notes 58.6 KB
Newer Older
Francois Gygi committed
1
--------------------------------------------------------------------------------
Francois Gygi committed
2 3 4 5 6 7
rel1_63_4
--------------------------------------------------------------------------------
r1844,r1845,r1846: add qbox_maxforce.py script
r1835-r1843: B3LYP and BLYP spin-polarized implementation, SVWN updated
r1829-r1832: qbox_angle.py and qbox_torsion.py scripts
--------------------------------------------------------------------------------
Francois Gygi committed
8 9 10 11 12 13 14 15 16
rel1_63_3
--------------------------------------------------------------------------------
r1825: TorsionCmd.h: revert to previous sign convention for compatibility 
with VMD and consistency with torsion constraint.
--------------------------------------------------------------------------------
r1823: Revert to use of wf (rather than dwf) in preconditioner update
--------------------------------------------------------------------------------
r1818: Added set_velocity command.
--------------------------------------------------------------------------------
Francois Gygi committed
17 18 19
r1809-r1813: modified Context to accept MPI communicators as ctor argument.
Removed pimpl idiom from implementation of Context.
--------------------------------------------------------------------------------
Francois Gygi committed
20 21 22
r1801 moved sync_positions and sync_velocities to AtomSet set_positions and
set_velocities functions
--------------------------------------------------------------------------------
Francois Gygi committed
23 24 25 26 27
rel1_63_2
--------------------------------------------------------------------------------
r1797 BOSampleStepper.C removed timer used in onpe0 section
r1796 JDWavefunctionStepper.C fixed timer name
--------------------------------------------------------------------------------
Francois Gygi committed
28 29 30 31 32 33 34 35
r1792 rel1_63_1
--------------------------------------------------------------------------------
r1792 CGIonicStepper.C: reset velocities at end of CG step
r1791 BOSampleStepper.C: modified etotal_int convergence criterion
r1788 added timers in JDWavefunctionStepper.C
--------------------------------------------------------------------------------
r1786 rel1_63_0
--------------------------------------------------------------------------------
Francois Gygi committed
36 37 38 39
r1779-r1782 Implementation of Harris-Foulkes functional for calc of etotal_int
--------------------------------------------------------------------------------
rel1_62_7 r1776
--------------------------------------------------------------------------------
Francois Gygi committed
40 41 42
r1774: Fixed output of partial_charge command. 
Increased max iter in ConstraintSet (note: two changes in r1774. accidental)
--------------------------------------------------------------------------------
Francois Gygi committed
43
r1771 rel1_62_6
44 45 46 47
Implementation of partial_charge command
Implementation of iter_cmd and iter_cmd_period variables
JDWavefunctionStepper.C Fix: use dwf for preconditioning.
--------------------------------------------------------------------------------
Francois Gygi committed
48
rel1_62_5 r1760
Francois Gygi committed
49 50 51 52 53 54 55 56 57
r1758 GGIonicStepper.C
Reduced alpha_max to 5.0
Rescale alpha when displacement exceeds limit
r1757 testFourierTransform.C
Added MPI barriers for more accurate timing.
Added print of grid sizes.
r1756 AtomSet.C fix reset_vcm in randomize_velocities
r1754 r1755 ElectricEnthalpy.C remove omp pragmas to avoid race condition
--------------------------------------------------------------------------------
Francois Gygi committed
58 59 60 61 62 63 64 65 66 67 68 69 70 71 72
rel1_62_4 r1748
r1748 qb.C: Change URL in header to qboxcode.org
r1742-r1744 ExchangeOperator.C Removed implementation of quadratic correction
to exchange. Correction does not improve accuracy when far from asymptotic
convergence of kpoint sampling.
--------------------------------------------------------------------------------
rel1_62_3 r1735
r1733 Species.C: Fix bug in implementation of nonlocal potential f-projector
r1735 NonLocalPotential.C: Fix bug in nonlocal potential stress contribution
from f projectors
--------------------------------------------------------------------------------
rel1_62_2 r1725
ElectricEnthalpy.[Ch] Changed "polarization" to "dipole" to reflect the
correct physical definition of output. Adjusted output format.
--------------------------------------------------------------------------------
Francois Gygi committed
73 74 75 76 77 78 79
rel1_62_1 r1722
Species.C use 12 digit precision
Fix uninitialized variables
--------------------------------------------------------------------------------
rel1_62_0
Implementation of electric field
--------------------------------------------------------------------------------
80 81 82 83 84 85 86 87 88 89 90 91 92 93
rel1_61_0
Implementation of ONCV potentials
/xml/species.xsd
/xml/sample.xsd
/src/NonLocalPotential.C
/src/SpeciesHandler.C
/src/NonLocalPotential.h
/src/EnergyFunctional.C
/src/SpeciesHandler.h
/src/EnergyFunctional.h
/src/Species.C
/src/Species.h
/src/ChargeDensity.C
/src/ChargeDensity.h
Francois Gygi committed
94
--------------------------------------------------------------------------------
95 96 97 98 99 100 101 102 103
rel1_60_9
r1656 ExchangeOperator.C: changed default bisection tolerance to 1.0
--------------------------------------------------------------------------------
rel1_60_8
r1655 ExchangeOperator print exch time only if DEBUG defined
r1652 Bisection.C print nsweep only if TIMING defined
r1651 ExchangeOperator.C added omp directives in jade.C
r1649 ExchangeOperator.C, Bisection.C added BISECTION_NSWEEP debug option
--------------------------------------------------------------------------------
Francois Gygi committed
104 105 106 107 108 109 110
rel1_60_7
--------------------------------------------------------------------------------
r1645: Bisection.C: modified pair_fraction to reduce calls to overlap.
r1644: optimization of Bisection::overlap speeds up exchange on large problems
r1644: added detailed timers to ExchangeOperator.C
--------------------------------------------------------------------------------
rel1_60_6
Francois Gygi committed
111
--------------------------------------------------------------------------------
Francois Gygi committed
112 113 114 115 116 117
r1605: added -vlocal option to the plot command. Plot Vloc+VHart+Vxc.
r1570: cleanup testXMLGFPreprocessor.C
r1569: cleanup tab ExchangeOperator.C
--------------------------------------------------------------------------------
rel1_60_5
--------------------------------------------------------------------------------
Francois Gygi committed
118 119 120 121 122 123 124 125 126
r1564: modify FFTW3 use of threads
Added -pbc option to distance, angle and torsion functions
PlotCmd.C: fixed -wfs option.
r1552 CPSampleStepper.C: added stepper kinetic energy to econst
Added reset_vcm at end of randomize_v
--------------------------------------------------------------------------------
rel1_60_4 r1550
--------------------------------------------------------------------------------
added FFTW3 option and restored ESSL_FFT functionality
Francois Gygi committed
127 128
r1506: Fixed typo in AlphaPBE0.h
--------------------------------------------------------------------------------
Francois Gygi committed
129 130 131 132
rel1_60_2
CGCellStepper.C: revert to 1.60.0 use of matrix transformations
Use reduced alpha_init (0.002)
--------------------------------------------------------------------------------
Francois Gygi committed
133 134
rel1_60_1
CGCellStepper.C: fixed incorrect use of amat_inv() in calc of gradient.
Francois Gygi committed
135
Note: use was correct. later restored.
Francois Gygi committed
136 137
CGCellStepper.C: reduced initial alpha value to 0.01, max to 0.5.
--------------------------------------------------------------------------------
138 139 140 141
qbox_msd.py: print msd value only, not step index
--------------------------------------------------------------------------------
Context.C: fixed deprecated cast to const char*
--------------------------------------------------------------------------------
142 143 144 145 146 147
rel1_60_0
Added alpha_PBE0 variable
--------------------------------------------------------------------------------
rel1_59_0
Added scf_tol variable
--------------------------------------------------------------------------------
Francois Gygi committed
148 149 150
rel1_58_0
Added utility scripts
--------------------------------------------------------------------------------
Francois Gygi committed
151 152 153
rel1_57_15
--------------------------------------------------------------------------------
r1409: ExchangeOperator.C: fixed coeffs of divergent terms for empty states
Francois Gygi committed
154
r1407: XMLGFPreprocessor.C: add unistd header for close function
Francois Gygi committed
155
--------------------------------------------------------------------------------
Francois Gygi committed
156 157 158 159 160 161
rel1_57_14
--------------------------------------------------------------------------------
r1396: util/kpgen/kpgen.C: fixed odd numbered case and added test.
r1395: Species.C: fix for case of missing radial functions
r1394: BOSampleStepper.C: include weight info in eigenvalues
r1390,r1391: Fix exchange calculation with multiple k-points
Francois Gygi committed
162 163
r1388: Species.[Ch]: ensure that print outputs the same data as was read
from the pseudopotential file.
Francois Gygi committed
164 165
r1363: XMLGFPreprocessor.C: implemented sample loading using http connection.
--------------------------------------------------------------------------------
Francois Gygi committed
166 167
rel1_57_13
--------------------------------------------------------------------------------
Francois Gygi committed
168 169 170 171
r1358: ExchangeOperator.C: Fixed exchange contributions to stress.
KPGridConnectivity.[Ch]: Added cell_moved() member to update cell-dependent 
quantities during cell optimization.
--------------------------------------------------------------------------------
172 173
rel1_57_12
--------------------------------------------------------------------------------
Francois Gygi committed
174
r1354: Added cell_moved() member in ExchangeOperator to resize vbasis
175
--------------------------------------------------------------------------------
Francois Gygi committed
176 177 178 179 180
rel1_57_11
--------------------------------------------------------------------------------
r1349: modified Wavefunction::operator= to allow assignment between wfs with
different cell sizes. Needed for variable cell calculations.
--------------------------------------------------------------------------------
Francois Gygi committed
181 182 183 184 185 186
rel1_57_10
--------------------------------------------------------------------------------
r1344: removed dependency on Context in multiple classes
       SlaterDet uses MPI column communicator instead of Context
--------------------------------------------------------------------------------
rel1_57_9
187
--------------------------------------------------------------------------------
Francois Gygi committed
188 189
r1326: WavefunctionHandler.[Ch]: fixed current_gfdata_pos variable
--------------------------------------------------------------------------------
Francois Gygi committed
190 191 192 193 194 195 196 197 198 199 200 201 202 203
rel1_57_8
--------------------------------------------------------------------------------
r1317: undo r1312: keep positive constraint on delta_spin
r1316: Fixed loading of gfdata into slater_det with non-zero delta_spin
r1315: Restored correct preconditioning when using stress confinement
r1314: EnergyFunctional.[Ch]: removed dependency on ChargeDensity.h from header
r1313: XCOperator.[Ch]: removed dependency on ChargeDensity.h from header
r1312: allow negative delta_spin
r1311: MDWavefunctionStepper.C: removed unused vars
r1310: NonLocalPotential.C: removed unused vars
r1309: removed deprecated conversions from string const to char* in headers
--------------------------------------------------------------------------------
rel1_57_7
--------------------------------------------------------------------------------
Francois Gygi committed
204 205 206 207
r1304: BOSampleStepper.C: removed printing of delta_ehart and delta_eigsum.
Renamed variable nscf_converged.
r1303: Wavefunction.C: fixed add_kpoint to avoid modifying occ of existing kpts
This caused incorrect occupation numbers when loading wf with multiple kpts.
Francois Gygi committed
208 209
r1301: BOSampleStepper.C: print RC1 override msg on pe0 only
--------------------------------------------------------------------------------
Francois Gygi committed
210 211 212 213
rel1_57_6
--------------------------------------------------------------------------------
r1296: SampleHandler.C: set wfv to use same ctxt as s_.wf
--------------------------------------------------------------------------------
Francois Gygi committed
214 215 216 217 218 219 220 221
rel1_57_5
--------------------------------------------------------------------------------
r1292: fixed mlwf calc for spin-polarized case
r1291: ComputeMLWFCmd.C: added spin implementation
r1290: Anderson charge mixing on both spins simultaneously
r1288: BOSampleStepper: moved enthalpy definition out of onpe0 test
--------------------------------------------------------------------------------
r1286: rel1_57_4
Francois Gygi committed
222 223 224 225
r1283: PSDAWavefunctionStepper.C: fixed extrapolate flag
r1282: rewrite of kpgen.C
--------------------------------------------------------------------------------
rel1_57_3
Francois Gygi committed
226
r1275: fix sample read/write for nspin=2. Save cmd writes full species info.
227 228 229
--------------------------------------------------------------------------------
rel1_57_2
r1272: BOSampleStepper.C: fixed nite loop test for nite==0 case
Francois Gygi committed
230
--------------------------------------------------------------------------------
Francois Gygi committed
231
rel1_57_1
Francois Gygi committed
232 233 234
r1265: BOSampleStepper.C: changed behavior for nite=1, use eigenvalue_sum for
convergence test of nite loop, changed threshold value to 0.01*delta_ehart
r1264: RunCmd.C: changed default nite value to 0
Francois Gygi committed
235
r1268: ExchangeOperator.C: Added EXCHANGE_NOQUAD debug string. Cleanup.
Francois Gygi committed
236 237 238 239 240 241
--------------------------------------------------------------------------------
rel1_57_0 r1262
Cleanup of XCOperator and ExchangeOperator to include stress at gamma point
--------------------------------------------------------------------------------
rel1_56_2 r1259
r1257: EnergyFunctional: fix nspin=2 forces, stress.
Francois Gygi committed
242 243
BOSampleStepper: fixed bug in mixing with charge_mix_ndim=0
r1212: Adaptive preconditioner.
Francois Gygi committed
244 245 246
r1211: tolerance for non-self consistent iterations
--------------------------------------------------------------------------------
rel1_55_6
Francois Gygi committed
247 248 249 250 251 252 253
Redesign of Bisection and ExchangeOperator separates bisection transformation
and load-balancing permutation.
Fixed KPGridConnectivity
Added unit_cell info in BOSampleStepper output.
SlatedDet: added occ_ and eig_ to operator=
--------------------------------------------------------------------------------
rel1_55_5
Francois Gygi committed
254
Added polar decomposition in Matrix class.
Francois Gygi committed
255 256 257 258 259 260 261
Use polar in ortho_align, align, lowdin ortho.
--------------------------------------------------------------------------------
rel1_55_4
Added OpenMP pragmas
--------------------------------------------------------------------------------
rel1_55_0
merge of hfb functionality
Francois Gygi committed
262
--------------------------------------------------------------------------------
Francois Gygi committed
263 264 265
rel1_54_6
Added USE_DFFTW macro for platforms providing the dfftw.h header only
--------------------------------------------------------------------------------
Francois Gygi committed
266 267 268 269 270 271 272 273
rel1_54_5
Added enthalpy in BOSampleStepper for use in cell optimization.
BasisMapping.C: fix bug of serial version: MLWF calc of dipole wrong.
Added randomize_r command
removed printing on stdout in rseed command
Changed number of iterations in SlaterDet::{ortho_align,align,riccati}
--------------------------------------------------------------------------------
rel1_54_4
274 275 276 277 278 279 280
Added randomize_v command to set velocities to a Maxwell-Boltzmann distribution
Modified CGIonicStepper: project forces on constraints
Modified BMDIonicStepper: rescale velocity rather than stop
Other steppers: added synchronization calls to ensure consistency of positions
and unit cell values across tasks.
--------------------------------------------------------------------------------
rel1_54_3
281 282 283 284 285 286 287 288 289 290 291 292 293 294
Rewrite of CellStepper, SDCellStepper, CGCellStepper classes.
CGOptimizer and LineMinimizer restructured.
--------------------------------------------------------------------------------
rel1_54_2
fix CG algorithm in CGCellStepper.C
--------------------------------------------------------------------------------
rel1_54_1
CGCellStepper.C: fixed CG algorithm.
--------------------------------------------------------------------------------
rel1_54_1
Basis.C: fixed bug 26: cannot build basis for kpoint close to FCC BZ boundary
fixed in r924
--------------------------------------------------------------------------------
rel1_54_0
295 296 297 298 299 300 301
LineMinimizer.h: limited the number of iterations in bracketing mode to 4
UnitCell.C: accept unit cells with orientation leading to negative volume and
define the volume as fabs(a0*(a1^a2))
CellStepper.C, CGCellStepper.C: implemented CG algorithm to optimize both
cell parameters and atomic positions. Moved implementation of common CellStepper
member functions to CellStepper.C.
--------------------------------------------------------------------------------
Francois Gygi committed
302 303
rel1_53_0
RseedCmd.h: rseed command to initialize random number generator
Francois Gygi committed
304
BOSampleStepper.C: reintroduced wf extrapolation when nite>1 (leads to
Francois Gygi committed
305 306 307 308 309 310
much improved energy conservation in liquid Si)
Matrix.[Ch]: added IntegerMatrix, permutations
ComputeMLWF.C: test if not at Gamma point
StructureFactor.C, SampleWriter.C: added <cstring> for memset
XCPotential.h: moved header dependencies to XCPotential.C
--------------------------------------------------------------------------------
311
rel1_52_4
Francois Gygi committed
312
Introduced a USE_UUID macro in qb.C, uuid_str.[Ch] (some platforms have no
313
uuid library)
Francois Gygi committed
314
Fix bug 23: Wavefunction::set_nempty: added update occ when nempty=0.
315
--------------------------------------------------------------------------------
Francois Gygi committed
316 317 318 319 320 321 322
rel1_52_3
Fixed StructuredDocumentHandler.[Ch] and WavefunctionHandler.C for compilation
with Xerces-C 3.x.x
SampleReader.C: removed debug print
--------------------------------------------------------------------------------
rel1_52_2
RunCmd.h: updated help msg
Francois Gygi committed
323 324 325 326 327 328
rel1_52_2
RunCmd.h: updated help msg
LoadCmd.C: fix bug in reading a sample with atomset only. (unit_cell not set).
Add <cmd> </cmd> tags when echoing commands executed by qbox.
Add <eigenset> tag around <eigenvalues> for each kpoint and spin.
BOSampleStepper.C: Disabled wf extrapolation if nite>1 (unstable)
Francois Gygi committed
329
--------------------------------------------------------------------------------
Francois Gygi committed
330 331 332 333 334 335 336 337 338
rel1_52_1
SlaterDet::gram use beta=0 in herk, for consistency (complex case).
(does not affect results since Matrix ctor clears data).
SlaterDet: removed constraint on Im(c(G=0)) for complex case.
Note: this fixes a bug introduced in 1.51.1 which incorrectly set Im=0 for k!=0.
This fixes bug 2010-04-04T01:14:19Z
Matrix.C: parameters alpha and beta of pzherk and zherk must be double*
Moved files uuid.[Ch] to uuid_str.[Ch] to avoid name conflicts with uuid/uuid.h
--------------------------------------------------------------------------------
Francois Gygi committed
339 340 341 342 343 344 345
rel1_52_0
Added the rescale_v command (RescaleVCmd.h) to rescale all velocities.
Implemented the Bussi-Donadio-Parrinello thermostat.
Added files sampling.C sampling.h
Modified IonicStepper.h to add ekin_stepper member
BOSampleStepper.C: <econst> includes stepper kinetic energy when using BDP.
FourierTransform.C: included some OpenMP pragmas
Francois Gygi committed
346
Known bug: 2010-04-04T01:14:19Z
Francois Gygi committed
347 348
--------------------------------------------------------------------------------
rel1_51_1
Francois Gygi committed
349
Attempt to fix bug 2010-04-04T01:14:19Z
Francois Gygi committed
350
Small imaginary part in c(G=0), initialization in SlaterDet::resize.
Francois Gygi committed
351 352 353
Incorrect fix of 2010-04-04T01:14:19Z causes incorrect results in k!=0 wfs
Later corrected in 1.52.1
Known bug: 2010-04-04T01:14:19Z
Francois Gygi committed
354
--------------------------------------------------------------------------------
Francois Gygi committed
355 356 357 358 359 360 361 362
rel1_51_0
Added external forces: atomic, pair or global.
Added capability to load samples multiple times
Added capability to redefine species
Added uuid identifier in output
SlaterDet.C, Wavefunction.C modified clear, reset, init members
Species.C: modified Species::info to print XML elements
--------------------------------------------------------------------------------
Francois Gygi committed
363 364 365
rel1_50_4
ConstraintSet.C: Fixed uninitialized ndofs_ in ctor.
--------------------------------------------------------------------------------
Francois Gygi committed
366 367 368
rel1_50_3
SampleWriter.C: Fixed size calculation for serial version
--------------------------------------------------------------------------------
369 370 371 372 373
rel1_50_2
Updated several files to enable serial version (without MPI or ScaLAPACK)
Added include<cstring> in various files to get correct memcpy declaration.
(caused trouble with gcc 4.4.1 on Ubuntu).
--------------------------------------------------------------------------------
Francois Gygi committed
374 375 376
rel1_50_1
EnergyFunctional.C:732: use sigma only if compute_stress==true
--------------------------------------------------------------------------------
Francois Gygi committed
377 378 379 380 381 382
rel1_50_0
BOSampleStepper.C, RunCmd.C: added [-atomic_density] option to the run cmd.
AndersonMixer.C: iterative LS problem with adaptive Tikhonov parameter.
Matrix.[Ch]: added getsub for arbitrary block destination
JDWavefunctionStepper.[Ch]: Jacobi-Davidson WavefunctionStepper
--------------------------------------------------------------------------------
Francois Gygi committed
383 384 385 386
rel1_49_1
EnergyFunctional.C: increased criterion for determination of neighboring
cells in esr calculation.
--------------------------------------------------------------------------------
Francois Gygi committed
387 388 389 390 391 392 393
rel1_49_0
BOSampleStepper.C: introduced separate row-weighting of Anderson LS problem
with fixed cutoff rc1=3.0 a.u.
AndersonMixer.C: modified regularization
PlotCmd.C: white space
SlaterDet.C: white space
--------------------------------------------------------------------------------
Francois Gygi committed
394
rel1_48_1
Francois Gygi committed
395 396 397 398 399
SlaterDet.C: fix bug in SlaterDet::write for -text mode
BOSampleStepper.C: modified Kerker weights. Added mixer.reset() call.
AtomCmd.h: fixed text of help message.
AndersonMixer.C: added Tikhonov regularization. Bcast results from task 0.
PlotCmd.C: cleanup include.
Francois Gygi committed
400
--------------------------------------------------------------------------------
Francois Gygi committed
401 402 403 404 405
rel1_48_0
PlotCmd.[Ch]: added plot command. Generates cube format or xyz
{LDA,PBE,BLYP}Functional: modified API for compat. with future implem. of PBE0
SlaterDet.C: added timing ifdefs in gram ortho.
--------------------------------------------------------------------------------
Francois Gygi committed
406 407 408
rel1_47_1
Added a virtual member function in Constraint that returns the number of DOFs to
be subtracted due to that constraint. That number is 1 for all constraints,
Francois Gygi committed
409 410
except for PositionConstraint, for which it is 3. This function is used
by ConstraintSet to keep track of the total number of DOFs to be removed
Francois Gygi committed
411 412
when computing the system temperature. The ConstraintSet class maintains the
total number of DOFs and modifies it only when constraints are added or deleted.
Francois Gygi committed
413 414
MDIonicStepper::ekin() modified to compute kinetic energy correctly in the
presence of constraints.
Francois Gygi committed
415 416
Emass.h: allow reset to zero
BOSampleStepper.C: fix print format of etotal_int
Francois Gygi committed
417
--------------------------------------------------------------------------------
Francois Gygi committed
418 419 420 421 422 423 424 425
rel1_47_0
Add BMDIonicStepper class.
ConstraintCmd.h ConstraintSet.C: Added PositionConstraint class to lock atoms.
Species.C: modified calculation of ndft to ensure rmax>40 a.u.
This corrects the problem that ndft would depend on the number of mesh points
given in the species file.
WavefunctionHandler.C: fix XMLString::release() call for Xerces 3.0.1
--------------------------------------------------------------------------------
Francois Gygi committed
426
rel1_46_0
Francois Gygi committed
427
AndersonMixer.C, BOSampleStepper.C: Implemented multidimensional Anderson
Francois Gygi committed
428
acceleration of charge mixing.
Francois Gygi committed
429
Added charge_mix_ndim to specify dimension of Anderson acceleration of
Francois Gygi committed
430
charge mixing. charge_mix_ndim=0 results in simple mixing.
Francois Gygi committed
431 432 433 434 435
--------------------------------------------------------------------------------
rel1_45_3
UserInterface.C: modified server mode to allow multiple commands in input file.
Use file "<inputfile>.lock" to synchronize with client.
Output file in server mode is now a valid XML fragment, with fpmd namespace.
Francois Gygi committed
436 437
--------------------------------------------------------------------------------
rel1_45_2
Francois Gygi committed
438
qb.C, UserInterface.C: implemented -server option, cleaned up destructors.
Francois Gygi committed
439 440 441 442 443 444 445
AtomSet.C: implemented destructor (fix leaks)
qb.C: added delete s at end (fix leaks)
ConstraintSet: implemented destructor (fix leaks)
Constraint.h and derived classes: implemented virtual destructors.
StrainCmd.h: fix error in usage message.
XMLGFPreprocessor.C: new macro PARALLEL_FS. Limit the number of simultaneous
fread calls if PARALLEL_FS is not defined.
Francois Gygi committed
446
--------------------------------------------------------------------------------
Francois Gygi committed
447
rel1_45_1: fixed SDCellStepper.C: make local copy of sigma to avoid
Francois Gygi committed
448 449
PGI compiler error on franklin: "must be lvalue or...".
--------------------------------------------------------------------------------
Francois Gygi committed
450 451 452 453 454 455 456 457
rel1_45_0
Added strain command for deformation of the cell.
UnitCell.C: removed member compute_deda (moved calc to SDCellStepper). Added
symmetric matrix - vector product function.
SDCellStepper.C fixed calculation of cell correction from stress tensor.
BOSampleStepper.C: reintroduced wf extrapolation when nempty>0 for MD.
RunCmd.h: fixed help msg.
--------------------------------------------------------------------------------
Francois Gygi committed
458 459 460
rel1_44_5
BOSampleStepper.C: Fix uninitialized mlwft ptr. Fixed delete statements.
--------------------------------------------------------------------------------
Francois Gygi committed
461 462
rel1_44_4
BOSampleStepper.C: reintroduced feature that keeps memory of wfv between run
Francois Gygi committed
463
commands. Allows for smooth continuation of multiple runs. Added MLWF and
Francois Gygi committed
464 465 466 467
MLWFC calculation in the niter loop.
Modified wf extrapolation to include alignment in all cases. Use lowdin
orthogonalization after extrapolation.
WfDiag.h: Added MLWF and MLWFC option for the wf_diag variable: computes MLWFs
Francois Gygi committed
468
or MLWF centers at each ionic step.
Francois Gygi committed
469 470
SaveCmd.[Ch], SampleWriter.[Ch]: added -no_wfv option: save without wf velocity.
--------------------------------------------------------------------------------
Francois Gygi committed
471 472
rel1_44_3
UserInterface.h, Base64Transcoder.C: added include <cstring>
Francois Gygi committed
473
removed trailing blanks.
Francois Gygi committed
474
--------------------------------------------------------------------------------
Francois Gygi committed
475 476 477
rel1_44_2
Added copyright headers.
--------------------------------------------------------------------------------
478 479 480 481
rel1_44_1
EnergyFunctional.C: fixed calculation of Esr and Esr stress in cases where the
unit cell is small compared with rcps (initialized in AtomSet.C).
--------------------------------------------------------------------------------
Francois Gygi committed
482 483 484 485
rel1_44_0
WavefunctionHandler.[Ch], SampleReader.[Ch]: fixed compatibility with older
versions when reading samples with smaller grid sizes.
--------------------------------------------------------------------------------
Francois Gygi committed
486 487 488 489 490 491 492 493 494 495
rel1_43_5
BOSampleStepper.C: print energy at end of wf optimization when using niter=0.
Basis.C: modified grid size to cover all grids for any k-point
--------------------------------------------------------------------------------
rel1_43_4
Basis.C: np() yields same grid size for all kpoints
XMLGFPreprocessor.C, SampleReader.C: fixed reading samples with both real and
complex wavefunctions
Wavefunction.C: removed unneeded resize in add_kpoint
--------------------------------------------------------------------------------
Francois Gygi committed
496 497 498 499 500 501
rel1_43_3
TorsionCmd.h: fixed sign of torsion angle.
SlaterDet.[Ch]: fixed const-ness of some members.
Wavefunction.C: modif allocation in add_kpoint to avoid O(nkp**2) time
x8664_gcc.mk: link statically to gfortran libs for better portability of exec.
--------------------------------------------------------------------------------
502 503 504
rel1_43_2
SlaterDet.C: rewrite of the parallel I/O section, using less memory.
--------------------------------------------------------------------------------
Francois Gygi committed
505 506 507 508 509
rel1_43_1
BOSampleStepper.C, CPSampleStepper.C: fixed initialization of ekin_ion,temp_ion.
SampleWriter.C, Wavefunction.C, SlaterDet.C: implementation of parallel I/O
using SharedFilePtr class.
--------------------------------------------------------------------------------
Francois Gygi committed
510 511 512 513 514 515
rel1_43_0
SampleWriter.C, Wavefunction.C, SlaterDet.C: implemented MPI-IO parallel I/O
using individual file pointers, no shared pointers.
SlaterDet.C: fixed bug: base64 transcoding done twice on big endian platforms
when writing in parallel.
--------------------------------------------------------------------------------
Francois Gygi committed
516 517 518 519
rel1_42_0
SlaterDet.C, Wavefunction.C: implemented dynamic resize of ecut or nempty
without loss of data. Changes of cell also preserve wavefunctions.
--------------------------------------------------------------------------------
Francois Gygi committed
520
rel1_41_0
Francois Gygi committed
521
BOSampleStepper.C, CPSampleStepper.C: remove redundant printing of unitcell
Francois Gygi committed
522 523 524 525 526
LineMinimizer.h: new LineMinimizer class used in optimization algorithms
SDIonicStepper.C: back to simple dt^2/m steepest descent (back to rel1_39_0)
SDAIonicStepper.C: steepest descent with line minimization.
CGIonicStepper.C: conjugate gradient with line minimization.
--------------------------------------------------------------------------------
Francois Gygi committed
527 528 529 530 531 532
rel1_40_0
AtomsDyn.h,CGIonicStepper.[Ch]: added CG ionic stepper.
BOSampleStepper.C: enabled niter=0 in run command.
MDIonicStepper.C: removed trailing blanks.
SDAIonicStepper: reduced theta_max, test for energy increase.
SDIonicStepper: implemented line search, removed dt, mass dependency.
Francois Gygi committed
533
Known problems: SD, SDA, CG algorithms are not working properly
Francois Gygi committed
534
--------------------------------------------------------------------------------
Francois Gygi committed
535 536 537 538 539
rel1_39_0
SampleReader.C, SpeciesReader.C: set validation scheme to Val_Auto to allow
successful parsing in the absence of a local copy of sample.xsd or species.xsd.
Added fold_in_ws command: fold all atoms in the WS cell.
MDIonicStepper.C: removed collision debug info printout.
Francois Gygi committed
540
MDIonicStepper.C: make calc of collisions on task 0, then sync in LOWE and
Francois Gygi committed
541
ANDERSEN thermostats. Ensures that all velocities are consistent on all nodes.
Francois Gygi committed
542
PSDAWavefunctionStepper.C: removed psda_enhancement_factor which caused
Francois Gygi committed
543
oscillations in some PSDA optimizations.
Francois Gygi committed
544
BOSampleStepper.C: use wf velocity only inside BOSampleStepper. wfv is not
Francois Gygi committed
545 546
saved at end of steps. wfv is not used at first step for wf extrapolation.
--------------------------------------------------------------------------------
Francois Gygi committed
547 548
rel1_38_0
MDIonicStepper.C: Modified minimum image convention in LOWE thermostat to
Francois Gygi committed
549
conserve angular momentum in clusters. Fixed LOWE and ANDERSEN thermostats to
Francois Gygi committed
550 551 552 553 554 555 556 557
have correct collision rate.
UserInterface.C: fixed endl in output to avoid double endl.
Basis.C: remove pimpl implementation.
ChargeDensity.C: use factorizable sizes for density grid.
EnergyFunctional.C: corrected upper bound of ia1 in esr calculation.
EnergyFunctional.C: implemented multiple cell in esr calculation.
AtomSet.C: changed rcps value to 1.5. Changed interface to access cell.
--------------------------------------------------------------------------------
558 559 560
rel1_37_0
Cleaned up XML formatting of output. Removed comments. Use <timing> tag.
--------------------------------------------------------------------------------
561 562 563 564 565 566
rel1_36_0
Added unit cell to the sample schema. Modified AtomSet to contain a unit cell.
Included unit cell in saved samples.
--------------------------------------------------------------------------------
rel1_35_0
Implemented parallel I/O for writing sample files. Uses MPI-IO.
Francois Gygi committed
567
This does not work on BG/L with PVFS since PVFS does not support the
568 569 570
collective calls MPI_File_write_ordered and MPI_File_write_shared.
Option -serial added to the save command to use the old serial mode.
--------------------------------------------------------------------------------
Francois Gygi committed
571 572 573 574 575 576
rel1_34_4
Base64Transcoder.C: modif print functions to use larger string buffer for I/O.
SampleReader.C, SampleWriter.C: added timer.
Corrected lda arg in various BLACS calls. Did cause errors on
AIX/pessl. (Not a bug when using blacs lib compiled from netlib distribution).
--------------------------------------------------------------------------------
Francois Gygi committed
577 578 579 580 581
rel1_34_3
Wavefunction.C: fixed incorrect XML comments
Basis.C: fixed warning message printed by all tasks when k out of BZ.
AtomSet.C, SpeciesCmd.C: modif to always print species info when a species is
defined, i.e. also when loading from a sample file.
Francois Gygi committed
582
--------------------------------------------------------------------------------
Francois Gygi committed
583 584 585 586 587 588 589 590 591 592 593 594 595
rel1_34_2
WavefunctionHandler.C: fixed for compilation on BG/L
SampleReader.C: fixed for case where loading multiple k-points with wfv
NonLocalPotential.C: fixed calc of forces with multiple k-points
EnergyFunctional.C: fixed forces and stress with multiple k-points
MDWavefunctionStepper.C: fixed CP dynamics with k-points
MLWFTransform.C: changed syntax of blas call (zcopy instead of zcopy_)
NonLocalPotential.C: fix forces with k-point, fix bug introduced in 1.34.0.
SampleReader.C: multiple k-point and wf velocity functionality.
SlaterDet.C: fixed print() and write().
Wavefunction.C: changed context allocation. Fix update_occ, entropy.
PSDWavefunctionStepper.C: fixed complex case (k!=0)
--------------------------------------------------------------------------------
Francois Gygi committed
596 597 598 599 600 601 602
rel1_34_1
Several bug fixes for kpoint functionality.
CPSampleStepper.C: create wfv if absent.
ChargeDensity.C: increased grid size to avoid aliasing with k!=0
--------------------------------------------------------------------------------
rel1_34_0 (not for distribution)
Added kpoints. This release still has bugs. Not for distribution.
Francois Gygi committed
603 604 605 606
--------------------------------------------------------------------------------
rel1_33_5
removed trailing blanks in *.[Ch] *.mk Makefile
--------------------------------------------------------------------------------
Francois Gygi committed
607 608 609
rel1_33_4
ComputeMLWFCmd.C: fixed memory leak.
blas.h: added zgemm, dnrm2.
Francois Gygi committed
610
BOSampleStepper.C: disabled Anderson acceleration of charge mixing by default,
Francois Gygi committed
611 612 613
can be enabled with debug="AND_CHMIX"
AtomSet.C: removed unused variables.
--------------------------------------------------------------------------------
Francois Gygi committed
614 615 616 617 618 619 620
rel1_33_3
BOSampleStepper.C: extrapolation: restored alignment before extrapolation
ChargeMixCoeff.h: changed default value back to 0.5
Matrix.h: added iglobal and jglobal functions
SDAIonicStepper.h: modified default theta_max and theta_nc values
Species.[Ch]: added phi function
--------------------------------------------------------------------------------
Francois Gygi committed
621 622 623
rel1_33_2
Implemented calculation of total electronic and ionic dipole in MLWF.
--------------------------------------------------------------------------------
Francois Gygi committed
624 625 626 627 628 629 630 631 632
rel1_33_1
MLWFTransform.C: fixed bug in MLWF calc when cell sizes in x and y direction
differ.
--------------------------------------------------------------------------------
rel1_33_0 candidate
Implemented compute_mlwf command
Changed spline.C and sinft.C with new implementations.
Modified Species.C to use new spline and sinft interface.
--------------------------------------------------------------------------------
Francois Gygi committed
633
rel1_32_0
634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656
Dt.h, MDIonicStepper.C: modified to allow for negative time step.
Removed Sample.h dependency in WavefunctionStepper and derived classes.
Files affected are
BOSampleStepper.C
SDWavefunctionStepper.C
PSDWavefunctionStepper.C
PSDAWavefunctionStepper.C
EnergyFunctional.C
CPSampleStepper.C
MDWavefunctionStepper.C
WavefunctionStepper.h
SDWavefunctionStepper.h
PSDWavefunctionStepper.h
PSDAWavefunctionStepper.h
MDWavefunctionStepper.h
Removed facs, sigmas from Control.h. Moved vars to ConfinementPotential.
Use hardwired values 2.0 and 0.5 in
BOSampleStepper.C, CPSampleStepper.C
Removed namespace declarations in header files.
--------------------------------------------------------------------------------
rel1_31_0
Added class SampleWriter to separate write function from SaveCmd class.
--------------------------------------------------------------------------------
Francois Gygi committed
657 658 659 660 661 662 663 664
rel1_30_1
Wavefunction.C: typos
XMLGFPreprocessor.C: fixed bug in boundary adjustment.
jacobi.C: implement special case of fewer blocks than process columns.
BOSampleStepper.C: Moved Kerker preconditioning of charge density update
before Anderson acceleration.
ChargeMixCoeff.h: Changed default value to 1.0
ExtStress.h: initialize with zero in ctor
665
MDIonicStepper.C, Thermostat.h: corrected misspelled ANDERSEN
Francois Gygi committed
666
--------------------------------------------------------------------------------
Francois Gygi committed
667 668 669 670 671 672 673
rel1_30_0
D3vector.h: modified ctor to avoid accidental use with only one argument.
AtomSet.[Ch]: added functions to get/reset center of mass velocity.
StatusCmd.h: status cmd prints center of mass velocity.
MDIonicStepper.[Ch]: new thermostats ANDERSON LOWE. Old thermo renamed
to SCALING.
--------------------------------------------------------------------------------
Francois Gygi committed
674 675 676 677 678 679 680
rel1_29_1
BOSampleStepper.C: use wfmm only when needed. ASP extrapolation implemented.
Activate NTC or ASP extrapolation using debug variable.
XMLGFPreprocessor.C: added tests to avoid div by zero if no local grid
--------------------------------------------------------------------------------
rel1_29_0
BOSampleStepper.C: major rewrite:
Francois Gygi committed
681
added a wf_stepper->preprocess before the itscf loop to
Francois Gygi committed
682
get correct extrapolation when ions move.
Francois Gygi committed
683
Modified NTC extrapolation: activated if NTC_EXTRAPOLATION is found in the
Francois Gygi committed
684 685 686 687 688
debug variable.
ReadTSC.h: added missing #define statement
Debug.h: modified to take arbitrary strings
jacobi.C: new jacobi diagonalization. activate with ifdef in Wavefunction.C
--------------------------------------------------------------------------------
Francois Gygi committed
689 690 691 692 693 694 695 696 697 698 699 700
rel1_28_2
AtomSet.h: initialize nel_ in ctor.
XMLGFPreprocessor.C: use char buffer to read file.
Include timers in SlaterDet::ortho_align with #if TIMING
qb.C: remove <> brackets in processor names for XML compatibility (BGL)
AtomSetHandler.C, SpeciesHandler.C: removed msg about xlink, replaced with href
Species.C, SaveCmd.C: removed xlink namespace declaration in sample
SlaterDet.C: added #if TIMING and timers in ortho_align
MDIonicStepper.h: corrected comments
--------------------------------------------------------------------------------
rel1_28_1e{1234567} experimental versions containing
various modifications leading to rel1_28_2
701 702 703
--------------------------------------------------------------------------------
rel1_28_0
qb.C, SaveCmd.C, qbox_xmlns.C, xmlSpecies.C: change namespace to fpmd
Francois Gygi committed
704 705 706
--------------------------------------------------------------------------------
rel1_27_1
minor updates to make single-node version work.
Francois Gygi committed
707 708 709 710 711
--------------------------------------------------------------------------------
rel1_26_1e
redefine constraint command and subcommands, output format.
Introduce constraint names.
Remove ListConstraintsCmd.h
Francois Gygi committed
712
SDAIonicStepper.h: fixed bug:
Francois Gygi committed
713 714
Use of ndofs_ incorrect when ndofs<3*na (when constraints are defined).
Use CHOLESKY_REMAP macro value for size of square context in SlaterDet.C (bgl).
Francois Gygi committed
715
--------------------------------------------------------------------------------
Francois Gygi committed
716
rel1_26_0
Francois Gygi committed
717 718 719 720 721 722
Species.C: changed spline BC for local potential.
SlaterDet.C: randomize: return if basis size is zero.
Implementation of a new logic in all IonicStepper classes.
Implementation of the move command.
Implementation of constraints.
Implementation of distance, angle and torsion measurement commands.
Francois Gygi committed
723 724 725 726 727
--------------------------------------------------------------------------------
rel1_25_0
implementation of netcharge.
SpeciesCmd.C: print species information when adding species.
bug fix: MDWavefunctionStepper.C: correct dt2bye when ecuts>0.
Francois Gygi committed
728 729 730 731 732 733
--------------------------------------------------------------------------------
rel1_24_3
FourierTransform.C: removed unused code.
NonLocalPotential.C: cleanup calculation of G=0 in update_twnl.
BOSampleStepper.C: added APC counters
qb.C: added APC counters
Francois Gygi committed
734 735
--------------------------------------------------------------------------------
rel1_24_2
Francois Gygi committed
736
NonLocalPotential.C: Fixed bug in G=0 component of l=0 non-local projector in
Francois Gygi committed
737
semilocal form (merged bugfix from rel1_23_4)
Francois Gygi committed
738 739
--------------------------------------------------------------------------------
rel1_24_1
Francois Gygi committed
740
SlaterDet.C: fixed bug introduced in 1.24.0: Cholesky decomp was skipped if
Francois Gygi committed
741
CHOLESKY_REMAP is not defined.
Francois Gygi committed
742 743 744 745 746 747 748 749 750 751
--------------------------------------------------------------------------------
rel1_24_0
UnitCell.C: added space in output of lattice vectors.
Wavefunction.C: added syevx option for diagonalization (not active)
BOSampleStepper.C: added diag timer.
SlaterDet.C: Added CHOLESKY_REMAP macro to enable remapping to a square context
in SlaterDet::gram.
SlaterDet.C: rewritten communication in SlaterDet::print and SlaterDet::write
to avoid a deadlock on BGL.
Matrix.C: Added syevx and syevd functions
Francois Gygi committed
752
Note: modif of SlaterDet.C introduced a bug: see 1.24.1
753
--------------------------------------------------------------------------------
Francois Gygi committed
754 755 756
rel1_23_4 (on branch rel1_23_3_bf)
Fixed bug in NonLocalPotential.C: G=0 component of l=0 semilocal projector.
--------------------------------------------------------------------------------
757 758
rel1_23_3
NonLocalPotential.C: fixed bug: double fnl_size should be int fnl_size.
Francois Gygi committed
759 760 761
--------------------------------------------------------------------------------
rel1_23_2
FourierTransform.C: Fixed bug #39: When unit cells are non-orthogonal, the
Francois Gygi committed
762
transforms along x are not done correctly. Bounds including all non-zero
Francois Gygi committed
763 764 765
transforms are redefined.
Basis.C: Simplified basis set construction.
NonLocalPotential.C: removed variables used in old implementation (pre 1.23.0)
Francois Gygi committed
766
--------------------------------------------------------------------------------
Francois Gygi committed
767
rel1_23_1
Francois Gygi committed
768 769
PSDAWavefunctionStepper.C: Reset default theta for negative curvature to 0.0.
AndersonMixer: added settable default theta value for negative curvature.
Francois Gygi committed
770 771 772 773 774
--------------------------------------------------------------------------------
rel1_23_0
Added SDA algorithm for atoms dynamics: Anderson acceleration of SD.
New implementation of NonLocalPotential::energy, recomputing anl array at
every call.
Francois Gygi committed
775
Modified IonicStepper to make ekin and temp virtual. Implemented only in
Francois Gygi committed
776
MDIonicStepper.
777
--------------------------------------------------------------------------------
Francois Gygi committed
778 779 780
rel1_22_0
BOSampleStepper.C: new implementation of Kerker-Anderson charge mixing.
new variables charge_mix_rcut and charge_mix_coeff introduced: determine
Francois Gygi committed
781
the Kerker cutoff and mixing coefficient parameters.
Francois Gygi committed
782
--------------------------------------------------------------------------------
Francois Gygi committed
783 784 785 786 787 788 789 790 791 792
rel1_21_0
Context.[Ch]: redesigned Context to be column-major in all cases.
ChargeDensity.C: vcontext definition modified.
SlaterDet.C: new my_col_ctxt member: store single column Context.
Use modified Context allocation for my_col_ctxt to ensure that calls to
MPI_Comm_create are done with same arguments on all tasks.
Wavefunction.C: use simpler Context constructor (default is col-major).
UserInterface.C: removed printing of newline when echo==true.
Cleaned up timers in wf steppers.
--------------------------------------------------------------------------------
Francois Gygi committed
793 794
rel1_20_1
NonLocalPotential.C: fixed index calculation (bug 38).
Francois Gygi committed
795
--------------------------------------------------------------------------------
Francois Gygi committed
796 797 798 799 800 801 802
rel1_20_0
Wavefunction.C: Changed allocation of sd context to column-major order to get
contiguous nodes in  context columns.
Wavefunction.C: Changed maxiter to 500 and dmu to 2 eV in update_occ.
Nrowmax.h: add update_occ when changing nrowmax.
Matrix.C:219 and similar: removed assert. Some valptr may be 0 on some blocks.
SlaterDet.C: print sdcontext dimensions in SlaterDet::info.
Francois Gygi committed
803
ChargeDensity.C: added (void*) cast to delete statements (for xlC 7.0).
Francois Gygi committed
804
Known bug #38: incorrect forces with nrowmax=16 with 512 tasks. Occurs when
Francois Gygi committed
805
nrowmax <= (ntasks/nrowmax)/2.
Francois Gygi committed
806 807
--------------------------------------------------------------------------------
rel1_19_0 2004-10-04
Francois Gygi committed
808
BOSampleStepper.C: Implemented simple charge mixing for SCF iterations.
Francois Gygi committed
809
Disabled potential mixing.
Francois Gygi committed
810 811 812 813 814 815
SpeciesReader.C: fixed parsing of species files.
SlaterDet.C in print and write: fixed incorrect allocation of char buffer b:
caused segfaults when saving sample.
Base64Transcoder.[Ch]: added cstdio style interface for print function.
FourierTransform.[Ch]: implemented timers, activated if TIMING is defined.
testFourierTransform.C: updated to print timing info in readable form.
Francois Gygi committed
816 817
Known bug: Wavefunction::update_occ iteration on mu does not converge in some
systems.
Francois Gygi committed
818
--------------------------------------------------------------------------------
Francois Gygi committed
819
rel1_18_0 2004-09-14 (not for distribution)
Francois Gygi committed
820
BOSampleStepper modified for scf iterations. Update of charge density and
Francois Gygi committed
821 822 823 824
calculation of VHXC is taken out of EnergyFunctional.
RunCmd modified. Use run niter nitscf nite.
Added FermiTemp variable.
Modifications for calculation of occupation numbers if nempty > 0.
Francois Gygi committed
825
Added USE_XERCES macro. If not defined, the Xerces library is not used, and
Francois Gygi committed
826 827 828 829
only species files can be read. Loading of sample files without the Xerces lib
is not implemented yet.
SlaterDet.C modified to remove dependency on xercesc. Uses Base64Transcoder.
Makefile modified for libqb.a target for BGL.
Francois Gygi committed
830 831
Known bug: SpeciesReader.C incorrect if not USE_XERCES
Known bug: Base64 encoding not done in SlaterDet.C
Francois Gygi committed
832
--------------------------------------------------------------------------------
833
rel1_17_1 2004-08-18
Francois Gygi committed
834
Fixed bug #27: overrun of variable tmpfion in NonLocalPotential.C is due to
Francois Gygi committed
835 836 837 838
incorrect index calculation in situations where na[is] % (ntasks/nrowmax) != 0.
This is the case for (CdSe)_110 on 128 tasks, nrowmax=32, since na[is]/4 = 27.5.
Note: bug #27 does not affect calculations with a single non-local projector
(npr[is]==1).
839
Fixed bug #33 LDAFunctional.C: incorrect use of Perdew-Zunger caused small
840 841 842 843 844
differences (~1.e-3 a.u.) in total energy when compared to other codes.
The adjustment of the constant gamma to make the PZ energy function continuous
was incorrect. Instead, the constants C and D must be adjusted to ensure
continuity of Ec and its derivative at rs=1.
--------------------------------------------------------------------------------
Francois Gygi committed
845
rel1_17_0 2004-08-11
Francois Gygi committed
846
Fixed buffer overrun in Context::string_bcast. (note: bug #27 is not fixed).
Francois Gygi committed
847 848 849 850 851 852 853 854 855 856 857 858
Fixed bug 26: inconsistent qbox xmlns namespace in species file and qbox output.
Modified qb.C: use new qbox_xmlns() function to print qbox XML namespace.
EnergyFunctional.C:909: change lda argument to 14. This was done automatically
by the BLACS lib, but corrected line conforms to the BLACS convention that
lda >= m.
ChargeDensity.C: changed the <total_electronic_charge> output to an XML comment.
SaveCmd.C: include proper xmlns info when saving a sample.
blas.h: reorganized using the ADD_ macro, removed all platform-specific ifdefs.
XCPotential.C: removed underscores in blas calls.
SlaterDet.C: removed underscores in blas calls.
FourierTransform.C: use ADD_ for zdscal.
NonLocalPotential.C: removed underscores in blas calls, removed old OSF ifdefs.
Francois Gygi committed
859
--------------------------------------------------------------------------------
Francois Gygi committed
860 861 862 863
rel1_16_0
Implemented l=1,l=2 non-local stress.
Modified UnitCell.C to avoid infinite loops due to finite precision.
Modified mcr.mk to use library mkl_p4 instead of mkl: -lmkl_p4 before -lmkl
Francois Gygi committed
864
This change of library accelerates the si432 calculation by 12% overall
Francois Gygi committed
865
--------------------------------------------------------------------------------
Francois Gygi committed
866
rel1_15_2
Francois Gygi committed
867
Ecut.h: exit without any action if ecut is same as current value. Caused
Francois Gygi committed
868 869 870 871
zeroing of the wavefunction velocity when used in a redundant manner.
Added isodate.C/isodate.h and release.C/release.h files for separate access
to these functions from any other object.
Added a <description> tag in the sample file in SaveCmd.C including the ISO
Francois Gygi committed
872 873
date and the release of qbox that was used to create the file.
(Note: the tag was already allowed by the Schema specification, but the
Francois Gygi committed
874 875
save command did not write any description information.)
--------------------------------------------------------------------------------
Francois Gygi committed
876 877 878
rel1_15_1
Fixed bug: stop on assert in NonLocalPotential for l=1 or l=2 projectors
Fixed bug: Matrix::init_size() with zero dimensions.
Francois Gygi committed
879 880
Known bugs:
-wf_diag variable is ignored.
Francois Gygi committed
881
--------------------------------------------------------------------------------
Francois Gygi committed
882 883 884 885 886
rel1_15_0
Added R option for the cell_lock variable: rescale unit cell only (keep aspect
ratio fixed).
Corrected inconsistencies between BOSampleStepper.C and CPSampleStepper.C as
regards printing of variables during a run: unit_cell, enthalpy, pv.
Francois Gygi committed
887 888 889 890
Known bugs:
-Stops on assert in NonLocalPotential::update_twnl() for l=1 or l=2 projectors
-Crashes when defining a species without using it, i.e. species with zero atoms.
 Traced to incorrect initialization of sizes in Matrix.C
891
--------------------------------------------------------------------------------
Francois Gygi committed
892
rel1_14_3
Francois Gygi committed
893 894 895
Fixed calculation of ekin_e in MDWavefunctionStepper.C to avoid small error
when printing ekin_e at the first iteration of a CP run. Note: only the printed
ekin_e is affected, wfs are correct.
Francois Gygi committed
896
--------------------------------------------------------------------------------
Francois Gygi committed
897 898 899
rel1_14_2
Fixed Thermostat in MDIonicStepper.C
Fixed use of ionic velocities at first step in CPSampleStepper.C
Francois Gygi committed
900 901 902 903 904 905
Known bug:
Calculation of ekin_e in MDWavefunctionStepper.C at the first iteration uses
the wf velocity at t=0. This is second order accurate, but not consistent with
the calculation of ekin_e in subsequent steps, which introduces a small error
in the printed ekin_e at the first iteration. Ekin_e should be calculated using
a first-order expression, i.e. (wf0-wfm)/dt to be consistent.
Francois Gygi committed
906 907
--------------------------------------------------------------------------------
rel1_14_1a
Francois Gygi committed
908 909 910 911 912
SlaterDet.C: Removed messages from resize about cell being enclosed by ref_cell.
Note: the determination of enclosure should be revised.
SDCellStepper.C: removed debug messages. New "S" option to preserve shape.
BOSampleStepper.C: Added output of cell dimensions if cell is not locked.
Preconditioner.C: bug fixed in calculation of diag when using confinement.
Francois Gygi committed
913
Known bugs:
Francois Gygi committed
914 915
Does not use ionic velocities at first step of CP dynamics.
Thermostat is not working.
Francois Gygi committed
916 917
--------------------------------------------------------------------------------
rel1_14_0
Francois Gygi committed
918
Matrix.h Reintroduced the clear() call in the resize members. Working with
Francois Gygi committed
919 920 921 922
uninitialized matrices sometimes caused NaNs to appear in the padding areas
of the danl matrix in NonLocalPotential.C.
Note that the clear() call was removed in rel1_13_0, which invalidates 1_13_0.
Matrix.C: Added assert()'s in clear() functions.
923 924
BOSampleStepper.C: Introduced quadratic wf extrapolation option (switch
in BOSampleStepper.C, currently disabled in 1.14.0. Added calculation
Francois Gygi committed
925
of forces at each electronic step to monitor the convergence
926
of the force x velocity product (disabled in 1.14.0).
Francois Gygi committed
927
PSDWavefunctionStepper.C: Fixed bug in usage of preconditioner (affects
Francois Gygi committed
928 929
1_13_0 only).
PSDAWavefunctionStepper.C: Fixed bug in usage of preconditioner (see above).
Francois Gygi committed
930
SlaterDet.[Ch]: introduced new orthogonalization and alignment functions:lowdin,
Francois Gygi committed
931 932 933 934 935
align, ortho_align.


--------------------------------------------------------------------------------
rel1_13_0 (not for release, see Matrix clear() bug above)
936 937 938 939 940 941 942 943 944
Implemented stress calculation and variable cell dynamics
Stress calculation works for s-only non-local potentials.
Changed names of variables tau0, taup to r0, rp (and keep tau for scaled
coordinates)
modified the IonicStepper interface to separate the calculation of rp
from the update r0 := rp.
Removed a bug in calculation of eta at first step (was not using ekin_ion)
--------------------------------------------------------------------------------
rel1_13_0a1 (not for release)
Francois Gygi committed
945
Computes stress tensor. Limited to s-only n-l projectors. No cell eq. of
946 947
motion yet. Tested against GP results in cubic Si64.
--------------------------------------------------------------------------------
Francois Gygi committed
948 949 950
rel1_12_1
Removed Gauss-Jacobi quadrature in NonLocalPotential introduced in 1_12_0 and
reverted to trapezoidal rule. Tests on Si64 using trapezoidal, Simpson, Gauss-
Francois Gygi committed
951 952 953 954 955
Legendre and Gauss-Jacobi show that the trapezoidal rule is more efficient
than all other methods, likely because higher order methods are not in their
asymptotic range for reasonable numbers of points  (4-32). A possible
improvement over the present status may be to use Richardson extrapolation,
since the trapezoidal rule has O(h^2) error. However, from the example of Si64,
Francois Gygi committed
956 957
little improvement is obtained for small (4-8) numbers of points.
--------------------------------------------------------------------------------
Francois Gygi committed
958
rel1_12_0
Francois Gygi committed
959
Replaced trapezoidal integration in NonLocalPotential.C by a Gauss-Jacobi rule.
Francois Gygi committed
960
(Note: this was later found to be less efficient. Removed in 1.12.1e)
Francois Gygi committed
961 962 963
Fixed bug in PSDWavefunctionStepper.C and PSDAWavefunctionStepper.C:
use ecut if ecutprec==0.0. Caused nans when ecutprec was not set.
--------------------------------------------------------------------------------
964
rel1_11_2 2003-12-04
Francois Gygi committed
965
Fixed Elan allocation failure problem in SlaterDet::write. Problem was caused
966 967 968
by the large number of buffers allocated by the elan lib for all the messages
sent to task 0 before a receive was posted for them. A barrier in the loop
over states limits the number of messages sent to task 0 at any given time.
Francois Gygi committed
969 970
Note: the problem likely doesn't show on AIX since the MPI implementation may
limit the number of buffered received messages. The barrier is added in the
971 972
AIX code too (SlaterDet::print).
--------------------------------------------------------------------------------
Francois Gygi committed
973 974 975
rel1_11_1
Fixed uninitialized var eta_ in MDIonicStepper that caused errors on AIX.
Known problem: elan allocation failure on mcr when writing h2o64 sample
Francois Gygi committed
976
using 140 tasks on 70 nodes. Possible bug in SlaterDet::write if USE_CSTDIO_LFS.
Francois Gygi committed
977
When running on AIX (using SlaterDet::print instead of SlaterDet::write) no
Francois Gygi committed
978
problem arises, and memory usage per node is low.(fixed in 1_11_2).
Francois Gygi committed
979
--------------------------------------------------------------------------------
Francois Gygi committed
980
rel1_11_0
Francois Gygi committed
981
BOSampleStepper: changed to do extrapolation and ionic move before
Francois Gygi committed
982 983
smoothing the wf. Uses wf velocity if available. Creates it if not
Included PSDA wf stepper.
Francois Gygi committed
984
BO dyn Works ok with PSDA.
Francois Gygi committed
985 986 987 988
Tested 1pe vs 2pe on CH4 BO dynamics: ok.
Corrected bug in SampleReader.C (reading of wf velocity, appeared in rel1_9_0)
--------------------------------------------------------------------------------
rel1_10_0 (not for release) (Note: known bugs)
989 990 991
Complete rewrite of the SampleStepper hierarchy, including CP and BO classes.
Runs CP and BO/SD and BO/PSD tests ok. No extrapolation of wavefunctions yet.
Note: wavefunction extrapolation implemented yet.
Francois Gygi committed
992
Planned work: interchange nite iterations and ionic move in BO stepper, so
993 994
that the wfs at the end of the iteration are the GS for the ionic positions at
the same time.
Francois Gygi committed
995 996
XML files: a <description> tag (optional) was added to the sample.xsd file
to include any information about the sample that a user may want to include.
Francois Gygi committed
997
Bug in SampleReader.C: reading of density matrix for the
Francois Gygi committed
998 999
wavefunction velocity is incorrect. Causes out of sync MPI call and Abort
Corrected in 1_11_0 (candidate)
Francois Gygi committed
1000
--------------------------------------------------------------------------------
Francois Gygi committed
1001
rel1_9_0 (Note: known bugs)
Francois Gygi committed
1002
Large file support (LFS): LFS is not correctly supported for <iostream> in icc
Francois Gygi committed
1003
and gcc 3.2. A workaround is implemented in SaveCmd.C, Wavefunction.C,
Francois Gygi committed
1004 1005 1006 1007
SlaterDet.C. The workaround is activated by defining the USE_CSTDIO_LFS macro.
Occupation numbers moved to the SlaterDet class.
Occupation numbers are not fixed to 2.0 anymore. Load and save now use
occupation numbers.
Francois Gygi committed
1008
Bug in SampleReader.C: reading of density matrix for the
Francois Gygi committed
1009 1010
wavefunction velocity is incorrect. Causes out of sync MPI call and Abort
Corrected in 1_11_0 (candidate)
Francois Gygi committed
1011 1012
--------------------------------------------------------------------------------
rel1_8_2
Francois Gygi committed
1013 1014
Fixed problem with wfvtmp in SampleReader: cannot load sample and
then set wf_dyn = MD. Also, the order of load and set wf_dyn MD commands causes
Francois Gygi committed
1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036
a seg fault.
--------------------------------------------------------------------------------
rel1_8_1
Fixed large-file support for sample files.
Fixed resizing of wf velocity.
Defined Matrix::operator=.
Fixed bug in PSD optimization: G=0 coefficient had zero value of dt2bye.
Fixed bug in UnitCell::fold_in_ws: caused infinite loop in some cases.
--------------------------------------------------------------------------------
rel1_8_0
Added thermostat, th_time, th_temp.
Added emass variable.
--------------------------------------------------------------------------------
rel1_7_1
Fixed bug in calculation of electronic kinetic energy in SampleStepper.C which
caused small kink in ekin_e and spike in econst during restarts.
--------------------------------------------------------------------------------
rel1_7_0
Implemented parallel XML preprocessing of sample files for fast loading.
Added -serial option to the load command to force serial parsing of files.
Fixed a bug in Context::string_send: was incorrect for zero-length strings
initialization of ibuf removed, unnecessary.
Francois Gygi committed
1037
Added new dmin,dmax,imin,imax,string_send,string_recv,pmap functions in
Francois Gygi committed
1038 1039 1040 1041 1042 1043 1044 1045 1046
Context
Changed the block distribution of the slabs in FourierTransform to adopt the
same type of block distribution used in ScaLAPACK. Needed in SampleReader.C
in order to read from the gfdata matrix.
--------------------------------------------------------------------------------
rel1_6_1exp
2003-07-24:modified initialization of coefficients in SlaterDet constructor
to choose g vectors of minimum norm. Note: reverting to -O2 option using xlC
after noting that -O3 causes incorrect results in testBasis.
Francois Gygi committed
1047
Added dmin,dmax,imin,imax members to Context.C to identify process where
Francois Gygi committed
1048 1049 1050
max or min is found.
--------------------------------------------------------------------------------
rel1_6_0
Francois Gygi committed
1051
Implemented MD for wfs and for ions, print ekin_e, ekin_ion, econst in
Francois Gygi committed
1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086
SampleStepper.C. Use Stoermer's rule to compute velocities at end points.
Implemented load/save of wf velocities
--------------------------------------------------------------------------------
rel1_5_1
Fixed bug in NonLocalPotential that appeared for Contexts having multiple
columns and rows (computation of enl and fion incorrect).
--------------------------------------------------------------------------------
rel1_5_0    May 21, 2003
Parallel Load/Save XML sample implemented.
Load is slow: 6 min for 256 states on a (64)^3 grid (H2O_64, 73 Ry)
Save is ok (30 s.)
Bug found in NonLocalPotential::update_eigr: index of first local atom not
computed. Fixed. Affects calculations with multiple-column contexts.
Fixed bug in NonLocalPotential::energy: loop over fnl elements.
Added optional ecut attribute to the wavefunction element to insure
restart from xml sample in exact same conditions. If ecut attribute is not
specified in xml file, a value is inferred from the grid size.
Fixed incorrect initialization of dwf in EnergyFunctional::energy.
Implemented PSD for wf_dyn.
--------------------------------------------------------------------------------
rel1_4_0    May 16, 2003
Implemented byteswap operation when loading/saving XML base64 file on AIX.
(affects WavefunctionHandler.[Ch] and SlaterDet.[Ch].
All storage in base64 form is therefore little-endian. No byte swapping needed
on Intel platforms.
--------------------------------------------------------------------------------
rel1_3_0    May 16, 2003
New features in rel1_3_0:
XML input for sample, species, atomset, wavefunctions, including base64
encoding. New hiearchy of XML handler classes for parsing of sample files.
Parsing done with Apache xerces-c, 2.2.0.
Clean-up of FourierTransform: convention of fwd/bwd changed to be consistent
with usually accepted definitions (forward transform is Fourier analysis, i.e.
computation of Fourier coefficients, and involves scaling by 1/np012. Backward
transform is computation of real-space function from coefficients, no scaling).
Francois Gygi committed
1087
Load command includes reading of sample and appropriate resizing of all
Francois Gygi committed
1088 1089
variables.
The "locked" variable is removed from the Atom class, and will be reintroduced
Francois Gygi committed
1090
as a Constraint. This is to avoid having to include the "locked" info in the
Francois Gygi committed
1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104
XML definition of an Atom.
Builds and runs on Linux (linuc-pc_mpi_icc.mk) and on snow (aix_mpi.mk)
--------------------------------------------------------------------------------
Jan 24, 2003
Checking in release rel1_0_0:
performs SD steps with LDA and local pseudopotentials
--------------------------------------------------------------------------------
Thu Jan  9 16:01:42 PST 2003
Added UserInterface to qb. Commands Set, Print, Quit, Atom.
TO BE FIXED: SlaterDet cannot resize if more states than basis functions.
This forces the order in which ecut, cell and atoms are defined.
--------------------------------------------------------------------------------
Tue Sep 24 14:19:13 PDT 2002
SlaterDet can exist on any context.
Francois Gygi committed
1105
Developing a Wavefunction that can hold any number of SlaterDets for
Francois Gygi committed
1106 1107
arbitrary nspin and nkpoints.
--------------------------------------------------------------------------------