Fix benchmark results and prepare for new ones

3 files changed, 68 insertions, 48 deletions

diff --git a/benchmarks.csv b/benchmarks.csv
index 181da4e77..eb0ff0333 100644
--- a/benchmarks.csv
+++ b/benchmarks.csv
@@ -1,17 +1,23 @@
-ml_type,tr_size,te_size,sigma,mae,time
-CM,2500,1500,1000.0,26.97361909951274,282.1443384
-L-JM,2500,1500,1000.0,11.785532138202667,277.3047686
-CM,3000,1500,1000.0,24.641045831013365,368.9830951
-L-JM,3000,1500,1000.0,11.08713556535848,370.8802103
-CM,3500,1500,1000.0,23.152765029544195,467.1278212
-L-JM,3500,1500,1000.0,10.430573100461325,464.2503922
-CM,4000,1500,1000.0,22.15854674774742,562.7823053
-L-JM,4000,1500,1000.0,10.117842321543852,564.9598646000001
-CM,4500,1500,1000.0,21.180935112846054,655.8574701
-L-JM,4500,1500,1000.0,9.677330400431318,652.4534939
-CM,5000,1500,1000.0,20.30113013118839,755.6121498
-L-JM,5000,1500,1000.0,9.143465812164308,759.3658756
-CM,5500,1500,1000.0,19.749349939851125,867.1811531999999
-L-JM,5500,1500,1000.0,8.902193965087893,863.8858544000001
-CM,6000,1101,1000.0,18.989775833821966,934.9760266999999
-L-JM,6000,1101,1000.0,8.595942764490113,932.6673659
+ml_type,tr_size,te_size,kernel_s,mae,time,lj_s,lj_e,date_ran
+CM,1500,1500,1000.0,31.512240475332977,100.3640273,na,na,14/12/2019
+L-JM,1500,1500,1000.0,14.071581760048153,101.6336081,1,1,14/12/2019
+CM,2000,1500,1000.0,28.245321081132253,152.88077109999998,na,na,14/12/2019
+L-JM,2000,1500,1000.0,12.641839980374655,155.5011396,1,1,14/12/2019
+CM,2500,1500,1000.0,26.97361909951274,215.9536518,na,na,14/12/2019
+L-JM,2500,1500,1000.0,11.785532138202667,211.8681615,1,1,14/12/2019
+CM,3000,1500,1000.0,24.641045831013365,278.5150912,na,na,14/12/2019
+L-JM,3000,1500,1000.0,11.08713556535848,278.5971606,1,1,14/12/2019
+CM,3500,1500,1000.0,23.152765029544195,401.9234568,na,na,14/12/2019
+L-JM,3500,1500,1000.0,10.430573100461325,408.3161812,1,1,14/12/2019
+CM,4000,1500,1000.0,22.15854674774742,499.55023489999996,na,na,14/12/2019
+L-JM,4000,1500,1000.0,10.117842321543852,503.7487102,1,1,14/12/2019
+CM,4500,1500,1000.0,21.180935112846054,605.4631191999999,na,na,14/12/2019
+L-JM,4500,1500,1000.0,9.677330400431318,604.4122219,1,1,14/12/2019
+CM,5000,1500,1000.0,20.30113013118839,699.0641616,na,na,14/12/2019
+L-JM,5000,1500,1000.0,9.143465812164308,701.9964291,1,1,14/12/2019
+CM,5500,1500,1000.0,19.749349939851125,816.2225933,na,na,14/12/2019
+L-JM,5500,1500,1000.0,8.902193965087893,800.8945613,1,1,14/12/2019
+CM,6000,1101,1000.0,18.989775833821966,894.5558989,na,na,14/12/2019
+L-JM,6000,1101,1000.0,8.595942764490113,885.4234397,1,1,14/12/2019
+CM,6500,601,1000.0,19.424238707695146,956.2706457,na,na,14/12/2019
+L-JM,6500,601,1000.0,8.636351001125403,950.2348745,1,1,14/12/2019
diff --git a/lj_matrix.py b/lj_matrix.py
index 5cb1b5a8d..2a8e0d956 100644
--- a/lj_matrix.py
+++ b/lj_matrix.py
@@ -29,6 +29,8 @@ from numpy.linalg import eig
 
 def lj_matrix(mol_data,
               nc_data,
+              sigma=1.0,
+              epsilon=1.0,
               max_len=25,
               as_eig=True,
               bohr_radius_units=False):
@@ -92,11 +94,11 @@ def lj_matrix(mol_data,
                             # Conversion factor is included in r^2.
 
                             # 1/r^2
-                            r_2 = 1/(conversion_rate**2*(x + y + z))
+                            r_2 = sigma**2/(conversion_rate**2*(x + y + z))
 
                             r_6 = math.pow(r_2, 3)
                             r_12 = math.pow(r_6, 2)
-                            lj[i, j] = (4*(r_12 - r_6))
+                            lj[i, j] = (4*epsilon*(r_12 - r_6))
                     else:
                         break
 
@@ -150,11 +152,11 @@ def lj_matrix(mol_data,
                         # Conversion factor is included in r^2.
 
                         # 1/r^2
-                        r_2 = 1/(conversion_rate**2*(x + y + z))
+                        r_2 = sigma**2/(conversion_rate**2*(x + y + z))
 
                         r_6 = math.pow(r_2, 3)
                         r_12 = math.pow(r_6, 2)
-                        lj_row.append(4*(r_12 - r_6))
+                        lj_row.append(4*epsilon*(r_12 - r_6))
 
                 lj_temp.append(np.array(lj_row))
 
@@ -169,6 +171,8 @@ def lj_matrix(mol_data,
 def lj_matrix_multiple(mol_data,
                        nc_data,
                        pipe=None,
+                       sigma=1,
+                       epsilon=1,
                        max_len=25,
                        as_eig=True,
                        bohr_radius_units=False):
@@ -185,7 +189,13 @@ def lj_matrix_multiple(mol_data,
     printc('L-J Matrices calculation started.', 'CYAN')
     tic = time.perf_counter()
 
-    ljm_data = np.array([lj_matrix(mol, nc, max_len, as_eig, bohr_radius_units)
+    ljm_data = np.array([lj_matrix(mol,
+                                   nc,
+                                   sigma,
+                                   epsilon,
+                                   max_len,
+                                   as_eig,
+                                   bohr_radius_units)
                         for mol, nc in zip(mol_data, nc_data)])
 
     toc = time.perf_counter()
diff --git a/main.py b/main.py
index 9144099d5..88f0a26f5 100644
--- a/main.py
+++ b/main.py
@@ -43,37 +43,37 @@ def main():
     procs = []
     pipes = []
 
-    cm_recv, cm_send = Pipe(False)
-    p1 = Process(target=c_matrix_multiple,
-                 args=(molecules, nuclear_charge, cm_send))
-    procs.append(p1)
-    pipes.append(cm_recv)
-    p1.start()
+    # cm_recv, cm_send = Pipe(False)
+    # p1 = Process(target=c_matrix_multiple,
+    #              args=(molecules, nuclear_charge, cm_send))
+    # procs.append(p1)
+    # pipes.append(cm_recv)
+    # p1.start()
 
     ljm_recv, ljm_send = Pipe(False)
     p2 = Process(target=lj_matrix_multiple,
-                 args=(molecules, nuclear_charge, ljm_send))
+                 args=(molecules, nuclear_charge, ljm_send, 1.5))
     procs.append(p2)
     pipes.append(ljm_recv)
     p2.start()
 
-    cm_data = pipes[0].recv()
-    ljm_data = pipes[1].recv()
+    # cm_data = pipes[0].recv()
+    ljm_data = pipes[0].recv()
 
     for proc in procs:
         proc.join()
 
     # ML calculation.
     procs = []
-    cm_pipes = []
+    # cm_pipes = []
     ljm_pipes = []
-    for i in range(2500, 6000 + 1, 500):
-        cm_recv, cm_send = Pipe(False)
-        p1 = Process(target=do_ml,
-                     args=(cm_data, energy_pbe0, i, 'CM', cm_send))
-        procs.append(p1)
-        cm_pipes.append(cm_recv)
-        p1.start()
+    for i in range(1500, 6500 + 1, 500):
+        # cm_recv, cm_send = Pipe(False)
+        # p1 = Process(target=do_ml,
+        #              args=(cm_data, energy_pbe0, i, 'CM', cm_send))
+        # procs.append(p1)
+        # cm_pipes.append(cm_recv)
+        # p1.start()
 
         ljm_recv, ljm_send = Pipe(False)
         p2 = Process(target=do_ml,
@@ -82,21 +82,25 @@ def main():
         ljm_pipes.append(ljm_recv)
         p2.start()
 
-    cm_bench_results = []
+    # cm_bench_results = []
     ljm_bench_results = []
-    for cd_pipe, ljd_pipe in zip(cm_pipes, ljm_pipes):
-        cm_bench_results.append(cd_pipe.recv())
+    for ljd_pipe in ljm_pipes:  # cd_pipe, ljd_pipe in zip(cm_pipes, ljm_pipes):
+        # cm_bench_results.append(cd_pipe.recv())
         ljm_bench_results.append(ljd_pipe.recv())
 
     for proc in procs:
         proc.join()
 
-    with open('benchmarks.csv', 'w') as save_file:
-        save_file.write('ml_type,tr_size,te_size,sigma,mae,time\n')
-        for cm, ljm, in zip(cm_bench_results, ljm_bench_results):
-            cm_text = ','.join([str(field) for field in cm]) + '\n'
-            ljm_text = ','.join([str(field) for field in ljm]) + '\n'
-            save_file.write(cm_text)
+    with open('benchmarks.csv', 'a') as save_file:
+        # save_file.write(''.join(['ml_type,tr_size,te_size,kernel_s,',
+        #                          'mae,time,lj_s,lj_e,date_ran\n']))
+        date = '/'.join([str(field) for field in time.localtime()[:3][::-1]])
+        for ljm in ljm_bench_results:  # cm, ljm, in zip(cm_bench_results, ljm_bench_results):
+            # cm_text = ','.join([str(field) for field in cm])\
+            #     + ',' + date + '\n'
+            ljm_text = ','.join([str(field) for field in ljm])\
+                + ',1.5,1,' + date + '\n'
+            # save_file.write(cm_text)
             save_file.write(ljm_text)
 
     # End of program