1 |
+ |
2004-01-09 21:15 tim |
2 |
+ |
|
3 |
+ |
* libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub |
4 |
+ |
|
5 |
+ |
2004-01-09 15:29 gezelter |
6 |
+ |
|
7 |
+ |
* libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4) |
8 |
+ |
|
9 |
+ |
2004-01-08 17:25 chuckv |
10 |
+ |
|
11 |
+ |
* libmdtools/DumpWriter.cpp: A work in progress... |
12 |
+ |
|
13 |
+ |
2004-01-08 13:59 gezelter |
14 |
+ |
|
15 |
+ |
* libmdtools/DumpWriter.cpp: null terminate some strings just in |
16 |
+ |
case |
17 |
+ |
|
18 |
+ |
2004-01-08 13:13 mmeineke |
19 |
+ |
|
20 |
+ |
* libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS |
21 |
+ |
state bug. |
22 |
+ |
|
23 |
+ |
2004-01-08 13:05 gezelter |
24 |
+ |
|
25 |
+ |
* libmdtools/DumpWriter.cpp: added strncpy to DumpWriter |
26 |
+ |
|
27 |
+ |
2004-01-08 12:57 mmeineke |
28 |
+ |
|
29 |
+ |
* libmdtools/InitializeFromFile.cpp: fixed the restart from NVT |
30 |
+ |
exstended state bug |
31 |
+ |
|
32 |
+ |
2004-01-08 12:40 gezelter |
33 |
+ |
|
34 |
+ |
* libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter |
35 |
+ |
|
36 |
+ |
2004-01-08 10:44 mmeineke |
37 |
+ |
|
38 |
+ |
* libmdtools/InitializeFromFile.cpp: added support for the ignore |
39 |
+ |
XS state info flag |
40 |
+ |
|
41 |
+ |
2004-01-07 14:26 tim |
42 |
+ |
|
43 |
+ |
* libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp, |
44 |
+ |
samples/argon/argon.bass, samples/water/ssd.bass: Fixed a bug of |
45 |
+ |
sending message from master node to itself in DumpWriter.cpp and |
46 |
+ |
InitializeFromFile.cpp |
47 |
+ |
|
48 |
+ |
2004-01-06 14:49 chuckv |
49 |
+ |
|
50 |
+ |
* libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90: |
51 |
+ |
performance fixes in the dipole dipole and reaction field code |
52 |
+ |
|
53 |
+ |
2004-01-06 13:54 chuckv |
54 |
+ |
|
55 |
+ |
* libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a |
56 |
+ |
little more sane |
57 |
+ |
|
58 |
+ |
2004-01-05 17:49 chuckv |
59 |
+ |
|
60 |
+ |
* libmdtools/: calc_LJ_FF.F90, calc_dipole_dipole.F90, |
61 |
+ |
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
62 |
+ |
calc_sticky_pair.F90, do_Forces.F90: Attempting to increase |
63 |
+ |
performance by reducing spurious function calls |
64 |
+ |
|
65 |
+ |
2004-01-05 17:18 chuckv |
66 |
+ |
|
67 |
+ |
* libmdtools/do_Forces.F90: mangling forces even further |
68 |
+ |
|
69 |
+ |
2004-01-05 17:18 chuckv |
70 |
+ |
|
71 |
+ |
* configure, ac-tools/configure.in: mpich mucking |
72 |
+ |
|
73 |
+ |
2004-01-05 17:12 chuckv |
74 |
+ |
|
75 |
+ |
* libmdtools/do_Forces.F90: mangled do_forces... |
76 |
+ |
|
77 |
+ |
2004-01-05 16:00 chuckv |
78 |
+ |
|
79 |
+ |
* ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90, |
80 |
+ |
libmdtools/do_Forces.F90: Added bitmask to do_forces property |
81 |
+ |
lookup |
82 |
+ |
|
83 |
|
2003-12-29 14:56 chuckv |
84 |
|
|
85 |
|
* samples/metals/Au.bass, third-party/mt19937ar.c: Added |
438 |
|
* configure, ac-tools/configure.in, samples/water/ssd.bass, |
439 |
|
utils/sysbuilder/sysBuild.cpp: fixes for configure, sysBuild |
440 |
|
|
441 |
< |
2003-10-24 17:17 mmeineke |
441 |
> |
2003-10-24 18:17 mmeineke |
442 |
|
|
443 |
|
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
444 |
|
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, bilayerSys.cpp, |
447 |
|
overhauled latticeBilayer into its own program. Removed sysBuild |
448 |
|
from the Makefile |
449 |
|
|
450 |
< |
2003-10-24 12:36 gezelter |
450 |
> |
2003-10-24 13:36 gezelter |
451 |
|
|
452 |
|
* utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp, |
453 |
|
latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer |
454 |
|
builder |
455 |
|
|
456 |
< |
2003-10-24 12:35 gezelter |
456 |
> |
2003-10-24 13:35 gezelter |
457 |
|
|
458 |
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a |
459 |
|
merge problem |
460 |
|
|
461 |
< |
2003-10-23 14:57 mmeineke |
461 |
> |
2003-10-23 15:57 mmeineke |
462 |
|
|
463 |
|
* samples/metals/Makefile.in: added eam ForceField files to the |
464 |
|
init |
467 |
|
|
468 |
|
added the init file to the makefile |
469 |
|
|
470 |
< |
2003-10-23 14:57 mmeineke |
470 |
> |
2003-10-23 15:57 mmeineke |
471 |
|
|
472 |
|
* libmdtools/: EAM_FF.cpp, SimSetup.cpp: added eam ForceField files |
473 |
|
to the init |
474 |
|
|
475 |
|
fixed an eam mpi parmeter setup bug |
476 |
|
|
477 |
< |
2003-10-23 14:57 mmeineke |
477 |
> |
2003-10-23 15:57 mmeineke |
478 |
|
|
479 |
|
* forceFields/Makefile.in: added eam ForceField files to the init |
480 |
|
|
481 |
< |
2003-10-22 16:17 mmeineke |
481 |
> |
2003-10-22 17:17 mmeineke |
482 |
|
|
483 |
|
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Makefile.in, |
484 |
|
NPTxym.cpp, NPTxyz.cpp, NPTzm.cpp, SimSetup.cpp: added a new NPT |
485 |
|
integrator, NPTxyz. It scales the x, y, and z direction sepeartely. |
486 |
|
no box skew allowed. |
487 |
|
|
488 |
< |
2003-10-21 14:33 mmeineke |
488 |
> |
2003-10-21 15:33 mmeineke |
489 |
|
|
490 |
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
491 |
|
libmdtools/SimSetup.cpp, staticProps/GofRtheta.cpp, |
494 |
|
of the time stamp in the .init file * default=> useInitTime = |
495 |
|
true; |
496 |
|
|
497 |
< |
2003-10-17 16:19 mmeineke |
497 |
> |
2003-10-17 17:19 mmeineke |
498 |
|
|
499 |
|
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, GofR.cpp, |
500 |
|
Makefile.in, PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
504 |
|
fixed a number of bugs in the staticProps code. gofr is now |
505 |
|
working. |
506 |
|
|
507 |
< |
2003-10-17 16:18 mmeineke |
507 |
> |
2003-10-17 17:18 mmeineke |
508 |
|
|
509 |
|
* ac-tools/configure.in: added the staticProps directory to the |
510 |
|
build list for both configure and configure.in |
511 |
|
|
512 |
< |
2003-10-17 16:17 mmeineke |
512 |
> |
2003-10-17 17:17 mmeineke |
513 |
|
|
514 |
|
* configure: added the staticProps directory to the build list |
515 |
|
|
516 |
< |
2003-10-16 14:16 mmeineke |
516 |
> |
2003-10-16 15:16 mmeineke |
517 |
|
|
518 |
|
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, Exclude.cpp, |
519 |
|
Integrator.cpp, Makefile.in, ReadWrite.hpp: Changed DumpReader to |
527 |
|
a frame is written. This lets the .eor file represent the last |
528 |
|
written frame of a simulation. |
529 |
|
|
530 |
< |
2003-10-10 12:10 mmeineke |
530 |
> |
2003-10-10 13:10 mmeineke |
531 |
|
|
532 |
< |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, |
533 |
< |
CorrWrap.hpp, GofR.cpp, Makefile.in, PairCorrList.cpp, |
534 |
< |
PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
535 |
< |
staticProps.cpp: removed the props directory, and moved everything |
536 |
< |
over to staticProps |
532 |
> |
* props/AllCorr.cpp, props/AllCorr.hpp, props/CorrWrap.cpp, |
533 |
> |
props/CorrWrap.hpp, props/GofR.cpp, props/PairCorrList.cpp, |
534 |
> |
props/PairCorrList.hpp, props/PairCorrType.cpp, |
535 |
> |
props/PairCorrType.hpp, props/staticProps.cpp, |
536 |
> |
staticProps/AllCorr.cpp, staticProps/AllCorr.hpp, |
537 |
> |
staticProps/CorrWrap.cpp, staticProps/CorrWrap.hpp, |
538 |
> |
staticProps/GofR.cpp, staticProps/Makefile.in, |
539 |
> |
staticProps/PairCorrList.cpp, staticProps/PairCorrList.hpp, |
540 |
> |
staticProps/PairCorrType.cpp, staticProps/PairCorrType.hpp, |
541 |
> |
staticProps/staticProps.cpp: removed the props directory, and moved |
542 |
> |
everything over to staticProps |
543 |
|
|
544 |
< |
2003-10-09 17:09 mmeineke |
544 |
> |
2003-10-09 18:09 mmeineke |
545 |
|
|
546 |
< |
* libmdtools/Atom.hpp: Contiuned work on staticProps. should be in |
546 |
> |
* libmdtools/Atom.hpp, props/AllCorr.cpp, props/AllCorr.hpp, |
547 |
> |
props/CorrWrap.cpp, props/CorrWrap.hpp, props/GofR.cpp, |
548 |
> |
props/PairCorrType.cpp, props/PairCorrType.hpp, |
549 |
> |
props/staticProps.cpp: Contiuned work on staticProps. should be in |
550 |
|
a position where it will compile and run first runs. |
551 |
|
|
552 |
< |
2003-10-04 13:46 chuckv |
552 |
> |
2003-10-04 14:46 chuckv |
553 |
|
|
554 |
|
* libmdtools/calc_eam.F90, libmdtools/do_Forces.F90, |
555 |
|
samples/metals/Au.bass: Fixed bug in calc_eam. |
556 |
|
|
557 |
< |
2003-10-04 13:08 chuckv |
557 |
> |
2003-10-04 14:08 chuckv |
558 |
|
|
559 |
|
* samples/metals/init_au.in: added Au init file for eam. |
560 |
|
|
561 |
< |
2003-10-03 17:11 mmeineke |
561 |
> |
2003-10-03 18:11 mmeineke |
562 |
|
|
563 |
|
* libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed |
564 |
|
entahlpy from the statwriter and thermo. |
565 |
|
|
566 |
< |
2003-10-03 17:02 mmeineke |
566 |
> |
2003-10-03 18:02 mmeineke |
567 |
|
|
568 |
+ |
* props/: AllCorr.cpp, AllCorr.hpp, PairCorrList.cpp, |
569 |
+ |
PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
570 |
+ |
staticProps.cpp: changed the formating ogf the error statements in |
571 |
+ |
simError |
572 |
+ |
|
573 |
+ |
added a function to get the maxCutoff |
574 |
+ |
|
575 |
+ |
near completion of the staticProps code. still needs the pair loop, |
576 |
+ |
and the loop to allocate and read each frame. |
577 |
+ |
|
578 |
+ |
2003-10-03 18:02 mmeineke |
579 |
+ |
|
580 |
|
* libmdtools/SimInfo.hpp: changed the formating ogf the error |
581 |
|
statements in simError |
582 |
|
|
583 |
|
added a function to get the maxCutoff |
584 |
|
|
585 |
< |
2003-10-03 17:01 mmeineke |
585 |
> |
2003-10-03 18:01 mmeineke |
586 |
|
|
587 |
|
* libBASS/simError.c: changed the formating ogf the error |
588 |
|
statements in simError |
589 |
|
|
590 |
< |
2003-09-30 11:00 mmeineke |
590 |
> |
2003-10-02 18:06 mmeineke |
591 |
|
|
592 |
+ |
* props/: AllCorr.cpp, AllCorr.hpp, PairCorrList.cpp, |
593 |
+ |
PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
594 |
+ |
staticProps.cpp: finishing up the constructs needed to get this |
595 |
+ |
program up and running |
596 |
+ |
|
597 |
+ |
2003-09-30 12:00 mmeineke |
598 |
+ |
|
599 |
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed |
600 |
|
f90Flags so they are no longer overwritten by the compiler. |
601 |
|
|
602 |
< |
2003-09-29 17:06 mmeineke |
602 |
> |
2003-09-29 18:06 mmeineke |
603 |
|
|
604 |
|
* libmdtools/fortranWrappers.cpp: added mpif90 mod check back same |
605 |
|
for conifig.in |
606 |
|
|
607 |
|
fixed wrappers to extern "C" |
608 |
|
|
609 |
< |
2003-09-29 17:06 mmeineke |
609 |
> |
2003-09-29 18:06 mmeineke |
610 |
|
|
611 |
|
* ac-tools/configure.in: added mpif90 mod check back same for |
612 |
|
conifig.in |
613 |
|
|
614 |
< |
2003-09-29 17:05 mmeineke |
614 |
> |
2003-09-29 18:05 mmeineke |
615 |
|
|
616 |
|
* configure: added mpif90 mod check back |
617 |
|
|
618 |
< |
2003-09-29 16:16 mmeineke |
618 |
> |
2003-09-29 17:16 mmeineke |
619 |
|
|
620 |
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
621 |
|
libBASS/BendStamp.cpp, libBASS/BondStamp.cpp, |
627 |
|
libmdtools/fortranWrappers.cpp: fixed a lot of warnings and errors |
628 |
|
found with SUN's SUNWspro.s1s7 |
629 |
|
|
630 |
< |
2003-09-29 12:38 mmeineke |
630 |
> |
2003-09-29 13:38 mmeineke |
631 |
|
|
632 |
|
* libmdtools/GenericData.hpp: light change in syntax. no |
633 |
|
signifigant change. |
634 |
|
|
635 |
< |
2003-09-25 16:17 mmeineke |
635 |
> |
2003-09-25 17:17 mmeineke |
636 |
|
|
637 |
|
* libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some |
638 |
|
additional remarks from icc -w3 (extra verbose output) |
639 |
|
|
640 |
< |
2003-09-25 14:27 mmeineke |
640 |
> |
2003-09-25 15:27 mmeineke |
641 |
|
|
642 |
|
* libBASS/parse_tree.c, libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
643 |
|
libmdtools/DirectionalAtom.cpp, libmdtools/DumpWriter.cpp, |
651 |
|
libmdtools/mpiSimulation.cpp, src/oopse.cpp: cleaned things with |
652 |
|
gcc -Wall and g++ -Wall |
653 |
|
|
654 |
< |
2003-09-25 13:54 gezelter |
654 |
> |
2003-09-25 14:54 gezelter |
655 |
|
|
656 |
|
* configure, ac-tools/configure.in: fixed a bug in configure |
657 |
|
|
658 |
< |
2003-09-25 11:42 gezelter |
658 |
> |
2003-09-25 12:42 gezelter |
659 |
|
|
660 |
|
* Makefile.in, configure, ac-tools/aclocal.m4, |
661 |
|
ac-tools/configure.in, libBASS/Makefile.in, libmdtools/Makefile.in, |
662 |
|
src/Makefile.in, utils/Makefile.in, utils/sysbuilder/Makefile.in: |
663 |
|
fixes for configure |
664 |
|
|
665 |
< |
2003-09-24 14:34 mmeineke |
665 |
> |
2003-09-24 15:34 mmeineke |
666 |
|
|
667 |
|
* libmdtools/Integrator.cpp: moved readyCheck in the integrator so |
668 |
|
that it is called before the first Statistics are written. |
669 |
|
|
670 |
< |
2003-09-23 15:36 gezelter |
670 |
> |
2003-09-23 16:36 gezelter |
671 |
|
|
672 |
|
* src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a |
673 |
|
bunch of Make.dep files to CVS |
674 |
|
|
675 |
< |
2003-09-23 15:34 mmeineke |
675 |
> |
2003-09-23 16:34 mmeineke |
676 |
|
|
677 |
|
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, |
678 |
|
SimSetup.cpp: Removed NPTfm from Integrator.hpp. |
679 |
|
|
680 |
|
Some small syntax cleaning in NPTfm and SimSetup |
681 |
|
|
682 |
< |
2003-09-22 18:07 tim |
682 |
> |
2003-09-22 19:07 tim |
683 |
|
|
684 |
|
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
685 |
|
SimInfo.hpp: fix bug in calculating maxCutoff |
686 |
|
|
687 |
< |
2003-09-22 16:23 mmeineke |
687 |
> |
2003-09-22 17:23 mmeineke |
688 |
|
|
689 |
|
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Make.dep, |
690 |
|
Makefile.in, NPT.cpp, NPTf.cpp, NPTfm.cpp, NPTim.cpp, SimSetup.cpp: |
692 |
|
|
693 |
|
Removed NPTfm and NPTim from cvs |
694 |
|
|
695 |
< |
2003-09-19 15:00 mmeineke |
695 |
> |
2003-09-19 16:00 mmeineke |
696 |
|
|
697 |
|
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
698 |
|
NPT.cpp, NPTf.cpp, NPTi.cpp, NVT.cpp, SimSetup.cpp: added NPT base |
699 |
|
class. NPTi is up to date. NPTf is not. |
700 |
|
|
701 |
< |
2003-09-19 11:03 mmeineke |
701 |
> |
2003-09-19 12:03 mmeineke |
702 |
|
|
703 |
|
* utils/Makefile.in, src/Makefile.in: removed mpi++ from the |
704 |
|
makefile |
705 |
|
|
706 |
< |
2003-09-19 11:01 gezelter |
706 |
> |
2003-09-19 12:01 gezelter |
707 |
|
|
708 |
|
* samples/water/ssd.bass: goofing off to test NPTf and NPTi |
709 |
|
|
710 |
< |
2003-09-19 11:01 gezelter |
710 |
> |
2003-09-19 12:01 gezelter |
711 |
|
|
712 |
|
* libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found |
713 |
|
(nearly) conserved quantities for both NPTi and NPTf |
714 |
|
|
715 |
< |
2003-09-19 10:20 mmeineke |
715 |
> |
2003-09-19 11:20 mmeineke |
716 |
|
|
717 |
|
* utils/Makefile.in: fixed a typo in the makefile. |
718 |
|
|
719 |
< |
2003-09-19 09:55 gezelter |
719 |
> |
2003-09-19 10:55 gezelter |
720 |
|
|
721 |
|
* libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp, |
722 |
|
samples/water/ssd.bass: [no log message] |
723 |
|
|
724 |
< |
2003-09-19 09:22 tim |
724 |
> |
2003-09-19 10:22 tim |
725 |
|
|
726 |
|
* libmdtools/: NPTi.cpp, NVT.cpp: [no log message] |
727 |
|
|
728 |
< |
2003-09-17 09:22 mmeineke |
728 |
> |
2003-09-17 10:22 mmeineke |
729 |
|
|
730 |
|
* libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now |
731 |
|
work with constraints. |
732 |
|
|
733 |
< |
2003-09-16 15:02 tim |
733 |
> |
2003-09-16 16:02 tim |
734 |
|
|
735 |
|
* libmdtools/: Integrator.hpp, NPTf.cpp, NPTfm.cpp, NPTi.cpp, |
736 |
|
SimInfo.cpp, SimInfo.hpp: fixed ecr grow in SimInfo |
739 |
|
|
740 |
|
NPTi appears very stable. |
741 |
|
|
742 |
< |
2003-09-15 11:52 tim |
742 |
> |
2003-09-15 12:52 tim |
743 |
|
|
744 |
|
* libmdtools/AbstractClasses.hpp, libmdtools/Integrator.cpp, |
745 |
|
libmdtools/Integrator.hpp, libmdtools/NPTf.cpp, |
750 |
|
utils/sysbuilder/bilayerSys.cpp: add conserved quantity to |
751 |
|
statWriter fix bug of vector wrapping at NPTi |
752 |
|
|
753 |
< |
2003-09-12 11:20 gezelter |
753 |
> |
2003-09-12 16:51 mmeineke |
754 |
|
|
755 |
+ |
* props/: AllCorr.cpp, AllCorr.hpp, GofR.cpp, PairCorrType.cpp, |
756 |
+ |
PairCorrType.hpp: added AllCorr. It eill still need some work |
757 |
+ |
|
758 |
+ |
2003-09-12 12:20 gezelter |
759 |
+ |
|
760 |
|
* libmdtools/: Make.dep, Makefile.in: Added integrators to |
761 |
|
Makefile.in |
762 |
|
|
763 |
< |
2003-09-12 11:20 gezelter |
763 |
> |
2003-09-12 12:20 gezelter |
764 |
|
|
765 |
|
* ChangeLog: Entered changes for configure into ChangeLog |
766 |
|
|
767 |
< |
2003-09-09 15:35 mmeineke |
767 |
> |
2003-09-10 17:28 mmeineke |
768 |
|
|
769 |
+ |
* props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added more |
770 |
+ |
work on getting gofR working. |
771 |
+ |
|
772 |
+ |
2003-09-09 17:50 mmeineke |
773 |
+ |
|
774 |
+ |
* props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added the |
775 |
+ |
beginings of the GofR pair correlation. |
776 |
+ |
|
777 |
+ |
added identification of identI in matchI. |
778 |
+ |
|
779 |
+ |
2003-09-09 16:35 mmeineke |
780 |
+ |
|
781 |
|
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTxym.cpp, |
782 |
|
NPTzm.cpp, Thermo.cpp, Thermo.hpp: updated the ChangeLog |
783 |
|
|
784 |
|
added two new NPT integrators, they still need work. |
785 |
|
|
786 |
< |
2003-09-09 15:34 mmeineke |
786 |
> |
2003-09-09 16:34 mmeineke |
787 |
|
|
788 |
|
* ChangeLog: updated the ChangeLog |
789 |
|
|
790 |
< |
2003-09-05 17:45 gezelter |
790 |
> |
2003-09-05 18:45 gezelter |
791 |
|
|
792 |
|
* libmdtools/Make.dep: dependency on config.h |
793 |
|
|
794 |
< |
2003-09-05 17:36 gezelter |
794 |
> |
2003-09-05 18:36 gezelter |
795 |
|
|
796 |
|
* configure, ac-tools/aclocal.m4: fixed sprng problem |
797 |
|
|
798 |
< |
2003-09-05 16:29 gezelter |
798 |
> |
2003-09-05 17:29 gezelter |
799 |
|
|
800 |
|
* samples/metals/Makefile.in: New Makefile for metals sample |
801 |
|
|
802 |
< |
2003-09-05 16:27 gezelter |
802 |
> |
2003-09-05 17:27 gezelter |
803 |
|
|
804 |
|
* Makefile, Makefile.in, ac-tools/aclocal.m4, |
805 |
|
ac-tools/configure.in, ac-tools/fortran90.m4, forceFields/Makefile, |
823 |
|
utils/sysbuilder/Makefile, utils/sysbuilder/Makefile.in: Changes to |
824 |
|
autoconf / configure method of configuring OOPSE |
825 |
|
|
826 |
< |
2003-09-04 16:48 mmeineke |
826 |
> |
2003-09-04 17:48 mmeineke |
827 |
|
|
828 |
|
* libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
829 |
|
libmdtools/Makefile, libmdtools/NPTf.cpp, libmdtools/NPTfm.cpp, |
833 |
|
|
834 |
|
added ability to reset the integrators in the NVT and NPT family. |
835 |
|
|
836 |
< |
2003-09-04 16:48 mmeineke |
836 |
> |
2003-09-04 17:48 mmeineke |
837 |
|
|
838 |
|
* libBASS/: Globals.cpp, Globals.hpp: added resetTime to the Global |
839 |
|
namespace. |
840 |
|
|
841 |
< |
2003-09-02 09:30 tim |
841 |
> |
2003-09-02 10:30 tim |
842 |
|
|
843 |
|
* libmdtools/: Integrator.hpp, Makefile, SimSetup.cpp, |
844 |
|
ZConsWriter.cpp, ZConstraint.cpp: fix a bug at MPI version of |
845 |
|
PolicyByMass |
846 |
|
|
847 |
< |
2003-08-28 16:09 tim |
847 |
> |
2003-08-28 17:09 tim |
848 |
|
|
849 |
|
* ChangeLog, libmdtools/GenericData.cpp, |
850 |
|
libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp, |
851 |
|
libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex |
852 |
|
|
853 |
< |
2003-08-27 14:23 tim |
853 |
> |
2003-08-28 12:59 mmeineke |
854 |
|
|
855 |
+ |
* props/: PairCorrType.cpp, PairCorrType.hpp, staticProps.cpp: |
856 |
+ |
added the first functional parts of the PairCorrType Abstract |
857 |
+ |
classes. |
858 |
+ |
|
859 |
+ |
2003-08-27 15:23 tim |
860 |
+ |
|
861 |
|
* libmdtools/: Integrator.cpp, SimSetup.cpp, ZConstraint.cpp: fix |
862 |
|
bug of MPI_Allreduce in ZConstraint, the MPITYPE is set to |
863 |
|
MPI_DOUBLE, however, the corret type is MPI_INT. Therefore, when we |
864 |
|
turn on the optimization flag, it causes a seg fault |
865 |
|
|
866 |
< |
2003-08-27 11:25 gezelter |
866 |
> |
2003-08-27 12:25 gezelter |
867 |
|
|
868 |
|
* libmdtools/: calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, |
869 |
|
calc_reaction_field.F90, calc_sticky_pair.F90: More fixes for |
870 |
|
stress tensor parallel bug. |
871 |
|
|
872 |
< |
2003-08-27 11:16 tim |
872 |
> |
2003-08-27 12:16 tim |
873 |
|
|
874 |
|
* ChangeLog, libmdtools/DUFF.cpp, |
875 |
|
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90: |
876 |
|
fix bug in calc_dipole_dipole.F90 and calc_stikcy_pair.F90 |
877 |
|
molMembershipList use global index instead of local index |
878 |
|
|
879 |
< |
2003-08-26 15:37 tim |
879 |
> |
2003-08-26 16:37 tim |
880 |
|
|
881 |
|
* libmdtools/: Integrator.cpp, ZConstraint.cpp, do_Forces.F90, |
882 |
|
mpiSimulation.cpp: set default force substraction policy to |
883 |
|
PolicyByMass |
884 |
|
|
885 |
< |
2003-08-26 15:29 tim |
885 |
> |
2003-08-26 16:29 tim |
886 |
|
|
887 |
|
* libmdtools/Integrator.cpp: [no log message] |
888 |
|
|
889 |
< |
2003-08-26 15:13 mmeineke |
889 |
> |
2003-08-26 16:13 mmeineke |
890 |
|
|
891 |
|
* utils/sysbuilder/bilayerSys.cpp: added define statemewnt to |
892 |
|
Statwriter and Dumpwriter to handle files larger than 2 gb. |
895 |
|
|
896 |
|
hard coding some system init into bilayer.sys |
897 |
|
|
898 |
< |
2003-08-26 15:12 mmeineke |
898 |
> |
2003-08-26 16:12 mmeineke |
899 |
|
|
900 |
|
* libmdtools/: DumpWriter.cpp, StatWriter.cpp, ZConstraint.cpp: |
901 |
|
added define statemewnt to Statwriter and Dumpwriter to handle |
903 |
|
|
904 |
|
commented out some print statements in Zconstraint |
905 |
|
|
906 |
< |
2003-08-26 15:02 tim |
906 |
> |
2003-08-26 16:02 tim |
907 |
|
|
908 |
|
* libmdtools/SimSetup.cpp: Use make_sprng_seed() to generate seed |
909 |
|
and check the seed which is specified by user at least contains 9 |
910 |
|
digits |
911 |
|
|
912 |
< |
2003-08-26 13:32 mmeineke |
912 |
> |
2003-08-26 14:32 mmeineke |
913 |
|
|
914 |
|
* libmdtools/DUFF.cpp: changed the Makefiel a litle. |
915 |
|
|
917 |
|
constucted in MPI. (The MPI struct had 6 doubles declared versus |
918 |
|
the actual 11) |
919 |
|
|
920 |
< |
2003-08-26 13:30 mmeineke |
920 |
> |
2003-08-26 14:30 mmeineke |
921 |
|
|
922 |
|
* Makefile: changed the Makefiel a litle. |
923 |
|
|
924 |
< |
2003-08-25 17:17 gezelter |
924 |
> |
2003-08-25 18:17 gezelter |
925 |
|
|
926 |
|
* utils/sysbuilder/Makefile: More FreeBSD fixes |
927 |
|
|
928 |
< |
2003-08-25 16:51 gezelter |
928 |
> |
2003-08-25 17:51 gezelter |
929 |
|
|
930 |
|
* libBASS/BASSlex.l, libBASS/Makefile, libmdtools/Integrator.hpp, |
931 |
|
libmdtools/Makefile, src/Makefile: [no log message] |
932 |
|
|
933 |
< |
2003-08-22 15:04 mmeineke |
933 |
> |
2003-08-22 16:04 mmeineke |
934 |
|
|
935 |
|
* libmdtools/: Integrator.cpp, ZConstraint.cpp: small bug fix on |
936 |
|
frequency of output dumps. |
937 |
|
|
938 |
< |
2003-08-20 17:23 tim |
938 |
> |
2003-08-20 18:23 tim |
939 |
|
|
940 |
|
* libBASS/Globals.hpp, libmdtools/SimInfo.hpp, |
941 |
|
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
943 |
|
if he does not specify any value for seed, oopse will take the |
944 |
|
value of seconds of system time as seed |
945 |
|
|
946 |
< |
2003-08-20 14:42 mmeineke |
946 |
> |
2003-08-20 15:42 mmeineke |
947 |
|
|
948 |
|
* libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
949 |
|
libmdtools/GhostBend.cpp, libmdtools/SRI.hpp, |
956 |
|
fixed a bug where ghostbend atom b was not being set. ( recent bug |
957 |
|
from SimState conversion) |
958 |
|
|
959 |
< |
2003-08-20 14:41 mmeineke |
959 |
> |
2003-08-20 15:41 mmeineke |
960 |
|
|
961 |
|
* libBASS/Globals.hpp: updated the Changelog. |
962 |
|
|
963 |
|
added some bug fixes for setting the random number generator seed |
964 |
|
value. |
965 |
|
|
966 |
< |
2003-08-20 14:41 mmeineke |
966 |
> |
2003-08-20 15:41 mmeineke |
967 |
|
|
968 |
|
* ChangeLog: updated the Changelog. |
969 |
|
|
970 |
< |
2003-08-20 14:11 tim |
970 |
> |
2003-08-20 15:11 tim |
971 |
|
|
972 |
|
* libBASS/Globals.cpp, libmdtools/DUFF.cpp, |
973 |
|
libmdtools/GhostBend.cpp, libmdtools/SRI.hpp: bug fixed in ghost |
974 |
|
bend class |
975 |
|
|
976 |
< |
2003-08-20 10:13 mmeineke |
976 |
> |
2003-08-20 11:13 mmeineke |
977 |
|
|
978 |
|
* utils/: Makefile, sysbuilder/Makefile: quick makefile fix, in |
979 |
|
make links. added -f to ln -s. |
980 |
|
|
981 |
< |
2003-08-20 09:50 tim |
981 |
> |
2003-08-20 10:50 tim |
982 |
|
|
983 |
|
* libmdtools/: ZConsWriter.cpp, ZConstraint.cpp: [no log message] |
984 |
|
|
985 |
< |
2003-08-20 09:34 tim |
985 |
> |
2003-08-20 10:34 tim |
986 |
|
|
987 |
|
* libmdtools/: Integrator.hpp, SimSetup.cpp, ZConsWriter.cpp, |
988 |
|
ZConstraint.cpp: reformmating ZConstraint and fixe bug of error msg |
989 |
|
printing |
990 |
|
|
991 |
< |
2003-08-18 15:59 chuckv |
991 |
> |
2003-08-18 16:59 chuckv |
992 |
|
|
993 |
|
* utils/sysbuilder/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
994 |
|
latticeBuilder.cpp, latticeBuilder.hpp, nanoBuilder.cpp, |
995 |
|
sysBuild.cpp, sysBuild.hpp: Fixed sysBuild -bilayer works. |
996 |
|
Nanobuilder still broke. |
997 |
|
|
998 |
< |
2003-08-15 14:24 tim |
998 |
> |
2003-08-15 15:24 tim |
999 |
|
|
1000 |
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
1001 |
|
libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
1004 |
|
libmdtools/ZConstraint.cpp: Tested MPI version of Z-Constraint |
1005 |
|
Method |
1006 |
|
|
1007 |
< |
2003-08-14 11:16 tim |
1007 |
> |
2003-08-14 12:16 tim |
1008 |
|
|
1009 |
|
* libmdtools/: Integrator.hpp, ZConstraint.cpp: Stable ZConstraint |
1010 |
|
with average force substraction strategy |
1011 |
|
|
1012 |
< |
2003-08-13 16:20 chuckv |
1012 |
> |
2003-08-13 17:20 chuckv |
1013 |
|
|
1014 |
|
* libmdtools/: do_Forces.F90, mpiSimulation_module.F90: Added some |
1015 |
|
profiling code -DPROFILE. |
1016 |
|
|
1017 |
< |
2003-08-13 14:21 tim |
1017 |
> |
2003-08-13 15:21 tim |
1018 |
|
|
1019 |
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
1020 |
|
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
1021 |
|
libmdtools/SimSetup.cpp, libmdtools/ZConstraint.cpp: harmonic |
1022 |
|
potential & z-contraint method |
1023 |
|
|
1024 |
< |
2003-08-12 16:44 mmeineke |
1024 |
> |
2003-08-12 17:44 mmeineke |
1025 |
|
|
1026 |
|
* libBASS/BASS_interface.cpp, libBASS/Globals.hpp, |
1027 |
|
libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
1030 |
|
annoying bug in Directional Atom, where mu was getting written to |
1031 |
|
pseudorandom memory location. |
1032 |
|
|
1033 |
< |
2003-08-12 14:56 tim |
1033 |
> |
2003-08-12 15:56 tim |
1034 |
|
|
1035 |
|
* libBASS/BASS_interface.cpp, libBASS/Globals.cpp, |
1036 |
|
libBASS/Globals.hpp, libmdtools/Atom.hpp, |
1037 |
|
libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp, |
1038 |
|
libmdtools/SimSetup.cpp: debugging globals |
1039 |
|
|
1040 |
< |
2003-08-12 13:40 gezelter |
1040 |
> |
2003-08-12 14:40 gezelter |
1041 |
|
|
1042 |
|
* forceFields/: DUFF.frc, EAM_FF.frc, LJFF.frc: formatting fixes |
1043 |
|
and new atypes in LJFF |
1044 |
|
|
1045 |
< |
2003-08-12 13:15 gezelter |
1045 |
> |
2003-08-12 14:15 gezelter |
1046 |
|
|
1047 |
|
* forceFields/: DUFF.frc, LJFF.frc: fixed a few references to older |
1048 |
|
stuff... |
1049 |
|
|
1050 |
< |
2003-08-12 13:14 chuckv |
1050 |
> |
2003-08-12 14:14 chuckv |
1051 |
|
|
1052 |
|
* utils/sysbuilder/sysBuild.ggo: Added comment line for getgetopt. |
1053 |
|
|
1054 |
< |
2003-08-12 13:04 chuckv |
1054 |
> |
2003-08-12 14:04 chuckv |
1055 |
|
|
1056 |
|
* utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp: |
1057 |
|
Missed del of files before. |
1058 |
|
|
1059 |
< |
2003-08-12 13:03 chuckv |
1059 |
> |
2003-08-12 14:03 chuckv |
1060 |
|
|
1061 |
|
* utils/sysbuilder/: MPIobj/placeHolder, obj/placeHolder: [no log |
1062 |
|
message] |
1063 |
|
|
1064 |
< |
2003-08-12 13:01 chuckv |
1064 |
> |
2003-08-12 14:01 chuckv |
1065 |
|
|
1066 |
|
* utils/sysbuilder/Makefile: commit makefile |
1067 |
|
|
1068 |
< |
2003-08-12 12:51 tim |
1068 |
> |
2003-08-12 13:51 tim |
1069 |
|
|
1070 |
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
1071 |
|
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
1073 |
|
libmdtools/SimSetup.hpp, libmdtools/ZConstraint.cpp: added |
1074 |
|
harmonical potential to z-constraint method |
1075 |
|
|
1076 |
< |
2003-08-11 17:31 chuckv |
1076 |
> |
2003-08-11 18:31 chuckv |
1077 |
|
|
1078 |
|
* utils/Makefile: Changed makefile to only build quicklate. |
1079 |
|
|
1080 |
< |
2003-08-11 17:25 chuckv |
1080 |
> |
2003-08-11 18:25 chuckv |
1081 |
|
|
1082 |
|
* ac-tools/configure.in: added utils/sysbuilder to be built. |
1083 |
|
|
1084 |
< |
2003-08-11 17:12 chuckv |
1084 |
> |
2003-08-11 18:12 chuckv |
1085 |
|
|
1086 |
|
* utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
1087 |
|
bilayerSys.hpp, latticeBuilder.cpp, latticeBuilder.hpp, |
1095 |
|
sysbuilder into a subdirectory. Fixed some of sysbuilder to work |
1096 |
|
with new atom allocation in libmdtools. |
1097 |
|
|
1098 |
< |
2003-08-11 14:41 tim |
1098 |
> |
2003-08-11 15:41 tim |
1099 |
|
|
1100 |
|
* libmdtools/: Integrator.cpp, Integrator.hpp: added method of |
1101 |
|
moving zconstraint molecules to specified positions |
1102 |
|
|
1103 |
< |
2003-08-11 14:39 tim |
1103 |
> |
2003-08-11 15:39 tim |
1104 |
|
|
1105 |
|
* libmdtools/: SimSetup.cpp, ZConstraint.cpp: [no log message] |
1106 |
|
|
1107 |
< |
2003-08-11 14:38 mmeineke |
1107 |
> |
2003-08-11 15:38 mmeineke |
1108 |
|
|
1109 |
|
* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
1110 |
|
libBASS/BASS_parse.c, libBASS/BASSyacc.y, libBASS/Globals.cpp, |
1115 |
|
libBASS/parse_tree.c, libmdtools/SimInfo.hpp: Added zConstraint |
1116 |
|
into the BASS language syntax. |
1117 |
|
|
1118 |
< |
2003-08-11 13:29 mmeineke |
1118 |
> |
2003-08-11 14:29 mmeineke |
1119 |
|
|
1120 |
|
* libmdtools/: SimInfo.cpp, SimInfo.hpp: changed the number of |
1121 |
|
degrees of freedom to account for zConstreints |
1122 |
|
|
1123 |
< |
2003-08-08 16:22 chuckv |
1123 |
> |
2003-08-08 17:22 chuckv |
1124 |
|
|
1125 |
|
* libmdtools/EAM_FF.cpp, libmdtools/calc_eam.F90, |
1126 |
|
libmdtools/do_Forces.F90, libmdtools/neighborLists.F90, |
1127 |
|
samples/metals/Au.bass: EAM works...... Neighbor list also |
1128 |
|
works..... |
1129 |
|
|
1130 |
< |
2003-08-08 12:48 mmeineke |
1130 |
> |
2003-08-08 14:32 mmeineke |
1131 |
|
|
1132 |
+ |
* props/: frameCount.c, frameCount.h, props.cpp, staticProps.cpp: |
1133 |
+ |
moved frameCount's functionality into DumpReader. also split props |
1134 |
+ |
into staticProps and dynamicProps. (currently only have |
1135 |
+ |
staticProps) |
1136 |
+ |
|
1137 |
+ |
2003-08-08 13:48 mmeineke |
1138 |
+ |
|
1139 |
|
* libmdtools/: Makefile, ZConstraint.cpp: fixed a deprcated |
1140 |
|
instance of Atom::setZ and Atom::getZ in ZConstaint. |
1141 |
|
|
1142 |
< |
2003-08-07 16:47 mmeineke |
1142 |
> |
2003-08-07 17:47 mmeineke |
1143 |
|
|
1144 |
|
* libmdtools/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, |
1145 |
|
DirectionalAtom.cpp, DumpWriter.cpp, ForceFields.cpp, |
1148 |
|
SimState.hpp, Torsion.cpp: switched SimInfo to use a system |
1149 |
|
configuration from SimState rather than arrays from Atom |
1150 |
|
|
1151 |
< |
2003-08-06 19:47 chuckv |
1151 |
> |
2003-08-06 20:47 chuckv |
1152 |
|
|
1153 |
|
* libmdtools/Atom.hpp, libmdtools/EAM_FF.cpp, |
1154 |
|
libmdtools/SimInfo.cpp, libmdtools/calc_eam.F90, |
1155 |
|
libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
1156 |
|
samples/metals/Au.bass: Bug fixes for eam... |
1157 |
|
|
1158 |
< |
2003-08-01 11:18 tim |
1158 |
> |
2003-08-01 12:18 tim |
1159 |
|
|
1160 |
|
* libmdtools/: SimSetup.cpp, ZConstraint.cpp: stable version of |
1161 |
|
Z-Constraint |
1162 |
|
|
1163 |
< |
2003-07-31 14:59 tim |
1163 |
> |
2003-07-31 15:59 tim |
1164 |
|
|
1165 |
|
* ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1166 |
|
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
1167 |
|
libmdtools/ZConstraint.cpp: add index range checking into |
1168 |
|
ZConstraint |
1169 |
|
|
1170 |
< |
2003-07-31 10:38 tim |
1170 |
> |
2003-07-31 11:38 tim |
1171 |
|
|
1172 |
|
* libBASS/: Globals.cpp, Globals.hpp: added z-constraint parameters |
1173 |
|
to the globals |
1174 |
|
|
1175 |
< |
2003-07-31 10:35 tim |
1175 |
> |
2003-07-31 11:35 tim |
1176 |
|
|
1177 |
|
* libmdtools/: AllIntegrator.hpp, GenericData.cpp, GenericData.hpp, |
1178 |
|
Integrator.hpp, Makefile, Molecule.cpp, Molecule.hpp, NPTf.cpp, |
1180 |
|
SimSetup.cpp, ZConsWriter.cpp, ZConsWriter.hpp, ZConstraint.cpp: |
1181 |
|
Added Z constraint. |
1182 |
|
|
1183 |
< |
2003-07-30 16:17 chuckv |
1183 |
> |
2003-07-30 17:17 chuckv |
1184 |
|
|
1185 |
|
* libmdtools/EAM_FF.cpp, libmdtools/ForceFields.hpp, |
1186 |
|
libmdtools/ReadWrite.hpp, libmdtools/calc_eam.F90, |
1187 |
|
libmdtools/do_Forces.F90, libmdtools/wrappers.F90, |
1188 |
|
samples/metals/Au.bass: More bug fixes for eam. |
1189 |
|
|
1190 |
< |
2003-07-29 11:32 mmeineke |
1190 |
> |
2003-07-29 12:32 mmeineke |
1191 |
|
|
1192 |
|
* libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp, |
1193 |
< |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile: |
1194 |
< |
working on the props code |
1193 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
1194 |
> |
props/frameCount.c, props/frameCount.h, props/props.cpp, |
1195 |
> |
src/Makefile: working on the props code |
1196 |
|
|
1197 |
< |
2003-07-29 11:32 mmeineke |
1197 |
> |
2003-07-29 12:32 mmeineke |
1198 |
|
|
1199 |
|
* libBASS/Globals.cpp: [no log message] |
1200 |
|
|
1201 |
< |
2003-07-25 15:05 chuckv |
1201 |
> |
2003-07-25 16:05 chuckv |
1202 |
|
|
1203 |
|
* samples/metals/: Au.bass, metals.mdl: Added bass models for |
1204 |
|
metals |
1205 |
|
|
1206 |
< |
2003-07-25 15:00 chuckv |
1206 |
> |
2003-07-25 16:00 chuckv |
1207 |
|
|
1208 |
|
* libmdtools/: Makefile, SimSetup.cpp, calc_eam.F90, |
1209 |
|
notifyCutoffs.F90: Added eam to simSetup and added changecutoffeam. |
1210 |
|
|
1211 |
< |
2003-07-24 16:22 chuckv |
1211 |
> |
2003-07-24 17:22 chuckv |
1212 |
|
|
1213 |
|
* ac-tools/configure.in: Changed configure to look for both upper |
1214 |
|
and lower cass .mod files |
1215 |
|
|
1216 |
< |
2003-07-24 14:57 chuckv |
1216 |
> |
2003-07-24 15:57 chuckv |
1217 |
|
|
1218 |
|
* libmdtools/: calc_eam.F90, do_Forces.F90: module use fixes for |
1219 |
|
eam and do_forces. |
1220 |
|
|
1221 |
< |
2003-07-23 17:13 chuckv |
1221 |
> |
2003-07-23 18:13 chuckv |
1222 |
|
|
1223 |
|
* libmdtools/: Makefile, calc_eam.F90, do_Forces.F90, |
1224 |
|
force_globals.F90, simulation_module.F90, status_module.F90: |
1225 |
|
Finished most code for eam.... |
1226 |
|
|
1227 |
< |
2003-07-22 16:49 mmeineke |
1227 |
> |
2003-07-22 17:49 mmeineke |
1228 |
|
|
1229 |
|
* libmdtools/: DumpReader.cpp, ReadWrite.hpp: added the scan |
1230 |
|
function to the DumpReader. It should now save the start of each |
1231 |
|
frame in a vector. |
1232 |
|
|
1233 |
< |
2003-07-22 15:05 mmeineke |
1233 |
> |
2003-07-22 16:05 mmeineke |
1234 |
|
|
1235 |
|
* libmdtools/: DumpReader.cpp, ReadWrite.hpp: making some changes |
1236 |
|
to read dump files |
1237 |
|
|
1238 |
< |
2003-07-22 14:54 tim |
1238 |
> |
2003-07-22 15:54 tim |
1239 |
|
|
1240 |
|
* libmdtools/: AbstractClasses.hpp, AllIntegrator.hpp, |
1241 |
|
Integrator.cpp, Integrator.hpp, Makefile, NPTf.cpp, NPTfm.cpp, |
1242 |
|
NPTi.cpp, NPTim.cpp, NVT.cpp, SimSetup.cpp, SimSetup.hpp: [no log |
1243 |
|
message] |
1244 |
|
|
1245 |
< |
2003-07-22 11:41 mmeineke |
1245 |
> |
2003-07-22 12:41 mmeineke |
1246 |
|
|
1247 |
|
* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, SimInfo.hpp, |
1248 |
|
SimSetup.cpp: Fixed a current time initialization bug in |
1249 |
|
InitFromFile. |
1250 |
|
|
1251 |
< |
2003-07-21 16:27 mmeineke |
1251 |
> |
2003-07-21 17:27 mmeineke |
1252 |
|
|
1253 |
|
* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp, |
1254 |
|
Integrator.cpp, SimInfo.hpp: some initial changes to Dumpwriter and |
1255 |
|
friends to accomadate random file access |
1256 |
|
|
1257 |
< |
2003-07-21 11:23 mmeineke |
1257 |
> |
2003-07-21 12:23 mmeineke |
1258 |
|
|
1259 |
|
* libmdtools/SimInfo.cpp: Initialized currentTime to 0, in case no |
1260 |
|
one sets it. |
1261 |
|
|
1262 |
< |
2003-07-21 11:23 mmeineke |
1262 |
> |
2003-07-21 12:23 mmeineke |
1263 |
|
|
1264 |
|
* libmdtools/: InitializeFromFile.cpp, Integrator.cpp, |
1265 |
|
ReadWrite.hpp: fixed Initializefrom file to start the simulation |
1266 |
|
from the time specified in the init file. |
1267 |
|
|
1268 |
< |
2003-07-17 16:49 gezelter |
1268 |
> |
2003-07-17 17:49 gezelter |
1269 |
|
|
1270 |
|
* libmdtools/: Integrator.cpp, ReadWrite.hpp, SimInfo.hpp, |
1271 |
|
DumpReader.cpp: Started work on a DumpReader |
1272 |
|
|
1273 |
< |
2003-07-17 15:38 gezelter |
1273 |
> |
2003-07-17 16:38 gezelter |
1274 |
|
|
1275 |
|
* libmdtools/calc_sticky_pair.F90: Fixes for SSD/E |
1276 |
|
|
1277 |
< |
2003-07-17 15:32 gezelter |
1277 |
> |
2003-07-17 16:32 gezelter |
1278 |
|
|
1279 |
|
* forceFields/DUFF.frc, libmdtools/DUFF.cpp, |
1280 |
|
libmdtools/calc_sticky_pair.F90, libmdtools/fortranWrapDefines.hpp: |
1281 |
|
Changes for SSD/E |
1282 |
|
|
1283 |
< |
2003-07-17 14:38 mmeineke |
1283 |
> |
2003-07-17 15:38 mmeineke |
1284 |
|
|
1285 |
|
* libmdtools/do_Forces.F90: commented out an eam line |
1286 |
|
|
1287 |
< |
2003-07-17 14:32 chuckv |
1287 |
> |
2003-07-17 15:32 chuckv |
1288 |
|
|
1289 |
|
* libmdtools/atype_module.F90: fixed spelling issue |
1290 |
|
|
1291 |
< |
2003-07-17 14:29 chuckv |
1291 |
> |
2003-07-17 15:29 chuckv |
1292 |
|
|
1293 |
|
* libmdtools/: fInfo.c, status_module.F90: added info module |
1294 |
|
|
1295 |
< |
2003-07-17 14:25 chuckv |
1295 |
> |
2003-07-17 15:25 chuckv |
1296 |
|
|
1297 |
|
* libmdtools/: Atom.hpp, DUFF.cpp, EAM_FF.cpp, LJFF.cpp, Makefile, |
1298 |
|
atype_module.F90, calc_eam.F90, do_Forces.F90, |
1299 |
|
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
1300 |
|
mpiSimulation_module.F90: Added massive changes for eam.... |
1301 |
|
|
1302 |
< |
2003-07-16 16:49 chuckv |
1302 |
> |
2003-07-16 17:49 chuckv |
1303 |
|
|
1304 |
|
* libmdtools/EAM_FF.cpp: More up to date version of EAM_FF |
1305 |
|
|
1306 |
< |
2003-07-16 16:30 mmeineke |
1306 |
> |
2003-07-16 17:30 mmeineke |
1307 |
|
|
1308 |
|
* libmdtools/: ForceFields.cpp, Makefile, SimInfo.cpp, SimInfo.hpp, |
1309 |
|
SimSetup.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
1314 |
|
notifyCutoffs in Fortran notifies those who need the information of |
1315 |
|
any changes to cutoffs. |
1316 |
|
|
1317 |
< |
2003-07-16 12:35 gezelter |
1317 |
> |
2003-07-16 13:35 gezelter |
1318 |
|
|
1319 |
|
* utils/: Makefile, quickLate.c: Made quickLate aware of Hmat. |
1320 |
|
quickLate is now somewhat more intelligent about periodic |
1321 |
|
boundaries and wrapping. |
1322 |
|
|
1323 |
< |
2003-07-16 11:40 chuckv |
1323 |
> |
2003-07-16 12:40 chuckv |
1324 |
|
|
1325 |
|
* libmdtools/calc_LJ_FF.F90: Fixed bug in updating mixing lists |
1326 |
|
|
1327 |
< |
2003-07-16 10:34 mmeineke |
1327 |
> |
2003-07-16 11:34 mmeineke |
1328 |
|
|
1329 |
|
* scripts/cleanSrc: added a quick wipe-and-update script for quick |
1330 |
|
rebuilds on BoB |
1331 |
|
|
1332 |
< |
2003-07-15 21:11 gezelter |
1332 |
> |
2003-07-15 22:11 gezelter |
1333 |
|
|
1334 |
|
* libmdtools/: ForceFields.cpp, SimInfo.cpp, SimInfo.hpp, |
1335 |
|
SimSetup.cpp, calc_dipole_dipole.F90, calc_reaction_field.F90: more |
1336 |
|
fixes for box changes |
1337 |
|
|
1338 |
< |
2003-07-15 17:29 mmeineke |
1338 |
> |
2003-07-15 18:29 mmeineke |
1339 |
|
|
1340 |
|
* libmdtools/simulation_module.F90: removed some debugging print |
1341 |
|
statements. |
1342 |
|
|
1343 |
< |
2003-07-15 17:22 mmeineke |
1343 |
> |
2003-07-15 18:22 mmeineke |
1344 |
|
|
1345 |
|
* libmdtools/: SimInfo.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
1346 |
|
do_Forces.F90, simulation_module.F90: fixed a long lived bug in |
1349 |
|
cutoff region to be to small. Also led to the removal of the taper |
1350 |
|
region to buffer the dipole cutoff. |
1351 |
|
|
1352 |
< |
2003-07-15 16:34 mmeineke |
1352 |
> |
2003-07-15 17:34 mmeineke |
1353 |
|
|
1354 |
|
* libmdtools/: SimInfo.cpp, simulation_module.F90: working on |
1355 |
|
fixing ssd bug |
1356 |
|
|
1357 |
< |
2003-07-15 14:56 gezelter |
1357 |
> |
2003-07-15 15:56 gezelter |
1358 |
|
|
1359 |
|
* libmdtools/: NPTf.cpp, NPTfm.cpp, NPTi.cpp, SimInfo.cpp: Fixes |
1360 |
|
for the NPT ensembles |
1361 |
|
|
1362 |
< |
2003-07-15 13:52 mmeineke |
1362 |
> |
2003-07-15 14:52 mmeineke |
1363 |
|
|
1364 |
|
* libmdtools/: Makefile, SimSetup.cpp, SimSetup.hpp: cleaned up |
1365 |
|
simSetup |
1366 |
|
|
1367 |
< |
2003-07-15 12:57 mmeineke |
1367 |
> |
2003-07-15 13:57 mmeineke |
1368 |
|
|
1369 |
|
* libmdtools/: Integrator.cpp, NPTi.cpp, SRI.hpp, SimSetup.cpp, |
1370 |
|
SimSetup.hpp, Thermo.cpp, Thermo.hpp, f_verlet_constrained.F90: |
1371 |
|
fixed some bugs, Changed entry_plug to info where appropriate |
1372 |
|
|
1373 |
< |
2003-07-15 12:25 chuckv |
1373 |
> |
2003-07-15 13:25 chuckv |
1374 |
|
|
1375 |
|
* utils/sysBuild.ggo: added more command line arguments |
1376 |
|
|
1377 |
< |
2003-07-15 12:11 gezelter |
1377 |
> |
2003-07-15 13:11 gezelter |
1378 |
|
|
1379 |
|
* samples/: alkane/butane.bass, lipid/5x5.bass, water/ssd.bass: |
1380 |
|
Fixing force field line |
1381 |
|
|
1382 |
< |
2003-07-15 12:10 gezelter |
1382 |
> |
2003-07-15 13:10 gezelter |
1383 |
|
|
1384 |
|
* libmdtools/: Atom.hpp, NPTi.cpp, NPTim.cpp, Thermo.cpp, |
1385 |
|
calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, |
1386 |
|
calc_reaction_field.F90, calc_sticky_pair.F90: Fixing pressure |
1387 |
|
tensor |
1388 |
|
|
1389 |
< |
2003-07-15 10:50 gezelter |
1389 |
> |
2003-07-15 11:50 gezelter |
1390 |
|
|
1391 |
|
* libmdtools/: Bond.cpp, Molecule.cpp: more archaic code fixes |
1392 |
|
|
1393 |
< |
2003-07-15 10:42 gezelter |
1393 |
> |
2003-07-15 11:42 gezelter |
1394 |
|
|
1395 |
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, Verlet.cpp: |
1396 |
|
removed old outdated code |
1397 |
|
|
1398 |
< |
2003-07-15 09:45 gezelter |
1398 |
> |
2003-07-15 10:45 gezelter |
1399 |
|
|
1400 |
|
* libmdtools/Thermo.cpp: fixes to get rid of get_vx and set_vx |
1401 |
|
|
1402 |
< |
2003-07-15 09:28 gezelter |
1402 |
> |
2003-07-15 10:28 gezelter |
1403 |
|
|
1404 |
|
* libmdtools/Molecule.cpp: removing get_vx |
1405 |
|
|
1406 |
< |
2003-07-14 22:28 gezelter |
1406 |
> |
2003-07-14 23:28 gezelter |
1407 |
|
|
1408 |
|
* libmdtools/NPTfm.cpp: Added NPTfm |
1409 |
|
|
1410 |
< |
2003-07-14 22:27 gezelter |
1410 |
> |
2003-07-14 23:27 gezelter |
1411 |
|
|
1412 |
|
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: |
1413 |
|
Bugfix in NPTim, fixes for NPTfm |
1414 |
|
|
1415 |
< |
2003-07-14 22:08 gezelter |
1415 |
> |
2003-07-14 23:08 gezelter |
1416 |
|
|
1417 |
|
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: |
1418 |
|
Checking in changes for NPTim |
1419 |
|
|
1420 |
< |
2003-07-14 18:06 gezelter |
1420 |
> |
2003-07-14 19:06 gezelter |
1421 |
|
|
1422 |
|
* utils/Makefile: Broken SysBuilder |
1423 |
|
|
1424 |
< |
2003-07-14 18:06 gezelter |
1424 |
> |
2003-07-14 19:06 gezelter |
1425 |
|
|
1426 |
|
* samples/: alkane/init_butane.eor, argon/argon.bass, |
1427 |
|
argon/init_argon.eor, lipid/init_5x5.eor, water/init_ssd.eor: Fixes |
1428 |
|
for samples |
1429 |
|
|
1430 |
< |
2003-07-14 18:06 gezelter |
1430 |
> |
2003-07-14 19:06 gezelter |
1431 |
|
|
1432 |
|
* libmdtools/: Integrator.cpp, do_Forces.F90: Removed some |
1433 |
|
debugging write statements |
1434 |
|
|
1435 |
< |
2003-07-14 17:38 gezelter |
1435 |
> |
2003-07-14 18:38 gezelter |
1436 |
|
|
1437 |
|
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, NPTi.cpp, |
1438 |
|
NVT.cpp: Fixes for get and set routines in Atom and DirectionalAtom |
1439 |
|
|
1440 |
< |
2003-07-14 16:48 mmeineke |
1440 |
> |
2003-07-14 17:48 mmeineke |
1441 |
|
|
1442 |
|
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp: added get |
1443 |
|
and set routines to Atom and DirectionalAtom |
1444 |
|
|
1445 |
< |
2003-07-14 16:35 chuckv |
1445 |
> |
2003-07-14 17:35 chuckv |
1446 |
|
|
1447 |
|
* utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp, |
1448 |
|
sysBuild.cpp, sysBuild.ggo, sysBuild.hpp: added a nanoSysBuilder |
1449 |
|
that takes different cmd line arguments. |
1450 |
|
|
1451 |
< |
2003-07-14 16:28 mmeineke |
1451 |
> |
2003-07-14 17:28 mmeineke |
1452 |
|
|
1453 |
|
* libmdtools/: Atom.hpp, BondExtensions.cpp, DirectionalAtom.cpp, |
1454 |
|
ForceFields.cpp, Integrator.cpp, Integrator.hpp, Makefile, |
1455 |
|
SimInfo.cpp, SimInfo.hpp, do_Forces.F90: found a bug. Unit vectors |
1456 |
|
were not being updated |
1457 |
|
|
1458 |
< |
2003-07-14 10:04 gezelter |
1458 |
> |
2003-07-14 11:04 gezelter |
1459 |
|
|
1460 |
|
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp: Working on |
1461 |
|
NPTim |
1462 |
|
|
1463 |
< |
2003-07-14 09:55 mmeineke |
1463 |
> |
2003-07-14 10:55 mmeineke |
1464 |
|
|
1465 |
|
* forceFields/DUFF.frc: Switched the bond in the force field back |
1466 |
|
to constrained, to preserve energy |
1467 |
|
|
1468 |
< |
2003-07-11 17:34 mmeineke |
1468 |
> |
2003-07-11 18:34 mmeineke |
1469 |
|
|
1470 |
|
* libmdtools/: BondExtensions.cpp, DUFF.cpp, Integrator.cpp, |
1471 |
|
Integrator.hpp: working on som integrator bugs |
1472 |
|
|
1473 |
< |
2003-07-11 10:26 gezelter |
1473 |
> |
2003-07-11 11:26 gezelter |
1474 |
|
|
1475 |
|
* libmdtools/: StreamTokenizer.cpp, StreamTokenizer.hpp: Starting |
1476 |
|
to worry about all the strtok() calls in our code |
1477 |
|
|
1478 |
< |
2003-07-11 09:49 gezelter |
1478 |
> |
2003-07-11 10:49 gezelter |
1479 |
|
|
1480 |
|
* utils/nanoBuilder.cpp: Fixed Hmat and some namespace strangeness |
1481 |
|
|
1482 |
< |
2003-07-10 20:15 gezelter |
1482 |
> |
2003-07-10 21:15 gezelter |
1483 |
|
|
1484 |
|
* libmdtools/DumpWriter.cpp: Fixed hmat in DumpWriter (MPI) and |
1485 |
|
eor. |
1486 |
|
|
1487 |
< |
2003-07-10 17:15 mmeineke |
1487 |
> |
2003-07-10 18:15 mmeineke |
1488 |
|
|
1489 |
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, NPTf.cpp, |
1490 |
|
SimInfo.cpp, Thermo.cpp: fixed some bugs |
1491 |
|
|
1492 |
< |
2003-07-10 14:53 chuckv |
1492 |
> |
2003-07-10 15:53 chuckv |
1493 |
|
|
1494 |
|
* utils/: Makefile, latticeBuilder.cpp, latticeBuilder.hpp, |
1495 |
|
nanoBuilder.cpp, nanoBuilder.hpp, sysBuild.cpp, sysBuild.hpp: Added |
1496 |
|
nanoBuilder and a general Lattice builder. |
1497 |
|
|
1498 |
< |
2003-07-10 12:10 gezelter |
1498 |
> |
2003-07-10 13:10 gezelter |
1499 |
|
|
1500 |
|
* libmdtools/: Integrator.hpp, NPTf.cpp, SimInfo.cpp, SimInfo.hpp, |
1501 |
|
Thermo.cpp, Thermo.hpp: Bunch of 1-d array -> 2-d array stuff |
1502 |
|
|
1503 |
< |
2003-07-09 17:14 mmeineke |
1503 |
> |
2003-07-09 18:14 mmeineke |
1504 |
|
|
1505 |
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, |
1506 |
|
Integrator.hpp, NPTf.cpp, NPTi.cpp, ReadWrite.hpp, SimInfo.cpp, |
1507 |
|
SimSetup.cpp: Bug fixing NPTi and NPTf. there is some error in the |
1508 |
|
caclulation of HmatInverse. |
1509 |
|
|
1510 |
< |
2003-07-09 10:34 mmeineke |
1510 |
> |
2003-07-09 11:34 mmeineke |
1511 |
|
|
1512 |
|
* libBASS/MoleculeStamp.hpp: starting some work for xlate |
1513 |
|
|
1514 |
< |
2003-07-09 10:33 mmeineke |
1514 |
> |
2003-07-09 11:33 mmeineke |
1515 |
|
|
1516 |
|
* libmdtools/: SimSetup.cpp, Thermo.cpp: adding in dan's NPT stuff |
1517 |
|
|
1518 |
< |
2003-07-09 08:56 gezelter |
1518 |
> |
2003-07-09 09:56 gezelter |
1519 |
|
|
1520 |
|
* libmdtools/: NPTf.cpp, SimSetup.cpp: Fixes and merging NPTf |
1521 |
|
|
1522 |
< |
2003-07-09 08:56 gezelter |
1522 |
> |
2003-07-09 09:56 gezelter |
1523 |
|
|
1524 |
|
* libBASS/Globals.cpp: Removed Qmass |
1525 |
|
|
1526 |
< |
2003-07-08 21:15 gezelter |
1526 |
> |
2003-07-08 22:15 gezelter |
1527 |
|
|
1528 |
|
* libmdtools/: Makefile, NPTf.cpp, NPTi.cpp: Fixes for both NPTf |
1529 |
|
and NPTi |
1530 |
|
|
1531 |
< |
2003-07-08 20:41 gezelter |
1531 |
> |
2003-07-08 21:41 gezelter |
1532 |
|
|
1533 |
|
* libmdtools/: NPTf.cpp, NPTi.cpp: Fixes in NPTi migrated into NPTf |
1534 |
|
|
1535 |
< |
2003-07-08 16:10 gezelter |
1535 |
> |
2003-07-08 17:10 gezelter |
1536 |
|
|
1537 |
|
* libmdtools/: Integrator.hpp, NPTf.cpp: [no log message] |
1538 |
|
|
1539 |
< |
2003-07-08 16:06 gezelter |
1539 |
> |
2003-07-08 17:06 gezelter |
1540 |
|
|
1541 |
|
* libmdtools/NPTi.cpp: fixed box scaling |
1542 |
|
|
1543 |
< |
2003-07-08 15:56 gezelter |
1543 |
> |
2003-07-08 16:56 gezelter |
1544 |
|
|
1545 |
|
* libmdtools/: Integrator.hpp, Makefile, NPTi.cpp, SimInfo.cpp, |
1546 |
|
SimInfo.hpp, Thermo.cpp: NPTi |
1547 |
|
|
1548 |
< |
2003-07-03 14:41 mmeineke |
1548 |
> |
2003-07-03 15:41 mmeineke |
1549 |
|
|
1550 |
|
* libBASS/Makefile, libmdtools/Makefile, src/Makefile, |
1551 |
|
utils/Makefile, utils/bilayerSys.cpp: cleaned up the dependecy |
1552 |
|
scripts in the makefiles |
1553 |
|
|
1554 |
< |
2003-07-02 16:26 mmeineke |
1554 |
> |
2003-07-02 17:26 mmeineke |
1555 |
|
|
1556 |
|
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
1557 |
|
libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
1562 |
|
utils/Makefile: fixed the bugs introduced by switching the periodic |
1563 |
|
box to a matrix |
1564 |
|
|
1565 |
< |
2003-07-01 17:39 gezelter |
1565 |
> |
2003-07-01 18:39 gezelter |
1566 |
|
|
1567 |
|
* libmdtools/do_Forces.F90: Fortran flexi-BOX |
1568 |
|
|
1569 |
< |
2003-07-01 17:29 gezelter |
1569 |
> |
2003-07-01 18:29 gezelter |
1570 |
|
|
1571 |
|
* libmdtools/simulation_module.F90: Fixes for flexi-BOX |
1572 |
|
|
1573 |
< |
2003-07-01 16:33 mmeineke |
1573 |
> |
2003-07-01 17:33 mmeineke |
1574 |
|
|
1575 |
|
* libmdtools/: SimInfo.cpp, SimInfo.hpp, fSimulation.h, |
1576 |
|
fortranWrapDefines.hpp, simulation_module.F90: working on adding |
1577 |
|
the box matrix to everything. |
1578 |
|
|
1579 |
< |
2003-06-30 17:03 mmeineke |
1579 |
> |
2003-06-30 18:03 mmeineke |
1580 |
|
|
1581 |
|
* ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1582 |
|
src/oopse.cpp: |
1583 |
|
Updated the ChangeLog, and Converted most of the SImInfo to use |
1584 |
|
non-Isotropic boxes. wrapVector needs to be finished. |
1585 |
|
|
1586 |
< |
2003-06-25 16:12 mmeineke |
1586 |
> |
2003-06-25 17:12 mmeineke |
1587 |
|
|
1588 |
|
* libmdtools/: Integrator.cpp, SimSetup.cpp: Changed over the bonds |
1589 |
|
to Harmonic bonds in the DUFF frc file |
1590 |
|
|
1591 |
|
fixed constraints. |
1592 |
|
|
1593 |
< |
2003-06-25 16:11 mmeineke |
1593 |
> |
2003-06-25 17:11 mmeineke |
1594 |
|
|
1595 |
|
* forceFields/DUFF.frc: Changed over the bonds to Harmonic bonds in |
1596 |
|
the DUFF frc file |
1597 |
|
|
1598 |
< |
2003-06-24 17:51 gezelter |
1598 |
> |
2003-06-24 18:51 gezelter |
1599 |
|
|
1600 |
|
* libmdtools/: Integrator.hpp, NVT.cpp: Fixes to NVT. Check them! |
1601 |
|
|
1602 |
< |
2003-06-24 14:57 mmeineke |
1602 |
> |
2003-06-24 15:57 mmeineke |
1603 |
|
|
1604 |
|
* forceFields/DUFF.frc, libmdtools/BondExtensions.cpp, |
1605 |
|
libmdtools/DUFF.cpp, libmdtools/SRI.hpp: added Harmonic bod into |
1606 |
|
the DUFF forcefield and BondExtensions.cpp |
1607 |
|
|
1608 |
< |
2003-06-23 16:24 mmeineke |
1608 |
> |
2003-06-23 17:24 mmeineke |
1609 |
|
|
1610 |
|
* libmdtools/Integrator.cpp: Doing some work to debug the |
1611 |
|
constraint code. |
1612 |
|
|
1613 |
< |
2003-06-20 15:50 gezelter |
1613 |
> |
2003-06-20 16:50 gezelter |
1614 |
|
|
1615 |
|
* libmdtools/Integrator.hpp: NPT fix |
1616 |
|
|
1617 |
< |
2003-06-20 15:29 mmeineke |
1617 |
> |
2003-06-20 16:29 mmeineke |
1618 |
|
|
1619 |
|
* libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
1620 |
|
libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
1623 |
|
libmdtools/Thermo.hpp, src/Makefile, utils/Makefile: Most of the |
1624 |
|
integrator and NVT seem to be working now. |
1625 |
|
|
1626 |
< |
2003-06-20 11:49 gezelter |
1626 |
> |
2003-06-20 12:49 gezelter |
1627 |
|
|
1628 |
|
* libmdtools/: Integrator.hpp, NVT.cpp: NVT additions |
1629 |
|
|
1630 |
< |
2003-06-19 17:02 mmeineke |
1630 |
> |
2003-06-19 18:02 mmeineke |
1631 |
|
|
1632 |
|
* forceFields/DUFF.frc, forceFields/LJFF.frc, |
1633 |
|
forceFields/LJ_FF.frc, forceFields/Makefile, |
1638 |
|
libmdtools/TraPPEFF.cpp: slowly converting to new integrator and |
1639 |
|
forcefield names. |
1640 |
|
|
1641 |
< |
2003-06-19 14:21 mmeineke |
1641 |
> |
2003-06-19 15:21 mmeineke |
1642 |
|
|
1643 |
|
* libmdtools/: Integrator.cpp, SimSetup.cpp, Symplectic.cpp: |
1644 |
|
finished the basics of the integrator and SimSetup.cpp |
1645 |
|
|
1646 |
< |
2003-06-19 14:11 mmeineke |
1646 |
> |
2003-06-19 15:11 mmeineke |
1647 |
|
|
1648 |
|
* libmdtools/SimSetup.cpp: doing some work on SimSetup to clean it |
1649 |
|
up / get it to work with the new Integrator. |
1650 |
|
|
1651 |
< |
2003-06-18 17:20 mmeineke |
1651 |
> |
2003-06-18 18:20 mmeineke |
1652 |
|
|
1653 |
|
* libmdtools/Symplectic.cpp: minor changes in an attempt to fix |
1654 |
|
output times. |
1655 |
|
|
1656 |
< |
2003-06-17 16:56 mmeineke |
1656 |
> |
2003-06-17 17:56 mmeineke |
1657 |
|
|
1658 |
|
* libmdtools/: Integrator.hpp, SimSetup.cpp: Added Teng's parmeters |
1659 |
|
fro the ghost Bend in TraPPE_Ex |
1660 |
|
|
1661 |
|
some work on the integrator. ( incomplete) |
1662 |
|
|
1663 |
< |
2003-06-17 16:55 mmeineke |
1663 |
> |
2003-06-17 17:55 mmeineke |
1664 |
|
|
1665 |
|
* forceFields/TraPPE_Ex.frc: Added Teng's parmeters fro the ghost |
1666 |
|
Bend in TraPPE_Ex |
1667 |
|
|
1668 |
< |
2003-06-04 16:06 mmeineke |
1668 |
> |
2003-06-04 17:06 mmeineke |
1669 |
|
|
1670 |
|
* libmdtools/: Integrator.hpp, Symplectic.cpp: added constrainA and |
1671 |
|
constrainB to the Symplectic integrator |
1672 |
|
|
1673 |
< |
2003-05-30 16:32 mmeineke |
1673 |
> |
2003-05-30 17:32 mmeineke |
1674 |
|
|
1675 |
|
* utils/bilayerSys.cpp: currently modifiying Symplectic to become |
1676 |
|
the basic integrator. |
1677 |
|
|
1678 |
|
bilayerSys.cpp altered for building tb3. |
1679 |
|
|
1680 |
< |
2003-05-30 16:31 mmeineke |
1680 |
> |
2003-05-30 17:31 mmeineke |
1681 |
|
|
1682 |
|
* libmdtools/: Integrator.hpp, SimInfo.hpp, Symplectic.cpp, |
1683 |
|
TraPPE_ExFF.cpp, Verlet.cpp, f_verlet_constrained.F90: currently |
1684 |
|
modifiying Symplectic to become the basic integrator. |
1685 |
|
|
1686 |
< |
2003-05-30 15:19 mmeineke |
1686 |
> |
2003-05-30 16:19 mmeineke |
1687 |
|
|
1688 |
|
* libmdtools/Integrator.hpp: added some member variables for |
1689 |
|
position, velocity, etc. |
1690 |
|
|
1691 |
< |
2003-05-30 14:07 mmeineke |
1691 |
> |
2003-05-30 15:07 mmeineke |
1692 |
|
|
1693 |
|
* libmdtools/: AbstractClasses.hpp, Integrator.hpp: changed how NVT |
1694 |
|
is now derived from Integrator |
1695 |
|
|
1696 |
< |
2003-05-20 11:44 mmeineke |
1696 |
> |
2003-05-20 12:44 mmeineke |
1697 |
|
|
1698 |
|
* libmdtools/GhostBend.cpp: fixed an a mismatched Ghostbend bug. |
1699 |
|
|
1700 |
< |
2003-05-17 11:57 mmeineke |
1700 |
> |
2003-05-17 12:57 mmeineke |
1701 |
|
|
1702 |
|
* utils/: Makefile, MoLocator.cpp, bilayerSys.cpp: all seems to be |
1703 |
|
working |
1704 |
|
|
1705 |
< |
2003-05-16 16:37 mmeineke |
1705 |
> |
2003-05-16 17:37 mmeineke |
1706 |
|
|
1707 |
|
* utils/bilayerSys.cpp: still working on the bilayer code |
1708 |
|
|
1709 |
< |
2003-05-16 09:28 mmeineke |
1709 |
> |
2003-05-16 10:28 mmeineke |
1710 |
|
|
1711 |
|
* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: doing some |
1712 |
|
work to overhaul sysbuild. |
1713 |
|
|
1714 |
< |
2003-05-13 16:23 mmeineke |
1714 |
> |
2003-05-13 17:23 mmeineke |
1715 |
|
|
1716 |
|
* libmdtools/calc_sticky_pair.F90: optimized the ssd calc loop |
1717 |
|
|
1718 |
< |
2003-05-13 15:47 mmeineke |
1718 |
> |
2003-05-13 16:47 mmeineke |
1719 |
|
|
1720 |
|
* samples/: Makefile, beadLipid/Makefile, beadLipid/beadLipid.mdl, |
1721 |
|
beadLipid/water.mdl: Added bead lipid model to the sample directory |
1722 |
|
|
1723 |
< |
2003-05-13 15:34 mmeineke |
1723 |
> |
2003-05-13 16:34 mmeineke |
1724 |
|
|
1725 |
|
* forceFields/TraPPE_Ex.frc: finished adding the Tail beads into |
1726 |
|
the Trappe extended force field |
1727 |
|
|
1728 |
< |
2003-05-13 12:01 mmeineke |
1728 |
> |
2003-05-13 13:01 mmeineke |
1729 |
|
|
1730 |
|
* forceFields/TraPPE_Ex.frc: added the TailBead atom types to the |
1731 |
|
TraPPe_Ex forceField |
1732 |
|
|
1733 |
< |
2003-05-09 14:51 mmeineke |
1733 |
> |
2003-05-09 15:51 mmeineke |
1734 |
|
|
1735 |
|
* samples/lipid/lipid.mdl: fixed up the TraPPE_Ex force field. |
1736 |
|
there were some duplicate entries |
1737 |
|
|
1738 |
|
added a two chain lipid to the lipid.mdl in sample |
1739 |
|
|
1740 |
< |
2003-05-09 14:51 mmeineke |
1740 |
> |
2003-05-09 15:51 mmeineke |
1741 |
|
|
1742 |
|
* forceFields/TraPPE_Ex.frc: fixed up the TraPPE_Ex force field. |
1743 |
|
there were some duplicate entries |
1744 |
|
|
1745 |
< |
2003-05-09 11:56 mmeineke |
1745 |
> |
2003-05-09 12:56 mmeineke |
1746 |
|
|
1747 |
|
* forceFields/TraPPE_Ex.frc: added the utils subdirectory to the |
1748 |
|
configure script |
1749 |
|
|
1750 |
|
added the CH branching group to the TraPPE_Ex fource field |
1751 |
|
|
1752 |
< |
2003-05-09 11:55 mmeineke |
1752 |
> |
2003-05-09 12:55 mmeineke |
1753 |
|
|
1754 |
|
* ac-tools/configure.in: added the utils subdirectory to the |
1755 |
|
configure script |
1756 |
|
|
1757 |
< |
2003-04-25 11:02 mmeineke |
1757 |
> |
2003-04-25 12:02 mmeineke |
1758 |
|
|
1759 |
|
* utils/bilayerSys.cpp: i quick fix to th distance in the random |
1760 |
|
bilayer builder |
1761 |
|
|
1762 |
< |
2003-04-24 21:00 mmeineke |
1762 |
> |
2003-04-24 22:00 mmeineke |
1763 |
|
|
1764 |
|
* libmdtools/f_verlet_constrained.F90: added a new test for |
1765 |
|
constraint failure |
1766 |
|
|
1767 |
< |
2003-04-17 16:54 mmeineke |
1767 |
> |
2003-04-17 17:54 mmeineke |
1768 |
|
|
1769 |
|
* libBASS/BASS_interface.h, libmdtools/SimSetup.cpp, |
1770 |
|
utils/Makefile, utils/MoLocator.cpp, utils/MoLocator.hpp, |
1771 |
|
utils/bilayerSys.cpp: fixed up sysBuild to where it should now |
1772 |
|
build our systems |
1773 |
|
|
1774 |
< |
2003-04-16 16:11 mmeineke |
1774 |
> |
2003-04-16 17:11 mmeineke |
1775 |
|
|
1776 |
|
* utils/: MoLocator.cpp, MoLocator.hpp: almost finished. |
1777 |
|
|
1778 |
< |
2003-04-15 16:47 mmeineke |
1778 |
> |
2003-04-15 17:47 mmeineke |
1779 |
|
|
1780 |
|
* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: bilayerSys |
1781 |
|
and sysBuild both will build now. woot! |
1782 |
|
|
1783 |
< |
2003-04-15 16:20 mmeineke |
1783 |
> |
2003-04-15 17:20 mmeineke |
1784 |
|
|
1785 |
|
* utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
1786 |
|
bilayerSys.hpp, sysBuild.cpp, sysBuild.hpp: finished bilayerSys.cpp |
1789 |
|
|
1790 |
|
MoLocator.cpp is currently empty |
1791 |
|
|
1792 |
< |
2003-04-15 15:40 chuckv |
1792 |
> |
2003-04-15 16:40 chuckv |
1793 |
|
|
1794 |
|
* forceFields/EAM_FF.frc, forceFields/agu3.eam, |
1795 |
|
forceFields/auu3.eam, forceFields/cuu3.eam, forceFields/niu3.eam, |
1796 |
|
forceFields/pdu3.eam, forceFields/ptu3.eam, |
1797 |
|
libmdtools/ForceFields.hpp: Added eam force files... |
1798 |
|
|
1799 |
< |
2003-04-15 11:37 chuckv |
1799 |
> |
2003-04-15 12:37 chuckv |
1800 |
|
|
1801 |
|
* libmdtools/EAM_FF.cpp: More eam work. |
1802 |
|
|
1803 |
< |
2003-04-14 16:22 mmeineke |
1803 |
> |
2003-04-14 17:22 mmeineke |
1804 |
|
|
1805 |
|
* libmdtools/SimSetup.hpp, utils/Makefile, utils/bilayerSys.cpp, |
1806 |
|
utils/bilayerSys.hpp, utils/sysBuild.cpp, utils/sysBuild.hpp: |
1807 |
|
working on the system builder |
1808 |
|
|
1809 |
< |
2003-04-14 16:16 chuckv |
1809 |
> |
2003-04-14 17:16 chuckv |
1810 |
|
|
1811 |
|
* libmdtools/: Symplectic.cpp, Verlet.cpp, calc_eam.F90: Fixed |
1812 |
|
ordering on NVT calculation in integrators. |
1813 |
|
|
1814 |
< |
2003-04-14 14:51 mmeineke |
1814 |
> |
2003-04-14 15:51 mmeineke |
1815 |
|
|
1816 |
|
* utils/: Makefile, sysBuild.cpp, MPIobj/placeHolder, |
1817 |
|
obj/placeHolder: working on a system builder |
1818 |
|
|
1819 |
< |
2003-04-14 14:04 mmeineke |
1819 |
> |
2003-04-14 15:04 mmeineke |
1820 |
|
|
1821 |
|
* utils/Makefile: added Ghost bends to the TraPPE_Ex forceField |
1822 |
|
|
1823 |
|
added sysBuild to the utils Makefile |
1824 |
|
|
1825 |
< |
2003-04-14 14:03 mmeineke |
1825 |
> |
2003-04-14 15:03 mmeineke |
1826 |
|
|
1827 |
|
* forceFields/TraPPE_Ex.frc, libmdtools/TraPPE_ExFF.cpp: added |
1828 |
|
Ghost bends to the TraPPE_Ex forceField |
1829 |
|
|
1830 |
< |
2003-04-14 13:19 chuckv |
1830 |
> |
2003-04-14 14:19 chuckv |
1831 |
|
|
1832 |
|
* libmdtools/calc_eam.F90: Added first mangling of EAM. |
1833 |
|
|
1834 |
< |
2003-04-11 13:46 mmeineke |
1834 |
> |
2003-04-11 14:46 mmeineke |
1835 |
|
|
1836 |
|
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90, force_globals.F90, |
1837 |
|
simulation_module.F90: fixed a memory bug in Fortran, where |
1838 |
|
molMembershipArray was declared nLocal instead of nGlobal. |
1839 |
|
|
1840 |
< |
2003-04-11 10:16 gezelter |
1840 |
> |
2003-04-11 11:16 gezelter |
1841 |
|
|
1842 |
|
* libmdtools/: Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
1843 |
|
SimSetup.cpp, calc_LJ_FF.F90, do_Forces.F90, |
1844 |
|
fortranWrapDefines.hpp, simulation_module.F90: Bug fix in progress |
1845 |
|
for NPT |
1846 |
|
|
1847 |
< |
2003-04-10 15:08 mmeineke |
1847 |
> |
2003-04-10 16:08 mmeineke |
1848 |
|
|
1849 |
|
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: added a |
1850 |
|
globalIndex counter to Molecule |
1851 |
|
|
1852 |
< |
2003-04-10 11:35 gezelter |
1852 |
> |
2003-04-10 12:35 gezelter |
1853 |
|
|
1854 |
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp: Working on |
1855 |
|
ConstantStress |
1856 |
|
|
1857 |
< |
2003-04-10 11:27 mmeineke |
1857 |
> |
2003-04-10 12:27 mmeineke |
1858 |
|
|
1859 |
|
* libmdtools/SimSetup.cpp: fixed a n mpi init bug in SimSetup. |
1860 |
|
caused a miscalculation of nLocal. |
1861 |
|
|
1862 |
< |
2003-04-10 11:21 mmeineke |
1862 |
> |
2003-04-10 12:21 mmeineke |
1863 |
|
|
1864 |
|
* libmdtools/: Symplectic.cpp, Thermo.cpp, calc_dipole_dipole.F90, |
1865 |
|
do_Forces.F90: fixed a bug in symplectic, where presure was only |
1866 |
|
being calculated the first time through. |
1867 |
|
|
1868 |
< |
2003-04-09 11:20 chuckv |
1868 |
> |
2003-04-09 12:20 chuckv |
1869 |
|
|
1870 |
|
* samples/alkane/alkanes.mdl: added pentane to the alkane model |
1871 |
|
file |
1872 |
|
|
1873 |
< |
2003-04-09 08:59 gezelter |
1873 |
> |
2003-04-09 09:59 gezelter |
1874 |
|
|
1875 |
|
* libmdtools/: ExtendedSystem.cpp, ForceFields.cpp, StatWriter.cpp, |
1876 |
|
Thermo.cpp, Thermo.hpp: Added volume and enthalpy to status file |
1877 |
|
|
1878 |
< |
2003-04-08 23:06 gezelter |
1878 |
> |
2003-04-09 00:06 gezelter |
1879 |
|
|
1880 |
|
* libmdtools/: DumpWriter.cpp, ExtendedSystem.cpp, |
1881 |
|
ExtendedSystem.hpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
1885 |
|
fortranWrapDefines.hpp, simulation_module.F90: fixes for NPT and |
1886 |
|
NVT |
1887 |
|
|
1888 |
< |
2003-04-08 17:38 chuckv |
1888 |
> |
2003-04-08 18:38 chuckv |
1889 |
|
|
1890 |
|
* libmdtools/SimInfo.cpp, libmdtools/Symplectic.cpp, |
1891 |
|
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
1893 |
|
libmdtools/simulation_module.F90, samples/water/ssd.bass: It works |
1894 |
|
(kinda)... |
1895 |
|
|
1896 |
< |
2003-04-08 16:35 gezelter |
1896 |
> |
2003-04-08 17:35 gezelter |
1897 |
|
|
1898 |
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
1899 |
|
libmdtools/ExtendedSystem.cpp, libmdtools/ExtendedSystem.hpp, |
1900 |
|
libmdtools/SimSetup.cpp: Fixes for NPT / NVT |
1901 |
|
|
1902 |
< |
2003-04-08 12:16 chuckv |
1902 |
> |
2003-04-08 13:16 chuckv |
1903 |
|
|
1904 |
|
* libmdtools/: do_Forces.F90, neighborLists.F90, |
1905 |
|
simulation_module.F90: Moved expand neighborlist to init_FF. |
1906 |
|
|
1907 |
< |
2003-04-08 10:20 chuckv |
1907 |
> |
2003-04-08 11:20 chuckv |
1908 |
|
|
1909 |
|
* libmdtools/: ForceFields.cpp, Thermo.cpp, Verlet.cpp: fixes for |
1910 |
|
NVT |
1911 |
|
|
1912 |
< |
2003-04-08 09:39 gezelter |
1912 |
> |
2003-04-08 10:39 gezelter |
1913 |
|
|
1914 |
|
* libmdtools/Verlet.cpp: fixes for nvt / npt |
1915 |
|
|
1916 |
< |
2003-04-08 09:34 gezelter |
1916 |
> |
2003-04-08 10:34 gezelter |
1917 |
|
|
1918 |
|
* libmdtools/: ExtendedSystem.cpp, StatWriter.cpp, Symplectic.cpp, |
1919 |
|
Thermo.cpp, Verlet.cpp: dt/2 fix in nvt |
1920 |
|
|
1921 |
< |
2003-04-08 07:50 gezelter |
1921 |
> |
2003-04-08 08:50 gezelter |
1922 |
|
|
1923 |
|
* libmdtools/ExtendedSystem.cpp: Fixes for affine transform |
1924 |
|
|
1925 |
< |
2003-04-08 07:44 gezelter |
1925 |
> |
2003-04-08 08:44 gezelter |
1926 |
|
|
1927 |
|
* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, |
1928 |
|
Symplectic.cpp, Thermo.cpp, Verlet.cpp: Changes to integrate the |
1929 |
|
NVT and NPT ensembles |
1930 |
|
|
1931 |
< |
2003-04-07 16:42 gezelter |
1931 |
> |
2003-04-07 17:42 gezelter |
1932 |
|
|
1933 |
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
1934 |
|
libmdtools/ExtendedSystem.cpp, libmdtools/SimInfo.cpp, |
1935 |
|
libmdtools/SimSetup.cpp: Fixes for NPT and NVT |
1936 |
|
|
1937 |
< |
2003-04-07 16:20 mmeineke |
1937 |
> |
2003-04-07 17:20 mmeineke |
1938 |
|
|
1939 |
|
* libmdtools/calc_sticky_pair.F90: fixed a sign error in the radial |
1940 |
|
portion of SSD. |
1941 |
|
|
1942 |
< |
2003-04-07 16:16 mmeineke |
1942 |
> |
2003-04-07 17:16 mmeineke |
1943 |
|
|
1944 |
|
* libmdtools/: ForceFields.cpp, Symplectic.cpp: |
1945 |
|
doing some testing in sticky through Symplectic. |
1946 |
|
|
1947 |
< |
2003-04-07 15:51 gezelter |
1947 |
> |
2003-04-07 16:51 gezelter |
1948 |
|
|
1949 |
|
* libmdtools/: ExtendedSystem.cpp, Verlet.cpp: Working on NVT |
1950 |
|
|
1951 |
< |
2003-04-07 15:50 chuckv |
1951 |
> |
2003-04-07 16:50 chuckv |
1952 |
|
|
1953 |
|
* libmdtools/do_Forces.F90: Fixed transpose bug in mpi reduce for |
1954 |
|
tau and virial. |
1955 |
|
|
1956 |
< |
2003-04-07 15:06 mmeineke |
1956 |
> |
2003-04-07 16:06 mmeineke |
1957 |
|
|
1958 |
|
* libmdtools/DumpWriter.cpp, libmdtools/SimInfo.cpp, |
1959 |
|
libmdtools/SimSetup.cpp, libmdtools/Symplectic.cpp, |
1960 |
|
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90, |
1961 |
|
src/Makefile: bug fixes |
1962 |
|
|
1963 |
< |
2003-04-07 11:56 gezelter |
1963 |
> |
2003-04-07 12:56 gezelter |
1964 |
|
|
1965 |
|
* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, |
1966 |
|
StatWriter.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, Verlet.cpp: |
1967 |
|
Many fixes to add extended system |
1968 |
|
|
1969 |
< |
2003-04-07 09:30 gezelter |
1969 |
> |
2003-04-07 10:30 gezelter |
1970 |
|
|
1971 |
|
* src/Makefile: Fixed a bug caused by my experimentation |
1972 |
|
|
1973 |
< |
2003-04-07 09:30 gezelter |
1973 |
> |
2003-04-07 10:30 gezelter |
1974 |
|
|
1975 |
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, |
1976 |
|
Integrator.hpp, Makefile, SimSetup.cpp, Symplectic.cpp, Verlet.cpp: |
1977 |
|
Added ExtendedSystem infrastructure for NPT and NVT calculations |
1978 |
|
|
1979 |
< |
2003-04-07 09:30 gezelter |
1979 |
> |
2003-04-07 10:30 gezelter |
1980 |
|
|
1981 |
|
* libBASS/: Globals.cpp, Globals.hpp: Added targetPressure to BASS |
1982 |
|
|
2329 |
|
|
2330 |
|
2003-03-24 20:07 gezelter |
2331 |
|
|
2332 |
< |
* samples/Makefile: moving tests to samples |
2332 |
> |
* samples/Makefile, tests/Makefile: moving tests to samples |
2333 |
|
|
2334 |
|
2003-03-24 20:06 gezelter |
2335 |
|
|
2336 |
< |
* samples/: alkane/Makefile, alkane/alkanes.mdl, |
2337 |
< |
alkane/butane.bass, alkane/init_butane.eor, argon/Makefile, |
2338 |
< |
argon/argon.bass, argon/init_argon.eor, argon/lj.mdl, |
2339 |
< |
lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor, |
2340 |
< |
lipid/lipid.mdl, lipid/water.mdl, water/Makefile, |
2341 |
< |
water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to |
2342 |
< |
samples |
2336 |
> |
* samples/alkane/Makefile, samples/alkane/alkanes.mdl, |
2337 |
> |
samples/alkane/butane.bass, samples/alkane/init_butane.eor, |
2338 |
> |
samples/argon/Makefile, samples/argon/argon.bass, |
2339 |
> |
samples/argon/init_argon.eor, samples/argon/lj.mdl, |
2340 |
> |
samples/lipid/5x5.bass, samples/lipid/Makefile, |
2341 |
> |
samples/lipid/init_5x5.eor, samples/lipid/lipid.mdl, |
2342 |
> |
samples/lipid/water.mdl, samples/water/Makefile, |
2343 |
> |
samples/water/init_ssd.eor, samples/water/ssd.bass, |
2344 |
> |
samples/water/water.mdl, tests/alkane/Makefile, |
2345 |
> |
tests/alkane/alkanes.mdl, tests/alkane/butane.bass, |
2346 |
> |
tests/alkane/init_butane.eor, tests/argon/Makefile, |
2347 |
> |
tests/argon/argon.bass, tests/argon/init_argon.eor, |
2348 |
> |
tests/argon/lj.mdl, tests/lipid/5x5.bass, tests/lipid/Makefile, |
2349 |
> |
tests/lipid/init_5x5.eor, tests/lipid/lipid.mdl, |
2350 |
> |
tests/lipid/water.mdl, tests/water/Makefile, |
2351 |
> |
tests/water/init_ssd.eor, tests/water/ssd.bass, |
2352 |
> |
tests/water/water.mdl: moved tests to samples |
2353 |
|
|
2354 |
|
2003-03-24 19:51 gezelter |
2355 |
|
|
2357 |
|
|
2358 |
|
2003-03-24 19:46 gezelter |
2359 |
|
|
2360 |
< |
* ac-tools/Make.conf.in: Added makefiles in tests directories |
2360 |
> |
* ac-tools/Make.conf.in, tests/Makefile, tests/alkane/Makefile, |
2361 |
> |
tests/argon/Makefile, tests/lipid/Makefile, tests/water/Makefile: |
2362 |
> |
Added makefiles in tests directories |
2363 |
|
|
2364 |
|
2003-03-24 16:55 gezelter |
2365 |
|
|
2376 |
|
* libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp, |
2377 |
|
do_Forces.F90: little bug fixes here and there |
2378 |
|
|
2379 |
+ |
2003-03-24 11:04 mmeineke |
2380 |
+ |
|
2381 |
+ |
* tests/argon/: argon.bass, init_argon.eor, lj.mdl: added an argon |
2382 |
+ |
test simulation |
2383 |
+ |
|
2384 |
+ |
2003-03-24 11:02 mmeineke |
2385 |
+ |
|
2386 |
+ |
* tests/: lipid/5x5.bass, lipid/init_5x5.eor, lipid/lipid.mdl, |
2387 |
+ |
lipid/water.mdl, water/init_ssd.eor, water/ssd.bass, |
2388 |
+ |
water/water.mdl: [no log message] |
2389 |
+ |
|
2390 |
+ |
2003-03-24 11:02 mmeineke |
2391 |
+ |
|
2392 |
+ |
* tests/alkane/: alkanes.mdl, butane.bass, init_butane.eor: added |
2393 |
+ |
some test bass files for experimenting with |
2394 |
+ |
|
2395 |
|
2003-03-24 10:26 mmeineke |
2396 |
|
|
2397 |
|
* libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug |