create the folder for each system of GO

pyxtal/optimize/GA.py

@@ -113,7 +113,7 @@ def __init__(self,
 
     def full_str(self):
         s = str(self)
-        s +=  "\n------Vanila Genetic Algorithm------"
+        s += "\nMethod    : Genetic Algorithm"
         s += "\nGeneration: {:4d}".format(self.N_gen)
         s += "\nPopulation: {:4d}".format(self.N_pop)
         s += "\nFraction  : {:4.2f} {:4.2f} {:4.2f}".format(*self.fracs)
@@ -191,7 +191,7 @@ def run(self, ref_pmg=None, ref_eng=None, ref_pxrd=None):
                     self.block,
                     self.num_block,
                     self.atom_info,
-                    self.workdir,
+                    self.workdir + '/' + 'calc',
                     self.sg,
                     self.composition,
                     self.lattice,
@@ -253,7 +253,7 @@ def run(self, ref_pmg=None, ref_eng=None, ref_pxrd=None):
                         if xtal.energy < 9999:
                             if self.verbose:
                                 print("Add qualified structure", id, xtal.energy)
-                            with open(self.cif, 'a+') as f:
+                            with open(self.workdir+'/'+self.cif, 'a+') as f:
                                 label = self.tag + '-g' + str(gen) + '-p' + str(id)
                                 f.writelines(xtal.to_file(header=label))
                         #else:
@@ -361,8 +361,9 @@ def _crossover(self, x1, x2):
     ncpu = options.ncpu
     ffopt = options.ffopt
     db_name, name = 'pyxtal/database/test.db', 'ACSALA'
-    wdir = 'tmp'
+    wdir = name
     os.makedirs(wdir, exist_ok=True)
+    os.makedirs(wdir+'/calc', exist_ok=True)
 
     db = database(db_name)
     row = db.get_row(name)
@@ -373,8 +374,8 @@ def _crossover(self, x1, x2):
         if 'charmm_info' in row.data.keys():
             # prepare charmm input
             chm_info = row.data['charmm_info']
-            prm = open(wdir+'/pyxtal.prm', 'w'); prm.write(chm_info['prm']); prm.close()
-            rtf = open(wdir+'/pyxtal.rtf', 'w'); rtf.write(chm_info['rtf']); rtf.close()
+            prm = open(wdir+'/calc/pyxtal.prm', 'w'); prm.write(chm_info['prm']); prm.close()
+            rtf = open(wdir+'/calc/pyxtal.rtf', 'w'); rtf.write(chm_info['rtf']); rtf.close()
         else:
             # Make sure we generate the initial guess from ambertools
             if os.path.exists('parameters.xml'): os.remove('parameters.xml')

pyxtal/optimize/base.py

@@ -140,7 +140,7 @@ def __init__(self,
                 else:
                     print("No FF parameter file exists, using the default setting", ff_style)
                     params0 = self.parameters.params_init.copy()
-                    self.parameters.export_parameters(self.ff_parameters, params0)
+                    self.parameters.export_parameters(self.wdir+'/'+self.ff_parameters, params0)
 
                 self.prepare_chm_info(params0)
 
@@ -152,7 +152,7 @@ def __init__(self,
         self.tag = tag
         self.cif = cif
         if cif is not None:
-            with open(cif, 'w') as f: f.writelines(str(self))
+            with open(self.workdir+'/'+cif, 'w') as f: f.writelines(str(self))
         #print(self)
 
     def __str__(self):
@@ -433,7 +433,7 @@ def ff_optimization(self, xtals, N_added, N_min=50, dE=2.5, FMSE=2.5):
 
         return N_added
 
-    def prepare_chm_info(self, params0, params1=None, suffix='pyxtal0'):
+    def prepare_chm_info(self, params0, params1=None, suffix='calc/pyxtal0'):
         """
         TODO: A base classs for optimization
         prepar_chm_info with the updated params.