.00 1.5000 -bond 6 15 222.00 1.8100 -bond 6 16 222.00 1.8100 -bond 6 20 320.00 1.4250 -bond 6 24 337.00 1.4490 -bond 6 44 382.00 1.4480 -bond 6 47 317.00 1.5100 -bond 6 51 260.00 1.5260 -bond 6 53 367.00 1.4710 -bond 6 55 337.00 1.4630 -bond 6 79 222.00 1.8100 -bond 6 105 337.00 1.4750 -bond 7 20 553.00 0.9450 -bond 7 25 340.00 0.1000 -bond 9 9 530.00 1.3400 -bond 9 11 530.00 1.3400 -bond 9 14 530.00 1.3400 -bond 10 10 260.00 1.5260 -bond 10 11 317.00 1.5000 -bond 10 14 317.00 1.5000 -bond 10 20 320.00 1.4250 -bond 10 24 337.00 1.4490 -bond 10 44 382.00 1.4480 -bond 10 105 337.00 1.4750 -bond 11 11 530.00 1.3400 -bond 11 13 317.00 1.5000 -bond 11 14 530.00 1.3400 -bond 11 79 222.00 1.7600 -bond 12 12 469.00 1.4000 -bond 12 48 469.00 1.4000 -bond 12 60 469.00 1.4000 -bond 12 81 469.00 1.4000 -bond 13 13 268.00 1.5290 -bond 13 14 317.00 1.5000 -bond 13 15 222.00 1.8100 -bond 13 16 222.00 1.8100 -bond 13 18 390.00 1.4300 -bond 13 19 390.00 1.4700 -bond 13 20 320.00 1.4100 -bond 13 21 245.00 1.7810 -bond 13 22 340.00 1.7900 -bond 13 24 337.00 1.4490 -bond 13 25 340.00 0.3000 -bond 13 44 382.00 1.4480 -bond 13 46 340.00 1.0900 -bond 13 47 317.00 1.5100 -bond 13 48 317.00 1.5100 -bond 13 50 317.00 1.5100 -bond 13 51 268.00 1.5290 -bond 13 53 367.00 1.4710 -bond 13 55 337.00 1.4630 -bond 13 56 337.00 1.4490 -bond 13 57 337.00 1.4750 -bond 13 60 317.00 1.5100 -bond 13 64 212.00 1.8430 -bond 13 65 245.00 1.9450 -bond 13 66 200.00 2.1900 -bond 13 79 340.00 1.7700 -bond 13 80 317.00 1.4950 -bond 13 83 317.00 1.5040 -bond 13 84 317.00 1.5040 -bond 13 85 317.00 1.5040 -bond 13 87 317.00 1.4950 -bond 13 90 337.00 1.4490 -bond 13 91 280.00 1.5100 -bond 13 95 532.80 1.4600 -bond 13 101 382.00 1.4480 -bond 13 102 375.00 1.4900 -bond 13 104 212.00 1.8200 -bond 13 105 337.00 1.4750 -bond 13 107 337.00 1.4490 -bond 13 108 187.00 1.8600 -bond 13 109 317.00 1.5100 -bond 14 14 530.00 1.3400 -bond 15 17 274.00 1.3360 -bond 15 48 250.00 1.7400 -bond 16 16 166.00 2.0380 -bond 16 19 300.00 1.6850 -bond 16 24 250.00 1.7300 -bond 16 25 340.00 0.5000 -bond 16 47 250.00 1.7600 -bond 16 48 250.00 1.7600 -bond 16 61 250.00 1.7300 -bond 16 82 250.00 1.7600 -bond 16 84 250.00 1.7400 -bond 16 91 222.00 1.8100 -bond 16 108 144.00 2.1500 -bond 17 25 340.00 0.1000 -bond 18 18 550.00 1.1200 -bond 18 19 650.00 1.1570 -bond 18 48 400.00 1.4100 -bond 18 56 550.00 1.2400 -bond 19 19 1150.00 1.2100 -bond 19 21 330.00 1.6370 -bond 19 46 420.00 1.0800 -bond 19 47 400.00 1.4260 -bond 19 48 400.00 1.4510 -bond 19 50 400.00 1.4260 -bond 19 65 330.00 1.7840 -bond 19 88 400.00 1.4510 -bond 19 91 400.00 1.4510 -bond 20 20 250.00 1.4700 -bond 20 21 200.00 1.6900 -bond 20 24 320.00 1.4500 -bond 20 25 340.00 0.3000 -bond 20 44 320.00 1.4500 -bond 20 47 450.00 1.3700 -bond 20 48 450.00 1.3640 -bond 20 51 320.00 1.3800 -bond 20 60 340.00 1.3600 -bond 20 61 462.00 1.3990 -bond 20 64 230.00 1.6100 -bond 20 82 462.00 1.3570 -bond 20 84 340.00 1.3600 -bond 20 108 374.00 1.6400 -bond 21 25 300.00 0.3000 -bond 21 47 300.00 1.7250 -bond 21 48 300.00 1.7250 -bond 21 82 300.00 1.7250 -bond 21 83 300.00 1.7250 -bond 21 84 300.00 1.7250 -bond 21 87 300.00 1.7250 -bond 21 88 300.00 1.7250 -bond 21 108 223.00 2.0200 -bond 22 23 700.00 1.5300 -bond 22 25 340.00 0.5000 -bond 23 25 340.00 0.3000 -bond 23 79 700.00 1.4400 -bond 24 25 367.00 0.3000 -bond 24 45 434.00 1.0100 -bond 24 48 427.00 1.3810 -bond 24 59 427.00 1.3810 -bond 24 79 434.00 1.6700 -bond 24 84 427.00 1.3810 -bond 24 88 427.00 1.3810 -bond 24 91 337.00 1.4490 -bond 24 103 500.00 1.2700 -bond 24 106 40.00 2.0500 -bond 25 25 340.00 0.3000 -bond 25 44 340.00 0.3000 -bond 25 45 340.00 0.1000 -bond 25 46 340.00 0.3000 -bond 25 47 340.00 0.3000 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47 48 427.00 1.4330 -bond 47 50 549.00 1.3400 -bond 47 57 448.00 1.3650 -bond 47 58 367.00 1.0800 -bond 47 65 300.00 1.9000 -bond 47 66 250.00 2.0800 -bond 47 86 385.00 1.4600 -bond 47 91 317.00 1.5100 -bond 47 105 448.00 1.3650 -bond 47 110 700.00 1.3050 -bond 48 48 469.00 1.4000 -bond 48 49 367.00 1.0800 -bond 48 50 427.00 1.4330 -bond 48 53 400.00 1.4500 -bond 48 55 481.00 1.3400 -bond 48 56 483.00 1.3390 -bond 48 57 427.00 1.3810 -bond 48 60 469.00 1.4040 -bond 48 61 414.00 1.3910 -bond 48 64 220.00 1.7800 -bond 48 65 300.00 1.8700 -bond 48 66 250.00 2.0800 -bond 48 79 340.00 1.7700 -bond 48 81 469.00 1.4000 -bond 48 84 546.00 1.3670 -bond 48 86 469.00 1.4000 -bond 48 88 469.00 1.4210 -bond 48 91 317.00 1.4900 -bond 48 101 382.00 1.3850 -bond 48 102 400.00 1.4600 -bond 48 109 427.00 1.4330 -bond 49 59 367.00 1.0800 -bond 49 62 340.00 1.0800 -bond 49 82 367.00 1.0800 -bond 49 83 367.00 1.0800 -bond 49 84 367.00 1.0800 -bond 49 85 367.00 1.0800 -bond 49 87 367.00 1.0800 -bond 49 88 367.00 1.0800 -bond 50 50 385.00 1.4600 -bond 50 56 457.00 1.2900 -bond 50 84 549.00 1.3650 -bond 50 109 385.00 1.4600 -bond 51 105 337.00 1.4750 -bond 52 64 525.00 1.4800 -bond 53 54 434.00 1.0100 -bond 54 55 434.00 1.0100 -bond 55 59 481.00 1.3400 -bond 55 82 481.00 1.3400 -bond 56 56 500.00 1.3200 -bond 56 59 502.00 1.3240 -bond 56 60 461.00 1.3540 -bond 56 82 461.00 1.3540 -bond 56 86 483.00 1.3390 -bond 56 103 550.00 1.2100 -bond 56 109 457.00 1.2900 -bond 57 60 436.00 1.3740 -bond 57 61 400.00 1.3490 -bond 57 62 440.00 1.3710 -bond 57 81 428.00 1.3800 -bond 57 82 477.00 1.3430 -bond 57 84 427.00 1.3810 -bond 57 85 427.00 1.3810 -bond 57 86 385.00 1.4400 -bond 58 83 367.00 1.0800 -bond 58 84 367.00 1.0800 -bond 59 63 367.00 1.0800 -bond 60 60 520.00 1.3700 -bond 60 61 414.00 1.3910 -bond 60 80 388.00 1.4590 -bond 60 81 447.00 1.4190 -bond 60 87 469.00 1.4240 -bond 60 105 436.00 1.3740 -bond 61 61 400.00 1.2800 -bond 61 62 529.00 1.3040 -bond 61 82 488.00 1.3350 -bond 61 83 410.00 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-bond 102 103 550.00 1.2250 -bond 108 108 94.00 2.3200 -bond 109 109 549.00 1.3450 ################################ @@ -1378,2040 +98,7 @@ bond 109 109 549.00 1.3450 ################################ -angle 25 1 25 33.00 109.47 -angle 1 2 2 50.00 109.50 -angle 2 2 2 63.00 112.40 -angle 2 2 3 63.00 112.40 -angle 2 2 5 80.00 109.50 -angle 2 2 6 63.00 112.40 -angle 6 2 6 63.00 112.40 -angle 5 2 6 80.00 109.50 -angle 2 2 10 63.00 112.40 -angle 3 2 10 63.00 112.40 -angle 6 2 10 63.00 112.40 -angle 10 2 10 63.00 112.40 -angle 5 2 10 80.00 109.50 -angle 10 2 12 63.00 114.00 -angle 6 2 13 63.00 112.40 -angle 10 2 15 50.00 108.60 -angle 2 2 16 50.00 114.70 -angle 10 2 16 50.00 114.70 -angle 2 2 20 80.00 109.50 -angle 6 2 20 80.00 109.50 -angle 10 2 20 80.00 109.50 -angle 3 2 24 80.00 110.30 -angle 2 2 24 80.00 111.20 -angle 2 2 44 56.20 109.47 -angle 6 2 44 56.20 109.47 -angle 10 2 44 56.20 109.47 -angle 13 2 44 56.20 109.47 -angle 3 2 44 80.00 111.20 -angle 2 2 48 63.00 112.40 -angle 10 2 48 63.00 114.00 -angle 2 2 51 63.00 112.40 -angle 6 2 51 63.00 112.40 -angle 2 2 53 80.00 111.20 -angle 2 2 55 80.00 111.20 -angle 10 2 80 63.00 115.60 -angle 2 3 4 80.00 120.40 -angle 1 3 4 80.00 121.00 -angle 3 3 4 80.00 121.40 -angle 4 3 4 80.00 126.00 -angle 4 3 5 80.00 121.00 -angle 4 3 6 80.00 120.40 -angle 5 3 10 70.00 115.00 -angle 4 3 10 80.00 120.40 -angle 5 3 12 70.00 120.00 -angle 12 3 12 85.00 120.00 -angle 5 3 13 70.00 108.00 -angle 13 3 13 70.00 116.00 -angle 1 3 13 80.00 111.00 -angle 3 3 13 80.00 117.20 -angle 4 3 13 80.00 120.40 -angle 10 3 20 81.00 111.40 -angle 13 3 20 81.00 111.40 -angle 4 3 20 83.00 123.40 -angle 13 3 21 75.00 109.00 -angle 4 3 21 75.00 119.00 -angle 24 3 24 70.00 114.20 -angle 2 3 24 70.00 116.60 -angle 3 3 24 70.00 116.60 -angle 6 3 24 70.00 116.60 -angle 10 3 24 70.00 116.60 -angle 13 3 24 70.00 116.60 -angle 4 3 24 80.00 122.90 -angle 20 3 24 81.00 111.40 -angle 13 3 44 70.00 116.00 -angle 4 3 44 80.00 120.40 -angle 13 3 46 35.00 115.00 -angle 46 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64 20 100.00 108.23 -angle 4 64 48 45.00 109.50 -angle 5 64 48 45.00 109.50 -angle 20 64 48 45.00 109.50 -angle 5 64 52 45.00 108.23 -angle 13 64 52 45.00 109.50 -angle 20 64 52 100.00 108.23 -angle 52 64 52 140.00 119.90 -angle 25 65 25 33.00 109.47 -angle 25 66 25 33.00 109.47 -angle 78 77 78 150.00 180.00 -angle 6 79 11 62.00 98.90 -angle 13 79 13 62.00 102.00 -angle 5 79 13 75.00 96.40 -angle 5 79 23 74.00 108.70 -angle 13 79 23 74.00 108.90 -angle 23 79 23 104.00 119.00 -angle 13 79 24 100.00 103.00 -angle 23 79 24 120.00 107.00 -angle 13 79 44 62.00 102.00 -angle 23 79 44 74.00 108.90 -angle 13 79 48 62.00 102.00 -angle 23 79 48 74.00 107.20 -angle 5 79 48 75.00 96.40 -angle 24 79 48 100.00 103.00 -angle 13 79 82 62.00 102.00 -angle 46 80 60 35.00 126.80 -angle 2 80 60 70.00 128.60 -angle 13 80 60 70.00 128.60 -angle 46 80 84 35.00 126.80 -angle 2 80 84 70.00 125.00 -angle 13 80 84 70.00 125.00 -angle 60 80 84 85.00 106.40 -angle 12 81 57 70.00 132.80 -angle 48 81 57 70.00 132.80 -angle 57 81 60 70.00 104.40 -angle 12 81 60 85.00 122.70 -angle 48 81 60 85.00 122.70 -angle 13 82 16 70.00 125.00 -angle 16 82 24 70.00 125.00 -angle 16 82 44 70.00 120.20 -angle 20 82 49 35.00 117.00 -angle 16 82 49 35.00 125.00 -angle 49 82 57 35.00 120.00 -angle 57 82 57 70.00 120.00 -angle 13 82 57 70.00 125.00 -angle 48 82 57 70.00 125.00 -angle 56 82 57 70.00 126.20 -angle 49 82 61 35.00 120.00 -angle 16 82 61 70.00 113.60 -angle 16 82 61 70.00 115.00 -angle 20 82 61 70.00 115.00 -angle 57 82 61 70.00 120.00 -angle 13 82 61 70.00 125.00 -angle 44 82 61 70.00 126.10 -angle 24 82 61 70.00 126.20 -angle 57 82 79 70.00 120.00 -angle 61 82 79 70.00 120.00 -angle 20 82 86 70.00 122.00 -angle 61 82 86 70.00 130.00 -angle 57 82 87 70.00 106.20 -angle 56 82 87 70.00 127.70 -angle 49 83 61 35.00 120.00 -angle 48 83 61 70.00 111.00 -angle 13 83 61 70.00 124.50 -angle 49 83 84 35.00 128.20 -angle 61 83 84 70.00 111.00 -angle 13 83 84 70.00 130.70 -angle 13 84 16 70.00 125.00 -angle 13 84 20 70.00 121.60 -angle 16 84 24 70.00 125.00 -angle 20 84 49 35.00 113.40 -angle 16 84 49 35.00 125.00 -angle 48 84 49 35.00 130.70 -angle 49 84 50 35.00 130.70 -angle 20 84 50 70.00 110.00 -angle 49 84 57 35.00 121.60 -angle 13 84 57 70.00 121.60 -angle 48 84 57 70.00 121.60 -angle 3 84 57 85.00 120.00 -angle 57 84 58 35.00 120.00 -angle 13 84 61 70.00 118.90 -angle 49 84 80 35.00 120.00 -angle 57 84 80 70.00 108.70 -angle 49 84 83 35.00 130.70 -angle 57 84 83 70.00 106.30 -angle 20 84 83 70.00 108.00 -angle 16 84 83 70.00 111.00 -angle 13 84 83 70.00 130.70 -angle 13 84 84 70.00 120.00 -angle 57 84 84 70.00 120.00 -angle 61 84 84 70.00 120.00 -angle 20 84 86 70.00 121.60 -angle 57 84 86 70.00 121.60 -angle 49 84 87 35.00 132.10 -angle 57 84 87 70.00 107.70 -angle 20 84 87 70.00 110.60 -angle 16 84 87 70.00 111.00 -angle 61 84 87 70.00 111.90 -angle 13 84 87 70.00 132.10 -angle 48 84 87 70.00 132.10 -angle 86 84 87 70.00 132.10 -angle 3 84 87 85.00 120.00 -angle 49 85 57 35.00 120.00 -angle 13 85 57 70.00 121.60 -angle 49 85 85 35.00 130.70 -angle 57 85 85 70.00 106.30 -angle 13 85 85 70.00 130.70 -angle 48 86 48 63.00 120.00 -angle 48 86 56 70.00 124.00 -angle 48 86 82 63.00 120.00 -angle 48 86 83 63.00 120.00 -angle 48 86 84 63.00 120.00 -angle 48 86 86 63.00 120.00 -angle 56 86 86 70.00 124.00 -angle 48 86 87 63.00 120.00 -angle 48 86 88 63.00 120.00 -angle 49 87 60 35.00 120.00 -angle 46 87 60 35.00 126.80 -angle 13 87 60 70.00 128.60 -angle 49 87 84 35.00 125.70 -angle 46 87 84 35.00 126.80 -angle 84 87 84 70.00 103.80 -angle 82 87 84 70.00 110.40 -angle 2 87 84 70.00 125.00 -angle 13 87 84 70.00 125.00 -angle 3 87 84 70.00 130.00 -angle 60 87 84 85.00 106.40 -angle 84 87 86 70.00 125.70 -angle 49 87 87 35.00 127.50 -angle 60 87 87 70.00 107.30 -angle 84 87 87 70.00 107.30 -angle 86 87 87 70.00 127.50 -angle 84 87 88 70.00 103.80 -angle 48 88 49 35.00 128.60 -angle 49 88 61 35.00 118.90 -angle 13 88 61 70.00 118.90 -angle 19 88 61 70.00 118.90 -angle 61 88 87 70.00 111.90 -angle 4 89 90 80.00 134.00 -angle 90 89 91 70.00 91.00 -angle 4 89 91 80.00 134.00 -angle 13 90 89 55.00 127.00 -angle 89 90 91 50.00 94.00 -angle 13 90 91 50.00 126.00 -angle 24 91 46 35.00 108.00 -angle 13 91 46 35.00 114.30 -angle 44 91 46 35.00 114.30 -angle 46 91 46 35.00 114.30 -angle 16 91 46 37.50 108.00 -angle 46 91 47 35.00 109.50 -angle 46 91 89 37.50 110.00 -angle 24 91 89 70.00 117.00 -angle 46 91 90 35.00 111.00 -angle 16 91 90 55.00 109.00 -angle 91 91 91 30.00 79.20 -angle 13 91 91 37.50 117.20 -angle 44 91 91 37.50 117.20 -angle 46 91 91 37.50 117.20 -angle 24 91 91 37.50 126.00 -angle 16 91 91 55.00 128.00 -angle 89 91 91 63.00 85.00 -angle 47 91 91 63.00 114.00 -angle 90 91 91 80.00 89.00 -angle 13 95 13 172.80 120.00 -angle 13 95 46 144.00 120.00 -angle 13 101 45 35.00 109.50 -angle 45 101 45 43.60 106.40 -angle 45 101 48 50.00 112.50 -angle 13 101 48 50.00 120.50 -angle 13 102 103 80.00 117.50 -angle 48 102 103 80.00 117.50 -angle 103 102 103 80.00 125.00 -angle 25 103 25 10.00 109.50 -angle 25 103 102 10.00 109.50 -angle 13 104 13 45.00 109.50 -angle 3 105 10 70.00 117.60 -angle 3 105 13 70.00 117.60 -angle 3 105 45 35.00 119.20 -angle 45 105 47 35.00 119.20 -angle 13 105 47 70.00 121.20 -angle 3 105 47 70.00 121.60 -angle 3 105 51 70.00 117.60 -angle 47 105 51 70.00 121.20 -angle 45 105 60 30.00 125.80 -angle 6 105 60 70.00 125.80 -angle 10 105 60 70.00 125.80 -angle 13 105 60 70.00 125.80 -angle 51 105 60 70.00 125.80 -angle 45 105 62 30.00 128.80 -angle 60 105 62 70.00 105.40 -angle 6 105 62 70.00 128.80 -angle 10 105 62 70.00 128.80 -angle 13 105 62 70.00 128.80 -angle 51 105 62 70.00 128.80 -angle 4 106 24 20.00 109.50 -angle 24 106 24 20.00 109.50 -angle 13 107 13 50.00 118.00 -angle 3 107 13 50.00 121.90 -angle 1 108 13 35.00 110.50 -angle 13 108 13 60.00 110.00 -angle 13 108 20 60.00 100.00 -angle 20 108 20 60.00 110.00 -angle 13 108 21 35.00 110.50 -angle 45 108 45 35.00 109.50 -angle 13 108 45 35.00 110.50 -angle 46 108 46 35.00 109.50 -angle 13 108 46 35.00 110.50 -angle 13 108 65 35.00 110.50 -angle 13 108 66 35.00 110.50 -angle 13 108 108 50.00 112.00 -angle 46 109 48 35.00 123.30 -angle 46 109 50 35.00 120.00 -angle 13 109 50 70.00 124.00 -angle 46 109 109 35.00 120.00 -angle 13 109 109 70.00 124.00 -angle 50 109 109 70.00 124.00 -angle 48 109 109 85.00 117.00 -angle 4 110 47 160.00 180.00 -angle 47 110 47 160.00 180.00 - - - ################################ - ## ## - ## Urey-Bradley Parameters ## - ## ## - ################################ - - -ureybrad 35 34 35 38.25 1.5537 - - - ##################################### - ## ## - ## Improper Torsional Parameters ## - ## ## - ##################################### - - -imptors 0 0 3 4 21.000 180.0 2 -imptors 0 0 3 52 21.000 180.0 2 -imptors 0 0 24 0 5.000 180.0 2 -imptors 0 0 47 0 30.000 180.0 2 -imptors 0 0 48 0 5.000 180.0 2 - - - ############################ - ## ## - ## Torsional Parameters ## - ## ## - ############################ - - - ################################################################### - ## ## - ## Alternative Torsional Parameter Values for Use with OPLS-AA ## - ## ## - ## For some torsions, OPLS-AA has multiple possible parameter ## - ## values; the list below shows functional groups for which ## - ## these alternate (commented) values should be preferred; the ## - ## values are in the same order as in the full parameter list ## - ## ## - ## 4 3 3 36 generic (default) ## - ## 4 3 3 36 dicarbonyls ## - ## 36 3 3 36 hydrocarbon (default) ## - ## 36 3 3 36 dicarbonyls ## - ## 13 3 5 7 carboxylic acid (default) ## - ## 13 3 5 7 1,2-diacid monoanion ## - ## 4 3 13 13 peptide (default) ## - ## 4 3 13 13 propanamide ## - ## 4 3 13 13 carboxylic acid ## - ## 4 3 13 13 dicarboxylic acid ## - ## 4 3 13 13 aldyhyde, ketone, acyl halide ## - ## 4 3 13 13 1,2-diacid monoanion ## - ## 5 3 13 13 carboxylic acid (default) ## - ## 5 3 13 13 dicarboxylic acid ## - ## 35 3 13 13 peptide psi' (default) ## - ## 35 3 13 13 propanamide ## - ## 35 3 13 13 beta-3-peptide, last psi ## - ## 4 3 29 13 esters (default) ## - ## 4 3 29 13 benzoic esters ## - ## 7 5 13 13 alcohols (default) ## - ## 7 5 13 13 trifluoroethanol ## - ## 7 5 13 13 hexopyranoses ## - ## 7 5 13 36 alcohols (default) ## - ## 7 5 13 36 axial cyclohexanol ## - ## 7 5 13 36 trifluoroethanol ## - ## 0 13 13 13 alcohols, ethers (default) ## - ## 0 13 13 13 hexopyranoses ## - ## 3 13 13 3 dicarboxylic acid (default) ## - ## 3 13 13 3 1,2-diacid monoanion ## - ## 3 13 13 13 butanamide (default) ## - ## 3 13 13 13 carboxylate ion ## - ## 3 13 13 13 aldyhyde, ketone, acyl halide ## - ## 3 13 13 36 all carbonyls (default) ## - ## 3 13 13 36 dicarboxylic acid ## - ## 3 13 13 36 aldehyde, ketone, acyl halide ## - ## 5 13 13 5 diols only (default) ## - ## 5 13 13 5 triols only ## - ## 5 13 13 5 hexopyranoses ## - ## 13 13 13 13 hydrocarbon (default) ## - ## 13 13 13 13 perfluoroalkane ## - ## 13 13 13 35 peptide chi-1 (default) ## - ## 13 13 13 35 N-propylformamide ## - ## 36 13 13 69 generic (default) ## - ## 36 13 13 69 sulfone ## - ## 13 13 33 13 amine (default) ## - ## 13 13 33 13 exocyclic amine ## - ## 13 13 33 13 exocyclic 1,4-diamine ## - ## 13 13 33 34 amine (default) ## - ## 13 13 33 34 azetidine, 4-ring ## - ## 13 13 33 34 pyrrolidine, 5-ring ## - ## 13 13 33 34 cyclic amine ## - ## 13 13 33 34 cyclic 1,4-diamine ## - ## 13 13 35 3 peptide phi' (default) ## - ## 13 13 35 3 N-ethylformamide ## - ## 13 13 35 3 beta-3-peptide, first theta tors ## - ## 13 13 35 13 proline, CD-N-CA-CB (default) ## - ## 13 13 35 13 proline, CG-CD-N-CA ## - ## 36 13 35 3 peptide phi'' (default) ## - ## 36 13 35 3 N-methylformamide ## - ## 13 13 47 0 imidazole, indole, purine (default) ## - ## 13 13 47 0 nucleoside chi ## - ## 13 13 47 52 nucleoside (default) ## - ## 13 13 47 52 imidazole, indole, purine ## - ## 29 13 47 0 imidazole, indole, purine (default) ## - ## 29 13 47 0 nucleoside chi ## - ## 29 13 95 52 nucleoside (default) ## - ## 29 13 95 52 imidazole, indole, purine ## - ## 13 13 97 13 generic (default) ## - ## 13 13 97 13 generic ## - ## 17 15 38 0 aromatic thiol (default) ## - ## 17 15 38 0 aromatic thiol, N-C-S-H ## - ## 13 29 54 42 phosphonates (default) ## - ## 13 29 54 42 dimethyl phosphate ## - ## 34 35 72 16 diaryl amine (default) ## - ## 34 35 72 16 aniline-like ## - ## 34 35 72 29 diaryl amine (default) ## - ## 34 35 72 29 aniline-like ## - ## 13 40 40 37 diene (default) ## - ## 13 40 40 37 2-methyl-1,3-butadiene ## - ## 0 46 72 0 generic (default) ## - ## 0 46 72 0 generic ## - ## 0 47 72 0 generic (default) ## - ## 0 47 72 0 generic ## - ## 0 47 74 0 generic (default) ## - ## 0 47 74 0 generic ## - ## 0 47 74 0 generic ## - ## 0 51 72 0 generic (default) ## - ## 0 51 72 0 HA-CR-NB-?? or N?-CR-NB-?? ## - ## 0 72 77 0 generic (default) ## - ## 0 72 77 0 biphenyl-like, N-C-C-C ## - ## ## - ################################################################### - - -torsion 0 2 2 2 -2.500 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 0 2 2 6 -2.500 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 1 2 2 2 -2.000 0.0 1 0.700 180.0 2 3.000 0.0 3 -torsion 1 2 2 6 -2.000 0.0 1 0.700 180.0 2 3.000 0.0 3 -torsion 2 2 2 2 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 2 2 2 6 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 2 2 2 10 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 2 2 2 13 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 2 2 2 65 -2.000 0.0 1 0.500 180.0 2 3.250 0.0 3 -torsion 6 2 2 6 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 6 2 2 65 -2.000 0.0 1 0.500 180.0 2 3.250 0.0 3 -torsion 10 2 2 10 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 2 2 5 7 0.300 0.0 1 0.000 180.0 2 1.300 0.0 3 -torsion 6 2 5 7 0.300 0.0 1 0.000 180.0 2 1.300 0.0 3 -torsion 10 2 5 7 0.300 0.0 1 0.000 180.0 2 1.300 0.0 3 -torsion 0 2 10 2 -2.500 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 2 2 10 2 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 2 2 13 2 -3.400 0.0 1 1.250 180.0 2 3.100 0.0 3 -torsion 6 2 20 2 -7.400 0.0 1 3.000 180.0 2 1.800 0.0 3 -torsion 6 2 20 6 -8.400 0.0 1 3.000 180.0 2 1.800 0.0 3 -torsion 4 3 3 4 1.600 0.0 1 3.200 180.0 2 0.000 0.0 3 -torsion 4 3 3 13 0.000 0.0 1 0.500 180.0 2 0.000 0.0 3 -torsion 4 3 3 24 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 4 3 3 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -#torsion 4 3 3 36 0.000 0.0 1 0.200 180.0 2 0.000 0.0 3 -torsion 13 3 3 13 0.700 0.0 1 -1.500 180.0 2 0.000 0.0 3 -torsion 13 3 3 24 -0.500 0.0 1 0.200 180.0 2 0.000 0.0 3 -torsion 13 3 3 46 0.800 0.0 1 -0.760 180.0 2 0.000 0.0 3 -torsion 24 3 3 46 -0.900 0.0 1 0.300 180.0 2 0.000 0.0 3 -torsion 46 3 3 46 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -#torsion 36 3 3 36 0.800 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 3 3 5 7 3.000 0.0 1 5.500 180.0 2 0.000 0.0 3 -torsion 4 3 5 7 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 13 3 5 7 1.500 0.0 1 5.500 180.0 2 0.000 0.0 3 -#torsion 13 3 5 7 3.200 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 24 3 5 7 -2.000 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 46 3 5 7 1.500 0.0 1 5.500 180.0 2 0.000 0.0 3 -torsion 48 3 5 7 4.000 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 1 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 1 3 13 46 0.000 0.0 1 0.000 180.0 2 0.360 0.0 3 -torsion 3 3 13 46 0.000 0.0 1 0.000 180.0 2 0.085 0.0 3 -torsion 4 3 13 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 4 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -#torsion 4 3 13 13 0.000 0.0 1 1.166 180.0 2 0.000 0.0 3 -#torsion 4 3 13 13 0.000 0.0 1 0.546 180.0 2 0.000 0.0 3 -#torsion 4 3 13 13 -0.750 0.0 1 -0.550 180.0 2 -0.250 0.0 3 -#torsion 4 3 13 13 -0.277 0.0 1 1.228 180.0 2 -0.694 0.0 3 -#torsion 4 3 13 13 -1.000 0.0 1 -1.900 180.0 2 -0.900 0.0 3 -torsion 4 3 13 21 -0.650 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 4 3 13 44 0.000 0.0 1 0.820 180.0 2 0.000 0.0 3 -torsion 4 3 13 24 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 4 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 4 3 13 48 0.000 0.0 1 0.546 180.0 2 0.000 0.0 3 -torsion 5 3 13 13 0.000 0.0 1 1.412 180.0 2 0.000 0.0 3 -#torsion 5 3 13 13 1.000 0.0 1 0.546 180.0 2 0.450 0.0 3 -torsion 5 3 13 44 5.260 0.0 1 0.820 180.0 2 0.000 0.0 3 -torsion 5 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 13 3 13 13 1.454 0.0 1 -0.144 180.0 2 -0.775 0.0 3 -torsion 13 3 13 46 0.000 0.0 1 0.000 180.0 2 0.275 0.0 3 -torsion 20 3 13 13 0.000 0.0 1 0.000 180.0 2 -0.553 0.0 3 -torsion 20 3 13 46 0.000 0.0 1 0.000 180.0 2 0.132 0.0 3 -torsion 21 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 21 3 13 46 0.000 0.0 1 0.000 180.0 2 0.360 0.0 3 -torsion 24 3 13 13 1.173 0.0 1 0.189 180.0 2 -1.200 0.0 3 -#torsion 35 3 13 13 3.250 0.0 1 -0.402 180.0 2 -0.136 0.0 3 -#torsion 35 3 13 13 3.260 0.0 1 0.440 180.0 2 0.600 0.0 3 -torsion 24 3 13 21 0.650 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 24 3 13 24 1.816 0.0 1 1.222 180.0 2 1.581 0.0 3 -torsion 24 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 46 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 46 3 13 46 0.000 0.0 1 0.000 180.0 2 0.360 0.0 3 -torsion 48 3 13 46 0.000 0.0 1 0.000 180.0 2 0.275 0.0 3 -torsion 52 3 13 13 0.000 0.0 1 0.820 180.0 2 0.000 0.0 3 -torsion 52 3 13 44 0.000 0.0 1 0.820 180.0 2 0.000 0.0 3 -torsion 52 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 65 3 13 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 65 3 13 46 0.000 0.0 1 0.000 180.0 2 0.360 0.0 3 -torsion 107 3 13 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 4 3 20 13 0.000 0.0 1 5.124 180.0 2 0.000 0.0 3 -#torsion 4 3 29 13 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 4 3 20 48 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 13 3 20 13 4.669 0.0 1 5.124 180.0 2 0.000 0.0 3 -torsion 13 3 20 48 1.500 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 24 3 20 13 -2.000 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 46 3 20 13 4.669 0.0 1 5.124 180.0 2 0.000 0.0 3 -torsion 48 3 20 13 4.000 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 3 3 24 13 0.400 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 3 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 4 3 24 5 0.000 0.0 1 6.603 180.0 2 0.000 0.0 3 -torsion 4 3 24 13 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 4 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 4 3 24 47 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 4 3 24 48 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 4 3 24 91 0.000 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 5 3 24 13 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 5 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 13 3 24 5 4.542 0.0 1 6.603 180.0 2 1.045 0.0 3 -torsion 13 3 24 13 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 13 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 13 3 24 48 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 20 3 24 13 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 20 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 24 3 24 3 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 24 3 24 13 4.600 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 24 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 46 3 24 13 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 46 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 47 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 48 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 48 3 24 48 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 48 3 24 84 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 48 3 24 87 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 84 3 24 48 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 84 3 24 84 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 84 3 24 87 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 87 3 24 45 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 87 3 24 48 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 87 3 24 84 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 87 3 24 87 2.300 0.0 1 6.089 180.0 2 0.000 0.0 3 -torsion 0 3 47 13 0.900 0.0 1 0.230 180.0 2 -0.505 0.0 3 -torsion 4 3 47 46 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 4 3 47 47 2.500 0.0 1 6.000 180.0 2 0.000 0.0 3 -torsion 5 3 47 47 3.200 0.0 1 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2 0.000 0.0 3 -torsion 46 3 56 45 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 0 3 60 0 0.000 0.0 1 7.000 180.0 2 0.000 0.0 3 -torsion 4 3 60 0 0.000 0.0 1 7.000 180.0 2 0.000 0.0 3 -torsion 4 3 82 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 4 3 82 57 2.000 0.0 1 1.000 180.0 2 0.000 0.0 3 -torsion 4 3 82 61 0.000 0.0 1 1.000 180.0 2 0.000 0.0 3 -torsion 82 3 82 57 -2.000 0.0 1 1.000 180.0 2 0.000 0.0 3 -torsion 82 3 82 61 0.000 0.0 1 1.000 180.0 2 0.000 0.0 3 -torsion 4 3 84 20 -0.750 0.0 1 1.500 180.0 2 0.000 0.0 3 -torsion 4 3 84 87 0.750 0.0 1 1.500 180.0 2 0.000 0.0 3 -torsion 84 3 84 20 0.000 0.0 1 1.500 180.0 2 0.000 0.0 3 -torsion 84 3 84 87 0.000 0.0 1 1.500 180.0 2 0.000 0.0 3 -torsion 48 3 86 48 0.000 0.0 1 2.170 180.0 2 0.000 0.0 3 -torsion 0 3 87 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 4 3 87 84 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3 -torsion 4 3 87 87 0.000 0.0 1 2.100 180.0 2 0.000 0.0 3 -torsion 24 3 87 84 0.000 0.0 1 1.100 180.0 2 0.000 0.0 3 -torsion 24 3 87 87 0.000 0.0 1 1.100 180.0 2 0.000 0.0 3 -torsion 4 3 107 13 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 13 3 107 13 0.000 0.0 1 4.900 180.0 2 0.000 0.0 3 -torsion 4 3 109 109 2.500 0.0 1 6.000 180.0 2 0.000 0.0 3 -torsion 5 3 109 109 3.200 0.0 1 -3.000 180.0 2 0.000 0.0 3 -torsion 0 4 106 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 7 5 10 2 0.300 0.0 1 0.000 180.0 2 0.500 0.0 3 -torsion 7 5 10 6 0.300 0.0 1 0.000 180.0 2 0.500 0.0 3 -torsion 7 5 13 2 0.000 0.0 1 0.000 180.0 2 0.200 0.0 3 -torsion 7 5 13 6 0.000 0.0 1 0.000 180.0 2 0.200 0.0 3 -torsion 7 5 13 13 -0.356 0.0 1 -0.174 180.0 2 0.492 0.0 3 -#torsion 7 5 13 13 4.478 0.0 1 -2.175 180.0 2 0.000 0.0 3 -#torsion 7 5 13 13 2.674 0.0 1 -2.883 180.0 2 1.026 0.0 3 -torsion 7 5 13 46 0.000 0.0 1 0.000 180.0 2 0.352 0.0 3 -#torsion 7 5 13 36 -2.589 0.0 1 -1.123 180.0 2 0.270 0.0 3 -#torsion 7 5 13 36 0.000 0.0 1 0.000 180.0 2 0.476 0.0 3 -torsion 7 5 13 47 -0.900 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 7 5 13 48 -0.900 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 7 5 13 50 -0.900 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 7 5 44 13 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -torsion 7 5 44 45 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -torsion 7 5 24 3 5.519 0.0 1 -6.700 180.0 2 0.581 0.0 3 -torsion 7 5 24 45 2.722 0.0 1 -5.154 180.0 2 0.000 0.0 3 -torsion 7 5 47 47 0.000 0.0 1 1.682 180.0 2 0.000 0.0 3 -torsion 7 5 48 48 0.000 0.0 1 1.682 180.0 2 0.000 0.0 3 -torsion 7 5 51 20 -1.257 0.0 1 -1.806 180.0 2 0.003 0.0 3 -torsion 7 5 56 3 3.000 0.0 1 3.000 180.0 2 0.000 0.0 3 -torsion 7 5 64 4 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 7 5 64 5 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 7 5 79 13 -0.750 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 7 5 79 23 0.750 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 7 5 79 48 2.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 0 13 13 3 -4.344 0.0 1 -1.714 180.0 2 0.000 0.0 3 -torsion 0 13 13 13 1.711 0.0 1 -0.500 180.0 2 0.663 0.0 3 -#torsion 0 13 13 13 -1.336 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 0 13 13 24 1.428 0.0 1 0.086 180.0 2 0.029 0.0 3 -torsion 1 13 13 1 -2.500 0.0 1 0.000 180.0 2 0.250 0.0 3 -torsion 1 13 13 5 0.000 0.0 1 0.000 180.0 2 0.540 0.0 3 -torsion 1 13 13 13 0.300 0.0 1 -0.400 180.0 2 0.400 0.0 3 -torsion 1 13 13 46 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 -torsion 3 13 13 3 -0.550 0.0 1 0.000 180.0 2 1.000 0.0 3 -#torsion 3 13 13 3 0.800 0.0 1 0.000 180.0 2 0.900 0.0 3 -torsion 3 13 13 5 -6.180 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 3 13 13 13 -2.060 0.0 1 -0.313 180.0 2 0.315 0.0 3 -#torsion 3 13 13 13 -3.185 0.0 1 -0.825 180.0 2 0.493 0.0 3 -#torsion 3 13 13 13 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3 -torsion 3 13 13 15 -4.344 0.0 1 -1.714 180.0 2 0.000 0.0 3 -torsion 3 13 13 16 -4.344 0.0 1 -1.714 180.0 2 0.000 0.0 3 -torsion 3 13 13 24 -9.000 0.0 1 2.000 180.0 2 0.800 0.0 3 -torsion 3 13 13 46 0.000 0.0 1 0.000 180.0 2 -0.100 0.0 3 -#torsion 3 13 13 36 0.000 0.0 1 0.000 180.0 2 0.074 0.0 3 -#torsion 3 13 13 36 0.000 0.0 1 0.000 180.0 2 -0.076 0.0 3 -torsion 3 13 13 48 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3 -torsion 3 13 13 80 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3 -torsion 5 13 13 5 9.508 0.0 1 0.000 180.0 2 0.000 0.0 3 -#torsion 5 13 13 5 12.234 0.0 1 0.000 180.0 2 0.000 0.0 3 -#torsion 5 13 13 5 9.066 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 5 13 13 13 -1.552 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 5 13 13 20 4.319 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 5 13 13 44 8.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 5 13 13 24 6.280 0.0 1 -1.467 180.0 2 2.030 0.0 3 -torsion 5 13 13 46 0.000 0.0 1 0.000 180.0 2 0.468 0.0 3 -torsion 13 13 13 13 1.300 0.0 1 -0.050 180.0 2 0.200 0.0 3 -#torsion 13 13 13 13 6.622 0. 1 0.948 180. 2 -1.388 0. 3 -2.118 180. 4 -torsion 13 13 13 15 1.262 0.0 1 -0.198 180.0 2 0.465 0.0 3 -torsion 13 13 13 16 2.619 0.0 1 -0.620 180.0 2 0.258 0.0 3 -torsion 13 13 13 19 0.000 0.0 1 -0.650 180.0 2 0.000 0.0 3 -torsion 13 13 13 21 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 -torsion 13 13 13 44 2.392 0.0 1 -0.674 180.0 2 0.550 0.0 3 -torsion 13 13 13 24 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3 -#torsion 13 13 13 35 1.964 0.0 1 0.000 180.0 2 0.659 0.0 3 -torsion 13 13 13 46 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -torsion 13 13 13 51 1.300 0.0 1 -0.050 180.0 2 0.200 0.0 3 -torsion 13 13 13 53 2.732 0.0 1 -0.229 180.0 2 0.485 0.0 3 -torsion 13 13 13 65 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 -torsion 13 13 13 66 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 -torsion 13 13 13 79 1.262 0.0 1 -0.198 180.0 2 0.465 0.0 3 -torsion 13 13 13 107 1.964 0.0 1 0.000 180.0 2 0.659 0.0 3 -torsion 13 13 13 108 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 15 13 13 46 0.000 0.0 1 0.000 180.0 2 0.452 0.0 3 -torsion 16 13 13 46 0.000 0.0 1 0.000 180.0 2 0.452 0.0 3 -torsion 19 13 13 46 0.000 0.0 1 0.000 180.0 2 0.366 0.0 3 -torsion 20 13 13 20 -0.550 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 20 13 13 46 0.000 0.0 1 0.000 180.0 2 0.468 0.0 3 -torsion 21 13 13 21 -0.250 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 21 13 13 44 2.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 21 13 13 46 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 -torsion 44 13 13 44 11.035 0.0 1 -0.968 180.0 2 0.270 0.0 3 -torsion 44 13 13 46 -1.013 0.0 1 -0.709 180.0 2 0.473 0.0 3 -torsion 44 13 13 48 -0.800 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 24 13 13 46 0.000 0.0 1 0.000 180.0 2 0.464 0.0 3 -torsion 24 13 13 48 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3 -torsion 24 13 13 80 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3 -torsion 46 13 13 46 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -torsion 46 13 13 47 0.000 0.0 1 0.000 180.0 2 0.366 0.0 3 -torsion 46 13 13 48 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 -torsion 46 13 13 51 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -torsion 46 13 13 53 0.000 0.0 1 0.000 180.0 2 0.384 0.0 3 -torsion 46 13 13 55 0.000 0.0 1 0.000 180.0 2 -0.582 0.0 3 -torsion 46 13 13 59 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 -torsion 46 13 13 62 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 -torsion 46 13 13 65 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 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2 0.680 0.0 3 -torsion 46 13 15 17 0.000 0.0 1 0.000 180.0 2 0.480 0.0 3 -torsion 13 13 16 13 0.925 0.0 1 -0.576 180.0 2 0.677 0.0 3 -torsion 13 13 16 16 1.941 0.0 1 -0.836 180.0 2 0.935 0.0 3 -torsion 46 13 16 13 0.000 0.0 1 0.000 180.0 2 0.647 0.0 3 -torsion 46 13 16 16 0.000 0.0 1 0.000 180.0 2 0.558 0.0 3 -torsion 46 13 16 48 0.000 0.0 1 0.000 180.0 2 0.647 0.0 3 -torsion 0 13 18 19 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 46 13 18 19 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 0 13 19 18 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 0 13 19 19 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 13 13 19 19 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 46 13 19 19 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 0 13 20 13 -0.521 0.0 1 -2.018 180.0 2 1.996 0.0 3 -torsion 56 13 20 13 -0.500 0.0 1 -1.500 180.0 2 1.000 0.0 3 -torsion 57 13 20 13 -0.500 0.0 1 -1.500 180.0 2 1.000 0.0 3 -torsion 13 13 20 3 -1.220 0.0 1 -0.126 180.0 2 0.422 0.0 3 -torsion 13 13 20 13 0.650 0.0 1 -0.250 180.0 2 0.670 0.0 3 -torsion 13 13 20 64 -1.420 0.0 1 -0.620 180.0 2 0.100 0.0 3 -torsion 46 13 20 0 0.000 0.0 1 0.000 180.0 2 0.760 0.0 3 -torsion 46 13 20 3 0.000 0.0 1 0.000 180.0 2 0.198 0.0 3 -torsion 46 13 20 47 0.000 0.0 1 0.000 180.0 2 0.760 0.0 3 -torsion 46 13 20 48 0.000 0.0 1 0.000 180.0 2 0.760 0.0 3 -torsion 46 13 20 51 0.000 0.0 1 0.000 180.0 2 0.760 0.0 3 -torsion 46 13 20 64 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 -torsion 13 13 44 13 0.416 0.0 1 -0.128 180.0 2 0.695 0.0 3 -#torsion 13 13 33 13 1.536 0.0 1 -0.128 180.0 2 0.695 0.0 3 -#torsion 13 13 33 13 1.464 0.0 1 -0.128 180.0 2 0.695 0.0 3 -torsion 13 13 44 45 -0.190 0.0 1 -0.417 180.0 2 0.418 0.0 3 -#torsion 13 13 33 34 0.000 0.0 1 4.000 180.0 2 0.000 0.0 3 -#torsion 13 13 33 34 0.200 0.0 1 -0.417 180.0 2 0.418 0.0 3 -#torsion 13 13 33 34 0.819 0.0 1 -0.417 180.0 2 0.418 0.0 3 -#torsion 13 13 33 34 1.522 0.0 1 -0.417 180.0 2 0.418 0.0 3 -torsion 46 13 44 13 0.000 0.0 1 0.000 180.0 2 0.560 0.0 3 -torsion 46 13 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1 14.000 180.0 2 0.000 0.0 3 -torsion 48 109 109 48 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 48 109 109 50 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 48 109 109 109 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 50 109 109 50 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 50 109 109 109 0.000 0.0 1 14.000 180.0 2 0.000 0.0 3 -torsion 109 109 109 109 1.423 0.0 1 4.055 180.0 2 0.858 0.0 3 - - - ################################################################ - ## ## - ## Additional Torsional Parameter Values Used with OPLS-AA ## - ## ## - ## The torsions listed below were added to official OPLS-AA ## - ## to complete the set needed for proteins; the values were ## - ## obtained by analogy from the closest OPLS-AA torsions; ## - ## most of the added values are for HIP or N-terminal AAs; ## - ## ## - ################################################################ - - -torsion 24 3 13 53 1.816 0.0 1 1.222 180.0 2 1.581 0.0 3 -torsion 52 3 13 24 0.000 0.0 1 0.820 180.0 2 0.000 0.0 3 -torsion 3 13 13 53 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 3 13 13 83 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3 -torsion 3 13 13 84 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3 -torsion 3 13 13 85 -1.697 0.0 1 -0.456 180.0 2 0.585 0.0 3 -torsion 5 13 13 53 6.280 0.0 1 -1.467 180.0 2 2.030 0.0 3 -torsion 15 13 13 53 1.428 0.0 1 0.086 180.0 2 0.029 0.0 3 -torsion 16 13 13 53 1.428 0.0 1 0.086 180.0 2 0.029 0.0 3 -torsion 13 13 13 55 2.732 0.0 1 -0.229 180.0 2 0.485 0.0 3 -torsion 24 13 13 83 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3 -torsion 53 13 13 83 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 24 13 13 84 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3 -torsion 53 13 13 84 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 24 13 13 85 0.845 0.0 1 -0.962 180.0 2 0.713 0.0 3 -torsion 46 13 13 85 0.000 0.0 1 0.000 180.0 2 0.462 0.0 3 -torsion 53 13 13 85 1.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 3 13 53 13 1.438 0.0 1 -0.124 180.0 2 0.264 0.0 3 -torsion 3 13 53 54 0.000 0.0 1 0.000 180.0 2 0.347 0.0 3 -torsion 13 13 53 54 0.000 0.0 1 0.000 180.0 2 0.347 0.0 3 -torsion 46 13 55 54 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 13 13 85 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 13 13 85 57 1.700 0.0 1 -0.600 180.0 2 0.000 0.0 3 -torsion 46 13 85 0 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 -torsion 55 48 55 54 0.000 0.0 1 3.900 180.0 2 0.000 0.0 3 -torsion 0 48 81 0 0.000 0.0 1 7.250 180.0 2 0.000 0.0 3 -torsion 0 57 85 0 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 -torsion 0 85 85 0 0.000 0.0 1 10.750 180.0 2 0.000 0.0 3 - - - ################################################################ - ## ## - ## Additional Torsional Parameter Values Used with OPLS-AA ## - ## ## - ## The torsions listed below were added to official OPLS-AA ## - ## to complete the values needed for selected organics ## - ## ## - ################################################################ - - -torsion 13 13 13 20 1.300 0.0 1 -0.050 180.0 2 0.200 0.0 3 -torsion 13 13 13 47 1.300 0.0 1 -0.050 180.0 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-charge 770 -0.1000 -charge 771 0.2900 -charge 772 0.0900 -charge 773 0.1500 -charge 774 0.2100 -charge 775 0.2700 -charge 776 0.0960 -charge 777 -0.0390 -charge 778 0.0270 -charge 779 0.0110 -charge 780 0.0740 -charge 781 -0.0290 -charge 782 0.7000 -charge 783 -0.3520 -charge 784 -0.7090 -charge 785 0.3170 -charge 786 -0.2200 -charge 787 0.0200 -charge 788 0.1000 -charge 789 0.1200 -charge 790 0.2200 -charge 791 0.3600 -charge 792 0.2400 -charge 793 0.1200 -charge 794 0.4800 -charge 795 -0.1200 -charge 796 0.2500 -charge 797 0.1500 -charge 798 -0.0800 -charge 799 -0.1060 -charge 800 -0.2000 -charge 801 -0.0060 -charge 802 0.1030 -charge 803 0.0970 -charge 804 0.2000 -charge 805 -0.2000 -charge 806 -0.0060 -charge 807 0.1030 -charge 808 0.0970 -charge 809 0.2000 -charge 810 -0.0800 -charge 811 -0.0800 -charge 812 -0.0800 -charge 813 0.1000 -charge 814 -0.2500 -charge 815 0.6000 -charge 816 -0.1500 -charge 817 -0.0250 -charge 818 -0.0450 -charge 819 0.1450 -charge 820 0.8880 -charge 821 1.0030 -charge 822 -0.6580 -charge 823 -0.6340 -charge 824 0.4110 -charge 825 -0.4420 -charge 826 0.4350 -charge 827 0.2250 -charge 828 0.2550 -charge 829 -0.0340 -charge 830 0.0030 -charge 831 0.3000 -charge 832 -0.0400 -charge 833 -0.0575 -charge 834 2.0000 -charge 835 -0.0700 -charge 836 0.0300 -charge 837 0.1300 -charge 838 -0.1300 -charge 839 0.1000 -charge 840 -0.6850 -charge 841 0.1550 -charge 842 -0.1000 -charge 843 -0.4270 -charge 844 0.2180 -charge 845 0.6000 -charge 846 -0.6000 -charge 847 -0.3600 -charge 848 0.0000 -charge 849 0.0600 -charge 850 0.1200 -charge 851 0.1800 -charge 852 0.0600 -charge 853 0.5700 -charge 854 -0.5700 -charge 855 0.0000 -charge 856 0.0200 -charge 857 -0.0400 -charge 858 0.0000 -charge 859 0.0600 -charge 860 -0.0700 -charge 861 -0.1400 -charge 862 0.1700 -charge 863 0.1100 -charge 864 0.1500 -charge 865 0.1700 -charge 866 1.0000 -charge 867 0.8500 -charge 868 0.7000 -charge 869 0.5500 -charge 870 -0.1000 -charge 871 -0.4300 -charge 872 -0.3700 -charge 873 -0.3100 -charge 874 -0.2500 -charge 875 -1.0000 -charge 876 -1.0000 -charge 877 -1.0000 -charge 878 -1.0000 -charge 879 1.0000 -charge 880 1.0000 -charge 881 1.0000 -charge 882 1.0000 -charge 883 1.0000 -charge 884 2.0000 -charge 885 2.0000 -charge 886 2.0000 -charge 887 2.0000 -charge 888 -0.0500 -charge 889 0.0500 -charge 890 0.1500 -charge 891 0.2500 -charge 892 0.1000 -charge 893 0.1150 -charge 894 0.1350 -charge 895 0.0150 -charge 896 0.1550 -charge 897 0.0000 -charge 898 -0.1150 -charge 899 0.1500 -charge 900 -0.2500 -charge 901 -0.1000 -charge 902 0.0500 -charge 903 -0.1000 -charge 904 0.2000 -charge 905 -0.2500 -charge 906 0.0880 - - - ######################################## - ## ## - ## Biopolymer Atom Type Conversions ## - ## ## - ######################################## - - -biotype 1 N "Glycine" 180 -biotype 2 CA "Glycine" 165 -biotype 3 C "Glycine" 177 -biotype 4 HN "Glycine" 183 -biotype 5 O "Glycine" 178 -biotype 6 HA "Glycine" 85 -biotype 7 N "Alanine" 180 -biotype 8 CA "Alanine" 166 -biotype 9 C "Alanine" 177 -biotype 10 HN "Alanine" 183 -biotype 11 O "Alanine" 178 -biotype 12 HA "Alanine" 85 -biotype 13 CB "Alanine" 80 -biotype 14 HB "Alanine" 85 -biotype 15 N "Valine" 180 -biotype 16 CA "Valine" 166 -biotype 17 C "Valine" 177 -biotype 18 HN "Valine" 183 -biotype 19 O "Valine" 178 -biotype 20 HA "Valine" 85 -biotype 21 CB "Valine" 82 -biotype 22 HB "Valine" 85 -biotype 23 CG1 "Valine" 80 -biotype 24 HG1 "Valine" 85 -biotype 25 CG2 "Valine" 80 -biotype 26 HG2 "Valine" 85 -biotype 27 N "Leucine" 180 -biotype 28 CA "Leucine" 166 -biotype 29 C "Leucine" 177 -biotype 30 HN "Leucine" 183 -biotype 31 O "Leucine" 178 -biotype 32 HA "Leucine" 85 -biotype 33 CB "Leucine" 81 -biotype 34 HB "Leucine" 85 -biotype 35 CG "Leucine" 82 -biotype 36 HG "Leucine" 85 -biotype 37 CD1 "Leucine" 80 -biotype 38 HD1 "Leucine" 85 -biotype 39 CD2 "Leucine" 80 -biotype 40 HD2 "Leucine" 85 -biotype 41 N "Isoleucine" 180 -biotype 42 CA "Isoleucine" 166 -biotype 43 C "Isoleucine" 177 -biotype 44 HN "Isoleucine" 183 -biotype 45 O "Isoleucine" 178 -biotype 46 HA "Isoleucine" 85 -biotype 47 CB "Isoleucine" 82 -biotype 48 HB "Isoleucine" 85 -biotype 49 CG1 "Isoleucine" 80 -biotype 50 HG1 "Isoleucine" 85 -biotype 51 CG2 "Isoleucine" 81 -biotype 52 HG2 "Isoleucine" 85 -biotype 53 CD "Isoleucine" 80 -biotype 54 HD "Isoleucine" 85 -biotype 55 N "Serine" 180 -biotype 56 CA "Serine" 166 -biotype 57 C "Serine" 177 -biotype 58 HN "Serine" 183 -biotype 59 O "Serine" 178 -biotype 60 HA "Serine" 85 -biotype 61 CB "Serine" 99 -biotype 62 HB "Serine" 85 -biotype 63 OG "Serine" 96 -biotype 64 HG "Serine" 97 -biotype 65 N "Threonine" 180 -biotype 66 CA "Threonine" 166 -biotype 67 C "Threonine" 177 -biotype 68 HN "Threonine" 183 -biotype 69 O "Threonine" 178 -biotype 70 HA "Threonine" 85 -biotype 71 CB "Threonine" 100 -biotype 72 HB "Threonine" 85 -biotype 73 OG1 "Threonine" 96 -biotype 74 HG1 "Threonine" 97 -biotype 75 CG2 "Threonine" 80 -biotype 76 HG2 "Threonine" 85 -biotype 77 N "Cysteine (SH)" 180 -biotype 78 CA "Cysteine (SH)" 166 -biotype 79 C "Cysteine (SH)" 177 -biotype 80 HN "Cysteine (SH)" 183 -biotype 81 O "Cysteine (SH)" 178 -biotype 82 HA "Cysteine (SH)" 85 -biotype 83 CB "Cysteine (SH)" 148 -biotype 84 HB "Cysteine (SH)" 85 -biotype 85 SG "Cysteine (SH)" 142 -biotype 86 HG "Cysteine (SH)" 146 -biotype 87 N "Cystine (SS)" 180 -biotype 88 CA "Cystine (SS)" 166 -biotype 89 C "Cystine (SS)" 177 -biotype 90 HN "Cystine (SS)" 183 -biotype 91 O "Cystine (SS)" 178 -biotype 92 HA "Cystine (SS)" 85 -biotype 93 CB "Cystine (SS)" 156 -biotype 94 HB "Cystine (SS)" 85 -biotype 95 SG "Cystine (SS)" 145 -biotype 96 N "Cysteine (S-)" -1 -biotype 97 CA "Cysteine (S-)" -1 -biotype 98 C "Cysteine (S-)" -1 -biotype 99 HN "Cysteine (S-)" -1 -biotype 100 O "Cysteine (S-)" -1 -biotype 101 HA "Cysteine (S-)" -1 -biotype 102 CB "Cysteine (S-)" -1 -biotype 103 HB "Cysteine (S-)" -1 -biotype 104 SG "Cysteine (S-)" -1 -biotype 105 N "Proline" 181 -biotype 106 CA "Proline" 188 -biotype 107 C "Proline" 177 -biotype 108 O "Proline" 178 -biotype 109 HA "Proline" 85 -biotype 110 CB "Proline" 81 -biotype 111 HB "Proline" 85 -biotype 112 CG "Proline" 81 -biotype 113 HG "Proline" 85 -biotype 114 CD "Proline" 187 -biotype 115 HD "Proline" 85 -biotype 116 N "Phenylalanine" 180 -biotype 117 CA "Phenylalanine" 166 -biotype 118 C "Phenylalanine" 177 -biotype 119 HN "Phenylalanine" 183 -biotype 120 O "Phenylalanine" 178 -biotype 121 HA "Phenylalanine" 85 -biotype 122 CB "Phenylalanine" 94 -biotype 123 HB "Phenylalanine" 85 -biotype 124 CG "Phenylalanine" 90 -biotype 125 CD "Phenylalanine" 90 -biotype 126 HD "Phenylalanine" 91 -biotype 127 CE "Phenylalanine" 90 -biotype 128 HE "Phenylalanine" 91 -biotype 129 CZ "Phenylalanine" 90 -biotype 130 HZ "Phenylalanine" 91 -biotype 131 N "Tyrosine" 180 -biotype 132 CA "Tyrosine" 166 -biotype 133 C "Tyrosine" 177 -biotype 134 HN "Tyrosine" 183 -biotype 135 O "Tyrosine" 178 -biotype 136 HA "Tyrosine" 85 -biotype 137 CB "Tyrosine" 94 -biotype 138 HB "Tyrosine" 85 -biotype 139 CG "Tyrosine" 90 -biotype 140 CD "Tyrosine" 90 -biotype 141 HD "Tyrosine" 91 -biotype 142 CE "Tyrosine" 90 -biotype 143 HE "Tyrosine" 91 -biotype 144 CZ "Tyrosine" 108 -biotype 145 OH "Tyrosine" 109 -biotype 146 HH "Tyrosine" 110 -biotype 147 N "Tyrosine (O-)" -1 -biotype 148 CA "Tyrosine (O-)" -1 -biotype 149 C "Tyrosine (O-)" -1 -biotype 150 HN "Tyrosine (O-)" -1 -biotype 151 O "Tyrosine (O-)" -1 -biotype 152 HA "Tyrosine (O-)" -1 -biotype 153 CB "Tyrosine (O-)" -1 -biotype 154 HB "Tyrosine (O-)" -1 -biotype 155 CG "Tyrosine (O-)" -1 -biotype 156 CD "Tyrosine (O-)" -1 -biotype 157 HD "Tyrosine (O-)" -1 -biotype 158 CE "Tyrosine (O-)" -1 -biotype 159 HE "Tyrosine (O-)" -1 -biotype 160 CZ "Tyrosine (O-)" -1 -biotype 161 OH "Tyrosine (O-)" -1 -biotype 162 N "Tryptophan" 180 -biotype 163 CA "Tryptophan" 166 -biotype 164 C "Tryptophan" 177 -biotype 165 HN "Tryptophan" 183 -biotype 166 O "Tryptophan" 178 -biotype 167 HA "Tryptophan" 85 -biotype 168 CB "Tryptophan" 81 -biotype 169 HB "Tryptophan" 85 -biotype 170 CG "Tryptophan" 441 -biotype 171 CD1 "Tryptophan" 455 -biotype 172 HD1 "Tryptophan" 91 -biotype 173 CD2 "Tryptophan" 442 -biotype 174 NE1 "Tryptophan" 444 -biotype 175 HE1 "Tryptophan" 445 -biotype 176 CE2 "Tryptophan" 443 -biotype 177 CE3 "Tryptophan" 90 -biotype 178 HE3 "Tryptophan" 91 -biotype 179 CZ2 "Tryptophan" 90 -biotype 180 HZ2 "Tryptophan" 91 -biotype 181 CZ3 "Tryptophan" 90 -biotype 182 HZ3 "Tryptophan" 91 -biotype 183 CH2 "Tryptophan" 90 -biotype 184 HH2 "Tryptophan" 91 -biotype 185 N "Histidine (+)" 180 -biotype 186 CA "Histidine (+)" 166 -biotype 187 C "Histidine (+)" 177 -biotype 188 HN "Histidine (+)" 183 -biotype 189 O "Histidine (+)" 178 -biotype 190 HA "Histidine (+)" 85 -biotype 191 CB "Histidine (+)" 446 -biotype 192 HB "Histidine (+)" 85 -biotype 193 CG "Histidine (+)" 451 -biotype 194 ND1 "Histidine (+)" 453 -biotype 195 HD1 "Histidine (+)" 454 -biotype 196 CD2 "Histidine (+)" 451 -biotype 197 HD2 "Histidine (+)" 91 -biotype 198 CE1 "Histidine (+)" 450 -biotype 199 HE1 "Histidine (+)" 91 -biotype 200 NE2 "Histidine (+)" 453 -biotype 201 HE2 "Histidine (+)" 454 -biotype 202 N "Histidine (HD)" 180 -biotype 203 CA "Histidine (HD)" 166 -biotype 204 C "Histidine (HD)" 177 -biotype 205 HN "Histidine (HD)" 183 -biotype 206 O "Histidine (HD)" 178 -biotype 207 HA "Histidine (HD)" 85 -biotype 208 CB "Histidine (HD)" 446 -biotype 209 HB "Histidine (HD)" 85 -biotype 210 CG "Histidine (HD)" 449 -biotype 211 ND1 "Histidine (HD)" 444 -biotype 212 HD1 "Histidine (HD)" 445 -biotype 213 CD2 "Histidine (HD)" 448 -biotype 214 HD2 "Histidine (HD)" 91 -biotype 215 CE1 "Histidine (HD)" 447 -biotype 216 HE1 "Histidine (HD)" 91 -biotype 217 NE2 "Histidine (HD)" 452 -biotype 218 N "Histidine (HE)" 180 -biotype 219 CA "Histidine (HE)" 166 -biotype 220 C "Histidine (HE)" 177 -biotype 221 HN "Histidine (HE)" 183 -biotype 222 O "Histidine (HE)" 178 -biotype 223 HA "Histidine (HE)" 85 -biotype 224 CB "Histidine (HE)" 446 -biotype 225 HB "Histidine (HE)" 85 -biotype 226 CG "Histidine (HE)" 448 -biotype 227 ND1 "Histidine (HE)" 452 -biotype 228 CD2 "Histidine (HE)" 449 -biotype 229 HD2 "Histidine (HE)" 91 -biotype 230 CE1 "Histidine (HE)" 447 -biotype 231 HE1 "Histidine (HE)" 91 -biotype 232 NE2 "Histidine (HE)" 444 -biotype 233 HE2 "Histidine (HE)" 445 -biotype 234 N "Aspartic Acid" 180 -biotype 235 CA "Aspartic Acid" 166 -biotype 236 C "Aspartic Acid" 177 -biotype 237 HN "Aspartic Acid" 183 -biotype 238 O "Aspartic Acid" 178 -biotype 239 HA "Aspartic Acid" 85 -biotype 240 CB "Aspartic Acid" 216 -biotype 241 HB "Aspartic Acid" 85 -biotype 242 CG "Aspartic Acid" 213 -biotype 243 OD "Aspartic Acid" 214 -biotype 244 N "Aspartic Acid (COOH)" -1 -biotype 245 CA "Aspartic Acid (COOH)" -1 -biotype 246 C "Aspartic Acid (COOH)" -1 -biotype 247 HN "Aspartic Acid (COOH)" -1 -biotype 248 O "Aspartic Acid (COOH)" -1 -biotype 249 HA "Aspartic Acid (COOH)" -1 -biotype 250 CB "Aspartic Acid (COOH)" -1 -biotype 251 HB "Aspartic Acid (COOH)" -1 -biotype 252 CG "Aspartic Acid (COOH)" -1 -biotype 253 OD1 "Aspartic Acid (COOH)" -1 -biotype 254 OD2 "Aspartic Acid (COOH)" -1 -biotype 255 HD2 "Aspartic Acid (COOH)" -1 -biotype 256 N "Asparagine" 180 -biotype 257 CA "Asparagine" 166 -biotype 258 C "Asparagine" 177 -biotype 259 HN "Asparagine" 183 -biotype 260 O "Asparagine" 178 -biotype 261 HA "Asparagine" 85 -biotype 262 CB "Asparagine" 81 -biotype 263 HB "Asparagine" 85 -biotype 264 CG "Asparagine" 177 -biotype 265 OD1 "Asparagine" 178 -biotype 266 ND2 "Asparagine" 179 -biotype 267 HD2 "Asparagine" 182 -biotype 268 N "Glutamic Acid" 180 -biotype 269 CA "Glutamic Acid" 166 -biotype 270 C "Glutamic Acid" 177 -biotype 271 HN "Glutamic Acid" 183 -biotype 272 O "Glutamic Acid" 178 -biotype 273 HA "Glutamic Acid" 85 -biotype 274 CB "Glutamic Acid" 81 -biotype 275 HB "Glutamic Acid" 85 -biotype 276 CG "Glutamic Acid" 216 -biotype 277 HG "Glutamic Acid" 85 -biotype 278 CD "Glutamic Acid" 213 -biotype 279 OE "Glutamic Acid" 214 -biotype 280 N "Glutamic Acid (COOH)" -1 -biotype 281 CA "Glutamic Acid (COOH)" -1 -biotype 282 C "Glutamic Acid (COOH)" -1 -biotype 283 HN "Glutamic Acid (COOH)" -1 -biotype 284 O "Glutamic Acid (COOH)" -1 -biotype 285 HA "Glutamic Acid (COOH)" -1 -biotype 286 CB "Glutamic Acid (COOH)" -1 -biotype 287 HB "Glutamic Acid (COOH)" -1 -biotype 288 CG "Glutamic Acid (COOH)" -1 -biotype 289 HG "Glutamic Acid (COOH)" -1 -biotype 290 CD "Glutamic Acid (COOH)" -1 -biotype 291 OE1 "Glutamic Acid (COOH)" -1 -biotype 292 OE2 "Glutamic Acid (COOH)" -1 -biotype 293 HE2 "Glutamic Acid (COOH)" -1 -biotype 294 N "Glutamine" 180 -biotype 295 CA "Glutamine" 166 -biotype 296 C "Glutamine" 177 -biotype 297 HN "Glutamine" 183 -biotype 298 O "Glutamine" 178 -biotype 299 HA "Glutamine" 85 -biotype 300 CB "Glutamine" 81 -biotype 301 HB "Glutamine" 85 -biotype 302 CG "Glutamine" 81 -biotype 303 HG "Glutamine" 85 -biotype 304 CD "Glutamine" 177 -biotype 305 OE1 "Glutamine" 178 -biotype 306 NE2 "Glutamine" 179 -biotype 307 HE2 "Glutamine" 182 -biotype 308 N "Methionine" 180 -biotype 309 CA "Methionine" 166 -biotype 310 C "Methionine" 177 -biotype 311 HN "Methionine" 183 -biotype 312 O "Methionine" 178 -biotype 313 HA "Methionine" 85 -biotype 314 CB "Methionine" 81 -biotype 315 HB "Methionine" 85 -biotype 316 CG "Methionine" 152 -biotype 317 HG "Methionine" 85 -biotype 318 SD "Methionine" 144 -biotype 319 CE "Methionine" 151 -biotype 320 HE "Methionine" 85 -biotype 321 N "Lysine" 180 -biotype 322 CA "Lysine" 166 -biotype 323 C "Lysine" 177 -biotype 324 HN "Lysine" 183 -biotype 325 O "Lysine" 178 -biotype 326 HA "Lysine" 85 -biotype 327 CB "Lysine" 81 -biotype 328 HB "Lysine" 85 -biotype 329 CG "Lysine" 81 -biotype 330 HG "Lysine" 85 -biotype 331 CD "Lysine" 81 -biotype 332 HD "Lysine" 85 -biotype 333 CE "Lysine" 235 -biotype 334 HE "Lysine" 85 -biotype 335 NZ "Lysine" 230 -biotype 336 HZ "Lysine" 233 -biotype 337 N "Lysine (NH2)" -1 -biotype 338 CA "Lysine (NH2)" -1 -biotype 339 C "Lysine (NH2)" -1 -biotype 340 HN "Lysine (NH2)" -1 -biotype 341 O "Lysine (NH2)" -1 -biotype 342 HA "Lysine (NH2)" -1 -biotype 343 CB "Lysine (NH2)" -1 -biotype 344 HB "Lysine (NH2)" -1 -biotype 345 CG "Lysine (NH2)" -1 -biotype 346 HG "Lysine (NH2)" -1 -biotype 347 CD "Lysine (NH2)" -1 -biotype 348 HD "Lysine (NH2)" -1 -biotype 349 CE "Lysine (NH2)" -1 -biotype 350 HE "Lysine (NH2)" -1 -biotype 351 NZ "Lysine (NH2)" -1 -biotype 352 HZ "Lysine (NH2)" -1 -biotype 353 N "Arginine" 180 -biotype 354 CA "Arginine" 166 -biotype 355 C "Arginine" 177 -biotype 356 HN "Arginine" 183 -biotype 357 O "Arginine" 178 -biotype 358 HA "Arginine" 85 -biotype 359 CB "Arginine" 81 -biotype 360 HB "Arginine" 85 -biotype 361 CG "Arginine" 251 -biotype 362 HG "Arginine" 85 -biotype 363 CD "Arginine" 250 -biotype 364 HD "Arginine" 85 -biotype 365 NE "Arginine" 246 -biotype 366 HE "Arginine" 247 -biotype 367 CZ "Arginine" 245 -biotype 368 NH "Arginine" 243 -biotype 369 HH "Arginine" 244 -biotype 370 N "Ornithine" 180 -biotype 371 CA "Ornithine" 166 -biotype 372 C "Ornithine" 177 -biotype 373 HN "Ornithine" 183 -biotype 374 O "Ornithine" 178 -biotype 375 HA "Ornithine" 85 -biotype 376 CB "Ornithine" 81 -biotype 377 HB "Ornithine" 85 -biotype 378 CG "Ornithine" 81 -biotype 379 HG "Ornithine" 85 -biotype 380 CD "Ornithine" 235 -biotype 381 HD "Ornithine" 85 -biotype 382 NE "Ornithine" 230 -biotype 383 HE "Ornithine" 233 -biotype 384 N "MethylAlanine (AIB)" 180 -biotype 385 CA "MethylAlanine (AIB)" 167 -biotype 386 C "MethylAlanine (AIB)" 177 -biotype 387 HN "MethylAlanine (AIB)" 183 -biotype 388 O "MethylAlanine (AIB)" 178 -biotype 389 CB "MethylAlanine (AIB)" 80 -biotype 390 HB "MethylAlanine (AIB)" 85 -biotype 391 N "Pyroglutamic Acid" 180 -biotype 392 CA "Pyroglutamic Acid" 166 -biotype 393 C "Pyroglutamic Acid" 177 -biotype 394 HN "Pyroglutamic Acid" 183 -biotype 395 O "Pyroglutamic Acid" 178 -biotype 396 HA "Pyroglutamic Acid" 85 -biotype 397 CB "Pyroglutamic Acid" 81 -biotype 398 HB "Pyroglutamic Acid" 85 -biotype 399 CG "Pyroglutamic Acid" 216 -biotype 400 HG "Pyroglutamic Acid" 85 -biotype 401 CD "Pyroglutamic Acid" 177 -biotype 402 OE "Pyroglutamic Acid" 178 -biotype 403 N "N-Terminal GLY" 230 -biotype 404 CA "N-Terminal GLY" 235 -biotype 405 C "N-Terminal GLY" 177 -biotype 406 HN "N-Terminal GLY" 233 -biotype 407 O "N-Terminal GLY" 178 -biotype 408 HA "N-Terminal GLY" 85 -biotype 409 N "N-Terminal ALA" 230 -biotype 410 CA "N-Terminal ALA" 236 -biotype 411 C "N-Terminal ALA" 177 -biotype 412 HN "N-Terminal ALA" 233 -biotype 413 O "N-Terminal ALA" 178 -biotype 414 HA "N-Terminal ALA" 85 -biotype 415 N "N-Terminal VAL" 230 -biotype 416 CA "N-Terminal VAL" 236 -biotype 417 C "N-Terminal VAL" 177 -biotype 418 HN "N-Terminal VAL" 233 -biotype 419 O "N-Terminal VAL" 178 -biotype 420 HA "N-Terminal VAL" 85 -biotype 421 N "N-Terminal LEU" 230 -biotype 422 CA "N-Terminal LEU" 236 -biotype 423 C "N-Terminal LEU" 177 -biotype 424 HN "N-Terminal LEU" 233 -biotype 425 O "N-Terminal LEU" 178 -biotype 426 HA "N-Terminal LEU" 85 -biotype 427 N "N-Terminal ILE" 230 -biotype 428 CA "N-Terminal ILE" 236 -biotype 429 C "N-Terminal ILE" 177 -biotype 430 HN "N-Terminal ILE" 233 -biotype 431 O "N-Terminal ILE" 178 -biotype 432 HA "N-Terminal ILE" 85 -biotype 433 N "N-Terminal SER" 230 -biotype 434 CA "N-Terminal SER" 236 -biotype 435 C "N-Terminal SER" 177 -biotype 436 HN "N-Terminal SER" 233 -biotype 437 O "N-Terminal SER" 178 -biotype 438 HA "N-Terminal SER" 85 -biotype 439 N "N-Terminal THR" 230 -biotype 440 CA "N-Terminal THR" 236 -biotype 441 C "N-Terminal THR" 177 -biotype 442 HN "N-Terminal THR" 233 -biotype 443 O "N-Terminal THR" 178 -biotype 444 HA "N-Terminal THR" 85 -biotype 445 N "N-Terminal CYS (SH)" 230 -biotype 446 CA "N-Terminal CYS (SH)" 236 -biotype 447 C "N-Terminal CYS (SH)" 177 -biotype 448 HN "N-Terminal CYS (SH)" 233 -biotype 449 O "N-Terminal CYS (SH)" 178 -biotype 450 HA "N-Terminal CYS (SH)" 85 -biotype 451 N "N-Terminal CYX (SS)" 230 -biotype 452 CA "N-Terminal CYX (SS)" 236 -biotype 453 C "N-Terminal CYX (SS)" 177 -biotype 454 HN "N-Terminal CYX (SS)" 233 -biotype 455 O "N-Terminal CYX (SS)" 178 -biotype 456 HA "N-Terminal CYX (SS)" 85 -biotype 457 N "N-Terminal CYD (S-)" -1 -biotype 458 CA "N-Terminal CYD (S-)" -1 -biotype 459 C "N-Terminal CYD (S-)" -1 -biotype 460 HN "N-Terminal CYD (S-)" -1 -biotype 461 O "N-Terminal CYD (S-)" -1 -biotype 462 HA "N-Terminal CYD (S-)" -1 -biotype 463 N "N-Terminal PRO" 252 -biotype 464 CA "N-Terminal PRO" 238 -biotype 465 C "N-Terminal PRO" 177 -biotype 466 HN "N-Terminal PRO" 253 -biotype 467 O "N-Terminal PRO" 178 -biotype 468 HA "N-Terminal PRO" 85 -biotype 469 CD "N-Terminal PRO" 239 -biotype 470 HD "N-Terminal PRO" 85 -biotype 471 N "N-Terminal PHE" 230 -biotype 472 CA "N-Terminal PHE" 236 -biotype 473 C "N-Terminal PHE" 177 -biotype 474 HN "N-Terminal PHE" 233 -biotype 475 O "N-Terminal PHE" 178 -biotype 476 HA "N-Terminal PHE" 85 -biotype 477 N "N-Terminal TYR" 230 -biotype 478 CA "N-Terminal TYR" 236 -biotype 479 C "N-Terminal TYR" 177 -biotype 480 HN "N-Terminal TYR" 233 -biotype 481 O "N-Terminal TYR" 178 -biotype 482 HA "N-Terminal TYR" 85 -biotype 483 N "N-Terminal TYD (O-)" -1 -biotype 484 CA "N-Terminal TYD (O-)" -1 -biotype 485 C "N-Terminal TYD (O-)" -1 -biotype 486 HN "N-Terminal TYD (O-)" -1 -biotype 487 O "N-Terminal TYD (O-)" -1 -biotype 488 HA "N-Terminal TYD (O-)" -1 -biotype 489 N "N-Terminal TRP" 230 -biotype 490 CA "N-Terminal TRP" 236 -biotype 491 C "N-Terminal TRP" 177 -biotype 492 HN "N-Terminal TRP" 233 -biotype 493 O "N-Terminal TRP" 178 -biotype 494 HA "N-Terminal TRP" 85 -biotype 495 N "N-Terminal HIS (+)" 230 -biotype 496 CA "N-Terminal HIS (+)" 236 -biotype 497 C "N-Terminal HIS (+)" 177 -biotype 498 HN "N-Terminal HIS (+)" 233 -biotype 499 O "N-Terminal HIS (+)" 178 -biotype 500 HA "N-Terminal HIS (+)" 85 -biotype 501 N "N-Terminal HIS (HD)" 230 -biotype 502 CA "N-Terminal HIS (HD)" 236 -biotype 503 C "N-Terminal HIS (HD)" 177 -biotype 504 HN "N-Terminal HIS (HD)" 233 -biotype 505 O "N-Terminal HIS (HD)" 178 -biotype 506 HA "N-Terminal HIS (HD)" 85 -biotype 507 N "N-Terminal HIS (HE)" 230 -biotype 508 CA "N-Terminal HIS (HE)" 236 -biotype 509 C "N-Terminal HIS (HE)" 177 -biotype 510 HN "N-Terminal HIS (HE)" 233 -biotype 511 O "N-Terminal HIS (HE)" 178 -biotype 512 HA "N-Terminal HIS (HE)" 85 -biotype 513 N "N-Terminal ASP" 230 -biotype 514 CA "N-Terminal ASP" 236 -biotype 515 C "N-Terminal ASP" 177 -biotype 516 HN "N-Terminal ASP" 233 -biotype 517 O "N-Terminal ASP" 178 -biotype 518 HA "N-Terminal ASP" 85 -biotype 519 N "N-Terminal ASH (COOH)" -1 -biotype 520 CA "N-Terminal ASH (COOH)" -1 -biotype 521 C "N-Terminal ASH (COOH)" -1 -biotype 522 HN "N-Terminal ASH (COOH)" -1 -biotype 523 O "N-Terminal ASH (COOH)" -1 -biotype 524 HA "N-Terminal ASH (COOH)" -1 -biotype 525 N "N-Terminal ASN" 230 -biotype 526 CA "N-Terminal ASN" 236 -biotype 527 C "N-Terminal ASN" 177 -biotype 528 HN "N-Terminal ASN" 233 -biotype 529 O "N-Terminal ASN" 178 -biotype 530 HA "N-Terminal ASN" 85 -biotype 531 N "N-Terminal GLU" 230 -biotype 532 CA "N-Terminal GLU" 236 -biotype 533 C "N-Terminal GLU" 177 -biotype 534 HN "N-Terminal GLU" 233 -biotype 535 O "N-Terminal GLU" 178 -biotype 536 HA "N-Terminal GLU" 85 -biotype 537 N "N-Terminal GLH (COOH)" -1 -biotype 538 CA "N-Terminal GLH (COOH)" -1 -biotype 539 C "N-Terminal GLH (COOH)" -1 -biotype 540 HN "N-Terminal GLH (COOH)" -1 -biotype 541 O "N-Terminal GLH (COOH)" -1 -biotype 542 HA "N-Terminal GLH (COOH)" -1 -biotype 543 N "N-Terminal GLN" 230 -biotype 544 CA "N-Terminal GLN" 236 -biotype 545 C "N-Terminal GLN" 177 -biotype 546 HN "N-Terminal GLN" 233 -biotype 547 O "N-Terminal GLN" 178 -biotype 548 HA "N-Terminal GLN" 85 -biotype 549 N "N-Terminal MET" 230 -biotype 550 CA "N-Terminal MET" 236 -biotype 551 C "N-Terminal MET" 177 -biotype 552 HN "N-Terminal MET" 233 -biotype 553 O "N-Terminal MET" 178 -biotype 554 HA "N-Terminal MET" 85 -biotype 555 N "N-Terminal LYS" 230 -biotype 556 CA "N-Terminal LYS" 236 -biotype 557 C "N-Terminal LYS" 177 -biotype 558 HN "N-Terminal LYS" 233 -biotype 559 O "N-Terminal LYS" 178 -biotype 560 HA "N-Terminal LYS" 85 -biotype 561 N "N-Terminal LYD (NH2)" -1 -biotype 562 CA "N-Terminal LYD (NH2)" -1 -biotype 563 C "N-Terminal LYD (NH2)" -1 -biotype 564 HN "N-Terminal LYD (NH2)" -1 -biotype 565 O "N-Terminal LYD (NH2)" -1 -biotype 566 HA "N-Terminal LYD (NH2)" -1 -biotype 567 N "N-Terminal ARG" 230 -biotype 568 CA "N-Terminal ARG" 236 -biotype 569 C "N-Terminal ARG" 177 -biotype 570 HN "N-Terminal ARG" 233 -biotype 571 O "N-Terminal ARG" 178 -biotype 572 HA "N-Terminal ARG" 85 -biotype 573 N "N-Terminal ORN" 230 -biotype 574 CA "N-Terminal ORN" 236 -biotype 575 C "N-Terminal ORN" 177 -biotype 576 HN "N-Terminal ORN" 233 -biotype 577 O "N-Terminal ORN" 178 -biotype 578 HA "N-Terminal ORN" 85 -biotype 579 N "N-Terminal AIB" 230 -biotype 580 CA "N-Terminal AIB" 237 -biotype 581 C "N-Terminal AIB" 177 -biotype 582 HN "N-Terminal AIB" 233 -biotype 583 O "N-Terminal AIB" 178 -biotype 584 N "C-Terminal GLY" 180 -biotype 585 CA "C-Terminal GLY" 226 -biotype 586 C "C-Terminal GLY" 213 -biotype 587 HN "C-Terminal GLY" 183 -biotype 588 OXT "C-Terminal GLY" 214 -biotype 589 HA "C-Terminal GLY" 85 -biotype 590 N "C-Terminal ALA" 180 -biotype 591 CA "C-Terminal ALA" 225 -biotype 592 C "C-Terminal ALA" 213 -biotype 593 HN "C-Terminal ALA" 183 -biotype 594 OXT "C-Terminal ALA" 214 -biotype 595 HA "C-Terminal ALA" 85 -biotype 596 N "C-Terminal VAL" 180 -biotype 597 CA "C-Terminal VAL" 225 -biotype 598 C "C-Terminal VAL" 213 -biotype 599 HN "C-Terminal VAL" 183 -biotype 600 OXT "C-Terminal VAL" 214 -biotype 601 HA "C-Terminal VAL" 85 -biotype 602 N "C-Terminal LEU" 180 -biotype 603 CA "C-Terminal LEU" 225 -biotype 604 C "C-Terminal LEU" 213 -biotype 605 HN "C-Terminal LEU" 183 -biotype 606 OXT "C-Terminal LEU" 214 -biotype 607 HA "C-Terminal LEU" 85 -biotype 608 N "C-Terminal ILE" 180 -biotype 609 CA "C-Terminal ILE" 225 -biotype 610 C "C-Terminal ILE" 213 -biotype 611 HN "C-Terminal ILE" 183 -biotype 612 OXT "C-Terminal ILE" 214 -biotype 613 HA "C-Terminal ILE" 85 -biotype 614 N "C-Terminal SER" 180 -biotype 615 CA "C-Terminal SER" 225 -biotype 616 C "C-Terminal SER" 213 -biotype 617 HN "C-Terminal SER" 183 -biotype 618 OXT "C-Terminal SER" 214 -biotype 619 HA "C-Terminal SER" 85 -biotype 620 N "C-Terminal THR" 180 -biotype 621 CA "C-Terminal THR" 225 -biotype 622 C "C-Terminal THR" 213 -biotype 623 HN "C-Terminal THR" 183 -biotype 624 OXT "C-Terminal THR" 214 -biotype 625 HA "C-Terminal THR" 85 -biotype 626 N "C-Terminal CYS (SH)" 180 -biotype 627 CA "C-Terminal CYS (SH)" 225 -biotype 628 C "C-Terminal CYS (SH)" 213 -biotype 629 HN "C-Terminal CYS (SH)" 183 -biotype 630 OXT "C-Terminal CYS (SH)" 214 -biotype 631 HA "C-Terminal CYS (SH)" 85 -biotype 632 N "C-Terminal CYX (SS)" 180 -biotype 633 CA "C-Terminal CYX (SS)" 225 -biotype 634 C "C-Terminal CYX (SS)" 213 -biotype 635 HN "C-Terminal CYX (SS)" 183 -biotype 636 OXT "C-Terminal CYX (SS)" 214 -biotype 637 HA "C-Terminal CYX (SS)" 85 -biotype 638 N "C-Terminal CYD (S-)" -1 -biotype 639 CA "C-Terminal CYD (S-)" -1 -biotype 640 C "C-Terminal CYD (S-)" -1 -biotype 641 HN "C-Terminal CYD (S-)" -1 -biotype 642 OXT "C-Terminal CYD (S-)" -1 -biotype 643 HA "C-Terminal CYD (S-)" -1 -biotype 644 N "C-Terminal PRO" 181 -biotype 645 CA "C-Terminal PRO" 228 -biotype 646 C "C-Terminal PRO" 213 -biotype 647 OXT "C-Terminal PRO" 214 -biotype 648 HA "C-Terminal PRO" 85 -biotype 649 N "C-Terminal PHE" 180 -biotype 650 CA "C-Terminal PHE" 225 -biotype 651 C "C-Terminal PHE" 213 -biotype 652 HN "C-Terminal PHE" 183 -biotype 653 OXT "C-Terminal PHE" 214 -biotype 654 HA "C-Terminal PHE" 85 -biotype 655 N "C-Terminal TYR" 180 -biotype 656 CA "C-Terminal TYR" 225 -biotype 657 C "C-Terminal TYR" 213 -biotype 658 HN "C-Terminal TYR" 183 -biotype 659 OXT "C-Terminal TYR" 214 -biotype 660 HA "C-Terminal TYR" 85 -biotype 661 N "C-Terminal TYD (O-)" -1 -biotype 662 CA "C-Terminal TYD (O-)" -1 -biotype 663 C "C-Terminal TYD (O-)" -1 -biotype 664 HN "C-Terminal TYD (O-)" -1 -biotype 665 OXT "C-Terminal TYD (O-)" -1 -biotype 666 HA "C-Terminal TYD (O-)" -1 -biotype 667 N "C-Terminal TRP" 180 -biotype 668 CA "C-Terminal TRP" 225 -biotype 669 C "C-Terminal TRP" 213 -biotype 670 HN "C-Terminal TRP" 183 -biotype 671 OXT "C-Terminal TRP" 214 -biotype 672 HA "C-Terminal TRP" 85 -biotype 673 N "C-Terminal HIS (+)" 180 -biotype 674 CA "C-Terminal HIS (+)" 225 -biotype 675 C "C-Terminal HIS (+)" 213 -biotype 676 HN "C-Terminal HIS (+)" 183 -biotype 677 OXT "C-Terminal HIS (+)" 214 -biotype 678 HA "C-Terminal HIS (+)" 85 -biotype 679 N "C-Terminal HIS (HD)" 180 -biotype 680 CA "C-Terminal HIS (HD)" 225 -biotype 681 C "C-Terminal HIS (HD)" 213 -biotype 682 HN "C-Terminal HIS (HD)" 183 -biotype 683 OXT "C-Terminal HIS (HD)" 214 -biotype 684 HA "C-Terminal HIS (HD)" 85 -biotype 685 N "C-Terminal HIS (HE)" 180 -biotype 686 CA "C-Terminal HIS (HE)" 225 -biotype 687 C "C-Terminal HIS (HE)" 213 -biotype 688 HN "C-Terminal HIS (HE)" 183 -biotype 689 OXT "C-Terminal HIS (HE)" 214 -biotype 690 HA "C-Terminal HIS (HE)" 85 -biotype 691 N "C-Terminal ASP" 180 -biotype 692 CA "C-Terminal ASP" 225 -biotype 693 C "C-Terminal ASP" 213 -biotype 694 HN "C-Terminal ASP" 183 -biotype 695 OXT "C-Terminal ASP" 214 -biotype 696 HA "C-Terminal ASP" 85 -biotype 697 N "C-Terminal ASH (COOH)" -1 -biotype 698 CA "C-Terminal ASH (COOH)" -1 -biotype 699 C "C-Terminal ASH (COOH)" -1 -biotype 700 HN "C-Terminal ASH (COOH)" -1 -biotype 701 OXT "C-Terminal ASH (COOH)" -1 -biotype 702 HA "C-Terminal ASH (COOH)" -1 -biotype 703 N "C-Terminal ASN" 180 -biotype 704 CA "C-Terminal ASN" 225 -biotype 705 C "C-Terminal ASN" 213 -biotype 706 HN "C-Terminal ASN" 183 -biotype 707 OXT "C-Terminal ASN" 214 -biotype 708 HA "C-Terminal ASN" 85 -biotype 709 N "C-Terminal GLU" 180 -biotype 710 CA "C-Terminal GLU" 225 -biotype 711 C "C-Terminal GLU" 213 -biotype 712 HN "C-Terminal GLU" 183 -biotype 713 OXT "C-Terminal GLU" 214 -biotype 714 HA "C-Terminal GLU" 85 -biotype 715 N "C-Terminal GLH (COOH)" -1 -biotype 716 CA "C-Terminal GLH (COOH)" -1 -biotype 717 C "C-Terminal GLH (COOH)" -1 -biotype 718 HN "C-Terminal GLH (COOH)" -1 -biotype 719 OXT "C-Terminal GLH (COOH)" -1 -biotype 720 HA "C-Terminal GLH (COOH)" -1 -biotype 721 N "C-Terminal GLN" 180 -biotype 722 CA "C-Terminal GLN" 225 -biotype 723 C "C-Terminal GLN" 213 -biotype 724 HN "C-Terminal GLN" 183 -biotype 725 OXT "C-Terminal GLN" 214 -biotype 726 HA "C-Terminal GLN" 85 -biotype 727 N "C-Terminal MET" 180 -biotype 728 CA "C-Terminal MET" 225 -biotype 729 C "C-Terminal MET" 213 -biotype 730 HN "C-Terminal MET" 183 -biotype 731 OXT "C-Terminal MET" 214 -biotype 732 HA "C-Terminal MET" 85 -biotype 733 N "C-Terminal LYS" 180 -biotype 734 CA "C-Terminal LYS" 225 -biotype 735 C "C-Terminal LYS" 213 -biotype 736 HN "C-Terminal LYS" 183 -biotype 737 OXT "C-Terminal LYS" 214 -biotype 738 HA "C-Terminal LYS" 85 -biotype 739 N "C-Terminal LYD (NH2)" -1 -biotype 740 CA "C-Terminal LYD (NH2)" -1 -biotype 741 C "C-Terminal LYD (NH2)" -1 -biotype 742 HN "C-Terminal LYD (NH2)" -1 -biotype 743 OXT "C-Terminal LYD (NH2)" -1 -biotype 744 HA "C-Terminal LYD (NH2)" -1 -biotype 745 N "C-Terminal ARG" 180 -biotype 746 CA "C-Terminal ARG" 225 -biotype 747 C "C-Terminal ARG" 213 -biotype 748 HN "C-Terminal ARG" 183 -biotype 749 OXT "C-Terminal ARG" 214 -biotype 750 HA "C-Terminal ARG" 85 -biotype 751 N "C-Terminal ORN" 180 -biotype 752 CA "C-Terminal ORN" 225 -biotype 753 C "C-Terminal ORN" 213 -biotype 754 HN "C-Terminal ORN" 183 -biotype 755 OXT "C-Terminal ORN" 214 -biotype 756 HA "C-Terminal ORN" 85 -biotype 757 N "C-Terminal AIB" 180 -biotype 758 CA "C-Terminal AIB" 227 -biotype 759 C "C-Terminal AIB" 213 -biotype 760 HN "C-Terminal AIB" 183 -biotype 761 OXT "C-Terminal AIB" 214 -biotype 762 N "Deprotonated N-Terminus" -1 -biotype 763 H "Deprotonated N-Terminus" -1 -biotype 764 C "Formyl N-Terminus" 177 -biotype 765 H "Formyl N-Terminus" 221 -biotype 766 O "Formyl N-Terminus" 178 -biotype 767 CH3 "Acetyl N-Terminus" 80 -biotype 768 H "Acetyl N-Terminus" 85 -biotype 769 C "Acetyl N-Terminus" 177 -biotype 770 O "Acetyl N-Terminus" 178 -biotype 771 C "Protonated C-Terminus" -1 -biotype 772 O "Protonated C-Terminus" -1 -biotype 773 OH "Protonated C-Terminus" -1 -biotype 774 HO "Protonated C-Terminus" -1 -biotype 775 N "Amide C-Terminus" 179 -biotype 776 HN "Amide C-Terminus" 182 -biotype 777 N "N-MeAmide C-Terminus" 180 -biotype 778 HN "N-MeAmide C-Terminus" 183 -biotype 779 CH3 "N-MeAmide C-Terminus" 184 -biotype 780 H "N-MeAmide C-Terminus" 85 -biotype 2001 O "Water" 63 -biotype 2002 H "Water" 64 -biotype 2003 NA "Sodium Ion" -1 -biotype 2004 K "Potassium Ion" -1 -biotype 2005 MG "Magnesium Ion" -1 -biotype 2006 CA "Calcium Ion" -1 -biotype 2007 CL "Chloride Ion" -1 diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_explicit/aluminum_crystal_strain/README.TXT b/tools/moltemplate/examples/all_atom_examples/force_field_explicit/aluminum_crystal_strain/README.TXT index 355fe42831..115c1fab35 100644 --- a/tools/moltemplate/examples/all_atom_examples/force_field_explicit/aluminum_crystal_strain/README.TXT +++ b/tools/moltemplate/examples/all_atom_examples/force_field_explicit/aluminum_crystal_strain/README.TXT @@ -27,11 +27,11 @@ system.data, system.in.init, system.in.settings. --- To run LAMMPS, try a command like: --- -lmp_linux -i run.in +lmp_mpi -i run.in or (if you have mpi installed) -mpirun -np 4 lmp_linux -i run.in +mpirun -np 4 lmp_mpi -i run.in This will create an ordinary LAMMPS dump file you can visualize with VMD traj.lammpstrj (See README_visualize.txt) diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_explicit/ice_crystal/README_run.sh b/tools/moltemplate/examples/all_atom_examples/force_field_explicit/ice_crystal/README_run.sh index 56b784d5ab..4a1e130642 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_explicit/ice_crystal/README_run.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_explicit/ice_crystal/README_run.sh @@ -7,15 +7,15 @@ # If not, carry out the instructions in "README_setup.sh". # # -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, +# If "lmp_mpi" is the name of the command you use to invoke lammps, # then you would run lammps on these files this way: -lmp_linux -i run.in.npt # minimization and simulation at constant pressure +lmp_mpi -i run.in.npt # minimization and simulation at constant pressure # to be followed by -lmp_linux -i run.in.nvt # simulation at constant volume +lmp_mpi -i run.in.nvt # simulation at constant volume #(Note: The constant volume simulation lacks pressure equilibration. These are # completely separate simulations. The results of the constant pressure @@ -27,7 +27,7 @@ lmp_linux -i run.in.nvt # simulation at constant volume # If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.npt # or -#mpirun -np 4 lmp_linux -i run.in.nvt +#mpirun -np 4 lmp_mpi -i run.in.nvt # (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/README_run.sh b/tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/README_run.sh index 8a470b9551..ee5e5665aa 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/README_run.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/README_run.sh @@ -7,18 +7,18 @@ # If not, carry out the instructions in "README_setup.sh". # # -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, +# If "lmp_mpi" is the name of the command you use to invoke lammps, # then you would run lammps on these files this way: -lmp_linux -i run.in.nvt # minimization and simulation at constant volume -lmp_linux -i run.in.npt # minimization and simulation at constant pressure +lmp_mpi -i run.in.nvt # minimization and simulation at constant volume +lmp_mpi -i run.in.npt # minimization and simulation at constant pressure # (WARNING: The "run.in.npt" example has not been # rigorously tested and may fail.) # If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.npt -#mpirun -np 4 lmp_linux -i run.in.nvt +#mpirun -np 4 lmp_mpi -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.nvt # (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/moltemplate_files/graphene.lt b/tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/moltemplate_files/graphene.lt index 1410cac9bb..c54a380f62 100644 --- a/tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/moltemplate_files/graphene.lt +++ b/tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/moltemplate_files/graphene.lt @@ -25,6 +25,9 @@ Graphene { group Cgraphene type @atom:C } write_once("In Init") { + # -- Default styles (used in this file for graphene carbon) -- + units real + atom_style full #(full enables you to to add other molecules later) pair_style hybrid lj/cut/coul/long 10.0 } } # Graphene diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/moltemplate_files/spce.lt index f0f141d655..e1bf2390a0 100644 --- a/tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/moltemplate_files/spce.lt +++ b/tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/moltemplate_files/spce.lt @@ -27,10 +27,10 @@ SPCE { } write_once("In Settings") { - bond_coeff @bond:OH harmonic 1000.0 1.0 - angle_coeff @angle:HOH harmonic 1000.0 109.47 - pair_coeff @atom:O @atom:O lj/cut/coul/long 0.1553 3.166 - pair_coeff @atom:H @atom:H lj/cut/coul/long 0.0 2.058 + bond_coeff @bond:OH harmonic 600.0 1.0 + angle_coeff @angle:HOH harmonic 75.0 109.47 + pair_coeff @atom:O @atom:O lj/cut/coul/long 0.1553 3.166 + pair_coeff @atom:H @atom:H lj/cut/coul/long 0.0 2.058 group spce type @atom:O @atom:H fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH # (Remember to "unfix" fShakeSPCE during minimization.) @@ -41,12 +41,11 @@ SPCE { units real atom_style full # (Hybrid force fields were not necessary but are used for portability.) - pair_style hybrid lj/cut/coul/long 10.0 + pair_style hybrid lj/cut/coul/long 9.0 bond_style hybrid harmonic angle_style hybrid harmonic kspace_style pppm 0.0001 - pair_modify mix arithmetic - pair_modify shift yes + #pair_modify mix arithmetic # LEAVE THIS UNSPECIFIED! } } # end of definition of "SPCE" water molecule type diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/moltemplate_files/watmw.lt b/tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/moltemplate_files/watmw.lt new file mode 100644 index 0000000000..c7aaecebbc --- /dev/null +++ b/tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/moltemplate_files/watmw.lt @@ -0,0 +1,54 @@ +# This file stores LAMMPS data for the "mW" water model. +# (Molinero, V. and Moore, E.B., J. Phys. Chem. B 2009, 113, 4008-4016) +# +# In this model, each water molecule is represented by a single "mW" particle. +# These particles interact with their neighbors via 3-body Stillinger-Weber +# forces whose parameters are tuned to mimic directional hydrogen-bonding +# in liquid water (as well as hexagonal ice, type II ice, and +# low-density super-cooled liquid/amorphous water phases). + +WatMW { + write("Data Atoms") { + $atom:mW $mol:. @atom:mW 0.0 0.0 0.0 0.0 + } + + write_once("Data Masses") { + @atom:mW 18.02 + } + + write_once("system.in.sw") { + mW mW mW 6.189 2.3925 1.8 23.15 1.2 -0.333333333 7.049556277 0.602224558 4 0 0 + } + + write_once("In Init") { + # -- Default styles for "WatMW" -- + units real + pair_style sw + } + + write_once("In Settings") { + # --Now indicate which atom type(s) are simulated using the "sw" pair style + # -- In this case only one of the atom types is used (the mW water "atom"). + + pair_coeff * * sw system.in.sw mW NULL NULL NULL + + # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so + # -- the atoms are identified by order in the list, not by name. (The "mW" + # -- refers to to an identifier in the system.in.sw file, not watmw.lt.) + # -- This command says that the first atom type corresponds to the "mW" + # -- atom in system.in.sw, and to ignore the remaining three atom types + # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt. + # -- We don't want to use the "sw" force field for interactions involving + # -- these atom types, so we put "NULL" there.) + # -- Note: For this to work, you should probably run moltemplate this way: + # -- moltemplate.sh -a "@atom:WatMW/mW 1" system.lt + # -- This assigns the atom type named @atom:WatMW/mW to 1 (the first atom) + } + + # -- optional -- + + write_once("In Settings") { + group WatMW type @atom:mW #(Atoms of this type belong to the "WatMW" group) + } + +} # WatMW diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/run.in.npt b/tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/run.in.npt index 6bd4fd8a18..ab6c4bbf9c 100644 --- a/tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/run.in.npt +++ b/tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/run.in.npt @@ -25,6 +25,8 @@ include system.in.settings # Only the Cgraphene atoms are immobile. group mobile subtract all Cgraphene +# (Note: The "Cgraphene" group was defined in system.in.settings.) + # Unfortunately you can not use the LAMMPS "minimize" command on this system # because there is no way to immobilize the carbon graphene & nanotube atoms diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/run.in.nvt index f457702a03..a86e9227a2 100644 --- a/tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/run.in.nvt +++ b/tools/moltemplate/examples/all_atom_examples/force_field_explicit/nanotube+water/run.in.nvt @@ -24,13 +24,11 @@ include system.in.settings -# Optional: Improve efficiency by omitting the calcuation of interactions -# between immobile atoms. (Note: This is not optional under NPT conditions.) -neigh_modify exclude group Cgraphene Cgraphene - # Only the Cgraphene atoms are immobile. group mobile subtract all Cgraphene +# (Note: The "Cgraphene" group was defined in system.in.settings.) + # -- minimization protocol -- diff --git a/tools/moltemplate/examples/all_atom_examples/force_field_explicit/waterSPCE+Na+Cl/README_run.sh b/tools/moltemplate/examples/all_atom_examples/force_field_explicit/waterSPCE+Na+Cl/README_run.sh index cf51fa8705..70c34bd6f4 100755 --- a/tools/moltemplate/examples/all_atom_examples/force_field_explicit/waterSPCE+Na+Cl/README_run.sh +++ b/tools/moltemplate/examples/all_atom_examples/force_field_explicit/waterSPCE+Na+Cl/README_run.sh @@ -7,15 +7,15 @@ # If not, carry out the instructions in "README_setup.sh". # # -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, +# If "lmp_mpi" is the name of the command you use to invoke lammps, # then you would run lammps on these files this way: -lmp_linux -i run.in.npt # minimization and simulation at constant pressure +lmp_mpi -i run.in.npt # minimization and simulation at constant pressure # or -lmp_linux -i run.in.nvt # minimization and simulation at constant volume +lmp_mpi -i run.in.nvt # minimization and simulation at constant volume #(Note: The constant volume simulation lacks pressure equilibration. These are # completely separate simulations. The results of the constant pressure @@ -27,7 +27,7 @@ lmp_linux -i run.in.nvt # minimization and simulation at constant volume # If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.npt # or -#mpirun -np 4 lmp_linux -i run.in.nvt +#mpirun -np 4 lmp_mpi -i run.in.nvt # (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/README_run.sh index 8220a755c4..68acee49b9 100755 --- a/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/README_run.sh +++ b/tools/moltemplate/examples/coarse_grained_examples/3bodyWater+hydrocarbons_MW+TraPPE/README_run.sh @@ -7,12 +7,12 @@ # If not, carry out the instructions in "README_setup.sh". # # -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, +# If "lmp_mpi" is the name of the command you use to invoke lammps, # then you would run lammps on these files this way: -lmp_linux -i run.in.npt # minimization and simulation at constant pressure -lmp_linux -i run.in.nvt # minimization and simulation at constant volume +lmp_mpi -i run.in.npt # minimization and simulation at constant pressure +lmp_mpi -i run.in.nvt # minimization and simulation at constant volume #(Note: The constant volume simulation lacks pressure equilibration. These are # completely separate simulations. The results of the constant pressure @@ -26,6 +26,6 @@ lmp_linux -i run.in.nvt # minimization and simulation at constant volume # If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.npt -#mpirun -np 4 lmp_linux -i run.in.nvt +#mpirun -np 4 lmp_mpi -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.nvt # (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/README_run.sh index edb6b2698b..9d2b0fbc5a 100755 --- a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/README_run.sh +++ b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/README_run.sh @@ -7,15 +7,15 @@ # If not, carry out the instructions in "README_setup.sh". # # -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, +# If "lmp_mpi" is the name of the command you use to invoke lammps, # then you would run lammps on these files this way: -lmp_linux -i run.in.min # minimization -lmp_linux -i run.in.npt # simulation at constant pressure -lmp_linux -i run.in.nvt # simulation at constant volume +lmp_mpi -i run.in.min # minimization +lmp_mpi -i run.in.npt # simulation at constant pressure +lmp_mpi -i run.in.nvt # simulation at constant volume # If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.npt -#mpirun -np 4 lmp_linux -i run.in.nvt +#mpirun -np 4 lmp_mpi -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.nvt # (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/moltemplate_files/lipid.lt b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/moltemplate_files/lipid.lt index 3507a6035e..3fe1b55305 100644 --- a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/moltemplate_files/lipid.lt +++ b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_formation_PACKMOL/moltemplate_files/lipid.lt @@ -7,7 +7,6 @@ DPPC { angle_style hybrid cosine/squared dihedral_style none improper_style none - #pair_style hybrid lj/gromacs/coul/gromacs 9 12 0.000001 12 pair_style hybrid lj/gromacs/coul/gromacs 9 12 0.000001 12 special_bonds lj/coul 0 1 1 dielectric 15 diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/README_run.sh index e163a10696..8cc857a5b4 100755 --- a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/README_run.sh +++ b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/README_run.sh @@ -7,15 +7,15 @@ # If not, carry out the instructions in "README_setup.sh". # # -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, +# If "lmp_mpi" is the name of the command you use to invoke lammps, # then you would run lammps on these files this way: -lmp_linux -i run.in.min # minimization -lmp_linux -i run.in.npt # simulation at constant pressure -lmp_linux -i run.in.nvt # simulation at constant volume +lmp_mpi -i run.in.min # minimization +lmp_mpi -i run.in.npt # simulation at constant pressure +lmp_mpi -i run.in.nvt # simulation at constant volume # If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.npt -#mpirun -np 4 lmp_linux -i run.in.nvt +#mpirun -np 4 lmp_mpi -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.nvt # (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/moltemplate_files/lipid.lt b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/moltemplate_files/lipid.lt index 0d045eaf8c..df92940b18 100644 --- a/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/moltemplate_files/lipid.lt +++ b/tools/moltemplate/examples/coarse_grained_examples/MARTINI_examples/DPPC_bilayer_preformed/moltemplate_files/lipid.lt @@ -7,7 +7,6 @@ DPPC { angle_style hybrid cosine/squared dihedral_style none improper_style none - #pair_style hybrid lj/charmm/coul/charmm 9 12 0.000001 12 pair_style hybrid lj/gromacs/coul/gromacs 9 12 0.000001 12 special_bonds lj/coul 0 1 1 dielectric 15 diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/README_run.sh index 1347aebbb4..8bf8e27648 100755 --- a/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/README_run.sh +++ b/tools/moltemplate/examples/coarse_grained_examples/abstract_2bead_heteropolymer/README_run.sh @@ -7,14 +7,14 @@ # If not, carry out the instructions in "README_setup.sh". # # -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, +# If "lmp_mpi" is the name of the command you use to invoke lammps, # then you would run lammps on these files this way: -lmp_linux -i run.in.nvt +lmp_mpi -i run.in.nvt # If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.nvt +#mpirun -np 4 lmp_mpi -i run.in.nvt # (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/README_run.sh index ac21c4c45e..9343d763f7 100755 --- a/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/README_run.sh +++ b/tools/moltemplate/examples/coarse_grained_examples/abstract_random_heteropolymer/README_run.sh @@ -7,8 +7,8 @@ # If not, carry out the instructions in "README_setup.sh". # # -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, +# If "lmp_mpi" is the name of the command you use to invoke lammps, # then you would run lammps on these files this way: -lmp_linux -i run.in.nvt +lmp_mpi -i run.in.nvt diff --git a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/README_run.sh index 7078918d5a..0828a7f098 100755 --- a/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/README_run.sh +++ b/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/README_run.sh @@ -7,22 +7,22 @@ # If not, carry out the instructions in "README_setup.sh". # # -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, +# If "lmp_mpi" is the name of the command you use to invoke lammps, # then you would run lammps on these files this way: -lmp_linux -i run.in.nvt # Run a simulation at constant volume +lmp_mpi -i run.in.nvt # Run a simulation at constant volume #or -lmp_linux -i run.in.npt # Run a simulation at constant pressure +lmp_mpi -i run.in.npt # Run a simulation at constant pressure # (Note: Constant pressure conditions have not been # well tested. The "run.in.npt" script may fail.) # If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.nvt +#mpirun -np 4 lmp_mpi -i run.in.nvt #or -#mpirun -np 4 lmp_linux -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.npt # (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/README_run.sh index 2ed2e747d2..19674c88bd 100755 --- a/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/README_run.sh +++ b/tools/moltemplate/examples/coarse_grained_examples/chromosome_metaphase_Naumova2013/README_run.sh @@ -1,7 +1,7 @@ # Run lammps using the following 3 commands: -# (assuming "lmp_linux" is the name of your LAMMPS binary) +# (assuming "lmp_mpi" is the name of your LAMMPS binary) -lmp_linux -i run.in.min -lmp_linux -i run.in.stage1 -lmp_linux -i run.in.stage2 +lmp_mpi -i run.in.min +lmp_mpi -i run.in.stage1 +lmp_mpi -i run.in.stage2 diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/README.TXT b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/README.TXT similarity index 100% rename from tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/README.TXT rename to tools/moltemplate/examples/coarse_grained_examples/membrane+protein/README.TXT diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/README_WARNING.TXT b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/README_WARNING.TXT new file mode 100644 index 0000000000..f60da6c3f8 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/README_WARNING.TXT @@ -0,0 +1,12 @@ +WARNING: + This is not a realistic simulation of a protein in a lipid membrane. + + When I released this example in 2013, the simulations ran without crashing and produced no obvious visual flaws. However recently (2015) I've noticed that there are some serious problems: Currently, the protein no-longer remains perpendicular to the membrane during the simulations. (In some cases, it also unfolds.) The original version of this example did not behave this way. I'm not sure what changed since then. + + This example was created to demonstrate how to combine totally different kinds of coarse-grained molecules (with different kinds of force-fields) together in the same simulation in LAMMPS. Tuning the force-field parameters to get realistic results was not the goal. + + One day I might tinker with the shape of the protein and the force-field parameters to try and avoid this unsightly outcome. (Probably shortening the length of the helices would help.) Either way, I doubt it would make the simulations any more accurate. + + I apologize that the simulations no longer produce the same pretty images shown on the web page. + +Andrew 2015-8-02 diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/README_run.sh similarity index 75% rename from tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/README_run.sh rename to tools/moltemplate/examples/coarse_grained_examples/membrane+protein/README_run.sh index 9598e3b08d..d7ea305695 100755 --- a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/README_run.sh +++ b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/README_run.sh @@ -7,15 +7,15 @@ # If not, carry out the instructions in "README_setup.sh". # # -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, +# If "lmp_mpi" is the name of the command you use to invoke lammps, # then you would run lammps on these files this way: -lmp_linux -i run.in.npt # Run a simulation at constant pressure (tension) +lmp_mpi -i run.in.npt # Run a simulation at constant pressure (tension) #or -lmp_linux -i run.in.nvt # Run a simulation at constant volume +lmp_mpi -i run.in.nvt # Run a simulation at constant volume #(Note: The constant volume simulation lacks pressure equilibration. These are # completely separate simulations. The results of the constant pressure @@ -27,7 +27,7 @@ lmp_linux -i run.in.nvt # Run a simulation at constant volume # If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.npt #or -#mpirun -np 4 lmp_linux -i run.in.nvt +#mpirun -np 4 lmp_mpi -i run.in.nvt # (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/README_setup.sh b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/README_setup.sh similarity index 100% rename from tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/README_setup.sh rename to tools/moltemplate/examples/coarse_grained_examples/membrane+protein/README_setup.sh diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/README_visualize.txt b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/README_visualize.txt similarity index 100% rename from tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/README_visualize.txt rename to tools/moltemplate/examples/coarse_grained_examples/membrane+protein/README_visualize.txt diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg similarity index 100% rename from tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg rename to tools/moltemplate/examples/coarse_grained_examples/membrane+protein/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/images/membrane+protein_t=0ps_LR.jpg b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/images/membrane+protein_t=0ps_LR.jpg similarity index 100% rename from tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/images/membrane+protein_t=0ps_LR.jpg rename to tools/moltemplate/examples/coarse_grained_examples/membrane+protein/images/membrane+protein_t=0ps_LR.jpg diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/images/membrane+protein_t=0ps_no_pbc_LR.jpg b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/images/membrane+protein_t=0ps_no_pbc_LR.jpg similarity index 100% rename from tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/images/membrane+protein_t=0ps_no_pbc_LR.jpg rename to tools/moltemplate/examples/coarse_grained_examples/membrane+protein/images/membrane+protein_t=0ps_no_pbc_LR.jpg diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/images/membrane+protein_t=0ps_top_LR.jpg b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/images/membrane+protein_t=0ps_top_LR.jpg similarity index 100% rename from tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/images/membrane+protein_t=0ps_top_LR.jpg rename to tools/moltemplate/examples/coarse_grained_examples/membrane+protein/images/membrane+protein_t=0ps_top_LR.jpg diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/images/membrane+protein_t=5000ps_LR.jpg b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/images/membrane+protein_t=5000ps_LR.jpg similarity index 100% rename from tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/images/membrane+protein_t=5000ps_LR.jpg rename to tools/moltemplate/examples/coarse_grained_examples/membrane+protein/images/membrane+protein_t=5000ps_LR.jpg diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010.lt b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/1beadProtSci2010.lt similarity index 90% rename from tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010.lt rename to tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/1beadProtSci2010.lt index a5df81056d..d2aa805a5b 100644 --- a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010.lt +++ b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/1beadProtSci2010.lt @@ -187,10 +187,6 @@ } - - # We use the same bond-angle forces whenever - # there are 3 consecutively-bonded atoms: - # # angleType atomtypes1 2 3 bondtypes1 2 write_once("Data Angles By Type") { @@ -203,18 +199,13 @@ } - - - # Dihedral interactions are also determined by atom-type name in this case. - # I chose atoms whose type-names begin with "t" to be "turn" atoms. - # Atoms whose type-names begin with "s" could be either helices or sheets. - # (In this case, helices. In this example, we use the @dihedral:delta65_0 - # parameters. This corresponds to the "AUF2" model from the - # Bellesia et. al 2010 paper.) - # dihedralType atomtypes1 2 3 4 bondtypes1 2 3 write_once("Data Dihedrals By Type") { + # For a chain of sH and sL atoms, use the @dihedral:delta65_0 + # parameters. (This corresponds to the "AUF2" model from the + # Bellesia et. al 2010 paper.) + @dihedral:delta65_0 @atom:s* @atom:s* @atom:s* @atom:s* * * * # If "tN" (turn) atoms are present, use the @dihedral:turn parameters @@ -222,20 +213,8 @@ @dihedral:turn @atom:tN @atom:* @atom:* @atom:* * * * } - - # From the Bellesia et al 2010 paper: - # for helices: U_{dih}(\phi) = 1.2*(cos(3\phi) + cos(\phi+\delta)) - # for turns: U_{dih}(\phi) = 0.2*cos(3\phi) - # - # General formula used for "dihedral_style fourier": - # U_{dih}(\phi) = \Sum_{i=1}^m K_i [ 1.0 + cos(n_i \phi - d_i) ] - # - # Syntax: - # dihedralType dihedralstyle m K_1 n_1 d_1 K2 n_2 d_2 ... - write_once("In Settings") { dihedral_coeff @dihedral:delta60_0 fourier 2 2.167862 3 0 2.167862 1 -60.0 - dihedral_coeff @dihedral:delta62_5 fourier 2 2.167862 3 0 2.167862 1 -62.5 dihedral_coeff @dihedral:delta65_0 fourier 2 2.167862 3 0 2.167862 1 -65.0 dihedral_coeff @dihedral:turn fourier 1 0.361310 3 0 # Note: 2.167862=1.2*epsilon and 0.361310=0.2*epsilon. diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010_variations.lt b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt similarity index 100% rename from tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010_variations.lt rename to tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/moltemplate_files/CGLipidBr2005.lt b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/CGLipidBr2005.lt similarity index 89% rename from tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/moltemplate_files/CGLipidBr2005.lt rename to tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/CGLipidBr2005.lt index ed8fe89dfe..24be50aced 100644 --- a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/moltemplate_files/CGLipidBr2005.lt +++ b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/CGLipidBr2005.lt @@ -46,13 +46,12 @@ CGLipidBr2005 { dihedral_style none improper_style none + pair_style hybrid table linear 1130 & lj/charmm/coul/charmm/inter es4k4l 14.5 15 + pair_modify mix arithmetic special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" - - neighbor 2.0 multi # <- perhaps unnecessary - comm_modify mode multi # <- perhaps unnecessary } @@ -81,8 +80,9 @@ CGLipidBr2005 { @atom:head 200.0 } write_once("In Settings") { - pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:../tail @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 } } #DPPC @@ -109,8 +109,9 @@ CGLipidBr2005 { @atom:head 200.0 } write_once("In Settings") { - pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:../tail @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 } } #DLPC @@ -120,7 +121,6 @@ CGLipidBr2005 { write_once("Data Masses") { @atom:int 200.0 @atom:tail 200.0 - @atom:head 200.0 #<- Default head type. We may override it later. } write_once("In Settings") { @@ -153,23 +153,21 @@ CGLipidBr2005 { # Unfortunately, mixing lj/charmm and "table" pair styles in the same # simulation is very inneficient. - pair_coeff @atom:int @atom:int table table_int.dat INT + pair_coeff @atom:int @atom:int table table_int.dat INT # The interaction of tail beads with eachother is given by the formula below # and with other atoms ...using Lorenz-Berthelot and "repulsive wins" rules: # epsilon*(0.4*(sigma/r)^12 - 1.0*(sigma/r)^6), - pair_coeff @atom:tail @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 - pair_coeff @atom:int @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 - - # The interaction of head beads which all other beads is given by: - # epsilon*(0.4*(sigma/r)^12 - 0.0*(sigma/r)^6), - - pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:tail @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 + pair_coeff @atom:int @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 + # The interaction between head beads from different types of lipids + # is (currently) repulsive: + pair_coeff @atom:DPPC/head @atom:DLPC/head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 } # write_once("In Settings") + # Note: I divided epsilon by 4 to get "0.1643" because we are using the # "es4k4l" coeffstyle, corresponding to U(r)=eps(4*K*(s/r)^12 + 4*L*(s/r)^6) # (The "es4k4l" coeffstyle is the default.) Using this convention makes it diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py similarity index 100% rename from tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py rename to tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py similarity index 100% rename from tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py rename to tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/system.lt new file mode 100644 index 0000000000..6ffe9a58b2 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/system.lt @@ -0,0 +1,178 @@ +# Description: + +# This example shows how to put a protein (inclusion) in a +# lipid bilayer mixture composed of two different lipids (DPPC and DLPC). +# The DPPC lipid model is described here: +# G. Brannigan, P.F. Philips, and F.L.H. Brown, +# Physical Review E, Vol 72, 011915 (2005) +# The protein model is described here: +# G. Bellesia, AI Jewett, and J-E Shea, +# Protein Science, Vol19 141-154 (2010) +# The new DLPC model is a truncated version of DPPC, +# (Its behaviour has not been rigorously tested.) +# Note that 50%/50% mixtures of DPPC & DLPC are commonly used to +# build liposomes http://www.ncbi.nlm.nih.gov/pubmed/10620293 + +# Note: +# This example may require additional features to be added to LAMMPS. +# If LAMMPS complains about an "Invalid pair_style", then copy the code +# in the "additional_lammps_code" directory into your LAMMPS "src" directory +# and recompile LAMMPS. + + + +import "CGLipidBr2005.lt" + +using namespace CGLipidBr2005 + +# The "= new random" syntax chooses one of several molecules at random + +lipids = new random([DPPC, DLPC], [0.5,0.5], 1234) #"1234"=random_seed + [13].move(7.5, 0, 0) + [15].move(3.75, 6.49519, 0) # <-- hexagonal lattice + [2].rot(180, 1, 0, 0) # <-- 2 monolayers + +# Move all the lipds up to the center of the box + +lipids[*][*][*].move(0,0,75.0) + + + + +# Although this patch of lipids is not square or rectangular, (it looks +# like a parallelogram), this is no longer the case after rectangular +# periodic boundary conditions are applied. (Check by visualising in VMD.) + + +write_once("Data Boundary") { + 0 97.5 xlo xhi + 0 97.42785792 ylo yhi + 0 150.0 zlo zhi +} + + +# A note on geometry: +# We want to create a bilayer arranged in a hexagonal lattice consisting of +# 15 rows (each row is aligned with the x-axis) +# 13 columns (aligned at a 60 degree angle from the x axis) +# The lattice spacing is 7.5 Angstroms. +# When wrapped onto a rectangular box, the dimensions of the system are: +# 13 * 7.5 Angstroms in the X direction +# 15 * 7.5*sqrt(3)/2 Angstroms in the Y direction + + + + + + + +# ------------------- protein inclusion --------------------- + +import "1beadProtSci2010.lt" + +using namespace 1beadProtSci2010 + +protein = new 4HelixInsideOut + +protein.move(45.0, 25.98076211, 75.0) + + +# Delete a hole in the membrane to create space for the protein. +# (In the future moltemplate will be able to avoid occlusion automatically.) + + +delete lipids[4][2][*] +delete lipids[6][2][*] +delete lipids[3-6][3][*] +delete lipids[3-5][4][*] +delete lipids[2-5][5][*] +delete lipids[2][6][*] +delete lipids[4][6][*] + + +# -------- interactions between protein and lipids ---------- + +# Note: All atom types must include the full path (the name of +# the namespace which defined them as well as the atom type name). +# (This is because we are no longer inside that namespace.) + + +write_once("In Settings") { + + # Interactions between the protein and lipid atoms are usually + # determined by mixing rules. (However this is not possible some + # for atoms, such as the "int" atoms in the lipid model which + # interact using -1/r^2 attraction.) Mixing rules do not make + # sense for these atoms so we must explicitly define their + # interaction with all other atoms. + + # i j pairstylename eps sig K L + + pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 6.0 1 -1 + pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0 + pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0 + + # We want the interactions between hydrophobic residues and atoms in + # the interior of the lipd to be energetically similar to the attractive + # interactions between hydrophobic residues. (See 1beadProtSci2010.) + + pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 6.0 1 -1 + + # We also add an artificial attractive interaction between the + # turn residues of the protein and the lipid head groups in + # order to keep the protein upright. Probably not necessary. + + pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 6.0 1 -1 + pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 6.0 1 -1 + + # All other interactions between proteins and lipids are steric. + pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0 + pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0 + pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0 + pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0 + pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0 + pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0 + + + # Add a weak attractive interaction between hydrophilic "sL" beads + # (Whose strength mimics the strength of interaction between tail beads + # in the lipid. This was absent from the original protein model. + # However without some kind of weak attraction between residues, + # the negative pressure in the interior of the bilayer membrane + # allways pulls the protein apart. Recall that in the membrane, + # the hydrophobic beads in the protein will face outwards towards the lipid + # tails leaving the hydrophilic amino acids of the protein in the interior. + # In reality, these polar groups form hydrogen bonds with each other.) + + pair_coeff @atom:1beadProtSci2010/sL @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.3286 7.5 0.4 -1 + + # However these hydrophilic amino acids are not attrected to + # the bilayer interior. + + pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 + +} + + + + +# Finally, we must combine the two force-field styles which were used for +# the coarse-grained lipid and protein. To do that, we write one last time +# to the "In Init" section. When reading the "Init" section LAMMPS will +# read these commands last and this will override any earlier settings. + +write_once("In Init") { + # -- These styles override earlier settings -- + units real + atom_style full + # (Hybrid force field styles were used for portability.) + bond_style hybrid harmonic + angle_style hybrid cosine/delta harmonic + dihedral_style hybrid fourier + improper_style none + pair_style hybrid table linear 1001 lj/charmm/coul/charmm/inter es4k4l 14.5 15 + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" +} + diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/moltemplate_files/table_int.dat b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/table_int.dat similarity index 100% rename from tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/moltemplate_files/table_int.dat rename to tools/moltemplate/examples/coarse_grained_examples/membrane+protein/moltemplate_files/table_int.dat diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/run.in.min b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/run.in.min similarity index 100% rename from tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/run.in.min rename to tools/moltemplate/examples/coarse_grained_examples/membrane+protein/run.in.min diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/run.in.npt b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/run.in.npt similarity index 96% rename from tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/run.in.npt rename to tools/moltemplate/examples/coarse_grained_examples/membrane+protein/run.in.npt index dab8a4469e..2dc4bbe035 100644 --- a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/run.in.npt +++ b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/run.in.npt @@ -2,7 +2,7 @@ # # You must use moltemplate.sh to create 3 files: # system.data system.in.init system.in.settings -# (See README_setup.sh for details.) +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) # # -------- REQUIREMENTS: --------- # 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/run.in.nvt b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/run.in.nvt similarity index 96% rename from tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/run.in.nvt rename to tools/moltemplate/examples/coarse_grained_examples/membrane+protein/run.in.nvt index a16b16430c..c9195b4e62 100644 --- a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/run.in.nvt +++ b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein/run.in.nvt @@ -2,7 +2,7 @@ # # 1) You must use moltemplate.sh to create 3 files: # system.data system.in.init system.in.settings -# (See README_setup.sh for details.) +# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) # 2) You must equilibrate the system beforehand using "run.in.npt". # This will create the file "system_after_npt.data" which this file reads. # (Note: I have not verified that this equilibration protocol works well.) diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/moltemplate_files/system.lt deleted file mode 100644 index 9072293c7b..0000000000 --- a/tools/moltemplate/examples/coarse_grained_examples/membrane+protein_Brannigan2005+Bellesia2010/moltemplate_files/system.lt +++ /dev/null @@ -1,219 +0,0 @@ -# Description: - -# This example shows how to put a protein (inclusion) in a -# lipid bilayer mixture composed of two different lipids (DPPC and DLPC). -# The DPPC lipid model is described here: -# G. Brannigan, P.F. Philips, and F.L.H. Brown, -# Physical Review E, Vol 72, 011915 (2005) -# The protein model is described here: -# G. Bellesia, AI Jewett, and J-E Shea, -# Protein Science, Vol19 141-154 (2010) -# The new DLPC model is a truncated version of DPPC, -# (Its behaviour has not been rigorously tested.) -# Note that 50%/50% mixtures of DPPC & DLPC are commonly used to -# build liposomes http://www.ncbi.nlm.nih.gov/pubmed/10620293 - -# Note: -# This example may require additional features to be added to LAMMPS. -# If LAMMPS complains about an "Invalid pair_style", then copy the code -# in the "additional_lammps_code" directory into your LAMMPS "src" directory -# and recompile LAMMPS. - - - -import "CGLipidBr2005.lt" - -using namespace CGLipidBr2005 - -# The "= new random" syntax chooses one of several molecules at random - -lipids = new random([DPPC, DLPC], [195,195], 1234) #"1234"=random_seed - [13].move(7.5, 0, 0) - [15].move(3.75, 6.49519, 0) # <-- hexagonal lattice - [2].rot(180, 1, 0, 0) # <-- 2 monolayers - - -# Note 195 + 195 must equal the number of lipids created (13x15x2) -# -# ALTERNATE METHOD: Choose each lipid independently (50%,50% probability): -# lipids = new random([DPPC, DLPC], [0.5,0.5], 1234) -# [13].move(7.5, 0, 0) -# [15].move(3.75, 6.49519, 0) -# [2].rot(180, 1, 0, 0) - - - - -# Now move all the lipds up to the center of the box - -lipids[*][*][*].move(0,0,75.0) - - - - -# Although this patch of lipids is not square or rectangular, (it looks -# like a parallelogram), this is no longer the case after rectangular -# periodic boundary conditions are applied. (Check by visualising in VMD.) - - -write_once("Data Boundary") { - 0 97.5 xlo xhi - 0 97.42785792 ylo yhi - 0 150.0 zlo zhi -} - - -# A note on geometry: -# We want to create a bilayer arranged in a hexagonal lattice consisting of -# 13 rows (each row is aligned with the x-axis) -# 15 columns (aligned at a 60 degree angle from the x axis) -# The lattice spacing is 7.5 Angstroms. -# When wrapped onto a rectangular box, the dimensions of the system are: -# 13 * 7.5 Angstroms in the X direction -# 15 * 7.5*sqrt(3)/2 Angstroms in the Y direction - - - - - - - -# ------------------- protein inclusion --------------------- - -import "1beadProtSci2010.lt" - -using namespace 1beadProtSci2010 - -protein = new 4HelixInsideOut - -protein.move(45.0, 25.98076211, 75.0) - - -# Delete a hole in the membrane to create space for the protein. - -delete lipids[4][2][*] -delete lipids[6][2][*] -delete lipids[3-6][3][*] -delete lipids[3-5][4][*] -delete lipids[2-5][5][*] -delete lipids[2][6][*] -delete lipids[4][6][*] - -# Note: All atom types must include the full path (the name of -# the namespace which defined them as well as the atom type name). -# (This is because we are no longer inside that namespace.) - - -write_once("In Settings") { - - # ----------------------------------------------------------- - # -------- interactions between protein and lipids ---------- - # ----------------------------------------------------------- - - # Interactions between the protein and lipid atoms are usually - # determined by mixing rules. (However this is not possible some - # for atoms, such as the "int" atoms in the lipid model which - # interact using -1/r^2 attraction.) Mixing rules do not make - # sense for these atoms so we must explicitly define their - # interaction with all other atoms. - - # We want the hydrophobic interactions between hydrophobic residues in - # the protein and beads the interior of the lipid to be energetically - # similar to the attractive interactions between the lipid tails. - # - # Note: I made the width of the outward-facing protein beads slightly larger - # ("12.5") whenever they interact with the "tail" beads in each lipid - # (in order to make the protein wider there). - # This hopefully relieves some of the internal negative pressure in the center - # of the bilayer which can otherwise rip apart the protein or suck it into - # the bilaer. (This is a hack, and I'm not sure if it is necessary. - # For different protein or lipid models, you probably don't need this.) - # - # i j pairstylename eps sig K L - - pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 12.5 0.4 -1 - pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 - - # To help keep the protein from tilting 90 degrees and burying itself - # within the lipid bilayer, we make the turn regions at either - # end of the protein (strongly) attracted to the head groups - # of the lipid. (In reality, they would probably be attracted - # to the water as well.) - - pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 - pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 - - # All other interactions between proteins and lipids are steric. - - pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - - pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - - pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - - pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - - - # ----------------------------------------------------------- - # -------- Modifications to the protein model: -------------- - # ----------------------------------------------------------- - # - # Turn off attraction between the hydrophobic "@atom:sH" beads: - # (These beads are located in the outside of a trans-membrane protein.) - - pair_coeff @atom:1beadProtSci2010/sH @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0 - - # (Why: These beads are only attracted to - # each other in an aqueous environment) - - # ... and - # Turn ON attraction between the hydrophilic "@atom:sL" beads. - # (These beads are located in the interior of a trans-membrane protein.) - - pair_coeff @atom:1beadProtSci2010/sL @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 - - # Why? - # In reality, polar groups in the interior of trans-membrane - # proteins do form hydrogen bonds with each other. This was - # absent from the original protein model because, in an aqueous - # environment, these groups preferentially interact with the water. - # - # Why is this necessary? - # Shouldn't attraction between lipid tails and the protein create - # an effective force which brings the hydrophilic beads together? - # (similar to the hydrophobic effect, but in reverse?). - # Answer: - # Unlike an aqueous environment (~zero pressure, or +1atm), there is - # a large negative pressure in the interior of some bilayer membrane - # models (such as this one). Without some kind of direct attraction - # between interior residues, the protein will get pulled apart. - # (Perhaps the attractive force I am using is too strong?) - -} - - - - -# Finally, we must combine the two force-field styles which were used for -# the coarse-grained lipid and protein. To do that, we write one last time -# to the "In Init" section. When reading the "Init" section LAMMPS will -# read these commands last and this will override any earlier settings. - -write_once("In Init") { - # -- These styles override earlier settings -- - units real - atom_style full - # (Hybrid force field styles were used for portability.) - bond_style hybrid harmonic - angle_style hybrid cosine/delta harmonic - dihedral_style hybrid fourier - improper_style none - pair_style hybrid table linear 1130 lj/charmm/coul/charmm/inter es4k4l 14.5 15 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" -} - diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/README_run.sh index 9598e3b08d..d7ea305695 100755 --- a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/README_run.sh +++ b/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/README_run.sh @@ -7,15 +7,15 @@ # If not, carry out the instructions in "README_setup.sh". # # -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, +# If "lmp_mpi" is the name of the command you use to invoke lammps, # then you would run lammps on these files this way: -lmp_linux -i run.in.npt # Run a simulation at constant pressure (tension) +lmp_mpi -i run.in.npt # Run a simulation at constant pressure (tension) #or -lmp_linux -i run.in.nvt # Run a simulation at constant volume +lmp_mpi -i run.in.nvt # Run a simulation at constant volume #(Note: The constant volume simulation lacks pressure equilibration. These are # completely separate simulations. The results of the constant pressure @@ -27,7 +27,7 @@ lmp_linux -i run.in.nvt # Run a simulation at constant volume # If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.npt #or -#mpirun -np 4 lmp_linux -i run.in.nvt +#mpirun -np 4 lmp_mpi -i run.in.nvt # (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005Orig.lt b/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005Orig.lt index c994f7d1c2..a12eb0681c 100644 --- a/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005Orig.lt +++ b/tools/moltemplate/examples/coarse_grained_examples/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005Orig.lt @@ -51,9 +51,6 @@ CGLipidBr2005 { lj/charmm/coul/charmm/inter es4k4l 14.5 15 pair_modify mix arithmetic special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" - - neighbor 2.0 multi # <- perhaps unnecessary - comm_modify mode multi # <- perhaps unnecessary } diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh index 45bd2d451d..d5ae1fe5a3 100755 --- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh +++ b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh @@ -13,10 +13,10 @@ -LAMMPS_COMMAND="lmp_ubuntu" +LAMMPS_COMMAND="lmp_mpi" # Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps -# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. +# (such as lmp_ubuntu, lmp_mac_mpi, lmp_cygwin etc...). Change if necessary. # Run lammps using the following 3 commands: diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh index 45bd2d451d..d5ae1fe5a3 100755 --- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh +++ b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh @@ -13,10 +13,10 @@ -LAMMPS_COMMAND="lmp_ubuntu" +LAMMPS_COMMAND="lmp_mpi" # Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps -# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. +# (such as lmp_ubuntu, lmp_mac_mpi, lmp_cygwin etc...). Change if necessary. # Run lammps using the following 3 commands: diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/README_run.sh index 99338c7708..6c5417239b 100755 --- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/README_run.sh +++ b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/frustrated/README_run.sh @@ -9,10 +9,10 @@ # ----------------------------------- -LAMMPS_COMMAND="lmp_ubuntu" +LAMMPS_COMMAND="lmp_mpi" # Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps -# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. +# (such as lmp_ubuntu, lmp_mac_mpi, lmp_cygwin etc...). Change if necessary. # Run lammps using the following 3 commands: diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh index 45bd2d451d..d5ae1fe5a3 100755 --- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh +++ b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh @@ -13,10 +13,10 @@ -LAMMPS_COMMAND="lmp_ubuntu" +LAMMPS_COMMAND="lmp_mpi" # Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps -# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. +# (such as lmp_ubuntu, lmp_mac_mpi, lmp_cygwin etc...). Change if necessary. # Run lammps using the following 3 commands: diff --git a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/README_run.sh index 45bd2d451d..4b0229453e 100755 --- a/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/README_run.sh +++ b/tools/moltemplate/examples/coarse_grained_examples/protein_folding_examples/1beadProtSci2010/README_run.sh @@ -13,10 +13,10 @@ -LAMMPS_COMMAND="lmp_ubuntu" +LAMMPS_COMMAND="lmp_mpi" # Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps -# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. +# (such as lmp_ubuntu, lmp_mac_mpi, lmp_cygwin etc...) Change if necessary. # Run lammps using the following 3 commands: diff --git a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/README_WARNING.TXT b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/README_WARNING.TXT new file mode 100644 index 0000000000..1a4ecd094a --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/README_WARNING.TXT @@ -0,0 +1,14 @@ +WARNING: + This is not a realistic simulation of proteins in a lipid membrane. + + When I released this example in 2013, the simulations ran without crashing and produced no obvious visual flaws. However recently (2015) I've noticed that there are some serious problems: Currently, the protein no-longer remains perpendicular to the membrane during the simulations. (In some cases, it also unfolds.) The original version of this example did not behave this way. I'm not sure what changed since then. + + In addition, I have also noticed that newer versions of PACKMOL do not always succeed at generating a spherical vesicle in a reasonable amount of time. (You will probably have to play with the .inp files in the packmol_files directory to get PACKMOL to produce any files at all.) + + This example was created to demonstrate how to combine totally different kinds of coarse-grained molecules (with different kinds of force-fields) together in the same simulation in LAMMPS. Tuning the force-field parameters to get realistic results was not the goal. + + One day I might tinker with the shape of the protein and the force-field parameters to try and avoid this unsightly outcome. (Probably shortening the length of the helices would help.) Either way, I doubt it would make the simulations any more accurate. + + I apologize that the simulations no longer produce the same pretty images shown on the web page. + +Andrew 2015-8-02 diff --git a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/README_run.sh b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/README_run.sh index 99f39891e4..ab62f6fb59 100755 --- a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/README_run.sh +++ b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/README_run.sh @@ -8,17 +8,17 @@ # If not, carry out the instructions in "README_setup.sh". # # -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, +# If "lmp_mpi" is the name of the command you use to invoke lammps, # then you would run lammps on these files this way: -lmp_linux -i run.in.min # Minimize the system (important, and very slow) +lmp_mpi -i run.in.min # Minimize the system (important, and very slow) -lmp_linux -i run.in.nvt # Run a simulation at constant volume +lmp_mpi -i run.in.nvt # Run a simulation at constant volume # If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.min +#mpirun -np 4 lmp_mpi -i run.in.min #or -#mpirun -np 4 lmp_linux -i run.in.nvt +#mpirun -np 4 lmp_mpi -i run.in.nvt # (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/CGLipidBr2005.lt b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/CGLipidBr2005.lt index ed8fe89dfe..2388f3afd9 100644 --- a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/CGLipidBr2005.lt +++ b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/CGLipidBr2005.lt @@ -50,9 +50,6 @@ CGLipidBr2005 { lj/charmm/coul/charmm/inter es4k4l 14.5 15 pair_modify mix arithmetic special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" - - neighbor 2.0 multi # <- perhaps unnecessary - comm_modify mode multi # <- perhaps unnecessary } diff --git a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/system.lt index 98213116d8..a470e1bf89 100644 --- a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/system.lt +++ b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/system.lt @@ -45,8 +45,8 @@ using namespace 1beadProtSci2010 # b) then we add 9500 DLPC lipids to the inner monolayer # # step3) Keeping the coordinates from steps 1 and 2 fixed, -# a) first we add 12500 DPPC lipids to the outer monolayer -# b) then we add 12500 DLPC lipids to the outer monolayer +# a) first we add 12700 DPPC lipids to the outer monolayer +# b) then we add 12700 DLPC lipids to the outer monolayer # # The order that molecules are created in moltemplate should match the order # they appear in the final XYZ file created by PACKMOL. (See above.) @@ -63,9 +63,9 @@ dppc_in = new DPPC [9500] dlpc_in = new DLPC [9500] # Step 3a) ---- outer monolayer ---- -dppc_out = new DPPC [12500] +dppc_out = new DPPC [12700] # Step 3b) -dlpc_out = new DLPC [12500] +dlpc_out = new DLPC [12700] @@ -187,6 +187,5 @@ write_once("In Init") { pair_style hybrid table linear 1130 lj/charmm/coul/charmm/inter es4k4l 14.5 15 pair_modify mix arithmetic special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" - communicate multi } diff --git a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/run.in.min b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/run.in.min index 9cb2d93003..25ed25ad77 100644 --- a/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/run.in.min +++ b/tools/moltemplate/examples/coarse_grained_examples/vesicle_Brannigan2005+Bellesia2010/run.in.min @@ -28,10 +28,14 @@ include system.in.settings # -- Run section -- -dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz +dump 1 all custom 250 traj_min.lammpstrj id mol type x y z ix iy iz # minimize +#balance 1.3 rcb + +min_style quickmin +min_modify dmax 0.1 minimize 1.0e-5 1.0e-7 5000 20000 # If minimization crashes, then instead try Langevin dynamics diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step3_run_lammps.sh b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step3_run_lammps.sh index 813c406c0e..ab9a7dc6e8 100755 --- a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step3_run_lammps.sh +++ b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step3_run_lammps.sh @@ -7,10 +7,10 @@ # If not, carry out the instructions in "README_run_moltemplate.sh". # # -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, +# If "lmp_mpi" is the name of the command you use to invoke lammps, # then you would run lammps this way: -lmp_linux -i run.in.nvt +lmp_mpi -i run.in.nvt # NOTE: BECAUSE ALL OF THE ORIGINAL FORCE FIELD PARAMETERS WERE INTENTIONALLY # REMOVED, THE SYSTEM WILL MOVE IN A VERY UNREALISTIC WAY. diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/junk.in b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/junk.in deleted file mode 100644 index 22bfd7170d..0000000000 --- a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/junk.in +++ /dev/null @@ -1 +0,0 @@ -atom_style full diff --git a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh b/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh index 022c53ce3b..2944f68403 100755 --- a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh +++ b/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh @@ -7,12 +7,12 @@ # If not, carry out the instructions in "README_setup.sh". # # -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, +# If "lmp_mpi" is the name of the command you use to invoke lammps, # then you would run lammps on these files this way: -lmp_linux -i run.in.npt # minimization and simulation at constant pressure -lmp_linux -i run.in.nvt # minimization and simulation at constant volume +lmp_mpi -i run.in.npt # minimization and simulation at constant pressure +lmp_mpi -i run.in.nvt # minimization and simulation at constant volume #(Note: The constant volume simulation lacks pressure equilibration. These are # completely separate simulations. The results of the constant pressure @@ -26,6 +26,6 @@ lmp_linux -i run.in.nvt # minimization and simulation at constant volume # If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.npt -#mpirun -np 4 lmp_linux -i run.in.nvt +#mpirun -np 4 lmp_mpi -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.nvt # (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/README.TXT b/tools/moltemplate/examples/misc_examples/menger_sponge/README.TXT index 6bc152b186..4d3a9d2f85 100644 --- a/tools/moltemplate/examples/misc_examples/menger_sponge/README.TXT +++ b/tools/moltemplate/examples/misc_examples/menger_sponge/README.TXT @@ -35,11 +35,11 @@ system.data, system.in.init, system.in.settings. --- To run LAMMPS, try a command like: --- -lmp_linux -i run.in +lmp_mpi -i run.in or (if you have mpi installed) -mpirun -np 4 lmp_linux -i run.in +mpirun -np 4 lmp_mpi -i run.in This will create an ordinary LAMMPS dump file you can visualize with VMD traj.lammpstrj (See README_visualize.txt) diff --git a/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/README.TXT b/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/README.TXT index 76caac02cc..3e985be859 100644 --- a/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/README.TXT +++ b/tools/moltemplate/examples/misc_examples/pyramids_vs_gravity/README.TXT @@ -17,6 +17,7 @@ to bounce off of. So I added a graphene surface at the bottom as scenery. (It does not exert any force on the atoms.) (Random comment: This could be a fun example to illustrate the Boltzmann - distribution. Because there is no damping, in a small region, the particle - heights should eventually approach the Boltzmann distribution for some - suitable temperature.) + distribution. Because there is no damping, in a small region, I'm guessing + the particle heights should eventually approach the Boltzmann distribution + for some temperature consistent with the initial potential energy of the + system.) diff --git a/tools/moltemplate/moltemplate_manual.pdf b/tools/moltemplate/moltemplate_manual.pdf index 4ead6c064b..6c23a2986c 100644 Binary files a/tools/moltemplate/moltemplate_manual.pdf and b/tools/moltemplate/moltemplate_manual.pdf differ diff --git a/tools/moltemplate/src/dump2data.py b/tools/moltemplate/src/dump2data.py index fb5fb74014..553a164c38 100755 --- a/tools/moltemplate/src/dump2data.py +++ b/tools/moltemplate/src/dump2data.py @@ -949,7 +949,7 @@ if __name__ == "__main__": if (is_triclinic and (len(tokens) > 2)): frame_xy_str = tokens[2] bvec[0] = float(frame_xy_str) - #See http://lammps.sandia.gov/doc/Section_howto.html#howto_12 + #See http://lammps.sandia.gov/doc/Section_howto.html#howto-12 #sys.stderr.write('avec='+str(avec)+'\n') elif not frame_ylo_str: @@ -960,7 +960,7 @@ if __name__ == "__main__": if (is_triclinic and (len(tokens) > 2)): frame_xz_str = tokens[2] cvec[0] = float(frame_xz_str) - #See http://lammps.sandia.gov/doc/Section_howto.html#howto_12 + #See http://lammps.sandia.gov/doc/Section_howto.html#howto-12 #sys.stderr.write('bvec='+str(bvec)+'\n') elif not frame_zlo_str: @@ -971,7 +971,7 @@ if __name__ == "__main__": if (is_triclinic and (len(tokens) > 2)): frame_yz_str = tokens[2] cvec[1] = float(frame_yz_str) - #See http://lammps.sandia.gov/doc/Section_howto.html#howto_12 + #See http://lammps.sandia.gov/doc/Section_howto.html#howto-12 #sys.stderr.write('cvec='+str(cvec)+'\n') elif (section.find('ITEM: ATOMS') == 0): @@ -1002,9 +1002,6 @@ if __name__ == "__main__": y = float(ylo_str) + xs*avec[1] + ys*bvec[1] + zs*cvec[1] z = float(zlo_str) + xs*avec[2] + ys*bvec[2] + zs*cvec[2] - # avec, bvec, cvec described here: - #http://lammps.sandia.gov/doc/Section_howto.html#howto_12 - elif ((i_xsu != -1) and (i_ysu != -1) and (i_zsu != -1)): xsu = float(tokens[i_xsu]) #i_xs determined above ysu = float(tokens[i_ysu]) diff --git a/tools/moltemplate/src/ltemplify.py b/tools/moltemplate/src/ltemplify.py index d765573c35..97ee00e9f7 100755 --- a/tools/moltemplate/src/ltemplify.py +++ b/tools/moltemplate/src/ltemplify.py @@ -44,6 +44,13 @@ def Intify(s): return s +def IsNumber(s): + try: + float(s) + return True + except ValueError, TypeError: + return False + def StringToInterval(sel_str, slice_delim='*'): # Split a string into 1-3 tokens using the slice_delim and convert to int. # What a mess. I should rewrite this function @@ -210,8 +217,8 @@ def BelongsToSel(i, sel): try: g_program_name = __file__.split('/')[-1] # = 'ltemplify.py' - g_version_str = '0.45' - g_date_str = '2014-12-17' + g_version_str = '0.48' + g_date_str = '2015-8-02' sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+'\n') non_empty_output = False @@ -288,6 +295,9 @@ try: i_atomid = None i_atomtype = None i_molid = None + i_x = None + i_y = None + i_z = None l_in_init = [] l_in_settings = [] @@ -309,6 +319,7 @@ try: l_data_dihedral_coeffs = [] l_data_improper_coeffs = [] l_data_pair_coeffs = [] + l_data_pairij_coeffs = [] l_data_atoms = [] l_data_velocities = [] l_data_bonds = [] @@ -317,6 +328,14 @@ try: l_data_impropers = [] # class2 force fields + #l_in_bondbond_coeffs = [] <--not needed, included in l_in_angle_coeff + #l_in_bondangle_coeffs = [] <--not needed, included in l_in_angle_coeff + #l_in_middlebondtorsion_coeffs = [] not needed, included in l_in_dihedral_coeff + #l_in_endbondtorsion_coeffs = [] <--not needed, included in l_in_dihedral_coeff + #l_in_angletorsion_coeffs = [] <--not needed, included in l_in_dihedral_coeff + #l_in_angleangletorsion_coeffs = [] not needed, included in l_in_dihedral_coeff + #l_in_bondbond13_coeffs = [] <--not needed, included in l_in_dihedral_coeff + #l_in_angleangle_coeffs = [] <--not needed, included in l_in_improper_coeff l_data_bondbond_coeffs = [] l_data_bondangle_coeffs = [] l_data_middlebondtorsion_coeffs = [] @@ -340,7 +359,7 @@ try: some_pair_coeffs_read = False complained_atom_style_mismatch = False infer_types_from_comments = False - + remove_coeffs_from_data_file = True argv = sys.argv @@ -403,6 +422,13 @@ try: sys.stderr.write('\n \"Atoms\" column format:\n') sys.stderr.write(' '+(' '.join(column_names))+'\n') i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names) + # Which columns contain the coordinates? + ii_coords = ColNames2Coords(column_names) + assert(len(ii_coords) == 1) + i_x = ii_coords[0][0] + i_y = ii_coords[0][1] + i_z = ii_coords[0][2] + if i_molid: sys.stderr.write(' (i_atomid='+str(i_atomid+1)+', i_atomtype='+str(i_atomtype+1)+', i_molid='+str(i_molid+1)+')\n\n') else: @@ -467,6 +493,17 @@ try: else: i += 1 + # We might need to parse the simulation boundary-box. + # If so, use these variables. (None means uninitialized.) + boundary_xlo = None + boundary_xhi = None + boundary_ylo = None + boundary_yhi = None + boundary_zlo = None + boundary_zhi = None + boundary_xy = None + boundary_yz = None + boundary_xz = None # atom type names atomtypes_name2int = {} @@ -480,6 +517,12 @@ try: # The default atom_style is "full" column_names = AtomStyle2ColNames('full') i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names) + # Which columns contain the coordinates? + ii_coords = ColNames2Coords(column_names) + assert(len(ii_coords) == 1) + i_x = ii_coords[0][0] + i_y = ii_coords[0][1] + i_z = ii_coords[0][2] #--------------------------------------------------------- #-- The remaining arguments are files that the user wants @@ -565,6 +608,12 @@ try: column_names = AtomStyle2ColNames(line.split()[1]) i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names) + # Which columns contain the coordinates? + ii_coords = ColNames2Coords(column_names) + assert(len(ii_coords) == 1) + i_x = ii_coords[0][0] + i_y = ii_coords[0][1] + i_z = ii_coords[0][2] sys.stderr.write('\n \"Atoms\" column format:\n') sys.stderr.write(' '+(' '.join(column_names))+'\n') @@ -599,6 +648,53 @@ try: elif (line.strip() == 'Atoms'): sys.stderr.write(' reading \"'+line.strip()+'\"\n') atoms_already_read = True + + # Before attempting to read atomic coordinates, first find + # the lattice vectors of the simulation's boundary box: + # Why do we care about the Simulation Boundary? + # Some LAMMPS data files store atomic coordinates in a + # complex format with 6 numbers, 3 floats, and 3 integers. + # The 3 floats are x,y,z coordinates. Any additional numbers + # following these are integers which tell LAMMPS which cell + # the particle belongs to, (in case it has wandered out of + # the original periodic boundary box). In order to find + # the true location of the particle, we need to offset that + # particle's position with the unit-cell lattice vectors: + # avec, bvec, cvec (or multiples thereof) + # avec, bvec, cvec are the axis of the parallelepiped which + # define the simulation's boundary. They are described here: + #http://lammps.sandia.gov/doc/Section_howto.html#howto-12 + if ((not boundary_xlo) or (not boundary_xhi) or + (not boundary_ylo) or (not boundary_yhi) or + (not boundary_zlo) or (not boundary_zhi)): + raise InputError('Error: The DATA file lacks a boundary-box header. You must specify:\n' + ' xlo xhi ylo yhi zlo zhi (and xy xz yz if triclinic)\n' + ' These numbers should appear before the \"Atoms\" section.\n' + ' Use this format (example):\n' + ' -100.0 100.0 xhi xlo\n' + ' 0.0 200.0 yhi ylo\n' + ' -25.0 50.0 zhi zlo\n' + '\n' + 'For details, see http://lammps.sandia.gov/doc/read_data.html\n' + '\n' + ' (NOTE: If the atom coordinates are NOT followed by integers, then\n' + ' these numbers are all ignored, however you must still specify\n' + ' xlo, xhi, ylo, yhi, zlo, zhi. You can set them all to 0.0.)\n') + + if not (boundary_xy and boundary_yz and boundary_xz): + # Then use a simple rectangular boundary box: + avec = (boundary_xhi-boundary_xlo, 0.0, 0.0) + bvec = (0.0, boundary_yhi-boundary_ylo, 0.0) + cvec = (0.0, 0.0, boundary_zhi-boundary_zlo) + else: + # Triclinic geometry in LAMMPS is explained here: + # http://lammps.sandia.gov/doc/Section_howto.html#howto-12 + # http://lammps.sandia.gov/doc/read_data.html + avec = (boundary_xhi-boundary_xlo, 0.0, 0.0) + bvec = (boundary_xy, boundary_yhi-boundary_ylo, 0.0) + cvec = (boundary_xz, boundary_yz, boundary_zhi-boundary_zlo) + + while lex: line = lex.ReadLine() if line.strip() in data_file_header_names: @@ -613,7 +709,8 @@ try: raise InputError('Error: The number of columns in the \"Atoms\" section does\n' ' not match the atom_style (see column name list above).\n') elif ((len(tokens) != len(column_names)) and - (not complained_atom_style_mismatch)): + (len(tokens) != len(column_names)+3) and + (not complained_atom_style_mismatch)): complained_atom_style_mismatch = True sys.stderr.write('Warning: The number of columns in the \"Atoms\" section does\n' ' not match the atom_style (see column name list above).\n') @@ -645,7 +742,38 @@ try: atomtypes_int2name[atomtype] = atomtype_name tokens[i_atomtype] = '@atom:'+atomtype_name - # I can't use atomids_int2names or atomtypes_int2names yet + # Interpreting unit-cell counters + # If present, then unit-cell "flags" must be + # added to the x,y,z coordinates. + # + # For more details on unit-cell "flags", see: + # http://lammps.sandia.gov/doc/read_data.html + # "In the data file, atom lines (all lines or + # none of them) can optionally list 3 trailing + # integer values (nx,ny,nz), which are used to + # initialize the atom’s image flags. + # If nx,ny,nz values are not listed in the + # data file, LAMMPS initializes them to 0. + # Note that the image flags are immediately + # updated if an atom’s coordinates need to + # wrapped back into the simulation box." + + if (len(tokens) == len(column_names)+3): + nx = int(tokens[-3]) + ny = int(tokens[-2]) + nz = int(tokens[-1]) + x = float(tokens[i_x]) + nx*avec[0]+ny*bvec[0]+nz*cvec[0] + y = float(tokens[i_y]) + nx*avec[1]+ny*bvec[1]+nz*cvec[1] + z = float(tokens[i_z]) + nx*avec[2]+ny*bvec[2]+nz*cvec[2] + tokens[i_x] = str(x) + tokens[i_y] = str(y) + tokens[i_z] = str(z) + # Now get rid of them: + del tokens[-3:] + + + + # I can't use atomids_int2name or atomtypes_int2name yet # because they probably have not been defined yet. # (Instead assign these names in a later pass.) @@ -747,8 +875,11 @@ try: if (BelongsToSel(atomid, atomid_selection) and BelongsToSel(atomtype, atomtype_selection) and BelongsToSel(molid, molid_selection)): - #tokens[0] = '$atom:id'+tokens[0] - tokens[0] = '$atom:'+atomids_int2name[atomid] + tokens[0] = '$atom:id'+tokens[0] + #tokens[0] = '$atom:'+atomids_int2name[atomid] + #NOTE:I can't use "atomids_int2name" yet because + # they probably have not been defined yet. + # (Instead assign these names in a later pass.) l_data_velocities.append((' '*indent)+(' '.join(tokens)+'\n')) # non-point-like-particles: @@ -771,8 +902,11 @@ try: if (BelongsToSel(atomid, atomid_selection) and BelongsToSel(atomtype, atomtype_selection) and BelongsToSel(molid, molid_selection)): - #tokens[0] = '$atom:id'+tokens[0] - tokens[0] = '$atom:'+atomids_int2name[atomid] + tokens[0] = '$atom:id'+tokens[0] + #tokens[0] = '$atom:'+atomids_int2name[atomid] + #NOTE:I can't use "atomids_int2name" yet because + # they probably have not been defined yet. + # (Instead assign these names in a later pass.) l_data_ellipsoids.append((' '*indent)+(' '.join(tokens)+'\n')) elif (line.strip() == 'Lines'): sys.stderr.write(' reading \"'+line.strip()+'\"\n') @@ -793,8 +927,11 @@ try: if (BelongsToSel(atomid, atomid_selection) and BelongsToSel(atomtype, atomtype_selection) and BelongsToSel(molid, molid_selection)): - #tokens[0] = '$atom:id'+tokens[0] - tokens[0] = '$atom:'+atomids_int2name[atomid] + tokens[0] = '$atom:id'+tokens[0] + #tokens[0] = '$atom:'+atomids_int2name[atomid] + #NOTE:I can't use "atomids_int2name" yet because + # they probably have not been defined yet. + # (Instead assign these names in a later pass.) l_data_lines.append((' '*indent)+(' '.join(tokens)+'\n')) elif (line.strip() == 'Triangles'): sys.stderr.write(' reading \"'+line.strip()+'\"\n') @@ -815,8 +952,11 @@ try: if (BelongsToSel(atomid, atomid_selection) and BelongsToSel(atomtype, atomtype_selection) and BelongsToSel(molid, molid_selection)): - #tokens[0] = '$atom:id'+tokens[0] - tokens[0] = '$atom:'+atomids_int2name[atomid] + tokens[0] = '$atom:id'+tokens[0] + #tokens[0] = '$atom:'+atomids_int2name[atomid] + #NOTE:I can't use "atomids_int2name" yet because + # they probably have not been defined yet. + # (Instead assign these names in a later pass.) l_data_triangles.append((' '*indent)+(' '.join(tokens)+'\n')) elif (line.strip() == 'Bonds'): @@ -1083,7 +1223,7 @@ try: atomtype_i_str = tokens[0] if '*' in atomtype_i_str: raise InputError('PROBLEM near or before '+ErrorLeader(infile, lineno)+'\n' - ' As of 2012-7, moltemplate forbids use of the "\*\" wildcard\n' + ' As of 2015-8, moltemplate forbids use of the "\*\" wildcard\n' ' character in the \"Pair Coeffs\" section.\n') else: i = int(atomtype_i_str) @@ -1093,6 +1233,37 @@ try: tokens[0] = i_str l_data_pair_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + elif (line.strip() == 'PairIJ Coeffs'): + sys.stderr.write(' reading \"'+line.strip()+'\"\n') + some_pair_coeffs_read = True + while lex: + line = lex.ReadLine() + if line.strip() in data_file_header_names: + lex.push_raw_text(line) # <- Save line for later + break + tokens = line.strip().split() + if len(tokens) > 0: + if (len(tokens) < 2): + raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' + ' Nonsensical line in Pair Coeffs section:\n' + ' \"'+line.strip()+'\"\n') + atomtype_i_str = tokens[0] + atomtype_j_str = tokens[1] + if (('*' in atomtype_i_str) or ('*' in atomtype_j_str)): + raise InputError('PROBLEM near or before '+ErrorLeader(infile, lineno)+'\n' + ' As of 2015-8, moltemplate forbids use of the "\*\" wildcard\n' + ' character in the \"PairIJ Coeffs\" section.\n') + else: + i = int(atomtype_i_str) + j = int(atomtype_j_str) + if (((not i) or BelongsToSel(i, atomtype_selection)) and + ((not j) or BelongsToSel(j, atomtype_selection))): + i_str = '@atom:type'+str(i) + j_str = '@atom:type'+str(j) + tokens[0] = i_str + tokens[1] = j_str + l_data_pair_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) + elif (tokens[0] == 'pair_coeff'): some_pair_coeffs_read = True if (len(tokens) < 3): @@ -1151,7 +1322,7 @@ try: break tokens = line.strip().split() if len(tokens) > 0: - tokens[0] = '@angle:type'+tokens[0] + #tokens[0] = '@angle:type'+tokens[0] l_data_bondbond_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) elif (line.strip() == 'BondAngle Coeffs'): @@ -1163,7 +1334,7 @@ try: break tokens = line.strip().split() if len(tokens) > 0: - tokens[0] = '@angle:type'+tokens[0] + #tokens[0] = '@angle:type'+tokens[0] l_data_bondangle_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) elif (line.strip() == 'MiddleBondTorsion Coeffs'): @@ -1175,7 +1346,7 @@ try: break tokens = line.strip().split() if len(tokens) > 0: - tokens[0] = '@dihedral:type'+tokens[0] + #tokens[0] = '@dihedral:type'+tokens[0] l_data_middlebondtorsion_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) elif (line.strip() == 'EndBondTorsion Coeffs'): @@ -1187,7 +1358,7 @@ try: break tokens = line.strip().split() if len(tokens) > 0: - tokens[0] = '@dihedral:type'+tokens[0] + #tokens[0] = '@dihedral:type'+tokens[0] l_data_endbondtorsion_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) elif (line.strip() == 'AngleTorsion Coeffs'): @@ -1199,7 +1370,7 @@ try: break tokens = line.strip().split() if len(tokens) > 0: - tokens[0] = '@dihedral:type'+tokens[0] + #tokens[0] = '@dihedral:type'+tokens[0] l_data_angletorsion_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) elif (line.strip() == 'AngleAngleTorsion Coeffs'): @@ -1211,7 +1382,7 @@ try: break tokens = line.strip().split() if len(tokens) > 0: - tokens[0] = '@dihedral:type'+tokens[0] + #tokens[0] = '@dihedral:type'+tokens[0] l_data_angleangletorsion_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) elif (line.strip() == 'BondBond13 Coeffs'): @@ -1223,7 +1394,7 @@ try: break tokens = line.strip().split() if len(tokens) > 0: - tokens[0] = '@dihedral:type'+tokens[0] + #tokens[0] = '@dihedral:type'+tokens[0] l_data_bondbond13_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) elif (line.strip() == 'AngleAngle Coeffs'): @@ -1235,7 +1406,7 @@ try: break tokens = line.strip().split() if len(tokens) > 0: - tokens[0] = '@improper:type'+tokens[0] + #tokens[0] = '@improper:type'+tokens[0] l_data_angleangle_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) elif (line.strip() == 'Angles By Type'): @@ -1274,6 +1445,43 @@ try: tokens[0] = '@improper:type'+tokens[0] l_data_impropers_by_type.append((' '*indent)+(' '.join(tokens)+'\n')) + + # Figure out the size of the simulation box boundary: + elif ((len(tokens)==4) and + (tokens[2] == 'xlo') and + (tokens[3] == 'xhi') and + IsNumber(tokens[0]) and + IsNumber(tokens[1])): + boundary_xlo = float(tokens[0]) + boundary_xhi = float(tokens[1]) + + elif ((len(tokens)==4) and + (tokens[2] == 'ylo') and + (tokens[3] == 'yhi') and + IsNumber(tokens[0]) and + IsNumber(tokens[1])): + boundary_ylo = float(tokens[0]) + boundary_yhi = float(tokens[1]) + + elif ((len(tokens)==4) and + (tokens[2] == 'zlo') and + (tokens[3] == 'zhi') and + IsNumber(tokens[0]) and + IsNumber(tokens[1])): + boundary_zlo = float(tokens[0]) + boundary_zhi = float(tokens[1]) + + elif ((len(tokens)==6) and + (tokens[3] == 'xy') and + (tokens[4] == 'xz') and + (tokens[5] == 'yz') and + IsNumber(tokens[0]) and + IsNumber(tokens[1]) and + IsNumber(tokens[2])): + boundary_xy = float(tokens[0]) + boundary_xz = float(tokens[1]) + boundary_yz = float(tokens[2]) + elif (tokens[0] == 'group'): if (len(tokens) < 3): raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' @@ -1457,6 +1665,29 @@ try: else: i_line += 1 + # delete data_pairij_coeffs for atom types we don't care about anymore: + i_line = 0 + while i_line < len(l_data_pairij_coeffs): + line = l_data_pairij_coeffs[i_line] + tokens = line.strip().split() + assert(len(tokens) > 0) + split_colon_I = tokens[0].split(':') + assert(len(split_colon_I) == 2) + atomtype_I = Intify(split_colon_I[1]) + split_colon_J = tokens[1].split(':') + assert(len(split_colon_J) == 2) + atomtype_J = Intify(split_colon_J[1]) + if (((not (atomtype_I in needed_atomtypes)) and + (not ((len(atomtype_selection) > 0) and + BelongsToSel(atomtype_I, atomtype_selection)))) + or + ((not (atomtype_J in needed_atomtypes)) and + (not ((len(atomtype_selection) > 0) and + BelongsToSel(atomtype_J, atomtype_selection))))): + del l_data_pairij_coeffs[i_line] + else: + i_line += 1 + # delete in_pair_coeffs for atom we don't care about anymore: i_line = 0 while i_line < len(l_in_pair_coeffs): @@ -1838,6 +2069,39 @@ try: l_data_angle_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') i_line += 1 + # --- class2specific ---- + # Do the same for BondBond and BondAngle Coeffs: + # NOTE: LAMMPS INPUT SCRIPTS, ALL CLASS2 COEFFS are represented by: + # angle_coeff, dihedral_coeff, and improper_coeff commands. + # THERE ARE NO bondbond_coeff commands, or bondangle_coeff commands, + # etc..., so we dont have to worry about l_in_bondbond_coeffs,... + # delete data_bondbond_coeffs for angletypes we don't care about anymore: + i_line = 0 + while i_line < len(l_data_bondbond_coeffs): + line = l_data_bondbond_coeffs[i_line] + tokens = line.strip().split() + angletype = Intify(tokens[0]) + if (not (angletype in needed_angletypes)): + del l_data_bondbond_coeffs[i_line] + else: + tokens[0] = '@angle:type'+str(angletype) + l_data_bondbond_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + # delete data_bondangle_coeffs for angletypes we don't care about anymore: + i_line = 0 + while i_line < len(l_data_bondangle_coeffs): + line = l_data_bondangle_coeffs[i_line] + tokens = line.strip().split() + angletype = Intify(tokens[0]) + if (not (angletype in needed_angletypes)): + del l_data_bondangle_coeffs[i_line] + else: + tokens[0] = '@angle:type'+str(angletype) + l_data_bondangle_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + # --- end of class2specific ---- + + # delete in_angle_coeffs for angletypes we don't care about anymore: for angletype in needed_angletypes: assert(type(angletype) is int) @@ -1910,6 +2174,7 @@ try: + # --- DIHEDRALS AND DIHEDRAL COEFFS --- # delete lines from data_dihedrals if they involve atoms we don't care about @@ -1958,6 +2223,76 @@ try: l_data_dihedral_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') i_line += 1 + # --- class2specific ---- + # Do the same for MiddleBondTorsion, EndBondTorsion, AngleTorsion, + # AngleAngleTorsion, and BondBond13 Coeffs + # NOTE: LAMMPS INPUT SCRIPTS, ALL CLASS2 COEFFS are represented by: + # angle_coeff, dihedral_coeff, and improper_coeff commands. + # THERE ARE NO "middlebondtorsion_coeff" commands, etc...so we don't + # have to worry about dealing with "l_in_middlebondtorsion_coeffs",... + # delete data_middlebondtorsion_coeffs for dihedraltypes we don't care about anymore: + i_line = 0 + while i_line < len(l_data_middlebondtorsion_coeffs): + line = l_data_middlebondtorsion_coeffs[i_line] + tokens = line.strip().split() + dihedraltype = Intify(tokens[0]) + if (not (dihedraltype in needed_dihedraltypes)): + del l_data_middlebondtorsion_coeffs[i_line] + else: + tokens[0] = '@dihedral:type'+str(dihedraltype) + l_data_middlebondtorsion_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + # delete data_endbondtorsion_coeffs for dihedraltypes we don't care about anymore: + i_line = 0 + while i_line < len(l_data_endbondtorsion_coeffs): + line = l_data_endbondtorsion_coeffs[i_line] + tokens = line.strip().split() + dihedraltype = Intify(tokens[0]) + if (not (dihedraltype in needed_dihedraltypes)): + del l_data_endbondtorsion_coeffs[i_line] + else: + tokens[0] = '@dihedral:type'+str(dihedraltype) + l_data_endbondtorsion_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + # delete data_angletorsion_coeffs for dihedraltypes we don't care about anymore: + i_line = 0 + while i_line < len(l_data_angletorsion_coeffs): + line = l_data_angletorsion_coeffs[i_line] + tokens = line.strip().split() + dihedraltype = Intify(tokens[0]) + if (not (dihedraltype in needed_dihedraltypes)): + del l_data_angletorsion_coeffs[i_line] + else: + tokens[0] = '@dihedral:type'+str(dihedraltype) + l_data_angletorsion_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + # delete data_angleangletorsion_coeffs for dihedraltypes we don't care about anymore: + i_line = 0 + while i_line < len(l_data_angleangletorsion_coeffs): + line = l_data_angleangletorsion_coeffs[i_line] + tokens = line.strip().split() + dihedraltype = Intify(tokens[0]) + if (not (dihedraltype in needed_dihedraltypes)): + del l_data_angleangletorsion_coeffs[i_line] + else: + tokens[0] = '@dihedral:type'+str(dihedraltype) + l_data_angleangletorsion_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + # delete data_bondbond13_coeffs for dihedraltypes we don't care about anymore: + i_line = 0 + while i_line < len(l_data_bondbond13_coeffs): + line = l_data_bondbond13_coeffs[i_line] + tokens = line.strip().split() + dihedraltype = Intify(tokens[0]) + if (not (dihedraltype in needed_dihedraltypes)): + del l_data_bondbond13_coeffs[i_line] + else: + tokens[0] = '@dihedral:type'+str(dihedraltype) + l_data_bondbond13_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + # --- end of class2specific ---- + + # delete in_dihedral_coeffs for dihedraltypes we don't care about anymore: for dihedraltype in needed_dihedraltypes: assert(type(dihedraltype) is int) @@ -2078,6 +2413,28 @@ try: l_data_improper_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') i_line += 1 + # --- class2specific ---- + # Do the same for AngleAngle Coeffs + # NOTE: LAMMPS INPUT SCRIPTS, ALL CLASS2 COEFFS are represented by: + # angle_coeff, dihedral_coeff, and improper_coeff commands. + # THERE ARE NO "angleangle_coeff" commands, etc...so we don't + # have to worry about dealing with "l_in_angleangle_coeffs",... + # delete data_middlebondtorsion_coeffs for dihedraltypes we don't care about anymore: + # delete data_angleangle_coeffs for impropertypes we don't care about anymore: + i_line = 0 + while i_line < len(l_data_angleangle_coeffs): + line = l_data_angleangle_coeffs[i_line] + tokens = line.strip().split() + impropertype = Intify(tokens[0]) + if (not (impropertype in needed_impropertypes)): + del l_data_angleangle_coeffs[i_line] + else: + tokens[0] = '@improper:type'+str(impropertype) + l_data_angleangle_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') + i_line += 1 + # --- end of class2specific ---- + + # delete in_improper_coeffs for impropertypes we don't care about anymore: for impropertype in needed_impropertypes: assert(type(impropertype) is int) @@ -2155,12 +2512,12 @@ try: # If so, then save the group and write it out. # (I hate trying to parse this kind of text.) - if len(l_in_group) > 0: - sys.stderr.write('\n' - ' --groups-- Attempting to parse \"group\" commands.\n' - ' This may cause '+g_program_name+' to crash.\n' - ' If so, comment out all group commands in your input script(s), and\n' - ' try again. (And please report the error. -Andrew 2014-10-30)\n') + #if len(l_in_group) > 0: + # sys.stderr.write('\n' + # ' --groups-- Attempting to parse \"group\" commands.\n' + # ' This may cause '+g_program_name+' to crash.\n' + # ' If so, comment out all group commands in your input script(s), and\n' + # ' try again. (And please report the error. -Andrew 2014-10-30)\n') i_line = 0 groups_needed = set(['all']) @@ -2610,30 +2967,104 @@ try: sys.stdout.write('\n') sys.stdout.write(''.join(l_in_masses)) non_empty_output = True + + + if remove_coeffs_from_data_file: + if len(l_data_pair_coeffs) > 0: + for line in l_data_pair_coeffs: + tokens = line.strip().split() + atomtype_str = tokens[0] + l_in_pair_coeffs.append((' '*cindent)+' pair_coeff '+atomtype_str+' '+atomtype_str+' '+' '.join(tokens[1:])+'\n') + l_data_pair_coeffs = [] + if len(l_data_pairij_coeffs) > 0: + for line in l_data_pairij_coeffs: + l_in_pair_coeffs.append((' '*cindent)+' pair_coeff '+line.strip()+'\n') + l_data_pairij_coeffs = [] if len(l_in_pair_coeffs) > 0: l_in_pair_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') l_in_pair_coeffs.append((' '*cindent)+'}\n') sys.stdout.write('\n') sys.stdout.write(''.join(l_in_pair_coeffs)) non_empty_output = True + + + if (remove_coeffs_from_data_file and (len(l_data_bond_coeffs) > 0)): + for line in l_data_bond_coeffs: + l_in_bond_coeffs.append((' '*cindent)+' bond_coeff '+line.strip()+'\n') + l_data_bond_coeffs = [] if len(l_in_bond_coeffs) > 0: l_in_bond_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') l_in_bond_coeffs.append((' '*cindent)+'}\n') sys.stdout.write('\n') sys.stdout.write(''.join(l_in_bond_coeffs)) non_empty_output = True + + if (remove_coeffs_from_data_file and (len(l_data_angle_coeffs) > 0)): + for line in l_data_angle_coeffs: + l_in_angle_coeffs.append((' '*cindent)+' angle_coeff '+line.strip()+'\n') + l_data_angle_coeffs = [] + for line in l_data_bondbond_coeffs: + tokens = line.strip().split() + l_in_angle_coeffs.append((' '*cindent)+' angle_coeff '+tokens[0]+' bb '+' '.join(tokens[1:])+'\n') + l_data_bondbond_coeffs = [] + for line in l_data_bondangle_coeffs: + tokens = line.strip().split() + l_in_angle_coeffs.append((' '*cindent)+' angle_coeff '+tokens[0]+' ba '+' '.join(tokens[1:])+'\n') + l_data_bondangle_coeffs = [] if len(l_in_angle_coeffs) > 0: l_in_angle_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') l_in_angle_coeffs.append((' '*cindent)+'}\n') sys.stdout.write('\n') sys.stdout.write(''.join(l_in_angle_coeffs)) non_empty_output = True + + if (remove_coeffs_from_data_file and (len(l_data_dihedral_coeffs) > 0)): + for line in l_data_dihedral_coeffs: + l_in_dihedral_coeffs.append((' '*cindent)+' dihedral_coeff '+line.strip()+'\n') + l_data_dihedral_coeffs = [] + + for line in l_data_middlebondtorsion_coeffs: + tokens = line.strip().split() + l_in_dihedral_coeffs.append((' '*cindent)+' dihedral_coeff '+tokens[0]+' mbt '+' '.join(tokens[1:])+'\n') + l_data_middlebondtorsion_coeffs = [] + + for line in l_data_endbondtorsion_coeffs: + tokens = line.strip().split() + l_in_dihedral_coeffs.append((' '*cindent)+' dihedral_coeff '+tokens[0]+' ebt '+' '.join(tokens[1:])+'\n') + l_data_endbondtorsion_coeffs = [] + + for line in l_data_angletorsion_coeffs: + tokens = line.strip().split() + l_in_dihedral_coeffs.append((' '*cindent)+' dihedral_coeff '+tokens[0]+' at '+' '.join(tokens[1:])+'\n') + l_data_angletorsion_coeffs = [] + + for line in l_data_angleangletorsion_coeffs: + tokens = line.strip().split() + l_in_dihedral_coeffs.append((' '*cindent)+' dihedral_coeff '+tokens[0]+' aat '+' '.join(tokens[1:])+'\n') + l_data_angleangletorsion_coeffs = [] + + for line in l_data_bondbond13_coeffs: + tokens = line.strip().split() + l_in_dihedral_coeffs.append((' '*cindent)+' dihedral_coeff '+tokens[0]+' bb13 '+' '.join(tokens[1:])+'\n') + l_data_bondbond13_coeffs = [] + if len(l_in_dihedral_coeffs) > 0: l_in_dihedral_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') l_in_dihedral_coeffs.append((' '*cindent)+'}\n') sys.stdout.write('\n') sys.stdout.write(''.join(l_in_dihedral_coeffs)) non_empty_output = True + + if (remove_coeffs_from_data_file and (len(l_data_improper_coeffs) > 0)): + for line in l_data_improper_coeffs: + l_in_improper_coeffs.append((' '*cindent)+' improper_coeff '+line.strip()+'\n') + l_data_improper_coeffs = [] + + for line in l_data_angleangle_coeffs: + tokens = line.strip().split() + l_in_improper_coeffs.append((' '*cindent)+' improper_coeff '+tokens[0]+' aa '+' '.join(tokens[1:])+'\n') + l_data_angleangle_coeffs = [] + if len(l_in_improper_coeffs) > 0: l_in_improper_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') l_in_improper_coeffs.append((' '*cindent)+'}\n') @@ -2680,6 +3111,12 @@ try: sys.stdout.write('\n') sys.stdout.write(''.join(l_data_pair_coeffs)) non_empty_output = True + if len(l_data_pairij_coeffs) > 0: + l_data_pairij_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_pairij_coeffs+'\") {\n') + l_data_pairij_coeffs.append((' '*cindent)+'}\n') + sys.stdout.write('\n') + sys.stdout.write(''.join(l_data_pairij_coeffs)) + non_empty_output = True # class2 force fields: if len(l_data_bondbond_coeffs) > 0: @@ -2779,11 +3216,17 @@ try: sys.stdout.write('\n') sys.stdout.write(''.join(l_data_triangles)) - if len(l_data_velocities) > 0: - l_data_velocities.insert(0, (' '*cindent)+'write(\"'+data_velocities+'\") {\n') - l_data_velocities.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_velocities)) + # DO NOT WRITE OUT VELOCITY DATA + # (Why: because it makes it difficult to combine this molecular template + # with molecule templates from other sources which lack velocity data. + # LAMMPS (and topotools) will crash if the number of entries in the + # Velocities section of a data file does not match the number of atoms.) + # COMMENTING OUT: + #if len(l_data_velocities) > 0: + # l_data_velocities.insert(0, (' '*cindent)+'write(\"'+data_velocities+'\") {\n') + # l_data_velocities.append((' '*cindent)+'}\n') + # sys.stdout.write('\n') + # sys.stdout.write(''.join(l_data_velocities)) if len(l_data_bonds) > 0: l_data_bonds.insert(0, (' '*cindent)+'write(\"'+data_bonds+'\") {\n') l_data_bonds.append((' '*cindent)+'}\n') @@ -2815,11 +3258,11 @@ try: l_in_group.append((' '*cindent)+'}\n') sys.stdout.write('\n') sys.stdout.write(''.join(l_in_group)) - sys.stderr.write('######################################################\n' - 'WARNING: One or more \"group\" commands appear to refer to relevant atoms.\n' - ' Please check to make sure that the group(s) generated by\n' - ' '+g_program_name+' contain the correct atoms. (-Andrew 2014-10-30)\n' - '######################################################\n') + #sys.stderr.write('######################################################\n' + # 'WARNING: One or more \"group\" commands appear to refer to relevant atoms.\n' + # ' Please check to make sure that the group(s) generated by\n' + # ' '+g_program_name+' contain the correct atoms. (-Andrew 2014-10-30)\n' + # '######################################################\n') assert(non_empty_output) if len(l_in_fix_rigid) > 0: @@ -2890,12 +3333,12 @@ try: if non_empty_output: sys.stderr.write('WARNING: The '+g_program_name+' script has not been rigorously tested.\n' ' Exotic (many-body) pair-styles and pair-styles with\n' - ' unusual syntax (such as hbond/dreiding) are not understood\n' + ' unusual syntax (such hbond/dreiding) are not understood\n' ' by '+g_program_name+' (...although they are supported by moltemplate).\n' ' Please look over the resulting LT file and check for errors.\n' ' Convert any remaining atom, bond, angle, dihedral, or improper id\n' ' or type numbers to the corresponding $ or @-style counter variables.\n' - ' Feel free to report any bugs you find. (-Andrew Jewett 2014-10-30)\n') + ' Feel free to report any bugs you find. (-Andrew Jewett 2015-8-02)\n') diff --git a/tools/moltemplate/src/moltemplate.sh b/tools/moltemplate/src/moltemplate.sh index d7b280d4e1..2e04cb17e9 100755 --- a/tools/moltemplate/src/moltemplate.sh +++ b/tools/moltemplate/src/moltemplate.sh @@ -1,5 +1,5 @@ #!/usr/bin/env bash -# (note: Classic Bourne shell (#!/bin/sh) also seems to work.) +# (note: Classic Bourne shell (#!/bin/sh) also worked at some point.) # Author: Andrew Jewett (jewett.aij at g mail) @@ -9,8 +9,8 @@ # All rights reserved. G_PROGRAM_NAME="moltemplate.sh" -G_VERSION="1.29" -G_DATE="2014-12-19" +G_VERSION="1.31" +G_DATE="2015-8-02" echo "${G_PROGRAM_NAME} v${G_VERSION} ${G_DATE}" >&2 echo "" >&2 @@ -138,6 +138,7 @@ data_angle_coeffs="Data Angle Coeffs" data_dihedral_coeffs="Data Dihedral Coeffs" data_improper_coeffs="Data Improper Coeffs" data_pair_coeffs="Data Pair Coeffs" +data_pairij_coeffs="Data PairIJ Coeffs" # interactions-by-type (not id. This is not part of the LAMMPS standard.) data_bonds_by_type="Data Bonds By Type" @@ -193,6 +194,7 @@ ttree_assignments.txt $tmp_atom_coords $data_masses $data_pair_coeffs +$data_pairij_coeffs $data_bond_coeffs $data_angle_coeffs $data_dihedral_coeffs @@ -367,6 +369,7 @@ done TTREE_ARGS="" ATOM_STYLE="" +ATOM_STYLE_ARG="" i=0 while [ "$i" -lt "$ARGC" ]; do @@ -533,13 +536,14 @@ while [ "$i" -lt "$ARGC" ]; do #echo " (atom_style=\"$A\")" >&2 #echo "" >&2 - ATOM_STYLE="-atomstyle \"$A\"" + ATOM_STYLE="$A" + ATOM_STYLE_ARG="-atomstyle \"$A\"" - # (minor detail: $ATOM_STYLE should also be appended to TTREE_ARGS) + # (minor detail: $ATOM_STYLE_ARG should also be appended to TTREE_ARGS) if [ -z "$TTREE_ARGS" ]; then - TTREE_ARGS="$ATOM_STYLE" + TTREE_ARGS="$ATOM_STYLE_ARG" else - TTREE_ARGS="${TTREE_ARGS} $ATOM_STYLE" + TTREE_ARGS="${TTREE_ARGS} $ATOM_STYLE_ARG" fi @@ -646,6 +650,28 @@ fi echo "" >&2 + + + +# Attempt to remove any the DOS return-cairrage characters +# from inside the standard LAMMPS files generated by the user: +# (Users are free to put whatever weird characters they want in other +# (custom) auxilliary files. But not in the standard LAMMPS files.) +OIFS=$IFS +#IFS=$'\n' +IFS=" +" +for file in $MOLTEMPLATE_TEMP_FILES; do + if [ -e "$file" ]; then + #dos2unix < "$file" > "$file.dos2unix" + tr -d '\r' < "$file" > "$file.dos2unix" + rm -f "$file" >/dev/null 2>&1 || true + mv -f "$file.dos2unix" "$file" + fi +done +IFS=$OIFS + + if [ -s "${data_atoms}" ]; then if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicate_atoms.py" \ < "${data_atoms}" \ @@ -1480,13 +1506,21 @@ else echo "WARNING: missing file \"$data_masses\"" >&2 fi - if [ -s "$data_pair_coeffs" ]; then echo "Pair Coeffs" >> "$OUT_FILE_DATA" echo "" >> "$OUT_FILE_DATA" cat "$data_pair_coeffs" >> "$OUT_FILE_DATA" echo "" >> "$OUT_FILE_DATA" -else + PAIR_COEFFS_IN_DATA="true" +fi +if [ -s "$data_pairij_coeffs" ]; then + echo "PairIJ Coeffs" >> "$OUT_FILE_DATA" + echo "" >> "$OUT_FILE_DATA" + cat "$data_pairij_coeffs" >> "$OUT_FILE_DATA" + echo "" >> "$OUT_FILE_DATA" + PAIR_COEFFS_IN_DATA="true" +fi +if [ -n "$PAIR_COEFFS_IN_DATA" ]; then if [ ! -s "$in_settings" ] || (! grep -q pair_coeff "$in_settings"); then echo "WARNING: no pair coeffs have been set!" >&2 fi @@ -1598,9 +1632,12 @@ if [ -s "$data_angleangle_coeffs" ]; then fi - if [ -s "$data_atoms" ]; then - echo "Atoms" >> "$OUT_FILE_DATA" + if [ -n "$ATOM_STYLE" ]; then + echo "Atoms # $ATOM_STYLE" >> "$OUT_FILE_DATA" + else + echo "Atoms # full" >> "$OUT_FILE_DATA" + fi if [ -s "$tmp_atom_coords" ]; then echo "# (Note: x,y,z coordinates may overlap and can be modified later.)" >> "$OUT_FILE_DATA" else @@ -1735,7 +1772,7 @@ if [ -s "$tmp_atom_coords" ]; then # Copy the coordinates in $tmp_atom_coords into $OUT_FILE_DATA rm -f "$OUT_FILE_COORDS" - if ! eval $PYTHON_COMMAND "${SCRIPT_DIR}/raw2data.py" $ATOM_STYLE "$OUT_FILE_DATA" < "$tmp_atom_coords" > "$OUT_FILE_COORDS"; then + if ! eval $PYTHON_COMMAND "${SCRIPT_DIR}/raw2data.py" $ATOM_STYLE_ARG "$OUT_FILE_DATA" < "$tmp_atom_coords" > "$OUT_FILE_COORDS"; then ERR_INTERNAL fi mv -f "$OUT_FILE_COORDS" "$OUT_FILE_DATA" @@ -1790,10 +1827,7 @@ for file in $MOLTEMPLATE_TEMP_FILES; do if [ -e "$file" ]; then rm -f "output_ttree/$file" >/dev/null 2>&1 || true #echo "file=\"$file\"" - #mv "$file" output_ttree/ >/dev/null 2>&1 || true - #dos2unix < "$file" > "output_ttree/$file" - tr -d '\r' < "$file" > "output_ttree/$file" - rm -f "$file" >/dev/null 2>&1 || true + mv "$file" output_ttree/ >/dev/null 2>&1 || true fi done IFS=$OIFS @@ -1805,17 +1839,19 @@ IFS=$OIFS # ############## DEAL WITH CUSTOM NON-STANDARD SECTIONS ################ -N_data_prefix=`expr length "$data_prefix"` +# N_data_prefix=`expr length "$data_prefix"` <-- not posix compliant. AVOID +N_data_prefix=${#data_prefix} #<-- works even if $data_prefix contains spaces ls "${data_prefix}"* 2> /dev/null | while read file_name; do #If using bash: - #section_name="${file_name:$N_data_prefix}" + #SECTION_NAME="${file_name:$N_data_prefix}" #If using sh: - section_name=`expr substr "$file_name" $(($N_data_prefix+1)) 1000000` + #SECTION_NAME=`expr substr "$file_name" $(($N_data_prefix+1)) 1000000` <-- not posix compliant. AVOID + SECTION_NAME=`echo "" | awk "END{print substr(\"$file_name\",$((N_data_prefix+1)),1000000)}"` # Create a new section in the data file # matching the portion of the name of # the file after the data_prefix. echo "" >> "$OUT_FILE_DATA" - echo "$section_name" >> "$OUT_FILE_DATA" + echo "$SECTION_NAME" >> "$OUT_FILE_DATA" echo "" >> "$OUT_FILE_DATA" cat "$file_name" >> "$OUT_FILE_DATA" echo "" >> "$OUT_FILE_DATA" @@ -1840,13 +1876,14 @@ if [ -e "$OUT_FILE_DATA" ]; then fi - -N_in_prefix=`expr length "$in_prefix"` +#N_in_prefix=`expr length "$in_prefix"` <-- not posix compliant. AVOID. +N_in_prefix=${#in_prefix} #<-- works even if $in_prefix contains spaces ls "${in_prefix}"* 2> /dev/null | while read file_name; do #If using bash: - #section_name="${file_name:$N_in_prefix}" + #SECTION_NAME="${file_name:$N_in_prefix}" #If using sh: - SECTION_NAME=`expr substr "$file_name" $(($N_in_prefix+1)) 1000000` + #SECTION_NAME=`expr substr "$file_name" $(($N_in_prefix+1)) 1000000` <-- not posix compliant. AVOID + SECTION_NAME=`echo "" | awk "END{print substr(\"$file_name\",$((N_in_prefix+1)),1000000)}"` FILE_SUFFIX=`echo "$SECTION_NAME" | awk '{print tolower($0)}'` # Create a new section in the lammps input script # matching the portion of the name of @@ -1954,7 +1991,8 @@ echo "# -- ALTERNATELY, run at constant volume (Nose-Hoover) --" >> $OUT_FILE_I echo "# fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1" >> $OUT_FILE_INPUT_SCRIPT echo "# -- ALTERNATELY, run at constant volume using Langevin dynamics. --" >> $OUT_FILE_INPUT_SCRIPT echo "# -- (This is good for sparse CG polymers in implicit solvent.) --" >> $OUT_FILE_INPUT_SCRIPT -echo "# fix fxlan all langevin 300.0 300.0 5000 48279" >> $OUT_FILE_INPUT_SCRIPT +echo "# fix fxLAN all langevin 300.0 300.0 5000 48279" >> $OUT_FILE_INPUT_SCRIPT +echo "# fix fxNVE all nve #(<--needed by fix langevin)" >> $OUT_FILE_INPUT_SCRIPT echo "# -- Now, finally run the simulation --" >> $OUT_FILE_INPUT_SCRIPT echo "# run 50000" >> $OUT_FILE_INPUT_SCRIPT #echo "# write_restart system_after_nvt.rst" >> $OUT_FILE_INPUT_SCRIPT diff --git a/tools/moltemplate/src/oplsaa_moltemplate.py b/tools/moltemplate/src/oplsaa_moltemplate.py index e8884c9502..fd590a3fda 100755 --- a/tools/moltemplate/src/oplsaa_moltemplate.py +++ b/tools/moltemplate/src/oplsaa_moltemplate.py @@ -6,7 +6,9 @@ __author__="Jason Lambert" # (some additional corrections by Miguel Gonzalez and Andrew Jewett) -__version__="0.18" +__version__="0.20" + + import sys import os @@ -14,7 +16,7 @@ from operator import itemgetter g_program_name = __file__.split('/')[-1] -# To do that, first make a copy of the \"oplsaa.prm\" file +# First make a copy of the \"oplsaa.prm\" file # (which can be downloaded from the TINKER web site). # The lines in this file beginning with the word \"atoms\" should # define the atoms which you plan to put in your simulation. All other @@ -23,8 +25,23 @@ g_program_name = __file__.split('/')[-1] #""") +if sys.version > '3': + import io +else: + import cStringIO -#input data from file containing opls aa force field parameters. +try: + if sys.version < '2.7': + raise Exception('Error: Using python '+sys.version+'\n'+ + ' Alas, your version of python is too old.\n' + ' You must upgrade to a newer version of python (2.7 or later).') +except Exception as err: + sys.stderr.write('\n\n'+str(err)+'\n') + sys.exit(-1) + + + +#input data from file containing oplsaa force field parameters. try: f=open(sys.argv[1],"r") except: @@ -88,7 +105,6 @@ if num_atomTypes > 25: " file beginning with \"atom\" which you do not need.)\n\n") #temporary storage file -h=open("temp.txt","w+") atom_lookup={} #this dictionary contains all the atom ffid's as a key and the number of atoms with that key #atom=[[10000,10000] for i in range(906)] <- don't assume there are 906 atoms atom=[[-10000,-10000] for i in range(0,max_atomType+1)] @@ -180,15 +196,18 @@ for line in lines: improper.append([int(line[1]), int(line[2]), int(line[3]), int(line[4]), float(line[5]), float(line[6])]) -if len(atom) > 600: - sys.stderr.write("WARNING: The number of atom types in your file exceeds 600\n" - " (You were supposed to edit out the atoms you don't need.\n" - " Not doing this may crash your computer.)\n" - "\n" - " Proceed? (Y/N): ") - reply = sys.stdin.readline() - if find(reply.strip().lower(), 'y') != 0: - exit(0) + +#if len(atom) > 600: +# sys.stderr.write("WARNING: The number of atom types in your file exceeds 600\n" +# " (You were supposed to edit out the atoms you don't need.\n" +# " Not doing this may crash your computer.)\n" +# "\n" +# " Proceed? (Y/N): ") +# reply = sys.stdin.readline() +# if find(reply.strip().lower(), 'y') != 0: +# exit(0) + + #adding the charge and Lennard Jones parameters to #to each atom type. @@ -266,120 +285,160 @@ for x in atom: atom_lookup[x[1]]=[x[0]] atom_ffid=x[1] atom_lookup[0]=["*"] + #-------------------------------------------------------------# - - #writing out the bond coefficients and bond parameters# #-------------------------------------------------------------# -g.write(" write_once(\"In Settings\") {\n") -index1=0 + +# First check if the atoms in system can potentially form bonds +might_have_bonds = False for x in bond: for y in atom_lookup.get(x[0],[]): for z in atom_lookup.get(x[1],[]): - #g.write(" bond_coeff @bond:{}-{} harmonic {} {}\n".format(y,z,x[2]/2,x[3])) - # Miguel Gonzales corrected this line to: - g.write(" bond_coeff @bond:{}-{} harmonic {} {}\n".format(y,z,x[2],x[3])) - h.write(" @bond:{0}-{1} @atom:{0} @atom:{1}\n".format(y,z)) -g.write(" } #(end of bond_coeffs)\n\n") -h.seek(0,0) -g.write(" write_once(\"Data Bonds By Type\") {\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of bonds by type)\n\n") -del(bond) -h.close() -#-----------------------------------------------------------# -h=open("temp.txt","w+") + might_have_bonds = True +if might_have_bonds: + h=open("temp.txt","w+") + g.write(" write_once(\"In Settings\") {\n") + index1=0 + for x in bond: + for y in atom_lookup.get(x[0],[]): + for z in atom_lookup.get(x[1],[]): + #g.write(" bond_coeff @bond:{}-{} harmonic {} {}\n".format(y,z,x[2]/2,x[3])) + # Miguel Gonzales corrected this line to: + g.write(" bond_coeff @bond:{}-{} harmonic {} {}\n".format(y,z,x[2],x[3])) + h.write(" @bond:{0}-{1} @atom:{0} @atom:{1}\n".format(y,z)) + g.write(" } #(end of bond_coeffs)\n\n") + h.seek(0,0) + g.write(" write_once(\"Data Bonds By Type\") {\n") + for line in h.readlines(): + g.write(line) + g.write(" } #(end of bonds by type)\n\n") + del(bond) + h.close() + + +#-----------------------------------------------------------# #writing out angle coefficients and angles by type.---------# #-----------------------------------------------------------# -g.write(" write_once(\"Data Angles By Type\"){\n") + +# First check if the atoms in system can potentially form angle interactions +might_have_angles = False for x in angle: for y in atom_lookup.get(x[0],[]): for z in atom_lookup.get(x[1],[]): for u in atom_lookup.get(x[2],[]): - #print(y,z,u,x) - #h.write(" angle_coeff @angle:{}-{}-{} harmonic {} {}\n".format(y,z,u,x[3]/2.0,x[4])) - # Miguel Gonzales corrected this line: - h.write(" angle_coeff @angle:{}-{}-{} harmonic {} {}\n".format(y,z,u,x[3],x[4])) - g.write(" @angle:{0}-{1}-{2} @atom:{0} @atom:{1} @atom:{2}\n".format(y,z,u)) + might_have_angles = True +if might_have_angles: + h=open("temp.txt","w+") + g.write(" write_once(\"Data Angles By Type\"){\n") + for x in angle: + for y in atom_lookup.get(x[0],[]): + for z in atom_lookup.get(x[1],[]): + for u in atom_lookup.get(x[2],[]): + #print(y,z,u,x) + #h.write(" angle_coeff @angle:{}-{}-{} harmonic {} {}\n".format(y,z,u,x[3]/2.0,x[4])) + # Miguel Gonzales corrected this line: + h.write(" angle_coeff @angle:{}-{}-{} harmonic {} {}\n".format(y,z,u,x[3],x[4])) + g.write(" @angle:{0}-{1}-{2} @atom:{0} @atom:{1} @atom:{2}\n".format(y,z,u)) -g.write(" } #(end of angles by type)\n\n") -h.seek(0,0) -g.write(" write_once(\"In Settings\" ){\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of angle_coeffs)\n\n") -del(angle) -h.close() + g.write(" } #(end of angles by type)\n\n") + h.seek(0,0) + g.write(" write_once(\"In Settings\" ){\n") + for line in h.readlines(): + g.write(line) + g.write(" } #(end of angle_coeffs)\n\n") + del(angle) + h.close() + +#----------------------------------------------------------# +#writing dihedrals by type and dihedral coefficients-------# #----------------------------------------------------------# -#writing dihedrals by type and dihedral coefficients-------# -h=h=open("temp.txt","w+") -g.write(" write_once(\"Data Dihedrals By Type\") {\n") -#print(atom_lookup) +# First check if the atoms in system can potentially form dihedral interactions +might_have_dihedrals = False for x in dihedral: for y in atom_lookup.get(x[0],[]): for z in atom_lookup.get(x[1],[]): for u in atom_lookup.get(x[2],[]): for v in atom_lookup.get(x[3],[]): - if x[0]!=0 and x[3]!=0: - g.write(" @dihedral:{0}-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( - y,z,u,v)) - h.write(" dihedral_coeff @dihedral:{}-{}-{}-{} opls {} {} {} {}\n".format( - y,z,u,v,x[4],x[5],x[6],x[7])) - elif x[0]==0 and x[3]!=0: - g.write(" @dihedral:0-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( - y,z,u,v)) - h.write(" dihedral_coeff @dihedral:0-{}-{}-{} opls {} {} {} {}\n".format( - z,u,v,x[4],x[5],x[6],x[7])) - elif x[0]==0 and x[3]==0: - g.write(" @dihedral:0-{1}-{2}-0 @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( - y,z,u,v)) - #h.write(" dihedral_coeff @dihedral:0-{}-{}-0 harmonic {} {} {} {}\n".format( - h.write(" dihedral_coeff @dihedral:0-{}-{}-0 opls {} {} {} {}\n".format( - z,u,x[4],x[5],x[6],x[7])) + might_have_dihedrals = True + +if might_have_dihedrals: + h=open("temp.txt","w+") + g.write(" write_once(\"Data Dihedrals By Type\") {\n") + #print(atom_lookup) + for x in dihedral: + for y in atom_lookup.get(x[0],[]): + for z in atom_lookup.get(x[1],[]): + for u in atom_lookup.get(x[2],[]): + for v in atom_lookup.get(x[3],[]): + if x[0]!=0 and x[3]!=0: + g.write(" @dihedral:{0}-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v)) + h.write(" dihedral_coeff @dihedral:{}-{}-{}-{} opls {} {} {} {}\n".format(y,z,u,v,x[4],x[5],x[6],x[7])) + elif x[0]==0 and x[3]!=0: + g.write(" @dihedral:0-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( + y,z,u,v)) + h.write(" dihedral_coeff @dihedral:0-{}-{}-{} opls {} {} {} {}\n".format(z,u,v,x[4],x[5],x[6],x[7])) + elif x[0]==0 and x[3]==0: + g.write(" @dihedral:0-{1}-{2}-0 @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v)) + #h.write(" dihedral_coeff @dihedral:0-{}-{}-0 harmonic {} {} {} {}\n".format(z,u,x[4],x[5],x[6],x[7])) + h.write(" dihedral_coeff @dihedral:0-{}-{}-0 opls {} {} {} {}\n".format(z,u,x[4],x[5],x[6],x[7])) -del(dihedral) -g.write(" } #(end of Dihedrals by type)\n\n") -h.seek(0,0) -g.write(" write_once(\"In Settings\") {\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of dihedral_coeffs)\n\n") -h.close() + del(dihedral) + g.write(" } #(end of Dihedrals by type)\n\n") + h.seek(0,0) + g.write(" write_once(\"In Settings\") {\n") + for line in h.readlines(): + g.write(line) + g.write(" } #(end of dihedral_coeffs)\n\n") + h.close() + +#-----------------------------------------------------------------------# +#----writing out improper coefficients and impropers by type------------# #-----------------------------------------------------------------------# -#----writing out improper coefficients and impropers by type------------# -h=open("temp.txt","w+") -g.write(" write_once(\"Data Impropers By Type (opls_imp.py)\") {\n") +# First check if the atoms in system can potentially form improper interactions +might_have_impropers = False for x in improper: for y in atom_lookup.get(x[0],[]): for z in atom_lookup.get(x[1],[]): for u in atom_lookup.get(x[2],[]): for v in atom_lookup.get(x[3],[]): - # Notation: let I,J,K,L denote the atom types ("biotypes") - # listed in the order they appear in the "oplsaa.prm" file. - # (I think J and L are represented by "u" and "v" in the code here.) - # It looks like the "oplsaa.prm" file distributed with tinker - # treats the third atom ("K") as the central atom. - # After checking the code, it appears that the improper angle is - # calculated as the angle between the I,J,K and the J,K,L planes - if x[0]==0 and x[1]==0 and x[3]==0: - g.write(" @improper:0-0-{2}-0 @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v)) - h.write(" improper_coeff @improper:0-0-{2}-0 harmonic {4} {5} \n".format(y,z,u,v,x[4]/2,180)) - else: - g.write(" @improper:0-0-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v)) - h.write(" improper_coeff @improper:0-0-{2}-{3} harmonic {4} {5} \n".format(y,z,u,v,x[4]/2,180)) + might_have_impropers = True + +if might_have_impropers: + h=open("temp.txt","w+") + g.write(" write_once(\"Data Impropers By Type (opls_imp.py)\") {\n") + for x in improper: + for y in atom_lookup.get(x[0],[]): + for z in atom_lookup.get(x[1],[]): + for u in atom_lookup.get(x[2],[]): + for v in atom_lookup.get(x[3],[]): + # Notation: let I,J,K,L denote the atom types ("biotypes") + # listed in the order they appear in the "oplsaa.prm" file. + # (I think J and L are represented by "u" and "v" in the code here.) + # It looks like the "oplsaa.prm" file distributed with tinker + # treats the third atom ("K") as the central atom. + # After checking the code, it appears that the improper angle is + # calculated as the angle between the I,J,K and the J,K,L planes + if x[0]==0 and x[1]==0 and x[3]==0: + g.write(" @improper:0-0-{2}-0 @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v)) + h.write(" improper_coeff @improper:0-0-{2}-0 harmonic {4} {5} \n".format(y,z,u,v,x[4]/2,180)) + else: + g.write(" @improper:0-0-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v)) + h.write(" improper_coeff @improper:0-0-{2}-{3} harmonic {4} {5} \n".format(y,z,u,v,x[4]/2,180)) -g.write(" } #(end of impropers by type)\n\n") -h.seek(0,0) -g.write(" write_once(\"In Settings\") {\n") -for line in h.readlines(): - g.write(line) -g.write(" } #(end of improp_coeffs)\n\n") + g.write(" } #(end of impropers by type)\n\n") + h.seek(0,0) + g.write(" write_once(\"In Settings\") {\n") + for line in h.readlines(): + g.write(line) + g.write(" } #(end of improp_coeffs)\n\n") + h.close() + #-----------------------------------------------------------------------# #This section writes out the input parameters required for an opls-aa simulation @@ -400,12 +459,8 @@ g.write(" } #end of init parameters\n\n") g.write("} # OPLSAA\n") f.close() g.close() -h.close() os.remove("temp.txt") sys.stderr.write("...finished.\n") - - - diff --git a/tools/smd/Makefile b/tools/smd/Makefile new file mode 100644 index 0000000000..618bd0ab39 --- /dev/null +++ b/tools/smd/Makefile @@ -0,0 +1,7 @@ +all: + clang++ -o dump2vtk_tris dump2vtk_tris.cpp -I/usr/include/vtk-5.8/ -lvtkCommon -lvtkIO -lvtkFiltering -lvtkRendering + + +clean: + rm -f *.o + diff --git a/tools/smd/dump2vtk_tris.cpp b/tools/smd/dump2vtk_tris.cpp new file mode 100644 index 0000000000..2486f8c4e3 --- /dev/null +++ b/tools/smd/dump2vtk_tris.cpp @@ -0,0 +1,235 @@ +/* + * convert a LAMMPS / Smooth-Mach Dynamics triangle output file into a VTK unstructured grid file. + * LAMMPS output file contains STL triangle vertices + * + * ASSUMPTIONS: + * + * A compute exists for and STL triangulated surface, which computes the triangl vertices with a command like this: + * compute F tri_group smd/triangle_vertices + * c_F[1-9] now hold the triangle vertices. + * + * LAMMPS dump file has the following entries per atom line: + * id type mol x y z c_F[1] c_F[2] c_F[3] c_F[4] c_F[5] c_F[6] c_F[7] c_F[8] c_F[9] + * + */ + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include + +using namespace std; + +#define RENDER 0 // switch on / off rendering of snapshots + +void WriteVTU(std::string filename, int ntime, vtkSmartPointer unstructuredGrid) { + vtkSmartPointer writer = vtkSmartPointer::New(); + // create filename with the current timestep + std::ostringstream oss; + oss << ntime; + filename += "." + oss.str() + ".vtu"; + + writer->SetFileName(filename.c_str()); + #if VTK_MAJOR_VERSION <= 5 + writer->SetInput(unstructuredGrid); + #else + writer->SetInputData(unstructuredGrid); + #endif + writer->Write(); +} + +void WriteVTK(std::string filename, int ntime, vtkSmartPointer unstructuredGrid) { + vtkSmartPointer writer = vtkSmartPointer::New(); + // create filename with the current timestep + std::ostringstream oss; + oss << ntime; + filename += "_" + oss.str() + ".vtk"; + + writer->SetFileName(filename.c_str()); + #if VTK_MAJOR_VERSION <= 5 + writer->SetInput(unstructuredGrid); + #else + writer->SetInputData(unstructuredGrid); + #endif + writer->Write(); +} + +int main(int argc, char *argv[]) { + + string line; + vtkSmartPointer points; + vtkSmartPointer vertices; + vtkSmartPointer cellArray; + vtkIdType id_v1, id_v2, id_v3; + vtkSmartPointer tri = vtkSmartPointer::New(); // create an empty tri; + vtkSmartPointer unstructuredGrid; + + + unstructuredGrid = vtkSmartPointer::New(); + + // Parse command line arguments + if (argc != 3) { + std::cout << "Required arguments: InputFilename OutputFile_Basename" + << std::endl; + return EXIT_FAILURE; + } + + std::string lammps_dump = argv[1]; + std::string filename = argv[2]; + + ifstream myfile(lammps_dump.c_str()); + + int nlines_read = 0; + int count = -1; + int ntime; + int N; // number of atoms in this timestep + int id, type, mol; + double x, y, z, v1x, v1y, v1z, v2x, v2y, v2z, v3x, v3y, v3z; + if (myfile.is_open()) { + + while (getline(myfile, line)) { + std::size_t found = line.find("TIMESTEP"); + if (found != std::string::npos) { + cout << line << endl; + count = 0; + nlines_read = 0; + + // reinitialize VTK arrays so they are empty + points = vtkSmartPointer::New(); + vertices = vtkSmartPointer::New(); + cellArray = vtkSmartPointer::New(); + } + if (count >= 0) + count++; + + if (count == 2) { + istringstream convert(line); + convert >> ntime; + cout << "timestep is: " << ntime << endl; + } + + if (count == 4) { + istringstream convert(line); + convert >> N; + cout << "number of particles is: " << N << endl; + } + + if (count > 9) { + //cout << line << endl; + //const vector words = split(line, " "); + + std::istringstream is(line); + std::istream_iterator eos; + std::vector out(std::istream_iterator(is), eos); + + /* + * we expect the following entries in a data line: + * id type mol x y z v1x v1y v1z v2x v2y v2z v3x v3y v3z + */ + + id = out[0]; + type = out[1]; + mol = out[2]; + x = out[3]; // triangle center + y = out[4]; + z = out[5]; + v1x = out[6]; // triangle vertex 1 + v1y = out[7]; + v1z = out[8]; + v2x = out[9]; // triangle vertex 2 + v2y = out[10]; + v2z = out[11]; + v3x = out[12]; // triangle vertex 3 + v3y = out[13]; + v3z = out[14]; + + id_v1 = points->InsertNextPoint(v1x, v1y, v1z); // store tri vertices in points array and retain indices + id_v2 = points->InsertNextPoint(v2x, v2y, v2z); + id_v3 = points->InsertNextPoint(v3x, v3y, v3z); + + + + tri->GetPointIds()->SetId(0, id_v1); // fill triangle with retained indices + tri->GetPointIds()->SetId(1, id_v2); + tri->GetPointIds()->SetId(2, id_v3); + + cellArray->InsertNextCell(tri); // insert tri into array of cells + + nlines_read += 1; + + } + + if (count % (9 + N) == 0) { // we have reached the end of this snapshot + printf( + "----------------------------------------------------\n"); + printf("number of lines read from lammps dump file: %d\n", + nlines_read); + + + unstructuredGrid->SetPoints(points); + unstructuredGrid->SetCells(VTK_TRIANGLE, cellArray); + + WriteVTK(filename, ntime, unstructuredGrid); + + +// if (ntime > 100) { +// return 0; +// } + +#if RENDER == 1 + // Read and display file for verification that it was written correclty + vtkSmartPointer reader = + vtkSmartPointer::New(); + reader->SetFileName(filename.c_str()); + reader->Update(); + + vtkSmartPointer mapper = vtkSmartPointer< + vtkDataSetMapper>::New(); + mapper->SetInputConnection(reader->GetOutputPort()); + + vtkSmartPointer actor = + vtkSmartPointer::New(); + actor->SetMapper(mapper); + + vtkSmartPointer renderer = vtkSmartPointer< + vtkRenderer>::New(); + vtkSmartPointer renderWindow = vtkSmartPointer< + vtkRenderWindow>::New(); + renderWindow->AddRenderer(renderer); + vtkSmartPointer renderWindowInteractor = + vtkSmartPointer::New(); + renderWindowInteractor->SetRenderWindow(renderWindow); + + renderer->AddActor(actor); + renderer->SetBackground(.3, .6, .3); // Background color green + + renderWindow->Render(); + renderWindowInteractor->Start(); +#endif + } + + } + myfile.close(); + } else { + cout << "Unable to open file"; + } + + return EXIT_SUCCESS; +}

    angle
    peri atom-ID atom-type volume density x y z
    sphere
    smdatom-ID atom-type molecule volume mass kernel_radius contact_radius x y z
    sphere atom-ID atom-type diameter density x y z
    template
    template atom-ID molecule-ID template-index template-atom atom-type x y z
    tri
    tri atom-ID molecule-ID atom-type triangleflag density x y z
    wavepacket
    wavepacket atom-ID atom-type charge spin eradius etag cs_re cs_im x y z
    hybrid
    hybrid atom-ID atom-type x y z sub-style1 sub-style2 ...