diff --git a/README.md b/README.md index 24a80b21a9dd44c2aa5025e0734a726fb95757e1..d83249845cf63e5623acb8ff1173f506ca65d761 100644 --- a/README.md +++ b/README.md @@ -1,50 +1,18 @@ -This is the main repository of the [NOMAD](http://nomad-lab.eu) parser for +This is the main repository of the [NOMAD](https://www.nomad-coe.eu/) parser for [CPMD](http://www.cpmd.org/). -# Installation -This parser is a submodule of the nomad-lab-base repository. Developers within -the NoMaD project will automatically get a copy of this repository when they -download and install the base repository. - -# Structure -The scala layer can access the parser functionality through the -scalainterface.py file, by calling the following command: - -```python - python scalainterface.py path/to/main/file -``` - -This scala interface is separated into it's own file to separate it from the -rest of the code. Some parsers will have the interface in the same file as the -parsing code, but I feel that this is a cleaner approach. - -The parser is designed to support multiple versions of CPMD with a -[DRY](https://en.wikipedia.org/wiki/Don%27t_repeat_yourself) approach: The -initial parser class is based on CPMD v4.1, and other versions will be -subclassed from it. By sublassing, all the previous functionality will be -preserved, new functionality can be easily created, and old functionality -overridden only where necesssary. - - -# Standalone Mode -The parser is designed to be usable also outside the NoMaD project as a -separate python package. This standalone python-only mode is primarily for -people who want to easily access the parser without the need to setup the whole -"NOMAD Stack". It is also used when running custom unit tests found in the -folder *cpmd/test/unittests*. Here is an example of the call syntax: - +# Example ```python from cpmdparser import CPMDParser import matplotlib.pyplot as mpl - # 1. Initialize a parser by giving a path to the CPMD output file and a list of - # default units - path = "path/to/main.file" + # 1. Initialize a parser with a set of default units. default_units = ["eV"] - parser = CPMDParser(path, default_units=default_units) + parser = CPMDParser(default_units=default_units) - # 2. Parse - results = parser.parse() + # 2. Parse a file + path = "path/to/main.file" + results = parser.parse(path) # 3. Query the results with using the id's created specifically for NOMAD. scf_energies = results["energy_total_scf_iteration"] @@ -52,51 +20,31 @@ folder *cpmd/test/unittests*. Here is an example of the call syntax: mpl.show() ``` -To install this standalone version, you need to clone the repositories -"python-common", "nomad-meta-info", and "parser-cpmd" into the same folder. -Then install the python-common according to the instructions found in the -README. After that, you can install this package by running: +# Installation +The code is python 2 and python 3 compatible. First download and install +the nomadcore package: ```sh -python setup.py develop --user +git clone https://gitlab.mpcdf.mpg.de/nomad-lab/python-common.git +cd python-common +pip install -r requirements.txt +pip install -e . ``` -# Tools and Methods -This section describes some of the guidelines that are used in the development -of this parser. - -## Documentation -This parser tries to follow the [google style -guide](https://google.github.io/styleguide/pyguide.html?showone=Comments#Comments) -for documenting python code. Documenting makes it much easier to follow the -logic behind your parser. +Then download the metainfo definitions to the same folder where the +'python-common' repository was cloned: -## Testing -The parsers can become quite complicated and maintaining them without -systematic testing is impossible. There are general tests that are -performed automatically in the scala layer for all parsers. This is essential, -but can only test that the data is outputted in the correct format and -according to some general rules. These tests cannot verify that the contents -are correct. +```sh +git clone https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info.git +``` -In order to truly test the parser output, regression testing is needed. The -tests for this parser are located in -**/cpmd/parser/parser-cpmd/cpmdparser/regtest**. Tests provide one way to test -each parseable quantity and python has a very good [library for unit -testing](https://docs.python.org/2/library/unittest.html). When the parser -supports a new quantity it is quite fast to create unit tests for it. These -tests will validate the parsing, and also easily detect bugs that may rise when -the code is modified in the future. +Finally download and install the parser: -## Profiling -The parsers have to be reasonably fast. For some codes there is already -significant amount of data in the NoMaD repository and the time taken to parse -it will depend on the performance of the parser. Also each time the parser -evolves after system deployment, the existing data may have to be reparsed at -least partially. +```sh +git clone https://gitlab.mpcdf.mpg.de/nomad-lab/parser-cp2k.git +cd parser-cp2k +pip install -e . +``` -By profiling what functions take the most computational time and memory during -parsing you can identify the bottlenecks in the parser. There are already -existing profiling tools such as -[cProfile](https://docs.python.org/2/library/profile.html#module-cProfile) -which you can plug into your scripts very easily. +# Notes +The parser is based on CPMD 4.1. diff --git a/parser/parser-cpmd/cpmdparser/parser.py b/parser/parser-cpmd/cpmdparser/parser.py index 476bedb81259165ce2e3777e05c19fb48b26167a..55f61725a2315a6ade42c8a4a4e56e0931259f96 100644 --- a/parser/parser-cpmd/cpmdparser/parser.py +++ b/parser/parser-cpmd/cpmdparser/parser.py @@ -8,14 +8,12 @@ from nomadcore.baseclasses import ParserInterface logger = logging.getLogger("nomad") -#=============================================================================== class CPMDRunType(object): def __init__(self, module_name, class_name): self.module_name = module_name self.class_name = class_name -#=============================================================================== class CPMDParser(ParserInterface): """This class handles the initial setup before any parsing can happen. It determines which version of CPMD was used to generate the output and then @@ -24,8 +22,8 @@ class CPMDParser(ParserInterface): After the implementation has been setup, you can parse the files with parse(). """ - def __init__(self, main_file, metainfo_to_keep=None, backend=None, default_units=None, metainfo_units=None, debug=True, log_level=logging.ERROR, store=True): - super(CPMDParser, self).__init__(main_file, metainfo_to_keep, backend, default_units, metainfo_units, debug, log_level, store) + def __init__(self, metainfo_to_keep=None, backend=None, default_units=None, metainfo_units=None, debug=True, log_level=logging.ERROR, store=True): + super(CPMDParser, self).__init__(metainfo_to_keep, backend, default_units, metainfo_units, debug, log_level, store) def setup_version(self): """Setups the version by looking at the output file and the version diff --git a/parser/parser-cpmd/cpmdparser/regtest/README.md b/parser/parser-cpmd/cpmdparser/regtest/README.md deleted file mode 100644 index 550be2b7a0711f971e5cc927234a6c4b44181aff..0000000000000000000000000000000000000000 --- a/parser/parser-cpmd/cpmdparser/regtest/README.md +++ /dev/null @@ -1,6 +0,0 @@ -# Unit tests -This directory contains unit tests to evaluate the correctness of the parser in -a systematic way. Ideally each parsed metainfo should have at least one unit -test, and if the resulting values are predetermined, the available values -should all be tested individually. Also certain scenarios that should produce a -parsing error should be tested. diff --git a/parser/parser-cpmd/cpmdparser/scalainterface.py b/parser/parser-cpmd/cpmdparser/scalainterface.py index eb0a691fa7f6b3659acc9f138b3c39bb706d501c..b6b4e853c5c4905f4455b4faa37da904f45d9d38 100644 --- a/parser/parser-cpmd/cpmdparser/scalainterface.py +++ b/parser/parser-cpmd/cpmdparser/scalainterface.py @@ -13,5 +13,5 @@ if __name__ == "__main__": # Initialise the parser with the main filename and a JSON backend main_file = sys.argv[1] - parser = CPMDParser(main_file, backend=JsonParseEventsWriterBackend) - parser.parse() + parser = CPMDParser(backend=JsonParseEventsWriterBackend) + parser.parse(main_file) diff --git a/parser/parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py b/parser/parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py index f151bb29c06ac802e4f1df12249f760aa9430c9e..861480ec77bfafb5c8cebdd39c8feef43b0c0857 100644 --- a/parser/parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py +++ b/parser/parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py @@ -10,7 +10,6 @@ from .inputparser import CPMDInputParser logger = logging.getLogger("nomad") -#=============================================================================== class CPMDCommonParser(CommonParser): """ This class is used to store and instantiate common parts of the diff --git a/parser/parser-cpmd/cpmdparser/versions/cpmd41/geooptparser.py b/parser/parser-cpmd/cpmdparser/versions/cpmd41/geooptparser.py index 51fb78342fee4de26f06fd68d6994d7893197185..254d2ca31d93b3aaed95b19c9583da154444b7e7 100644 --- a/parser/parser-cpmd/cpmdparser/versions/cpmd41/geooptparser.py +++ b/parser/parser-cpmd/cpmdparser/versions/cpmd41/geooptparser.py @@ -8,7 +8,6 @@ import logging LOGGER = logging.getLogger("nomad") -#=============================================================================== class CPMDGeoOptParser(MainHierarchicalParser): """The main parser class that is called for all run types. Parses the CPMD output file. diff --git a/parser/parser-cpmd/cpmdparser/versions/cpmd41/inputparser.py b/parser/parser-cpmd/cpmdparser/versions/cpmd41/inputparser.py index 1515b45bb1e5618d55f47c3c28025c7b6c3e91a7..cd4d73aac753d78d34842e642ba3f45eac04b807 100644 --- a/parser/parser-cpmd/cpmdparser/versions/cpmd41/inputparser.py +++ b/parser/parser-cpmd/cpmdparser/versions/cpmd41/inputparser.py @@ -7,7 +7,6 @@ from cpmdparser.generic.inputparsing import metainfo_data_prefix, metainfo_secti logger = logging.getLogger("nomad") -#=============================================================================== class CPMDInputParser(AbstractBaseParser): """Parses the CPMD input file. """ diff --git a/parser/parser-cpmd/cpmdparser/versions/cpmd41/mdparser.py b/parser/parser-cpmd/cpmdparser/versions/cpmd41/mdparser.py index 0890e032d8c9996630f223989a0bb795742ed879..b08a13c216ab0248dd336fa35476f6842aaa1c07 100644 --- a/parser/parser-cpmd/cpmdparser/versions/cpmd41/mdparser.py +++ b/parser/parser-cpmd/cpmdparser/versions/cpmd41/mdparser.py @@ -10,7 +10,6 @@ import nomadcore.configurationreading LOGGER = logging.getLogger("nomad") -#=============================================================================== class CPMDMDParser(MainHierarchicalParser): """The main parser class that is called for all run types. Parses the CPMD output file. diff --git a/parser/parser-cpmd/cpmdparser/versions/cpmd41/propertiesparser.py b/parser/parser-cpmd/cpmdparser/versions/cpmd41/propertiesparser.py index 61b5f10ff78e501d034c6ccba515f421ecd413b4..f0321b2d16cc2578d7835a70c1dfa09f5ad07d33 100644 --- a/parser/parser-cpmd/cpmdparser/versions/cpmd41/propertiesparser.py +++ b/parser/parser-cpmd/cpmdparser/versions/cpmd41/propertiesparser.py @@ -8,7 +8,6 @@ import logging LOGGER = logging.getLogger("nomad") -#=============================================================================== class CPMDPropertiesParser(MainHierarchicalParser): """The main parser class that is called for all run types. Parses the CPMD output file. diff --git a/parser/parser-cpmd/cpmdparser/versions/cpmd41/vibrationparser.py b/parser/parser-cpmd/cpmdparser/versions/cpmd41/vibrationparser.py index 93e825c89aa6b1f01267d89f76817da0cd328848..60b71269f7b6feea6a403f124113e01ce9ce66af 100644 --- a/parser/parser-cpmd/cpmdparser/versions/cpmd41/vibrationparser.py +++ b/parser/parser-cpmd/cpmdparser/versions/cpmd41/vibrationparser.py @@ -8,7 +8,6 @@ import logging LOGGER = logging.getLogger("nomad") -#=============================================================================== class CPMDVibrationParser(MainHierarchicalParser): """The main parser class that is called for all run types. Parses the CPMD output file. diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/H_CVB_BLYP.psp b/regtests/cpmd_4.1/H_CVB_BLYP.psp similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/H_CVB_BLYP.psp rename to regtests/cpmd_4.1/H_CVB_BLYP.psp diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/H_MT_LDA.psp b/regtests/cpmd_4.1/H_MT_LDA.psp similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/H_MT_LDA.psp rename to regtests/cpmd_4.1/H_MT_LDA.psp diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/O_MT_BLYP.psp b/regtests/cpmd_4.1/O_MT_BLYP.psp similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/O_MT_BLYP.psp rename to regtests/cpmd_4.1/O_MT_BLYP.psp diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/periodicity/bulk/GEOMETRY b/regtests/cpmd_4.1/dos/GEOMETRY similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/periodicity/bulk/GEOMETRY rename to 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diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/lda/input.inp b/regtests/cpmd_4.1/single_point/input.inp similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/lda/input.inp rename to regtests/cpmd_4.1/single_point/input.inp diff --git a/regtests/cpmd_4.1/single_point/output.out b/regtests/cpmd_4.1/single_point/output.out new file mode 100644 index 0000000000000000000000000000000000000000..b7fb802822bc95d7164dab1cff250c4b764493de --- /dev/null +++ b/regtests/cpmd_4.1/single_point/output.out @@ -0,0 +1,286 @@ + cp_groups: we are using a 1 x 1 grid (groups x nprocs). + PROGRAM CPMD STARTED AT: 2016-07-04 14:05:06.851 + SETCNST| USING: CODATA 2006 UNITS + + + ****** ****** **** **** ****** + ******* ******* ********** ******* + *** ** *** ** **** ** ** *** + ** ** *** ** ** ** ** ** + ** ******* ** ** ** ** + *** ****** ** ** ** *** + ******* ** ** ** ******* + ****** ** ** ** ****** + + VERSION 4.1-rUnversioned directory + + COPYRIGHT + IBM RESEARCH DIVISION + MPI FESTKOERPERFORSCHUNG STUTTGART + + The CPMD consortium + Home Page: http://www.cpmd.org + Mailing List: cpmd-list@cpmd.org + E-mail: cpmd@cpmd.org + + + *** Jun 22 2016 -- 12:41:05 *** + + THE INPUT FILE IS: input.inp + THIS JOB RUNS ON: lenovo700 + THE CURRENT DIRECTORY IS: + /home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/h2 + THE TEMPORARY DIRECTORY IS: + /home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/h2 + THE PROCESS ID IS: 32589 + THE JOB WAS SUBMITTED BY: lauri + + + ****************************************************************************** + * INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO * + ****************************************************************************** + * isolated hydrogen molecule. * + * single point calculation. * + ****************************************************************************** + + SINGLE POINT DENSITY OPTIMIZATION + + USING SEED 123456 TO INIT. PSEUDO RANDOM NUMBER GEN. + PATH TO THE RESTART FILES: ./ + GRAM-SCHMIDT ORTHOGONALIZATION + MAXIMUM NUMBER OF STEPS: 10000 STEPS + MAXIMUM NUMBER OF ITERATIONS FOR SC: 10000 STEPS + PRINT INTERMEDIATE RESULTS EVERY 10001 STEPS + STORE INTERMEDIATE RESULTS EVERY 10001 STEPS + NUMBER OF DISTINCT RESTART FILES: 1 + TEMPERATURE IS CALCULATED ASSUMING EXTENDED BULK BEHAVIOR + FICTITIOUS ELECTRON MASS: 400.0000 + TIME STEP FOR ELECTRONS: 5.0000 + TIME STEP FOR IONS: 5.0000 + CONVERGENCE CRITERIA FOR WAVEFUNCTION OPTIMIZATION: 1.0000E-07 + WAVEFUNCTION OPTIMIZATION BY PRECONDITIONED DIIS + THRESHOLD FOR THE WF-HESSIAN IS 0.5000 + MAXIMUM NUMBER OF VECTORS RETAINED FOR DIIS: 10 + STEPS UNTIL DIIS RESET ON POOR PROGRESS: 10 + FULL ELECTRONIC GRADIENT IS USED + SPLINE INTERPOLATION IN G-SPACE FOR PSEUDOPOTENTIAL FUNCTIONS + NUMBER OF SPLINE POINTS: 5000 + + EXCHANGE CORRELATION FUNCTIONALS + LDA EXCHANGE: NONE + LDA XC THROUGH PADE APPROXIMATION + S.GOEDECKER, J.HUTTER, M.TETER PRB 541703 (1996) + + *** DETSP| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + ***************************** ATOMS **************************** + NR TYPE X(BOHR) Y(BOHR) Z(BOHR) MBL + 1 H 8.259993 7.558904 7.558904 3 + 2 H 6.857816 7.558904 7.558904 3 + **************************************************************** + + NUMBER OF STATES: 1 + NUMBER OF ELECTRONS: 2.00000 + CHARGE: 0.00000 + ELECTRON TEMPERATURE(KELVIN): 0.00000 + OCCUPATION + 2.0 + + ============================================================ + | Pseudopotential Report Thu Jan 11 18:21:49 1996 | + ------------------------------------------------------------ + | Atomic Symbol : H | + | Atomic Number : 1 | + | Number of core states : 0 | + | Number of valence states : 1 | + | Exchange-Correlation Functional : | + | Slater exchange : .6667 | + | LDA correlation : Ceperley-Alder | + | Electron Configuration : N L Occupation | + | 1 S 1.0000 | + | Full Potential Total Energy -.445894 | + | Trouiller-Martins normconserving PP | + | n l rc energy | + | 1 S .5000 -.23366 | + | 2 P .5000 -.23366 | + | Number of Mesh Points : 511 | + | Pseudoatom Total Energy -.445889 | + ============================================================ + + **************************************************************** + * ATOM MASS RAGGIO NLCC PSEUDOPOTENTIAL * + * H 1.0080 1.2000 NO S LOCAL * + **************************************************************** + + + PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA + NCPU NGW NHG PLANES GXRAYS HXRAYS ORBITALS Z-PLANES + 0 17133 136605 90 1281 5089 1 1 + G=0 COMPONENT ON PROCESSOR : 0 + PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA + + *** loadpa| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + OPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPEN + NUMBER OF CPUS PER TASK 1 + OPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPEN + + *** rggen| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + ************************** SUPERCELL *************************** + SYMMETRY: SIMPLE CUBIC + LATTICE CONSTANT(a.u.): 15.11781 + CELL DIMENSION: 15.1178 1.0000 1.0000 0.0000 0.0000 0.0000 + VOLUME(OMEGA IN BOHR^3): 3455.14726 + LATTICE VECTOR A1(BOHR): 15.1178 0.0000 0.0000 + LATTICE VECTOR A2(BOHR): 0.0000 15.1178 0.0000 + LATTICE VECTOR A3(BOHR): 0.0000 0.0000 15.1178 + RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0661 0.0000 0.0000 + RECIP. LAT. VEC. B2(2Pi/BOHR): 0.0000 0.0661 0.0000 + RECIP. LAT. VEC. B3(2Pi/BOHR): 0.0000 0.0000 0.0661 + REAL SPACE MESH: 90 90 90 + WAVEFUNCTION CUTOFF(RYDBERG): 70.00000 + DENSITY CUTOFF(RYDBERG): (DUAL= 4.00) 280.00000 + NUMBER OF PLANE WAVES FOR WAVEFUNCTION CUTOFF: 17133 + NUMBER OF PLANE WAVES FOR DENSITY CUTOFF: 136605 + **************************************************************** + + *** RINFORCE| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + *** FFTPRP| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + GENERATE ATOMIC BASIS SET + H SLATER ORBITALS + 1S ALPHA= 1.0000 OCCUPATION= 1.00 + + + INITIALIZATION TIME: 0.48 SECONDS + + *** WFOPTS| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + *** PHFAC| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + NOTE: ATOMIC GUESS USING DISTRIBUTED LINALG WITH LANCZOS + *** ATOMWF| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + ATRHO| CHARGE(R-SPACE): 2.000000 (G-SPACE): 2.000000 + + ATOM COORDINATES GRADIENTS (-FORCES) + 1 H 8.2600 7.5589 7.5589 0.000E+00 0.000E+00 0.000E+00 + 2 H 6.8578 7.5589 7.5589 0.000E+00 0.000E+00 0.000E+00 + + TIME FOR WAVEFUNCTION INITIALIZATION: 0.83 SECONDS + *** RWFOPT| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + EWALD| SUM IN REAL SPACE OVER 1* 1* 1 CELLS + + TOTAL INTEGRATED ELECTRONIC DENSITY + IN G-SPACE = 2.0000000000 + IN R-SPACE = 2.0000000000 + + (K+E1+L+N+X) TOTAL ENERGY = -1.09689770 A.U. + (K) KINETIC ENERGY = 0.81247072 A.U. + (E1=A-S+R) ELECTROSTATIC ENERGY = -0.48640053 A.U. + (S) ESELF = 0.66490380 A.U. + (R) ESR = 0.17302593 A.U. + (L) LOCAL PSEUDOPOTENTIAL ENERGY = -0.84879440 A.U. + (N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U. + (X) EXCHANGE-CORRELATION ENERGY = -0.57417350 A.U. + + NFI GEMAX CNORM ETOT DETOT TCPU + 1 3.816E-02 2.886E-03 -1.096898 0.000E+00 0.23 + 2 8.628E-03 1.041E-03 -1.130803 -3.391E-02 0.22 + 3 2.736E-03 2.293E-04 -1.132376 -1.572E-03 0.22 + 4 6.115E-04 4.235E-05 -1.132456 -8.056E-05 0.22 + 5 1.532E-04 7.007E-06 -1.132459 -3.315E-06 0.24 + 6 3.895E-05 1.396E-06 -1.132460 -1.338E-07 0.22 + 7 6.288E-06 4.459E-07 -1.132460 -7.717E-09 0.22 + 8 7.941E-07 1.282E-07 -1.132460 -4.283E-10 0.22 + 9 1.237E-07 2.861E-08 -1.132460 -1.992E-11 0.22 + 10 2.278E-08 5.401E-09 -1.132460 -8.606E-13 0.22 + + RESTART INFORMATION WRITTEN ON FILE ./RESTART.1 + *** RWFOPT| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + **************************************************************** + * * + * FINAL RESULTS * + * * + **************************************************************** + + ATOM COORDINATES GRADIENTS (-FORCES) + 1 H 8.2600 7.5589 7.5589 1.780E-02 -1.104E-16 -9.425E-17 + 2 H 6.8578 7.5589 7.5589 -1.780E-02 -1.867E-16 -1.490E-16 + + **************************************************************** + + + ELECTRONIC GRADIENT: + MAX. COMPONENT = 1.15980E-08 NORM = 1.11525E-09 + NUCLEAR GRADIENT: + MAX. COMPONENT = 1.77985E-02 NORM = 1.02760E-02 + + + TOTAL INTEGRATED ELECTRONIC DENSITY + IN G-SPACE = 2.0000000000 + IN R-SPACE = 2.0000000000 + + (K+E1+L+N+X) TOTAL ENERGY = -1.13245953 A.U. + (K) KINETIC ENERGY = 1.09007149 A.U. + (E1=A-S+R) ELECTROSTATIC ENERGY = -0.47319176 A.U. + (S) ESELF = 0.66490380 A.U. + (R) ESR = 0.17302593 A.U. + (L) LOCAL PSEUDOPOTENTIAL ENERGY = -1.09902228 A.U. + (N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U. + (X) EXCHANGE-CORRELATION ENERGY = -0.65031699 A.U. + + **************************************************************** + + + + **************************************************************** + * * + * TIMING * + * * + **************************************************************** + SUBROUTINE CALLS SELF TIME TOTAL TIME + AVERAGE MAXIMUM AVERAGE MAXIMUM + cpmd 1 0.00 0.00 3.67 3.67 + rwfopt 1 0.00 0.00 3.20 3.20 + updwf 11 0.00 0.00 2.37 2.37 + forcedr 11 0.00 0.00 2.33 2.33 + forces 11 0.00 0.00 2.33 2.33 + forces_a 11 0.00 0.00 1.80 1.80 + rscpot 11 0.00 0.00 1.80 1.80 + vofrho 12 0.00 0.00 1.79 1.79 + VOFRHOB 12 0.04 0.04 1.22 1.22 + INVFFTN 37 1.12 1.12 1.12 1.12 + initrun 1 0.00 0.00 0.82 0.82 + rinitwf 1 0.00 0.00 0.82 0.82 + ATOMWF 1 0.00 0.00 0.82 0.82 + FWFFTN 25 0.69 0.69 0.69 0.69 + xcener_new 12 0.04 0.04 0.67 0.67 + mikeu 12 0.63 0.63 0.63 0.63 + vpsi 13 0.06 0.06 0.63 0.63 + VOFRHOA 12 0.03 0.03 0.57 0.57 + ATRHO 1 0.35 0.35 0.39 0.39 + rhoofr 11 0.07 0.07 0.34 0.34 + rinit 1 0.00 0.00 0.26 0.26 + rggen 1 0.01 0.01 0.26 0.26 + loadpa 1 0.01 0.01 0.25 0.25 + dist_ksmat 1 0.00 0.00 0.11 0.11 + RINFORCE 1 0.00 0.00 0.10 0.10 + NUMPW 1 0.10 0.10 0.10 0.10 + loadpa_b 1 0.10 0.10 0.10 0.10 + loadpa_c 1 0.10 0.10 0.10 0.10 + FORMFN 1 0.10 0.10 0.10 0.10 + ppener 12 0.06 0.06 0.06 0.06 + loadpa_a 1 0.04 0.04 0.04 0.04 + EICALC 12 0.04 0.04 0.04 0.04 + odiis 11 0.04 0.04 0.04 0.04 + PUTPS 1 0.01 0.01 0.01 0.01 + forces_b 11 0.00 0.00 0.01 0.01 + potfor 1 0.01 0.01 0.01 0.01 + fftprp 1 0.00 0.00 0.00 0.00 + **************************************************************** + + CPU TIME : 0 HOURS 0 MINUTES 3.67 SECONDS + ELAPSED TIME : 0 HOURS 0 MINUTES 3.67 SECONDS + *** CPMD| SIZE OF THE PROGRAM IS NOT AVAILABLE *** + + PROGRAM CPMD ENDED AT: 2016-07-04 14:05:10.523 diff --git a/regtests/cpmd_4.1/single_point/run.sh b/regtests/cpmd_4.1/single_point/run.sh new file mode 100755 index 0000000000000000000000000000000000000000..222042e49aa219ad6e922865b7797f786e068428 --- /dev/null +++ b/regtests/cpmd_4.1/single_point/run.sh @@ -0,0 +1,3 @@ +export CPMD_PP_LIBRARY_PATH=../ +export OMP_NUM_THREADS=1 +cpmd41 input.inp > output.out diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/b1lyp/GEOMETRY b/regtests/cpmd_4.1/xc_functional/b1lyp/GEOMETRY similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/b1lyp/GEOMETRY rename to regtests/cpmd_4.1/xc_functional/b1lyp/GEOMETRY diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/b1lyp/GEOMETRY.xyz b/regtests/cpmd_4.1/xc_functional/b1lyp/GEOMETRY.xyz similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/b1lyp/GEOMETRY.xyz rename to regtests/cpmd_4.1/xc_functional/b1lyp/GEOMETRY.xyz diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/b3lyp/LATEST b/regtests/cpmd_4.1/xc_functional/b1lyp/LATEST similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/b3lyp/LATEST rename to regtests/cpmd_4.1/xc_functional/b1lyp/LATEST diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/b1lyp/RESTART.1 b/regtests/cpmd_4.1/xc_functional/b1lyp/RESTART.1 similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/b1lyp/RESTART.1 rename to regtests/cpmd_4.1/xc_functional/b1lyp/RESTART.1 diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/b1lyp/input.inp b/regtests/cpmd_4.1/xc_functional/b1lyp/input.inp similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/b1lyp/input.inp rename to regtests/cpmd_4.1/xc_functional/b1lyp/input.inp diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/b1lyp/output.out b/regtests/cpmd_4.1/xc_functional/b1lyp/output.out similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/b1lyp/output.out rename to regtests/cpmd_4.1/xc_functional/b1lyp/output.out diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/b1lyp/run.sh b/regtests/cpmd_4.1/xc_functional/b1lyp/run.sh similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/b1lyp/run.sh rename to regtests/cpmd_4.1/xc_functional/b1lyp/run.sh diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/b3lyp/GEOMETRY b/regtests/cpmd_4.1/xc_functional/b3lyp/GEOMETRY similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/b3lyp/GEOMETRY rename to regtests/cpmd_4.1/xc_functional/b3lyp/GEOMETRY diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/b3lyp/GEOMETRY.xyz b/regtests/cpmd_4.1/xc_functional/b3lyp/GEOMETRY.xyz similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/b3lyp/GEOMETRY.xyz rename to regtests/cpmd_4.1/xc_functional/b3lyp/GEOMETRY.xyz diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/blyp/LATEST b/regtests/cpmd_4.1/xc_functional/b3lyp/LATEST similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/blyp/LATEST rename to regtests/cpmd_4.1/xc_functional/b3lyp/LATEST diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/b3lyp/RESTART.1 b/regtests/cpmd_4.1/xc_functional/b3lyp/RESTART.1 similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/b3lyp/RESTART.1 rename to regtests/cpmd_4.1/xc_functional/b3lyp/RESTART.1 diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/b3lyp/input.inp b/regtests/cpmd_4.1/xc_functional/b3lyp/input.inp similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/b3lyp/input.inp rename to regtests/cpmd_4.1/xc_functional/b3lyp/input.inp diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/b3lyp/output.out b/regtests/cpmd_4.1/xc_functional/b3lyp/output.out similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/b3lyp/output.out rename to regtests/cpmd_4.1/xc_functional/b3lyp/output.out diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/b3lyp/run.sh b/regtests/cpmd_4.1/xc_functional/b3lyp/run.sh similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/b3lyp/run.sh rename to regtests/cpmd_4.1/xc_functional/b3lyp/run.sh diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/blyp/GEOMETRY b/regtests/cpmd_4.1/xc_functional/blyp/GEOMETRY similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/blyp/GEOMETRY rename to regtests/cpmd_4.1/xc_functional/blyp/GEOMETRY diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/blyp/GEOMETRY.xyz b/regtests/cpmd_4.1/xc_functional/blyp/GEOMETRY.xyz similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/blyp/GEOMETRY.xyz rename to regtests/cpmd_4.1/xc_functional/blyp/GEOMETRY.xyz diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/bp/LATEST b/regtests/cpmd_4.1/xc_functional/blyp/LATEST similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/bp/LATEST rename to regtests/cpmd_4.1/xc_functional/blyp/LATEST diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/blyp/RESTART.1 b/regtests/cpmd_4.1/xc_functional/blyp/RESTART.1 similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/blyp/RESTART.1 rename to regtests/cpmd_4.1/xc_functional/blyp/RESTART.1 diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/blyp/input.inp b/regtests/cpmd_4.1/xc_functional/blyp/input.inp similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/blyp/input.inp rename to regtests/cpmd_4.1/xc_functional/blyp/input.inp diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/blyp/output.out b/regtests/cpmd_4.1/xc_functional/blyp/output.out similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/blyp/output.out rename to regtests/cpmd_4.1/xc_functional/blyp/output.out diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/blyp/run.sh b/regtests/cpmd_4.1/xc_functional/blyp/run.sh similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/blyp/run.sh rename to regtests/cpmd_4.1/xc_functional/blyp/run.sh diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/bp/GEOMETRY b/regtests/cpmd_4.1/xc_functional/bp/GEOMETRY similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/bp/GEOMETRY rename to regtests/cpmd_4.1/xc_functional/bp/GEOMETRY diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/bp/GEOMETRY.xyz b/regtests/cpmd_4.1/xc_functional/bp/GEOMETRY.xyz similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/bp/GEOMETRY.xyz rename to regtests/cpmd_4.1/xc_functional/bp/GEOMETRY.xyz diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/hcth/LATEST 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from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/hse06/input.inp rename to regtests/cpmd_4.1/xc_functional/hse06/input.inp diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/hse06/output.out b/regtests/cpmd_4.1/xc_functional/hse06/output.out similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/hse06/output.out rename to regtests/cpmd_4.1/xc_functional/hse06/output.out diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/hse06/run.sh b/regtests/cpmd_4.1/xc_functional/hse06/run.sh similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/hse06/run.sh rename to regtests/cpmd_4.1/xc_functional/hse06/run.sh diff --git a/regtests/cpmd_4.1/xc_functional/lda/GEOMETRY b/regtests/cpmd_4.1/xc_functional/lda/GEOMETRY new file mode 100644 index 0000000000000000000000000000000000000000..4fc346d8d03ee55cc5ed943b11eb14af91be77a4 --- /dev/null +++ b/regtests/cpmd_4.1/xc_functional/lda/GEOMETRY @@ -0,0 +1,2 @@ + 8.259992891426 7.558904499132 7.558904499132 0.017798524379 -0.000000000000 -0.000000000000 + 6.857816106837 7.558904499132 7.558904499132 -0.017798524379 -0.000000000000 -0.000000000000 diff --git a/regtests/cpmd_4.1/xc_functional/lda/GEOMETRY.xyz b/regtests/cpmd_4.1/xc_functional/lda/GEOMETRY.xyz new file mode 100644 index 0000000000000000000000000000000000000000..b13c48d0b6644a53a06502a83cea74fb0265e4e1 --- /dev/null +++ b/regtests/cpmd_4.1/xc_functional/lda/GEOMETRY.xyz @@ -0,0 +1,4 @@ + 2 +GEOMETRY FILE / created by CPMD + H 4.371000000000 4.000000000000 4.000000000000 0.009418573488 -0.000000000000 -0.000000000000 + H 3.629000000000 4.000000000000 4.000000000000 -0.009418573488 -0.000000000000 -0.000000000000 diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/olyp/LATEST b/regtests/cpmd_4.1/xc_functional/lda/LATEST similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/olyp/LATEST rename to regtests/cpmd_4.1/xc_functional/lda/LATEST diff --git a/regtests/cpmd_4.1/xc_functional/lda/RESTART.1 b/regtests/cpmd_4.1/xc_functional/lda/RESTART.1 new file mode 100644 index 0000000000000000000000000000000000000000..88b00a1a01f06fe6a5955b36cc01256a544cf1ce Binary files /dev/null and b/regtests/cpmd_4.1/xc_functional/lda/RESTART.1 differ diff --git a/regtests/cpmd_4.1/xc_functional/lda/input.inp b/regtests/cpmd_4.1/xc_functional/lda/input.inp new file mode 100755 index 0000000000000000000000000000000000000000..c1b5c8a868f3b0aec8910af9399c6bfabec9fa3d --- /dev/null +++ b/regtests/cpmd_4.1/xc_functional/lda/input.inp @@ -0,0 +1,35 @@ +&INFO +isolated hydrogen molecule. +single point calculation. +&END + +&CPMD + OPTIMIZE WAVEFUNCTION + CONVERGENCE ORBITALS + 1.0d-7 + CENTER MOLECULE ON + PRINT FORCES ON +&END + +&SYSTEM + SYMMETRY + 1 + ANGSTROM + CELL + 8.00 1.0 1.0 0.0 0.0 0.0 + CUTOFF + 70.0 +&END + +&DFT + FUNCTIONAL LDA +&END + +&ATOMS +*H_MT_LDA.psp + LMAX=S + 2 + 4.371 4.000 4.000 + 3.629 4.000 4.000 +&END + diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/lda/output.out b/regtests/cpmd_4.1/xc_functional/lda/output.out similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/lda/output.out rename to regtests/cpmd_4.1/xc_functional/lda/output.out diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/lda/run.sh b/regtests/cpmd_4.1/xc_functional/lda/run.sh similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/lda/run.sh rename to regtests/cpmd_4.1/xc_functional/lda/run.sh diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/olyp/GEOMETRY b/regtests/cpmd_4.1/xc_functional/olyp/GEOMETRY similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/olyp/GEOMETRY rename to 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a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/x3lyp/input.inp b/regtests/cpmd_4.1/xc_functional/x3lyp/input.inp similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/x3lyp/input.inp rename to regtests/cpmd_4.1/xc_functional/x3lyp/input.inp diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/x3lyp/output.out b/regtests/cpmd_4.1/xc_functional/x3lyp/output.out similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/x3lyp/output.out rename to regtests/cpmd_4.1/xc_functional/x3lyp/output.out diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/x3lyp/run.sh b/regtests/cpmd_4.1/xc_functional/x3lyp/run.sh similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/x3lyp/run.sh rename to regtests/cpmd_4.1/xc_functional/x3lyp/run.sh diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/xlyp/GEOMETRY b/regtests/cpmd_4.1/xc_functional/xlyp/GEOMETRY similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/xlyp/GEOMETRY rename to regtests/cpmd_4.1/xc_functional/xlyp/GEOMETRY diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/xlyp/GEOMETRY.xyz b/regtests/cpmd_4.1/xc_functional/xlyp/GEOMETRY.xyz similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/xlyp/GEOMETRY.xyz rename to regtests/cpmd_4.1/xc_functional/xlyp/GEOMETRY.xyz diff --git a/regtests/cpmd_4.1/xc_functional/xlyp/LATEST b/regtests/cpmd_4.1/xc_functional/xlyp/LATEST new file mode 100644 index 0000000000000000000000000000000000000000..0e4449210602fd9c3a45bd3bc780cd67ad8721b0 --- /dev/null +++ b/regtests/cpmd_4.1/xc_functional/xlyp/LATEST @@ -0,0 +1,2 @@ +./RESTART.1 + 1 diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/xlyp/RESTART.1 b/regtests/cpmd_4.1/xc_functional/xlyp/RESTART.1 similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/xlyp/RESTART.1 rename to regtests/cpmd_4.1/xc_functional/xlyp/RESTART.1 diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/xlyp/input.inp b/regtests/cpmd_4.1/xc_functional/xlyp/input.inp similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/xlyp/input.inp rename to regtests/cpmd_4.1/xc_functional/xlyp/input.inp diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/xlyp/output.out b/regtests/cpmd_4.1/xc_functional/xlyp/output.out similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/xlyp/output.out rename to regtests/cpmd_4.1/xc_functional/xlyp/output.out diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/xlyp/run.sh b/regtests/cpmd_4.1/xc_functional/xlyp/run.sh similarity index 100% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/xc_functional/xlyp/run.sh rename to regtests/cpmd_4.1/xc_functional/xlyp/run.sh diff --git a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/run_tests.py b/regtests/regtests.py similarity index 90% rename from parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/run_tests.py rename to regtests/regtests.py index 09a9a1ce3d4a7ec5a0733bf635ca0f04de4814ad..4377cab28b1d32105a7cd7a8b0ef8aa4e046960b 100644 --- a/parser/parser-cpmd/cpmdparser/regtest/cpmd_4.1/run_tests.py +++ b/regtests/regtests.py @@ -18,42 +18,32 @@ from cpmdparser import CPMDParser from nomadcore.unit_conversion.unit_conversion import convert_unit -#=============================================================================== -def get_results(folder, metainfo_to_keep=None): - """Get the given result from the calculation in the given folder by using - the Analyzer in the nomadtoolkit package. Tries to optimize the parsing by - giving the metainfo_to_keep argument. +def get_result(folder, metaname=None): + """Get the results from the calculation in the given folder. By default goes through different Args: folder: The folder relative to the directory of this script where the parsed calculation resides. - metaname: The quantity to extract. + metaname(str): Optional quantity to return. If not specified, returns + the full dictionary of results. """ dirname = os.path.dirname(__file__) - filename = os.path.join(dirname, folder, "output.out") - parser = CPMDParser(filename, None, debug=True, log_level=logging.WARNING) - results = parser.parse() - return results + filename = os.path.join("cpmd_{}".format(VERSION), dirname, folder, "output.out") + parser = CPMDParser(None, debug=True, log_level=logging.CRITICAL) + results = parser.parse(filename) - -#=============================================================================== -def get_result(folder, metaname, optimize=True): - if optimize: - results = get_results(folder, None) + if metaname is None: + return results else: - results = get_results(folder) - result = results[metaname] - return result + return results[metaname] -#=============================================================================== class TestInputParser(unittest.TestCase): """Tests that the parser can handle single-point calculations. """ - @classmethod def setUpClass(cls): - cls.results = get_results("single_point", "section_run") + cls.results = get_result("single_point") # cls.results.print_summary() def test_x_cpmd_input_functional(self): @@ -76,14 +66,12 @@ class TestInputParser(unittest.TestCase): self.results["x_cpmd_section_input_CPMD.OPTIMIZE_WAVEFUNCTION"] -#=============================================================================== class TestSinglePoint(unittest.TestCase): """Tests that the parser can handle single-point calculations. """ - @classmethod def setUpClass(cls): - cls.results = get_results("single_point", "section_run") + cls.results = get_result("single_point") # cls.results.print_summary() def test_program_name(self): @@ -239,12 +227,12 @@ class TestSinglePoint(unittest.TestCase): # self.assertEqual(multiplicity, 1) -#=============================================================================== class TestGeoOpt(unittest.TestCase): - + """Geometry optimization tests. + """ @classmethod def setUpClass(cls): - cls.results = get_results("geo_opt/bfgs", "section_run") + cls.results = get_result("geo_opt/bfgs") def test_program_name(self): result = self.results["program_name"] @@ -351,12 +339,12 @@ class TestGeoOpt(unittest.TestCase): self.assertTrue(np.array_equal(result, expected_result)) -#=============================================================================== class TestMD(unittest.TestCase): - + """Moleculer dynamics tests. + """ @classmethod def setUpClass(cls): - cls.results = get_results("md/nve", "section_run") + cls.results = get_result("md/nve") cls.temp = convert_unit( np.array([ 110.096, @@ -546,11 +534,11 @@ class TestMD(unittest.TestCase): self.assertTrue(np.allclose(result[1], expected_result[1], rtol=0, atol=0.0001)) -#=============================================================================== class TestMDTrajFormats(unittest.TestCase): - + """Tests for different MD trajectory formats. + """ def test_dcd(self): - results = get_results("md/dcd", "section_run") + results = get_result("md/dcd") positions = results["atom_positions"] expected_start = convert_unit( np.array([ @@ -570,7 +558,7 @@ class TestMDTrajFormats(unittest.TestCase): self.assertTrue(np.allclose(positions[-1, :], expected_end, rtol=0, atol=0.0000001e-11)) def test_xyz(self): - results = get_results("md/xyz", "section_run") + results = get_result("md/xyz") positions = results["atom_positions"] expected_start = convert_unit( np.array([ @@ -590,7 +578,7 @@ class TestMDTrajFormats(unittest.TestCase): self.assertTrue(np.allclose(positions[-1, :], expected_end, rtol=0, atol=0.00001e-11)) def test_trajectory(self): - results = get_results("md/trajectory", "section_run") + results = get_result("md/trajectory") positions = results["atom_positions"] expected_start = convert_unit( np.array([ @@ -610,7 +598,7 @@ class TestMDTrajFormats(unittest.TestCase): self.assertTrue(np.allclose(positions[-1, :], expected_end, rtol=0, atol=0.00001e-11)) def test_ftrajectory(self): - results = get_results("md/ftrajectory", "section_run") + results = get_result("md/ftrajectory") positions = results["atom_positions"] expected_start = convert_unit( np.array([ @@ -630,7 +618,6 @@ class TestMDTrajFormats(unittest.TestCase): self.assertTrue(np.allclose(positions[-1, :], expected_end, rtol=0, atol=0.00001e-11)) -#=============================================================================== class TestMDPrintSettings(unittest.TestCase): """Test that the print settings are interpreted corrrectly. """ @@ -640,7 +627,7 @@ class TestMDPrintSettings(unittest.TestCase): TRAJEC.xyz/dcd file exists can the trajectory be read, because it is not affected by range. """ - results = get_results("md/range", "section_run") + results = get_result("md/range") results["atom_positions"] with self.assertRaises(LookupError): results["atom_velocities"] @@ -648,7 +635,7 @@ class TestMDPrintSettings(unittest.TestCase): results["atom_forces"] def test_sample(self): - results = get_results("md/sample", "section_run") + results = get_result("md/sample") # Seet that the pos, vel and forces are associated with the correct scc sccs = results["section_single_configuration_calculation"] @@ -671,51 +658,48 @@ class TestMDPrintSettings(unittest.TestCase): self.assertEqual(forces, None) -#=============================================================================== class TestPeriodicity(unittest.TestCase): """Test the parsing of cell periodicity. """ def test_bulk(self): - results = get_results("periodicity/bulk") + results = get_result("periodicity/bulk") periodicity = results["configuration_periodic_dimensions"] self.assertTrue(np.array_equal(periodicity, np.array([True, True, True]))) def test_cluster(self): - results = get_results("periodicity/cluster") + results = get_result("periodicity/cluster") periodicity = results["configuration_periodic_dimensions"] self.assertTrue(np.array_equal(periodicity, np.array([False, False, False]))) def test_isolated(self): - results = get_results("periodicity/isolated") + results = get_result("periodicity/isolated") periodicity = results["configuration_periodic_dimensions"] self.assertTrue(np.array_equal(periodicity, np.array([False, False, False]))) def test_polymer(self): - results = get_results("periodicity/polymer") + results = get_result("periodicity/polymer") periodicity = results["configuration_periodic_dimensions"] self.assertTrue(np.array_equal(periodicity, np.array([True, False, False]))) def test_surface_xy(self): - results = get_results("periodicity/surface_xy") + results = get_result("periodicity/surface_xy") periodicity = results["configuration_periodic_dimensions"] self.assertTrue(np.array_equal(periodicity, np.array([True, True, False]))) def test_surface_xz(self): - results = get_results("periodicity/surface_xz") + results = get_result("periodicity/surface_xz") periodicity = results["configuration_periodic_dimensions"] self.assertTrue(np.array_equal(periodicity, np.array([True, False, True]))) def test_surface_yz(self): - results = get_results("periodicity/surface_yz") + results = get_result("periodicity/surface_yz") periodicity = results["configuration_periodic_dimensions"] self.assertTrue(np.array_equal(periodicity, np.array([False, True, True]))) -#=============================================================================== class TestXCFunctional(unittest.TestCase): """Tests that the XC functionals can be properly parsed. """ - def test_lda(self): xc = get_result("xc_functional/lda", "XC_functional") self.assertEqual(xc, "1*LDA_XC_TETER93") @@ -777,7 +761,6 @@ class TestXCFunctional(unittest.TestCase): self.assertEqual(xc, "1*HYB_GGA_XC_HSE06") -# #=============================================================================== # class TestSCFConvergence(unittest.TestCase): # """Tests whether the convergence status and number of SCF step can be # parsed correctly. @@ -792,7 +775,6 @@ class TestXCFunctional(unittest.TestCase): # self.assertFalse(result) -# # =============================================================================== # class TestGeoOptTrajFormats(unittest.TestCase): # def test_xyz(self): @@ -848,7 +830,6 @@ class TestXCFunctional(unittest.TestCase): # self.assertEqual(frames, 7) -# #=============================================================================== # class TestGeoOptOptimizers(unittest.TestCase): # def test_bfgs(self): @@ -860,7 +841,6 @@ class TestXCFunctional(unittest.TestCase): # self.assertEqual(result, "bfgs") -# #=============================================================================== # class TestGeoOptTrajectory(unittest.TestCase): # def test_each_and_add_last(self): @@ -927,9 +907,7 @@ class TestXCFunctional(unittest.TestCase): # i_conf += 1 -# #=============================================================================== # class TestMDEnsembles(unittest.TestCase): - # @classmethod # def setUpClass(cls): # cls.pressure = convert_unit( @@ -1006,16 +984,18 @@ class TestXCFunctional(unittest.TestCase): # self.assertTrue(np.array_equal(expected_cell_end, simulation_cell[-1,:,:])) -#=============================================================================== if __name__ == '__main__': - suites = [] - suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSinglePoint)) - suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOpt)) - suites.append(unittest.TestLoader().loadTestsFromTestCase(TestInputParser)) - suites.append(unittest.TestLoader().loadTestsFromTestCase(TestMD)) - suites.append(unittest.TestLoader().loadTestsFromTestCase(TestMDTrajFormats)) - suites.append(unittest.TestLoader().loadTestsFromTestCase(TestMDPrintSettings)) - suites.append(unittest.TestLoader().loadTestsFromTestCase(TestPeriodicity)) - suites.append(unittest.TestLoader().loadTestsFromTestCase(TestXCFunctional)) - alltests = unittest.TestSuite(suites) - unittest.TextTestRunner(verbosity=0).run(alltests) + + VERSIONS = ["4.1"] + for VERSION in VERSIONS: + suites = [] + suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSinglePoint)) + suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOpt)) + suites.append(unittest.TestLoader().loadTestsFromTestCase(TestInputParser)) + suites.append(unittest.TestLoader().loadTestsFromTestCase(TestMD)) + suites.append(unittest.TestLoader().loadTestsFromTestCase(TestMDTrajFormats)) + suites.append(unittest.TestLoader().loadTestsFromTestCase(TestMDPrintSettings)) + suites.append(unittest.TestLoader().loadTestsFromTestCase(TestPeriodicity)) + suites.append(unittest.TestLoader().loadTestsFromTestCase(TestXCFunctional)) + alltests = unittest.TestSuite(suites) + unittest.TextTestRunner(verbosity=0).run(alltests)