Merge branch 'develop'

README.md

@@ -38,7 +38,7 @@ Surfaxe primarily supports the [VASP](https://www.vasp.at/) DFT code, however mo
 ![Bond analysis example](example_data/figures/bond_analysis_plot.png)
 
 **Surface energy convergence checks with respect to vacuum and slab thickness**
-![Surface energy convergence example](example_data/figures/110_surface_energy.png)
+![Surface energy convergence example](example_data/figures/010_surface_energy.png)
 
 See the [tutorials directory](tutorials/) for more examples.
 
@@ -78,21 +78,22 @@ Generation:
 
 Convergence:
 
-* `surfaxe-parsefols`: Parses the convergence folders set up with `surfaxe-generate` where calculations were run with VASP. Extracts the relevant data and plots convergence graphs of the variation of surface energy and energy per atom with respect to slab and vacuum thickness.
+* `surfaxe-parse-energies`: Extracts the relevant data from the convergence folders set up with `surfaxe-generate` where calculations were run with VASP. Plots convergence graphs of the variation of surface energy with respect to slab and vacuum thickness. Can optionally parse core atom and vacuum energies as well.
+* `surfaxe-parse-structures`: Collects the structures' metadata into a json file and optionally performs bond analysis as in `surfaxe-bonds`.
 
 Analysis:
 
 * `surfaxe-bonds`: Parses the structure, looking for bonds between specified atoms.
 * `surfaxe-simplenn`: Predicts the coordination environment of atoms for simple structures.
 * `surfaxe-complexnn`: Predcts the coordination environment of atoms in more complex structures where the default prediction algorithm fails.
-* `surfaxe-potential`: Calculates and optionally plots the planar and macroscopic potential of the slab along c-axis.
+* `surfaxe-potential`: Calculates the planar potential of the slab along c-axis, the gradient of the planar potential and optionally macroscopic potential.
 * `surfaxe-cartdisp`: Calculates the Cartesian displacements of atoms during relaxation from intial and final structures.
 
 Plotting:
 
 * `surfaxe-plot-surfen` and `surfaxe-plot-enatom`: Plot the surface energy and energy per atom based on data from `surfaxe-parsefols` with individual customisability
 * `surfaxe-plot-bonds`: Plots the bond distance with respect to fractional coordinate, based on `surfaxe-bonds`
-* `surfaxe-plot-potential`: Plots the planar and macroscopic potential based on data already analysed with `surfaxe-potential`
+* `surfaxe-plot-potential`: Plots the planar (and macroscopic) potential based on data already analysed with `surfaxe-potential`
 
 Data:
 
@@ -142,6 +143,7 @@ Surfaxe is compatible with python 3.7+ and requires the following packages:
 * [Pandas](https://pandas.pydata.org/)
 * [Matplotlib](https://matplotlib.org/)
 * [Numpy](https://numpy.org/)
+* [Scikit-learn](https://scikit-learn.org/stable/)
 
 ## Contributors
 

docs/command_line_examples.rst

@@ -105,16 +105,21 @@ minimum vacuum thickness of 30 Å.
 Post-processing commands
 ========================
 
-**surfaxe-parsefols**: Parses data produced by electronic structure codes once calculations
+**surfaxe-parse-energies**: Parses data produced by electronic structure codes once calculations
 have been run in then directory structures produced by the pre-processing commands. 
+Can optionally collect vacuum and core energies. 
 
-Example: :mod:`surfaxe-parsefols --hkl 0,0,1 -b 8.83099` saves a csv file of surface energies
-and energies per atom for each slab-vacuum combination, as well as plots for each. See the 
-Tutorials directory for examples. 
+Example: :mod:`surfaxe-parse-energies --hkl 0,0,1 -b 8.83099` saves a csv file of surface energies
+and energies per atom for each slab-vacuum combination. See the Tutorials directory for examples. 
 
 **surfaxe-plot-surfen** and **surfaxe-plot-enatom** can be used to customise the surface 
 energy and energy per atom plots independetnly based on the data already collated 
-with **surfaxe-parsefols**. 
+with **surfaxe-parse-energies**. 
+
+**surfaxe-parse-structures**: Parses the (relaxed) structures from convergence calculations
+and collates them into the same json format as is created when surface slabs are generated. Can 
+optionally perform bond analysis for multiple specified bonds. Useful for comparison of relaxed 
+and unrelaxed surfaces slabs and determination of convergence.
 
 =================
 Analysis commands

docs/tutorials.rst

@@ -48,9 +48,12 @@ on SnO2 slabs, we could set up the config dict as follows:
     }
     }
 
-Alternatively, one of the ready-made :mod:`surfaxe` config dicts (:mod:`PBEsol_config.json`, 
-:mod:`PBE_config.json` or :mod:`HSE06_config.json`) can be used and further modified 
-using :mod:`user_incar_settings`, :mod:`user_kpoints_settings` and :mod:`user_potcar_settings`
+Alternatively, one of the ready-made :mod:`surfaxe` config dicts (:mod:`PBEsol.json`, 
+:mod:`PBEsol_relax.json`, :mod:`PBE.json`, :mod:`PBE_relax.json` or :mod:`HSE06.json`) 
+can be used and further modified using :mod:`user_incar_settings`, 
+:mod:`user_kpoints_settings` and :mod:`user_potcar_settings`. The :mod:`relax` config dicts 
+contain additional parameters necessary for geometric relaxations of slabs. 
+The POTCAR functional (i.e. PBE, PBE_54) can be chosen with :mod:`user_potcar_functional`.  
 
 `Pymatgen documentation <https://pymatgen.org/pymatgen.io.vasp.sets.html#pymatgen.io.vasp.sets.DictSet>`_ 
 covers exact behaviour of the :mod:`user_incar_settings`, :mod:`user_kpoints_settings` and :mod:`user_potcar_settings` 

example_data/convergence/Y2Ti2S2O5/010_data.csv

@@ -0,0 +1,29 @@
+,hkl_string,hkl_tuple,slab_thickness,vac_thickness,slab_index,atoms,area,bandgap,slab_energy,slab_per_atom,time_taken,surface_energy,surface_energy_ev,vacuum_potential,vacuum_gradient,surface_energy_fm,surface_energy_boettger,surface_energy_ouc,surface_energy_prim
+0,10,"(0, 1, 0)",10,10,0,24,26.109033226959006,2.0735,-185.11670083,-7.713195867916667,82.966,0.6182291598998413,0.038591083639191,5.989,-0.0010909507996537,0.624414524227934,,0.6201775886163629,0.6242678804464569
+1,10,"(0, 1, 0)",20,10,0,48,26.109033226959006,2.1285,-372.26815681,-7.755586600208333,238.487,0.6122150316693984,0.0382156698919724,8.004,-27.83894302436476,0.6245857603255839,0.6234152793254065,0.6161118891024416,0.6242924727626296
+2,10,"(0, 1, 0)",30,10,0,72,26.109033226959006,2.1312,-559.41826332,-7.769698101666667,512.387,0.6066149078413943,0.0378660991161919,9.013,-42.77089474741916,0.6251710008256812,0.6243953733210382,0.6124601939909592,0.6247310694812499
+3,10,"(0, 1, 0)",40,10,0,96,26.109033226959006,2.132,-746.56943472,-7.776764945,1057.408,0.6006880860148462,0.0374961352069192,9.617,-31.64388527254158,0.6254295433272173,0.6256677188925434,0.6084818008809328,0.6248429682013087
+4,10,"(0, 1, 0)",50,10,0,120,26.109033226959006,2.1321,-933.72164294,-7.781013691166667,1958.69,0.5944431777954221,0.0371063157175669,10.02,-25.957897822820776,0.6253699994358771,0.6255677205708391,0.6041853213780303,0.6246367805284914
+5,10,"(0, 1, 0)",60,10,0,144,26.109033226959006,2.132,-1120.87378597,-7.783845735902777,2627.405,0.5882182692403387,0.0367177446467127,10.312,-20.827615338039227,0.6253304552089126,0.6303012076183377,0.5999088415394686,0.6244505925200498
+6,10,"(0, 1, 0)",70,10,0,168,26.109033226959006,2.1321000000000003,-1308.02850051,-7.785883931607143,3436.714,0.5812044461773388,0.0362799279761135,10.529,-18.56130894730448,0.6245019964739968,,0.5948434471930251,0.6234754900036569
+7,10,"(0, 1, 0)",10,20,0,24,26.109033226959006,2.0736,-185.11974419,-7.713322674583334,110.146,0.6172954863552089,0.038532801894832,3.993,0.0003095252147527,0.6234415039416388,,0.6192439150717305,0.6233342069018245
+8,10,"(0, 1, 0)",20,20,0,48,26.109033226959006,2.1285,-372.27097932,-7.7556454025,333.479,0.6113491127782863,0.0381616175267344,6.003,0.0012092054648693,0.6236411479511461,0.6220338605732418,0.6152459702113294,0.6234265538715176
+9,10,"(0, 1, 0)",30,20,0,72,26.109033226959006,2.1316,-559.42024568,-7.769725634444445,699.293,0.6060067388808085,0.0378281360100379,7.211,0.0153266809930384,0.6244447916400894,0.6229865459172204,0.6118520250303733,0.624122900520664
+10,10,"(0, 1, 0)",40,20,0,96,26.109033226959006,2.1321,-746.57054715,-7.776776532812501,1325.026,0.6003468032020045,0.0374748316605495,8.017,-13.904195398747328,0.6249308735477241,0.624309978221156,0.608140518068091,0.624501685388467
+11,10,"(0, 1, 0)",50,20,0,120,26.109033226959006,2.1321,-933.72192707,-7.781016058916666,2102.562,0.5943560094472167,0.0371008744973293,8.594,-25.676865880598363,0.6250860973793749,0.6275318753620306,0.6040981530298247,0.624549612180286
+12,10,"(0, 1, 0)",60,20,0,144,26.109033226959006,2.1293,-1120.87540738,-7.783856995694445,2450.94,0.5877208362642539,0.0366866938991419,9.189,-21.562867439498785,0.6245969417828158,0.6310657138841974,0.5994114085633836,0.623953159543965
+13,10,"(0, 1, 0)",70,20,0,168,26.109033226959006,2.132,-1308.03080748,-7.785897663571428,4547.272,0.5804966899942632,0.0362357484390925,9.365,-18.88490601554195,0.6235188130992987,,0.5941356910099496,0.6227677338205811
+14,10,"(0, 1, 0)",10,30,0,24,26.109033226959006,2.0755000000000003,-185.11949463,-7.71331227625,134.06,0.6173720489602943,0.0385375810836638,3.028,-0.2004808007991027,0.6237197074108916,,0.6193204776768159,0.6234107695069099
+15,10,"(0, 1, 0)",20,30,0,48,26.109033226959006,2.1285,-372.27001096,-7.755625228333333,426.152,0.6116461963023136,0.0381801620663117,4.803,-0.0016303806538539,0.6243415132035082,0.6218781951388214,0.615543053735357,0.6237236373955449
+16,10,"(0, 1, 0)",30,30,0,72,26.109033226959006,2.1318,-559.41853944,-7.769701936666667,944.82,0.6065301968840598,0.0378608112911398,6.008,0.0011377676644748,0.625573172235843,0.6232062538415826,0.6123754830336247,0.6246463585239154
+17,10,"(0, 1, 0)",40,30,0,96,26.109033226959006,2.1276,-746.56851088,-7.776755321666666,1150.802,0.6009715112315522,0.037513827168012,7.042,-0.6069821149785554,0.6263621450339413,0.626883860467861,0.6087652260976386,0.6251263934180147
+18,10,"(0, 1, 0)",50,30,0,120,26.109033226959006,2.1325000000000003,-933.72147916,-7.781012326333333,2413.666,0.594493423922475,0.0371094521799297,7.563,-0.25530708120691,0.62623171617547,0.629762229090268,0.6042355675050831,0.6246870266555443
+19,10,"(0, 1, 0)",60,30,0,144,26.109033226959006,2.1326,-1120.87632388,-7.783863360277778,3220.328,0.5874396628889164,0.0366691425024292,8.1,-8.185983737437137,0.6255256135924825,0.6323024901800101,0.5991302351880461,0.6236719861686274
+20,10,"(0, 1, 0)",70,30,0,168,26.109033226959006,2.1321,-1308.03254862,-7.7859080275,5174.478,0.5799625250070675,0.036202404806933,8.472,-19.089171826224625,0.6243961341612396,,0.5936015260227536,0.6222335688333853
+21,10,"(0, 1, 0)",10,40,0,24,26.109033226959006,2.0736,-185.11929839,-7.713304099583333,200.246,0.6174322535027672,0.0385413391699605,2.396,0.0007412872583242,0.6239804531932147,,0.6193806822192888,0.6234709740493828
+22,10,"(0, 1, 0)",20,40,0,48,26.109033226959006,2.1285,-372.26887949,-7.755601656041667,534.265,0.611993320403804,0.0382018302374409,4.002,0.0001361447826771,0.6250897197846992,0.6224871893654808,0.6158901778368474,0.6240707614970353
+23,10,"(0, 1, 0)",30,40,0,72,26.109033226959006,2.1318,-559.41783476,-7.769692149444444,1196.542,0.6067463859229658,0.0378743062373886,5.15,-0.0011061609051547,0.6263909849943083,0.6243988093732378,0.6125916720725306,0.6248625475628212
+24,10,"(0, 1, 0)",40,40,0,96,26.109033226959006,2.1245,-746.56886704,-7.776759031666667,1331.967,0.6008622447728751,0.0375070065401295,6.127,0.0506209535859644,0.6270550435346652,0.6279661064535512,0.6086559596389617,0.6250171269593375
+25,10,"(0, 1, 0)",50,40,0,120,26.109033226959006,2.1297,-933.72280627,-7.781023385583333,2095.765,0.5940862793527061,0.0370840374127781,6.814,-0.0321019918556597,0.6268272778049437,0.6312377343133156,0.6038284229353142,0.6242798820857755
+26,10,"(0, 1, 0)",60,40,0,144,26.109033226959006,2.1312,-1120.87887831,-7.783881099374999,3081.298,0.5866559883605842,0.0366202239925458,7.31,-0.1817689545497925,0.6259451865032694,0.6291997933706984,0.598346560659714,0.6228883116402953
+27,10,"(0, 1, 0)",70,40,0,168,26.109033226959006,2.1255,-1308.03384322,-7.785915733452382,3405.351,0.5795653541922318,0.0361776126212379,7.813,-0.3958670338727575,0.6254027520253296,,0.5932043552079181,0.6218363980185498

setup.py

@@ -25,7 +25,7 @@
       license='MIT',
       packages=['surfaxe'],
       zip_safe=False,
-      install_requires=['scipy', 'numpy', 'spglib', 'pymatgen','pandas'],
+      install_requires=['scipy', 'numpy', 'spglib', 'pymatgen','pandas','scikit-learn'],
       python_requires='>=3.7',
       classifiers=[
         'Programming Language :: Python',
@@ -36,7 +36,8 @@
       ],
       entry_points={
         'console_scripts': [
-          'surfaxe-parsefols = surfaxe.cli.parsefols:main', 
+          'surfaxe-parse-energy = surfaxe.cli.parseenergy:main', 
+          'surfaxe-parse-structures = surfaxe.cli.parsestructures:main', 
           'surfaxe-bonds = surfaxe.cli.bonds:main', 
           'surfaxe-simplenn = surfaxe.cli.simplenn:main', 
           'surfaxe-complexnn = surfaxe.cli.complexnn:main',