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rel1_63_3
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r1825: TorsionCmd.h: revert to previous sign convention for compatibility 
with VMD and consistency with torsion constraint.
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r1823: Revert to use of wf (rather than dwf) in preconditioner update
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r1818: Added set_velocity command.
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r1809-r1813: modified Context to accept MPI communicators as ctor argument.
Removed pimpl idiom from implementation of Context.
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r1801 moved sync_positions and sync_velocities to AtomSet set_positions and
set_velocities functions
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rel1_63_2
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r1797 BOSampleStepper.C removed timer used in onpe0 section
r1796 JDWavefunctionStepper.C fixed timer name
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r1792 rel1_63_1
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r1792 CGIonicStepper.C: reset velocities at end of CG step
r1791 BOSampleStepper.C: modified etotal_int convergence criterion
r1788 added timers in JDWavefunctionStepper.C
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r1786 rel1_63_0
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r1779-r1782 Implementation of Harris-Foulkes functional for calc of etotal_int
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rel1_62_7 r1776
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r1774: Fixed output of partial_charge command. 
Increased max iter in ConstraintSet (note: two changes in r1774. accidental)
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r1771 rel1_62_6
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Implementation of partial_charge command
Implementation of iter_cmd and iter_cmd_period variables
JDWavefunctionStepper.C Fix: use dwf for preconditioning.
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rel1_62_5 r1760
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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
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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.
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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
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rel1_62_2 r1725
ElectricEnthalpy.[Ch] Changed "polarization" to "dipole" to reflect the
correct physical definition of output. Adjusted output format.
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rel1_62_1 r1722
Species.C use 12 digit precision
Fix uninitialized variables
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rel1_62_0
Implementation of electric field
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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
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rel1_60_9
r1656 ExchangeOperator.C: changed default bisection tolerance to 1.0
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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
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rel1_60_7
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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
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rel1_60_6
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r1605: added -vlocal option to the plot command. Plot Vloc+VHart+Vxc.
r1570: cleanup testXMLGFPreprocessor.C
r1569: cleanup tab ExchangeOperator.C
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rel1_60_5
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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
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rel1_60_4 r1550
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added FFTW3 option and restored ESSL_FFT functionality
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r1506: Fixed typo in AlphaPBE0.h
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rel1_60_2
CGCellStepper.C: revert to 1.60.0 use of matrix transformations
Use reduced alpha_init (0.002)
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rel1_60_1
CGCellStepper.C: fixed incorrect use of amat_inv() in calc of gradient.
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Note: use was correct. later restored.
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CGCellStepper.C: reduced initial alpha value to 0.01, max to 0.5.
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qbox_msd.py: print msd value only, not step index
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Context.C: fixed deprecated cast to const char*
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rel1_60_0
Added alpha_PBE0 variable
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rel1_59_0
Added scf_tol variable
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rel1_58_0
Added utility scripts
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rel1_57_15
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r1409: ExchangeOperator.C: fixed coeffs of divergent terms for empty states
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r1407: XMLGFPreprocessor.C: add unistd header for close function
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rel1_57_14
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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
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r1388: Species.[Ch]: ensure that print outputs the same data as was read
from the pseudopotential file.
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r1363: XMLGFPreprocessor.C: implemented sample loading using http connection.
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rel1_57_13
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r1358: ExchangeOperator.C: Fixed exchange contributions to stress.
KPGridConnectivity.[Ch]: Added cell_moved() member to update cell-dependent 
quantities during cell optimization.
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rel1_57_12
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r1354: Added cell_moved() member in ExchangeOperator to resize vbasis
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rel1_57_11
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r1349: modified Wavefunction::operator= to allow assignment between wfs with
different cell sizes. Needed for variable cell calculations.
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rel1_57_10
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r1344: removed dependency on Context in multiple classes
       SlaterDet uses MPI column communicator instead of Context
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rel1_57_9
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r1326: WavefunctionHandler.[Ch]: fixed current_gfdata_pos variable
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rel1_57_8
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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
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rel1_57_7
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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.
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r1301: BOSampleStepper.C: print RC1 override msg on pe0 only
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rel1_57_6
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r1296: SampleHandler.C: set wfv to use same ctxt as s_.wf
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rel1_57_5
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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
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r1286: rel1_57_4
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r1283: PSDAWavefunctionStepper.C: fixed extrapolate flag
r1282: rewrite of kpgen.C
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rel1_57_3
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r1275: fix sample read/write for nspin=2. Save cmd writes full species info.
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rel1_57_2
r1272: BOSampleStepper.C: fixed nite loop test for nite==0 case
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rel1_57_1
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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
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r1268: ExchangeOperator.C: Added EXCHANGE_NOQUAD debug string. Cleanup.
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rel1_57_0 r1262
Cleanup of XCOperator and ExchangeOperator to include stress at gamma point
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rel1_56_2 r1259
r1257: EnergyFunctional: fix nspin=2 forces, stress.
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BOSampleStepper: fixed bug in mixing with charge_mix_ndim=0
r1212: Adaptive preconditioner.
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r1211: tolerance for non-self consistent iterations
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rel1_55_6
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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=
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rel1_55_5
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Added polar decomposition in Matrix class.
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Use polar in ortho_align, align, lowdin ortho.
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rel1_55_4
Added OpenMP pragmas
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rel1_55_0
merge of hfb functionality
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rel1_54_6
Added USE_DFFTW macro for platforms providing the dfftw.h header only
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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}
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rel1_54_4
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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.
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rel1_54_3
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Rewrite of CellStepper, SDCellStepper, CGCellStepper classes.
CGOptimizer and LineMinimizer restructured.
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rel1_54_2
fix CG algorithm in CGCellStepper.C
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rel1_54_1
CGCellStepper.C: fixed CG algorithm.
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rel1_54_1
Basis.C: fixed bug 26: cannot build basis for kpoint close to FCC BZ boundary
fixed in r924
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rel1_54_0
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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.
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rel1_53_0
RseedCmd.h: rseed command to initialize random number generator
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BOSampleStepper.C: reintroduced wf extrapolation when nite>1 (leads to
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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
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rel1_52_4
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Introduced a USE_UUID macro in qb.C, uuid_str.[Ch] (some platforms have no
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uuid library)
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Fix bug 23: Wavefunction::set_nempty: added update occ when nempty=0.
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rel1_52_3
Fixed StructuredDocumentHandler.[Ch] and WavefunctionHandler.C for compilation
with Xerces-C 3.x.x
SampleReader.C: removed debug print
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rel1_52_2
RunCmd.h: updated help msg
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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)
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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
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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
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Known bug: 2010-04-04T01:14:19Z
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rel1_51_1
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Attempt to fix bug 2010-04-04T01:14:19Z
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Small imaginary part in c(G=0), initialization in SlaterDet::resize.
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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
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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
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rel1_50_4
ConstraintSet.C: Fixed uninitialized ndofs_ in ctor.
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rel1_50_3
SampleWriter.C: Fixed size calculation for serial version
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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).
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rel1_50_1
EnergyFunctional.C:732: use sigma only if compute_stress==true
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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
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rel1_49_1
EnergyFunctional.C: increased criterion for determination of neighboring
cells in esr calculation.
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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
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rel1_48_1
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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.
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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.
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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,
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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
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when computing the system temperature. The ConstraintSet class maintains the
total number of DOFs and modifies it only when constraints are added or deleted.
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MDIonicStepper::ekin() modified to compute kinetic energy correctly in the
presence of constraints.
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Emass.h: allow reset to zero
BOSampleStepper.C: fix print format of etotal_int
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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
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rel1_46_0
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AndersonMixer.C, BOSampleStepper.C: Implemented multidimensional Anderson
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acceleration of charge mixing.
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Added charge_mix_ndim to specify dimension of Anderson acceleration of
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charge mixing. charge_mix_ndim=0 results in simple mixing.
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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.
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rel1_45_2
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qb.C, UserInterface.C: implemented -server option, cleaned up destructors.
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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.
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rel1_45_1: fixed SDCellStepper.C: make local copy of sigma to avoid
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PGI compiler error on franklin: "must be lvalue or...".
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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.
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rel1_44_5
BOSampleStepper.C: Fix uninitialized mlwft ptr. Fixed delete statements.
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rel1_44_4
BOSampleStepper.C: reintroduced feature that keeps memory of wfv between run
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commands. Allows for smooth continuation of multiple runs. Added MLWF and
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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
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or MLWF centers at each ionic step.
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SaveCmd.[Ch], SampleWriter.[Ch]: added -no_wfv option: save without wf velocity.
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rel1_44_3
UserInterface.h, Base64Transcoder.C: added include <cstring>
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removed trailing blanks.
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rel1_44_2
Added copyright headers.
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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).
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rel1_44_0
WavefunctionHandler.[Ch], SampleReader.[Ch]: fixed compatibility with older
versions when reading samples with smaller grid sizes.
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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
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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
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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.
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rel1_43_2
SlaterDet.C: rewrite of the parallel I/O section, using less memory.
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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.
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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.
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rel1_42_0
SlaterDet.C, Wavefunction.C: implemented dynamic resize of ecut or nempty
without loss of data. Changes of cell also preserve wavefunctions.
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rel1_41_0
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BOSampleStepper.C, CPSampleStepper.C: remove redundant printing of unitcell
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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.
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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.
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Known problems: SD, SDA, CG algorithms are not working properly
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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.
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534
MDIonicStepper.C: make calc of collisions on task 0, then sync in LOWE and
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535
ANDERSEN thermostats. Ensures that all velocities are consistent on all nodes.
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536
PSDAWavefunctionStepper.C: removed psda_enhancement_factor which caused
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537
oscillations in some PSDA optimizations.
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538
BOSampleStepper.C: use wf velocity only inside BOSampleStepper. wfv is not
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saved at end of steps. wfv is not used at first step for wf extrapolation.
--------------------------------------------------------------------------------
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rel1_38_0
MDIonicStepper.C: Modified minimum image convention in LOWE thermostat to
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543
conserve angular momentum in clusters. Fixed LOWE and ANDERSEN thermostats to
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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.
--------------------------------------------------------------------------------
552 553 554
rel1_37_0
Cleaned up XML formatting of output. Removed comments. Use <timing> tag.
--------------------------------------------------------------------------------
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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.
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This does not work on BG/L with PVFS since PVFS does not support the
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collective calls MPI_File_write_ordered and MPI_File_write_shared.
Option -serial added to the save command to use the old serial mode.
--------------------------------------------------------------------------------
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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).
--------------------------------------------------------------------------------
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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.
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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)
--------------------------------------------------------------------------------
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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.
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--------------------------------------------------------------------------------
rel1_33_5
removed trailing blanks in *.[Ch] *.mk Makefile
--------------------------------------------------------------------------------
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rel1_33_4
ComputeMLWFCmd.C: fixed memory leak.
blas.h: added zgemm, dnrm2.
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604
BOSampleStepper.C: disabled Anderson acceleration of charge mixing by default,
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can be enabled with debug="AND_CHMIX"
AtomSet.C: removed unused variables.
--------------------------------------------------------------------------------
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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
--------------------------------------------------------------------------------
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rel1_33_2
Implemented calculation of total electronic and ionic dipole in MLWF.
--------------------------------------------------------------------------------
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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.
--------------------------------------------------------------------------------
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rel1_32_0
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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.
--------------------------------------------------------------------------------
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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
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MDIonicStepper.C, Thermostat.h: corrected misspelled ANDERSEN
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--------------------------------------------------------------------------------
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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.
--------------------------------------------------------------------------------
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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:
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added a wf_stepper->preprocess before the itscf loop to
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get correct extrapolation when ions move.
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Modified NTC extrapolation: activated if NTC_EXTRAPOLATION is found in the
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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
--------------------------------------------------------------------------------
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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
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--------------------------------------------------------------------------------
rel1_28_0
qb.C, SaveCmd.C, qbox_xmlns.C, xmlSpecies.C: change namespace to fpmd
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--------------------------------------------------------------------------------
rel1_27_1
minor updates to make single-node version work.
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--------------------------------------------------------------------------------
rel1_26_1e
redefine constraint command and subcommands, output format.
Introduce constraint names.
Remove ListConstraintsCmd.h
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SDAIonicStepper.h: fixed bug:
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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).
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--------------------------------------------------------------------------------
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rel1_26_0
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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.
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--------------------------------------------------------------------------------
rel1_25_0
implementation of netcharge.
SpeciesCmd.C: print species information when adding species.
bug fix: MDWavefunctionStepper.C: correct dt2bye when ecuts>0.
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--------------------------------------------------------------------------------
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
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--------------------------------------------------------------------------------
rel1_24_2
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730
NonLocalPotential.C: Fixed bug in G=0 component of l=0 non-local projector in
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semilocal form (merged bugfix from rel1_23_4)
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--------------------------------------------------------------------------------
rel1_24_1
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SlaterDet.C: fixed bug introduced in 1.24.0: Cholesky decomp was skipped if
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CHOLESKY_REMAP is not defined.
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--------------------------------------------------------------------------------
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
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Note: modif of SlaterDet.C introduced a bug: see 1.24.1
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--------------------------------------------------------------------------------
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rel1_23_4 (on branch rel1_23_3_bf)
Fixed bug in NonLocalPotential.C: G=0 component of l=0 semilocal projector.
--------------------------------------------------------------------------------
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rel1_23_3
NonLocalPotential.C: fixed bug: double fnl_size should be int fnl_size.
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--------------------------------------------------------------------------------
rel1_23_2
FourierTransform.C: Fixed bug #39: When unit cells are non-orthogonal, the
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756
transforms along x are not done correctly. Bounds including all non-zero
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transforms are redefined.
Basis.C: Simplified basis set construction.
NonLocalPotential.C: removed variables used in old implementation (pre 1.23.0)
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--------------------------------------------------------------------------------
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rel1_23_1
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PSDAWavefunctionStepper.C: Reset default theta for negative curvature to 0.0.
AndersonMixer: added settable default theta value for negative curvature.
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--------------------------------------------------------------------------------
rel1_23_0
Added SDA algorithm for atoms dynamics: Anderson acceleration of SD.
New implementation of NonLocalPotential::energy, recomputing anl array at
every call.
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Modified IonicStepper to make ekin and temp virtual. Implemented only in
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MDIonicStepper.
771
--------------------------------------------------------------------------------
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rel1_22_0
BOSampleStepper.C: new implementation of Kerker-Anderson charge mixing.
new variables charge_mix_rcut and charge_mix_coeff introduced: determine
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the Kerker cutoff and mixing coefficient parameters.
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--------------------------------------------------------------------------------
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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.
--------------------------------------------------------------------------------
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rel1_20_1
NonLocalPotential.C: fixed index calculation (bug 38).
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--------------------------------------------------------------------------------
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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
797
ChargeDensity.C: added (void*) cast to delete statements (for xlC 7.0).
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798
Known bug #38: incorrect forces with nrowmax=16 with 512 tasks. Occurs when
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799
nrowmax <= (ntasks/nrowmax)/2.
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--------------------------------------------------------------------------------
rel1_19_0 2004-10-04
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BOSampleStepper.C: Implemented simple charge mixing for SCF iterations.
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Disabled potential mixing.
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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.
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Known bug: Wavefunction::update_occ iteration on mu does not converge in some
systems.
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--------------------------------------------------------------------------------
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rel1_18_0 2004-09-14 (not for distribution)
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814
BOSampleStepper modified for scf iterations. Update of charge density and
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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.
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819
Added USE_XERCES macro. If not defined, the Xerces library is not used, and
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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.
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Known bug: SpeciesReader.C incorrect if not USE_XERCES
Known bug: Base64 encoding not done in SlaterDet.C
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--------------------------------------------------------------------------------
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rel1_17_1 2004-08-18
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Fixed bug #27: overrun of variable tmpfion in NonLocalPotential.C is due to
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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).
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Fixed bug #33 LDAFunctional.C: incorrect use of Perdew-Zunger caused small
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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.
--------------------------------------------------------------------------------
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rel1_17_0 2004-08-11
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Fixed buffer overrun in Context::string_bcast. (note: bug #27 is not fixed).
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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.
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--------------------------------------------------------------------------------
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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
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This change of library accelerates the si432 calculation by 12% overall
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--------------------------------------------------------------------------------
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rel1_15_2
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Ecut.h: exit without any action if ecut is same as current value. Caused
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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
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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
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save command did not write any description information.)
--------------------------------------------------------------------------------
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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.
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Known bugs:
-wf_diag variable is ignored.
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--------------------------------------------------------------------------------
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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.
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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
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--------------------------------------------------------------------------------
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rel1_14_3
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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.
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--------------------------------------------------------------------------------
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rel1_14_2
Fixed Thermostat in MDIonicStepper.C
Fixed use of ionic velocities at first step in CPSampleStepper.C
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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.
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--------------------------------------------------------------------------------
rel1_14_1a
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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.
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Known bugs:
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Does not use ionic velocities at first step of CP dynamics.
Thermostat is not working.
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--------------------------------------------------------------------------------
rel1_14_0
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Matrix.h Reintroduced the clear() call in the resize members. Working with
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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.
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BOSampleStepper.C: Introduced quadratic wf extrapolation option (switch
in BOSampleStepper.C, currently disabled in 1.14.0. Added calculation
Francois Gygi committed
919
of forces at each electronic step to monitor the convergence
920
of the force x velocity product (disabled in 1.14.0).
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921
PSDWavefunctionStepper.C: Fixed bug in usage of preconditioner (affects
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1_13_0 only).
PSDAWavefunctionStepper.C: Fixed bug in usage of preconditioner (see above).
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SlaterDet.[Ch]: introduced new orthogonalization and alignment functions:lowdin,
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align, ortho_align.


--------------------------------------------------------------------------------
rel1_13_0 (not for release, see Matrix clear() bug above)
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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)
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Computes stress tensor. Limited to s-only n-l projectors. No cell eq. of
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motion yet. Tested against GP results in cubic Si64.
--------------------------------------------------------------------------------
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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
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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,
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little improvement is obtained for small (4-8) numbers of points.
--------------------------------------------------------------------------------
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rel1_12_0
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Replaced trapezoidal integration in NonLocalPotential.C by a Gauss-Jacobi rule.
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(Note: this was later found to be less efficient. Removed in 1.12.1e)
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Fixed bug in PSDWavefunctionStepper.C and PSDAWavefunctionStepper.C:
use ecut if ecutprec==0.0. Caused nans when ecutprec was not set.
--------------------------------------------------------------------------------
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rel1_11_2 2003-12-04
Francois Gygi committed
959
Fixed Elan allocation failure problem in SlaterDet::write. Problem was caused
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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.
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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
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AIX code too (SlaterDet::print).
--------------------------------------------------------------------------------
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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
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using 140 tasks on 70 nodes. Possible bug in SlaterDet::write if USE_CSTDIO_LFS.
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When running on AIX (using SlaterDet::print instead of SlaterDet::write) no
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problem arises, and memory usage per node is low.(fixed in 1_11_2).
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--------------------------------------------------------------------------------
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rel1_11_0
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BOSampleStepper: changed to do extrapolation and ionic move before
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smoothing the wf. Uses wf velocity if available. Creates it if not
Included PSDA wf stepper.
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BO dyn Works ok with PSDA.
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Tested 1pe vs 2pe on CH4 BO dynamics: ok.
Corrected bug in SampleReader.C (reading of wf velocity, appeared in rel1_9_0)
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rel1_10_0 (not for release) (Note: known bugs)
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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.
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Planned work: interchange nite iterations and ionic move in BO stepper, so
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that the wfs at the end of the iteration are the GS for the ionic positions at
the same time.
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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.
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Bug in SampleReader.C: reading of density matrix for the
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wavefunction velocity is incorrect. Causes out of sync MPI call and Abort
Corrected in 1_11_0 (candidate)
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rel1_9_0 (Note: known bugs)
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Large file support (LFS): LFS is not correctly supported for <iostream> in icc
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and gcc 3.2. A workaround is implemented in SaveCmd.C, Wavefunction.C,
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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.
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Bug in SampleReader.C: reading of density matrix for the
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wavefunction velocity is incorrect. Causes out of sync MPI call and Abort
Corrected in 1_11_0 (candidate)
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rel1_8_2
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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
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a seg fault.
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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.
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rel1_8_0
Added thermostat, th_time, th_temp.
Added emass variable.
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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.
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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.
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Added new dmin,dmax,imin,imax,string_send,string_recv,pmap functions in
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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.
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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.
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Added dmin,dmax,imin,imax members to Context.C to identify process where
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max or min is found.
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rel1_6_0
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Implemented MD for wfs and for ions, print ekin_e, ekin_ion, econst in
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SampleStepper.C. Use Stoermer's rule to compute velocities at end points.
Implemented load/save of wf velocities
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rel1_5_1
Fixed bug in NonLocalPotential that appeared for Contexts having multiple
columns and rows (computation of enl and fion incorrect).
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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.
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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.
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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).
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Load command includes reading of sample and appropriate resizing of all
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variables.
The "locked" variable is removed from the Atom class, and will be reintroduced
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as a Constraint. This is to avoid having to include the "locked" info in the
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XML definition of an Atom.
Builds and runs on Linux (linuc-pc_mpi_icc.mk) and on snow (aix_mpi.mk)
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Jan 24, 2003
Checking in release rel1_0_0:
performs SD steps with LDA and local pseudopotentials
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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.
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Tue Sep 24 14:19:13 PDT 2002
SlaterDet can exist on any context.
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Developing a Wavefunction that can hold any number of SlaterDets for
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arbitrary nspin and nkpoints.
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