update ML and DFT (aims)

AppOutputExtractor/FHIaims/FHIaimsVib.py

@@ -0,0 +1,137 @@
+from AppOutputExtractor.OutputExtractor import BaseExtractor
+from AppOutputExtractor.FHIaims.FHIaimsMolecule import molecule as fmol
+from AppOutputExtractor.FHIaims.FHIaimsMolecule import calculate_rmsd_molecules
+from AppOutputExtractor.FHIaims.FHIaimsOutputExtractor import extractor
+
+from ShellCommand import shellcommand
+import ParsingSupport
+
+import os
+import shutil
+import string,json
+
+
+class aimsvibcalc(BaseExtractor):
+
+    def __init__(self, app_version='22', tag=None):
+        '''
+        '''
+        app_output = './aims.out'
+        self.extractor = extractor()
+        self.extractor.set_output_filepath(app_output)
+        self.no_atoms = self.extractor.get_no_atoms()
+        self.geometries = self.extractor.get_geometries(self.no_atoms)
+        self.order = self.extractor.get_atom_order(self.no_atoms)
+        self.species = self.extractor.get_species(self.order)
+
+
+        self.ucl_id = 'uccatka'
+        self.job_time = '2:00:00'
+        #self.job_name = 'test'
+        self.memory = '2'
+        self.cpu_core = '40'  # for Young 40 core = 1 node
+        self.payment = 'Gold'
+        self.budgets = 'UCL_chemM_Woodley'
+        self.path_binary = '/home/uccatka/software/fhi-aims.221103/build/aims.221103.scalapack.mpi.x'
+        self.vib_path_binary = '/home/uccatka/software/fhi-aims.221103/build/src/vibrations/numerical_vibrations.pl'
+        self.path_fhiaims_species = '/home/uccatka/software/fhi-aims.221103/species_defaults/defaults_2020/light'
+        self.step_size = 0.05
+
+        super().__init__(app='FHIaims',version=app_version)
+
+        # set app output patterns
+        module_path = os.path.dirname(os.path.abspath(__file__)) + '/OutputPattern' # getting this module path, '__file__'
+        self.patterns = self.load_patterns(module_path)
+
+        # memo
+        self.tag = tag
+
+        # shellcommand obj
+        self.shell = shellcommand()
+
+        return None
+
+    def make_job_submit(self, job_name, loc='./vibration', step_size='0.0025'):
+        ''' Write 'submit.sh' job script for SGE system '''
+        path = os.path.join(loc, 'submit.sh')
+        with open(path, 'a') as f:
+            f.write("#!/bin/bash -l\n")
+            f.write("\n")
+            f.write("#$ -S /bin/bash\n")
+            f.write(f"#$ -l h_rt={self.job_time}\n")
+            f.write(f"#$ -l mem={self.memory}G\n")
+            f.write(f"#$ -N {job_name}\n")
+            f.write(f"#$ -pe mpi {self.cpu_core}\n")
+            f.write("#$ -cwd\n")
+            f.write("\n")
+            f.write(f"#$ -P {self.payment}\n")
+            f.write(f"#$ -A {self.budgets}\n")
+            f.write("\n")
+            f.write("#$ -m e\n")
+            f.write(f"#$ -M {self.ucl_id}@ucl.ac.uk\n")
+            f.write("\n")
+            f.write("module purge\n")
+            f.write("module load gerun\n")
+            f.write("module load userscripts\n")
+            f.write("module load gcc-libs/4.9.2\n")
+            f.write("module unload -f compilers mpi\n")
+            f.write("module load beta-modules\n")
+            f.write("module load gcc-libs/10.2.0\n")
+            f.write("module load openblas/0.3.7-serial/gnu-4.9.2\n")
+            f.write("module load compilers/intel/2019/update5\n")
+            f.write("module load mpi/intel/2018/update3/intel\n")
+            f.write("module load cmake/3.21.1\n\n")            
+
+            f.write(f"{self.vib_path_binary} {job_name}_{step_size} {step_size} > vibres.out\n")
+
+    @property
+    def vib_calc_prep(self):
+        #shutil.copy('./control.in', './vibration')        
+        geo_next = 'geometry.in.next_step'
+        geo = 'geometry.in'
+        vib_dir = 'vibration'
+        geometry_files = [x for x in os.listdir('./') if '.in' in x]
+        if os.path.exists(geo_next):
+            shutil.copy(geo_next, f'{vib_dir}/{geo}')
+            shutil.copy('hessian.aims', vib_dir)
+        else:
+            shutil.copy(geo, vib_dir)
+
+        basis_set_files = [os.path.join(self.path_fhiaims_species, x) for x in os.listdir(self.path_fhiaims_species)]
+        basis_set_all = [x.split('_')[1] for x in os.listdir(self.path_fhiaims_species)]
+        basis_set_index = [basis_set_all.index(x) for x in basis_set_all if x in self.species]
+
+        with open(os.path.join(vib_dir, 'control.in'), 'a') as f:
+            f.write("xc                 pbesol\n")
+            f.write("spin               none\n")
+            f.write("relativistic       atomic_zora scalar\n")
+            f.write("charge             0.\n\n")
+            f.write("#  SCF convergence\n")
+            f.write("occupation_type    gaussian 0.01\n")
+            f.write("mixer              pulay\n")
+            f.write("n_max_pulay        10\n")
+            f.write("charge_mix_param   0.5\n")
+            f.write("sc_accuracy_rho    1E-5\n")
+            f.write("sc_accuracy_eev    1E-3\n")
+            f.write("sc_accuracy_etot   1E-6\n")
+            f.write("sc_accuracy_forces 1E-4\n")
+            f.write("sc_iter_limit      1500\n\n")
+
+            for i in basis_set_index:
+                with open(basis_set_files[i], 'r') as ff:
+                    lines = ff.read()
+                f.write(lines)
+                f.write('\n')
+        return None
+
+if __name__ == "__main__":
+    vib = aimsvibcalc()
+    os.mkdir('vibration')
+    vib.vib_calc_prep
+    current_dir_name = os.path.basename(os.getcwd())
+    vib.make_job_submit(f'n{current_dir_name}')
+    os.chdir('vibration')
+    os.system('qsub submit.sh')
+
+
+

AppOutputExtractor/FHIaims/MLTTV_spliter.py

@@ -0,0 +1,37 @@
+from ase import io 
+
+def split_xyz_file(input_file, train_file, valid_file, test_file):
+    with open(input_file, 'r') as infile:
+        train_out = open(train_file, 'w')
+        valid_out = open(valid_file, 'w')
+        test_out = open(test_file, 'w')
+
+        while True:
+            # Read the header line containing the number of atoms
+            header = infile.readline()
+            if not header:
+                break  # End of file
+
+            num_atoms = int(header.strip())
+            block_lines = [infile.readline() for _ in range(num_atoms + 1)]
+
+            # Determine which file to write to based on the current index
+            i = infile.tell()  # Get current position in file
+            if i % 5 < 3:
+                output_file = train_out
+            elif i % 5 == 3:
+                output_file = valid_out
+            else:
+                output_file = test_out
+
+            # Write the block to the chosen file
+            output_file.write(header)
+            output_file.writelines(block_lines)
+
+        train_out.close()
+        valid_out.close()
+        test_out.close()
+
+# Usage:
+split_xyz_file('Training_set.xyz', 'Training_set_test.xyz', 'Validation_set_test.xyz', 'Testing_set_test.xyz')
+