v0 of FeatherBench

2024-12-22 04:13:52 +01:00 · 2024-08-30 20:15:39 +02:00 · 2024-08-30 20:15:39 +02:00 · 2c312cfc57
commit 2c312cfc57
parent 2ca8557cb3
7 changed files with 223 additions and 100 deletions
--- a/src/LR/ppLR.f90
+++ b/src/LR/ppLR.f90
@ -72,38 +72,43 @@ subroutine ppLR(TDA, nOO, nVV, Bpp, Cpp, Dpp, Om1, X1, Y1, Om2, X2, Y2, EcRPA)
    M(    1:nVV    ,nVV+1:nOO+nVV) = -           Bpp(1:nVV,1:nOO)
    M(nVV+1:nOO+nVV,    1:nVV)     = + transpose(Bpp(1:nVV,1:nOO))

-    !! Diagonalize the p-p matrix
-    !if(nOO+nVV > 0) call diagonalize_general_matrix(nOO+nVV, M, Om, Z)
-    !! Split the various quantities in p-p and h-h parts
-    !call sort_ppRPA(nOO, nVV, Om, Z, Om1, X1, Y1, Om2, X2, Y2)
+    if((nOO .eq. 0) .or. (nVV .eq. 0)) then

+      ! Diagonalize the p-p matrix
+      if(nOO+nVV > 0) call diagonalize_general_matrix(nOO+nVV, M, Om, Z)
+      ! Split the various quantities in p-p and h-h parts
+      call sort_ppRPA(nOO, nVV, Om, Z, Om1, X1, Y1, Om2, X2, Y2)

-    thr_d   = 1d-6   ! to determine if     diagonal elements of L.T x R are close enouph to 1
-    thr_nd  = 1d-6   ! to determine if non-diagonal elements of L.T x R are close enouph to 1
-    thr_deg = 1d-8   ! to determine if two eigenvectors are degenerate or not
-    imp_bio = .True. ! impose bi-orthogonality
-    verbose = .False.
-    call diagonalize_nonsym_matrix(N, M, Z, Om, thr_d, thr_nd, thr_deg, imp_bio, verbose)
+    else

-    do i = 1, nOO
-      Om2(i) = Om(i)
-      do j = 1, nVV
-        X2(j,i) = Z(j,i)
-      enddo
-      do j = 1, nOO
-        Y2(j,i) = Z(nVV+j,i)
-      enddo
-    enddo
+        thr_d   = 1d-6   ! to determine if     diagonal elements of L.T x R are close enouph to 1
+        thr_nd  = 1d-6   ! to determine if non-diagonal elements of L.T x R are close enouph to 1
+        thr_deg = 1d-8   ! to determine if two eigenvectors are degenerate or not
+        imp_bio = .True. ! impose bi-orthogonality
+        verbose = .False.
+        call diagonalize_nonsym_matrix(N, M, Z, Om, thr_d, thr_nd, thr_deg, imp_bio, verbose)
    
-    do i = 1, nVV
-      Om1(i) = Om(nOO+i)
-      do j = 1, nVV
-        X1(j,i) = M(j,nOO+i)
-      enddo
-      do j = 1, nOO
-        Y1(j,i) = M(nVV+j,nOO+i)
-      enddo
-    enddo
+        do i = 1, nOO
+          Om2(i) = Om(i)
+          do j = 1, nVV
+            X2(j,i) = Z(j,i)
+          enddo
+          do j = 1, nOO
+            Y2(j,i) = Z(nVV+j,i)
+          enddo
+        enddo
+    
+        do i = 1, nVV
+          Om1(i) = Om(nOO+i)
+          do j = 1, nVV
+            X1(j,i) = M(j,nOO+i)
+          enddo
+          do j = 1, nOO
+            Y1(j,i) = M(nVV+j,nOO+i)
+          enddo
+        enddo
+
+    endif

  end if

--- a/test/export_tobench.py
+++ b/test/export_tobench.py
@ -0,0 +1,26 @@
+
+import sys
+
+
+def read_quantities_from_file(filename):
+    quantities = {}
+
+    with open(filename, 'r') as file:
+        lines = file.readlines()
+        for i in range(0, len(lines), 2):
+            # Remove any leading or trailing whitespace/newline characters
+            quantity_name = lines[i].strip()
+            quantity_value = float(lines[i+1].strip())
+            quantities[quantity_name] = quantity_value
+
+    return quantities
+
+def print_quantities(quantities):
+    for key, value in quantities.items():
+        print(f'"{key}": {value},')
+
+filename = sys.argv[1]
+
+quantities = read_quantities_from_file(filename)
+print_quantities(quantities)
+
--- a/tests/create_database.py
+++ b/tests/create_database.py
@ -1,12 +1,39 @@

-import sqlite3
+import argparse

 from molecule import save_molecules_to_json, load_molecules_from_json
-from molecule import create_database, add_molecule_to_db
+from molecule import create_database, add_molecule_to_db, remove_database

 from feather_bench import FeatherBench


+parser = argparse.ArgumentParser(description="Benchmark Data Sets")
+
+parser.add_argument(
+    '-s', '--set_type',
+    choices=['light', 'medium', 'heavy'],
+    default='light',
+    help="Specify the type of data set: light (default), medium, or heavy."
+)
+
+
+args = parser.parse_args()
+
+if args.set_type == 'light':
+    bench = 'FeatherBench'
+    bench_title = "\n\nSelected Light Benchmark: {}\n\n".format(bench)
+elif args.set_type == 'medium':
+    bench = 'BalanceBench'
+    bench_title = "\n\nSelected Medium Benchmark: {}\n\n".format(bench)
+elif args.set_type == 'heavy':
+    bench = 'TitanBench'
+    bench_title = "\n\nSelected Heavy Benchmark: {}\n\n".format(bench)
+else:
+    bench_title = "\n\nSelected Light Benchmark: {}\n\n".format(bench)
+
+
+db_name = '{}.db'.format(bench)
+

 # Save molecules to JSON
 #save_molecules_to_json(FeatherBench, 'FeatherBench.json')
@ -15,8 +42,8 @@ from feather_bench import FeatherBench
 #loaded_molecules = load_molecules_from_json('FeatherBench.json')
 #print(loaded_molecules)

-# Create a database and add molecules
-db_name = 'FeatherBench.db'
+#remove_database(db_name)
+
 create_database(db_name)
 for molecule in FeatherBench:
    add_molecule_to_db(db_name, molecule)
--- a/tests/feather_bench.py
+++ b/tests/feather_bench.py
@ -11,43 +11,35 @@ He = Molecule(
    properties={
        "properties_rhf":{
            "6-31g": {
-                "RHF energy": -2.855160426884076,
-                "RHF HOMO energy": -0.914126628614305,
-                "RHF LUMO energy": 1.399859335225087,
-                "RHF dipole moment": 0.000000000000000,
-                "RMP2 correlation energy": -0.011200122910187,
-                "CCD correlation energy": -0.014985063408247,
-                "DCD correlation energy": -0.014985062907429,
-                "CCSD correlation energy": -0.015001711549550,
-                "drCCD correlation energy": -0.018845374502248,
-                "rCCD correlation energy": -0.016836324636164,
-                "crCCD correlation energy": 0.008524677369855,
-                "lCCD correlation energy": -0.008082420815100,
-                "pCCD correlation energy": -0.014985062519068,
-                "RCIS singlet excitation energy": 1.911193619935257,
-                "RCIS triplet excitation energy": 1.455852629402236,
-                "phRRPA correlation energy": -0.018845374129105,
-                "phRRPAx correlation energy": -0.015760565121283,
-                "crRRPA correlation energy": -0.008868581132405,
-                "ppRRPA correlation energy": -0.008082420815100,
-                "RG0F2 correlation energy": -0.011438430540374,
-                "RG0F2 HOMO energy": -0.882696116247871,
-                "RG0F2 LUMO energy": 1.383080391811630,
-                "evRGF2 correlation energy": -0.011448483158486,
-                "evRGF2 HOMO energy": -0.881327878713477,
-                "evRGF2 LUMO energy": 1.382458968133448,
-                "RG0W0 correlation energy": -0.019314094399756,
-                "RG0W0 HOMO energy": -0.870533880190454,
-                "RG0W0 LUMO energy": 1.377171287010956,
-                "evRGW correlation energy": -0.019335511771724,
-                "evRGW HOMO energy": -0.868460640957913,
-                "evRGW LUMO energy": 1.376287581471769,
-                "RG0T0pp correlation energy": -0.008082420815100,
-                "RG0T0pp HOMO energy": -0.914126628614305,
-                "RG0T0pp LUMO energy": 1.399859335225087,
-                "evRGTpp correlation energy": -0.008082420815100,
-                "evRGTpp HOMO energy": -0.914126628614305,
-                "evRGTpp LUMO energy": 1.399859335225087
+                "RHF energy": -2.855160426154444,
+                "RHF HOMO energy": -0.914126628640145,
+                "RHF LUMO energy": 1.399859335255765,
+                "RHF dipole moment": 0.0,
+                "MP2 correlation energy": -0.011200122909934,
+                "CCD correlation energy": -0.014985063116,
+                "CCSD correlation energy": -0.015001711549092,
+                "drCCD correlation energy": -0.01884537385338,
+                "rCCD correlation energy": -0.016836322809386,
+                "crCCD correlation energy": 0.008524676641474,
+                "lCCD correlation energy": -0.00808242082105,
+                "CIS singlet excitation energy": 1.911193619991987,
+                "CIS triplet excitation energy": 1.455852629458543,
+                "phRPA correlation energy": -0.018845374128748,
+                "phRPAx correlation energy": -0.015760565120758,
+                "crRPA correlation energy": -0.008868581132249,
+                "ppRPA correlation energy": -0.008082420814972,
+                "G0F2 correlation energy": -0.011438430540104,
+                "G0F2 HOMO energy": -0.882696116274599,
+                "G0F2 LUMO energy": 1.383080391842522,
+                "G0W0 correlation energy": -0.019314094399372,
+                "G0W0 HOMO energy": -0.87053388021722,
+                "G0W0 LUMO energy": 1.377171287041735,
+                "evGW correlation energy": -0.019335511771337,
+                "evGW HOMO energy": -0.868460640984803,
+                "evGW LUMO energy": 1.376287581502582,
+                "G0T0pp correlation energy": -0.008161908540634,
+                "G0T0pp HOMO energy": -0.898869172597701,
+                "G0T0pp LUMO energy": 1.383928087417952,
            }
        },
        "properties_uhf":{
@ -58,8 +50,51 @@ He = Molecule(
            "6-31g": {
            }
        },
-        "properties_rohf":{
-            "6-31g": {
+    }
+)
+
+# ---
+
+H2O = Molecule(
+    name="H2O",
+    multiplicity=1,
+    geometry=[
+        {"element": "O", "x":  0.0000, "y": 0.0000, "z": 0.0000},
+        {"element": "H", "x":  0.7571, "y": 0.0000, "z": 0.5861},
+        {"element": "H", "x": -0.7571, "y": 0.0000, "z": 0.5861}
+    ],
+    properties={
+        "properties_rhf":{
+            "cc-pvdz": {
+                "RHF energy": -85.21935817501823,
+                "RHF HOMO energy": -0.493132793449897,
+                "RHF LUMO energy": 0.185534869842355,
+                "RHF dipole moment": 0.233813698748474,
+                "MP2 correlation energy": -0.203978216774657,
+                "CCD correlation energy": -0.212571260121257,
+                "CCSD correlation energy": -0.213302190845899,
+                "drCCD correlation energy": -0.231281853419338,
+                "rCCD correlation energy": -0.277238348710547,
+                "crCCD correlation energy": 0.18014617422324,
+                "lCCD correlation energy": -0.15128653432796,
+                "CIS singlet excitation energy": 0.338828950934568,
+                "CIS triplet excitation energy": 0.304873339484139,
+                "phRPA correlation energy": -0.231281866582435,
+                "phRPAx correlation energy": -0.310796738307943,
+                "crRPA correlation energy": -0.246289801609294,
+                "ppRPA correlation energy": -0.151286536255888,
+                "G0F2 correlation energy": -0.217807591229668,
+                "G0F2 HOMO energy": -0.404541451101377,
+                "G0F2 LUMO energy": 0.16650398400197,
+                "G0W0 correlation energy": -0.23853664665404,
+                "G0W0 HOMO energy": -0.446828623007469,
+                "G0W0 LUMO energy": 0.173026609033024,
+                "evGW correlation energy": -0.239414217281308,
+                "evGW HOMO energy": -0.443076613314424,
+                "evGW LUMO energy": 0.172691758111392,
+                "G0T0pp correlation energy": -0.156214864467344,
+                "G0T0pp HOMO energy": -0.452117482732615,
+                "G0T0pp LUMO energy": 0.16679206983464,
            }
        }
    }
@ -67,24 +102,9 @@ He = Molecule(

 # ---

-#H2O = Molecule(
-#    name="H2O",
-#    multiplicity=1,
-#    geometry=[
-#        {"element": "O", "x":  0.0000, "y": 0.0000, "z": 0.0000},
-#        {"element": "H", "x":  0.7571, "y": 0.0000, "z": 0.5861},
-#        {"element": "H", "x": -0.7571, "y": 0.0000, "z": 0.5861}
-#    ],
-#    properties={
-#        "cc-pvdz": {
-#    }
-#)
-
-# ---
-
 FeatherBench = [
    He, 
-    #H2O
+    H2O
 ]


--- a/tests/inp/methods.RHF
+++ b/tests/inp/methods.RHF
@ -3,7 +3,7 @@
 # MP2 MP3
  T   T
 # CCD pCCD DCD CCSD CCSD(T)
-  T   T    T   T    F
+  T   F    F   T    F
 # drCCD rCCD crCCD lCCD
  T     T    T     T
 # CIS CIS(D) CID CISD FCI
@ -11,11 +11,11 @@
 # phRPA phRPAx crRPA ppRPA
  T     T      T     T 
 # G0F2 evGF2 qsGF2 ufGF2 G0F3 evGF3
-  T    T     F     F    F    F
+  T    F     F     F    F    F
 # G0W0 evGW qsGW SRG-qsGW ufG0W0 ufGW
  T    T    F    F        F      F
 # G0T0pp evGTpp qsGTpp ufG0T0pp
-  T      T      F      F
+  T      F      F      F
 # G0T0eh evGTeh qsGTeh
  F      F      F
 # Rtest Utest Gtest
--- a/tests/lunch_bench.py
+++ b/tests/lunch_bench.py
@ -181,7 +181,7 @@ class Quack_Job:
                    if(diff <= THRESH):
                        print_col(f"        🙂 {key}: ✔️ ", "green")
                    else:
-                        print_col(f"        ☹️ {key}: ❌ {data_ref[key]} ≠ {data_new[key]}", "red")
+                        print_col(f"        ☹️  {key}: ❌ {data_ref[key]} ≠ {data_new[key]}", "red")
        except FileNotFoundError:
            print_col(f"Error: The file '{filepath}' does not exist.", "red")
            sys.exist(1)
--- a/tests/molecule.py
+++ b/tests/molecule.py
@ -1,7 +1,11 @@

+import os
 import json
 import sqlite3

+from utils import print_col
+
+
 class Molecule:
    def __init__(self, name, multiplicity, geometry, properties):
        self.name = name
@ -38,23 +42,64 @@ def load_molecules_from_json(filename):


 def create_database(db_name):
-    conn = sqlite3.connect(db_name)
-    cursor = conn.cursor()
-    cursor.execute('''CREATE TABLE IF NOT EXISTS molecules
-                      (name TEXT, multiplicity INTEGER, geometry TEXT, properties TEXT)''')
-    conn.commit()
-    conn.close()
+    if os.path.exists(db_name):
+        conn = sqlite3.connect(db_name)
+        cursor = conn.cursor()
+        # Check if the table already exists
+        cursor.execute("SELECT name FROM sqlite_master WHERE type='table' AND name='molecules';")
+        table_exists = cursor.fetchone()
+        
+        if table_exists:
+            print_col(f"Database '{db_name}' already exists and table 'molecules' is already created.", "yellow")
+        else:
+            # Create the table if it does not exist
+            cursor.execute('''CREATE TABLE molecules
+                              (name TEXT, multiplicity INTEGER, geometry TEXT, properties TEXT)''')
+            conn.commit()
+            print_col(f"Table 'molecules' created in existing database '{db_name}' successfully.", "green")
+        conn.close()
+    else:
+        # Create the database and table
+        conn = sqlite3.connect(db_name)
+        cursor = conn.cursor()
+        cursor.execute('''CREATE TABLE molecules
+                          (name TEXT, multiplicity INTEGER, geometry TEXT, properties TEXT)''')
+        conn.commit()
+        conn.close()
+        print_col(f"Database '{db_name}' created and table 'molecules' added successfully.", "green")

 def add_molecule_to_db(db_name, molecule):
+
    conn = sqlite3.connect(db_name)
    cursor = conn.cursor()
+
+    # Convert geometry and properties to JSON strings
    geometry_str = json.dumps(molecule.geometry)
    energies_str = json.dumps(molecule.properties)
-    cursor.execute("INSERT INTO molecules VALUES (?, ?, ?, ?)",
-                   (molecule.name, molecule.multiplicity, geometry_str, energies_str))
-    conn.commit()
+
+    # Check if the molecule already exists
+    cursor.execute("SELECT COUNT(*) FROM molecules WHERE name = ?", (molecule.name,))
+    count = cursor.fetchone()[0]
+    
+    if count > 0:
+        print_col(f"Molecule '{molecule.name}' already exists in {db_name}.", "yellow")
+    else:
+        # Insert the molecule if it does not exist
+        cursor.execute("INSERT INTO molecules (name, multiplicity, geometry, properties) VALUES (?, ?, ?, ?)",
+                       (molecule.name, molecule.multiplicity, geometry_str, energies_str))
+        conn.commit()
+        print_col(f"'{molecule.name}' added to {db_name} successfully.", "green")
+    
    conn.close()

+
+def remove_database(db_name):
+    if os.path.exists(db_name):
+        os.remove(db_name)
+        print_col(f"Database '{db_name}' removed successfully.", "red")
+    else:
+        print_col(f"Database '{db_name}' does not exist.", "red")
+
 def get_molecules_from_db(db_name):
    conn = sqlite3.connect(db_name)
    cursor = conn.cursor()