| 1 |
+ |
2003-09-10 16:28 mmeineke |
| 2 |
+ |
|
| 3 |
+ |
* props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added more |
| 4 |
+ |
work on getting gofR working. |
| 5 |
+ |
|
| 6 |
+ |
2003-09-09 16:50 mmeineke |
| 7 |
+ |
|
| 8 |
+ |
* props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added the |
| 9 |
+ |
beginings of the GofR pair correlation. |
| 10 |
+ |
|
| 11 |
+ |
added identification of identI in matchI. |
| 12 |
+ |
|
| 13 |
+ |
2003-09-09 15:35 mmeineke |
| 14 |
+ |
|
| 15 |
+ |
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTxym.cpp, |
| 16 |
+ |
NPTzm.cpp, Thermo.cpp, Thermo.hpp: updated the ChangeLog |
| 17 |
+ |
|
| 18 |
+ |
added two new NPT integrators, they still need work. |
| 19 |
+ |
|
| 20 |
+ |
2003-09-09 15:34 mmeineke |
| 21 |
+ |
|
| 22 |
+ |
* ChangeLog: updated the ChangeLog |
| 23 |
+ |
|
| 24 |
+ |
2003-09-05 17:45 gezelter |
| 25 |
+ |
|
| 26 |
+ |
* libmdtools/Make.dep: dependency on config.h |
| 27 |
+ |
|
| 28 |
+ |
2003-09-05 17:36 gezelter |
| 29 |
+ |
|
| 30 |
+ |
* configure, ac-tools/aclocal.m4: fixed sprng problem |
| 31 |
+ |
|
| 32 |
+ |
2003-09-05 16:29 gezelter |
| 33 |
+ |
|
| 34 |
+ |
* samples/metals/Makefile.in: New Makefile for metals sample |
| 35 |
+ |
|
| 36 |
+ |
2003-09-05 16:27 gezelter |
| 37 |
+ |
|
| 38 |
+ |
* Makefile, Makefile.in, ac-tools/aclocal.m4, |
| 39 |
+ |
ac-tools/configure.in, ac-tools/fortran90.m4, forceFields/Makefile, |
| 40 |
+ |
forceFields/Makefile.in, libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 41 |
+ |
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile, |
| 42 |
+ |
libBASS/Makefile.in, libmdtools/Integrator.hpp, |
| 43 |
+ |
libmdtools/Linux_ifc_machdep.F90, libmdtools/Make.dep, |
| 44 |
+ |
libmdtools/Makefile, libmdtools/Makefile.in, |
| 45 |
+ |
libmdtools/calc_eam.F90, libmdtools/config.h.in, |
| 46 |
+ |
libmdtools/definitions_module.F90, libmdtools/fInfo.c, |
| 47 |
+ |
libmdtools/fortranWrappers.cpp, |
| 48 |
+ |
libmdtools/mpiSimulation_module.F90, libmdtools/neighborLists.F90, |
| 49 |
+ |
libmdtools/simulation_module.F90, samples/Makefile, |
| 50 |
+ |
samples/Makefile.in, samples/alkane/Makefile, |
| 51 |
+ |
samples/alkane/Makefile.in, samples/argon/Makefile, |
| 52 |
+ |
samples/argon/Makefile.in, samples/argon/argon.bass, |
| 53 |
+ |
samples/beadLipid/Makefile, samples/beadLipid/Makefile.in, |
| 54 |
+ |
samples/lipid/Makefile, samples/lipid/Makefile.in, |
| 55 |
+ |
samples/water/Makefile, samples/water/Makefile.in, src/Makefile, |
| 56 |
+ |
src/Makefile.in, utils/Makefile, utils/Makefile.in, |
| 57 |
+ |
utils/sysbuilder/Makefile, utils/sysbuilder/Makefile.in: Changes to |
| 58 |
+ |
autoconf / configure method of configuring OOPSE |
| 59 |
+ |
|
| 60 |
+ |
2003-09-04 16:48 mmeineke |
| 61 |
+ |
|
| 62 |
+ |
* libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
| 63 |
+ |
libmdtools/Makefile, libmdtools/NPTf.cpp, libmdtools/NPTfm.cpp, |
| 64 |
+ |
libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, libmdtools/NVT.cpp, |
| 65 |
+ |
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, src/Makefile: |
| 66 |
+ |
added resetTime to the Global namespace. |
| 67 |
+ |
|
| 68 |
+ |
added ability to reset the integrators in the NVT and NPT family. |
| 69 |
+ |
|
| 70 |
+ |
2003-09-04 16:48 mmeineke |
| 71 |
+ |
|
| 72 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: added resetTime to the Global |
| 73 |
+ |
namespace. |
| 74 |
+ |
|
| 75 |
+ |
2003-09-02 09:30 tim |
| 76 |
+ |
|
| 77 |
+ |
* libmdtools/: Integrator.hpp, Makefile, SimSetup.cpp, |
| 78 |
+ |
ZConsWriter.cpp, ZConstraint.cpp: fix a bug at MPI version of |
| 79 |
+ |
PolicyByMass |
| 80 |
+ |
|
| 81 |
+ |
2003-08-28 16:09 tim |
| 82 |
+ |
|
| 83 |
+ |
* ChangeLog, libmdtools/GenericData.cpp, |
| 84 |
+ |
libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp, |
| 85 |
+ |
libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex |
| 86 |
+ |
|
| 87 |
+ |
2003-08-28 11:59 mmeineke |
| 88 |
+ |
|
| 89 |
+ |
* props/: PairCorrType.cpp, PairCorrType.hpp, staticProps.cpp: |
| 90 |
+ |
added the first functional parts of the PairCorrType Abstract |
| 91 |
+ |
classes. |
| 92 |
+ |
|
| 93 |
+ |
2003-08-27 14:23 tim |
| 94 |
+ |
|
| 95 |
+ |
* libmdtools/: Integrator.cpp, SimSetup.cpp, ZConstraint.cpp: fix |
| 96 |
+ |
bug of MPI_Allreduce in ZConstraint, the MPITYPE is set to |
| 97 |
+ |
MPI_DOUBLE, however, the corret type is MPI_INT. Therefore, when we |
| 98 |
+ |
turn on the optimization flag, it causes a seg fault |
| 99 |
+ |
|
| 100 |
+ |
2003-08-27 11:25 gezelter |
| 101 |
+ |
|
| 102 |
+ |
* libmdtools/: calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, |
| 103 |
+ |
calc_reaction_field.F90, calc_sticky_pair.F90: More fixes for |
| 104 |
+ |
stress tensor parallel bug. |
| 105 |
+ |
|
| 106 |
+ |
2003-08-27 11:16 tim |
| 107 |
+ |
|
| 108 |
+ |
* ChangeLog, libmdtools/DUFF.cpp, |
| 109 |
+ |
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90: |
| 110 |
+ |
fix bug in calc_dipole_dipole.F90 and calc_stikcy_pair.F90 |
| 111 |
+ |
molMembershipList use global index instead of local index |
| 112 |
+ |
|
| 113 |
+ |
2003-08-26 15:37 tim |
| 114 |
+ |
|
| 115 |
+ |
* libmdtools/: Integrator.cpp, ZConstraint.cpp, do_Forces.F90, |
| 116 |
+ |
mpiSimulation.cpp: set default force substraction policy to |
| 117 |
+ |
PolicyByMass |
| 118 |
+ |
|
| 119 |
+ |
2003-08-26 15:29 tim |
| 120 |
+ |
|
| 121 |
+ |
* libmdtools/Integrator.cpp: [no log message] |
| 122 |
+ |
|
| 123 |
+ |
2003-08-26 15:13 mmeineke |
| 124 |
+ |
|
| 125 |
+ |
* utils/sysbuilder/bilayerSys.cpp: added define statemewnt to |
| 126 |
+ |
Statwriter and Dumpwriter to handle files larger than 2 gb. |
| 127 |
+ |
|
| 128 |
+ |
commented out some print statements in Zconstraint |
| 129 |
+ |
|
| 130 |
+ |
hard coding some system init into bilayer.sys |
| 131 |
+ |
|
| 132 |
+ |
2003-08-26 15:12 mmeineke |
| 133 |
+ |
|
| 134 |
+ |
* libmdtools/: DumpWriter.cpp, StatWriter.cpp, ZConstraint.cpp: |
| 135 |
+ |
added define statemewnt to Statwriter and Dumpwriter to handle |
| 136 |
+ |
files larger than 2 gb. |
| 137 |
+ |
|
| 138 |
+ |
commented out some print statements in Zconstraint |
| 139 |
+ |
|
| 140 |
+ |
2003-08-26 15:02 tim |
| 141 |
+ |
|
| 142 |
+ |
* libmdtools/SimSetup.cpp: Use make_sprng_seed() to generate seed |
| 143 |
+ |
and check the seed which is specified by user at least contains 9 |
| 144 |
+ |
digits |
| 145 |
+ |
|
| 146 |
+ |
2003-08-26 13:32 mmeineke |
| 147 |
+ |
|
| 148 |
+ |
* libmdtools/DUFF.cpp: changed the Makefiel a litle. |
| 149 |
+ |
|
| 150 |
+ |
Fixed a bug in MPI_DUFF. The atom block type was not being properly |
| 151 |
+ |
constucted in MPI. (The MPI struct had 6 doubles declared versus |
| 152 |
+ |
the actual 11) |
| 153 |
+ |
|
| 154 |
+ |
2003-08-26 13:30 mmeineke |
| 155 |
+ |
|
| 156 |
+ |
* Makefile: changed the Makefiel a litle. |
| 157 |
+ |
|
| 158 |
+ |
2003-08-25 17:17 gezelter |
| 159 |
+ |
|
| 160 |
+ |
* utils/sysbuilder/Makefile: More FreeBSD fixes |
| 161 |
+ |
|
| 162 |
+ |
2003-08-25 16:51 gezelter |
| 163 |
+ |
|
| 164 |
+ |
* libBASS/BASSlex.l, libBASS/Makefile, libmdtools/Integrator.hpp, |
| 165 |
+ |
libmdtools/Makefile, src/Makefile: [no log message] |
| 166 |
+ |
|
| 167 |
+ |
2003-08-22 15:04 mmeineke |
| 168 |
+ |
|
| 169 |
+ |
* libmdtools/: Integrator.cpp, ZConstraint.cpp: small bug fix on |
| 170 |
+ |
frequency of output dumps. |
| 171 |
+ |
|
| 172 |
+ |
2003-08-20 17:23 tim |
| 173 |
+ |
|
| 174 |
+ |
* libBASS/Globals.hpp, libmdtools/SimInfo.hpp, |
| 175 |
+ |
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
| 176 |
+ |
libmdtools/mpiSimulation.cpp: user can setup seed in bass file now, |
| 177 |
+ |
if he does not specify any value for seed, oopse will take the |
| 178 |
+ |
value of seconds of system time as seed |
| 179 |
+ |
|
| 180 |
+ |
2003-08-20 14:42 mmeineke |
| 181 |
+ |
|
| 182 |
+ |
* libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
| 183 |
+ |
libmdtools/GhostBend.cpp, libmdtools/SRI.hpp, |
| 184 |
+ |
libmdtools/SimSetup.cpp, libmdtools/SimState.cpp, |
| 185 |
+ |
utils/sysbuilder/bilayerSys.cpp: updated the Changelog. |
| 186 |
+ |
|
| 187 |
+ |
added some bug fixes for setting the random number generator seed |
| 188 |
+ |
value. |
| 189 |
+ |
|
| 190 |
+ |
fixed a bug where ghostbend atom b was not being set. ( recent bug |
| 191 |
+ |
from SimState conversion) |
| 192 |
+ |
|
| 193 |
+ |
2003-08-20 14:41 mmeineke |
| 194 |
+ |
|
| 195 |
+ |
* libBASS/Globals.hpp: updated the Changelog. |
| 196 |
+ |
|
| 197 |
+ |
added some bug fixes for setting the random number generator seed |
| 198 |
+ |
value. |
| 199 |
+ |
|
| 200 |
+ |
2003-08-20 14:41 mmeineke |
| 201 |
+ |
|
| 202 |
+ |
* ChangeLog: updated the Changelog. |
| 203 |
+ |
|
| 204 |
+ |
2003-08-20 14:11 tim |
| 205 |
+ |
|
| 206 |
+ |
* libBASS/Globals.cpp, libmdtools/DUFF.cpp, |
| 207 |
+ |
libmdtools/GhostBend.cpp, libmdtools/SRI.hpp: bug fixed in ghost |
| 208 |
+ |
bend class |
| 209 |
+ |
|
| 210 |
+ |
2003-08-20 10:13 mmeineke |
| 211 |
+ |
|
| 212 |
+ |
* utils/: Makefile, sysbuilder/Makefile: quick makefile fix, in |
| 213 |
+ |
make links. added -f to ln -s. |
| 214 |
+ |
|
| 215 |
+ |
2003-08-20 09:50 tim |
| 216 |
+ |
|
| 217 |
+ |
* libmdtools/: ZConsWriter.cpp, ZConstraint.cpp: [no log message] |
| 218 |
+ |
|
| 219 |
+ |
2003-08-20 09:34 tim |
| 220 |
+ |
|
| 221 |
+ |
* libmdtools/: Integrator.hpp, SimSetup.cpp, ZConsWriter.cpp, |
| 222 |
+ |
ZConstraint.cpp: reformmating ZConstraint and fixe bug of error msg |
| 223 |
+ |
printing |
| 224 |
+ |
|
| 225 |
|
2003-08-18 15:59 chuckv |
| 226 |
|
|
| 227 |
|
* utils/sysbuilder/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
| 1563 |
|
|
| 1564 |
|
2003-03-24 20:07 gezelter |
| 1565 |
|
|
| 1566 |
< |
* samples/Makefile: moving tests to samples |
| 1566 |
> |
* samples/Makefile, tests/Makefile: moving tests to samples |
| 1567 |
|
|
| 1568 |
|
2003-03-24 20:06 gezelter |
| 1569 |
|
|
| 1570 |
< |
* samples/: alkane/Makefile, alkane/alkanes.mdl, |
| 1571 |
< |
alkane/butane.bass, alkane/init_butane.eor, argon/Makefile, |
| 1572 |
< |
argon/argon.bass, argon/init_argon.eor, argon/lj.mdl, |
| 1573 |
< |
lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor, |
| 1574 |
< |
lipid/lipid.mdl, lipid/water.mdl, water/Makefile, |
| 1575 |
< |
water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to |
| 1576 |
< |
samples |
| 1570 |
> |
* samples/alkane/Makefile, samples/alkane/alkanes.mdl, |
| 1571 |
> |
samples/alkane/butane.bass, samples/alkane/init_butane.eor, |
| 1572 |
> |
samples/argon/Makefile, samples/argon/argon.bass, |
| 1573 |
> |
samples/argon/init_argon.eor, samples/argon/lj.mdl, |
| 1574 |
> |
samples/lipid/5x5.bass, samples/lipid/Makefile, |
| 1575 |
> |
samples/lipid/init_5x5.eor, samples/lipid/lipid.mdl, |
| 1576 |
> |
samples/lipid/water.mdl, samples/water/Makefile, |
| 1577 |
> |
samples/water/init_ssd.eor, samples/water/ssd.bass, |
| 1578 |
> |
samples/water/water.mdl, tests/alkane/Makefile, |
| 1579 |
> |
tests/alkane/alkanes.mdl, tests/alkane/butane.bass, |
| 1580 |
> |
tests/alkane/init_butane.eor, tests/argon/Makefile, |
| 1581 |
> |
tests/argon/argon.bass, tests/argon/init_argon.eor, |
| 1582 |
> |
tests/argon/lj.mdl, tests/lipid/5x5.bass, tests/lipid/Makefile, |
| 1583 |
> |
tests/lipid/init_5x5.eor, tests/lipid/lipid.mdl, |
| 1584 |
> |
tests/lipid/water.mdl, tests/water/Makefile, |
| 1585 |
> |
tests/water/init_ssd.eor, tests/water/ssd.bass, |
| 1586 |
> |
tests/water/water.mdl: moved tests to samples |
| 1587 |
|
|
| 1588 |
|
2003-03-24 19:51 gezelter |
| 1589 |
|
|
| 1591 |
|
|
| 1592 |
|
2003-03-24 19:46 gezelter |
| 1593 |
|
|
| 1594 |
< |
* ac-tools/Make.conf.in: Added makefiles in tests directories |
| 1594 |
> |
* ac-tools/Make.conf.in, tests/Makefile, tests/alkane/Makefile, |
| 1595 |
> |
tests/argon/Makefile, tests/lipid/Makefile, tests/water/Makefile: |
| 1596 |
> |
Added makefiles in tests directories |
| 1597 |
|
|
| 1598 |
|
2003-03-24 16:55 gezelter |
| 1599 |
|
|
| 1610 |
|
* libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp, |
| 1611 |
|
do_Forces.F90: little bug fixes here and there |
| 1612 |
|
|
| 1613 |
+ |
2003-03-24 11:04 mmeineke |
| 1614 |
+ |
|
| 1615 |
+ |
* tests/argon/: argon.bass, init_argon.eor, lj.mdl: added an argon |
| 1616 |
+ |
test simulation |
| 1617 |
+ |
|
| 1618 |
+ |
2003-03-24 11:02 mmeineke |
| 1619 |
+ |
|
| 1620 |
+ |
* tests/: lipid/5x5.bass, lipid/init_5x5.eor, lipid/lipid.mdl, |
| 1621 |
+ |
lipid/water.mdl, water/init_ssd.eor, water/ssd.bass, |
| 1622 |
+ |
water/water.mdl: [no log message] |
| 1623 |
+ |
|
| 1624 |
+ |
2003-03-24 11:02 mmeineke |
| 1625 |
+ |
|
| 1626 |
+ |
* tests/alkane/: alkanes.mdl, butane.bass, init_butane.eor: added |
| 1627 |
+ |
some test bass files for experimenting with |
| 1628 |
+ |
|
| 1629 |
|
2003-03-24 10:26 mmeineke |
| 1630 |
|
|
| 1631 |
|
* libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug |
| 1735 |
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
| 1736 |
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
| 1737 |
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
| 1738 |
< |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE |
| 1739 |
< |
Tree |
| 1738 |
> |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial |
| 1739 |
> |
revision |
| 1740 |
|
|
| 1741 |
|
2003-03-21 12:42 mmeineke |
| 1742 |
|
|
| 1793 |
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
| 1794 |
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
| 1795 |
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
| 1796 |
< |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial |
| 1797 |
< |
revision |
| 1796 |
> |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE |
| 1797 |
> |
Tree |
| 1798 |
|
|
