Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
6297a32d9b46
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Authored by Axel Kohlmeyer <akohlmey@gmail.com> on Aug 22 2013, 13:04.

Description

Merge remote-tracking branch 'lammps-ro/master' into lammps-icms

Respolved Conflicts:
doc/Manual.txt
lib/atc/CbEam.h
lib/atc/LammpsInterface.cpp
lib/atc/LammpsInterface.h

Details

Committed

Axel Kohlmeyer <akohlmey@gmail.com>

Aug 22 2013, 13:04

Pushed

junge

Oct 6 2016, 16:49

Parents

rLAMMPS3b265525df09: Adding new manual documentation for ATC version 2.0
rLAMMPS002ce0ee7d49: Merge branch 'lammps-icms' of git://git.icms.temple.edu/lammps-icms into lammps…

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Axel Kohlmeyer <akohlmey@gmail.com> committed rLAMMPS6297a32d9b46: Merge remote-tracking branch 'lammps-ro/master' into lammps-icms (authored by Axel Kohlmeyer <akohlmey@gmail.com>).Aug 22 2013, 13:04

Merged Changes

Commit	Author	Details	Committed
3b265525df09	jzimmer	Adding new manual documentation for ATC version 2.0	Aug 22 2013
87e146a37624	jzimmer	Deleting out-of-date documentation	Aug 22 2013
8b7b937f4199	jzimmer	Updating LAMMPS manual documentation files.	Aug 22 2013
ff968b7232d8	jzimmer	Removing dummy stdout file.	Aug 22 2013
2b9951bf5640	jzimmer	Including info on cauchy_born examples.	Aug 22 2013
3efd8133da8b	rjones	work in progress	Aug 22 2013
1144c1b3f957	rjones	first drafts of benchmark,py - numerical comparison of log files regression.sh…	Aug 22 2013
b22a8a7b61a5	rjones	ATC version 2.0, date: Aug21	Aug 22 2013
d77ab2f96a57	rjones	ATC version 2.0, date: Aug21	Aug 22 2013
0f69054d680a	rjones	ATC version 2.0, date: Aug21	Aug 22 2013
7d0fe14fdb33	jatempl	Updated to current set of examples.	Aug 22 2013
2d63313b2479	rjones	obsolete	Aug 22 2013
e2b9399b71eb	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10631 f3b2605a-c512-4ea7…	Aug 21 2013
7ece6ee79b5f	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10630 f3b2605a-c512-4ea7…	Aug 21 2013
184b8d155276	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10629 f3b2605a-c512-4ea7…	Aug 21 2013
5ad6f286a83a	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10628 f3b2605a-c512-4ea7…	Aug 21 2013
1a6312c5d891	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10627 f3b2605a-c512-4ea7…	Aug 21 2013
75119650946a	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10626 f3b2605a-c512-4ea7…	Aug 21 2013
2cbcde563fa3	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10624 f3b2605a-c512-4ea7…	Aug 21 2013
392ed29455c1	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10623 f3b2605a-c512-4ea7…	Aug 21 2013
e33d03ec2c19	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10622 f3b2605a-c512-4ea7…	Aug 21 2013

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M		doc/Manual.html
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A		doc/USER/atc/man_add_molecule.html
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M		doc/USER/atc/man_hardy_computes.html
M		doc/USER/atc/man_hardy_fields.html
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D		doc/USER/atc/man_hardy_set.html
M		doc/USER/atc/man_initial.html
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M		doc/USER/atc/man_mesh_output.html
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A		doc/USER/atc/man_momentum_time_integration.html
D		doc/USER/atc/man_neighbor_reset_frequency.html
A		doc/USER/atc/man_output.html
A		doc/USER/atc/man_output_elementset.html
A		doc/USER/atc/man_output_nodeset.html
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A		doc/USER/atc/man_poisson_solver.html
M		doc/USER/atc/man_read_restart.html
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A		doc/USER/atc/man_reset_time.html
A		doc/USER/atc/man_sample_frequency.html
A		doc/USER/atc/man_set.html
M		doc/USER/atc/man_source.html
A		doc/USER/atc/man_source_integration.html
A		doc/USER/atc/man_temperature_definition.html
D		doc/USER/atc/man_thermal_control.html
A		doc/USER/atc/man_thermal_time_integration.html
M		doc/USER/atc/man_time_filter.html
D		doc/USER/atc/man_time_integration.html
A		doc/USER/atc/man_track_displacement.html
D		doc/USER/atc/man_transfer_atomic_output.html
D		doc/USER/atc/man_transfer_boundary.html
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D		doc/USER/atc/man_transfer_output.html
M		doc/USER/atc/man_unfix_flux.html
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A		doc/USER/atc/man_write_atom_weights.html
M		doc/USER/atc/man_write_restart.html
D		doc/USER/atc/svn.stdout
M		doc/fix_rigid.html
M		doc/fix_rigid.txt
M		examples/USER/atc/README
D		examples/USER/atc/bar1d_thermal
D		examples/USER/atc/bar1d_thermal/Ar_thermal.mat
D		examples/USER/atc/bar1d_thermal/bar1d.log
D		examples/USER/atc/bar1d_thermal/bar1d_flux.log
D		examples/USER/atc/bar1d_thermal/in.bar1d
D		examples/USER/atc/bar1d_thermal/in.bar1d_flux
D		examples/USER/atc/bar1d_thermal/in.bar1d_frac_step
D		examples/USER/atc/bar1d_thermal/temp.init
D		examples/USER/atc/bar1d_two_temperature
D		examples/USER/atc/bar1d_two_temperature/Ar_ttm.mat
D		examples/USER/atc/bar1d_two_temperature/Cu_ttm.mat
D		examples/USER/atc/bar1d_two_temperature/bar1d_ttm.log
D		examples/USER/atc/bar1d_two_temperature/gaussianIC_ttm.log
D		examples/USER/atc/bar1d_two_temperature/in.bar1d_ttm
D		examples/USER/atc/bar1d_two_temperature/in.gaussianIC_ttm
D		examples/USER/atc/bar1d_two_temperature/in.no_atoms
D		examples/USER/atc/bar1d_two_temperature/in.uniform_exchange
D		examples/USER/atc/bar1d_two_temperature/in.uniform_heating
D		examples/USER/atc/bar1d_two_temperature/no_atoms.log
D		examples/USER/atc/bar1d_two_temperature/temp.init
D		examples/USER/atc/bar1d_two_temperature/uniform_exchange.log
D		examples/USER/atc/bar1d_two_temperature/uniform_exchange_init.data
D		examples/USER/atc/bar1d_two_temperature/uniform_heating.log
D		examples/USER/atc/bar1d_two_temperature/uniform_heating_init.data
M		examples/USER/atc/cauchy_born/cb_biaxial.screen
M		examples/USER/atc/cauchy_born/cb_shear.screen
M		examples/USER/atc/cauchy_born/cb_unistrain.screen
M		examples/USER/atc/cauchy_born/cb_unistrain_eam.screen
M		examples/USER/atc/cauchy_born/cb_unistrain_eam_linear.screen
M		examples/USER/atc/cauchy_born/cb_unistrain_linear.screen
M		examples/USER/atc/cauchy_born/cb_volumetric.screen
M		examples/USER/atc/cauchy_born/flying_cube.screen
M		examples/USER/atc/cauchy_born/ftcb_constV.screen
M		examples/USER/atc/cauchy_born/in.cb_biaxial
M		examples/USER/atc/cauchy_born/in.cb_shear
M		examples/USER/atc/cauchy_born/in.cb_volumetric
M		examples/USER/atc/cauchy_born/read_xref.screen
M		examples/USER/atc/drift_diffusion/convective_pulse.screen
M		examples/USER/atc/drift_diffusion/ddm_schrodinger.screen
M		examples/USER/atc/drift_diffusion/finite_well.screen
M		examples/USER/atc/drift_diffusion/no_atoms_ddm.screen
M		examples/USER/atc/drift_diffusion/null_material_ddm.screen
M		examples/USER/atc/drift_diffusion/poisson1d_noatoms.screen
M		examples/USER/atc/drift_diffusion/poisson2d_noatoms.screen
M		examples/USER/atc/drift_diffusion/schrodinger-poisson2d_Jconstraint.screen
M		examples/USER/atc/drift_diffusion/schrodinger-poisson2d_convective.screen
M		examples/USER/atc/drift_diffusion/schrodinger-poisson2d_noatoms.screen
M		examples/USER/atc/elastic/CNT_electrostatic2.mat
M		examples/USER/atc/elastic/bar1d.screen
M		examples/USER/atc/elastic/bar1d_damped.screen
M		examples/USER/atc/elastic/bar1d_flux.screen
M		examples/USER/atc/elastic/bar1d_frac_step.screen
M		examples/USER/atc/elastic/bar1d_ghost_flux.screen
M		examples/USER/atc/elastic/bar1d_thermo_elastic.screen
M		examples/USER/atc/elastic/cnt_electrostatic.screen
M		examples/USER/atc/elastic/cnt_electrostatic2.screen
M		examples/USER/atc/elastic/cnt_fixed_charge.screen
M		examples/USER/atc/elastic/eam_energy.screen
M		examples/USER/atc/elastic/electron_density.screen
M		examples/USER/atc/elastic/electrostatic_bending.screen
M		examples/USER/atc/elastic/electrostatic_bending_dos.screen
M		examples/USER/atc/elastic/in.bar1d_damped
M		examples/USER/atc/elastic/no_atoms.screen
M		examples/USER/atc/elastic/no_atoms_cb.screen
M		examples/USER/atc/elastic/no_atoms_cb_linear.screen
M		examples/USER/atc/fluids/bar1d_fluids.screen
M		examples/USER/atc/fluids/concentration.screen
M		examples/USER/atc/fluids/conducting_interface.screen
M		examples/USER/atc/fluids/dielectric_interface.screen
M		examples/USER/atc/fluids/double_layer.screen
M		examples/USER/atc/fluids/liquid_electrostatic.screen
M		examples/USER/atc/fluids/opp_force.screen
M		examples/USER/atc/fluids/poisson.screen
M		examples/USER/atc/fluids/shear_flow.screen
M		examples/USER/atc/fluids/shear_no_atoms.screen
M		examples/USER/atc/hardy/consistency.screen
M		examples/USER/atc/hardy/eam_kernel_convergence.screen
M		examples/USER/atc/hardy/eam_unistrain_cell.screen
M		examples/USER/atc/hardy/eam_unistrain_mesh.screen
M		examples/USER/atc/hardy/eam_unistrain_qcylinder.screen
M		examples/USER/atc/hardy/eam_unistrain_qsphere.screen
M		examples/USER/atc/hardy/eam_unistrain_step.screen
M		examples/USER/atc/hardy/eam_volume_stretch.screen
M		examples/USER/atc/hardy/eshelby_static.screen
M		examples/USER/atc/hardy/nvt.screen
M		examples/USER/atc/mesh/gaussianIC1d_hex.screen
M		examples/USER/atc/mesh/gaussianIC2d_hex.screen
M		examples/USER/atc/mesh/gaussianIC2d_hex20_uniform.screen
M		examples/USER/atc/mesh/gaussianIC2d_hex27_uniform.screen
M		examples/USER/atc/mesh/gaussianIC2d_hex_uniform.screen
M		examples/USER/atc/mesh/gaussianIC2d_tet.screen
M		examples/USER/atc/mesh/kernel2d_hex.screen
M		examples/USER/atc/mesh/kernel2d_tet.screen
M		examples/USER/atc/mesh/mesh2d_tet.screen
M		examples/USER/atc/mesh/semicircle.screen
M		examples/USER/atc/molecule/harmonic_bonds.screen
M		examples/USER/atc/molecule/polarize.screen
M		examples/USER/atc/molecule/quartic_bonds.screen
M		examples/USER/atc/molecule/water.screen
M		examples/USER/atc/thermal/bar1d.screen
M		examples/USER/atc/thermal/bar1d_all_atoms.screen
M		examples/USER/atc/thermal/bar1d_combined.screen
M		examples/USER/atc/thermal/bar1d_flux.screen
M		examples/USER/atc/thermal/bar1d_frac_step.screen
M		examples/USER/atc/thermal/bar1d_hoover.screen
M		examples/USER/atc/thermal/bar1d_interpolate.screen
M		examples/USER/atc/thermal/bar1d_lumped.screen
M		examples/USER/atc/thermal/no_atoms.screen
M		examples/USER/atc/two_temperature/bar1d_ttm.screen
M		examples/USER/atc/two_temperature/cutout.screen
M		examples/USER/atc/two_temperature/gaussianIC_ttm.screen
M		examples/USER/atc/two_temperature/no_atoms.screen
M		examples/USER/atc/two_temperature/restart.screen
M		examples/USER/atc/two_temperature/uniform_exchange.screen
M		examples/USER/atc/two_temperature/uniform_heating.screen
M		lib/atc/ATC_Coupling.cpp
M		lib/atc/ATC_Coupling.h
M		lib/atc/ATC_CouplingEnergy.cpp
M		lib/atc/ATC_CouplingEnergy.h
M		lib/atc/ATC_CouplingMass.cpp
M		lib/atc/ATC_CouplingMass.h
M		lib/atc/ATC_CouplingMomentum.cpp
M		lib/atc/ATC_CouplingMomentum.h
M		lib/atc/ATC_CouplingMomentumEnergy.cpp
M		lib/atc/ATC_CouplingMomentumEnergy.h
M		lib/atc/ATC_Error.h
M		lib/atc/ATC_Method.cpp
M		lib/atc/ATC_Method.h
M		lib/atc/ATC_Transfer.cpp
M		lib/atc/ATC_Transfer.h
M		lib/atc/ATC_TransferKernel.cpp
M		lib/atc/ATC_TypeDefs.h
M		lib/atc/AtomToMoleculeTransfer.cpp
M		lib/atc/AtomToMoleculeTransfer.h
M		lib/atc/AtomicRegulator.cpp
M		lib/atc/AtomicRegulator.h
M		lib/atc/BodyForce.cpp
M		lib/atc/BodyForce.h
M		lib/atc/CBLattice.cpp
M		lib/atc/CBLattice.h
M		lib/atc/CbEam.h
M		lib/atc/ChargeRegulator.cpp
M		lib/atc/ChargeRegulator.h
M		lib/atc/CloneVector.h
M		lib/atc/ConcentrationRegulator.cpp
M		lib/atc/ConcentrationRegulator.h
M		lib/atc/DenseMatrix.h
M		lib/atc/DependencyManager.h
M		lib/atc/DiagonalMatrix.h
M		lib/atc/ElasticTimeIntegrator.cpp
M		lib/atc/ElasticTimeIntegrator.h
M		lib/atc/ElectronChargeDensity.cpp
M		lib/atc/ElectronChargeDensity.h
M		lib/atc/ElectronDragPower.cpp
M		lib/atc/ElectronDragPower.h
M		lib/atc/ElectronFlux.cpp
M		lib/atc/ElectronFlux.h
M		lib/atc/ElectronHeatCapacity.cpp
M		lib/atc/ElectronHeatCapacity.h
M		lib/atc/ElectronHeatFlux.cpp
M		lib/atc/ElectronHeatFlux.h
M		lib/atc/ElectronPhononExchange.cpp
M		lib/atc/ElectronPhononExchange.h
M		lib/atc/ExtrinsicModel.cpp
M		lib/atc/ExtrinsicModel.h
M		lib/atc/ExtrinsicModelDriftDiffusion.cpp
M		lib/atc/ExtrinsicModelDriftDiffusion.h
M		lib/atc/ExtrinsicModelElectrostatic.cpp
M		lib/atc/ExtrinsicModelElectrostatic.h
M		lib/atc/ExtrinsicModelTwoTemperature.cpp
M		lib/atc/ExtrinsicModelTwoTemperature.h
M		lib/atc/FE_Element.cpp
M		lib/atc/FE_Element.h
M		lib/atc/FE_Engine.cpp
M		lib/atc/FE_Engine.h
M		lib/atc/FE_Interpolate.cpp
M		lib/atc/FE_Interpolate.h
M		lib/atc/FE_Mesh.cpp
M		lib/atc/FE_Mesh.h
M		lib/atc/FE_Quadrature.h
M		lib/atc/FieldManager.cpp
M		lib/atc/FieldManager.h
M		lib/atc/Function.cpp
M		lib/atc/Function.h
M		lib/atc/FundamentalAtomicQuantity.cpp
M		lib/atc/FundamentalAtomicQuantity.h
A		lib/atc/GhostManager.cpp
A		lib/atc/GhostManager.h
M		lib/atc/InterscaleOperators.cpp
M		lib/atc/InterscaleOperators.h
M		lib/atc/KD_Tree.cpp
M		lib/atc/KD_Tree.h
M		lib/atc/KernelFunction.h
M		lib/atc/KinetoThermostat.cpp
M		lib/atc/KinetoThermostat.h
M		lib/atc/Kinetostat.cpp
M		lib/atc/Kinetostat.h
M		lib/atc/LammpsInterface.cpp
M		lib/atc/LammpsInterface.h
M		lib/atc/LinearSolver.cpp
M		lib/atc/LinearSolver.h
M		lib/atc/MPI_Wrappers.cpp
M		lib/atc/MPI_Wrappers.h
M		lib/atc/Material.cpp
M		lib/atc/Material.h
M		lib/atc/Matrix.h
M		lib/atc/MatrixDef.h
M		lib/atc/MeshReader.cpp
M		lib/atc/MeshReader.h
M		lib/atc/MoleculeSet.cpp
M		lib/atc/MoleculeSet.h
M		lib/atc/NonLinearSolver.cpp
M		lib/atc/NonLinearSolver.h
M		lib/atc/OutputManager.cpp
M		lib/atc/OutputManager.h
M		lib/atc/ParDenseMatrix.h
M		lib/atc/ParDiagonalMatrix.cpp
M		lib/atc/ParDiagonalMatrix.h
M		lib/atc/ParSparseMatrix.h
M		lib/atc/PerAtomQuantity-inl.h
M		lib/atc/PerAtomQuantity.h
M		lib/atc/PerAtomQuantityLibrary.cpp
M		lib/atc/PerAtomQuantityLibrary.h
M		lib/atc/PerPairQuantity.cpp
M		lib/atc/PerPairQuantity.h
M		lib/atc/PhysicsModel.cpp
M		lib/atc/PhysicsModel.h
M		lib/atc/PoissonSolver.cpp
M		lib/atc/PrescribedDataManager.cpp
M		lib/atc/PrescribedDataManager.h
M		lib/atc/Quadrature.h
M		lib/atc/SchrodingerSolver.cpp
M		lib/atc/SchrodingerSolver.h
M		lib/atc/SparseMatrix-inl.h
M		lib/atc/SparseMatrix.h
M		lib/atc/SparseVector-inl.h
M		lib/atc/SparseVector.h
M		lib/atc/SpeciesTimeIntegrator.cpp
M		lib/atc/SpeciesTimeIntegrator.h
M		lib/atc/Stress.cpp
M		lib/atc/Stress.h
M		lib/atc/ThermalTimeIntegrator.cpp
M		lib/atc/ThermalTimeIntegrator.h
M		lib/atc/Thermostat.cpp
M		lib/atc/Thermostat.h
M		lib/atc/TimeFilter.cpp
M		lib/atc/TimeFilter.h
M		lib/atc/TimeIntegrator.cpp
M		lib/atc/TimeIntegrator.h
M		lib/atc/TransferLibrary.cpp
M		lib/atc/TransferLibrary.h
M		lib/atc/TransferOperator.cpp
M		lib/atc/TransferOperator.h
M		lib/atc/Utility.h
M		lib/atc/Vector.h
M		lib/atc/ViscousStress.cpp
M		lib/atc/ViscousStress.h
M		lib/atc/WeakEquation.h
M		lib/atc/WeakEquationChargeDiffusion.cpp
M		lib/atc/WeakEquationChargeDiffusion.h
M		lib/atc/WeakEquationDiffusion.cpp
M		lib/atc/WeakEquationDiffusion.h
M		lib/atc/WeakEquationElectronContinuity.cpp
M		lib/atc/WeakEquationElectronContinuity.h
M		lib/atc/WeakEquationElectronMomentum.h
M		lib/atc/WeakEquationElectronTemperature.cpp
M		lib/atc/WeakEquationElectronTemperature.h
M		lib/atc/WeakEquationMassDiffusion.cpp
M		lib/atc/WeakEquationMassDiffusion.h
M		lib/atc/WeakEquationMomentum.h
M		lib/atc/WeakEquationPhononTemperature.cpp
M		lib/atc/WeakEquationPhononTemperature.h
M		lib/atc/WeakEquationPoisson.cpp
M		lib/atc/WeakEquationPoisson.h
M		lib/atc/WeakEquationSchrodinger.cpp
M		lib/atc/WeakEquationSchrodinger.h
A	(dir)	regress/
A		regress/benchmark.py
A	(dir)	regress/min/
A		regress/min/in.min
A		regress/min/in.min.box
A		regress/min/log.min.18Feb13.linux.1
A		regress/min/log.min.18Feb13.linux.4
A		regress/min/log.min.box.18Feb13.linux.1
A		regress/min/log.min.box.18Feb13.linux.4
A		regress/regression.sh
M		src/PERI/fix_peri_neigh.cpp
M		src/PERI/fix_peri_neigh.h
M		src/RIGID/fix_rigid.cpp
M		src/RIGID/fix_rigid.h
M		src/RIGID/fix_rigid_small.cpp
M		src/RIGID/fix_rigid_small.h
M		src/USER-ATC/fix_atc.cpp
M		src/USER-ATC/fix_atc.h
M		src/fix.cpp
M		src/fix.h
M		src/math_extra.h
M		src/version.h
M		src/write_restart.cpp