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View Code? Open in Web Editor NEWSet of quantum chemistry programs and libraries
Home Page: https://quantumpackage.github.io/qp2/
License: GNU General Public License v2.0
Set of quantum chemistry programs and libraries
Home Page: https://quantumpackage.github.io/qp2/
License: GNU General Public License v2.0
make dans ocaml
rm -f -- test_atom
ocamlbuild -j 0 -syntax camlp4o -cflags "-g -warn-error A" -lflags "-g -warn-error A" test_atom.byte -use-ocamlfind
+ ocamlfind ocamlc -c -g -warn-error A -thread -package core,sexplib.syntax,cryptokit -syntax camlp4o -o Point3d.cmi Point3d.mli
File "Point3d.mli", line 14, characters 26-50:
Error: Unbound module Qptypes.Positive_float
Command exited with code 2.
Compilation unsuccessful after building 12 targets (0 cached) in 00:00:00.
make[1]: *** [test_atom.byte] Error 10
make[1]: Leaving directory `/home/razoa/quantum_package/ocaml'
make: *** [build] Error 2
Create a global variable for the current output file
Precision in i2 = ceiling(0.5d0_(dsqrt(8.d0_dble(i1)+1.d0)-1.d0))
The result may be wrong. Check using bielec_integrals_index
When a test.irp.f file is present the directory doesn't compile.
cd src
make veryclean
make
...
IRPF90_temp/MonoInts/pot_ao_ints.irp.F90(102): error #6404: This name does not have a type, and must have an explicit type. [DO_PSEUDO]
if (do_pseudo.eqv..TRUE.) then ! MonoInts/pot_ao_ints.irp.f: 13
------^
compilation aborted for IRPF90_temp/MonoInts/pot_ao_ints.irp.F90 (code 1)
make[1]: *** [IRPF90_temp/MonoInts/pot_ao_ints.irp.o] Error 1
make[1]: *** Waiting for unfinished jobs....
make[1]: Leaving directory `/home/scemama/quantum_package/src/Bielec_integrals'
-------------------- Error --------------------
Build failed for module Bielec_integrals
-----------------------------------------------
make: *** [default] Error 255
Because MonoInts/EZFIO.cfg is does not rebuild do_pseudo in Bielec_integrals.
All EZFIO.cfg files should be transformed to *.irp.f files before.
Checking irpf90...
Traceback (most recent call last):
File "./configure", line 501, in
l_installed, l_install_descendant = checking(d_dependency)
File "./configure", line 260, in checking
r = check_availability(i)
File "./configure", line 211, in check_availability
version = check_output("irpf90 -v".split()).strip()
File "./configure", line 168, in check_output
stderr=subprocess.PIPE, _popenargs, *_kwargs)
File "/usr/lib64/python2.6/subprocess.py", line 642, in init
errread, errwrite)
File "/usr/lib64/python2.6/subprocess.py", line 1234, in _execute_child
raise child_exception
OSError: [Errno 8] Exec format error
Remove all EZFIO input checking in Fortran
I don't know what qp_convert.py
doing. I guess is convert somme file who can be recognize by result_file utility
to EZFIO
, but i not sure.
qp_convert_output_to_ezfio.py
. (Cause we a have a qp_convert_ezfio_v1_to_v2.sh
so it is a little tedious to have a qp_convert.py
)Long&explicit name for conversion script are relevant i think.
/script/ezfio_interface
folder seem logical too. (All the stuff related to the ezfio need to go inside).Have a nice day,
PS : I can do the change if you want. I was just asking, because is not my script : )
Thomas
It seem to have a bug.
The calculus of integrals for the Ti atom in cc-pvdz with BFD pseudo take a long long time
When compiling without openmp
flag and launch SCF binary
AO map initialized
Providing the AO integrals
forrtl: severe (193): Run-Time Check Failure. The variable 'bld_ao_bielec_integrals_in_map_$THREAD_NUM' is being used without being defined
Image PC Routine Line Source
SCF 00000000005BE803 provide_ao_bielec 133 ao_bi_integrals.irp.F90
SCF 000000000049687A bld_ao_bi_elec_in 616 Fock_matrix.irp.F90
SCF 000000000049B268 provide_fock_matr 519 Fock_matrix.irp.F90
SCF 000000000049E310 provide_fock_matr 734 Fock_matrix.irp.F90
SCF 000000000056D53F huckel_guess_ 41 huckel.irp.F90
SCF 000000000040377C MAIN__ 107 SCF.irp.F90
SCF 00000000004032E6 Unknown Unknown Unknown
libc.so.6 00007F1A949C3EC5 Unknown Unknown Unknown
SCF 00000000004031D9 Unknown Unknown Unknown
Automatic build of Readme.rst should be done only for the LCPQ branch. Forks should not automatically update Readme.rst because there are lots of conflicts durin merges.
REPO=$( git config --get remote.origin.url | cut -d ':' -f 2 )
should be LCPQ/quantum_package.git
. If not, update_readme.py
should do nothing.
A python script ezfio_interface.py
will read a DEPENDENCY
config file with ConfigParser
of the form (for example)
[n_det]
doc: Number of states to consider
ezfio_name: det_num
ezfio_type: integer
ezfio_dir: determinants
and will create the *.ezfio_config
file, and the ezfio_interface.irp.f
file.
from ezfio_with_default import EZFIO_Provider
can be used to generate ezfio_interface.irp.f
.
configure should give a clean error message with wrong ./config.* file.
$ ./configure ./config/ifort --production
Traceback (most recent call last):
File "/ccc/work/cont003/gen1738/scemama/quantum_package/scripts/compilation/qp_create_ninja.py", line 811, in <module>
l_string = ninja_create_env_variable(pwd_config_file)
File "/ccc/work/cont003/gen1738/scemama/quantum_package/scripts/compilation/qp_create_ninja.py", line 88, in ninja_create_env_variable
flag))
File "/ccc/work/cont003/gen1738/scemama/quantum_package/scripts/compilation/read_compilation_cfg.py", line 22, in get_compilation_option
if flag_name == "FC" and config.getboolean("OPTION","CACHE"):
File "/usr/lib64/python2.6/ConfigParser.py", line 349, in getboolean
v = self.get(section, option)
File "/usr/lib64/python2.6/ConfigParser.py", line 532, in get
raise NoSectionError(section)
ConfigParser.NoSectionError: No section: 'OPTION'
Creating build.ninja...
Traceback (most recent call last):
File "./configure", line 499, in <module>
create_ninja_and_rc(l_installed)
File "./configure", line 469, in create_ninja_and_rc
subprocess.check_call(" ".join(l), shell=True)
File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '/ccc/work/cont003/gen1738/scemama/quantum_package/scripts/compilation/qp_create_ninja.py create config/ifort --production' returned non-zero exit status 1
When you make build a a.out
appear...
Create a buildbot system to run tests
export OMP_NUM_THREADS=1
rm -r HBO.ezfio
source ~/quantum_package/quantum_package.rc
qp_create_ezfio_from_xyz -b "STO-3G" HBO.xyz
qp_edit -c HBO.ezfio
ezfio set_file HBO.ezfio
ezfio set integrals_bielec threshold_mo 1e-12
ezfio set integrals_bielec threshold_ao 1e-12
ezfio set perturbation do_pt2_end 0
ezfio set determinants n_det_max 10000
qp_run SCF HBO.ezfio
qp_set_mo_class HBO.ezfio -core "[1-2]" -inact "[3-5]" -act "[6-9]" -virt "[10-11]"
qp_run cas_sd_selected HBO.ezfio
ezfio set determinants threshold_generators 1
ezfio set determinants read_wf 1
qp_run mrcc_cassd HBO.ezfio
avx and sse4.2 give different results
We need to have a exit code on the ezfio for checking if the calcul fail or not.
Something like a file status with "Running" or "Finish" inside. Or a boolean.
Plz, stop commit in this repo. ๐ ๐ฟ (if anyone ever do this)
The new idea:
Witch the new IRPF90 version (1.6.1), the EZFIO folder in QP don't compile. Throw this error :
`bash -c "[[ -e ../libezfio.a ]] && rm ../lib/libezfio.a"
make[1]: [../lib/libezfio.a] Error 1 (ignored)
ar cru ../lib/libezfio.a IRPF90_temp/irp_stack.irp.o IRPF90_temp/libezfio_error.irp.o IRPF90_temp/libezfio_error.irp.module.o IRPF90_temp/libezfio_file.irp.o IRPF90_temp/libezfio_file.irp.module.o IRPF90_temp/libezfio_util.irp.o IRPF90_temp/libezfio_util.irp.module.o IRPF90_temp/libezfio_groups.irp.o IRPF90_temp/libezfio_groups.irp.module.o IRPF90_temp/irp_touches.irp.o IRPF90_temp/irp_checkpoint.irp.o
ar: IRPF90_temp/irp_checkpoint.irp.o: No such file or directory
make[1]: *** [../lib/libezfio.a] Error 1
make[1]: Leaving directory `/tmp/quantum_package/EZFIO/src'
make: *** [default] Error 2
In ${QPACKAGE_ROOT}/scripts/install_irpf90.sh
change
URL="https://github.com/LCPQ/${BASE}/archive/master.tar.gz"
into
URL="https://github.com/TApplencourt/${BASE}/archive/master.tar.gz"
Delete ${QPACKAGE_ROOT}/irp90
, and run setup_environement.sh
I am using ZSH as my shell. When I try to source setup_environment.sh I get the following:
muammar@ihacku โฎ ~/github/quantum_package โฎ โญ master โฎ . ~/github/quantum_package/setup_environment.sh
make: 'irpf90' is up to date.
quantum_package.rc:export:3: not valid in this context: PYTHONPATH+
If I print PYTHONPATH, it is empty in my environment. However, I paste here my sys.path:
muammar@ihacku โฎ ~/github/quantum_package โฎ โญ master โฎ python -c "import sys; print sys.path"
['', '/usr/local/lib/python2.7/dist-packages/MeshPy-2011.1-py2.7-linux-x86_64.egg', '/usr/lib/python2.7', '/usr/lib/python2.7/plat-x86_64-linux-gnu', '/usr/lib/python2.7/lib-tk', '/usr/lib/python2.7/lib-old', '/usr/lib/python2.7/lib-dynload', '/usr/local/lib/python2.7/dist-packages', '/usr/local/lib/python2.7/dist-packages/setuptools-0.6c11-py2.7.egg-info', '/usr/lib/python2.7/dist-packages', '/usr/lib/python2.7/dist-packages/PILcompat', '/usr/lib/python2.7/dist-packages/gtk-2.0', '/usr/lib/pymodules/python2.7']
Wouldn't it be better to use sys.path.append instead?
Regards,
qp_run cid_sc2_selection
CISD SC2
========
provide_ao_basis_ao_num: Error: Provider in an openMP section
For travis-cli, support of gfortran compiler need to be restored.
Not the case for:
For exemple :
BEGIN_PROVIDER [ character*(64), mo_label ]
implicit none
BEGIN_DOC
! Molecular orbital coefficients on AO basis set
! mo_coef(i,j) = coefficient of the ith ao on the jth mo
! mo_label : Label characterizing the MOS (local, canonical, natural, etc)
END_DOC
logical :: exists
PROVIDE ezfio_filename
call ezfio_has_mo_basis_mo_label(exists)
if (exists) then
call ezfio_get_mo_basis_mo_label(mo_label)
else
mo_label = 'no_label'
endif
END_PROVIDER
And more qp_edit is broken. He didn't show the mos value.
Put 2DM in a map
ocamlbuild -j 0 -syntax camlp4o -cflags "-g -warn-error A" -lflags "-g -warn-error A" -ocamlopt ocamlc.opt test_input.byte -use-ocamlfind
+ ocamlfind ocamlc -c -g -warn-error A -thread -package core,sexplib.syntax,cryptokit -syntax camlp4o -o Input_ao_basis.cmo Input_ao_basis.ml
File "Input_ao_basis.ml", line 23, characters 24-39:
Error: Unbound module AO_basis_name
Command exited with code 2.
We need to remove the ocaml/Input_$MODULE.ml
file is needed.
The ezfio seem to be not rebuild as well.
[9/30] Generate Png representtion of the Tree Dependencies of Electrons
FAILED: cd /mnt/fhgfs/scemama/quantum_package/src/Electrons ; module_handler.py create_png
Couldn't import dot_parser, loading of dot files will not be possible.
Traceback (most recent call last):
File "/mnt/fhgfs/scemama/quantum_package/scripts/module/module_handler.py", line 238, in <module>
m.create_png(l_module)
File "/mnt/fhgfs/scemama/quantum_package/scripts/module/module_handler.py", line 211, in create_png
graph.write_png(path)
File "/mnt/fhgfs/scemama/quantum_package/scripts/utility/pydot.py", line 1903, in <lambda>
prog=prog))
File "/mnt/fhgfs/scemama/quantum_package/scripts/utility/pydot.py", line 1999, in write
dot_fd.write(self.create(prog, format))
File "/mnt/fhgfs/scemama/quantum_package/scripts/utility/pydot.py", line 2039, in create
'GraphViz\'s executables not found')
pydot.InvocationException: GraphViz's executables not found
5
methane molecule
C 0.000000 0.000000 0.000000
H 0.000000 0.000000 1.089000
H 1.026719 0.000000 -0.363000
H -0.513360 -0.889165 -0.363000
H -0.513360 0.889165 -0.363000
$ ./qp_create_ezfio_from_xyz roger.xyz -b 3-21++g -m 3
Uncaught exception:
Gto.GTO_Read_Failure(" 1 3.6649800 -0.3958970 0.2364600 ")
Raised at file "Gto.ml", line 62, characters 19-49
Called from file "Gto.ml", line 64, characters 5-20
Called from file "Basis.ml", line 10, characters 16-39
Called from file "Basis.ml", line 11, characters 6-37
Called from file "lib/core_list.ml", line 404, characters 13-17
Called from file "lib/command.ml", line 1678, characters 6-68
Called from file "lib/exn.ml", line 80, characters 6-10
Check if multiple determinants D
are in the wf.
D
D_i
, binary search in the psi_det_sorted_bit array, when found remove from listD
to reduce the domain of search.For now update_readme.py can only work if the module have a IRP_MAN
and a tag.
But we never use irp on module who have not binarys.
The main idea is to alow update_reade
to udapte all the descendant module if needed.
All the global variable relatif to path are now stored in qp_path
.
We need to make the changen in the script.
Create bitmasks from input file for orbital classes.
qp_create_ezfio_from_xyz
create a tmpfile who contains ALL the element in the basis-set.
And if the Basis only have He, it will bug and say
Uncaught exception:
(Failure "Element C not found")
Maybe only get the element needed. (Aka call EMSL with --atom
arg)
If you check the EZFIO.cfg
in Pseudo we need aux_basis
.
And the module aux_basis
need Pseudo.
Some cyclic dependency.
The idea to fix it is to allow aux_basis
to write in the EZFIO folder pseudo
. I will do this.
Reading MO integrals should check the MD5 key of the MOs to be sure that they correspond.
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