Merge remote-tracking branch 'lammps-ro/master' into atc-merge
c931a450c093
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Authored by Axel Kohlmeyer <akohlmey@gmail.com> on Aug 8 2013, 14:02.

Description

Merge remote-tracking branch 'lammps-ro/master' into atc-merge

Resolved Conflicts:
doc/Manual.txt
src/USER-ATC/Install.sh
tools/msi2lmp/biosym_frc_files/README

Details

Committed

Axel Kohlmeyer <akohlmey@gmail.com>

Aug 8 2013, 14:02

Pushed

junge

Oct 6 2016, 16:49

Parents

rLAMMPS0ec1c854eb38: ATC version 2.0, date: Aug7
rLAMMPS7c7617f7e5ec: only update the charged particles list after reneighboring

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Event Timeline

Axel Kohlmeyer <akohlmey@gmail.com> committed rLAMMPSc931a450c093: Merge remote-tracking branch 'lammps-ro/master' into atc-merge (authored by Axel Kohlmeyer <akohlmey@gmail.com>).Aug 8 2013, 14:02

Merged Changes

Commit	Author	Details	Committed
0ec1c854eb38	rjones	ATC version 2.0, date: Aug7	Aug 7 2013
2629a8389dae	rjones	ATC version 2.0, date: Aug7	Aug 7 2013
7855ef6ddac4	rjones	ATC version 2.0, date: Aug7	Aug 7 2013
fafff431e931	rjones	ATC version 2.0, date: Aug7	Aug 7 2013
53c7162e9eb1	rjones	ATC version 2.0, date: Aug7	Aug 7 2013
666de878addc	rjones	ATC version 2.0, date: Aug7	Aug 7 2013
0e4d1e6b2274	rjones	ATC version 2.0, date: Aug7	Aug 7 2013
6d40d7c25d58	rjones	ATC version 2.0, date: Aug7	Aug 7 2013
2486323112f2	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10554 f3b2605a-c512-4ea7…	Aug 6 2013
0239cf54addc	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10553 f3b2605a-c512-4ea7…	Aug 6 2013
20d39d1e8d70	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10552 f3b2605a-c512-4ea7…	Aug 6 2013
1701830c12a0	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10551 f3b2605a-c512-4ea7…	Aug 6 2013
aff25bf5865a	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10550 f3b2605a-c512-4ea7…	Aug 6 2013
79a2a93f9cd9	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10549 f3b2605a-c512-4ea7…	Aug 6 2013
afef1c881485	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10548 f3b2605a-c512-4ea7…	Aug 6 2013
6420945660e7	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10535 f3b2605a-c512-4ea7…	Aug 5 2013
ebe6ead34839	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10534 f3b2605a-c512-4ea7…	Aug 5 2013

Changes (453)
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		Path
M		doc/Manual.html
M		doc/Manual.txt
A		doc/USER/atc/svn.stdout
M		doc/fix_deposit.html
M		doc/fix_deposit.txt
A	(dir)	examples/USER/atc/cauchy_born/
A		examples/USER/atc/cauchy_born/Ar_CauchyBorn.mat
A		examples/USER/atc/cauchy_born/Ar_CauchyBorn_linear.mat
A		examples/USER/atc/cauchy_born/Au_CauchyBorn.mat
A		examples/USER/atc/cauchy_born/Au_CauchyBorn_linear.mat
A		examples/USER/atc/cauchy_born/Au_eam.mat
A		examples/USER/atc/cauchy_born/Au_eam_linear.mat
A		examples/USER/atc/cauchy_born/Cu_CauchyBorn.mat
A		examples/USER/atc/cauchy_born/cb_biaxial.screen
A		examples/USER/atc/cauchy_born/cb_shear.screen
A		examples/USER/atc/cauchy_born/cb_unistrain.screen
A		examples/USER/atc/cauchy_born/cb_unistrain_eam.screen
A		examples/USER/atc/cauchy_born/cb_unistrain_eam_linear.screen
A		examples/USER/atc/cauchy_born/cb_unistrain_linear.screen
A		examples/USER/atc/cauchy_born/cb_volumetric.screen
A		examples/USER/atc/cauchy_born/flying_cube.screen
A		examples/USER/atc/cauchy_born/ftcb_constV.screen
A		examples/USER/atc/cauchy_born/in.cb_biaxial
A		examples/USER/atc/cauchy_born/in.cb_shear
A		examples/USER/atc/cauchy_born/in.cb_unistrain
A		examples/USER/atc/cauchy_born/in.cb_unistrain_eam
A		examples/USER/atc/cauchy_born/in.cb_unistrain_eam_linear
A		examples/USER/atc/cauchy_born/in.cb_unistrain_linear
A		examples/USER/atc/cauchy_born/in.cb_volumetric
A		examples/USER/atc/cauchy_born/in.flying_cube
A		examples/USER/atc/cauchy_born/in.ftcb_constV
A		examples/USER/atc/cauchy_born/in.read_xref
A		examples/USER/atc/cauchy_born/read_xref.screen
A	(dir)	examples/USER/atc/drift_diffusion/
A		examples/USER/atc/drift_diffusion/Ar_ddm.mat
A		examples/USER/atc/drift_diffusion/CNT_ddm.mat
A		examples/USER/atc/drift_diffusion/Cu_cddm.mat
A		examples/USER/atc/drift_diffusion/SiGe_ddm_schrodinger.mat
A		examples/USER/atc/drift_diffusion/SiVacuum_cddm_schrodinger.mat
A		examples/USER/atc/drift_diffusion/SiVacuum_ddm_schrodinger.mat
A		examples/USER/atc/drift_diffusion/Si_ddm.mat
A		examples/USER/atc/drift_diffusion/Si_ddm_eq.mat
A		examples/USER/atc/drift_diffusion/Si_ddm_schrodinger.mat
A		examples/USER/atc/drift_diffusion/Si_ddm_thermopower.mat
A		examples/USER/atc/drift_diffusion/convective_pulse.screen
A		examples/USER/atc/drift_diffusion/ddm_schrodinger.screen
A		examples/USER/atc/drift_diffusion/finite_well.screen
A		examples/USER/atc/drift_diffusion/in.convective_pulse
A		examples/USER/atc/drift_diffusion/in.ddm_schrodinger
A		examples/USER/atc/drift_diffusion/in.finite_well
A		examples/USER/atc/drift_diffusion/in.no_atoms_ddm
A		examples/USER/atc/drift_diffusion/in.null_material_ddm
A		examples/USER/atc/drift_diffusion/in.poisson1d_noatoms
A		examples/USER/atc/drift_diffusion/in.poisson2d_noatoms
A		examples/USER/atc/drift_diffusion/in.schrodinger-poisson2d_Jconstraint
A		examples/USER/atc/drift_diffusion/in.schrodinger-poisson2d_convective
A		examples/USER/atc/drift_diffusion/in.schrodinger-poisson2d_noatoms
A		examples/USER/atc/drift_diffusion/no_atoms_ddm.screen
A		examples/USER/atc/drift_diffusion/null_material_ddm.screen
A		examples/USER/atc/drift_diffusion/poisson1d_noatoms.screen
A		examples/USER/atc/drift_diffusion/poisson2d_noatoms.screen
A		examples/USER/atc/drift_diffusion/schrodinger-poisson2d_Jconstraint.screen
A		examples/USER/atc/drift_diffusion/schrodinger-poisson2d_convective.screen
A		examples/USER/atc/drift_diffusion/schrodinger-poisson2d_noatoms.screen
A	(dir)	examples/USER/atc/dxa/
A		examples/USER/atc/dxa/in.eam_tension_frame
A		examples/USER/atc/dxa/in.eam_tension_mesh_frame
A	(dir)	examples/USER/atc/elastic/
A		examples/USER/atc/elastic/Ar_CauchyBorn.mat
A		examples/USER/atc/elastic/Ar_CauchyBornLinear.mat
A		examples/USER/atc/elastic/Ar_damped.mat
A		examples/USER/atc/elastic/Ar_elastic.mat
A		examples/USER/atc/elastic/Ar_thermo_elastic.mat
A		examples/USER/atc/elastic/Au_elastic.mat
A		examples/USER/atc/elastic/CNT.mat
A		examples/USER/atc/elastic/CNT_electrostatic.mat
A		examples/USER/atc/elastic/CNT_electrostatic2.mat
A		examples/USER/atc/elastic/CNT_id.mat
A		examples/USER/atc/elastic/bar1d.screen
A		examples/USER/atc/elastic/bar1d_damped.screen
A		examples/USER/atc/elastic/bar1d_flux.screen
A		examples/USER/atc/elastic/bar1d_frac_step.screen
A		examples/USER/atc/elastic/bar1d_ghost_flux.screen
A		examples/USER/atc/elastic/bar1d_thermo_elastic.screen
A		examples/USER/atc/elastic/cnt_electrostatic.screen
A		examples/USER/atc/elastic/cnt_electrostatic2.screen
A		examples/USER/atc/elastic/cnt_fixed_charge.screen
A		examples/USER/atc/elastic/eam_energy.screen
A		examples/USER/atc/elastic/electron_density.screen
A		examples/USER/atc/elastic/electrostatic_bending.screen
A		examples/USER/atc/elastic/electrostatic_bending_dos.screen
A		examples/USER/atc/elastic/in.bar1d
A		examples/USER/atc/elastic/in.bar1d_damped
A		examples/USER/atc/elastic/in.bar1d_flux
A		examples/USER/atc/elastic/in.bar1d_frac_step
A		examples/USER/atc/elastic/in.bar1d_ghost_flux
A		examples/USER/atc/elastic/in.bar1d_thermo_elastic
A		examples/USER/atc/elastic/in.cnt_electrostatic
A		examples/USER/atc/elastic/in.cnt_electrostatic2
A		examples/USER/atc/elastic/in.cnt_fixed_charge
A		examples/USER/atc/elastic/in.eam_energy
A		examples/USER/atc/elastic/in.electron_density
A		examples/USER/atc/elastic/in.electrostatic_bending
A		examples/USER/atc/elastic/in.electrostatic_bending_dos
A		examples/USER/atc/elastic/in.no_atoms
A		examples/USER/atc/elastic/in.no_atoms_cb
A		examples/USER/atc/elastic/in.no_atoms_cb_linear
A		examples/USER/atc/elastic/no_atoms.screen
A		examples/USER/atc/elastic/no_atoms_cb.screen
A		examples/USER/atc/elastic/no_atoms_cb_linear.screen
A	(dir)	examples/USER/atc/fluids/
A		examples/USER/atc/fluids/Ar_elastic.mat
A		examples/USER/atc/fluids/Ar_electrostatic.mat
A		examples/USER/atc/fluids/Ar_liquid.mat
A		examples/USER/atc/fluids/Ar_species.mat
A		examples/USER/atc/fluids/Ar_species_dl.mat
A		examples/USER/atc/fluids/Ar_thermal.mat
A		examples/USER/atc/fluids/Ar_visc_no_atoms.mat
A		examples/USER/atc/fluids/Ar_viscosity.mat
A		examples/USER/atc/fluids/bar1d_fluids.screen
A		examples/USER/atc/fluids/concentration.screen
A		examples/USER/atc/fluids/conducting_interface.screen
A		examples/USER/atc/fluids/dielectric.mat
A		examples/USER/atc/fluids/dielectric_interface.screen
A		examples/USER/atc/fluids/double_layer.screen
A		examples/USER/atc/fluids/in.bar1d_fluids
A		examples/USER/atc/fluids/in.concentration
A		examples/USER/atc/fluids/in.conducting_interface
A		examples/USER/atc/fluids/in.dielectric_interface
A		examples/USER/atc/fluids/in.double_layer
A		examples/USER/atc/fluids/in.liquid_electrostatic
A		examples/USER/atc/fluids/in.opp_force
A		examples/USER/atc/fluids/in.poisson
A		examples/USER/atc/fluids/in.shear_flow
A		examples/USER/atc/fluids/in.shear_no_atoms
A		examples/USER/atc/fluids/liquid_electrostatic.screen
A		examples/USER/atc/fluids/opp_force.screen
A		examples/USER/atc/fluids/poisson.screen
A		examples/USER/atc/fluids/shear_flow.screen
A		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/in.consistency
M		examples/USER/atc/hardy/in.eam_kernel_convergence
P		examples/USER/atc/hardy/in.eam_unistrain_cell Copied from examples/USER/atc/hardy/in.eam_unistrain_mesh
P		examples/USER/atc/hardy/in.eam_unistrain_mesh Copied to multiple locations: examples/USER/atc/hardy/in.eam_unistrain_cell examples/USER/atc/hardy/in.eam_unistrain_qcylinder examples/USER/atc/hardy/in.eam_unistrain_qsphere examples/USER/atc/hardy/in.eam_unistrain_step
P		examples/USER/atc/hardy/in.eam_unistrain_qcylinder Copied from examples/USER/atc/hardy/in.eam_unistrain_mesh
P		examples/USER/atc/hardy/in.eam_unistrain_qsphere Copied from examples/USER/atc/hardy/in.eam_unistrain_mesh
P		examples/USER/atc/hardy/in.eam_unistrain_step Copied from examples/USER/atc/hardy/in.eam_unistrain_mesh
M		examples/USER/atc/hardy/in.eam_volume_stretch
M		examples/USER/atc/hardy/in.eshelby_static
M		examples/USER/atc/hardy/in.nvt
M		examples/USER/atc/hardy/nvt.screen
A	(dir)	examples/USER/atc/mesh/
A		examples/USER/atc/mesh/Ar_ttm.mat
A		examples/USER/atc/mesh/Si.mat
A		examples/USER/atc/mesh/gaussianIC1d_hex.screen
A		examples/USER/atc/mesh/gaussianIC2d_hex.screen
A		examples/USER/atc/mesh/gaussianIC2d_hex20_uniform.screen
A		examples/USER/atc/mesh/gaussianIC2d_hex27_uniform.screen
A		examples/USER/atc/mesh/gaussianIC2d_hex_uniform.screen
A		examples/USER/atc/mesh/gaussianIC2d_tet.screen
A		examples/USER/atc/mesh/in.gaussianIC1d_hex
A		examples/USER/atc/mesh/in.gaussianIC2d_hex
A		examples/USER/atc/mesh/in.gaussianIC2d_hex20_uniform
A		examples/USER/atc/mesh/in.gaussianIC2d_hex27_uniform
A		examples/USER/atc/mesh/in.gaussianIC2d_tet
A		examples/USER/atc/mesh/in.kernel2d_hex
A		examples/USER/atc/mesh/in.kernel2d_tet
A		examples/USER/atc/mesh/in.mesh2d_tet
A		examples/USER/atc/mesh/in.semicircle
A		examples/USER/atc/mesh/kernel2d_hex.screen
A		examples/USER/atc/mesh/kernel2d_tet.screen
A		examples/USER/atc/mesh/mesh2d_tet.screen
A		examples/USER/atc/mesh/semicircle.screen
A	(dir)	examples/USER/atc/molecule/
A		examples/USER/atc/molecule/harmonic_bonds.screen
A		examples/USER/atc/molecule/in.harmonic_bonds
A		examples/USER/atc/molecule/in.polarize
A		examples/USER/atc/molecule/in.quartic_bonds
A		examples/USER/atc/molecule/in.water
A		examples/USER/atc/molecule/polarize.screen
A		examples/USER/atc/molecule/quartic_bonds.screen
A		examples/USER/atc/molecule/water.mat
A		examples/USER/atc/molecule/water.screen
A		examples/USER/atc/svn.stdout
A	(dir)	examples/USER/atc/thermal/
A		examples/USER/atc/thermal/Ar_thermal.mat
A		examples/USER/atc/thermal/bar1d.screen
A		examples/USER/atc/thermal/bar1d_all_atoms.screen
A		examples/USER/atc/thermal/bar1d_combined.screen
A		examples/USER/atc/thermal/bar1d_flux.screen
A		examples/USER/atc/thermal/bar1d_frac_step.screen
A		examples/USER/atc/thermal/bar1d_hoover.screen
A		examples/USER/atc/thermal/bar1d_interpolate.screen
A		examples/USER/atc/thermal/bar1d_lumped.screen
A		examples/USER/atc/thermal/in.bar1d
A		examples/USER/atc/thermal/in.bar1d_all_atoms
A		examples/USER/atc/thermal/in.bar1d_combined
A		examples/USER/atc/thermal/in.bar1d_flux
A		examples/USER/atc/thermal/in.bar1d_frac_step
A		examples/USER/atc/thermal/in.bar1d_hoover
A		examples/USER/atc/thermal/in.bar1d_interpolate
A		examples/USER/atc/thermal/in.bar1d_lumped
A		examples/USER/atc/thermal/in.no_atoms
A		examples/USER/atc/thermal/no_atoms.screen
A	(dir)	examples/USER/atc/two_temperature/
A		examples/USER/atc/two_temperature/Ar_ttm.mat
A		examples/USER/atc/two_temperature/Cu_ttm.mat
A		examples/USER/atc/two_temperature/bar1d_ttm.screen
A		examples/USER/atc/two_temperature/cutout.screen
A		examples/USER/atc/two_temperature/gaussianIC_ttm.screen
A		examples/USER/atc/two_temperature/in.bar1d_ttm
A		examples/USER/atc/two_temperature/in.cutout
A		examples/USER/atc/two_temperature/in.gaussianIC_ttm
A		examples/USER/atc/two_temperature/in.no_atoms
A		examples/USER/atc/two_temperature/in.restart
A		examples/USER/atc/two_temperature/in.uniform_exchange
A		examples/USER/atc/two_temperature/in.uniform_heating
A		examples/USER/atc/two_temperature/no_atoms.screen
A		examples/USER/atc/two_temperature/restart.screen
A		examples/USER/atc/two_temperature/uniform_exchange.screen
A		examples/USER/atc/two_temperature/uniform_heating.screen
M		examples/friction/in.friction
A		lib/atc/ATC_Coupling.cpp
A		lib/atc/ATC_Coupling.h
A		lib/atc/ATC_CouplingEnergy.cpp
A		lib/atc/ATC_CouplingEnergy.h
A		lib/atc/ATC_CouplingMass.cpp
A		lib/atc/ATC_CouplingMass.h
A		lib/atc/ATC_CouplingMomentum.cpp
A		lib/atc/ATC_CouplingMomentum.h
A		lib/atc/ATC_CouplingMomentumEnergy.cpp
A		lib/atc/ATC_CouplingMomentumEnergy.h
M		lib/atc/ATC_Error.h
D		lib/atc/ATC_HardyKernel.cpp
D		lib/atc/ATC_HardyKernel.h
A		lib/atc/ATC_Method.cpp
A		lib/atc/ATC_Method.h
M		lib/atc/ATC_Transfer.cpp
M		lib/atc/ATC_Transfer.h
D		lib/atc/ATC_TransferHardy.cpp
D		lib/atc/ATC_TransferHardy.h
A		lib/atc/ATC_TransferKernel.cpp
A		lib/atc/ATC_TransferKernel.h
A		lib/atc/ATC_TransferPartitionOfUnity.cpp
A		lib/atc/ATC_TransferPartitionOfUnity.h
D		lib/atc/ATC_TransferThermal.cpp
D		lib/atc/ATC_TransferThermal.h
D		lib/atc/ATC_TransferUtility.cpp
M		lib/atc/ATC_TypeDefs.h
M		lib/atc/Array.h
M		lib/atc/Array2D.h
A		lib/atc/AtomToMoleculeTransfer.cpp
A		lib/atc/AtomToMoleculeTransfer.h
M		lib/atc/AtomicRegulator.cpp
M		lib/atc/AtomicRegulator.h
A		lib/atc/BodyForce.cpp
A		lib/atc/BodyForce.h
A		lib/atc/CBLattice.cpp
A		lib/atc/CBLattice.h
M		lib/atc/CG.h
A		lib/atc/CauchyBorn.cpp
A		lib/atc/CauchyBorn.h
A		lib/atc/CbEam.h
A		lib/atc/CbLjCut.h
A		lib/atc/CbLjSmoothLinear.h
A		lib/atc/CbPotential.cpp
A		lib/atc/CbPotential.h
A		lib/atc/ChargeRegulator.cpp
A		lib/atc/ChargeRegulator.h
M		lib/atc/CloneVector.h
A		lib/atc/ConcentrationRegulator.cpp
A		lib/atc/ConcentrationRegulator.h
M		lib/atc/DenseMatrix.h
M		lib/atc/DenseVector.h
A		lib/atc/DependencyManager.h
M		lib/atc/DiagonalMatrix.h
M		lib/atc/ElasticTimeIntegrator.cpp
M		lib/atc/ElasticTimeIntegrator.h
A		lib/atc/ElectronChargeDensity.cpp
A		lib/atc/ElectronChargeDensity.h
A		lib/atc/ElectronDragPower.cpp
A		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
A		lib/atc/ExtrinsicModelDriftDiffusion.cpp
A		lib/atc/ExtrinsicModelDriftDiffusion.h
A		lib/atc/ExtrinsicModelElectrostatic.cpp
A		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
A		lib/atc/FE_Interpolate.cpp
A		lib/atc/FE_Interpolate.h
M		lib/atc/FE_Mesh.cpp
M		lib/atc/FE_Mesh.h
A		lib/atc/FE_Quadrature.h
M		lib/atc/FieldEulerIntegrator.cpp
M		lib/atc/FieldEulerIntegrator.h
A		lib/atc/FieldManager.cpp
A		lib/atc/FieldManager.h
A		lib/atc/Function.cpp
A		lib/atc/Function.h
A		lib/atc/FundamentalAtomicQuantity.cpp
A		lib/atc/FundamentalAtomicQuantity.h
M		lib/atc/GMRES.h
M		lib/atc/ImplicitSolveOperator.cpp
M		lib/atc/ImplicitSolveOperator.h
A		lib/atc/InterscaleOperators.cpp
A		lib/atc/InterscaleOperators.h
A		lib/atc/KD_Tree.cpp
A		lib/atc/KD_Tree.h
A		lib/atc/KernelFunction.cpp
A		lib/atc/KernelFunction.h
A		lib/atc/KinetoThermostat.cpp
A		lib/atc/KinetoThermostat.h
M		lib/atc/Kinetostat.cpp
M		lib/atc/Kinetostat.h
M		lib/atc/LammpsInterface.cpp
M		lib/atc/LammpsInterface.h
A		lib/atc/LinearSolver.cpp
A		lib/atc/LinearSolver.h
A		lib/atc/MPI_Wrappers.cpp
A		lib/atc/MPI_Wrappers.h
A		lib/atc/Makefile.lammps
A		lib/atc/Makefile.mpic++
M		lib/atc/Material.cpp
M		lib/atc/Material.h
M		lib/atc/Matrix.cpp
M		lib/atc/Matrix.h
M		lib/atc/MatrixDef.h
M		lib/atc/MatrixLibrary.h
A		lib/atc/MeshReader.cpp
A		lib/atc/MeshReader.h
A		lib/atc/MoleculeSet.cpp
A		lib/atc/MoleculeSet.h
A		lib/atc/NonLinearSolver.cpp
A		lib/atc/NonLinearSolver.h
M		lib/atc/OutputManager.cpp
M		lib/atc/OutputManager.h
A		lib/atc/PaqAtcUtility.cpp
A		lib/atc/PaqAtcUtility.h
A		lib/atc/ParDenseMatrix.h
A		lib/atc/ParDiagonalMatrix.cpp
A		lib/atc/ParDiagonalMatrix.h
A		lib/atc/ParSparseMatrix.cpp
A		lib/atc/ParSparseMatrix.h
A		lib/atc/PerAtomQuantity-inl.h
A		lib/atc/PerAtomQuantity.h
A		lib/atc/PerAtomQuantityLibrary.cpp
A		lib/atc/PerAtomQuantityLibrary.h
A		lib/atc/PerPairQuantity.cpp
A		lib/atc/PerPairQuantity.h
A		lib/atc/PhysicsModel.cpp
M		lib/atc/PhysicsModel.h
D		lib/atc/PhysicsModelThermal.cpp
D		lib/atc/PhysicsModelThermal.h
D		lib/atc/PhysicsModelTwoTemperature.cpp
D		lib/atc/PhysicsModelTwoTemperature.h
A		lib/atc/PoissonSolver.cpp
A		lib/atc/PoissonSolver.h
V		lib/atc/{PolynomialSolver.cpp ← Solver.cpp}
V		lib/atc/{PolynomialSolver.h ← Solver.h}
M		lib/atc/PrescribedDataManager.cpp
M		lib/atc/PrescribedDataManager.h
V		lib/atc/{Quadrature.cpp ← Quadrature.h}
V		lib/atc/{Quadrature.h → Quadrature.cpp}
A		lib/atc/SchrodingerSolver.cpp
A		lib/atc/SchrodingerSolver.h
A		lib/atc/ShapeFunction.h
V		lib/atc/{Solver.cpp → PolynomialSolver.cpp}
V		lib/atc/{Solver.h → PolynomialSolver.h}
M		lib/atc/SparseMatrix-inl.h
M		lib/atc/SparseMatrix.h
M		lib/atc/SparseVector-inl.h
M		lib/atc/SparseVector.h
A		lib/atc/SpeciesTimeIntegrator.cpp
A		lib/atc/SpeciesTimeIntegrator.h
A		lib/atc/Stress.cpp
A		lib/atc/Stress.h
D		lib/atc/StringManip.h
A		lib/atc/ThermalTimeIntegrator.cpp
A		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
A		lib/atc/TransferLibrary.cpp
A		lib/atc/TransferLibrary.h
A		lib/atc/TransferOperator.cpp
A		lib/atc/TransferOperator.h
M		lib/atc/Utility.h
M		lib/atc/Vector.cpp
M		lib/atc/Vector.h
A		lib/atc/ViscousStress.cpp
A		lib/atc/ViscousStress.h
A		lib/atc/VoigtOperations.h
A		lib/atc/WeakEquation.h
A		lib/atc/WeakEquationChargeDiffusion.cpp
A		lib/atc/WeakEquationChargeDiffusion.h
A		lib/atc/WeakEquationDiffusion.cpp
A		lib/atc/WeakEquationDiffusion.h
A		lib/atc/WeakEquationElectronContinuity.cpp
A		lib/atc/WeakEquationElectronContinuity.h
A		lib/atc/WeakEquationElectronMomentum.cpp
A		lib/atc/WeakEquationElectronMomentum.h
A		lib/atc/WeakEquationElectronTemperature.cpp
A		lib/atc/WeakEquationElectronTemperature.h
A		lib/atc/WeakEquationMassDiffusion.cpp
A		lib/atc/WeakEquationMassDiffusion.h
A		lib/atc/WeakEquationMomentum.cpp
A		lib/atc/WeakEquationMomentum.h
A		lib/atc/WeakEquationPhononTemperature.cpp
A		lib/atc/WeakEquationPhononTemperature.h
A		lib/atc/WeakEquationPoisson.cpp
A		lib/atc/WeakEquationPoisson.h
A		lib/atc/WeakEquationSchrodinger.cpp
A		lib/atc/WeakEquationSchrodinger.h
D		lib/atc/XT_Function.cpp
D		lib/atc/XT_Function.h
A		lib/atc/build.log
A		lib/atc/libatc.a
A		lib/atc/svn.stdout
V		src/{MISC → }/fix_deposit.cpp
V		src/{MISC → }/fix_deposit.h
M		src/USER-ATC/fix_atc.cpp
M		src/USER-ATC/fix_atc.h
A		src/USER-ATC/svn.stdout
M		src/USER-COLVARS/fix_colvars.cpp
V		src/{ ← MISC}/fix_deposit.cpp
V		src/{ ← MISC}/fix_deposit.h
M		src/version.h