1.. index:: fix atc
2
3fix atc command
4===============
5
6Syntax
7""""""
8
9.. parsed-literal::
10
11   fix <fixID> <group> atc <type> <parameter_file>
12
13* fixID = name of fix
14* group = name of group fix is to be applied
15* type = *thermal* or *two_temperature* or *hardy* or *field*
16
17.. parsed-literal::
18
19    *thermal* = thermal coupling with fields: temperature
20    *two_temperature* = electron-phonon coupling with field: temperature and electron_temperature
21    *hardy* = on-the-fly post-processing using kernel localization functions
22    *field* = on-the-fly post-processing using mesh-based localization functions
23
24* parameter_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file
25
26Examples
27""""""""
28
29.. code-block:: LAMMPS
30
31   fix AtC internal atc thermal Ar_thermal.dat
32   fix AtC internal atc two_temperature Ar_ttm.mat
33   fix AtC internal atc hardy
34   fix AtC internal atc field
35
36Description
37"""""""""""
38
39This fix is the beginning to creating a coupled FE/MD simulation and/or
40an on-the-fly estimation of continuum fields. The coupled versions of
41this fix do Verlet integration and the post-processing does not. After
42instantiating this fix, several other fix_modify commands will be
43needed to set up the problem, e.g. define the finite element mesh and
44prescribe initial and boundary conditions.
45
46.. image:: JPG/atc_nanotube.jpg
47   :align: center
48
49The following coupling example is typical, but non-exhaustive:
50
51.. code-block:: LAMMPS
52
53    # ... commands to create and initialize the MD system
54
55    # initial fix to designate coupling type and group to apply it to
56    # tag group physics material_file
57    fix AtC internal atc thermal Ar_thermal.mat
58
59    # create a uniform 12 x 2 x 2 mesh that covers region contain the group
60    # nx ny nz region periodicity
61    fix_modify AtC mesh create 12 2 2 mdRegion f p p
62
63    # specify the control method for the type of coupling
64    # physics control_type
65    fix_modify AtC thermal control flux
66
67    # specify the initial values for the empirical field "temperature"
68    # field node_group value
69    fix_modify AtC initial temperature all 30
70
71    # create an output stream for nodal fields
72    # filename output_frequency
73    fix_modify AtC output atc_fe_output 100
74
75    run 1000
76
77likewise for this post-processing example:
78
79.. code-block:: LAMMPS
80
81    # ... commands to create and initialize the MD system
82
83    # initial fix to designate post-processing and the group to apply it to
84    # no material file is allowed nor required
85    fix AtC internal atc hardy
86
87    # for hardy fix, specific kernel function (function type and range) to # be used as a localization function
88    fix AtC kernel quartic_sphere 10.0
89
90    # create a uniform 1 x 1 x 1 mesh that covers region contain the group
91    # with periodicity this effectively creates a system average
92    fix_modify AtC mesh create 1 1 1 box p p p
93
94    # change from default lagrangian map to eulerian
95    # refreshed every 100 steps
96    fix_modify AtC atom_element_map eulerian 100
97
98    # start with no field defined
99    # add mass density, potential energy density, stress and temperature
100    fix_modify AtC fields add density energy stress temperature
101
102    # create an output stream for nodal fields
103    # filename output_frequency
104    fix_modify AtC output nvtFE 100 text
105
106    run 1000
107
108the mesh's linear interpolation functions can be used as the localization function
109by using the field option:
110
111.. code-block:: LAMMPS
112
113    fix AtC internal atc field
114    fix_modify AtC mesh create 1 1 1 box p p p
115    ...
116
117Note coupling and post-processing can be combined in the same simulations using separate fixes.
118
119----------
120
121Restart, fix_modify, output, run start/stop, minimize info
122"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
123
124No information about this fix is written to :doc:`binary restart files
125<restart>`.
126
127The :doc:`fix_modify <fix_modify>` *energy* option is not supported by
128this fix, but this fix does add the kinetic energy imparted to atoms
129by the momentum coupling mode of the AtC package to the global
130potential energy of the system as part of :doc:`thermodynamic output
131<thermo_style>`.
132
133Additional :doc:`fix_modify <fix_modify>` options relevant to this
134fix are listed below.
135
136This fix computes a global scalar which can be accessed by various
137:doc:`output commands <Howto_output>`.  The scalar is the energy
138discussed in the previous paragraph.  The scalar value is "extensive".
139
140No parameter of this fix can be used with the
141*start/stop* keywords of the :doc:`run <run>` command.  This fix is not
142invoked during :doc:`energy minimization <minimize>`.
143
144Restrictions
145""""""""""""
146
147Thermal and two_temperature (coupling) types use a Verlet
148time-integration algorithm. The hardy type does not contain its own
149time-integrator and must be used with a separate fix that does contain
150one, e.g. nve, nvt, etc. In addition, currently:
151
152* the coupling is restricted to thermal physics
153* the FE computations are done in serial on each processor.
154
155.. _atc_fix_modify:
156
157Related commands
158""""""""""""""""
159
160After specifying this fix in your input script, several
161:doc:`fix_modify AtC <fix_modify>` commands are used to setup the
162problem, e.g. define the finite element mesh and prescribe initial and
163boundary conditions.  Each of these options has its own doc page.
164
165*fix_modify* commands for setup:
166
167* :doc:`fix_modify AtC mesh create <atc_mesh_create>`
168* :doc:`fix_modify AtC mesh quadrature <atc_mesh_quadrature>`
169* :doc:`fix_modify AtC mesh read <atc_mesh_read>`
170* :doc:`fix_modify AtC mesh write <atc_mesh_write>`
171* :doc:`fix_modify AtC mesh create_nodeset <atc_mesh_create_nodeset>`
172* :doc:`fix_modify AtC mesh add_to_nodeset <atc_mesh_add_to_nodeset>`
173* :doc:`fix_modify AtC mesh create_faceset box <atc_mesh_create_faceset_box>`
174* :doc:`fix_modify AtC mesh create_faceset plane <atc_mesh_create_faceset_plane>`
175* :doc:`fix_modify AtC mesh create_elementset <atc_mesh_create_elementset>`
176* :doc:`fix_modify AtC mesh delete_elements <atc_mesh_delete_elements>`
177* :doc:`fix_modify AtC mesh nodeset_to_elementset <atc_mesh_nodeset_to_elementset>`
178* :doc:`fix_modify AtC boundary type <atc_boundary_type>`
179* :doc:`fix_modify AtC internal_quadrature <atc_internal_quadrature>`
180* :doc:`fix_modify AtC time_integration <atc_time_integration>`
181* :doc:`fix_modify AtC extrinsic electron_integration <atc_electron_integration>`
182* :doc:`fix_modify AtC internal_element_set <atc_internal_element_set>`
183* :doc:`fix_modify AtC decomposition <atc_decomposition>`
184
185*fix_modify* commands for boundary and initial conditions:
186
187* :doc:`fix_modify AtC initial <atc_initial>`
188* :doc:`fix_modify AtC fix <atc_fix>`
189* :doc:`fix_modify AtC unfix <atc_unfix>`
190* :doc:`fix_modify AtC fix_flux <atc_fix_flux>`
191* :doc:`fix_modify AtC unfix_flux <atc_unfix_flux>`
192* :doc:`fix_modify AtC source <atc_source>`
193* :doc:`fix_modify AtC remove_source <atc_remove_source>`
194
195*fix_modify* commands for control and filtering:
196
197* :doc:`fix_modify AtC control thermal <atc_control_thermal>`
198* :doc:`fix_modify AtC control momentum <atc_control_momentum>`
199* :doc:`fix_modify AtC control localized_lambda <atc_control_localized_lambda>`
200* :doc:`fix_modify AtC control lumped_lambda_solve <atc_lumped_lambda_solve>`
201* :doc:`fix_modify AtC control mask_direction <atc_mask_direction>`
202* :doc:`fix_modify AtC filter <atc_time_filter>`
203* :doc:`fix_modify AtC filter scale <atc_filter_scale>`
204* :doc:`fix_modify AtC filter type <atc_filter_type>`
205* :doc:`fix_modify AtC equilibrium_start <atc_equilibrium_start>`
206* :doc:`fix_modify AtC extrinsic exchange <atc_extrinsic_exchange>`
207* :doc:`fix_modify AtC poisson_solver <atc_poisson_solver>`
208
209*fix_modify* commands for output:
210
211* :doc:`fix_modify AtC output <atc_output>`
212* :doc:`fix_modify AtC output nodeset <atc_output_nodeset>`
213* :doc:`fix_modify AtC output volume_integral <atc_output_volume_integral>`
214* :doc:`fix_modify AtC output boundary_integral <atc_output_boundary_integral>`
215* :doc:`fix_modify AtC output contour_integral <atc_output_contour_integral>`
216* :doc:`fix_modify AtC mesh output <atc_mesh_output>`
217* :doc:`fix_modify AtC write_restart <atc_write_restart>`
218* :doc:`fix_modify AtC read_restart <atc_read_restart>`
219
220*fix_modify* commands for post-processing:
221
222* :doc:`fix_modify AtC kernel <atc_hardy_kernel>`
223* :doc:`fix_modify AtC fields <atc_hardy_fields>`
224* :doc:`fix_modify AtC gradients <atc_hardy_gradients>`
225* :doc:`fix_modify AtC rates <atc_hardy_rates>`
226* :doc:`fix_modify AtC computes <atc_hardy_computes>`
227* :doc:`fix_modify AtC on_the_fly <atc_hardy_on_the_fly>`
228* :doc:`fix_modify AtC pair/bond_interactions <atc_pair_interactions>`
229* :doc:`fix_modify AtC sample_frequency <atc_sample_frequency>`
230* :doc:`fix_modify AtC set <atc_set_reference_pe>`
231
232miscellaneous *fix_modify* commands:
233
234* :doc:`fix_modify AtC atom_element_map <atc_atom_element_map>`
235* :doc:`fix_modify AtC atom_weight <atc_atom_weight>`
236* :doc:`fix_modify AtC write_atom_weights <atc_write_atom_weights>`
237* :doc:`fix_modify AtC kernel_bandwidth <atc_kernel_bandwidth>`
238* :doc:`fix_modify AtC reset_time <atc_reset_time>`
239* :doc:`fix_modify AtC reset_atomic_reference_positions <atc_reset_atomic_reference>`
240* :doc:`fix_modify AtC fe_md_boundary <atc_fe_md_boundary>`
241* :doc:`fix_modify AtC boundary_faceset <atc_boundary_faceset>`
242* :doc:`fix_modify AtC consistent_fe_initialization <atc_consistent_fe_initialization>`
243* :doc:`fix_modify AtC mass_matrix <atc_mass_matrix>`
244* :doc:`fix_modify AtC material <atc_material>`
245* :doc:`fix_modify AtC atomic_charge <atc_atomic_charge>`
246* :doc:`fix_modify AtC source_integration <atc_source_integration>`
247* :doc:`fix_modify AtC temperature_definition <atc_temperature_definition>`
248* :doc:`fix_modify AtC track_displacement <atc_track_displacement>`
249* :doc:`fix_modify AtC boundary_dynamics <atc_boundary_dynamics>`
250* :doc:`fix_modify AtC add_species <atc_add_species>`
251* :doc:`fix_modify AtC add_molecule <atc_add_molecule>`
252* :doc:`fix_modify AtC remove_species <atc_remove_species>`
253* :doc:`fix_modify AtC remove_molecule <atc_remove_molecule>`
254
255Note: a set of example input files with the attendant material files
256are included in the ``examples/PACKAGES/atc`` folders.
257
258Default
259"""""""
260None
261
262----------
263
264For detailed exposition of the theory and algorithms please see:
265
266.. _Wagner:
267
268**(Wagner)** Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, "An
269 atomistic-to-continuum coupling method for heat transfer in solids."
270 Special Issue of Computer Methods and Applied Mechanics (2008)
271 197:3351.
272
273.. _Zimmeman2004:
274
275**(Zimmerman2004)** Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE;
276 Klein, PA; Bammann, DJ, "Calculation of stress in atomistic
277 simulation." Special Issue of Modelling and Simulation in Materials
278 Science and Engineering (2004), 12:S319.
279
280.. _Zimmerman2010:
281
282**(Zimmerman2010)** Zimmerman, JA; Jones, RE; Templeton, JA, "A
283 material frame approach for evaluating continuum variables in
284 atomistic simulations." Journal of Computational Physics (2010),
285 229:2364.
286
287.. _Templeton2010:
288
289**(Templeton2010)** Templeton, JA; Jones, RE; Wagner, GJ, "Application
290 of a field-based method to spatially varying thermal transport
291 problems in molecular dynamics." Modelling and Simulation in
292 Materials Science and Engineering (2010), 18:085007.
293
294.. _Jones:
295
296**(Jones)** Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine,
297 JA, "Electron transport enhanced molecular dynamics for metals and
298 semi-metals." International Journal for Numerical Methods in
299 Engineering (2010), 83:940.
300
301.. _Templeton2011:
302
303**(Templeton2011)** Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA;
304 Wong, BM, "A long-range electric field solver for molecular dynamics
305 based on atomistic-to-continuum modeling." Journal of Chemical Theory
306 and Computation (2011), 7:1736.
307
308.. _Mandadapu:
309
310**(Mandadapu)** Mandadapu, KK; Templeton, JA; Lee, JW, "Polarization
311 as a field variable from molecular dynamics simulations." Journal of
312 Chemical Physics (2013), 139:054115.
313
314Please refer to the standard finite element (FE) texts, e.g. T.J.R
315Hughes " The finite element method ", Dover 2003, for the basics of FE
316simulation.
317