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2004-10-20 00:52 tim |
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|
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* src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and |
4 |
SnapshotManager in design phase |
5 |
|
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2004-10-19 23:54 gezelter |
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|
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* src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace |
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problem prevented linking |
10 |
|
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2004-10-19 23:54 gezelter |
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|
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* src/UseTheForce/Shapes_FF.cpp: fixed include |
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|
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2004-10-19 23:26 gezelter |
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|
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* src/utils/: Makefile, definitions.F90, definitions_module.F90, |
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oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90: |
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more fortran name mangling |
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|
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2004-10-19 23:23 gezelter |
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|
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* src/profiling/timing.F90: yet more fortran renaming |
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|
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2004-10-19 23:19 gezelter |
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|
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* src/UseTheForce/: Makefile, doForces.F90, doForces_interface.h, |
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do_Forces.F90, do_Forces.h, notifyCutoffs.F90, |
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notifyCutoffs_interface.h, notifycutoffs_module_interface.h, |
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wrappers.F90: Fortran name cleanup continues |
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|
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2004-10-19 23:12 gezelter |
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|
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* src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some |
35 |
broken fortran stuff |
36 |
|
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2004-10-19 23:02 gezelter |
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|
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* src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, |
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atype_interface.h, atype_module.F90, atype_module_interface.h, |
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calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, |
42 |
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
43 |
calc_shapes.F90, calc_sticky_pair.F90, charge.F90, dipole.F90, |
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eam.F90, eam_interface.h, eam_module_inteface.h, gb.F90, |
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gb_interface.h, gb_module_interface.h, mpiSimulation.F90, |
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mpiSimulation_interface.h, mpiSimulation_module.F90, |
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mpisimulation_module_interface.h, reactionField.F90, shapes.F90, |
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shapes_interface.h, shapes_module.h, simulation.F90, |
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simulation_interface.h, simulation_module.F90, |
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simulation_module_interface.h, sticky.F90, sticky_interface.h, |
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sticky_pair_module_interface.h, switch_module.F90, switcheroo.F90: |
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name sanity on the fortran side |
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|
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2004-10-19 19:18 tim |
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|
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* test/math/SquareMatrix3TestCase.hpp: [no log message] |
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|
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2004-10-19 18:01 tim |
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|
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* src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
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src/math/SquareMatrix3.hpp, test/math/SquareMatrix3TestCase.cpp: |
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except diagonalize(), all of functions in math library pass the |
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test |
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|
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2004-10-19 17:43 chuckv |
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|
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* src/UseTheForce/do_Forces.h: Added correct prototypes for |
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C-fortran interface functions. |
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|
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2004-10-19 17:37 chuckv |
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|
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* src/UseTheForce/DarkSide/: atype_module_interface.h, |
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eam_module_inteface.h, gb_module_interface.h, |
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mpisimulation_module_interface.h, simulation_module_interface.h, |
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sticky_pair_module_interface.h: Added correct prototypes for |
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C-fortran interface functions. |
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|
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2004-10-19 16:28 tim |
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|
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* ChangeLog, src/math/Quaternion.hpp, src/math/RectMatrix.hpp, |
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src/math/SquareMatrix.hpp, src/math/Vector.hpp, |
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test/math/QuaternionTestCase.cpp, test/math/QuaternionTestCase.hpp, |
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test/math/RectMatrixTestCase.cpp, |
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test/math/SquareMatrix3TestCase.cpp, test/math/Vector3TestCase.cpp, |
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test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp: more |
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bugs get fixed at math library |
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|
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2004-10-19 15:43 chuckv |
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|
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* src/UseTheForce/: DarkSide/atype_module_interface.h, |
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DarkSide/eam_module_inteface.h, DarkSide/gb_module_interface.h, |
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DarkSide/mpisimulation_module_interface.h, |
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DarkSide/simulation_module_interface.h, |
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DarkSide/sticky_pair_module_interface.h, DarkSide/calc_eam.F90, |
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DarkSide/atype_module.F90, DarkSide/calc_gb.F90, |
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DarkSide/calc_sticky_pair.F90, DarkSide/mpiSimulation_module.F90, |
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DarkSide/simulation_module.F90, do_Forces.F90, |
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fortranWrapDefines.hpp, mpiComponentPlan.h, notifyCutoffs.F90, |
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notifycutoffs_module_interface.h: Added new files for fortran |
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interface. |
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|
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2004-10-19 15:43 gezelter |
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|
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* src/UseTheForce/Makefile: regressing |
105 |
|
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2004-10-19 15:40 gezelter |
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|
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* src/: UseTheForce/DarkSide/calc_shapes.F90, |
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UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp: |
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working on shapes for portability |
111 |
|
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2004-10-19 15:40 gezelter |
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|
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* src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes |
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|
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2004-10-19 13:21 chrisfen |
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|
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* src/utils/: StringUtils.cpp, StringUtils.hpp: changed around |
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findBegin |
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|
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2004-10-18 23:34 tim |
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|
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* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs |
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are fixed in Vector class |
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|
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2004-10-18 23:28 tim |
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|
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* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix |
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some bugs in RectMatrixTestCase |
130 |
|
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2004-10-18 23:21 tim |
132 |
|
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* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp, |
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test/math/RectMatrixTestCase.hpp, test/math/Vector3TestCase.cpp, |
135 |
test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp, |
136 |
test/math/VectorTestCase.hpp: implement more test cases |
137 |
|
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2004-10-18 18:13 tim |
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|
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* ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp, |
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src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
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src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
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src/utils/StringTokenizer.hpp, test/math/Makefile, |
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test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more |
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tests on math library |
146 |
|
147 |
2004-10-18 16:03 tim |
148 |
|
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* test/math/: Makefile, QuaternionTestCase.cpp, |
150 |
QuaternionTestCase.hpp, RectMatrixTestCase.cpp, |
151 |
SquareMatrix3TestCase.cpp, Vector3TestCase.cpp, |
152 |
Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding |
153 |
more testing units |
154 |
|
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2004-10-18 12:07 tim |
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|
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* src/: brains/SimSetup.hpp, io/FileReader.hpp, math/Euler3.cpp, |
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math/Euler3.hpp, math/Quaternion.hpp, math/SquareMatrix3.hpp, |
159 |
math/Vector3.hpp, types/ShapeType.cpp, types/ShapeType.hpp, |
160 |
utils/GenericFactory.hpp: fix some bugs in Quaternion class |
161 |
|
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2004-10-18 11:30 gezelter |
163 |
|
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* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: |
165 |
Your basic run of the mill real-valued versions of Y_l^m(\theta, |
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\phi) |
167 |
|
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2004-10-18 11:29 gezelter |
169 |
|
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* src/: math/Makefile, math/Matrix3x3d.hpp, math/Vector3.hpp, |
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types/Makefile, types/ShapeType.cpp, types/ShapeType.hpp, |
172 |
utils/StringUtils.cpp, utils/StringUtils.hpp: Working on getting |
173 |
Shapes into OOPSE |
174 |
|
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2004-10-18 10:21 gezelter |
176 |
|
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* src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType |
178 |
|
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2004-10-18 00:23 tim |
180 |
|
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* test/math/VectorTestCase.hpp: adding vector test case |
182 |
|
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2004-10-18 00:23 tim |
184 |
|
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* src/utils/GenericFactory.hpp: adding generic factory and vector |
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test case |
187 |
|
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2004-10-16 20:19 tim |
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|
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* src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp, |
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SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in |
192 |
progress |
193 |
|
194 |
2004-10-15 20:31 tim |
195 |
|
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* src/math/Quaternion.hpp: add quaternion class |
197 |
|
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2004-10-15 16:11 tim |
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|
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* test/io/: DUFF.frc, IfstrstreamTestCase.cpp, |
201 |
IfstrstreamTestCase.hpp: adding test file |
202 |
|
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2004-10-15 16:10 tim |
204 |
|
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* src/io/basic_ifstrstream.hpp: fix a bunch of bugs |
206 |
|
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2004-10-15 15:42 tim |
208 |
|
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* src/io/basic_ifstrstream.hpp: change const_cast to statc_const |
210 |
|
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2004-10-15 15:35 tim |
212 |
|
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* src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp |
214 |
|
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2004-10-15 15:34 tim |
216 |
|
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* test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use |
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namespace oopse |
219 |
|
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2004-10-15 14:38 chuckv |
221 |
|
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* configure, ac-tools/aclocal.m4: Changed optimization flags for |
223 |
XLF and XLC. |
224 |
|
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2004-10-15 13:28 tim |
226 |
|
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* test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp: |
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adding ifstrstream test case |
229 |
|
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2004-10-15 13:20 tim |
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|
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* src/io/basic_ifstrstream.hpp: fix include |
233 |
|
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2004-10-15 13:18 tim |
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|
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* src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi |
237 |
|
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2004-10-15 13:17 tim |
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|
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* test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile |
241 |
|
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2004-10-15 13:16 tim |
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|
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* test/io/: Makefile, ifstrstreamTestCase.cpp, |
245 |
ifstrstreamTestCase.hpp: adding test case for ifstrstream |
246 |
|
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2004-10-15 10:37 tim |
248 |
|
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* test/io/: IOTest.cpp, ifstrstreamTestCase.cpp, |
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ifstrstreamTestCase.hpp: add ifstrstreamTestCase |
251 |
|
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2004-10-15 10:20 tim |
253 |
|
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* src/io/basic_ifstrstream.hpp: add checkFilename Option |
255 |
|
256 |
2004-10-15 10:19 tim |
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|
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* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp, |
259 |
SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add |
260 |
SquareMatrixTestCase class |
261 |
|
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2004-10-15 02:52 tim |
263 |
|
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* src/io/basic_ifstrstream.hpp: adding basic_ifstrstream |
265 |
|
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2004-10-14 18:28 tim |
267 |
|
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* src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp, |
269 |
Vector.hpp: math library in progress |
270 |
|
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2004-10-14 18:27 tim |
272 |
|
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* src/io/FileReader.hpp: FileReader in progress |
274 |
|
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2004-10-13 18:53 tim |
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|
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* src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress, |
278 |
test in isOrthogonal of SquareMatrix is failed by some reasons |
279 |
|
280 |
2004-10-13 17:28 tim |
281 |
|
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* src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap |
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class |
284 |
|
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2004-10-13 17:27 tim |
286 |
|
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* test/math/: MainTest.cpp, RectMatrixTestCase.cpp, |
288 |
RectMatrixTestCase.hpp: adding testing unit |
289 |
|
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2004-10-13 17:24 tim |
291 |
|
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* src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix |
293 |
|
294 |
2004-10-13 01:51 tim |
295 |
|
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* src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp, |
297 |
Vector3.hpp: refactory vector and matrix classes |
298 |
|
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2004-10-13 01:50 tim |
300 |
|
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* src/math/Vector3d.hpp: Remove some Makefile.in |
302 |
|
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2004-10-12 18:57 tim |
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|
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* src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and |
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Matrix3x3d.hpp |
307 |
|
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2004-10-12 14:08 tim |
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|
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* doc/: cppstyle.html, style.css: adding c++ coding style |
311 |
|
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2004-10-11 17:15 tim |
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|
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* src/: constraints/AbstractClasses.hpp, |
315 |
integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp: |
316 |
change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp |
317 |
|
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2004-10-11 16:54 tim |
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|
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* scripts/filepp: fix a bug in filepp |
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|
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2004-10-11 16:13 tim |
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|
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* make/Makefile.in: using filepp to generate dependencies instead |
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of compilers |
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|
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2004-10-11 16:10 tim |
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|
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* scripts/filepp: filepp can be used to generate dependencies for |
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c/c++ now |
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|
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2004-10-11 13:40 tim |
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|
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* make/Makefile.in: remove -module from F90Options |
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|
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2004-10-11 13:01 tim |
337 |
|
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* make/Makefile.in: adding rules to move fortran 90 module to |
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target directory |
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|
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2004-10-11 10:43 gezelter |
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|
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* make/Makefile.in: fixed makefile.in |
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|
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2004-10-11 09:51 tim |
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|
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* scripts/filepp: remove "use bytes" which causes problem in sgi |
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machine |
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|
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2004-10-11 09:26 tim |
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|
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* forceFields/Makefile: add Makefile |
353 |
|
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2004-10-11 09:23 tim |
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|
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* samples/: water/dimer/Makefile, water/spce/Makefile, |
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water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile, |
358 |
water/tip4p/Makefile, zcons/Makefile: fix Makefile under water |
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directory |
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|
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2004-10-11 09:23 tim |
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|
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* samples/argon/Makefile: remove argon.dump and argon.eor from |
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Makefile |
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|
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2004-10-09 01:01 tim |
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|
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* samples/: alkane/Makefile.in, argon/Makefile.in, |
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lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in: |
370 |
Remove some Makefile.in |
371 |
|
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2004-10-08 18:15 tim |
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|
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* make/Makefile.in: [no log message] |
375 |
|
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2004-10-08 17:51 tim |
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|
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* make/Makefile.in: fix make install |
379 |
|
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2004-10-08 17:10 tim |
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|
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* make/Makefile.in: adding make install |
383 |
|
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2004-10-08 17:04 tim |
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|
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* samples/: alkane/Makefile, argon/Makefile, lipid/Makefile, |
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metals/Makefile, minimizer/Makefile, water/Makefile.in, |
388 |
water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile, |
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water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in, |
390 |
water/ssde/Makefile, water/ssde/Makefile.in, |
391 |
water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in, |
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water/tip4p/Makefile, water/tip4p/Makefile.in, zcons/Makefile, |
393 |
zcons/Makefile.in: add Makefile to sample directory |
394 |
|
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2004-10-06 18:03 gezelter |
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|
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* src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt |
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stuff |
399 |
|
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2004-10-06 18:03 gezelter |
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|
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* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
403 |
make/Doxyfile, src/applications/getopt.c, |
404 |
src/applications/getopt1.c, src/applications/gnugetopt.h: more |
405 |
build fixes |
406 |
|
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2004-10-06 17:20 tim |
408 |
|
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* make/: Doxyfile, Makefile.in: adding doxygen configuration file |
410 |
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2004-10-06 17:19 tim |
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|
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* scripts/filepp: filepp can handle different fortran module case |
414 |
and suffix |
415 |
|
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2004-10-06 16:27 gezelter |
417 |
|
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* src/restraints/Restraints.cpp: Chris doesn't know about the |
419 |
OOPSE-2.0 directory structure yet |
420 |
|
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2004-10-06 16:27 gezelter |
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|
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* ChangeLog: Yeah yeah, we'lll get around to it later |
424 |
|
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2004-10-06 16:22 gezelter |
426 |
|
427 |
* configure, ac-tools/configure.in, ac-tools/fortran90.m4, |
428 |
make/Makefile.in: cleaning up build process |
429 |
|
430 |
2004-10-06 15:01 chrisfen |
431 |
|
432 |
* src/restraints/Restraints.cpp: made the file reading in |
433 |
restraints more intelligent - no longer gives uninformative seg |
434 |
faults |
435 |
|
436 |
2004-10-06 14:55 gezelter |
437 |
|
438 |
* src/applications/simpleBuilder/Make.ftemp.old: cleaning up |
439 |
|
440 |
2004-10-06 14:51 gezelter |
441 |
|
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* LICENSE, MPIobj/dummy, make/Makefile, obj/dummy, |
443 |
scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit |
444 |
|
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2004-10-06 13:53 tim |
446 |
|
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* make/: Makefile, Makefile.in: fix make statistics |
448 |
|
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2004-10-06 13:18 tim |
450 |
|
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* make/: Makefile, Makefile.in: adding GNU make functions to |
452 |
combine all of the static libraries to a big library |
453 |
|
454 |
2004-10-05 17:57 tim |
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|
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* make/: Makefile, Makefile.in: adding shared library flag |
457 |
|
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2004-10-05 14:37 tim |
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|
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* src/: Makefile, UseTheForce/Makefile, |
461 |
UseTheForce/mpiSimulation_module.F90, |
462 |
UseTheForce/DarkSide/Makefile, |
463 |
UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move |
464 |
mpiSimulation_module to DarkSide |
465 |
|
466 |
2004-10-05 14:35 tim |
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|
468 |
* make/: Makefile, Makefile.in: building MPI version;using static |
469 |
library instead of shared library |
470 |
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2004-10-05 09:14 tim |
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|
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* make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90 |
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to filepp |
475 |
|
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2004-10-04 15:56 tim |
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|
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* make/: Makefile, Makefile.in: add make cvslog |
479 |
|
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2004-10-04 11:24 gezelter |
481 |
|
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* make/: Makefile, Makefile.in: more work on the parallel build |
483 |
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2004-10-04 11:06 gezelter |
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|
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* make/: Makefile, Makefile.in: changes to backport declare flags |
487 |
|
488 |
2004-10-04 10:27 gezelter |
489 |
|
490 |
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, |
491 |
DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging |
492 |
shapes |
493 |
|
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2004-10-01 23:40 tim |
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|
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* scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree |
497 |
|
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2004-10-01 23:22 tim |
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|
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* make/: Makefile, Makefile.in: add oopse_ as library prefix |
501 |
|
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2004-10-01 16:59 tim |
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|
504 |
* make/: Makefile, Makefile.in: fix a space trimming bug in filepp |
505 |
|
506 |
2004-10-01 16:22 gezelter |
507 |
|
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* Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A |
509 |
few minor build changes |
510 |
|
511 |
2004-10-01 16:11 tim |
512 |
|
513 |
* scripts/filepp: adding fortran90 make dependency tool |
514 |
|
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2004-09-30 10:41 tim |
516 |
|
517 |
* make/: Makefile, Makefile.in: make clean is smart enough to only |
518 |
remove object files belong to current package. turn off silent |
519 |
mode |
520 |
|
521 |
2004-09-29 16:55 tim |
522 |
|
523 |
* src/: Makefile, UseTheForce/Makefile, |
524 |
UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile, |
525 |
applications/oopse/Makefile, applications/simpleBuilder/Makefile, |
526 |
brains/Makedepend, brains/Makefile, constraints/Makefile, |
527 |
integrators/Makefile, io/Makefile, math/Makefile, |
528 |
minimizers/Makefile, primitives/Makefile, profiling/Makefile, |
529 |
restraints/Makefile, types/Makefile, utils/Makefile, |
530 |
visitors/Makefile: define DEV_ROOT as relative path |
531 |
|
532 |
2004-09-29 16:54 tim |
533 |
|
534 |
* make/: Makefile, Makefile.in: get the relative path by shell |
535 |
script |
536 |
|
537 |
2004-09-29 16:32 tim |
538 |
|
539 |
* make/Makefile: eliminate DEV_ROOT by relative path |
540 |
|
541 |
2004-09-29 13:37 tim |
542 |
|
543 |
* make/Makefile.in: add PackageLibs; fix dependency rule |
544 |
|
545 |
2004-09-29 12:57 gezelter |
546 |
|
547 |
* configure, ac-tools/configure.in: updates |
548 |
|
549 |
2004-09-29 12:56 gezelter |
550 |
|
551 |
* make/: Make.conf.in, Makefile.in: Working on make stuff |
552 |
|
553 |
2004-09-29 12:46 tim |
554 |
|
555 |
* Makefile: If makefile does not exist, print error message |
556 |
|
557 |
2004-09-29 12:12 tim |
558 |
|
559 |
* make/: Make.conf.in, Makefile: fix dependencies rule |
560 |
|
561 |
2004-09-29 10:58 gezelter |
562 |
|
563 |
* Makefile, make/Makefile: still working on build process |
564 |
|
565 |
2004-09-29 10:00 tim |
566 |
|
567 |
* make/Makefile: add print statment to rules |
568 |
|
569 |
2004-09-29 09:59 tim |
570 |
|
571 |
* src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile, |
572 |
applications/dump2Xyz/Makefile, applications/oopse/Makefile, |
573 |
applications/simpleBuilder/Makefile, brains/Makefile, |
574 |
constraints/Makefile, integrators/Makefile, io/Makefile, |
575 |
math/Makefile, minimizers/Makefile, primitives/Makefile, |
576 |
profiling/Makefile, restraints/Makefile, types/Makefile, |
577 |
utils/Makefile, visitors/Makefile: change Makefile to relative path |
578 |
|
579 |
2004-09-28 21:55 tim |
580 |
|
581 |
* src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c |
582 |
which cause headache in bulding libutils |
583 |
|
584 |
2004-09-28 18:24 tim |
585 |
|
586 |
* src/applications/: BaseLattice.cpp, BaseLattice.hpp, |
587 |
Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h, |
588 |
Lattice.cpp, Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, |
589 |
LatticeFactory.cpp, LatticeFactory.hpp, MoLocator.cpp, |
590 |
MoLocator.hpp, Vector3d.hpp, cmdline.c, cmdline.h, nanoBuilder.cpp, |
591 |
nanoBuilder.hpp, oopse.cpp, simpleBuilder.cpp, simpleBuilder.ggo, |
592 |
simpleBuilderCmd.c, simpleBuilderCmd.h, dump2Xyz/Dump2XYZ.cpp, |
593 |
dump2Xyz/Dump2XYZ.ggo, dump2Xyz/Dump2XYZCmd.c, |
594 |
dump2Xyz/Dump2XYZCmd.h, dump2Xyz/Makefile, oopse/Makefile, |
595 |
oopse/oopse.cpp, simpleBuilder/BaseLattice.cpp, |
596 |
simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, |
597 |
simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, |
598 |
simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, |
599 |
simpleBuilder/LatticeFactory.hpp, simpleBuilder/Make.ftemp.old, |
600 |
simpleBuilder/Makefile, simpleBuilder/MoLocator.cpp, |
601 |
simpleBuilder/MoLocator.hpp, simpleBuilder/Vector3d.hpp, |
602 |
simpleBuilder/simpleBuilder.cpp, simpleBuilder/simpleBuilder.ggo, |
603 |
simpleBuilder/simpleBuilderCmd.c, simpleBuilder/simpleBuilderCmd.h: |
604 |
change directory structure of application. Every executable file is |
605 |
replaced in seperate directory |
606 |
|
607 |
2004-09-28 17:15 gezelter |
608 |
|
609 |
* lib/dummy: Keep that lib around, please. |
610 |
|
611 |
2004-09-28 17:14 gezelter |
612 |
|
613 |
* Makefile, configure, ac-tools/configure.in, make/Make.conf.in: |
614 |
starting a configure version |
615 |
|
616 |
2004-09-28 16:08 tim |
617 |
|
618 |
* src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90, |
619 |
UseTheForce/DarkSide/Makefile, |
620 |
UseTheForce/DarkSide/notifyCutoffs.F90, |
621 |
UseTheForce/DarkSide/simulation_module.F90, brains/Makedepend, |
622 |
brains/Makefile, brains/simulation_module.F90: move fortran files |
623 |
around to solve dependency problem |
624 |
|
625 |
2004-09-28 15:43 tim |
626 |
|
627 |
* Makefile, src/UseTheForce/ForceFields.hpp, |
628 |
src/UseTheForce/Makefile, src/applications/BaseLattice.hpp, |
629 |
src/applications/Makedepend, src/applications/Makefile, |
630 |
src/brains/Makedepend, src/brains/simulation_module.F90, |
631 |
src/integrators/AllIntegrator.hpp, src/math/Euler3.cpp, |
632 |
src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp, |
633 |
src/utils/Makefile: [no log message] |
634 |
|
635 |
2004-09-28 15:41 tim |
636 |
|
637 |
* make/Makefile, scripts/sfmakedepend: fix fortran dependency |
638 |
problem |
639 |
|
640 |
2004-09-28 11:13 tim |
641 |
|
642 |
* make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y, |
643 |
src/io/Makefile: add yacc and lex rules |
644 |
|
645 |
2004-09-27 15:24 tim |
646 |
|
647 |
* make/Makefile: adding include path to F90Options |
648 |
|
649 |
2004-09-27 15:13 tim |
650 |
|
651 |
* make/Makefile: change suffix from .cc to .cpp |
652 |
|
653 |
2004-09-24 11:27 tim |
654 |
|
655 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
656 |
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
657 |
UseTheForce/LJFF.cpp, UseTheForce/WATER.cpp, |
658 |
UseTheForce/do_Forces.F90, UseTheForce/fortranWrapDefines.hpp, |
659 |
UseTheForce/fortranWrappers.cpp, UseTheForce/fortranWrappers.hpp, |
660 |
UseTheForce/mpiForceField.c, UseTheForce/mpiSimulation_module.F90, |
661 |
UseTheForce/DarkSide/calc_LJ_FF.F90, |
662 |
UseTheForce/DarkSide/notifyCutoffs.F90, |
663 |
UseTheForce/DarkSide/switch_module.F90, |
664 |
applications/BaseLattice.cpp, applications/Dump2XYZ.cpp, |
665 |
applications/Dump2XYZCmd.c, applications/Lattice.cpp, |
666 |
applications/Lattice.hpp, applications/LatticeCreator.cpp, |
667 |
applications/LatticeCreator.hpp, applications/LatticeFactory.cpp, |
668 |
applications/MoLocator.cpp, applications/MoLocator.hpp, |
669 |
applications/cmdline.c, applications/nanoBuilder.cpp, |
670 |
applications/oopse.cpp, applications/simpleBuilder.cpp, |
671 |
applications/simpleBuilderCmd.c, brains/Exclude.cpp, |
672 |
brains/ForceFields.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
673 |
brains/SimSetup.cpp, brains/SimSetup.hpp, brains/SimState.cpp, |
674 |
brains/SkipList.cpp, brains/Thermo.cpp, brains/Thermo.hpp, |
675 |
brains/mpiSimulation.cpp, brains/mpiSimulation.hpp, |
676 |
constraints/AbstractClasses.hpp, constraints/ZConstraint.cpp, |
677 |
integrators/AbstractClasses.hpp, integrators/Integrator.cpp, |
678 |
integrators/Integrator.hpp, integrators/NPT.cpp, |
679 |
integrators/NPTf.cpp, integrators/NPTi.cpp, integrators/NPTxyz.cpp, |
680 |
integrators/NVT.cpp, io/BASS_interface.cpp, io/BASS_parse.c, |
681 |
io/DumpReader.cpp, io/DumpWriter.cpp, io/Globals.cpp, |
682 |
io/Globals.hpp, io/InitializeFromFile.cpp, io/LinkedAssign.cpp, |
683 |
io/LinkedCommand.cpp, io/ReadWrite.hpp, io/StatWriter.cpp, |
684 |
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
685 |
io/ZConsWriter.hpp, io/interface.c, io/make_nodes.c, |
686 |
io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/parse_interface.h, |
687 |
io/parse_tree.c, io/parse_tree.h, math/Euler3.cpp, math/MatVec3.c, |
688 |
math/MatVec3.h, math/randomSPRNG.cpp, |
689 |
minimizers/CGFamilyMinimizer.cpp, minimizers/OOPSEMinimizer.cpp, |
690 |
minimizers/OOPSEMinimizer.hpp, minimizers/PRCG.cpp, |
691 |
minimizers/SDMinimizer.cpp, primitives/AbstractClasses.hpp, |
692 |
primitives/Atom.cpp, primitives/Atom.hpp, primitives/Bend.cpp, |
693 |
primitives/BendExtensions.cpp, primitives/Bond.cpp, |
694 |
primitives/BondExtensions.cpp, primitives/CutoffGroup.hpp, |
695 |
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
696 |
primitives/GhostBend.cpp, primitives/Molecule.cpp, |
697 |
primitives/Molecule.hpp, primitives/RigidBody.cpp, |
698 |
primitives/RigidBody.hpp, primitives/SRI.hpp, |
699 |
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
700 |
primitives/Torsion.cpp, primitives/TorsionExtensions.cpp, |
701 |
profiling/mdProfile.cpp, restraints/Restraints.cpp, |
702 |
restraints/Restraints.hpp, types/AtomStamp.cpp, |
703 |
types/AtomStamp.hpp, types/BendStamp.cpp, types/BendStamp.hpp, |
704 |
types/BondStamp.cpp, types/BondStamp.hpp, types/Component.cpp, |
705 |
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
706 |
types/MakeStamps.cpp, types/MakeStamps.hpp, |
707 |
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
708 |
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
709 |
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
710 |
types/ZconStamp.cpp, types/ZconStamp.hpp, utils/GenericData.cpp, |
711 |
utils/StreamTokenizer.cpp, utils/StringUtils.c, |
712 |
utils/StringUtils.cpp, utils/Utility.cpp, utils/fError.c, |
713 |
utils/simError.c, visitors/AtomVisitor.cpp, |
714 |
visitors/AtomVisitor.hpp, visitors/CompositeVisitor.cpp, |
715 |
visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, |
716 |
visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
717 |
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, |
718 |
visitors/ZconsVisitor.hpp: change the #include in source files |
719 |
|
720 |
2004-09-23 23:16 gezelter |
721 |
|
722 |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
723 |
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
724 |
src/constraints/Makefile, src/constraints/ZConstraint.cpp, |
725 |
src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, |
726 |
src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, |
727 |
src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, |
728 |
src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, |
729 |
src/UseTheForce/fForceField.h, |
730 |
src/UseTheForce/fSwitchingFunction.h, |
731 |
src/UseTheForce/fortranWrapDefines.hpp, |
732 |
src/UseTheForce/fortranWrappers.cpp, |
733 |
src/UseTheForce/fortranWrappers.hpp, |
734 |
src/UseTheForce/mpiComponentPlan.h, |
735 |
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
736 |
src/UseTheForce/mpiSimulation_module.F90, |
737 |
src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, |
738 |
src/UseTheForce/DarkSide/atype_module.F90, |
739 |
src/UseTheForce/DarkSide/calc_LJ_FF.F90, |
740 |
src/UseTheForce/DarkSide/calc_charge_charge.F90, |
741 |
src/UseTheForce/DarkSide/calc_dipole_dipole.F90, |
742 |
src/UseTheForce/DarkSide/calc_eam.F90, |
743 |
src/UseTheForce/DarkSide/calc_gb.F90, |
744 |
src/UseTheForce/DarkSide/calc_reaction_field.F90, |
745 |
src/UseTheForce/DarkSide/calc_sticky_pair.F90, |
746 |
src/UseTheForce/DarkSide/force_globals.F90, |
747 |
src/UseTheForce/DarkSide/neighborLists.F90, |
748 |
src/UseTheForce/DarkSide/notifyCutoffs.F90, |
749 |
src/UseTheForce/DarkSide/switch_module.F90, |
750 |
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
751 |
src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, |
752 |
src/io/DumpWriter.cpp, src/io/Globals.cpp, |
753 |
src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, |
754 |
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
755 |
src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, |
756 |
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
757 |
src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, |
758 |
src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, |
759 |
src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, |
760 |
src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, |
761 |
src/types/AtomStamp.hpp, src/types/BendStamp.cpp, |
762 |
src/types/BendStamp.hpp, src/types/BondStamp.cpp, |
763 |
src/types/BondStamp.hpp, src/types/Component.cpp, |
764 |
src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, |
765 |
src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, |
766 |
src/types/MakeStamps.hpp, src/types/Makefile, |
767 |
src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, |
768 |
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
769 |
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
770 |
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
771 |
src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, |
772 |
src/brains/Exclude.hpp, src/brains/ForceFields.cpp, |
773 |
src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, |
774 |
src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, |
775 |
src/brains/SimSetup.hpp, src/brains/SimState.cpp, |
776 |
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
777 |
src/brains/SkipList.hpp, src/brains/Thermo.cpp, |
778 |
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
779 |
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
780 |
src/brains/simulation_module.F90, src/io/BASS_interface.cpp, |
781 |
src/io/Globals.hpp, src/io/LinkedAssign.cpp, |
782 |
src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, |
783 |
src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, |
784 |
src/math/mt19937ar.c, src/math/randomSPRNG.cpp, |
785 |
src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, |
786 |
src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, |
787 |
src/minimizers/OOPSEMinimizer.cpp, |
788 |
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
789 |
src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, |
790 |
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
791 |
src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, |
792 |
src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, |
793 |
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
794 |
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
795 |
src/primitives/Makefile, src/primitives/Molecule.cpp, |
796 |
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
797 |
src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, |
798 |
src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, |
799 |
src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, |
800 |
src/restraints/Makefile, src/restraints/Restraints.cpp, |
801 |
src/restraints/Restraints.hpp, src/utils/GenericData.cpp, |
802 |
src/utils/GenericData.hpp, src/utils/Makefile, |
803 |
src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, |
804 |
src/utils/StringUtils.c, src/utils/StringUtils.cpp, |
805 |
src/utils/StringUtils.h, src/utils/StringUtils.hpp, |
806 |
src/utils/TypeInfo.hpp, src/utils/Utility.cpp, |
807 |
src/utils/Utility.hpp, src/utils/definitions_module.F90, |
808 |
src/utils/fError.c, src/utils/oopseMPI_module.F90, |
809 |
src/utils/simError.c, src/utils/simError.h, |
810 |
src/utils/status_module.F90, src/utils/vector_class.F90, |
811 |
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
812 |
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
813 |
src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, |
814 |
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
815 |
src/visitors/RigidBodyVisitor.cpp, |
816 |
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
817 |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
818 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
819 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
820 |
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
821 |
samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, |
822 |
samples/zcons/Makefile.in, samples/zcons/water.md, |
823 |
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
824 |
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
825 |
src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, |
826 |
src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, |
827 |
src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, |
828 |
src/applications/Lattice.cpp, src/applications/Lattice.hpp, |
829 |
src/applications/LatticeCreator.cpp, |
830 |
src/applications/LatticeCreator.hpp, |
831 |
src/applications/LatticeFactory.cpp, |
832 |
src/applications/LatticeFactory.hpp, src/applications/Makedepend, |
833 |
src/applications/Makefile, src/applications/MoLocator.cpp, |
834 |
src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, |
835 |
src/applications/cmdline.c, src/applications/cmdline.h, |
836 |
src/applications/getopt.c, src/applications/getopt1.c, |
837 |
src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, |
838 |
src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, |
839 |
src/applications/quickLate.c, src/applications/simpleBuilder.cpp, |
840 |
src/applications/simpleBuilder.ggo, |
841 |
src/applications/simpleBuilderCmd.c, |
842 |
src/integrators/AbstractClasses.hpp, |
843 |
src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, |
844 |
src/integrators/Integrator.hpp, src/integrators/Makefile, |
845 |
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
846 |
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
847 |
src/integrators/NVT.cpp, src/profiling/Makefile, |
848 |
src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, |
849 |
src/profiling/timing.F90, samples/metals/Au_bulk.in, |
850 |
samples/metals/Au_nanoparticle.in, samples/metals/metals.md, |
851 |
samples/water/Makefile.in, samples/water/dimer/Makefile.in, |
852 |
samples/water/dimer/two.in, samples/water/dimer/two.md, |
853 |
samples/water/dimer/water.md, samples/water/spce/Makefile.in, |
854 |
samples/water/spce/spce.in, samples/water/spce/spce.md, |
855 |
samples/water/spce/water.md, samples/water/ssde/Makefile.in, |
856 |
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
857 |
samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, |
858 |
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
859 |
samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, |
860 |
samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, |
861 |
samples/water/ssd/water.md, samples/water/tip4p/tp4.in, |
862 |
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
863 |
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
864 |
samples/alkane/butane.in, samples/alkane/butane.md, |
865 |
samples/argon/500.in, samples/argon/500.md, |
866 |
samples/argon/Makefile.in, samples/argon/ar864.in, |
867 |
samples/argon/ar864.md, samples/argon/argonNVT.in, |
868 |
samples/argon/argonNVT.md, samples/argon/lj.md, |
869 |
samples/lipid/5x5.in, samples/lipid/5x5.md, |
870 |
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
871 |
samples/lipid/water.md, samples/minimizer/Makefile.in, |
872 |
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
873 |
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, |
874 |
samples/minimizer/tip4p_two.md, samples/minimizer/water.md, |
875 |
samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, |
876 |
forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, |
877 |
forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, |
878 |
forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, |
879 |
forceFields/DUFF.frc, forceFields/DipoleTest.frc, |
880 |
forceFields/EAM.VC.frc, forceFields/EAM.frc, |
881 |
forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, |
882 |
forceFields/Makefile.in, forceFields/Ni.u3.funcfl, |
883 |
forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, |
884 |
forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, |
885 |
forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, |
886 |
scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, |
887 |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
888 |
ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
889 |
ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, |
890 |
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
891 |
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
892 |
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
893 |
forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0 |
894 |
|
895 |
2004-09-23 23:16 gezelter |
896 |
|
897 |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
898 |
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
899 |
src/constraints/Makefile, src/constraints/ZConstraint.cpp, |
900 |
src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, |
901 |
src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, |
902 |
src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, |
903 |
src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, |
904 |
src/UseTheForce/fForceField.h, |
905 |
src/UseTheForce/fSwitchingFunction.h, |
906 |
src/UseTheForce/fortranWrapDefines.hpp, |
907 |
src/UseTheForce/fortranWrappers.cpp, |
908 |
src/UseTheForce/fortranWrappers.hpp, |
909 |
src/UseTheForce/mpiComponentPlan.h, |
910 |
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
911 |
src/UseTheForce/mpiSimulation_module.F90, |
912 |
src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, |
913 |
src/UseTheForce/DarkSide/atype_module.F90, |
914 |
src/UseTheForce/DarkSide/calc_LJ_FF.F90, |
915 |
src/UseTheForce/DarkSide/calc_charge_charge.F90, |
916 |
src/UseTheForce/DarkSide/calc_dipole_dipole.F90, |
917 |
src/UseTheForce/DarkSide/calc_eam.F90, |
918 |
src/UseTheForce/DarkSide/calc_gb.F90, |
919 |
src/UseTheForce/DarkSide/calc_reaction_field.F90, |
920 |
src/UseTheForce/DarkSide/calc_sticky_pair.F90, |
921 |
src/UseTheForce/DarkSide/force_globals.F90, |
922 |
src/UseTheForce/DarkSide/neighborLists.F90, |
923 |
src/UseTheForce/DarkSide/notifyCutoffs.F90, |
924 |
src/UseTheForce/DarkSide/switch_module.F90, |
925 |
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
926 |
src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, |
927 |
src/io/DumpWriter.cpp, src/io/Globals.cpp, |
928 |
src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, |
929 |
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
930 |
src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, |
931 |
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
932 |
src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, |
933 |
src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, |
934 |
src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, |
935 |
src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, |
936 |
src/types/AtomStamp.hpp, src/types/BendStamp.cpp, |
937 |
src/types/BendStamp.hpp, src/types/BondStamp.cpp, |
938 |
src/types/BondStamp.hpp, src/types/Component.cpp, |
939 |
src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, |
940 |
src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, |
941 |
src/types/MakeStamps.hpp, src/types/Makefile, |
942 |
src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, |
943 |
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
944 |
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
945 |
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
946 |
src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, |
947 |
src/brains/Exclude.hpp, src/brains/ForceFields.cpp, |
948 |
src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, |
949 |
src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, |
950 |
src/brains/SimSetup.hpp, src/brains/SimState.cpp, |
951 |
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
952 |
src/brains/SkipList.hpp, src/brains/Thermo.cpp, |
953 |
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
954 |
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
955 |
src/brains/simulation_module.F90, src/io/BASS_interface.cpp, |
956 |
src/io/Globals.hpp, src/io/LinkedAssign.cpp, |
957 |
src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, |
958 |
src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, |
959 |
src/math/mt19937ar.c, src/math/randomSPRNG.cpp, |
960 |
src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, |
961 |
src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, |
962 |
src/minimizers/OOPSEMinimizer.cpp, |
963 |
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
964 |
src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, |
965 |
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
966 |
src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, |
967 |
src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, |
968 |
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
969 |
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
970 |
src/primitives/Makefile, src/primitives/Molecule.cpp, |
971 |
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
972 |
src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, |
973 |
src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, |
974 |
src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, |
975 |
src/restraints/Makefile, src/restraints/Restraints.cpp, |
976 |
src/restraints/Restraints.hpp, src/utils/GenericData.cpp, |
977 |
src/utils/GenericData.hpp, src/utils/Makefile, |
978 |
src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, |
979 |
src/utils/StringUtils.c, src/utils/StringUtils.cpp, |
980 |
src/utils/StringUtils.h, src/utils/StringUtils.hpp, |
981 |
src/utils/TypeInfo.hpp, src/utils/Utility.cpp, |
982 |
src/utils/Utility.hpp, src/utils/definitions_module.F90, |
983 |
src/utils/fError.c, src/utils/oopseMPI_module.F90, |
984 |
src/utils/simError.c, src/utils/simError.h, |
985 |
src/utils/status_module.F90, src/utils/vector_class.F90, |
986 |
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
987 |
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
988 |
src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, |
989 |
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
990 |
src/visitors/RigidBodyVisitor.cpp, |
991 |
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
992 |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
993 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
994 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
995 |
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
996 |
samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, |
997 |
samples/zcons/Makefile.in, samples/zcons/water.md, |
998 |
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
999 |
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
1000 |
src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, |
1001 |
src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, |
1002 |
src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, |
1003 |
src/applications/Lattice.cpp, src/applications/Lattice.hpp, |
1004 |
src/applications/LatticeCreator.cpp, |
1005 |
src/applications/LatticeCreator.hpp, |
1006 |
src/applications/LatticeFactory.cpp, |
1007 |
src/applications/LatticeFactory.hpp, src/applications/Makedepend, |
1008 |
src/applications/Makefile, src/applications/MoLocator.cpp, |
1009 |
src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, |
1010 |
src/applications/cmdline.c, src/applications/cmdline.h, |
1011 |
src/applications/getopt.c, src/applications/getopt1.c, |
1012 |
src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, |
1013 |
src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, |
1014 |
src/applications/quickLate.c, src/applications/simpleBuilder.cpp, |
1015 |
src/applications/simpleBuilder.ggo, |
1016 |
src/applications/simpleBuilderCmd.c, |
1017 |
src/integrators/AbstractClasses.hpp, |
1018 |
src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, |
1019 |
src/integrators/Integrator.hpp, src/integrators/Makefile, |
1020 |
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
1021 |
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
1022 |
src/integrators/NVT.cpp, src/profiling/Makefile, |
1023 |
src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, |
1024 |
src/profiling/timing.F90, samples/metals/Au_bulk.in, |
1025 |
samples/metals/Au_nanoparticle.in, samples/metals/metals.md, |
1026 |
samples/water/Makefile.in, samples/water/dimer/Makefile.in, |
1027 |
samples/water/dimer/two.in, samples/water/dimer/two.md, |
1028 |
samples/water/dimer/water.md, samples/water/spce/Makefile.in, |
1029 |
samples/water/spce/spce.in, samples/water/spce/spce.md, |
1030 |
samples/water/spce/water.md, samples/water/ssde/Makefile.in, |
1031 |
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
1032 |
samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, |
1033 |
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
1034 |
samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, |
1035 |
samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, |
1036 |
samples/water/ssd/water.md, samples/water/tip4p/tp4.in, |
1037 |
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
1038 |
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
1039 |
samples/alkane/butane.in, samples/alkane/butane.md, |
1040 |
samples/argon/500.in, samples/argon/500.md, |
1041 |
samples/argon/Makefile.in, samples/argon/ar864.in, |
1042 |
samples/argon/ar864.md, samples/argon/argonNVT.in, |
1043 |
samples/argon/argonNVT.md, samples/argon/lj.md, |
1044 |
samples/lipid/5x5.in, samples/lipid/5x5.md, |
1045 |
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
1046 |
samples/lipid/water.md, samples/minimizer/Makefile.in, |
1047 |
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
1048 |
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, |
1049 |
samples/minimizer/tip4p_two.md, samples/minimizer/water.md, |
1050 |
samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, |
1051 |
forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, |
1052 |
forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, |
1053 |
forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, |
1054 |
forceFields/DUFF.frc, forceFields/DipoleTest.frc, |
1055 |
forceFields/EAM.VC.frc, forceFields/EAM.frc, |
1056 |
forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, |
1057 |
forceFields/Makefile.in, forceFields/Ni.u3.funcfl, |
1058 |
forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, |
1059 |
forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, |
1060 |
forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, |
1061 |
scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, |
1062 |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
1063 |
ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
1064 |
ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, |
1065 |
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
1066 |
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
1067 |
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
1068 |
forceFields/Pt.VC.funcfl: Initial revision |
1069 |
|