forked from lijiext/lammps
Richard Berger
GitHub
commit
3ce020eab2
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@ -49,19 +49,19 @@ KOKKOS, o = USER-OMP, t = OPT.
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
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| :doc:`smd/tlsph/num/neighs <compute_smd_tlsph_num_neighs>` | :doc:`smd/tlsph/shape <compute_smd_tlsph_shape>` | :doc:`smd/tlsph/strain <compute_smd_tlsph_strain>` | :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>` | :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>` | :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>` |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
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| :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>` | :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>` | :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>` | :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>` | :doc:`smd/vol <compute_smd_vol>` | :doc:`sna/atom <compute_sna_atom>` |
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| :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>` | :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>` | :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>` | :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>` | :doc:`smd/vol <compute_smd_vol>` | :doc:`snap <compute_sna_atom>` |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
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| :doc:`snad/atom <compute_sna_atom>` | :doc:`snav/atom <compute_sna_atom>` | :doc:`spin <compute_spin>` | :doc:`stress/atom <compute_stress_atom>` | :doc:`stress/mop <compute_stress_mop>` | :doc:`stress/mop/profile <compute_stress_mop>` |
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| :doc:`sna/atom <compute_sna_atom>` | :doc:`snad/atom <compute_sna_atom>` | :doc:`snav/atom <compute_sna_atom>` | :doc:`spin <compute_spin>` | :doc:`stress/atom <compute_stress_atom>` | :doc:`stress/mop <compute_stress_mop>` |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
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| :doc:`stress/tally <compute_tally>` | :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>` | :doc:`temp (k) <compute_temp>` | :doc:`temp/asphere <compute_temp_asphere>` | :doc:`temp/body <compute_temp_body>` | :doc:`temp/chunk <compute_temp_chunk>` |
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| :doc:`stress/mop/profile <compute_stress_mop>` | :doc:`stress/tally <compute_tally>` | :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>` | :doc:`temp (k) <compute_temp>` | :doc:`temp/asphere <compute_temp_asphere>` | :doc:`temp/body <compute_temp_body>` |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
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| :doc:`temp/com <compute_temp_com>` | :doc:`temp/cs <compute_temp_cs>` | :doc:`temp/deform <compute_temp_deform>` | :doc:`temp/deform/eff <compute_temp_deform_eff>` | :doc:`temp/drude <compute_temp_drude>` | :doc:`temp/eff <compute_temp_eff>` |
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| :doc:`temp/chunk <compute_temp_chunk>` | :doc:`temp/com <compute_temp_com>` | :doc:`temp/cs <compute_temp_cs>` | :doc:`temp/deform <compute_temp_deform>` | :doc:`temp/deform/eff <compute_temp_deform_eff>` | :doc:`temp/drude <compute_temp_drude>` |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
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| :doc:`temp/partial <compute_temp_partial>` | :doc:`temp/profile <compute_temp_profile>` | :doc:`temp/ramp <compute_temp_ramp>` | :doc:`temp/region <compute_temp_region>` | :doc:`temp/region/eff <compute_temp_region_eff>` | :doc:`temp/rotate <compute_temp_rotate>` |
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| :doc:`temp/eff <compute_temp_eff>` | :doc:`temp/partial <compute_temp_partial>` | :doc:`temp/profile <compute_temp_profile>` | :doc:`temp/ramp <compute_temp_ramp>` | :doc:`temp/region <compute_temp_region>` | :doc:`temp/region/eff <compute_temp_region_eff>` |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
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| :doc:`temp/sphere <compute_temp_sphere>` | :doc:`temp/uef <compute_temp_uef>` | :doc:`ti <compute_ti>` | :doc:`torque/chunk <compute_torque_chunk>` | :doc:`vacf <compute_vacf>` | :doc:`vcm/chunk <compute_vcm_chunk>` |
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| :doc:`temp/rotate <compute_temp_rotate>` | :doc:`temp/sphere <compute_temp_sphere>` | :doc:`temp/uef <compute_temp_uef>` | :doc:`ti <compute_ti>` | :doc:`torque/chunk <compute_torque_chunk>` | :doc:`vacf <compute_vacf>` |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
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| :doc:`voronoi/atom <compute_voronoi_atom>` | :doc:`xrd <compute_xrd>` | | | | |
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| :doc:`vcm/chunk <compute_vcm_chunk>` | :doc:`voronoi/atom <compute_voronoi_atom>` | :doc:`xrd <compute_xrd>` | | | |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
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@ -287,9 +287,10 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` doc
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* :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>` -
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* :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>` - per-particle Cauchy stress tensor and von Mises equivalent stress in Smooth Mach Dynamics
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* :doc:`smd/vol <compute_smd_vol>` - per-particle volumes and their sum in Smooth Mach Dynamics
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* :doc:`sna/atom <compute_sna_atom>` - calculate bispectrum coefficients for each atom
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* :doc:`snad/atom <compute_sna_atom>` - derivative of bispectrum coefficients for each atom
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* :doc:`snav/atom <compute_sna_atom>` - virial contribution from bispectrum coefficients for each atom
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* :doc:`snap <compute_sna_atom>` - bispectrum components and related quantities for a group of atoms
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* :doc:`sna/atom <compute_sna_atom>` - bispectrum components for each atom
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* :doc:`snad/atom <compute_sna_atom>` - derivative of bispectrum components for each atom
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* :doc:`snav/atom <compute_sna_atom>` - virial contribution from bispectrum components for each atom
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* :doc:`spin <compute_spin>` - magnetic quantities for a system of atoms having spins
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* :doc:`stress/atom <compute_stress_atom>` - stress tensor for each atom
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* :doc:`stress/mop <compute_stress_mop>` - normal components of the local stress tensor using the method of planes
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@ -9,6 +9,9 @@ compute snad/atom command
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compute snav/atom command
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=========================
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compute snap command
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====================
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Syntax
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""""""
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@ -17,7 +20,8 @@ Syntax
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compute ID group-ID sna/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
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compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
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compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
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compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
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compute ID group-ID snap rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* sna/atom = style name of this compute command
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@ -53,12 +57,17 @@ Examples
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compute b all sna/atom 1.4 0.99363 6 2.0 2.4 0.75 1.0 rmin0 0.0
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compute db all sna/atom 1.4 0.95 6 2.0 1.0
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compute vb all sna/atom 1.4 0.95 6 2.0 1.0
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compute snap all snap 1.4 0.95 6 2.0 1.0
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Description
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"""""""""""
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Define a computation that calculates a set of bispectrum components
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for each atom in a group.
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Define a computation that calculates a set of quantities related to the
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bispectrum components of the atoms in a group. These computes are
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used primarily for calculating the dependence of energy, force, and
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stress components on the linear coefficients in the
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:doc:`snap pair\_style <pair_snap>`, which is useful when training a
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SNAP potential to match target data.
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Bispectrum components of an atom are order parameters characterizing
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the radial and angular distribution of neighbor atoms. The detailed
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@ -148,6 +157,30 @@ Again, the sum is over all atoms *i'* of atom type *I*\ . For each atom
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virial components, each atom type, and each bispectrum component. See
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section below on output for a detailed explanation.
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Compute *snap* calculates a global array contains information related
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to all three of the above per-atom computes *sna/atom*\ , *snad/atom*\ ,
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and *snav/atom*\ . The first row of the array contains the summation of
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*sna/atom* over all atoms, but broken out by type. The last six rows
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of the array contain the summation of *snav/atom* over all atoms, broken
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out by type. In between these are 3\*\ *N* rows containing the same values
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computed by *snad/atom* (these are already summed over all atoms and
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broken out by type). The element in the last column of each row contains
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the potential energy, force, or stress, according to the row.
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These quantities correspond to the user-specified reference potential
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that must be subtracted from the target data when fitting SNAP.
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The potential energy calculation uses the built in compute *thermo\_pe*.
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The stress calculation uses a compute called *snap\_press* that is
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automatically created behind the scenes, according to the following
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command:
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.. parsed-literal::
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compute snap_press all pressure NULL virial
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See section below on output for a detailed explanation of the data
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layout in the global array.
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The value of all bispectrum components will be zero for atoms not in
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the group. Neighbor atoms not in the group do not contribute to the
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bispectrum of atoms in the group.
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@ -239,10 +272,25 @@ block contains six sub-blocks corresponding to the *xx*\ , *yy*\ , *zz*\ ,
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notation. Each of these sub-blocks contains one column for each
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bispectrum component, the same as for compute *sna/atom*
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Compute *snap* evaluates a global array.
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The columns are arranged into
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*ntypes* blocks, listed in order of atom type *I*\ . Each block
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contains one column for each bispectrum component, the same as for compute
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*sna/atom*\ . A final column contains the corresponding energy, force component
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on an atom, or virial stress component. The rows of the array appear
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in the following order:
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* 1 row: *sna/atom* quantities summed for all atoms of type *I*
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* 3\*\ *N* rows: *snad/atom* quantities, with derivatives w.r.t. x, y, and z coordinate of atom *i* appearing in consecutive rows. The atoms are sorted based on atom ID.
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* 6 rows: *snav/atom* quantities summed for all atoms of type *I*
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For example, if *K* =30 and ntypes=1, the number of columns in the per-atom
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arrays generated by *sna/atom*\ , *snad/atom*\ , and *snav/atom*
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are 30, 90, and 180, respectively. With *quadratic* value=1,
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the numbers of columns are 930, 2790, and 5580, respectively.
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The number of columns in the global array generated by *snap*
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are 31, and 931, respectively, while the number of rows is
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1+3\*\ *N*\ +6, where *N* is the total number of atoms.
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If the *quadratic* keyword value is set to 1, then additional
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columns are generated, corresponding to
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@ -131,6 +131,7 @@ KOKKOS, o = USER-OMP, t = OPT.
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"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html,
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"smd/ulsph/stress"_compute_smd_ulsph_stress.html,
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"smd/vol"_compute_smd_vol.html,
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"snap"_compute_sna_atom.html,
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"sna/atom"_compute_sna_atom.html,
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"snad/atom"_compute_sna_atom.html,
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"snav/atom"_compute_sna_atom.html,
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@ -278,9 +278,10 @@ compute"_Commands_compute.html doc page are followed by one or more of
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"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html -
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"smd/ulsph/stress"_compute_smd_ulsph_stress.html - per-particle Cauchy stress tensor and von Mises equivalent stress in Smooth Mach Dynamics
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"smd/vol"_compute_smd_vol.html - per-particle volumes and their sum in Smooth Mach Dynamics
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"sna/atom"_compute_sna_atom.html - calculate bispectrum coefficients for each atom
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"snad/atom"_compute_sna_atom.html - derivative of bispectrum coefficients for each atom
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"snav/atom"_compute_sna_atom.html - virial contribution from bispectrum coefficients for each atom
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"snap"_compute_sna_atom.html - bispectrum components and related quantities for a group of atoms
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"sna/atom"_compute_sna_atom.html - bispectrum components for each atom
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"snad/atom"_compute_sna_atom.html - derivative of bispectrum components for each atom
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"snav/atom"_compute_sna_atom.html - virial contribution from bispectrum components for each atom
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"spin"_compute_spin.html - magnetic quantities for a system of atoms having spins
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"stress/atom"_compute_stress_atom.html - stress tensor for each atom
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"stress/mop"_compute_stress_mop.html - normal components of the local stress tensor using the method of planes
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@ -9,12 +9,14 @@
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compute sna/atom command :h3
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compute snad/atom command :h3
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compute snav/atom command :h3
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compute snap command :h3
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[Syntax:]
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compute ID group-ID sna/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
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compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
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compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... :pre
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compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
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compute ID group-ID snap rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... :pre
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ID, group-ID are documented in "compute"_compute.html command :ulb,l
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sna/atom = style name of this compute command :l
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@ -41,12 +43,17 @@ keyword = {rmin0} or {switchflag} or {bzeroflag} or {quadraticflag} :l
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compute b all sna/atom 1.4 0.99363 6 2.0 2.4 0.75 1.0 rmin0 0.0
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compute db all sna/atom 1.4 0.95 6 2.0 1.0
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compute vb all sna/atom 1.4 0.95 6 2.0 1.0 :pre
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compute vb all sna/atom 1.4 0.95 6 2.0 1.0
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compute snap all snap 1.4 0.95 6 2.0 1.0 :pre
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[Description:]
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Define a computation that calculates a set of bispectrum components
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for each atom in a group.
|
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Define a computation that calculates a set of quantities related to the
|
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bispectrum components of the atoms in a group. These computes are
|
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used primarily for calculating the dependence of energy, force, and
|
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stress components on the linear coefficients in the
|
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"snap pair_style"_pair_snap.html, which is useful when training a
|
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SNAP potential to match target data.
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Bispectrum components of an atom are order parameters characterizing
|
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the radial and angular distribution of neighbor atoms. The detailed
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@ -130,6 +137,27 @@ Again, the sum is over all atoms {i'} of atom type {I}. For each atom
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virial components, each atom type, and each bispectrum component. See
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section below on output for a detailed explanation.
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Compute {snap} calculates a global array contains information related
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to all three of the above per-atom computes {sna/atom}, {snad/atom},
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and {snav/atom}. The first row of the array contains the summation of
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{sna/atom} over all atoms, but broken out by type. The last six rows
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of the array contain the summation of {snav/atom} over all atoms, broken
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out by type. In between these are 3*{N} rows containing the same values
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computed by {snad/atom} (these are already summed over all atoms and
|
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broken out by type). The element in the last column of each row contains
|
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the potential energy, force, or stress, according to the row.
|
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These quantities correspond to the user-specified reference potential
|
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that must be subtracted from the target data when fitting SNAP.
|
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The potential energy calculation uses the built in compute {thermo_pe}.
|
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The stress calculation uses a compute called {snap_press} that is
|
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automatically created behind the scenes, according to the following
|
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command:
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compute snap_press all pressure NULL virial :pre
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See section below on output for a detailed explanation of the data
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layout in the global array.
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The value of all bispectrum components will be zero for atoms not in
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the group. Neighbor atoms not in the group do not contribute to the
|
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bispectrum of atoms in the group.
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|
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@ -214,10 +242,25 @@ block contains six sub-blocks corresponding to the {xx}, {yy}, {zz},
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notation. Each of these sub-blocks contains one column for each
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bispectrum component, the same as for compute {sna/atom}
|
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Compute {snap} evaluates a global array.
|
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The columns are arranged into
|
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{ntypes} blocks, listed in order of atom type {I}. Each block
|
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contains one column for each bispectrum component, the same as for compute
|
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{sna/atom}. A final column contains the corresponding energy, force component
|
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on an atom, or virial stress component. The rows of the array appear
|
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in the following order:
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1 row: {sna/atom} quantities summed for all atoms of type {I}
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3*{N} rows: {snad/atom} quantities, with derivatives w.r.t. x, y, and z coordinate of atom {i} appearing in consecutive rows. The atoms are sorted based on atom ID.
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6 rows: {snav/atom} quantities summed for all atoms of type {I} :ul
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For example, if {K} =30 and ntypes=1, the number of columns in the per-atom
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arrays generated by {sna/atom}, {snad/atom}, and {snav/atom}
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are 30, 90, and 180, respectively. With {quadratic} value=1,
|
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the numbers of columns are 930, 2790, and 5580, respectively.
|
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The number of columns in the global array generated by {snap}
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are 31, and 931, respectively, while the number of rows is
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1+3*{N}+6, where {N} is the total number of atoms.
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If the {quadratic} keyword value is set to 1, then additional
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columns are generated, corresponding to
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@ -0,0 +1,94 @@
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# Demonstrate bispectrum computes
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# initialize simulation
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variable nsteps index 0
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variable nrep equal 1
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#variable a equal 3.316
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variable a equal 2.0
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units metal
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# generate the box and atom positions using a BCC lattice
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variable nx equal ${nrep}
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variable ny equal ${nrep}
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variable nz equal ${nrep}
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boundary p p p
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lattice bcc $a
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region box block 0 ${nx} 0 ${ny} 0 ${nz}
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create_box 2 box
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create_atoms 2 box
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mass * 180.88
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displace_atoms all random 0.1 0.1 0.1 123456
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# choose SNA parameters
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variable twojmax equal 2
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variable rcutfac equal 1.0
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variable rfac0 equal 0.99363
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variable rmin0 equal 0
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variable radelem1 equal 2.3
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variable radelem2 equal 2.0
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variable wj1 equal 1.0
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variable wj2 equal 0.96
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variable snap_options string &
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"${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag 0 bzeroflag 0 switchflag 0"
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# set up dummy potential to satisfy cutoff
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pair_style zero ${rcutfac}
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pair_coeff * *
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# set up reference potential
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variable zblcutinner equal 4
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variable zblcutouter equal 4.8
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variable zblz equal 73
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pair_style zbl ${zblcutinner} ${zblcutouter}
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pair_coeff * * ${zblz} ${zblz}
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# set up per-atom computes
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compute b all sna/atom ${snap_options}
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compute vb all snav/atom ${snap_options}
|
||||
compute db all snad/atom ${snap_options}
|
||||
|
||||
# perform sums over atoms
|
||||
|
||||
group snapgroup1 type 1
|
||||
group snapgroup2 type 2
|
||||
compute bsum1 snapgroup1 reduce sum c_b[*]
|
||||
compute bsum2 snapgroup2 reduce sum c_b[*]
|
||||
# fix bsum1 all ave/time 1 1 1 c_bsum1 file bsum1.dat mode vector
|
||||
# fix bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
|
||||
compute vbsum all reduce sum c_vb[*]
|
||||
# fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
|
||||
|
||||
# set up compute snap generating global array
|
||||
|
||||
compute snap all snap ${snap_options}
|
||||
fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
|
||||
|
||||
thermo 100
|
||||
|
||||
# test output: 1: total potential energy
|
||||
# 2: xy component of stress tensor
|
||||
# 3: Sum(B_{000}^i, all i of type 2)
|
||||
# 4: xy component of Sum(Sum(r_j*dB_{222}^i/dr_j), all i of type 2), all j)
|
||||
# followed by counterparts from compute snap
|
||||
|
||||
thermo_style custom &
|
||||
pe pxy c_bsum2[1] c_vbsum[60] &
|
||||
c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[13][10]
|
||||
thermo_modify norm no
|
||||
|
||||
# dump mydump_db all custom 1000 dump_db id c_db[*]
|
||||
# dump_modify mydump_db sort id
|
||||
|
||||
# Run MD
|
||||
|
||||
run ${nsteps}
|
||||
|
|
@ -0,0 +1,526 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
/* IDEAS
|
||||
|
||||
-DONE: Need to define a local peratom array for snad and snad on local and ghost atoms
|
||||
-DONE: Reverse communicate local peratom array
|
||||
-DONE: Copy peratom array into output array
|
||||
-DONE: size_array_cols = nperdim (ncoeff [+quadratic])
|
||||
-DONE: size_array_rows = 1 + total number of atoms + 6
|
||||
-DONE: size_peratom = (3+6)*nperdim*ntypes
|
||||
INCOMPLETE: Mappy from local to global
|
||||
INCOMPLETE: modify->find_compute()
|
||||
DONE: eliminate local peratom array for viral, replace with fdotr
|
||||
|
||||
*/
|
||||
#include "compute_snap.h"
|
||||
#include <cstring>
|
||||
#include <cstdlib>
|
||||
#include "sna.h"
|
||||
#include "atom.h"
|
||||
#include "update.h"
|
||||
#include "modify.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neigh_request.h"
|
||||
#include "force.h"
|
||||
#include "pair.h"
|
||||
#include "comm.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
enum{SCALAR,VECTOR,ARRAY};
|
||||
|
||||
ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
|
||||
Compute(lmp, narg, arg), cutsq(NULL), list(NULL), snap(NULL),
|
||||
radelem(NULL), wjelem(NULL), snap_peratom(NULL), snapall(NULL)
|
||||
{
|
||||
|
||||
array_flag = 1;
|
||||
extarray = 0;
|
||||
|
||||
double rfac0, rmin0;
|
||||
int twojmax, switchflag, bzeroflag;
|
||||
radelem = NULL;
|
||||
wjelem = NULL;
|
||||
|
||||
int ntypes = atom->ntypes;
|
||||
int nargmin = 6+2*ntypes;
|
||||
|
||||
if (narg < nargmin) error->all(FLERR,"Illegal compute snap command");
|
||||
|
||||
// default values
|
||||
|
||||
rmin0 = 0.0;
|
||||
switchflag = 1;
|
||||
bzeroflag = 1;
|
||||
quadraticflag = 0;
|
||||
|
||||
// process required arguments
|
||||
|
||||
memory->create(radelem,ntypes+1,"snap:radelem"); // offset by 1 to match up with types
|
||||
memory->create(wjelem,ntypes+1,"snap:wjelem");
|
||||
rcutfac = atof(arg[3]);
|
||||
rfac0 = atof(arg[4]);
|
||||
twojmax = atoi(arg[5]);
|
||||
for(int i = 0; i < ntypes; i++)
|
||||
radelem[i+1] = atof(arg[6+i]);
|
||||
for(int i = 0; i < ntypes; i++)
|
||||
wjelem[i+1] = atof(arg[6+ntypes+i]);
|
||||
|
||||
// construct cutsq
|
||||
|
||||
double cut;
|
||||
cutmax = 0.0;
|
||||
memory->create(cutsq,ntypes+1,ntypes+1,"snap:cutsq");
|
||||
for(int i = 1; i <= ntypes; i++) {
|
||||
cut = 2.0*radelem[i]*rcutfac;
|
||||
if (cut > cutmax) cutmax = cut;
|
||||
cutsq[i][i] = cut*cut;
|
||||
for(int j = i+1; j <= ntypes; j++) {
|
||||
cut = (radelem[i]+radelem[j])*rcutfac;
|
||||
cutsq[i][j] = cutsq[j][i] = cut*cut;
|
||||
}
|
||||
}
|
||||
|
||||
// process optional args
|
||||
|
||||
int iarg = nargmin;
|
||||
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg],"rmin0") == 0) {
|
||||
if (iarg+2 > narg)
|
||||
error->all(FLERR,"Illegal compute snap command");
|
||||
rmin0 = atof(arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"bzeroflag") == 0) {
|
||||
if (iarg+2 > narg)
|
||||
error->all(FLERR,"Illegal compute snap command");
|
||||
bzeroflag = atoi(arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"switchflag") == 0) {
|
||||
if (iarg+2 > narg)
|
||||
error->all(FLERR,"Illegal compute snap command");
|
||||
switchflag = atoi(arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"quadraticflag") == 0) {
|
||||
if (iarg+2 > narg)
|
||||
error->all(FLERR,"Illegal compute snap command");
|
||||
quadraticflag = atoi(arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else error->all(FLERR,"Illegal compute snap command");
|
||||
}
|
||||
|
||||
snaptr = new SNA(lmp,rfac0,twojmax,
|
||||
rmin0,switchflag,bzeroflag);
|
||||
|
||||
ncoeff = snaptr->ncoeff;
|
||||
nperdim = ncoeff;
|
||||
if (quadraticflag) nperdim += (ncoeff*(ncoeff+1))/2;
|
||||
ndims_force = 3;
|
||||
ndims_virial = 6;
|
||||
yoffset = nperdim;
|
||||
zoffset = 2*nperdim;
|
||||
natoms = atom->natoms;
|
||||
size_array_rows = 1+ndims_force*natoms+ndims_virial;
|
||||
size_array_cols = nperdim*atom->ntypes+1;
|
||||
lastcol = size_array_cols-1;
|
||||
|
||||
ndims_peratom = ndims_force;
|
||||
size_peratom = ndims_peratom*nperdim*atom->ntypes;
|
||||
|
||||
nmax = 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ComputeSnap::~ComputeSnap()
|
||||
{
|
||||
memory->destroy(snap);
|
||||
memory->destroy(snapall);
|
||||
memory->destroy(snap_peratom);
|
||||
memory->destroy(radelem);
|
||||
memory->destroy(wjelem);
|
||||
memory->destroy(cutsq);
|
||||
delete snaptr;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputeSnap::init()
|
||||
{
|
||||
if (force->pair == NULL)
|
||||
error->all(FLERR,"Compute snap requires a pair style be defined");
|
||||
|
||||
if (cutmax > force->pair->cutforce)
|
||||
error->all(FLERR,"Compute snap cutoff is longer than pairwise cutoff");
|
||||
|
||||
// need an occasional full neighbor list
|
||||
|
||||
int irequest = neighbor->request(this,instance_me);
|
||||
neighbor->requests[irequest]->pair = 0;
|
||||
neighbor->requests[irequest]->compute = 1;
|
||||
neighbor->requests[irequest]->half = 0;
|
||||
neighbor->requests[irequest]->full = 1;
|
||||
neighbor->requests[irequest]->occasional = 1;
|
||||
|
||||
int count = 0;
|
||||
for (int i = 0; i < modify->ncompute; i++)
|
||||
if (strcmp(modify->compute[i]->style,"snap") == 0) count++;
|
||||
if (count > 1 && comm->me == 0)
|
||||
error->warning(FLERR,"More than one compute snap");
|
||||
snaptr->init();
|
||||
|
||||
// allocate memory for global array
|
||||
|
||||
memory->create(snap,size_array_rows,size_array_cols,
|
||||
"snap:snap");
|
||||
memory->create(snapall,size_array_rows,size_array_cols,
|
||||
"snap:snapall");
|
||||
array = snapall;
|
||||
|
||||
// INCOMPLETE: modify->find_compute()
|
||||
// was called 223960 times by snappy Ta example
|
||||
// that is over 600 times per config?
|
||||
// how is this possible???
|
||||
|
||||
// find compute for reference energy
|
||||
|
||||
char *id_pe = (char *) "thermo_pe";
|
||||
int ipe = modify->find_compute(id_pe);
|
||||
if (ipe == -1)
|
||||
error->all(FLERR,"compute thermo_pe does not exist.");
|
||||
c_pe = modify->compute[ipe];
|
||||
|
||||
// add compute for reference virial tensor
|
||||
|
||||
char *id_virial = (char *) "snap_press";
|
||||
char **newarg = new char*[5];
|
||||
newarg[0] = id_virial;
|
||||
newarg[1] = (char *) "all";
|
||||
newarg[2] = (char *) "pressure";
|
||||
newarg[3] = (char *) "NULL";
|
||||
newarg[4] = (char *) "virial";
|
||||
modify->add_compute(5,newarg);
|
||||
delete [] newarg;
|
||||
|
||||
int ivirial = modify->find_compute(id_virial);
|
||||
if (ivirial == -1)
|
||||
error->all(FLERR,"compute snap_press does not exist.");
|
||||
c_virial = modify->compute[ivirial];
|
||||
|
||||
}
|
||||
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputeSnap::init_list(int /*id*/, NeighList *ptr)
|
||||
{
|
||||
list = ptr;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputeSnap::compute_array()
|
||||
{
|
||||
int ntotal = atom->nlocal + atom->nghost;
|
||||
|
||||
invoked_array = update->ntimestep;
|
||||
|
||||
// grow snap_peratom array if necessary
|
||||
|
||||
if (atom->nmax > nmax) {
|
||||
memory->destroy(snap_peratom);
|
||||
nmax = atom->nmax;
|
||||
memory->create(snap_peratom,nmax,size_peratom,
|
||||
"snap:snap_peratom");
|
||||
}
|
||||
|
||||
// clear global array
|
||||
|
||||
for (int irow = 0; irow < size_array_rows; irow++)
|
||||
for (int icoeff = 0; icoeff < size_array_cols; icoeff++)
|
||||
snap[irow][icoeff] = 0.0;
|
||||
|
||||
// clear local peratom array
|
||||
|
||||
for (int i = 0; i < ntotal; i++)
|
||||
for (int icoeff = 0; icoeff < size_peratom; icoeff++) {
|
||||
snap_peratom[i][icoeff] = 0.0;
|
||||
}
|
||||
|
||||
// invoke full neighbor list (will copy or build if necessary)
|
||||
|
||||
neighbor->build_one(list);
|
||||
|
||||
const int inum = list->inum;
|
||||
const int* const ilist = list->ilist;
|
||||
const int* const numneigh = list->numneigh;
|
||||
int** const firstneigh = list->firstneigh;
|
||||
int * const type = atom->type;
|
||||
|
||||
// compute sna derivatives for each atom in group
|
||||
// use full neighbor list to count atoms less than cutoff
|
||||
|
||||
double** const x = atom->x;
|
||||
const int* const mask = atom->mask;
|
||||
|
||||
for (int ii = 0; ii < inum; ii++) {
|
||||
const int i = ilist[ii];
|
||||
if (mask[i] & groupbit) {
|
||||
|
||||
const double xtmp = x[i][0];
|
||||
const double ytmp = x[i][1];
|
||||
const double ztmp = x[i][2];
|
||||
const int itype = type[i];
|
||||
const double radi = radelem[itype];
|
||||
const int* const jlist = firstneigh[i];
|
||||
const int jnum = numneigh[i];
|
||||
const int typeoffset_local = ndims_peratom*nperdim*(itype-1);
|
||||
const int typeoffset_global = nperdim*(itype-1);
|
||||
|
||||
// insure rij, inside, and typej are of size jnum
|
||||
|
||||
snaptr->grow_rij(jnum);
|
||||
|
||||
// rij[][3] = displacements between atom I and those neighbors
|
||||
// inside = indices of neighbors of I within cutoff
|
||||
// typej = types of neighbors of I within cutoff
|
||||
// note Rij sign convention => dU/dRij = dU/dRj = -dU/dRi
|
||||
|
||||
int ninside = 0;
|
||||
for (int jj = 0; jj < jnum; jj++) {
|
||||
int j = jlist[jj];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
const double delx = x[j][0] - xtmp;
|
||||
const double dely = x[j][1] - ytmp;
|
||||
const double delz = x[j][2] - ztmp;
|
||||
const double rsq = delx*delx + dely*dely + delz*delz;
|
||||
int jtype = type[j];
|
||||
if (rsq < cutsq[itype][jtype]&&rsq>1e-20) {
|
||||
snaptr->rij[ninside][0] = delx;
|
||||
snaptr->rij[ninside][1] = dely;
|
||||
snaptr->rij[ninside][2] = delz;
|
||||
snaptr->inside[ninside] = j;
|
||||
snaptr->wj[ninside] = wjelem[jtype];
|
||||
snaptr->rcutij[ninside] = (radi+radelem[jtype])*rcutfac;
|
||||
ninside++;
|
||||
}
|
||||
}
|
||||
|
||||
snaptr->compute_ui(ninside);
|
||||
snaptr->compute_zi();
|
||||
snaptr->compute_bi();
|
||||
|
||||
for (int jj = 0; jj < ninside; jj++) {
|
||||
const int j = snaptr->inside[jj];
|
||||
snaptr->compute_duidrj(snaptr->rij[jj],
|
||||
snaptr->wj[jj],
|
||||
snaptr->rcutij[jj],jj);
|
||||
snaptr->compute_dbidrj();
|
||||
|
||||
// Accumulate dBi/dRi, -dBi/dRj
|
||||
|
||||
double *snadi = snap_peratom[i]+typeoffset_local;
|
||||
double *snadj = snap_peratom[j]+typeoffset_local;
|
||||
|
||||
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
|
||||
snadi[icoeff] += snaptr->dblist[icoeff][0];
|
||||
snadi[icoeff+yoffset] += snaptr->dblist[icoeff][1];
|
||||
snadi[icoeff+zoffset] += snaptr->dblist[icoeff][2];
|
||||
snadj[icoeff] -= snaptr->dblist[icoeff][0];
|
||||
snadj[icoeff+yoffset] -= snaptr->dblist[icoeff][1];
|
||||
snadj[icoeff+zoffset] -= snaptr->dblist[icoeff][2];
|
||||
}
|
||||
|
||||
if (quadraticflag) {
|
||||
const int quadraticoffset = ncoeff;
|
||||
snadi += quadraticoffset;
|
||||
snadj += quadraticoffset;
|
||||
int ncount = 0;
|
||||
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
|
||||
double bi = snaptr->blist[icoeff];
|
||||
double bix = snaptr->dblist[icoeff][0];
|
||||
double biy = snaptr->dblist[icoeff][1];
|
||||
double biz = snaptr->dblist[icoeff][2];
|
||||
|
||||
// diagonal elements of quadratic matrix
|
||||
|
||||
double dbxtmp = bi*bix;
|
||||
double dbytmp = bi*biy;
|
||||
double dbztmp = bi*biz;
|
||||
|
||||
snadi[ncount] += dbxtmp;
|
||||
snadi[ncount+yoffset] += dbytmp;
|
||||
snadi[ncount+zoffset] += dbztmp;
|
||||
snadj[ncount] -= dbxtmp;
|
||||
snadj[ncount+yoffset] -= dbytmp;
|
||||
snadj[ncount+zoffset] -= dbztmp;
|
||||
|
||||
ncount++;
|
||||
|
||||
// upper-triangular elements of quadratic matrix
|
||||
|
||||
for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
|
||||
double dbxtmp = bi*snaptr->dblist[jcoeff][0]
|
||||
+ bix*snaptr->blist[jcoeff];
|
||||
double dbytmp = bi*snaptr->dblist[jcoeff][1]
|
||||
+ biy*snaptr->blist[jcoeff];
|
||||
double dbztmp = bi*snaptr->dblist[jcoeff][2]
|
||||
+ biz*snaptr->blist[jcoeff];
|
||||
|
||||
snadi[ncount] += dbxtmp;
|
||||
snadi[ncount+yoffset] += dbytmp;
|
||||
snadi[ncount+zoffset] += dbztmp;
|
||||
snadj[ncount] -= dbxtmp;
|
||||
snadj[ncount+yoffset] -= dbytmp;
|
||||
snadj[ncount+zoffset] -= dbztmp;
|
||||
|
||||
ncount++;
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
// Accumulate Bi
|
||||
|
||||
// linear contributions
|
||||
|
||||
for (int icoeff = 0; icoeff < ncoeff; icoeff++)
|
||||
snap[0][icoeff+typeoffset_global] += snaptr->blist[icoeff];
|
||||
|
||||
// quadratic contributions
|
||||
|
||||
if (quadraticflag) {
|
||||
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
|
||||
double bveci = snaptr->blist[icoeff];
|
||||
snap[0][icoeff+typeoffset_global] += 0.5*bveci*bveci;
|
||||
for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
|
||||
double bvecj = snaptr->blist[jcoeff];
|
||||
snap[0][icoeff+typeoffset_global] += bveci*bvecj;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// accumulate bispectrum force contributions to global array
|
||||
|
||||
for (int itype = 0; itype < atom->ntypes; itype++) {
|
||||
const int typeoffset_local = ndims_peratom*nperdim*itype;
|
||||
const int typeoffset_global = nperdim*itype;
|
||||
for (int icoeff = 0; icoeff < nperdim; icoeff++) {
|
||||
int irow = 1;
|
||||
for (int i = 0; i < ntotal; i++) {
|
||||
double *snadi = snap_peratom[i]+typeoffset_local;
|
||||
int iglobal = atom->tag[i];
|
||||
int irow = 3*(iglobal-1)+1;
|
||||
snap[irow][icoeff+typeoffset_global] += snadi[icoeff];
|
||||
snap[irow+1][icoeff+typeoffset_global] += snadi[icoeff+yoffset];
|
||||
snap[irow+2][icoeff+typeoffset_global] += snadi[icoeff+zoffset];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// accumulate forces to global array
|
||||
|
||||
for (int i = 0; i < atom->nlocal; i++) {
|
||||
int iglobal = atom->tag[i];
|
||||
int irow = 3*(iglobal-1)+1;
|
||||
snap[irow][lastcol] = atom->f[i][0];
|
||||
snap[irow+1][lastcol] = atom->f[i][1];
|
||||
snap[irow+2][lastcol] = atom->f[i][2];
|
||||
}
|
||||
|
||||
// accumulate bispectrum virial contributions to global array
|
||||
|
||||
dbdotr_compute();
|
||||
|
||||
// sum up over all processes
|
||||
|
||||
MPI_Allreduce(&snap[0][0],&snapall[0][0],size_array_rows*size_array_cols,MPI_DOUBLE,MPI_SUM,world);
|
||||
|
||||
// assign energy to last column
|
||||
|
||||
int irow = 0;
|
||||
double reference_energy = c_pe->compute_scalar();
|
||||
snapall[irow++][lastcol] = reference_energy;
|
||||
|
||||
// assign virial stress to last column
|
||||
// switch to Voigt notation
|
||||
|
||||
c_virial->compute_vector();
|
||||
irow += 3*natoms;
|
||||
snapall[irow++][lastcol] = c_virial->vector[0];
|
||||
snapall[irow++][lastcol] = c_virial->vector[1];
|
||||
snapall[irow++][lastcol] = c_virial->vector[2];
|
||||
snapall[irow++][lastcol] = c_virial->vector[5];
|
||||
snapall[irow++][lastcol] = c_virial->vector[4];
|
||||
snapall[irow++][lastcol] = c_virial->vector[3];
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute global virial contributions via summing r_i.dB^j/dr_i over
|
||||
own & ghost atoms
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ComputeSnap::dbdotr_compute()
|
||||
{
|
||||
double **x = atom->x;
|
||||
int irow0 = 1+ndims_force*natoms;
|
||||
|
||||
// sum over bispectrum contributions to forces
|
||||
// on all particles including ghosts
|
||||
|
||||
int nall = atom->nlocal + atom->nghost;
|
||||
for (int i = 0; i < nall; i++)
|
||||
for (int itype = 0; itype < atom->ntypes; itype++) {
|
||||
const int typeoffset_local = ndims_peratom*nperdim*itype;
|
||||
const int typeoffset_global = nperdim*itype;
|
||||
double *snadi = snap_peratom[i]+typeoffset_local;
|
||||
for (int icoeff = 0; icoeff < nperdim; icoeff++) {
|
||||
double dbdx = snadi[icoeff];
|
||||
double dbdy = snadi[icoeff+yoffset];
|
||||
double dbdz = snadi[icoeff+zoffset];
|
||||
int irow = irow0;
|
||||
snap[irow++][icoeff+typeoffset_global] += dbdx*x[i][0];
|
||||
snap[irow++][icoeff+typeoffset_global] += dbdy*x[i][1];
|
||||
snap[irow++][icoeff+typeoffset_global] += dbdz*x[i][2];
|
||||
snap[irow++][icoeff+typeoffset_global] += dbdz*x[i][1];
|
||||
snap[irow++][icoeff+typeoffset_global] += dbdz*x[i][0];
|
||||
snap[irow++][icoeff+typeoffset_global] += dbdy*x[i][0];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
memory usage
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double ComputeSnap::memory_usage()
|
||||
{
|
||||
|
||||
double bytes = size_array_rows*size_array_cols *
|
||||
sizeof(double); // snap
|
||||
bytes += size_array_rows*size_array_cols *
|
||||
sizeof(double); // snapall
|
||||
bytes += nmax*size_peratom * sizeof(double); // snap_peratom
|
||||
bytes += snaptr->memory_usage(); // SNA object
|
||||
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -0,0 +1,82 @@
|
|||
/* -*- 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 COMPUTE_CLASS
|
||||
|
||||
ComputeStyle(snap,ComputeSnap)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_COMPUTE_SNAP_H
|
||||
#define LMP_COMPUTE_SNAP_H
|
||||
|
||||
#include "compute.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class ComputeSnap : public Compute {
|
||||
public:
|
||||
ComputeSnap(class LAMMPS *, int, char **);
|
||||
~ComputeSnap();
|
||||
void init();
|
||||
void init_list(int, class NeighList *);
|
||||
void compute_array();
|
||||
double memory_usage();
|
||||
|
||||
private:
|
||||
int natoms, nmax, size_peratom, lastcol;
|
||||
int ncoeff, nperdim, yoffset, zoffset;
|
||||
int ndims_peratom, ndims_force, ndims_virial;
|
||||
double **cutsq;
|
||||
class NeighList *list;
|
||||
double **snap, **snapall;
|
||||
double **snap_peratom;
|
||||
double rcutfac;
|
||||
double *radelem;
|
||||
double *wjelem;
|
||||
class SNA* snaptr;
|
||||
double cutmax;
|
||||
int quadraticflag;
|
||||
|
||||
Compute *c_pe;
|
||||
Compute *c_virial;
|
||||
|
||||
void dbdotr_compute();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#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: Compute snap requires a pair style be defined
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Compute snap cutoff is longer than pairwise cutoff
|
||||
|
||||
UNDOCUMENTED
|
||||
|
||||
W: More than one compute snad/atom
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
*/
|
||||
Loading…
Reference in New Issue