~nickpapior/siesta/trunk-kovalp : changes

~nickpapior/siesta/trunk-kovalp » Changes to Tests/h3po4_1 from revision 588

From Revision 588

Rev	Summary	Authors	Date
368	Incorporation of BSC code: mesh optimization; parallel fdf l... Incorporation of BSC code: mesh optimization; parallel fdf library * The ongoing collaboration with the Barcelona Supercomputer Center (through the department of Computer Applications in Science and Engineering) has resulted in two new main enhancements: - New code to improve the load-balance among processors in the operations carried out in the real-space mesh (involved in the computation of charge density, exchange-correlation potential, and matrix elements of the hamiltonian, among others). Since the different operations have different work-load patterns, it has been necessary to define and handle three separate data distributions, with appropriately optimized communication patterns. Most of the new code is contained in new specialized modules, and there are calls for data distribution handling in higher-level modules, notably dhscf. An overview of the rationale and implementation of the new functionality can be found in An efficient implementation of a QM-MM method in SIESTA, C. F. Sanz-Navarro, R. Grima, A. Garcia, E. A. Bea, A. Soba, J.M. Cela, and P. Ordejon, Theoretical Chemistry Accounts. Online pub Sep 2010. DOI: 10.1007/s00214-010-0816-5 We are working on a set of developer-oriented notes to facilitate future enhancements. - A new fdf library which avoids the 'master node bottleneck': each MPI processor now holds a copy of the relevant information, and can satisfy fdf queries without the need for interprocess communication or file access. The most noticeable change is in the processing of fdf blocks. The previous version of the library provided a Fortran unit number from which the user code could read the block contents. Now the user is given an abstract handle with which to perform explicitly the operations of reading lines, parse, and extract useful information. This paradigm was already present as a wrapper in previous versions of Siesta, but it is now mandatory. The two new developments, while formally independent, have been merged at the same time due to historical and logistical reasons. Even though the mesh enhancements affect directly only a relatively small number of files, many others have been modified: some by changes in memory allocation syntax and indentation, and some to clarify code patterns or interfaces (see below). The new treatment of fdf blocks and the removal of the explicit broadcast step in some existing fdf calls has meant changes to many other files. In all, this patch affects several dozen files in the Siesta distribution. * Other significant changes - The interface to the spherical-harmonics module in matel has been changed to avoid the creation of temporary arrays at run time. Also, some internal arrays in the spherical-harmonics module are now pre-allocated to avoid overhead. - Throughout the code most 'allocatable' arrays have been turned into pointers, to be able to exploit the functionality in the alloc module to resize them concisely. It can be argued that we have gone too far in some cases. We have invested a lot of effort in this work, but it is very likely that some issues have escaped us. A list of those known at this time can be found in the file Docs/KNOWN.ISSUES.BSC-patch removed: Src/FoX/arch.make Src/doping.F Src/fdf/fdf.f Src/fdf/fdf.h Src/fdf/fdf_mod.f Src/fdf/fdfdefs.h Src/fdf/io_for_fdf_tests.f Src/fdf/io_sample.f Src/fdf/parse.f Src/fdf/sample.f Src/m_efield.F Tests/bsc-compare.sh Tests/std-compare.sh Util/Denchar/Src/fdf/.dummy_dir Util/Gen-basis/fdf/.dummy_directory Util/TBTrans/Libs/ Util/TBTrans/Libs/.dummy_directory Util/TBTrans/MPI/ Util/TBTrans/MPI/.dummy_dir Util/TBTrans/fdf/ Util/VCA/fdf/.dummy_directory Util/Vibra/Src/fdf/.dummy_directory added: .bzrignore Docs/BSC.CHANGES Docs/KNOWN.ISSUES.BSC-patch Src/FoX/arch.make Src/Libs/dgetrs_lapack.f Src/Libs/dspev_lapack.f Src/Sys/altix-32b-par.make Src/Sys/altix-32b-ser.make Src/Sys/atto-pgf95-openmpi.make Src/Sys/finisterrae.make.moved Src/Sys/g95-macosx-netcdf.make Src/Sys/gfortran-macosx-netcdf.make Src/Sys/intel-mpi-checks-metis.make Src/Sys/intel10-openmpi.make Src/Sys/intel11-openmpi.make Src/Sys/macosx-openmpi.make Src/Sys/marenostrum-lanczos.make Src/Sys/marenostrum-mpi-metis-64.make Src/Sys/mn-32b-par.make Src/Sys/mn-32b-ser.make Src/Sys/mn-openmp.make Src/Sys/nano-intel10-mvapich.make Src/Sys/pgf95-pgimpi.make Src/Sys/rogeli-intel-par.make Src/bsc_cellxc.F Src/bsc_xcmod.F Src/cellxc_mod.F Src/debugmpi.F Src/doping_uniform.F Src/fdf.Standard Src/fdf/XY.fdf Src/fdf/arch.make Src/fdf/fdf.F90 Src/fdf/hostfile Src/fdf/io_fdf.F90 Src/fdf/iso_fortran_env.F90 Src/fdf/parse.F90 Src/fdf/prec.F90 Src/fdf/sample.F90 Src/fdf/submit.sh Src/fdf/tags Src/fdf/utils.F90 Src/final_H_f_stress.F Src/m_diagon.F Src/m_dscfcomm.F Src/m_efield.F Src/mesh.F Src/meshcomm.F Src/meshphi.F Src/moremeshsubs.F Src/qsort.F Src/schecomm.F Src/setup_H0.F Src/walltime.c Src/xc.f Tests/mgc-force/ Tests/mgc-force/makefile Tests/mgc-force/mgc-force.fdf Tests/mgc-force/mgc-force.pseudos Util/Denchar/Src/timer_local.f renamed: Src/atom.f => Src/atom.F Src/forhar.f => Src/forhar.F Src/hsparse.f => Src/hsparse.F Src/meshmatrix.F => Src/meshdscf.F Src/parallelsubs.f => Src/parallelsubs.F Src/rhooda.f => Src/rhooda.F Src/rhoofd.f => Src/rhoofd.F Src/sparse_matrices.F90 => Src/sparse_matrices.F Src/timer.f90 => Src/timer.F90 Src/vmat.f => Src/vmat.F modified: Docs/siesta.ind Docs/siesta.tex Src/MPI/generate.sh Src/MPI/mpi.F Src/MPI/mpi__include.f90 Src/Makefile Src/SiestaXC/lib-makefile Src/SiestaXC/makefile Src/Sys/finisterrae.make Src/Sys/gfortran-netcdf.make Src/Sys/marenostrum-mpi-32.make Src/Sys/nano-intel-mpi-cdf.make Src/Sys/nano-intel-mpi.make Src/alloc.F90 Src/arw.f Src/atm_transfer.f Src/atm_types.f Src/atmfuncs.f Src/atomlist.f Src/atomlwf.F Src/bands.F Src/basis_io.F Src/basis_specs.f Src/basis_types.f Src/bonds.f Src/born_charge.F Src/broadcast_basis.F Src/broyden_optim.F Src/cdiag.F Src/cell_broyden_optim.F Src/cell_fire_optim.F Src/cgvc.F Src/cgvc_zmatrix.F Src/cgwf.F Src/chemical.f Src/chempot.F Src/compute_dm.F Src/conjgr.f Src/constr.f Src/coor.F Src/denmat.F Src/denmatlomem.F Src/densematrix.f Src/detover.F Src/dfscf.f Src/dhscf.F Src/diag2g.F Src/diag2k.F Src/diagg.F Src/diagk.F Src/diagk_file.F Src/diagkp.F Src/diagon.F Src/diagpol.f Src/diagsprl.F Src/dipole.F Src/dnaefs.f Src/dynamics.f Src/egandd.F Src/eggbox.F Src/electrostatic.f Src/ener3.F Src/ener3lomem.F Src/fdf/Otherfile Src/fdf/README Src/fdf/coords.fdf Src/fdf/fdf.Standard Src/fdf/makefile Src/fdf/sample.fdf Src/fermid.F Src/fft.F Src/find_kgrid.F Src/fire_optim.F Src/fixed.F Src/get_target_stress.f Src/globalise.F Src/gradient.F Src/gradientlomem.F Src/grdsam.F Src/initatom.f Src/initparallel.F Src/iocg.f Src/iodm.F Src/iodm_netcdf.F90 Src/iodmhs_netcdf.F90 Src/ioeig.f Src/iofa.f Src/iogrid_netcdf.F90 Src/iokp.f Src/iolwf.F Src/iomd.f Src/iopipes.F90 Src/ioxv.F Src/iozm.F Src/kgrid.F Src/kgridinit.F Src/kinefsm.f Src/kpoint_grid.F90 Src/kpoint_pdos.F90 Src/ksv.f Src/ksvinit.F Src/linpack.F Src/listsc.f Src/local_DOS.F Src/m_broyden_mixing.f Src/m_fire_mixing.f Src/m_history.f90 Src/m_iodm.F Src/m_iorho.F Src/m_iostruct.f Src/m_memory.F Src/m_mpi_utils.F Src/m_pulay.F90 Src/m_sparse.F Src/m_spin.F90 Src/m_ts_in_siesta.F Src/m_ts_kpoints.F90 Src/m_ts_options.F90 Src/matel.f Src/memory.F Src/memoryinfo.F Src/meshsubs.F Src/metaforce.F Src/mixer.F Src/mneighb.f Src/molecularmechanics.F90 Src/moreParallelSubs.F90 Src/mulliken.F Src/naefs.f Src/new_dm.F Src/nlefsm.f Src/normalize_dm.F Src/obc.f Src/old_atmfuncs.f Src/optical.F Src/ordern.F Src/outcoor.f Src/overfsm.f Src/overlap.f Src/pdos.F Src/pdosg.F Src/pdosk.F Src/pdoskp.F Src/phirphi.f Src/phirphi_opt.f Src/phonon.F Src/pixmol.f Src/plcharge.F Src/poison.F Src/post_scf_work.F Src/precision.F Src/projected_DOS.F Src/proximity_check.F Src/pseudopotential.f Src/pxf.F90 Src/radfft.f Src/radial.f Src/rdiag.F Src/read_xc_info.F Src/readsp.F Src/redcel.F Src/reinit.F Src/reoptical.F Src/reord.f Src/rhoofdsp.f Src/savepsi.F Src/scfconvergence_test.F Src/setatomnodes.F Src/setspatial.f Src/setup_hamiltonian.F Src/setup_kscell.F Src/shaper.f Src/show_distribution.f Src/siesta.F Src/siesta_analysis.F Src/siesta_end.F Src/siesta_forces.F Src/siesta_init.F Src/siesta_move.F Src/siesta_options.F90 Src/sorting.f Src/spher_harm.f Src/state_analysis.F Src/state_init.F Src/struct_init.F Src/vmatsp.f Src/vmb.F Src/write_md_record.F Src/write_subs.F Src/writewave.F Src/wxml/m_wxml_array_str.f90 Src/wxml/m_wxml_buffer.f90 Src/wxml/m_wxml_core.f90 Src/wxml/m_wxml_dictionary.f90 Src/wxml/m_wxml_elstack.f90 Src/zm_broyden_optim.F Src/zm_fire_optim.F Src/zmatrix.F Tests/Makefile Util/Contrib/APostnikov/Makefile Util/Denchar/Src/Makefile Util/Denchar/Src/atompla.f Util/Denchar/Src/denchar.f Util/Denchar/Src/local_reinit.f Util/Denchar/Src/readpla.f Util/Denchar/Src/readsts.f Util/Gen-basis/Makefile Util/Gen-basis/gen-basis.F Util/HSX/iohs.F Util/Helpers/Makefile Util/Optimizer/Makefile Util/TBTrans/Makefile Util/TBTrans/green4.F Util/TBTrans/m_tbt_gf.F90 Util/TBTrans/m_tbt_options.F90 Util/TBTrans/mkqgrid.f Util/TBTrans/reinit_tb.F Util/TBTrans/tbtrans.F Util/VCA/Makefile Util/Vibra/Src/Makefile Util/Vibra/Src/fcbuild.f Util/Vibra/Src/klines.f Util/Vibra/Src/recoor.f Util/Vibra/Src/vibrator.f version.info Src/atom.F Src/forhar.F Src/hsparse.F Src/meshdscf.F Src/parallelsubs.F Src/rhooda.F Src/rhoofd.F Src/sparse_matrices.F Src/timer.F90 Src/vmat.F	Alberto Garcia	13 years ago
278	Assorted fixes (hsparse warnings, xc_check...) Assorted fixes (hsparse warnings, xc_check...) * Fix for overzealous multiple-image detection in hsparse Hsparse raised a warning regarding connectivity of multiple images without actually checking that the currently considered neighbor did indeed overlap with the base atom. * Add missing line in Util/Grid/grid2cube.f (P. Ordejon) * Initialize nspin_data in Util/pdosxml/m_pdos.f90. Update cli code. (Reported by P. Ordejon) * Fix revPBE section in xc_check in atom.f * Fixed calculation of fermi level for charged systems in Util/COOP/mprop.f90 (Thanks to Manuel Cobian) * Fixed labels and file names in some tests. (Reported by I. Silanes, IFCA) * Fix declarations in function numb in chempot (Thanks to Manuel Cobian) * Increase the number of fields for energy differences in Pseudo/atom/prdiff.f (Reported by V. Maslyuk) added: Tests/pd_ice/pd_ice.pseudos renamed: Tests/h3po4_atomlists_1 => Tests/h3po4_1 Tests/h3po4_atomlists_1/h3po4.fdf => Tests/h3po4_1/h3po4_1.fdf Tests/h3po4_atomlists_1/h3po4.pseudos => Tests/h3po4_1/h3po4_1.pseudos Tests/h3po4_atomlists_2 => Tests/h3po4_2 Tests/h3po4_atomlists_2/h3po4.fdf => Tests/h3po4_2/h3po4_2.fdf Tests/h3po4_atomlists_2/h3po4.pseudos => Tests/h3po4_2/h3po4_2.pseudos Tests/h3po4_atomlists_3 => Tests/h3po4_3 Tests/h3po4_atomlists_3/h3po4.fdf => Tests/h3po4_3/h3po4_3.fdf Tests/h3po4_atomlists_3/h3po4.pseudos => Tests/h3po4_3/h3po4_3.pseudos Tests/pd_h2o => Tests/pd_ice modified: Pseudo/atom/prdiff.f Src/atom.f Src/chempot.F Src/hsparse.f Tests/h3po4_1/makefile Tests/h3po4_2/makefile Tests/h3po4_3/makefile Tests/pd_ice/makefile Tests/ptcda/ptcda.fdf Util/COOP/io_hs.f90 Util/COOP/main_vars.f90 Util/COOP/mprop.f90 Util/Grid/grid2cube.f Util/pdosxml/f2kcli.F90 Util/pdosxml/m_pdos.f90 Tests/h3po4_1/h3po4_1.fdf Tests/h3po4_2/h3po4_2.fdf Tests/h3po4_3/h3po4_3.fdf	Alberto Garcia	15 years ago
228	Direct merge into master branch of initial BSC changes Direct merge into master branch of initial BSC changes The changes along the BSC branches, up to the end of the restructuring of siesta.F and associated changes, have been merged into a direct descendant of the main development line. The BSC work originally started as a branch of siesta-devel--reference--2.1--patch-29. Development along 2.1 continued, and a new continuation branch 2.3 has been created specifically for this merge. Main patches applied: * ref@bsc--2007/siesta-bsc--master--2.1--base-0 tag of siesta@uam.es--2006/siesta-bsc--reference--2.1--patch-7 * ref@bsc--2007/siesta-bsc--master--2.1--patch-1 Use of xalast in analysis routines. Exit of geometry loop * ref@bsc--2007/siesta-bsc--master--2.1--patch-2 Creation of a module to hold the siesta options * ref@bsc--2007/siesta-bsc--master--2.1--patch-3 New geometry module * ref@bsc--2007/siesta-bsc--master--2.1--patch-4 New stub module for sparse matrices * ref@bsc--2007/siesta-bsc--master--2.1--patch-5 More options for running tests * ref@bsc--2007/siesta-bsc--master--2.1--patch-6 Encapsulation of k-point handling * ref@bsc--2007/siesta-bsc--master--2.1--patch-7 Initialize iza in struct_init * ref@bsc--2007/siesta-bsc--master--2.1--patch-8 Siesta_todo slimming by M. Quero * ref@bsc--2007/siesta-bsc--master--2.1--patch-9 Fix import of no_l in born_charge * ref@bsc--2007/siesta-bsc--master--2.1--patch-10 Some conversions to Fortran90 by M. Quero * ref@bsc--2007/siesta-bsc--master--2.1--patch-11 Fourth session at the BSC * ref@bsc--2007/siesta-bsc--master--2.1--patch-12 Clarification of the scope of the stress variables * ref@bsc--2007/siesta-bsc--master--2.1--patch-13 Creation of siesta_forces * ref@bsc--2007/siesta-bsc--master--2.1--patch-14 Replacement of some allocatables by pointers and automatics * ref@bsc--2007/siesta-bsc--master--2.1--patch-15 New m_energies and m_steps modules. Back to old k-point behavior * ref@bsc--2007/siesta-bsc--master--2.1--patch-16 Merge of removal of integer and real variables from siesta_todo * ref@bsc--2007/siesta-bsc--master--2.1--patch-17 Fixes for troublesome bugs in reference code * ref@bsc--2007/siesta-bsc--master--2.1--patch-18 Final cleanup of siesta_todo * ref@bsc--2007/siesta-bsc--master--2.1--patch-19 Add character(len=) routines to alloc.F90 ref@bsc--2007/siesta-bsc--master--2.1--patch-20 Pointers in fixed and setspatial. si2x1h test added to bsc-Makefile * ref@bsc--2007/siesta-bsc--master--2.1--patch-21 Re-organization of pulay module * ref@bsc--2007/siesta-bsc--master--2.1--patch-22 Reorganization of hsparse/xijorb calls with new neighbor module * ref@bsc--2007/siesta-bsc--master--2.1--patch-23 VPATH-aware compilation for multiple executable versions * ref@bsc--2007/siesta-bsc--master--2.1--patch-24 Allocatables to pointers I * ref@bsc--2007/siesta-bsc--master--2.1--patch-25 Allocatables to pointers II * ref@bsc--2007/siesta-bsc--master--2.1--patch-26 Allocatables to pointers III * ref@bsc--2007/siesta-bsc--master--2.1--patch-27 Allocatables to pointers IV -- new neighbor code + nspecies fix * ref@bsc--2007/siesta-bsc--master--2.1--patch-28 Explicit array-ness in calls in initatom and cellxc * ref@bsc--2007/siesta-bsc--master--2.1--patch-29 Fix wrong allocations in cellxc.F * ref@bsc--2007/siesta-bsc--master--2.1--patch-30 Explicit array extents in initatom.f * ref@bsc--2007/siesta-bsc--master--2.1--patch-31 Avoid shrinking of density-matrix arrays for extrapol. * ref@bsc--2007/siesta-bsc--master--2.1--patch-32 Fix typo in state_init.F * ref@bsc--2007/siesta-bsc--master--2.1--patch-33 Execute SCF loop when nscf=1 * ref@bsc--2007/siesta-bsc--master--2.1--patch-34 Clarify bounds of SCF loop in siesta_forces. * ref@bsc--2007/siesta-bsc--master--2.2--base-0 tag of ref@bsc--2007/siesta-bsc--master--2.1--patch-31 * ref@bsc--2007/siesta-bsc--master--2.3--base-0 tag of ref@bsc--2007/siesta-bsc--master--2.2--base-0 * ref@bsc--2007/siesta-bsc--master--2.3--patch-1 Prepare CHANGES file * ref@bsc--2007/siesta-bsc--master--2.3--patch-2 Merge patch-log for patch-30 from 2.1 * ref@bsc--2007/siesta-bsc--master--2.3--patch-3 New treatment of fractional atoms in VCA. Bug fix in lmxo * ref@bsc--2007/siesta-bsc--master--2.3--patch-4 Re-enabling of kgrid update in variable-cell calculations * ref@bsc--2007/siesta-bsc--master--2.3--patch-5 Fix typo in state_init.F * ref@bsc--2007/siesta-bsc--master--2.3--patch-6 Merge filtering package by Eduardo Anglada * ref@bsc--2007/siesta-bsc--master--2.3--patch-7 Add graphite_c6_full test for more realistic vdW test * ref@bsc--2007/siesta-bsc--master--2.3--patch-8 Add patchlog for k-point fix * ref@bsc--2007/siesta-bsc--master--2.3--patch-9 Fix of zmatrix code to deal with degenerate case * ref@bsc--2007/siesta-bsc--master--2.3--patch-10 Units conversion in Util/Optical/optical.f. Scripts. Cosmetics * ref@bsc--2007/siesta-bsc--master--2.3--patch-11 Implementation of basis_enthalpy calculation. Zmatrix dependency * ref@bsc--2007/siesta-bsc--master--2.3--patch-12 Option to use fractional rc's for multiple zeta * ref@bsc--2007/siesta-bsc--master--2.3--patch-13 Sync vpath changes. Update siesta.tex * ref@bsc--2007/siesta-bsc--master--2.3--patch-14 Fix tag in MPI send/receive in mulliken * ref@bsc--2007/siesta-bsc--master--2.3--patch-15 Option to use fractional rc's for multiple zeta * ref@bsc--2007/siesta-bsc--master--2.3--patch-16 Merge of XML tester by Eduardo Anglada. Portability fixes * ref@bsc--2007/siesta-bsc--master--2.3--patch-17 Fix marenostrum-mpi.make. Syntax in compare_m.f90 * ref@bsc--2007/siesta-bsc--master--2.3--patch-18 MareNostrum fixes. zdrot to blas. obj_setup. compare_m syntax * ref@bsc--2007/siesta-bsc--master--2.3--patch-19 Sync to bsc--2.1. Change banner in CHANGES to bsc--2.3 * ref@bsc--2007/siesta-bsc--master--2.3--patch-20 Execute SCF loop when nscf=1 * ref@bsc--2007/siesta-bsc--master--2.3--patch-21 Refinements of XML tester. New ioncat program * ref@bsc--2007/siesta-bsc--master--2.3--patch-22 Undef var in kgridinit, iohs MPI write, pdosg array bound, Origin shift * ref@bsc--2007/siesta-bsc--master--2.3--patch-23 Zmatrix optimization enhancements. Sign change in MM stress. * ref@bsc--2007/siesta-bsc--master--2.3--patch-24 Clarify bounds of SCF loop in siesta_forces. * ref@bsc--2007/siesta-bsc--master--2.3--patch-25 Avoid MP-grid permutations in trivial gamma case * ref@bsc--2007/siesta-bsc--master--2.3--patch-26 Sync to reference--2.1 * siesta@uam.es--2006/siesta-bsc--reference--2.1--base-0 tag of siesta@uam.es--2006/siesta-devel--reference--2.1--patch-29 * siesta@uam.es--2006/siesta-bsc--reference--2.1--patch-1 First stage of siesta.F splitting at BSC * siesta@uam.es--2006/siesta-bsc--reference--2.1--patch-2 Created struct_init for initial geometry setup. New test force_2 * siesta@uam.es--2006/siesta-bsc--reference--2.1--patch-3 Consolidate geometry updates at the end of loop * siesta@uam.es--2006/siesta-bsc--reference--2.1--patch-4 Initialize vol2 correctly in m_check_supercell.f * siesta@uam.es--2006/siesta-bsc--reference--2.1--patch-5 Kgrid setup streamlined. Bands. Proximity check. Hsparse allocation * siesta@uam.es--2006/siesta-bsc--reference--2.1--patch-6 Work by Manuel Quero before the meeting on Feb 7th * siesta@uam.es--2006/siesta-bsc--reference--2.1--patch-7 Moved the Born-effective-charge code	Alberto Garcia	16 years ago
216	Merge of XML tester by Eduardo Anglada Merge of XML tester by Eduardo Anglada * New command-line interface * Merged new functionality into old test.mk * Some of the new tests are not yet properly integrated. (reference output files and xml files have to be re-generated).	Alberto Garcia	17 years ago